title: Chronc hypoxia 4

city: Beijing

first: Yiwei

last: Liu

address: No.167 North Lishi Road, Xicheng District

department: Pediatric Cardiac Surgery

institute: fuwai hosptial, PUMC & CAMS

data_processing:
bcl2fastq software was used for basecalling
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the Raw Data. The steps are:(1) Trim Smart-seq2 public primer sequence from the Reads;(2) Remove the contaminated reads for adapters; (3) Remove the low quality reads;(4) Remove the reads whose N base is more than 5% for total bases
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was then calculated to estimate the expression level of genes in each sample
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include Counts and FPKM values for each Sample

source_name: heart

extract_protocol:
Heart tissues from hypoxic (n = 4) and normoxic rats (n = 4) were collected for RNA extraction. Total RNA was extracted by Trizol™ Reagent (no. 15596018, Thermo Fisher Scientific, USA) following the manufacturer’s protocol.
The sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (no. E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina, USA) according to the manufacturer’s instructions.

value: Sprague Dawley

value: heart

value: Three months

tag: treatment

value: Chronic hypoxia


title: healthy tumor-surrounding mucosa of sample CRC.34

status: Public on Dec 17 2020

type: SRA

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

library_source: genomic

data_processing:
Library strategy: amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2020crc)

molecule: genomic DNA

organism: Homo sapiens

source_name: Colonic mucosa

growth_protocol: Tissue samples were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerLyzer PowerSoil Kit (Qiagen, Hilden, Germany)  162 Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: diagnosis

value: Surrounding healthy tissue

tag: Sex

value: M


title: GapmeR-HIF1A-As2 rep1

city: Manchester

first: Michela

last: Garofalo

address: Alderley Park

country: United Kingdom

institute: CRUK Manchester Institute

library_source: transcriptomic

data_processing:
RSubRead
FeatureCount
DESeq2
Genome_build: Hg19
Supplementary_files_format_and_content: DESeq2 output

molecule: total RNA

source_name: H1299 cells

growth_protocol: H1299 cells were cultured in RPMI 1640 medium containing 10% FBS.

extract_protocol:
Total RNA was isolated from cells using TRIzol according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

tag: gapmer target


title: colorectal mucosa of sample CRC.34

value: Colorectal adenocarcinoma tissue

tag: tnm classification

value: pT3 N0

tag: colorectal cancer stadium

value: II

tag: tumor localization

value: Cecum


title: 8-3-KI: Pten mutant sample 3

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq and differential gene expression analysis was carried out using R/Bioconductor DEseq2 package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count matrix calculated by using DESeq2.

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: brain

tag: age

tag: genotype/variation

value: PTEN C-terminus mutant


title: Chronc hypoxia 2

country: China

organism: Rattus norvegicus


title: healthy tumor-surrounding mucosa of sample CRC.32


title: GapmeR-KIMAT1 rep3


title: healthy tumor-surrounding mucosa of sample CRC.28

value: F


title: GapmeR-KIMAT1 rep2


title: colorectal mucosa of sample CRC.28

value: T2 N0

value: I

value: Ascending colon


title: Chronc hypoxia 1


title: H3K4me3

data_processing:
bowtie2
macs2
homer
Genome_build: Hg19
Supplementary_files_format_and_content: bw files and peak files (bed)

extract_protocol:
Genomic DNA was purified with QIAquick PCR purification Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody


title: input DNA


title: healthy tumor-surrounding mucosa of sample CRC.25


title: GapmeR-KIMAT1 rep1


title: colorectal mucosa of sample CRC.25

value: pT1 N0

value: Rectum


title: GapmeR-Ctrl rep3

value: Ctrl


title: healthy tumor-surrounding mucosa of sample CRC.23


title: colorectal mucosa of sample CRC.23

value: T3 N1a G2

value: IIIB

value: Splenic flexure


title: Control 4

value: Sprague Dawley

value: heart

value: Three months

value: Normoxia


title: GapmeR-Ctrl rep2


title: healthy tumor-surrounding mucosa of sample CRC.20

value: Surrounding healthy tissue

value: M


title: healthy tumor-surrounding mucosa of sample CRC.22


title: colorectal mucosa of sample CRC.32

value: Colorectal adenocarcinoma tissue

value: T3 N0

value: II


title: Chronc hypoxia 3

value: Chronic hypoxia


title: GapmeR-Ctrl rep1


title: colorectal mucosa of sample CRC.22

value: pT3 N1a


title: Control 3


title: healthy tumor-surrounding mucosa of sample CRC.18

value: F


title: colorectal mucosa of sample CRC.20

value: pT3 N0

value: Rectum


title: Control 1


title: GapmeR-HIF1A-As2 rep3_mRNA


title: GapmeR-HIF1A-As2 rep2_mRNA


title: Non-malignant 6

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

country: USA

institute: University of Minnesota

description:
Sample 19
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

data_processing:
Illumina CASAVA software (version 1.8.2) for basecalling.
RNA-Seq reads were aligned to the reference genome (GRCh38) with HISAT2.
Cleaned and name-sorted alignments were processed with the featureCounts tool from the subread package. Both mates of a read pair were required to map to a feature to be counted.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw_gene_counts_matrix_angio.txt: Tab-delimited text file includes raw counts of all annotated genes for all samples.

source_name: Lung

extract_protocol:
Total RNA was isolated from tissue samples using the TriPure Isolation Reagent (Roche Applied Science, Indianapolis, IN, USA). The RNeasy Mini Kit (Qiagen, Valencia, CA, USA) was used for clean-up according to the manufacturer's instructions.
Two µg of total RNA from each sample were quantified and assessed for quality. RNA-Seq libraries were generated using the TruSeq RNA sample preparation kit (Illumina Inc., San Diego, CA).

tag: tissue type

value: Non-malignant control


title: healthy tumor-surrounding mucosa of sample CRC.17


title: colorectal mucosa of sample CRC.17

value: pT1 N0

value: I

value: Sigmoid colon


title: Non-malignant 5

description:
Sample 18
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Spleen


title: GapmeR-HIF1A-As2 rep1_mRNA


title: healthy tumor-surrounding mucosa of sample CRC.16


title: colorectal mucosa of sample CRC.18

value: pT2 N1b

value: IIIA

value: Cecum


title: Non-malignant 4

description:
Sample 17
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Skeletal muscle


title: colorectal mucosa of sample CRC.16

value: Descending colon


title: Non-malignant 3

description:
Sample 16
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Breast tissue


title: colorectal mucosa of sample CRC.15

value: pT3 N1c

value: IIIB

value: M


title: GapmeR-KIMAT1 rep3_mRNA


title: GapmeR-KIMAT1 rep2_mRNA


title: healthy tumor-surrounding mucosa of sample CRC.14

value: Surrounding healthy tissue


title: colorectal mucosa of sample CRC.14

value: Colorectal adenocarcinoma tissue

value: II


title: healthy tumor-surrounding mucosa of sample CRC.15


title: Non-malignant 2

description:
Sample 15
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Skin


title: GapmeR-KIMAT1 rep1_mRNA


title: Control 2

value: Sprague Dawley

value: heart

value: Three months

value: Normoxia


title: Non-malignant 1

description:
Sample 14
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Submandibular gland

value: Non-malignant control


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_8_S8 (ChIP-seq)

city: Boulder

first: Thomas

last: Cech

state: CO

address: 3415 Colorado Ave., Jennie Smoly Caruthers Biotech BLDG

institute: University of Colorado Boulder

description:
Flag_SUZ12_count.csv
column header in *count.csv: 8_S8_R1_001_trimmed_nodups

data_processing:
[ChIP-seq]  Reads containing Illumina indexes were trimmed with trimmomatic/0.36 (Bolger et al., 2014), aligned to the hg38 genome with bowtie/2.2.9 (Langmead and Salzberg, 2012) using --very-sensitive, and duplicates were marked and removed with picard/2.6.0. Peak calling was performed with MACS/2.1.1 (Zhang et al., 2008) on merged replicates using the --broad setting and a false-discovery rate of 0.01. Consensus peak sets were generated by merging peak sets and removing ENCODE blacklist genomic regions with bedtools/2.25.0 (Quinlan and Hall, 2010). Metapeak plots and heatmaps were generated with deeptools/3.0.1 (Ramirez et al., 2016) using the computeMatrix function on the consensus peaks sets. ChIP-seq signal intensity plots over genomic regions were curated using CPM normalized bigwig files generated by deeptools and visualized with the Integrative Genomics Viewer (igv/2.8.0) (Robinson et al., 2011; Thorvaldsdottir et al., 2013).
Rstudio packages were used for gene centric analysis. To include promoter proximal reads, the slop function within bedtools/2.25.0 was used to add 2,500 base-pairs onto the upstream region of the 60,609 genes within the gencode hg38 annotation. Reads were counted over these annotated regions using featureCounts (Liao et al., 2014) within the Rsubread/1.32.4 package (Liao et al., 2019). P-values and fold change were calculated using DEseq2/1.26.0 (Love et al., 2014). Plotting was performed with ggplot2/3.2.1.
[RNA-seq]  Paired-end reads containing Illumina indexes were trimmed with trimmomatic/0.36 (Bolger et al., 2014), aligned to the hg38 genome with HISAT2/2.1.0 (Kim et al., 2015) using --very-sensitive, and duplicates were marked and removed with picard/2.6.0. RNA-seq signal intensity plots over genomic regions were curated using RPKM normalized bigwig files generated by deeptools/3.0.1 (Ramirez et al., 2016) and visualized with the Integrative Genomics Viewer (igv/2.8.0) (Robinson et al., 2011; Thorvaldsdottir et al., 2013). Reads were counted over gencode annotated genes in the hg38 genome with HTseq/0.9.1 (Anders et al., 2015). P-values and fold change were calculated using DEseq2/1.26.0 (Love et al., 2014). Plotting was performed with ggplot2/3.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: Comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation. Bigwig files are also provided for ChIP-seq data files

source_name: iPSC

growth_protocol: All experiments were performed in the human iPSC line GM25256 (WTC-11) purchased from the Coriell Institute (https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25256). Unless otherwise noted, cells were maintained on Vitronectin coated plates in Essential 8 Flex medium supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin at 37C/5%CO2. Cell splitting was performed using gentle conditions by incubating cells at 37C/5%CO2 for 5 min in PBS/0.5mM EDTA.

extract_protocol:
Total RNA was extracted with Trizol following manufactuer's protocol. DNA samples in ChIP-seq were extracted using phenol-chloroform.
KAPA RNA Hyperprep kit with riboerase (RNA-seq and fRIP-seq), KAPA HyperPlus Kit (ChIP-seq)

treatment_protocol: Refer to main text for complete ChIP-seq and RNA-seq methods

tag: differentiation state

value: undifferentiated

tag: clone

value: A2J2mut2 - polyclonal

tag: genotype

tag: cell type

value: iPSC

tag: fraction

value: DNA input

tag: biological replicate


title: GapmeR-Ctrl rep3_mRNA

tag: cell line

value: ctrl


title: GapmeR-Ctrl rep2_mRNA

tag: gapmer target


title: healthy tumor-surrounding mucosa of sample CRC.11

tag: diagnosis

tag: Sex


title: colorectal mucosa of sample CRC.11

tag: tnm classification

value: pT3 N0

tag: colorectal cancer stadium

tag: tumor localization

value: Sigmoid colon


title: Angiosarcoma 12

description:
Sample 12
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Parotid gland

value: Tumor


title: Angiosarcoma 13

description:
Sample 13
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Soft tissue


title: Angiosarcoma 11

description:
Sample 11
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Liver


title: healthy tumor-surrounding mucosa of sample CRC.10

value: M


title: KRASG12D rep3

data_processing:
RSubRead
FeatureCount
DESeq2
Genome_build: Hg19
Supplementary_files_format_and_content: Excel spreadsheet with raw count

tag: transfected with

value: KRAS G12D


title: Angiosarcoma 10

description:
Sample 10
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Breast


title: Skin_biopsy_Healthy_Leg_Margin4

type: RNA

city: North Grafton

first: Jillian

middle: M

last: Richmond

state: Massachusetts

address: 200 Westboro Road

department: Comparative Pathobiology

institute: Tufts Cummings School of Veterinary Medicine

hyb_protocol: Hybridizations were performed per Nanostring manufacturer's protocol overnight for 18h in a BioRad C1000 touch thermocycler

scan_protocol: Cartridges were run on a Nanostring Sprint machine

data_processing: Data were analyzed with nSolver software version 4.0

label: fluorescent probe

organism: Canis lupus familiaris

source_name: archival skin biopsy

label_protocol: Probe labeling was performed per Nanostring manufacturer's protocol

extract_protocol: RNA was isolated from 30 micron curls from archival skin biopsies using Qiagen FFPE RNEasy kit with Deparaffinization solution per the manufacturer's instructions.

tag: disease status

value: Healthy (leg margin)


title: Skin_biopsy_Healthy_Leg_Margin5


title: Skin_biopsy_Healthy_Leg_Margin2

description: 12yo_neuteredMale_GermanShepherdDogCross


title: KRASG12D rep2


title: colorectal mucosa of sample CRC.10

value: Colorectal adenocarcinoma tissue

value: II


title: healthy tumor-surrounding mucosa of sample CRC.13

value: Surrounding healthy tissue


title: Angiosarcoma 9

description:
Sample 9
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt


title: Skin_biopsy_Vitiligo_case1

value: vitiligo


title: Angiosarcoma 8

description:
Sample 8
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Left chest wall


title: colorectal mucosa of sample CRC.13

value: Rectum


title: colorectal mucosa of sample CRC.8

value: pT2 N0

value: I

value: Hepatic flexure

value: F


title: Angiosarcoma 7

description:
Sample 7
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Ovary


title: Skin_biopsy_VKH_case1

value: VKH


title: GapmeR-Ctrl rep1_mRNA

value: ctrl


title: Skin_biopsy_Healthy_Leg_Margin3


title: KRASWT rep2

value: KRAS WT


title: Angiosarcoma 6

description:
Sample 6
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Adrenal gland


title: colorectal mucosa of sample CRC.7

source_name: Colonic mucosa

value: pT3 N2b

value: IIIC

value: Ascending colon + splenic flexure


title: KRASWT rep1

source_name: H1299 cells


title: healthy tumor-surrounding mucosa of sample CRC.6

value: M


title: Angiosarcoma 5

description:
Sample 5
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

value: Tumor


title: healthy tumor-surrounding mucosa of sample CRC.8


title: Angiosarcoma 4

description:
Sample 4
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Heart


title: Skin_biopsy_Healthy_Leg_Margin1

description: 6yo_spayedFemale_Alaskan Malamute

value: Healthy (leg margin)


title: Angiosarcoma 3

description:
Sample 3
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Perihepatic tissue


title: colorectal mucosa of sample CRC.6

value: Colorectal adenocarcinoma tissue

value: T1 N0

value: Descending colon


title: KRASWT rep3


title: Skin_biopsy_VKH_case2


title: Angiosarcoma 2

description:
Sample 2
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Lung


title: Empty Vector rep3

value: empty vector


title: Empty Vector rep1


title: healthy tumor-surrounding mucosa of sample CRC.5

value: Surrounding healthy tissue


title: healthy tumor-surrounding mucosa of sample CRC.7


title: siNPM1 rep3

data_processing:
RSubRead
FeatureCount
DESeq2
Genome_build: Hg19

tag: knockdown


title: siNPM1 rep2


title: healthy tumor-surrounding mucosa of sample CRC.4


title: colorectal mucosa of sample CRC.5

value: pT3 N0

value: II

value: Splenic flexure


title: Transgenic, biological replicate3

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

institute: Tigem

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 .

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

label: biotin

source_name: liver of transgenic mouse

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: Conditional Tcfeb overxpressing mice were crossed with Alb-Cre line to get Tcfeb overexpression specifically in the liver

extract_protocol: Total RNAs from both wild-type and transgenic livers were purified by Trizol (Fisher Scientific, catalog no. 10296028 and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

treatment_protocol: Livers from wild-type and transgenic mice at P9 were used for the analysis

tag: tissue

value: liver

tag: genotype/variation

value: transgenic


title: colorectal mucosa of sample CRC.4

value: pT3a N1a

value: IIIB

value: Sigmoid colon


title: Transgenic, biological replicate2


title: Angiosarcoma 1

description:
Sample 1
Frozen tissue
RNA-Seq (paired-end, 2x50bp)
Raw_gene_counts_matrix_angio.txt

source_name: Omentum

tag: tissue type


title: Empty Vector rep2


title: siNPM1 rep1


title: CTL, biological replicate 3

source_name: liver of wild-type mouse

value: wild type


title: Transgenic, biological replicate1


title: CTL, biological replicate 2


title: RPE_TLA_Taxol_Resist

city: Amsterdam

first: Anna

last: Gonzalez Manjon

email: a.gonzalez@nki.nl, li.koob@nki.nl

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: TLA in RPE-1 taxol resistant cells replicate 1

data_processing:
Library strategy: TLA sequencing
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
RNA-seq: For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
DAMID: The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17. Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Supplementary_files_format_and_content: DamID: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins
Genome_build: RNA seq: Hg38
Genome_build: DAMID, ChIP-seq & TLA: Hg19

source_name: RPE-1 cells

growth_protocol: RPE-1 cells were grown in DMEMF12 with 6% FCS and 1%Pen/Strep

extract_protocol:
Sample collection was performed as described before by (de Vree et al Nat Gen 2014).
Library construction was performed as described before by (de Vree et al Nat Gen 2014).

tag: technique

value: TLA

value: Taxol resistant

tag: chip antibody


title: RPE_TLA_WT

description: TLA in RPE-1 cells replicate 1

value: WT


title: healthy tumor-surrounding mucosa of sample CRC.3

value: M


title: CTL, biological replicate 1


title: siDHX9 rep3


title: colorectal mucosa of sample CRC.3

value: Colorectal adenocarcinoma tissue

value: pT1 N0

value: I


title: siDHX9 rep1


title: healthy tumor-surrounding mucosa of sample CRC.1

value: Surrounding healthy tissue


title: siDHX9 rep2


title: RPE_LMNB1_CRISPRa_RUND_Rep2

description: DamID RPE-1 CRISPRa RUNDC3B Dam-LMNB1Replicate 2

data_processing:
Library strategy: DamID-seq
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
RNA-seq: For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
DAMID: The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17. Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Supplementary_files_format_and_content: DamID: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins
Genome_build: RNA seq: Hg38
Genome_build: DAMID, ChIP-seq & TLA: Hg19

extract_protocol:
Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, with the addition of a dephosphase step to prevent amplification of apoptotic fragments. 500 ng of genomic DNA was first dephosphorylated with rSAP (NEB), before digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. Following DpnII digestion of intact GATC sequences, DNA fragments were amplified with 22-26 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 9-12 PCR cycles with illumina index adapters.

treatment_protocol: 200.000 cells were plated in a 6-well plate in 2mL full medium, supplemented with 8 μg/mL polybrene to enhance viral transduction efficiency. Cells were transduced with either Dam-only lentivirus or Dam-LMNB1lentivirus. The following day, medium was refreshed. Three days after transduction, cells were harvested and genomic DNA was isolated.

value: DAMID


title: RPE_LMNB1_CRISPRa_Combo_Rep2

description: DamID RPE-1 CRISPRa ABCB4 and RUNDC3B Dam-LMNB1 Replicate 2


title: RPE_LMNB1_CRISPRa_ABCB4_Rep2

description: DamID RPE-1 CRISPRa ABCB4 Dam-LMNB1 Replicate 2


title: colorectal mucosa of sample CRC.1

value: pT2 N0


title: siCtrl rep3

value: siCtrl


title: RPE_ChIP_Input

description: Input DNA in RPE-1 WT

data_processing:
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
RNA-seq: For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
DAMID: The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17. Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Supplementary_files_format_and_content: DamID: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins
Genome_build: RNA seq: Hg38
Genome_build: DAMID, ChIP-seq & TLA: Hg19

extract_protocol:
Chromatin immunoprecipitations (ChIP) were performed as described (Stelloo et al. Oncogene 2018). For each ChIP 5 μg of specified antibody prebound to protein A beads were used.
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303 KAPA biosystems kit).

value: ChIP seq

value: none (input)


title: RPE_LMNB1_CRISPRa_WT_Rep2

description: DamID RPE-1 CRISPRa Dam-LMNB1 Replicate 2


title: siCtrl rep2


title: RPE_ChIP_H3K4me1_Rep2

description: ChIP in RPE-1 WT cells for H3k4me1


title: siCtrl rep1


title: Atl_4_3

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500 platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-houseperl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity (Grabherr et al, 2011) with min_kmer_cov set to 2 by default and all other parameters set default.
Genome_build: de novo sequencing without reference genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Cervus nippon

extract_protocol:
Antlers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNaseH- Clustering and sequencing (Novogene Experimental Department)）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. In the reaction buffer, dNTPs with dTTPwere replaced by dUTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structurewere ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μlUSER Enzyme (NEB， USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100system.

tag: breed

value: Shuangyang Sika deer

tag: developmental stage

value: antler


title: RPE_ChIP_H3K4me3_Rep2

description: ChIP in RPE-1 WT cells for H3k4me3

tag: cell line


title: RPE_LMNB1_TaxolRes_Dam_Rep2

description: DamID RPE-1 Taxol resistant Dam-LMNB1l Replicate 2


title: Atl_4_2


title: Atl_4_1


title: KRASG12D rep1

value: KRAS G12D


title: RPE_LMNB1_LBRKO_Rep2

description: DamID RPE-1 LBR KO Dam-LMNB1l Replicate 2

value: LBRKO


title: RPE_ChIP_H3K4me3_Rep1

description: ChIP in RPE-1 WT cells for H3k4me3


title: RPE_ChIP_H3K4me1_Rep1

description: ChIP in RPE-1 WT cells for H3k4me1


title: RPE_ChIP_H3K36me3_Rep2

description: ChIP in RPE-1 WT cells for H3k36me3


title: RPE_LMNB1_CRISPRa_ABCB1_Rep2

description: DamID RPE-1 CRISPRa ABCB1 Dam-LMNB1 Replicate 2


title: Atl_3_3


title: RPE_Dam_CRISPRa_RUND_Rep2

description:
DamID RPE-1 CRISPRa RUNDC3B Dam-control Replicate 2
pADamID-RPE_CRISPRa-RUNCD3B_Lmnb1-10kb-combined.bw


title: Atl_3_2


title: RPE_ChIP_H3K36me3_Rep1

description: ChIP in RPE-1 WT cells for H3k36me3


title: RPE_LMNB1_WT_Rep2

description: DamID RPE-1 WT Dam-LMNB1 Replicate 2


title: Genomic DNA from metastatic tissue 9

type: genomic

city: Campinas

first: Mariana

last: Maschietto

state: São Paulo

address: Rua Márcia Mendes, 619

department: Research Center

country: Brazil

institute: Boldrini Children's Hospital

description: metastatic tissue from lung

hyb_protocol: DNA was hybridized to each array according to the manufacturer's standard hybridization protocol.

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

data_processing: Scanned Illumina Infinium Human Methylation450 Beadchip were processed into IDAT files by GenomeStudio software v.2011.1, with methylation module v.1.9.0 using standard recommended Illumina scanner setting. Probes were annotated according to the Illumina annotation file using the Human GRCh37/hg19. Probes presenting unreliable fluorescence measurements, including multi-hit probes (n = 6830), located in XYS (n = 52,017) and failed probes (detP > 0.05, n = 73,045), were removed. Further, Quantile normalization was applied on the remaining 353,620 probes.

label: Biotin

source_name: metastatic tissue 9

label_protocol: As per manufacturer (Illumina)

extract_protocol: Genomic DNA was extracted and purified from formalin-fixed paraffin-embedded (FFPE) blocks samples using Qiagen DNeasy Kit and  recovered using Infinium HD FFPE Restore Protocol kit (Illumina, Inc, San Diego, CA, USA), according to standard instructions

value: metastatic tissue

tag: gender

value: Male

tag: age


title: RPE_Dam_CRISPRa_ABCB4_Rep2

description:
DamID RPE-1 CRISPRa ABCB4 Dam-control Replicate 2
pADamID-RPE_CRISPRa-ABCB4_Lmnb1-10kb-combined.bw


title: RPE_ChIP_H3K9me3_Rep2

description: ChIP in RPE-1 WT cells for H3k9me3

value: WT


title: Genomic DNA from normal kidney 9

description: normal kidney cortex

source_name: normal kidney 9

value: normal kidney


title: Atl_3_1


title: Atl_2_3


title: RPE_ChIP_H3K9me3_Rep1

description: ChIP in RPE-1 WT cells for H3k9me3


title: RPE_Dam_LBRKO_Rep2

description:
DamID RPE-1 LBR KO Dam-control Replicate 2
pADamID-RPE_LBR2KO_Lmnb1-10kb-combined.bw


title: Atl_2_2


title: RPE_Dam_CRISPRa_WT_Rep2

description:
DamID RPE-1 CRISPRa Dam-control Replicate 2
pADamID-RPE_CRISPRa-WT_Lmnb1-10kb-combined.bw


title: Genomic DNA from normal kidney 10

description: normal kidney cortex

source_name: normal kidney 10


title: Atl_2_1


title: RPE_Dam_TaxolRes_Dam_Rep2

description:
DamID RPE-1 Taxol resistant Dam-control Replicate 2
pADamID-RPE_s20_Lmnb1-10kb-combined.bw

value: Taxol resistant


title: Atl_1_3


title: Genomic DNA from metastatic tissue 10

description: metastatic tissue from lung

source_name: metastatic tissue 10


title: RPE_Dam_WT_Rep2

description:
DamID RPE-1 WT Dam-control Replicate 2
pADamID-RPE_wt_Lmnb1-10kb-combined.bw


title: RPE_LMNB1_CRISPRa_RUND_Rep1

description:
DamID RPE-1 CRISPRa RUNDC3B Dam-LMNB1Replicate 1
pADamID-RPE_CRISPRa-RUNCD3B_Lmnb1-10kb-combined.bw


title: Atl_1_2


title: Atl_1_1


title: miR_Atl_4

data_processing:
CASAVA  bcl2fastq-1.8.4 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Antlers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissus

value: Antler


title: RPE_LMNB1_CRISPRa_ABCB4_Rep1

description:
DamID RPE-1 CRISPRa ABCB4 Dam-LMNB1 Replicate 1
pADamID-RPE_CRISPRa-ABCB4_Lmnb1-10kb-combined.bw


title: miR_Atl_3


title: N4G

first: Li

last: Yanping

address: 1# Gaojingjia

institute: Civil Aviation General Hospital

data_processing:
Hisat2 v2.1.0 with parameters --dta –t –p 4 was used to compare the sequencing sequences of each sample with the reference genome
StringTie v1.3.2d with parameters -G ref.gtf was used to assemble reads.
HTSeq v0.6.0 with parameters -i gene_id -f bam -s no  -a 10 -q was used for estimation of gene expression.
Genome_build: Mus_musculus.GRCm38.90.chr
Supplementary_files_format_and_content: Counts for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The normal group was fed with normal chow, and the high salt group was fed with sodium-rich chow (containing 6% NaCl) for 6 weeks.

tag: strain

value: Liver

value: fed with sodium-rich chow (containing 6% NaCl)) for 6 weeks


title: Genomic DNA from Wilms tumor 10

description: Wilms tumor, blastemal component

source_name: Wilms tumor 10

value: Wilms tumor


title: Genomic DNA from Wilms tumor 6

description: Wilms tumor, blastemal component

source_name: Wilms tumor 6


title: Genomic DNA from metastatic tissue 6

description: metastatic tissue from lung

source_name: metastatic tissue 6


title: N3G


title: N2G


title: miR_Atl_2


title: Genomic DNA from Wilms tumor 9

description: Wilms tumor, blastemal component

source_name: Wilms tumor 9


title: N1G


title: RPE_LMNB1_CRISPRa_WT_Rep1

description:
DamID RPE-1 CRISPRa Dam-LMNB1 Replicate 1
pADamID-RPE_CRISPRa-WT_Lmnb1-10kb-combined.bw

value: DAMID


title: miR_Atl_1


title: Genomic DNA from normal kidney 6

description: normal kidney cortex

source_name: normal kidney 6


title: 4G

value: fed with normal chow


title: Genomic DNA from metastatic tissue 5

description: metastatic tissue from lung

source_name: metastatic tissue 5

value: Female


title: RPE_LMNB1_TaxolRes_Dam_Rep1

description:
DamID RPE-1 Taxol resistant Dam-LMNB1l Replicate 1
pADamID-RPE_s20_Lmnb1-10kb-combined.bw


title: RPE_LMNB1_LBRKO_Rep1

description:
DamID RPE-1 LBR KO Dam-LMNB1l Replicate 1
pADamID-RPE_LBR2KO_Lmnb1-10kb-combined.bw


title: Genomic DNA from Wilms tumor 5

description: Wilms tumor, blastemal component

source_name: Wilms tumor 5


title: Bone marrow, AML 4

city: Shanghai

first: Shuang

last: Li

address: 12 Wulumuqi Road Central

institute: Huashan Hospital of Fudan University

description:
[s5344]
Gene expresison without any treatment

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software.

source_name: Bone marrow, AML 4, M2a

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

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

treatment_protocol: Bone marrow samples were extracted from 5 MDS patients, 5 AML patients and 4 controls without any treatment.

tag: subject status

value: acute myeloid leukemia (AML)

value: male

tag: subtype

value: bone marrow


title: IL4,13

city: Denver

first: Donald

last: Leung

address: 1400 Jackson Street

department: Pediatrics

institute: National Jewish Health

description: IL4 [50 ng/mL], IL13 [50 ng/mL]  18 hrs

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Partek, RMA
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: Cell Culture

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Human epidermal keratinocytes were cultured on collagen matrix in serum-free and Ca2+-free EpiLife medium (Life Technologies, Grand Island, NY) supplemented with 0.06 mM CaCl2, 1% human keratinocyte growth Supplement S7 (Life Technologies), and 1% gentamicin/amphotericin in 5% CO2 at 37°C.

extract_protocol: Qiagen Rneasy kit

treatment_protocol: Incubated in culture with IL4, IL4 and IL13, or IL4,13 and IL31 for 18 hours

value: Neonatal

tag: agent

value: Human Epidermal Keratinocytes

tag: genotype

value: Commercial line, presumably wild-type


title: 2G


title: Bone marrow, AML 5

description:
[s2345]
Gene expresison without any treatment

source_name: Bone marrow, AML 5, M2a

value: female


title: IL13

description: IL13 [50 ng/mL] 18 hrs


title: IL4,13,31

description: IL4 [50 ng/mL], IL13 [50 ng/mL], IL31 [10 ng/mL]  18 hrs


title: Genomic DNA from metastatic tissue 3

description: metastatic tissue from lung

source_name: metastatic tissue 3

value: metastatic tissue

value: Male


title: 3G


title: RPE_LMNB1_WT_Rep1

description:
DamID RPE-1 WT Dam-LMNB1 Replicate 1
pADamID-RPE_wt_Lmnb1-10kb-combined.bw

source_name: RPE-1 cells

value: WT


title: Bone marrow, AML 3

description:
[s3922]
Gene expresison without any treatment

source_name: Bone marrow, AML 3, M2a


title: 1G


title: RPE_Dam_CRISPRa_Combo_Rep1

description: DamID RPE-1 CRISPRa ABCB4 and RUNDC3B Dam-control Replicate 1

value: CRISPRa_ABCB4 and RUNDC3B


title: 2D cardiac differentiation 3

city: Hannover

first: Robert

last: Zweigerdt

address: Carl-Neuberg-Str. 1

country: Germany

institute: Hannover Medical School

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of labeled cRNA were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  After normalization, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.  Finally, normalized processed data were imported into Omics Explorer software v3.5 (Qlucore) under default import settings for Agilent One Color mRNA Microarrays, except that any (further) normalization option during import was deselected. Accordingly, data processing steps during Omics Explorer import were: 1) removal of control measurements, 2) log base 2 transformation, 3) baseline transformation to the median.

source_name: HES3 NKX2.5-eGFP-derived cardiomyocytes

label_protocol: 110ng of total RNA were used as input. Synthesis of Cy3-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit One-Color’ (#5190-2305, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Prior to RNA isolation, single HFOs were incubated in 20 uL Collagenase II (Worthington) for 30 min at 37C for dissociation, whereby every 5 - 10 min, HFOs were disrupted by pipetting up and down. 330 uL RLT buffer (Qiagen) containing 1% β-Mercaptoethanol (Thermo Fisher Scientific) was added on top of the dissociated HFOs and vortexed for 15 s. Total RNA was prepared using the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. For RNA isolation from human embryonic hearts, cardiomyocytes from 2D differentiation, and hPSCs, samples were put into Trizol (Thermo Fisher Scientific) and mechanically disrupted by vortexing and pipetting. RNA isolation was performed using the NucleoSpin RNA Kit (Macherey-Nagel) according to manufacturer's instructions.


title: IL4

description: IL4 [50 ng/mL] 18 hrs

value: IL4 [50 ng/mL]


title: 2D cardiac differentiation 1


title: Media

description: Media control

value: Media control


title: Human heart 5-6 wk 2

description: Tissue procurement and processing were performed in accordance with institutional guidelines and was approved by the local research ethics committee (University Tübingen IRB #356/2008BO2 and #406/2011BO02). Human first trimester hearts (n = 4; 5 – 7 weeks of gestation) were obtained from elective aborted fetuses following informed consent and de-identification.

source_name: Human embryonic heart

value: 5-6 weeks of gestation


title: Spleen, VEH7

city: New Brunswick

first: Daniel

last: Herranz

state: New Jersey

address: 195 Little Albany Street

institute: Rutgers Cancer Institute of New Jersey

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Gene abundance estimates were obtained for each sample using kallisto 0.44.0, with the RefSeq mm10 transcriptome as the reference
The abundance levels were normalized using the DESeq between-sample normalization approach
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file includes the DESeq normalized counts for all samples

source_name: Spleen

growth_protocol: PE conditional knockout T-ALLs were injected intravenously in sub-lethally Irradiated mice

extract_protocol:
Leukemic spleens were removed, single-cell suspensions were obtained by pressing them through a 40mm filter, and subsequently subjected to red blood cell lysis. RNA was extracted using QIAGEN QIAshredder (#79656) and Rneasy Mini (#74106) kits. 1mg of Total RNA was used for the construction of sequencing libraries by Genewiz.
Strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with vehicle only (control: corn oil, C8267, Sigma-Aldrich) or tamoxifen (T5648, Sigma-Aldrich; 3 mg per mouse in corn oil) administered by intraperitoneal injection

tag: disease state

value: T-cell acute lymphoblastic leukaemia (T-ALL)

value: leukemic spleen

value: Control


title: 2D cardiac differentiation 2


title: Human heart 6-7 wk

value: 7 weeks of gestation


title: RPE_Dam_CRISPRa_ABCB4_Rep1

description: DamID RPE-1 CRISPRa ABCB4 Dam-control Replicate 1

value: DAMID


title: Spleen, VEH6

tag: tissue


title: Bone marrow, AML 1

description:
[s2750F1]
Gene expresison without any treatment

source_name: Bone marrow, AML 1, M2a, transformed from sample 2750

value: acute myeloid leukemia (AML)

value: male

value: bone marrow


title: Human heart 5-6 wk 1


title: RPE_Dam_CRISPRa_RUND_Rep1

description: DamID RPE-1 CRISPRa RUNDC3B Dam-control Replicate 1

tag: genotype/variation


title: Genomic DNA from Wilms tumor 3

description: Wilms tumor, blastemal component

source_name: Wilms tumor 3

value: Wilms tumor


title: Genomic DNA from metastatic tissue 2

description: metastatic tissue from lung

source_name: metastatic tissue 2


title: Genomic DNA from normal kidney 5

description: normal kidney cortex

source_name: normal kidney 5

value: normal kidney

value: Female


title: hPSCs 3

source_name: HES3 NKX2.5-eGFP cells cultured on monolayer

value: Pluripotent cells


title: Genomic DNA from normal kidney 2

description: normal kidney cortex

source_name: normal kidney 2

value: Male


title: Genomic DNA from Wilms tumor 1

description: Wilms tumor, blastemal component

source_name: Wilms tumor 1


title: Human heart 5 wk

value: 5 weeks of gestation


title: Genomic DNA from Wilms tumor 2

description: Wilms tumor, blastemal component

source_name: Wilms tumor 2


title: RPE_Dam_CRISPRa_ABCB1_Rep1

description: DamID RPE-1 CRISPRa ABCB1 Dam-control Replicate 1


title: Spleen, VEH1


title: Genomic DNA from normal kidney 3

description: normal kidney cortex

source_name: normal kidney 3


title: RPE_Dam_LBRKO_Rep1

description: DamID RPE-1 LBR KO Dam-control Replicate 1

value: LBRKO


title: Bone marrow, MDS 3

description:
[s5096]
Gene expresison without any treatment

source_name: Bone marrow, MDS 3, RAEB-1

value: myelodysplastic syndrome (MDS)


title: Genomic DNA from metastatic tissue 1

description: metastatic tissue from lung

source_name: metastatic tissue 1

value: metastatic tissue


title: Bone marrow, MDS 2

description:
[s6373]
Gene expresison without any treatment

source_name: Bone marrow, MDS 2, RAEB-1


title: Spleen, TMX5

value: T-cell acute lymphoblastic leukaemia (T-ALL)

value: Pten-enhancer deleted


title: RPE_Dam_WT_Rep1

description: DamID RPE-1 WT Dam-control Replicate 1

source_name: RPE-1 cells

value: WT


title: Bone marrow, MDS 1

description:
[s2750]
Gene expresison without any treatment

source_name: Bone marrow, MDS- 1, RAEB-1


title: Spleen, TMX6

value: leukemic spleen


title: Bone marrow, MDS 5

description:
[s10508]
Gene expresison without any treatment

source_name: Bone marrow, MDS 5, RAEB-1


title: RPE_Dam_TaxolRes_Dam_Rep1

description: DamID RPE-1 Taxol resistant Dam-control Replicate 1

value: DAMID

value: Taxol resistant


title: RPE_TaxolRes_RNAseq_R2

description:
RNAseq RPE-1 taxol resistant cells Replicate2
5735_bamstats.txt

extract_protocol: Cells were trypsinized and collected with 600uL of RLT vuffer

value: RNA seq


title: Bone marrow, MDS 4

description:
[s10849]
Gene expresison without any treatment

source_name: Bone marrow, MDS 4, RAEB-1

value: male

value: bone marrow


title: Bone marrow, Control 3

description:
[s0023A]
Gene expresison without any treatment

source_name: Bone marrow, Control 3, Leukopenia

value: control Leukopenia

value: female


title: RPE_TaxolRes_RNAseq_R1

description:
RNAseq RPE-1 taxol resistant cells Replicate1
5386_bamstats.txt


title: Spleen, TMX1

source_name: Spleen


title: NKX2.5-KO 2

source_name: HES3 NKX2.5-eGFP/eGFP-derived organoid (NKX2.5 knock-out)


title: Bone marrow, Control 4

description:
[s0034A]
Gene expresison without any treatment

source_name: Bone marrow, Control 4, Leukopenia


title: hPSCs 2

value: Pluripotent cells


title: RPEWT_RNAseq_R3

description:
RNAseq RPE-1 cells Replicate3
5386_bamstats.txt


title: NKX2.5-KO 1


title: Bone marrow, Control 1

description:
[s0009A]
Gene expresison without any treatment

source_name: Bone marrow, Control 1, Hypersplenism

value: control Hypersplenism


title: Bone marrow, Control 2

description:
[s0011A]
Gene expresison without any treatment

source_name: Bone marrow, Control 2, Thrombocytopenia

value: control Thrombocytopenia


title: RPEWT_RNAseq_R2

description:
RNAseq RPE-1 cells Replicate2
4280_bamstats.txt


title: Spleen, VEH5

value: Control


title: Spleen, TMX2


title: NKX2.5-KO 3


title: HFO 5

source_name: HES3 NKX2.5-eGFP-derived organoid


title: Genomic DNA from normal kidney 1

description: normal kidney cortex

source_name: normal kidney 1

value: normal kidney

value: Female


title: Normal skin keratinocytes_P.5-Untreated

city: Perth

first: Zhenjun

last: Deng

state: Western Australia

address: 35 Stirling Highway

country: Australia

institute: The University of Western Australia

data_processing:
Real Time Analysis (RTA) v3.4.4 software used for base-calling. Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Merge the two files for each sample prior to secondary analyses.
Fastp used for trimming.
STAR used for aligment and SAMtools used to generate bam files for further analyses.
DESeq2 used for differential gene expresson analyses.
Genome_build: hg19
Supplementary_files_format_and_content: CSV files with normalized abundance counts

source_name: Normal skin keratinocytes

growth_protocol: Fibroblasts were grown in DMEM/F12-Glutamax™ media with 10% FBS and 1% penicillin/streptomycin. Keratinocytes were grown in keratinocytes growth media (KGM, EpigrowTM, human epidermal keratinocyte complete culture media kit, Merck, Millipore, Massachusetts, USA) with 1% penicillin/streptomycin and 1.2 mM calcium chloride.

extract_protocol:
After treatment, cells were then collected using 0.05% trypsin and washed in PBS, before RNA was extracted. RNA was extracted using the RNeasy Mini kit protocol (Cat no-74104, Qiagen, Netherlands) according to the manufacturers’ protocol and stored at -80C for further analysis.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with/without 10 µM PXS-4787A for 48 hours.

tag: treatment

value: untreated

tag: cell type

value: keratinocytes


title: hPSCs 1

source_name: HES3 NKX2.5-eGFP cells cultured on monolayer


title: Normal skin keratinocytes_P.5-PXA-4787A

value: 10 uM PXS-4787A for 48 hours


title: Normal skin keratinocytes_P.4-PXA-4787A


title: RPEWT_RNAseq_R1

description:
RNAseq RPE-1 cells Replicate1
4280_bamstats.txt

tag: technique

value: WT

tag: chip antibody


title: TNBC GEMM 2208L 8800 Rep 2

city: Houston

first: Jarey

middle: Hao

last: Wang

state: Texas

address: 1 Baylor Plaza, 304B, Anderson Building

institute: Baylor College of Medicine

data_processing:
Raw read of fastq format were obtained after adapter removal in BaseSpace. Index of the mm10 mouse or hg38 human genome was built using hisat2-v2.0.4.
Proper paired-end reads were aligned to the reference genome using hisat2-v2.0.4.
The pysam python module was used to compute number of reads mapping to introns (in gtf format); reads mapping to features were then RPKM normalized.
Genome_build: mm10
Supplementary_files_format_and_content: gtf files for introns, along with two additional columns 1) number of reads mapped to the intron 2) number of reads mapped to or spanning the intron and 3) rpkm based on intronic reads

molecule: polyA RNA

source_name: GEMM 2208L

growth_protocol: T11, AT3, PyMT-M, 2208L GEMM tumors were transplanted orthotopically into C57BL/6 or Balbc females and then randomized onto 8800 or Vehicle.

extract_protocol:
Bulk tumor RNA isolated using RNeasy kit (Qiagen).
~300 bp insert strand specific library with polyA selection (TruSeq Stranded mRNA kit, Illumina).

treatment_protocol: Mice were treated with 8800 or Vehicle each day prior to take down (as specified in manuscript) and tumor preservation in RNAlater.

value: Balb/c

value: Breast tumor

value: 4-5 week mice at transplant

value: Drug

tag: phenotype

value: Responder


title: TNBC GEMM 2208L 8800 Rep 1


title: JURKAT_PTEN_enhancer_rep3

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Library strategy: 4C-Seq
The first nucleotides in each read (corresponding to barcode) and the nucleotides corresponding to theHindIII primer were trimmed from the 5' of the read
Mapping was performed using Bowtie2 to a reduced genome consisting of all unique 24 nucleotide-long regions surrounding DpnII sites allowing for zero mismatches.
Analysis of 4C-Seq signal was performed by building successive 25kb windows with 90% overlap and calculating the total number of reads per window.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: bedgraph files show total read count per 25kb window. Windows show 90% overlap.

source_name: JURKAT

growth_protocol: We performed cell culture of cell lines in standard conditions in a humidified atmosphere at 37°C under 5% CO2. DND41 (ACC 525), JURKAT (ACC 282), HPB-ALL (ACC 483) cells were obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). T-ALL cells were cultured in HyClone RPMI 1640 Media (SH3002701, Fisher Scientific) supplemented with 10% FBS (900-108, Gemini Bio-Products) and 1% penicillin-streptomycin (45000-652, VWR).

extract_protocol:
4C-Seq was prepared using HindIII and DpnII digestions.
The following primers were used for amplification (human PTEN promoter viewpoint: FW-AAATATCAACACTGAAGCTT and RV- GCCTCCAGTTGATTTCCAGA; human PE viewpoint FW- CAGCTTCTCCTTTTAAGCTT and RV- CACAGACATAATGCTGGGAA; mouse Pten promoter viewpoint FW- GTTCATCCTGAGTAAAGCTT and RV- CAAAAGATAATTGGTGAGCA; mouse PE viewpoint: FW- CCTCTATATGAGAGAAGCTT and RV- AAGAGCTGGCCACATGGTGA)

treatment_protocol: All samples were collected under same treatment conditions as described in growth protocol

value: leukemic cell line

tag: bait

tag: cell line

value: JURKAT


title: TNBC GEMM 2208L 8800 Rep 3

tag: age


title: Normal skin keratinocytes_P.4-Untreated


title: Normal skin keratinocytes_P.3-PXA-4787A


title: JURKAT_PTEN_enhancer_rep1


title: JURKAT_PTEN_enhancer_rep2


title: TNBC GEMM 2208L Veh Rep 3

value: Vehicle


title: TNBC GEMM 2208L Veh Rep 2


title: Normal skin keratinocytes_P.3-Untreated


title: JURKAT_PTEN_promoter_rep3


title: TNBC GEMM 2208L Veh Rep 1


title: Normal skin keratinocytes_P.2-PXA-4787A


title: TRA1ChIP_TRA1flag-TBSx3_72h_IP_rep2

city: Baltimore

first: Margaret

middle: R

last: Starostik

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq IP replicate 2
TRA1ChIP_TRA1flag-TBSx3_72h_rep2.narrowPeak

data_processing:
Raw small RNA-seq reads were trimmed for Illumina adapters and quality (SLIDING WINDOW: 4:25) using Trimmomatic 0.39 (Bolger et al., 2014).
Trimmed reads were then filtered using bbmap 38.23 (http://jgi.doe.gov/data-and-tools/bb-tools) to retain reads that were 15-30 nucleotides in length.
These filtered reads were aligned to the C. elegans WBcel235 (Cunningham et al., 2018) reference genome using Bowtie 1.1.1 (Langmead et al., 2009) with parameters -v 0 -k 5 --best --strata --tryhard.
Mapped reads were assigned to genomic features using featureCounts from Subread 1.6.3 (Liao et al., 2014), taking into account overlapping and multi-mapping reads (-O -M).
Raw counts were normalized within DESeq2 1.26.0 (Love et al., 2014).
For SNPC-1.3 and TRA-1 ChIP seq data, reads were trimmed for adapters and filtered for sequencing quality score > Q25 using Trim Galore! 0.5.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Filtered reads were aligned to C. elegans reference genome WBcel235 (Cunningham et al., 2018) using Bowtie2 2.3.4.2 (Langmead and Salzberg, 2012) with default parameters.
Post-alignment filtering was then performed to remove PCR duplicates using the MarkDuplicates utility within Picard 2.22.1 (http://broadinstitute.github.io/picard/).
In addition, SAMtools 1.9 was applied to remove unmapped reads and reads that mapped with MAPQ 30 but were not of primary alignment or failed sequence platform quality checks (SAMtools -F 1804 -q 30) (Li et al., 2009).
To identify DNA binding sites for SNPC-1.3, mapped and filtered SNPC-1.3 ChIP-seq reads were extended to 200 base pairs to account for the average length of ChIP fragments.
We then partitioned the genome into consecutive, non-overlapping 1,000 base pair bins and calculated read coverage, normalized by sequencing depth of each library, based on the total read count in each bin.
Bins with read coverages in the IP sample that fell below the median read coverage of piRNA-depleted regions on chromosome IV in the relevant input control were excluded from further analysis.
TRA-1 ChIP-seq peaks were called by callpeak within MACS 2.1.2 (Zhang et al., 2008) (--pvalue 0.05) with filtered TRA-1 ChIP-seq reads and relevant input controls.
Genome_build: WBcel235

organism: Caenorhabditis elegans

source_name: whole worms, gravid adult  (72 h, 20°C )

growth_protocol: Worms were grown in liquid culture at 20°C and fed E. coli strain HB101.

extract_protocol:
 After washing, the gut was cleared for 15 min by nutation in M9, followed by three washes in M9. Worms were live-crosslinked in 2.6% formaldehyde in water for 30 min at room temperature, nutating. Crosslinking was quenched with a final concentration of 125 mM glycine for 5 min with nutation. After three washes with water, worms were flash-frozen in liquid nitrogen. Frozen worms were ground into powder using a mixer mill MM400 (Retsch) for 2 rounds of 1 min at 30-1. Powder was resuspended in 1x RIPA buffer (1xPBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) for 10 min at 4°C. Crosslinked chromatin was sonicated using a Diagenode Bioruptor Pico for three 3-min cycles, 30 sec on/off. 10 µg chromatin was nutated overnight at 4°C with 2 µg of Flag antibody (Sigma-Aldrich, F1804) and then for 1.5 h with 50 µL mouse IgG Dynabeads (Invitrogen). Input amount was 10% of IP. Chromatin was decrosslinked and extracted as described previously (Weiser et al., 2017).
Libraries were prepared and multiplexed using the Ovation Ultralow Library Systems v2 (NuGEN Technologies) according to the manufacturer’s protocol. The NovaSeq 6000 platform was used to generate 50 bp paired-end reads.

value: whole worm

value: gravid adult (72h)

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk30)[snpc-1.3(3xtbs)] V

tag: replicate


title: Normal skin keratinocytes_P.2-Untreated


title: HFO 1

tag: developmental stage


title: JURKAT_PTEN_promoter_rep2


title: TNBC GEMM AT3 8800 Rep 2

source_name: GEMM AT3

tag: strain

value: Nonresponder


title: Normal skin keratinocytes_P.1-PXA-4787A


title: TRA1ChIP_TRA1flag-TBSx2_72h_IP_rep2

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seqIP replicate 2
TRA1ChIP_TRA1flag-TBSx2_72h_rep2.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk29)[snpc-1.3(2xtbs)] V


title: JURKAT_PTEN_promoter_rep1


title: Bone marrow, AML 2

description:
[s5651]
Gene expresison without any treatment

source_name: Bone marrow, AML 2, M2a

tag: subject status

value: acute myeloid leukemia (AML)

tag: gender

value: male

tag: subtype

value: bone marrow


title: TNBC GEMM AT3 8800 Rep 1

tag: genotype


title: TRA1ChIP_TRA1flag-TBSx1_72h_IP_rep2

description:
tra-1::3xflag;snpc-1.3(1xtbs) gravid adult (72h) TRA-1 ChIP-seq IP replicate 2
TRA1ChIP_TRA1flag-TBSx1_72h_rep2.narrowPeak

tag: tissue

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk28)[snpc-1.3(1xtbs)] V


title: HPBALL_PTEN_enhancer_rep3

source_name: HPBALL

value: HPBALL


title: Normal skin keratinocytes_P.1-Untreated

value: untreated

value: keratinocytes


title: Normal skin fibroblasts_P.6-Untreated

source_name: Normal skin fibroblasts

value: fibroblasts


title: TRA1ChIP_TRA1flag_72h_IP_rep2

description:
tra-1::3xflag gravid adult (72h) TRA-1 ChIP-seq IP replicate 2
TRA1ChIP_TRA1flag_72h_rep2.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III


title: TNBC GEMM AT3 Veh Rep 2

value: Breast tumor

value: 4-5 week mice at transplant


title: HPBALL_PTEN_enhancer_rep2

value: leukemic cell line


title: Spleen, TMX4

tag: disease state

value: T-cell acute lymphoblastic leukaemia (T-ALL)

value: leukemic spleen

value: Pten-enhancer deleted


title: TRA1ChIP_TRA1flag-TBSx3_72h_input_rep2

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 2
TRA1ChIP_TRA1flag-TBSx3_72h_rep2.narrowPeak

value: whole worm

value: gravid adult (72h)

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk30)[snpc-1.3(3xtbs)] V


title: Normal skin fibroblasts_P.6-PXA-4787A

tag: treatment

value: 10 uM PXS-4787A for 48 hours


title: TNBC GEMM AT3 Veh Rep 1

value: Vehicle

value: Nonresponder


title: TNBC GEMM PyMT-M 8800 Rep 4

source_name: GEMM PyMT-M

value: Drug

value: Responder


title: HPBALL_PTEN_enhancer_rep1

tag: cell type

value: HPBALL


title: TRA1ChIP_TRA1flag-TBSx2_72h_input_rep2

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 2
TRA1ChIP_TRA1flag-TBSx2_72h_rep2.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk29)[snpc-1.3(2xtbs)] V


title: Normal skin fibroblasts_P.5-PXA-4787A

value: fibroblasts


title: TNBC GEMM PyMT-M 8800 Rep 3

value: Breast tumor


title: TRA1ChIP_TRA1flag-TBSx1_72h_input_rep2

description:
tra-1::3xflag;snpc-1.3(1xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 2
TRA1ChIP_TRA1flag-TBSx1_72h_rep2.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk28)[snpc-1.3(1xtbs)] V


title: Normal skin fibroblasts_P.4-Untreated

value: untreated


title: TNBC GEMM PyMT-M 8800 Rep 2

value: 4-5 week mice at transplant


title: HPBALL_PTEN_promoter_rep2

value: leukemic cell line


title: HPBALL_PTEN_promoter_rep1


title: TRA1ChIP_TRA1flag_72h_input_rep2

description:
tra-1::3xflag gravid adult (72h) TRA-1 ChIP-seq input replicate 2
TRA1ChIP_TRA1flag_72h_rep2.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III


title: TNBC GEMM AT3 Veh Rep 3


title: DND41_PTEN_enhancer_rep3


title: TRA1ChIP_N2_72h_IP_rep2

description:
N2 gravid adult (72h) TRA-1 ChIP-seq IP replicate 2
TRA1ChIP_N2_72h_rep2.narrowPeak

value: whole worm


title: TNBC GEMM PyMT-M 8800 Rep 1


title: TRA1ChIP_N2_72h_input_rep2

description:
N2 gravid adult (72h) TRA-1 ChIP-seq input replicate 2
TRA1ChIP_N2_72h_rep2.narrowPeak

value: gravid adult (72h)


title: Normal skin fibroblasts_P.4-PXA-4787A


title: Normal skin fibroblasts_P.3-Untreated


title: DND41_PTEN_enhancer_rep2


title: Normal skin fibroblasts_P.5-Untreated


title: TNBC GEMM PyMT-M Veh Rep 4


title: TRA1ChIP_TRA1flag-TBSx3_72h_IP_rep1

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq IP replicate 1
TRA1ChIP_TRA1flag-TBSx3_72h_rep1.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk30)[snpc-1.3(3xtbs)] V


title: HPBALL_PTEN_promoter_rep3


title: DND41_PTEN_enhancer_rep1


title: TRA1ChIP_TRA1flag-TBSx2_72h_IP_rep1

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq IP replicate 1
TRA1ChIP_TRA1flag-TBSx2_72h_rep1.narrowPeak


title: Normal skin fibroblasts_P.2-Untreated


title: Normal skin fibroblasts_P.3-PXA-4787A

value: 10 uM PXS-4787A for 48 hours


title: DND41_PTEN_promoter_rep3


title: TRA1ChIP_TRA1flag-TBSx1_72h_IP_rep1

description:
tra-1::3xflag;snpc-1.3(1xtbs) gravid adult (72h) TRA-1 ChIP-seq IP replicate 1
TRA1ChIP_TRA1flag-TBSx1_72h_rep1.narrowPeak


title: TNBC GEMM PyMT-M Veh Rep 3

value: Vehicle


title: TNBC GEMM PyMT-M Veh Rep 2


title: Normal skin fibroblasts_P.2-PXA-4787A


title: TNBC GEMM PyMT-M Veh Rep 1


title: TRA1ChIP_TRA1flag_72h_IP_rep1

description:
tra-1::3xflag gravid adult (72h) TRA-1 ChIP-seq IP replicate 1
TRA1ChIP_TRA1flag_72h_rep1.narrowPeak


title: TNBC GEMM T11 8800 Rep 3

source_name: GEMM T11

value: Balb/c

value: Nonresponder


title: DND41_PTEN_promoter_rep1


title: TRA1ChIP_N2_72h_IP_rep1

description:
N2 gravid adult (72h) TRA-1 ChIP-seq IP replicate 1
TRA1ChIP_N2_72h_rep1.narrowPeak


title: Frameshifting-RNA mut-N-protein-0x 10mM-SDA In Vitro

city: Chapel Hill

first: Mark

middle: A

last: Boerneke

state: NC

address: Campus Box 3290

department: Chemistry

institute: University of North Carolina

data_processing:
Library strategy: SHAPE-MaP
Adduct locations identified by Shapemapper2 software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Reconstituted solution

extract_protocol: In vitro transcribed RNA was treated with 5NIA or DMSO (control) for SHAPE-MaP RNA structure probing experiments.  The binding of recombinantly expressed and purified SARS-CoV-2 N-protein at 160x, 80x, 20x, or 0x (control) molar excess concentrations to in vitro transcribed RNA was chemically probed using the bivalent chemical crosslinker SDA for RNP-MaP experiments. Chemically modified RNA samples from SHAPE-MaP and RNP-MaP experiments were subjected to MaP reverse transcription, which encodes the position of chemical adducts as non-templated nucleotides or deletions in the product cDNA. Sequencing libraries were generated using the Nextera XT workflow and sequenced on an Illumin MiSeq instrument.

value: isolate 2019-nCoV WHU01

value: 3J-UV and 10mM SDA

tag: target

value: Frameshifting-region RNA


title: Normal skin fibroblasts_P.1-PXA-4787A

value: fibroblasts


title: TNBC GEMM T11 8800 Rep 2

value: Breast tumor

value: Drug


title: TRA1ChIP_TRA1flag-TBSx3_72h_input_rep1

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 1
TRA1ChIP_TRA1flag-TBSx3_72h_rep1.narrowPeak


title: TNBC GEMM T11 8800 Rep 1


title: TRA1ChIP_TRA1flag-TBSx2_72h_input_rep1

description:
tra-1::3xflag;snpc-1.3(2xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 1
TRA1ChIP_TRA1flag-TBSx2_72h_rep1.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk29)[snpc-1.3(2xtbs)] V


title: Frameshifting-RNA mut-N-protein-160x 10mM-SDA In Vitro


title: TNBC GEMM T11 Veh Rep 3

value: 4-5 week mice at transplant


title: HFO sample 1

data_processing:
Compute resource: Raw data processing was conducted on a High Performance Computing cluster (HPC-seq). This cluster provides significant compute power (600 cores in 13 nodes, a total of 5 TB RAM, 300TB storage, Ubuntu Linux, SLURM job scheduler) to allow large workloads to be efficiently processed in a timely fashion, and furthermore provides the backbone for resource-intensive graphical applications such as the locally implemented MHH Galaxy instance. A three tiered storage system has been implemented, with jobs transiently stored on a fast 24TB SSD shelf, with important results saved into mid-term redundant NetApp shelves.
Raw data processing: BCL files were converted to FASTQ files using bcl2fastq Conversion Software (Illumina) using the respective sample sheet with utilized 10X barcodes. The proprietary 10x Genomics CellRanger pipeline (v3.0.2) was used with default parameters except for the setting of expected cells (--expect-cells 10000 ).
Genome_build: CellRanger was used to align read data to the reference genome provided by 10X Genomics (Human reference dataset 3.0.0; GrCh38) using the aligner STAR, counting aligned reads per gene, and calculating clustering and summary statistics.
Supplementary_files_format_and_content: The Loupe Cell Browser from 10x Genomics was used to view and revise annotated clusters, based on the implemented tSNE algorithm.

source_name: HES3 NKX2.5-eGFP reporter line

extract_protocol:
HFOs were dissociated into single cells using the STEMdiff Cardiomyocyte Dissociation Kit (Stemcell Technologies).
Library generation: Library preparation for single cell mRNA-Seq analysis was performed according to the Chromium NextGEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (Manual Part Number CG000204 Rev B; 10x Genomics). According to the protocol a given excess of cells was loaded to the 10x controller in order to reach a target number of 10000  cells per sample. Fragment length distribution of generated libraries was monitored using ‘Bioanalyzer High Sensitivity DNA Assay’ (5067-4626; Agilent Technologies). Quantification of libraries was performed by use of the ‘Qubit® dsDNA HS Assay Kit’ (Q32854; ThermoFisher Scientific). Sequencing run: Libraries were pooled, denatured with NaOH, and were finally diluted accordingly in order to be sequenced on an Illumina NovaSeq6000 sequencer using an S4 flowcell. Samples were sequenced according to the following settings: 150bp as sequence read 1; 150bp as sequence read 2; 8bp as index read 1; no index read 2. An average number of 283 million reads passing filter per sample were finally retrieved, yielding in roughly 49.000 reads per cell.

value: hPSC-derived organoid

tag: differentiation day


title: HFO sample 2


title: Frameshifting-RNA mut-N-protein-20x 10mM-SDA In Vitro


title: TRA1ChIP_TRA1flag-TBSx1_72h_input_rep1

description:
tra-1::3xflag;snpc-1.3(1xtbs) gravid adult (72h) TRA-1 ChIP-seq input replicate 1
TRA1ChIP_TRA1flag-TBSx1_72h_rep1.narrowPeak

value: tra-1(xk37)[3xflag::tra-1] III; snpc-1.3(xk28)[snpc-1.3(1xtbs)] V


title: TRA1ChIP_TRA1flag_72h_input_rep1

description:
tra-1::3xflag gravid adult (72h) TRA-1 ChIP-seq input replicate 1
TRA1ChIP_TRA1flag_72h_rep1.narrowPeak

value: whole worm

value: tra-1(xk37)[3xflag::tra-1] III


title: 5′-End RNA mut-N-protein-0x 10mM-SDA In Vitro

value: 5′-End RNA


title: TNBC GEMM T11 Veh Rep 2

tag: phenotype


title: Normal skin fibroblasts_P.1-Untreated

value: untreated


title: DND41_PTEN_promoter_rep2

value: leukemic cell line

tag: bait


title: TNBC GEMM T11 Veh Rep 1

value: Balb/c

value: Vehicle


title: TRA1ChIP_N2_72h_input_rep1

description:
N2 gravid adult (72h) TRA-1 ChIP-seq input replicate 1
TRA1ChIP_N2_72h_rep1.narrowPeak

value: gravid adult (72h)


title: 5′-End RNA mut-N-protein-160x 10mM-SDA In Vitro

value: isolate 2019-nCoV WHU01

value: 3J-UV and 10mM SDA


title: 2_4ss_H3K27Ac

city: Ithaca

first: Marcos

last: Simoes-Costa

state: New York

address: 526 Campus Rd

department: Molecular Biology and Genetics

institute: Cornell University

description: CUT&RUN data for H3K27Ac in chick neural crest cells

data_processing:
Paired-end sequencing reads from the CUT&RUN libraries were trimmed using Cutadapt (Martin, 2011). Reads were filtered for those with a minimum length of 25bp or longer and aligned to the reference chicken Galgal5 assembly using Bowtie2 (Langmead and Salzberg, 2012). Picard MarkDuplicates tool was used to mark duplicate reads and BAM files were filtered with SAMtools to discard unmapped reads (those that were not the primary alignment, reads failing platform/vendor quality checks, and PCR/optical duplicates (-f 2 -F 1804)). Bigwig plots were generated using deeptools v3.1.2 bamCoverage function with the following parameters: --binSize 5 --normalizeUsing RPGC --effectiveGenomeSize 1218492533 --extendReads.
Library strategy: CUT&RUN

organism: Gallus gallus

source_name: Neural folds

extract_protocol:
Neural folds were dissected from HH7-8 embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.

tag: condition

value: Wild type

tag: antibody


title: PSE-region-RNA N-protein-0x 10mM-SDA In Vitro

value: PSE-region RNA


title: Gilteritinib+MI3454_MOLM13_2

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

data_processing:
Quality trimming using Cutadapt version 2.1 with arguments: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT --nextseq-trim=20 --minimum-length 50
Indices generated using STAR v2.7.1a with options: --sjdbOverhang 99 --genomeSAsparseD 2
Sequences aligned using STAR v2.7.1a with options: --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within
Aligned reads counted using htseq-count from HTSeq v0.11.2 with options: -s reverse -r pos -f bam
Differential expression analysis using DESeq2 alpha < 0.05 lfcThreshold = log2(1.5)
Genome_build: GENCODE release 33 (GRCh38) primary assembly
Supplementary_files_format_and_content: tab-delimited files containing unnormalized count data

source_name: Acute monocytic leukemia cell line

growth_protocol: MOLM-13 cells were cultured in RPMI 1640 medium with 10% heat inactivated FBS and 1% pen/strep antibiotics.

extract_protocol:
Rneasy Mini Kit (Qiagen 74106)
Ribo depleted RNA was used to generate Illumina compatible TruSeq libraries

treatment_protocol: Cells were seeded at 3x10^5 cells/mL in triplicates and treated with Gilteritinib, MI3454, Gilteritinib+MI3454, or DMSO control.

tag: cells

value: Gilteritinib + MI3455


title: Gilteritinib+MI3454_MOLM13_1

value: Gilteritinib + MI3454


title: MI3454_MOLM13_3


title: RPE_Dam_CRISPRa_WT_Rep1

description: DamID RPE-1 CRISPRa Dam-control Replicate 1

data_processing:
Library strategy: DamID-seq
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
RNA-seq: For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
DAMID: The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17. Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Supplementary_files_format_and_content: DamID: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins
Genome_build: RNA seq: Hg38
Genome_build: DAMID, ChIP-seq & TLA: Hg19

source_name: RPE-1 cells

extract_protocol:
Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, with the addition of a dephosphase step to prevent amplification of apoptotic fragments. 500 ng of genomic DNA was first dephosphorylated with rSAP (NEB), before digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. Following DpnII digestion of intact GATC sequences, DNA fragments were amplified with 22-26 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 9-12 PCR cycles with illumina index adapters.

tag: technique

value: DAMID

tag: cell line

tag: genotype/variation

tag: chip antibody


title: PSE-region-RNA N-protein-20x 10mM-SDA In Vitro

tag: strain


title: NOTCH1-induced leukemia replicate1

data_processing:
The paired-end 42bp sequencing reads generated by Illumina sequencing are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads are removed.
Both data files were normalized to the same number of unique alignments (53.9 million) by downsampling.
Both reads are used for peak-calling. Peaks were identified using the MACS 1.4.2 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option.
To identify the density of transposition events along the genome, the genome was divided into 32bp bins and the number of fragments in each bin is determined. For this purpose, reads were extended to 200bp in order to smooth the data. This information was stored in a bigWig file.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files

source_name: mouse NOTCH1-induced leukemia

growth_protocol: A deltaE-NOTCH1-induced mouse primary leukemia was cultured in vitro in the presence of mouse IL-7(10ng/mL) until cells were able to continue proliferating without IL-7.

extract_protocol:
Cells were collected and frozen following Active Motif protocol guidelines.
Frozen samples were shipped to Active Motif, which prepared ATAC-seq libraries following standard procedures.

treatment_protocol: Two replicates were collected, without any treatment.

value: leukemic spleen

tag: experiment

value: Control


title: NOTCH1-induced leukemia replicate2

tag: tissue


title: presorted CD45-

city: Los Angeles

first: Hidekazu

last: Tsukamoto

state: CA

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

data_processing:
RNA-seq data was analyzed using the RNA-seq workflow in Partek Flow software (v3. Partek Inc., St. Louis, MO, USA).  Briefly, the raw sequencing reads were first trimmed based on the quality score (Phred QC>=20, min read length=25 nt)
Genome_build: The sequencing reads were mapped to mouse genome build mm10 using Tophat version 2.0.848 with default parameter settings and using Gencode M3 annotation 49 as guidance.  Gencode M3 was then used to quantify the aligned reads to genes using Partek E/M method.  The gene level aligned read counts were normalized for all samples using Upper Quartile normalization 50 before subjected to differential expression analysis using Partek Gene Specific Analysis method (genes with fewer than 10 aligned reads in any sample among a data set were excluded).
Supplementary_files_format_and_content: excel file containing genes expression comparison between R6 to R5, R6 to R8 and R6 to CD45- cells.

source_name: liver

extract_protocol:
The cells were centrifuged and total RNA was isolated with PicoPure RNA isolation kit (Thermo Fisher Scientific).
Prior to library construction RNA integrity was verified by Experion analysis (Bio-Rad).  PolyA selection was carried out using Illumina Truseq V2 polyA beads.  Material enriched for polyA was then introduced into the Kapa Biosystems stranded RNA-seq library prep kit at the elute-fragmentation-priming step then taken through the protocol according to manufacturer’s instructions.  Final PCR cycle numbers vary according to input amounts, for this set (low input got 12-14 cycles, higher input amounts 6-10) cycles was performed.  Libraries were visualized by Bioanalyzer analysis (Agilent) and quantified by qPCR (Kapa Biosystems Illumina Library Quantification Kit).

treatment_protocol: Mice were fed 40% of their daily caloric intake as ad libitum intake of high cholesterol fat diet (HCFD) and remaining 60% by intragastric feeding of alcohol-containing liquid diet.  They were also superimposed with weekly binge.

value: Alcoholic Hepatitis


title: 2_4ss_Sp5_1

description: CUT&RUN data for SP5 in chick neural crest cells

extract_protocol:
Neural folds were dissected from HH7-7 embryos (n=20 per CUT&RUN experiment). Cells were dissociated in Accumax for 20min at RT under mild agitation. CUT&RUN experiments were carried out as previously described (Rothstein and Simoes-Costa, 2019).
CUT&RUN libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, E7645) and sequenced with paired-end 37bp reads on an Illumina NextSeq500 instrument.

tag: developmental stage

value: Abcam, #ab36593


title: PSE-region-RNA N-protein-160x 10mM-SDA In Vitro

tag: treatment


title: MI3454_MOLM13_1


title: 5′-End RNA mut-N-protein-20x 10mM-SDA In Vitro

value: 5′-End RNA


title: dFezf1 24h 12/14/17

city: Boston

first: Jing

last: Peng

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing data were suitable for further analysis.
Reads were aligned to the Ensembl build BDGP6 of the D. melanogaster genome using STAR. Quality of alignments was assessed by checking for evenness of coverage, rRNA content, genomic context of alignments, complexity and other quality checks.
Expression quantification was performed with Salmon to identify transcript-level abundance estimates and then collapsed down to the gene-level using the R Bioconductor package tximport.
Differential expression was performed at the gene level using the R Bioconductor package DESeq2
Default parameters were used with the exception of the Cook’s distance filter, which was turned off. Significant genes were identified using an FDR threshold of 0.05.
Genome_build: Ensembl build BDGP6
Supplementary_files_format_and_content: The xlsx file contains the result for the differential expression analysis. The csv file has the raw counts information.

organism: Drosophila melanogaster

source_name: optic lobe

extract_protocol:
Total RNA was extracted using standard RNeasy protocol
cDNA libraries were prepared for sequencing with Illumina Nextera kit using Smart-seq2 protocols

tag: cell type

value: L3 lamina neurons

tag: genotype

value: 24h APF


title: Nucleocapsid -RNA N-protein-0x 10mM-SDA In Vitro

tag: target

value: Nucleocapsid RNA


title: dFezf1 24h 12/13/17


title: Nucleocapsid -RNA N-protein-20x 10mM-SDA In Vitro


title: Gilteritinib_MOLM13_3

value: Gilteritinib


title: Gilteritinib_MOLM13_2


title: Prom1-CD49f+CD45-


title: Prom1+CD49f+CD45-


title: dFezf1 24h 12/12/17


title: 2_4ss_Sp5_2


title: Gilteritinib_MOLM13_1


title: FRT40 24h 11/30/17

value: WT


title: MI3454_MOLM13_2


title: RNAseq: E17.5 distal fibroblast cells

city: Tokyo

first: Yasuhiro

last: Yamada

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

data_processing:
After trimming adaptor sequences and low-quality bases by cutadapt-1.16, the sequenced reads were mapped to the mouse reference genome (mm10) plus EGFP and tdTomato reporter sequences using HISAT2-2.1.0 with the GENCODE version M17 annotation gtf file. The uniquely mapped reads with high mapping quality were used for further analyses. The expression level of each gene (protein coding) was calculated as fragments per kilobase per million mapped reads (FPKM) by cufflinks-2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: processed_file.xlsx (cufflinks.FPKM)

source_name: stomach fibroblast cells

extract_protocol:
RNAeasy plus Micro Kit (QIAGEN) for RNA.
To generate RNA-seq libraries, Truseq Stranded mRNA LT sample prep kit (Illumina) was used according to the supplier’s instruction.

value: Sox2-EGFP; Gata4-td Tomato

value: stomach mesenchyme

value: distal fibroblast cells


title: HFO 3

source_name: HES3 NKX2.5-eGFP-derived organoid

extract_protocol: Prior to RNA isolation, single HFOs were incubated in 20 uL Collagenase II (Worthington) for 30 min at 37C for dissociation, whereby every 5 - 10 min, HFOs were disrupted by pipetting up and down. 330 uL RLT buffer (Qiagen) containing 1% β-Mercaptoethanol (Thermo Fisher Scientific) was added on top of the dissociated HFOs and vortexed for 15 s. Total RNA was prepared using the RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. For RNA isolation from human embryonic hearts, cardiomyocytes from 2D differentiation, and hPSCs, samples were put into Trizol (Thermo Fisher Scientific) and mechanically disrupted by vortexing and pipetting. RNA isolation was performed using the NucleoSpin RNA Kit (Macherey-Nagel) according to manufacturer's instructions.


title: Nucleocapsid-RNA N-protein-160x 10mM-SDA In Vitro

value: isolate 2019-nCoV WHU01

value: 3J-UV and 10mM SDA


title: RNAseq: E17.5 proximal fibroblast cells

value: proximal fibroblast cells


title: FRT40 24h 11/29/17


title: DMSO_MOLM13_3

value: DMSO


title: Frameshifting-RNA N-protein-20x 10mM-SDA In Vitro

value: Frameshifting-region RNA


title: DMSO_MOLM13_2


title: Prom1+CD49f+CD45+


title: FRT40 24h 11/28/17


title: RNAseq: E15.5 proximal fibroblast cells


title: RNAseq: E15.5 distal fibroblast cells


title: ATAC-seq 24h 9/27/17

data_processing:
Raw sequence reads were evaluated for quality using FASTQC.
Reads were filtered and  trimmed with Atropos.
High quality reads were mapped to the Ensembl build BDGP6  of the D. melanogaster genome using Bowtie2.
To call the peaks we used MACS2  v2.1.1 (43) with parameters “-g dm --nomodel --nolambda --keep-dup all”, and peaks were  filtered based on default settings and false discovery rate (FDR) < 0.05.
Peaks were  annotated to the nearest genes and to genomic elements such as transcription start sites  (TSS), transcription termination sites (TTS), exons and introns using the R Bioconductor  package ChIPseeker.
Genome_build: Ensembl build BDGP6
Supplementary_files_format_and_content: The bw files are the peak files for each sample

extract_protocol:
Upon dissociation, GFP-labeled L3 neurons were FACS sorted directly into 50 μL of lysis buffer (10 mM Tris-HCl ph7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, the nuclei were spun down at 800 g for 10 min at 4°C and the supernatant was carefully removed. The pellet was resuspended in the transposase reaction mix (25 μL of 2×TD buffer [Illumina Nextera DNA Library Prep kit], 2.5 μL of Transposase [Illumina Nextera DNA Library Prep kit] and 22.5 μL of nuclease-free water) and incubated at 37°C for 30 min. Following the transposition, the DNA sample was purified with Qiagen MinElute kit.
DNA libraries were constructed using Illumina Nextera protocols


title: DMSO_MOLM13_1


title: 5′-End RNA N-protein-0x 10mM-SDA In Vitro


title: RNAseq: E13.5 distal fibroblast cells


title: SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_IP_rep2

description:
snpc-1.3::3xflag; snpc-4::aid; TIR1 L4 (48h) SNPC-1.3 ChIP-seq IP replicate 2
SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_rep2_SignificantBins.txt

source_name: whole worms, L4 (48 h, 20°C )

extract_protocol:
 After washing, the gut was cleared for 15 min by nutation in M9, followed by three washes in M9. Worms were live-crosslinked in 2.6% formaldehyde in water for 30 min at room temperature, nutating. Crosslinking was quenched with a final concentration of 125 mM glycine for 5 min with nutation. After three washes with water, worms were flash-frozen in liquid nitrogen. Frozen worms were ground into powder using a mixer mill MM400 (Retsch) for 2 rounds of 1 min at 30-1. Powder was resuspended in 1x RIPA buffer (1xPBS, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) for 10 min at 4°C. Crosslinked chromatin was sonicated using a Diagenode Bioruptor Pico for three 3-min cycles, 30 sec on/off. 10 µg chromatin was nutated overnight at 4°C with 2 µg of Flag antibody (Sigma-Aldrich, F1804) and then for 1.5 h with 50 µL mouse IgG Dynabeads (Invitrogen). Input amount was 10% of IP. Chromatin was decrosslinked and extracted as described previously (Weiser et al., 2017).
Libraries were prepared and multiplexed using the Ovation Ultralow Library Systems v2 (NuGEN Technologies) according to the manufacturer’s protocol.  The Illumina HiSeq 4000 platform was used to generate 50 bp single-end reads.

treatment_protocol: 250 uM auxin was added 4 hours before collection

value: whole worm

tag: age

value: snpc-4(xk23) I ; unc-11(ed3) III; ieSi38 IV

tag: replicate


title: Frameshifting-RNA N-protein-160x 10mM-SDA In Vitro


title: ATAC-seq 24h 9/26/17


title: SNPC13ChIP_SNPC13flag_48h_IP_rep2

description:
snpc-1.3::3xflag L4 (48h) SNPC-1.3 ChIP-seq IP replicate 2
SNPC13ChIP_SNPC13flag_48h_rep2_SignificantBins.txt

value: snpc-1.3(xk32)[snpc-1.3a::3xflag] V


title: Frameshifting-RNA N-protein-0x 10mM-SDA In Vitro


title: RNAseq: E13.5 proximal fibroblast cells


title: ATAC-seq 24h 9/25/17


title: 5′-End RNA N-protein-80x 10mM-SDA In Vitro

value: 5′-End RNA


title: KO3_rep3

city: Seoul

first: CheolJun

last: Choi

address: 1, Gwanak-ro, Gwanak-gu, 29-310

institute: Seoul National University

description: GEO_processed excel file_YHLLAB.xlsx

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic0.38. (Trimmomatic option : ILLUMINACLIP:[TruSeq3-PE-2.fa]:2:30:10:5:true ,LEADING:3 , TRAILING:3 , SLIDINGWINDOW:4:15, MINLEN:36)
To estimate expression levels, the RNA-Seq reads were mapped to Mus musculus genome (mm10) using HISAT2 version 2.1.0, which is capable of reporting split-read alignments across splice junctions and determined using StringTie version 1.3.4d software in default options.
The read count data of filtered genes was normalized by RLE (Relative Log Expression) normalization with DESeq2. The nbinomWaldTest function in DESeq2 was used to test for differential expression. The output prints foldChange, p-value and FDR values which corrected by the Benjamin-Hochberg procedure.  DEGs was determined by |fold change|>=2 and p-value <0.05. For DEGs, hierarchical clustering analysis was performed with complete linkage method and Euclidean distance as a measure of similarity.
Gene-enrichment analysis and KEGG pathway analysis for DEGs were also performed based on Gene Ontology (http://geneontology.org/) and KEGG pathway (https://www.genome.jp/kegg/) database respectively. All statistical analysis and visualization of differentially expressed genes was conducted using R.3.5.1 (www.r-project.org).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include baseMean values for each Comparison

source_name: inguinal white adipose tissue

growth_protocol: Mice were fed a standard chow diet and were kept on a 12-h light/12-h dark cycle with free access to food and water at 22±1 °C.

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) and processed as per manufacturer’s instructions.
Libraries were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit, according to the manufacturer’s

value: untreated


title: RNAseq: E13.5 Gata4hi epithelial cells-2

source_name: stomach epithelial cells

value: stomach epithelium

value: epithelial cells


title: RNAseq: E13.5 Gata4hi epithelial cells-3


title: SNPC13ChIP_N2_48h_IP_rep2

description:
N2 L4 (48h) SNPC-1.3 ChIP-seq IP replicate 2
SNPC13ChIP_N2_48h_rep2_SignificantBins.txt


title: 5′-End RNA N-protein-160x 10mM-SDA In Vitro


title: Nucleocapsid RNA DMSO In Vitro

data_processing:
Library strategy: RNP-MaP
Adduct locations identified by Shapemapper2 software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

value: Nucleocapsid RNA


title: SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_input_rep2

description:
snpc-1.3::3xflag; snpc-4::aid; TIR1 L4 (48h) SNPC-1.3 ChIP-seq input replicate 2
SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_rep2_SignificantBins.txt


title: SNPC13ChIP_SNPC13flag_48h_input_rep2

description:
snpc-1.3::3xflag L4 (48h) SNPC-1.3 ChIP-seq input replicate 2
SNPC13ChIP_SNPC13flag_48h_rep2_SignificantBins.txt


title: HFO 2

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE1_107_Sep09.xml’.  Measurements of on-chip replicates (quintuplicates) were averaged using the geometric mean of processed intensity values of the green channel, ‘gProcessedSignal’ (gPS) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the normalized gPS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.   Averaged gPS values were normalized by global linear scaling: All gPS values of one sample were multiplied by an array-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the particular Microarray to be normalized (‘Array I’ in the formula shown below). Accordingly, normalized gPS values for all samples (microarray data sets) were calculated by the following formula:   normalized gPSArray i = gPSArray i  x (1500 / 75th PercentileArray i)  After normalization, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized gPS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.  Finally, normalized processed data were imported into Omics Explorer software v3.5 (Qlucore) under default import settings for Agilent One Color mRNA Microarrays, except that any (further) normalization option during import was deselected. Accordingly, data processing steps during Omics Explorer import were: 1) removal of control measurements, 2) log base 2 transformation, 3) baseline transformation to the median.


title: KO1_rep1

description: GEO_processed excel file_YHLLAB.xlsx


title: Nucleocapsid RNA 25mM 5NIA In Vitro

value: 25mM 5NIA


title: SNPC13ChIP_N2_48h_input_rep2

description:
N2 L4 (48h) SNPC-1.3 ChIP-seq input replicate 2
SNPC13ChIP_N2_48h_rep2_SignificantBins.txt


title: 5′-End RNA N-protein-20x 10mM-SDA In Vitro


title: PSE-region RNA DMSO In Vitro

value: PSE-region RNA


title: RNAseq: E13.5 Sox2midGata4mid epithelial cells-2

value: Sox2-EGFP; Gata4-td Tomato


title: SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_IP_rep1

description:
snpc-1.3::3xflag; snpc-4::aid; TIR1 L4 (48h) SNPC-1.3 ChIP-seq IP replicate 1
SNPC13ChIP_SNPC13flag-SNPC4aid-TIR1_48h_rep1_SignificantBins.txt


title: PSE-region RNA 25mM 5NIA In Vitro


title: RNAseq: E13.5 Sox2midGata4mid epithelial cells-1


title: SNPC13ChIP_SNPC13flag_48h_IP_rep1

description:
snpc-1.3::3xflag L4 (48h) SNPC-1.3 ChIP-seq IP replicate 1
SNPC13ChIP_SNPC13flag_48h_rep1_SignificantBins.txt


title: WT3_rep3

description: GEO_processed excel file_YHLLAB.xlsx

value: Wild-type


title: Frameshifting-region RNA DMSO In Vitro

value: isolate 2019-nCoV WHU01


title: RNAseq: E13.5 Sox2hi epithelial cells-3