title: Patient2 with LM primary CRC cancer tissue (miRNA)

description: miRNA expression

source_name: Tissue specimen

tag: disease state

value: Colorectal cancer (CRC) with liver metatasis

tag: gender

value: male

tag: tissue

value: colorectal cancer tissue


title: healthy donor1-1

status: Public on Feb 08 2021

type: RNA

city: shanghai

first: boke

last: zhang

address: 600 Yishan Road

country: China

institute: Shanghai Jiao Tong University Affiliated Sixth People's hospital

description:
1
Peripheral blood monocytes from healthy donor1 was not treated by INT-HA, which was considered as negative control

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

molecule: total RNA

organism: Homo sapiens

source_name: INT-HA-untreated

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-2000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis

tag: donor id

value: healthy donor1

tag: cell type

value: peripheral blood monocytes

tag: treated with

value: none (untreated control)


title: Det562_KO1_Input

type: SRA

city: Montreal

first: Jacek

last: Majewski

state: Quebec

address: 740 Dr. Penfield

department: Human Genetics

country: Canada

institute: McGill University

library_source: genomic

data_processing:
Sequences were all aligned to the GRCh38 analysis set.
Reads from ChIP-seq and targeted sequencing for knock-out validation were mapped using BWA v0.7.17 with default settings of the BWA-MEM algorithm.
WGBS/RNA-seq reads were adapter and quality (Q10) trimmed using BBDuk from BBTools v38.73 (https://sourceforge.net/projects/bbmap/) (t=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=10 minlen=2)
Trimmed WGBS reads were aligned as well as deduplicated using BISCUIT  v0.3.12 (https://github.com/zhou-lab/biscuit) with default options
Per-base methylation calling was performed with MethylDackel  v0.4.0 (https://github.com/dpryan79/MethylDackel) after excluding biased ends
Trimmed RNA-seq reads were aligned using STAR v2.7.3a based on GENCODE Release 33 annotations with the ENCODE standard options
ENCODE blacklisted regions were excluded from all analyses.
Variants were identified with GATK v4.1.5.0 using HaplotypeCaller.
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quantification files were obtained using Salmon v1.1.0 with default settings of the gentrome-based option
Supplementary_files_format_and_content: ChIP-seq bigWig files were obtained through first binning raw tag counts into 10 kb windows using bedtools76 v2.29.0 with intersectBed (-c) in combination with the makewindows command. Next, library size normalization consisted of dividing binned tag counts by the total number of mapped reads after filtering, while input normalization involved taking the log2 ratio of ChIP signals by those of the input (i.e., without immunoprecipitation) with the addition of pseudocount (1) to avoid division by 0. Additionally, quantitative normalization entailed the multiplication of original signal (either in CPM or as log2 ratio over input) by the genome-wide modification percentage information obtained from mass spectrometry.
Supplementary_files_format_and_content: narrowPeak of H3K27ac peaks were called using MACS v2.2.6 (-g hs -q 0.01)
Supplementary_files_format_and_content: WGBS bigWig files in 1 kb bins were calculated by taking per-base methylation calls and dividing the number of methylated base-calls divided by the total number of calls per window.
Supplementary_files_format_and_content: RNA-seq bigWig files were created through deepTools v3.3.1 with bamCoverage --normalizeUsing CPM
Supplementary_files_format_and_content: RData file containing the H3K27ac consensus peakset count matrix (dba.rda) was produced with DiffBind v2.14.0.
Supplementary_files_format_and_content: RData file containing a subsetted beta value matrix (mCG.450k.rda) was generated by filtering the genome-wide CpG matrix to include only CpG sites also covered by the Illumina 450k array.

molecule: genomic DNA

source_name: Detroit-562 cells & S2 cells (spiked-in)

extract_protocol:
About 10 million cells per cell line were grown and directly crosslinked on the plate with 1% formaldehyde (Sigma) for 10 minutes at room temperature and the reaction was stopped using 125nM Glycine for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped off the plate, pelleted, washed twice again in ice-cold PBS and flash frozen pellets stored at -80°C. Thawed pellets were resuspended in 500ul cell lysis buffer (5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate, EDTA-free Protease Inhibitor tablet) and incubated 30 minutes on ice. Samples were centrifugated and pellets resuspended in 500ul of nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and EDTA-free protease inhibitor tablet) and incubated 30 minutes on ice. Sonication of lysed nuclei was performed on a BioRuptor UCD-300 at max intensity for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis of a reversed cross-linked and purified aliquot. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing.
ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hr, followed by 20 min wash cycle using the provided wash buffers (DIAGENODE Immunoprecipitation Buffers, iDeal ChIP-seq kit for Histone). Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. Library preparation was carried out using KAPA Hyper Prep library preparation reagents, following the manufacturer’s protocol.

tag: chip antibody

tag: cell line

value: Patient-derived head and neck squamous cell carcinoma cell line

tag: genotype

value: NSD1 knock-out


title: Det562_KO1_RNA

library_source: transcriptomic

source_name: Detroit-562 cells

extract_protocol:
Total RNA was extracted from cell pellets of approximatively 1 million cells, washed with PBS, spun down and preserved at -80, using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions including DNAse treatment option.
Library preparation was performed with ribosomal RNA depletion according to the manufacturer’s instructions (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.


title: Det562_KO1_H3K27me3

value: H3K27me3 (Cell Signaling, 9733)


title: t0

city: Austin

first: Amy

last: Brock

state: TX

address: 107 West Dean Keeton St.

country: USA

institute: University of Texas at Austin

description: pre-treatment

data_processing:
The GTF file included with cellranger’s GRCh38 3.0.0 reference was modified to create a “pre-mRNA” GTF file so that pre-mRNAs would be included as counts in the later analysis.
Cellranger’s (v3.0.2) mkref command was then used to create a pre-mRNA reference from the GTF file and a genome FASTA file from the GRCh38 3.0.0 reference.
FASTQ files of the scRNA-seq libraries were then aligned to the new pre-mRNA reference using the cellranger count command, producing gene expression matrices.
Genome_build: GRCh38
Supplementary_files_format_and_content: filtered cell barcodes and gene expression counts produced by cellranger

molecule: polyA RNA

source_name: MDA-MB-231 cell line

extract_protocol:
Cryopreserved samples from drug-naïve and two samples of doxorubicin-treated cells frozen at 7 and 10 weeks post-treatment were harvested, sorted by FACS to collect the BFP+ population.
Cells were loaded into wells of a Chromium A Chip, and libraries were prepared using the 10XGenomics 3’ Single Cell Gene Expression (v2) protocol. Paired end (PE) sequencing of the libraries was conducted using a NovaSeq 6000 with an S1 chip (100 cycles) according to the manufacturer’s instructions (Illumina).

treatment_protocol: Cells were passaged into the center 60 wells of 96 well plates at a density of about 2000 cells per well. Two days later, cells were treated with a 24 hour pulse-treatment of doxorubicin at concentrations ranging from 0-1000 nM, with 6 replicates of each dose. Dosed media was applied to cells and treatment response was monitored using the Incucyte. After 24 hours, the dosed media was replaced with normal media and monitoring continued. Cells were fed fresh media every 2-3 days for the duration of the monitoring period (up to 5 weeks).

value: epithelial, adenocarinoma

tag: time point

value: pre-treatment

tag: agent


title: RNA_CH22_DTAG_T_0H_2

city: Houston

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

data_processing:
RNA-sequencing data was processed using the Genialis platform (www.genialis.com). In brief, reads were first preprocessed by BBDuk to remove adaptors. Preprocessed reads were aligned to HG19 by HISAT2 (Kim et al., 2019), per sample quantification was performed with Cuffquant, and Cuffnorm was used to estimate gene abundance (Trapnell et al., 2010). FPKM values were normalized to ERCC spike-in RNAs as described previously (Loven et al., 2012).
SLAM-seq data were processed as in the original SLAM-seq publication using the SlamDunk pipeline (https://t-neumann.github.io/slamdunk/index.html) with the following parameters ( -5 12 -n 100 -t 32 -m -rl 75).
Genome_build: HG19
Supplementary_files_format_and_content: Total RNA-seq: tab-delimited text files include FPKM values for each sample. SLAM-seq: tab-delimited text file including CPM values for all samples processed with the SlamDunk pipeline and conversion fraction of to identify nascent transcripts (a measure of the fraction of reads that have a converted C->T (indicative of metabolic labeling and therefore nascent transcription).

source_name: CH22 Sacral chordoma cell line

growth_protocol: UM-Chor1 chordoma cells were maintained in IMDM/RPMI (4:1) + 10% fetal bovine serum (FBS). CH22 chordoma cells were maintained in RPMI media + 10% FBS. All cell lines were maintained on tissue-culture treated plates.

extract_protocol:
Total RNA-seq: RNA extraction was performed using the RNA Clean and Concentrator-5 kit (Zymo R1017). ERCC RNA Spike-In Control Mixes (ThermoFisher 4456740) were added to each sample. SLAM-seq: RNA was extracted as described in Herzog et al., 2017. ERCC RNA Spike-In Control Mixes (ThermoFisher 4456740) were added to each sample.
Total RNA-seq: Libraries were constructed using the NEB Ultra II Directional Library Prep Kit for Illumina (NEB E7760L). SLAM-seq: Libraries were constructed using the Quant-seq 3’-end mRNA library preparation kit for Illumina (Lexogen 015)
Total RNA-seq: NEB Ultra II Directional Library Prep Kit for Illumina (NEB E7760L). SLAM-seq: Libraries were constructed using the Quant-seq 3’-end mRNA library preparation kit for Illumina (Lexogen 015).

treatment_protocol: Please see characteristics:treatment for each individual sample. Treatment was performed by addition of compound to growth media for the indiciated time point

tag: strain

value: Enginered cell ine derived from CH22 parental chordoma cell line

tag: treatment

value: No treatment


title: Det562_KO1_H3K36me2

value: H3K36me2 (Cell Signaling, 2901)


title: RNA_CH22_DTAG_T_THZ1_8H_1

value: Treated with 60 nM THZ1 for 8 hours


title: t7

description: 7 weeks after doxorubicin treatment

value: 7 weeks

value: doxorubicin


title: RNA_CH22_DTAG_T_0H_3


title: WT_IgG_CnR_rep2

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

description: Paired 2x150bp fastq

data_processing:
Library strategy: CUT&RUN
Paired-end FastQ files were downloaded from the sequencing facility’s website and processed through FastQC  (Galaxy Version 0.72+galaxy1) for quality control
Reads were trimmed to remove adaptor sequences using Trim Galore (Galaxy Version 0.6.3)
Bowtie2 (Galaxy Version 2.3.4.3+ galaxy 0) was used to map the reads against the hg19 genome assembly. The --very-sensitive-local parameter was applied. Any reads not considered the primary alignment or without mapped mate were excluded by using samtools (version 1.3.1).
For generation of BigWig files the deepTools package (version 3.3.0) was used. With the help of the ‘bamCompare’ command the controls IgG and were subtracted from the CUT&RUN tracks. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 50’  and ‘--centerReads’ for highest possible resolution and sharper signals.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig files representing CUT&RUN-seq for anti-MITF and anti-TFAP2a in SkMel28 WT and mutant cells lines

growth_protocol: SkMel28 cell lines were cultured in RPMI media containing 10% FBS and 1% PS. Cells were maintained in log-phase growth (approximately 80% confluent) and media changed every 24 hrs

extract_protocol: CUT&RUN libraries were prepared using the KAPA Hyper Prep Kit (Roche). Quality control post-library amplification was conducted using the 2100 Bioanalyzer for fragment analysis. Libraries were pooled to equimolar concentrations and sequenced with paired-end 150 bp reads on an Illumina NovaSeq 6000 instrument.

value: Melanoma cell

value: wildtype


title: RNA_DTAG_T_CH22_DEGRON_6DAY_03

value: Treated with 1 µM degron for 6 days


title: WT_IgG_CnR_rep1

description: Paired 2x150bp fastq


title: Det562_Input

value: NSD1 wild-type


title: RNA_CH22_DTAG_T_0H_1


title: WT_MITF_CnR_rep2

description: Paired 2x150bp fastq


title: RNA_DTAG_T_CH22_DEGRON_6DAY_01


title: Cal27_KO1_RNA

source_name: Cal-27 cells


title: WT_TFAP2a_CnR_rep2

description: Paired 2x150bp fastq


title: WT_TFAP2a_CnR_rep1

description: Paired 2x150bp fastq


title: RNA_DTAG_T_CH22_DEGRON_6DAY_02


title: RNA_CH22_DTAG_T_DEGRON_24H_3

value: Treated with 1 µM degron


title: Cal27_KO17_H3K27me3

source_name: Cal-27 cells & S2 cells (spiked-in)


title: Det562_H3K36me2


title: Det562_H3K27me3


title: RRBS_patient_2_iMS

city: Kensington

first: John

middle: E

last: Pimanda

state: NSW

address: Cnr High and Botany St

country: Australia

institute: UNSW

description:
AY16
RRBS iMS cells #2
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.

data_processing:
Quality and adapter trimming using trim_galore.
Alignment to hg38 genome using Bismark.
Merge bam files from same library.
Bam files converted to bigWig format.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig

source_name: Generated by in vitro reprogramming of mature adipocytes

growth_protocol: All cells were cultured in standard tissue culture conditions in complete Alpha MEM medium supplemented with autologous serum.

extract_protocol:
Adherent cells were trypsinized using TryPLE and used for genomic DNA extraction using Qiagen Miniprep kit, following manufacturer's instructions.
Restricted Representation Bisulphite Sequencing.

treatment_protocol: iMS cells were generated by in vitro reprogramming of primary adipocytes in the presence of AZA (2 days only) and rhPDGF-AB (25 days).

value: iMS

tag: sample type

value: Reprogrammed cell population

value: AZA and rhPDGF-AB


title: WT_MITF_CnR_rep1

description: Paired 2x150bp fastq


title: Healthy control patient 6

type: genomic

city: Badalona

first: Manel

last: Esteller

state: Barcelona

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

department: Cancer and Leukemia Epigenetics and Biology Program (PEBCL)

country: Spain

institute: Josep Carreras Leukaemia Research Institute (IJC)

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner settings

data_processing:
Minfi R package standard protocol. Normalization using ssNoob preprocessing method.
[intensities.csv] Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

growth_protocol: Not specified

extract_protocol: Total DNA was isolated by standard procedures using using conventional phenol:chloroform:isoamylalcohol (Sigma) extraction

treatment_protocol: No treatment applied

value: healthy control

tag: individual

value: Control 6

tag: population

value: Uruguayan population

value: Peripheral blood leukocytes


title: Healthy control patient 7

value: Control 7


title: RNA_CH22_DTAG_T_DEGRON_24H_2

value: Enginered cell ine derived from CH22 parental chordoma cell line


title: RRBS_patient_2_adMSC

description:
AY15
RRBS AdMSCs #2

source_name: Abdominal subcutaneous fat tissue

value: adipocytes

value: Control

value: Untreated


title: Cal27_KO17_H3K36me2

value: H3K36me2 (Cell Signaling, 2901)

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 knock-out


title: RNA_CH22_DTAG_T_DEGRON_24H_1


title: RRBS_patient_1_iMS

description:
AY14
RRBS iMS cells #1
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.


title: Cal27_KO1_H3K27me3

value: H3K27me3 (Cell Signaling, 9733)


title: RNA_CH22_PARENTAL_THZ1_8H_1

value: CH22 Parental

value: Treated with 60 nM THZ1 for 8 hours


title: RNA_CH22_DTAG_T_DEGRON_8H_3

value: Treated with 1 µM degron


title: Healthy control patient 4

value: Control 4


title: Healthy control patient 5

value: healthy control

value: Control 5


title: Cal27_KO1_H3K36me2


title: IgG-Control

data_processing:
ChIP-seq reads aligned to hg38 genome build using BWA.
Data filtered using Picard to remove duplicates and sorted.
Peak calls were called using macs2.
DiffBind (an R package) was used to identify differentially bound regions between iMS and adMSC in each histone mark.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: bigWig files

source_name: A mix of cell types

extract_protocol:
Adherent cells were fixed with 1% formaldehyde before cell lysis and nuclear isolation. Fixed Nuclei were stored in -80C. On the day of the experiment, nuclei were sonicated before Antibody based isolation of histone - DNA fragments.
The construction of the libraries is through the processes of end repairing, adding A to tails, purification, PCR amplification.
Paired-end (PE 150)

value: Mixed population

value: Mixed


title: RRBS_patient_1_adMSC

description:
AY13
RRBS AdMSCs #1


title: RNA_CH22_DTAG_T_DEGRON_8H_2


title: RNA_CH22_DTAG_T_DEGRON_8H_1


title: Healthy control patient 3

value: Control 3

value: Uruguayan population

value: Peripheral blood leukocytes


title: Healthy control patient 8

value: Control 8


title: Cal27_RNA

value: NSD1 wild-type


title: iMS_patient 2_H3K27me3

description:
H3K27me3_iMS cells#2
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.

value: iMS

value: Reprogrammed cell population

value: AZA and rhPDGF-AB

value: H3K27me3 (Diagenode C15410195)


title: Cal27_Input

value: Patient-derived head and neck squamous cell carcinoma cell line


title: iMS_patient 2_H3K4me3

description:
H3K4me3_iMS cells #2
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.


title: iMS_patient 2_H3K27Ac

description:
H3K27ac_iMS cells #2
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.


title: Cal27_H3K27me3

value: H3K27me3 (Cell Signaling, 9733)


title: Cal27_H3K36me2

value: H3K36me2 (Cell Signaling, 2901)


title: RNA_DTAG_T_CH22_DEGRON_0DAY_03

value: Enginered cell ine derived from CH22 parental chordoma cell line

value: No treatment


title: RNA_DTAG_T_CH22_DEGRON_0DAY_02


title: Healthy control patient 1

value: healthy control

value: Control 1


title: UMCHOR1_HA_BRACHYURY_INPUT

description: Input for UMCHOR1_HA_BRACHYURY

data_processing:
Library strategy: ChIPmentation (Schmidl et a., 2015; PMC4589892)
ChIPmentation datasets were aligned to the human HG19 genome using BWA ALN
MACS2 (Model-based Analysis of ChIP-seq) was used to identify enriched regions relative to background.
A P value threshold of enrichment of 1e-5 was used for all datasets and background datasets as described in characteristic: input
Genome_build: HG19
Supplementary_files_format_and_content: Raw fastq files, peak files in form of bedgraphs.

source_name: UM-Chor1 Clival chordoma cell line

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Tn5 enzyme and amplified using 2x NEBNext HiFi master mix.

value: UM-Chor1 Parental


title: Breast cancer patient 21

value: sporadic breast cancer

value: Patient 21


title: Breast cancer patient 20

value: Patient 20

value: Uruguayan population

value: Peripheral blood leukocytes


title: Healthy control patient 2

value: Control 2


title: RNA_DTAG_T_CH22_DEGRON_0DAY_01


title: mik2_6_1

city: Jinan

first: Shuguo

last: Hou

state: Shandong

address: Fengming Road 1000, Shandong Jianzhu University

department: School of Municipal & Environmental Engineering

institute: Shandong Jianzhu University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Arabidopsis thaliana

growth_protocol: Cold stratified seeds were surface-sterilized with 70% (v/v) ethanol for 5 min and were sown on ½ MS plates. Seedlings grown on plates vertically in a growth chamber at 20-23°C, 50% humidity, and 75-100 μE m-2 s-1 light with a 12-hr light/12-hr dark photoperiod.

extract_protocol: Total RNAs (5 μg) from two biological replicates were pooled for cDNA library construction. cDNA library preparation and sequencing were carried out on an Illumina HiSeq 4000 platform with 150-nucleotide pair-end reads.

treatment_protocol: Ten-day-old seedlings grown on ½ MS plates were incubated in 1 mL of liquid ½ MS medium overnight. Seedlings were then treated with or without 1 μM SCOOP12 for 1 or 6 hr and harvested for RNA isolation.

tag: developmental stages

value: 10-day old

value: 1 uM SCOOP12 for 6h

value: seedling


title: UMCHOR1_HA_BRACHYURY

description: Chromatin IP against HA (brachyury) in UM-Chor1 parental

value: HA-Tag (C29F4) Rabbit mAb #3724, lot8


title: mik2_1_2

value: 1 uM SCOOP12 for 1h


title: Breast cancer patient 22

tag: disease state

value: Patient 22


title: iMS_patient 1_H3K27Ac

description:
H3K27ac_iMS cells #1
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.

value: iMS

value: Reprogrammed cell population

value: AZA and rhPDGF-AB


title: Breast cancer patient 19

value: Patient 19


title: mik2_1_1


title: mik2_6_2


title: adMSC_patient 2_H3K27me3

value: adipocytes

value: Control

value: Untreated

value: H3K27me3 (Diagenode C15410195)


title: UMCHOR1_DTAG_T_G177D_K27AC_REP2

description: Chromatin IP against H3K27ac in UM-Chor1 HA-dTAG-T(G177D), T(-/-)

value: UM-Chor1 HA-dTAG-T(G177D), T(-/-)

value: Enginered cell line derived from UM-Chor1 parental chordoma cell line

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6


title: mik2_0_2

value: 10-day old


title: iMS_patient 1_H3K4me3

description:
H3K4me3_iMS cells #1
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.


title: Healthy control patient 9

value: healthy control

value: Control 9

value: Uruguayan population

value: Peripheral blood leukocytes


title: adMSC_patient 2_H3K4me3

description: H3K4me3_AdMSCs #2


title: UMCHOR1_DTAG_T_G177D_K27AC_INPUT_REP1

description: Input for UMCHOR1_DTAG_T_G177D_K27AC_REP1


title: Breast cancer patient 18

value: sporadic breast cancer

value: Patient 18


title: Breast cancer patient 17

value: Patient 17


title: adMSC_patient 2_H3K27Ac

description: H3K27ac_AdMSCs #2


title: mik2_0_1

value: seedling


title: UMCHOR1_DTAG_T_G177D_K27AC_REP1


title: Breast cancer patient 11

value: Patient 11


title: wild type_6_2

source_name: wild type_seedling

value: wild type

value: 1 uM SCOOP12 for 6h


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_INPUT_REP3

description: Input for UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP3


title: adMSC_patient 1_H3K27me3

value: adipocytes

value: Control

value: Untreated


title: RAPA_3

city: Changsha

first: Zhili

last: Deng

state: China

address: Xiangya Hospital, Central South University, Xiangya Road, Changsha, Hunan 410008, China.

department: Department of Dermatology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1).
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes gene readcount values for all Samples

organism: Mus musculus

source_name: Skin

extract_protocol:
Skin lesions were obtained, flash frozen in liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Skin

value: BALB/c

value: Control mouse treated with rapamycin


title: adMSC_patient 1_H3K4me3

description: H3K4me3_AdMSCs #1


title: Breast cancer patient 14

value: Patient 14


title: Breast cancer patient 12

value: Patient 12


title: Breast cancer patient 9

value: Patient 9

value: Uruguayan population


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP3

description: Chromatin IP against HA (brachyury) in UM-Chor1 HA-dTAG-T(G177D), T(-/-)

value: UM-Chor1 HA-dTAG-T(G177D), T(-/-)

value: Enginered cell line derived from UM-Chor1 parental chordoma cell line

value: HA-Tag (C29F4) Rabbit mAb #3724, lot8


title: Breast cancer patient 15

value: sporadic breast cancer

value: Patient 15

value: Peripheral blood leukocytes


title: RAPA_2

institute: Xiangya Hospital, Central South University


title: adMSC_patient 1_H3K27Ac

description: H3K27ac_AdMSCs #1


title: UMCHOR1_DTAG_T_G177D_K27AC_INPUT_REP2

description: Input for UMCHOR1_DTAG_T_G177D_K27AC_REP2


title: Breast cancer patient 8

value: Patient 8


title: RAPA_1


title: wild type_1_1

value: 10-day old

value: wild type

value: 1 uM SCOOP12 for 1h

value: seedling


title: Breast cancer patient 16

value: Patient 16


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP2


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_INPUT_REP2

description: Input for UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP2


title: PDX4_3

city: Philadelphia

first: Andrew

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

data_processing:
De-multiplexing and data aggregation was performed using the Braod Picard Pipeline
RNA sequencing fastq files were aligned to the GRCh38 human reference genome using Star aligner (v 2.6.1a), gencode v28
RSEM was used to quantify gene and transcript level expression
transcripts per million data were calculated using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file for log normalized transcripts per million for each sample

source_name: metastatic uveal melanoma cells

growth_protocol: MM66, MP38, MP46 and MP65 cells were grown in RPMI 1640 medium (20% FBS, 50 IU penicillin and 50 µg/ml streptomycin). PDX4 cells were cultured in RPMI 1640 medium (15% FBS, 50 IU penicillin and 50 µg/ml streptomycin)

extract_protocol:
Qiagen RNeasy mini kit
Illumina TruSeq™ Stranded mRNA Sample Preparation Kit

value: uveal melanoma cell line

tag: bap1 status

value: Loss


title: Breast cancer patient 10

value: Patient 10


title: wild type_1_2

tag: tissue


title: PDX4_2


title: iMS_patient 1_H3K27me3

description:
H3K27me3_iMS cells#1
iMS cells were generated from adipocytes by treatment with AZA and rhPDGF-AB.

value: iMS

value: Reprogrammed cell population

value: AZA and rhPDGF-AB

value: H3K27me3 (Diagenode C15410195)


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_INPUT_REP1

description: Input for UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP1

value: UM-Chor1 HA-dTAG-T(G177D), T(-/-)

value: Enginered cell line derived from UM-Chor1 parental chordoma cell line


title: wild type_0_2


title: L_R_3

value: Skin

value: BALB/c

value: LL37-induced rosacea-like mouse treated with rapamycin


title: L_R_2


title: wild type_0_1

value: 10-day old


title: PDX4_1


title: Healthy control patient 10

value: healthy control

value: Control 10

value: Uruguayan population

value: Peripheral blood leukocytes


title: UMCHOR1_DTAG_T_G177D_HA_BRACHYURY_REP1

value: HA-Tag (C29F4) Rabbit mAb #3724, lot8


title: AZ_160

city: Montpellier

first: Timothy

middle: John

last: TRANBARGER

address: 911 avenue agropolis BP 64501

department: Ecology, Biodiversity and Functioning of Continental Ecosystems (ECOBIO)

country: France

institute: Institut de Recherche pour le Développement

data_processing:
The 454 pyrosequence analysis, de novo assembly performed following the methods described previously using an automated pipeline previously described and with support of the SouthGreen Bioinformatics Platform (http://southgreen.cirad.fr/), and the high performance cluster of the Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes (Argout et al., 2008; Tranbarger et al., 2011).
For the Illumina samples, low quality reads were removed using Cutadapt. Trimmed reads were mapped using the BWA-MEM package with default parameters (Li 2012). Samtools was used to count mapped reads and the number of reads per kilobase and million reads (RPKM) were then calculated (Li et al., 2009]). The oil palm predicted transcripts used for mapping was downloaded from the NCBI website (http://www.ncbi.nlm.nih.gov/, GCF_000442705.1_EG5_rna.fna; January 2015).
Supplementary_files_format_and_content: xlsx; RPKM read counts

organism: Elaeis guineensis

source_name: Base of oil palm fruit (160 Days after pollination, DAP) containing abscission zone (AZ), collected from field, fruit abscission observed

growth_protocol: Oil palm (Elaeis guineensis Jacq.) cultivated at Krabi Golden Tenera plantation, from a tenera clone (clone C) produced in Thailand.

extract_protocol:
For RNA extractions, the fruit bunches were collected and the base of fruits containing the AZ were sampled as follows: the spikelets were removed from the bunches, rinsed in water, then individual fruit containing the base of the fruit containing the AZ were removed with scalpel, then the base of the fruit containing the AZ were dissected (approximately 50 AZ pieces were collected per sample), weighed at approximately 3 grams then froze immediately in liquid nitrogen. Backcross material were cleaned and processed with the same procedure. Total AZ weights were approximately 3-6 grams. Total RNA from mesocarp, pedicel and the base of the fruit enriched in AZs, treated or not with ethylene was extracted as previously described [Morcillo F et al.,Tree Physiol. 2006;26(5):585-594].
Total RNA (1 μg) was used to synthesize cDNA using the first-strand cDNA synthesis kit (ImProm-IITM Reverse Transcription System, Promega). The titanium kit was used (according to Roche GS FLX Titanium manual) and cDNAs derived from the different tissues and different ethylene treatment time points were tagged independently and then mixed together in one sample for 454 pyrosequencing carried out by the National Center for Genetic Engineering and Biotechnology (BIOTEC), Thailand. Sequencing of the three natural abscission samples (AZ30, AZ120 and AZ160) collected in Thailand was complete by the company GATC Biotech (www.gatc-biotech.com).

treatment_protocol: For each sample group, independent bunches were collected from distinct individuals of the same genotype. Spikelets were then collected in the centre of each bunch and sets of 6 spikelets were randomly sampled from them and put in individual hermetically sealed 50 l volume boxes. In absence of ethylene treatment, ethylene absorber (ETHYL-GONE, http://www.biosafer.com/ethyl-gone.php) was added in the box. All the boxes were kept at ambient temperature (approximately 30°C), and after 24 h of treatment the number of fruit separating from the spikelets were counted. Using the concentration of ethylene (10 μl l-1) that induced and synchronized the highest amount of fruit shedding (Roongsattham et al., 2012), fruit from 30 and 150 DAP were treated with ethylene. Spikelets were treated with or without ethylene, and every 3 h, treated or untreated spikelets were collected and shedding was quantified for each stage of development. For each time point, the pedicel and the base of the fruit containing the primary and adjacent AZs were isolated and frozen immediately in liquid nitrogen. Samples from two independent experiments were collected immediately after bunches were harvested.

value: Abscission zone (AZ) from fruit

tag: developmental stage

value: 160 DAP (160 Days after pollination)

value: Collected from the field, fruit abscission observed


title: MP65_3

source_name: primary uveal melanoma cells

tag: cell type

value: uveal melanoma cell line

value: Loss


title: CH22_PARENTAL_K27AC_INPUT_REP2

description: Input for CH22_PARENTAL_K27AC_INPUT_REP2

value: CH22 Parental


title: L_R_1


title: LL37_3

value: LL37-induced rosacea-like mouse


title: AZ_120

source_name: Base of oil palm fruit (120 Days after pollination, DAP) containing abscission zone (AZ), collected from field, no fruit abscission observed

value: 120 DAP (120 Days after pollination)

value: Collected from the field, no fruit abscission observed


title: Breast cancer patient 5

value: sporadic breast cancer

value: Patient 5


title: Breast cancer patient 2

value: Patient 2


title: LL37_2

value: Skin

value: BALB/c


title: CH22_PARENTAL_K27AC_REP2

description: Chromatin IP against H3K27ac in CH22 parental

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6


title: AZ_30

source_name: Base of oil palm fruit (30 Days after pollination, DAP) containing abscission zone (AZ), collected from field, no fruit abscission observed

value: 30 DAP (30 Days after pollination)


title: MP65_1


title: LL37_1


city: Memphis

first: Patrick

middle: Allen

last: Schreiner

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Children's Research Hospital

description:
total RNA depleted for rRNA
singleCopy - H3G34K Mutant - Replicate 3
singleCopy.counts.txt

data_processing:
Read alignment was performed using STAR software
Gene level quantification was performed by featureCounts (subread)
Differentially expressed genes were identified using limma voom. External RNA spike-ins were used to confirm no global expression changes amongst modified histones.
Genome_build: Schizosaccharomyces_pombe.ASM294v2.29
Supplementary_files_format_and_content: raw counts

organism: Schizosaccharomyces pombe

growth_protocol: Cultures were grown overnight in PMG complete media at 25°C to a density of 2.5 x 10-6 cells/ml in a 25mL culture

extract_protocol:
Hot phenol extraction was used to prepare total RNA (Leeds et al. 1991. PubMed PMID: 1748286). cells were pelleted by centrifugation and washed in DEPC H2O. The pellet was resuspended in 750 uL TES Buffer [50mM Tris-HCl pH 7.5, 10mM EDTA, 100mM NaCl, 0.5% SDS made in DEPC H2O] along with an equal volume of 5:1 phenol:chloroform pH 4.7 and incubated at 65°C for one hour with vortexing for 10 seconds every 10 minutes. The samples were then cooled on ice and centrifuged for five minutes at 13,000 RPM. The aqueous phase was transferred to a 2 mL phase lock tube and an additional phenol:chloroform extraction was performed. After centrifugation, the aqueous phase was transferred to a new tube and re-extracted using an equal volume of chloroform. To precipitate the RNA, the aqueous phase was transferred to a 2 mL microcentrifuge tube and three volumes of ice cold ethanol and 1/10th volume 3M NaOAc pH 5.2 were added and the samples were kept at -20°C overnight. The next day, samples were centrifuged at 14,000 RPM and 4°C for 15 minutes to pellet the RNA. The pellet was washed with ice cold 70% ethanol and air dried for 30 minutes. A Turbo DNAse (Ambion) reaction was set up with 100 ug of RNA in a 150 uL reaction containing 5 uL of Turbo DNAse. The reaction was incubated at 37°C for 30 minutes and another 5 uL of Turbo DNAse was added and incubated for an additional 30 minutes prior to the removal of the DNAse using 50 uL of inactivation beads. An RNeasy Mini kit (Sigma) was used to further clean up and concentrate the RNA which was eluted in a final volume of 30 uL of DEPC H2O. 5 ug total RNA was diluted to 10 ul, and 2 ul of a 1:20 dilution of ERCC RNA Spike-in mix (Invitrogen) was added to each sample. RNA-seq was performed by the St. Jude Hartwell Center. Ribosomal RNA was removed from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) following manufacturer instructions (Illumina).RNA was quantified using a Quant-iT assay (Life Technology). The quality was checked by 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or LabChip RNA Pico Sensitivity assay (Perkin Elmer) before library generation. Libraries were prepared from 2 ug of RNA.
Libraries were prepared using the TruSeq Strand Total RNA Library Prep Kit, beginning at Elution 2 – Fragment – Prime step immediately preceding cDNA synthesis according to the manufacturer instructions (Illumina) with the following modifications; the 94o C Elution 2 – Fragment – Prime incubation was reduced to five minutes and the PCR was reduced to 11 cycles. Libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies) or Kapa Library Quantification kit (Kapa Biosystems).
One hundred cycle paired end sequencing was performed on an Illumina HiSeq 4000 (single copy strains) or on an Illumina Novaseq 6000 (triple copy strains). Three biological replicates were used for each strain analyzed.  The total RNA was sequenced using stranded protocol with 2x100bp setting.

treatment_protocol: not applicable

tag: strain genotype


title: MP46_3


title: CH22_PARENTAL_K27AC_REP1

tag: chip antibody


title: wild type_6_1

value: 10-day old

value: wild type

value: 1 uM SCOOP12 for 6h

value: seedling


title: MP65_2

value: uveal melanoma cell line

tag: cell line


title: CON_3

value: Control mouse


description:
total RNA depleted for rRNA
singleCopy - H3G34K Mutant - Replicate 2
singleCopy.counts.txt


title: MP46_2

value: Loss


title: Breast cancer patient 3

value: Patient 3

value: Uruguayan population

value: Peripheral blood leukocytes


title: CH22_PARENTAL_HA_BRACHYURY_INPUT

description: Input for CH22_PARENTAL_HA_BRACHYURY

value: CH22 Parental


title: Breast cancer patient 1

value: sporadic breast cancer

value: Patient 1


title: CH22_PARENTAL_K27AC_INPUT_REP1

description: Input for CH22_PARENTAL_K27AC_INPUT_REP1


title: CON_2

value: Skin


title: singleCopy - Set2D Mutant - Replicate 3

description:
total RNA depleted for rRNA
singleCopy - Set2D Mutant - Replicate 3
singleCopy.counts.txt


description:
total RNA depleted for rRNA
singleCopy - H3G34K Mutant - Replicate 1
singleCopy.counts.txt


title: CON_1

value: BALB/c


title: MP38_3


title: CH22_DTAG_T_WT_HA_BRACHYURY_INPUT_REP2

description: Input for CH22_DTAG_T_WT_HA_BRACHYURY_REP2

value: CH22 HA-dTAG-T(WT), T(-/-)

value: Enginered cell line derived from CH22 parental chordoma cell line


title: LPS_IAA

city: tianjin

first: Yunhuan

last: Gao

address: Wei Jin Road No. 94

department: School of Medicine

institute: Nankai University

data_processing:
Basecalls performed using  Illumina BCL2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie1
Data were filtered using the NGS QC Toolkit
peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2

source_name: WEHI231 B cells

growth_protocol: WEHI231 B cells were seeded in 24-wells plate. The cells were then stimulated with IAA and LPS for 6 hrs,

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq 6000 following the manufacturer's protocols.

treatment_protocol: WEHI231 B cells were LPS/IAA treated for 6 hours.

value: B lymphocyte line

value: PXR(Cloud-clone Cat:PAD950Mu01)

value: treated with LPS and IAA for 6 hours


title: MP38_2


title: CH22_DTAG_T_WT_HA_BRACHYURY_REP2

description: Chromatin IP against HA (brachyury) in CH22 HA-dTAG-T(WT), T(-/-)

value: HA-Tag (C29F4) Rabbit mAb #3724, lot8


title: singleCopy - Set2D Mutant - Replicate 2

description:
total RNA depleted for rRNA
singleCopy - Set2D Mutant - Replicate 2
singleCopy.counts.txt


title: MP38_1

value: uveal melanoma cell line


title: MP46_1


title: CH22_PARENTAL_HA_BRACHYURY

description: Chromatin IP against HA (brachyury) in CH22 parental


description:
total RNA depleted for rRNA
singleCopy - H3G34V Mutant - Replicate 3
singleCopy.counts.txt


title: Breast cancer patient 7

value: Patient 7


title: LPS

value: treated with LPS for 6 hours


title: CH22_DTAG_T_WT_HA_BRACHYURY_INPUT_REP1

description: Input for CH22_DTAG_T_WT_HA_BRACHYURY_REP1


title: CH22_DTAG_T_WT_HA_BRACHYURY_REP1


title: MM66_3

value: Expressed


title: WT

value: untreated


title: 3_IAA

value: treated with IAA for 6 hours


title: MM66_1


description:
total RNA depleted for rRNA
singleCopy - H3G34V Mutant - Replicate 2
singleCopy.counts.txt


title: singleCopy - Set2D Mutant - Replicate 1

description:
total RNA depleted for rRNA
singleCopy - Set2D Mutant - Replicate 1
singleCopy.counts.txt


title: ScxLinDTR_Cre_Positive_D28_3

city: Rochester

first: Alayna

last: Loiselle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1.
Genome_build: GRCm38 + Gencode-M22 Annotation
Supplementary_files_format_and_content: *_deSeq2_counts_normalized.xlsx: Excel files containing DESeq2 normalized counts for each individual sample (12 total).
Supplementary_files_format_and_content: deSeq2_counts_normalized_all_samples.xlsx: Excel file containing DESeq2 normalized counts for all samples.
Supplementary_files_format_and_content: Cre+_vs_Cre-_D14andD28_Dataset_uploaded_to_IPA.xlsx: Data uploaded to ingenuity pathway analysis (IPA) for core analysis.

source_name: Repair Flexor Digitorum Longus Tendon

extract_protocol:
Repaired flexor tendons were removed, flash frozen using liquid nitrogen, and stored at -80 degrees Celsius. RNA was extracted using Trizol and the RNeasy Plus Micro Kit (Qiagen, Valencia, CA).
The TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols.

treatment_protocol: Diphtheria toxin (20ng/day) was administered to the right hindpaw for five consecutive days ending ten days prior to flexor tendon repair surgery to drive scleraxis lineage cell apoptosis.

tag: genotype/variation

value: ScxCre positive; DTR F/+

value: Flexor digitorum longus tendon

value: Acute flexor tendon injury and repair

tag: age at time of repair

value: 10-12 weeks

value: Day 28 post-repair


description:
total RNA depleted for rRNA
singleCopy - H3G34V Mutant - Replicate 1
singleCopy.counts.txt


title: Breast cancer patient 13

value: sporadic breast cancer

value: Patient 13

value: Uruguayan population

value: Peripheral blood leukocytes


title: ScxLinDTR_Cre_Positive_D28_2

tag: time point


title: Breast cancer patient 4

value: Patient 4


title: CH22_DTAG_T_G177D_K27AC_INPUT_REP1

description: Input for CH22_DTAG_T_G177D_K27AC_REP1

source_name: CH22 Sacral chordoma cell line

tag: strain

value: Enginered cell line derived from CH22 parental chordoma cell line


description:
total RNA depleted for rRNA
singleCopy - H3G34R Mutant - Replicate 3
singleCopy.counts.txt


title: FaDu_KO1_RNA

source_name: FaDu cells

value: FaDu

value: Patient-derived head and neck squamous cell carcinoma cell line

tag: genotype

value: NSD1 knock-out


description:
total RNA depleted for rRNA
singleCopy - H3G34R Mutant - Replicate 2
singleCopy.counts.txt


title: CH22_DTAG_T_G177D_K27AC_INPUT_REP2

description: Input for CH22_DTAG_T_G177D_K27AC_REP2


title: ScxLinDTR_Cre_Positive_D28_1

tag: treatment


title: Det562_KO4_H3K27ac

description: dba.rda

source_name: Detroit-562 cells & S2 cells (spiked-in)

value: H3K27ac (Cell Signaling, 8173)


title: CH22_DTAG_T_G177D_K27AC_REP1

description: Chromatin IP against H3K27ac in CH22 HA-dTAG-T(G177D), T(-/-)

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6


title: ScxLinDTR_Cre_Positive_D14_3

value: Day 14 post-repair


title: MM66_2

value: uveal melanoma cell line

value: Expressed


title: Breast cancer patient 6

tag: individual

value: Patient 6


title: singleCopy -H3G34R Mutant - Replicate 1

description:
total RNA depleted for rRNA
singleCopy -H3 G34R Mutant - Replicate 1
singleCopy.counts.txt


title: CH22_DTAG_T_G177D_HA_BRACHYURY_INPUT_REP2

description: Input for CH22_DTAG_T_G177D_HA_BRACHYURY_REP2


title: ScxLinDTR_Cre_Positive_D14_2

value: ScxCre positive; DTR F/+

value: Flexor digitorum longus tendon

value: Acute flexor tendon injury and repair

value: 10-12 weeks


title: Det562_KO1_H3K27ac

description: dba.rda


title: Det562_KO2_H3K27ac

description: dba.rda


title: ScxLinDTR_Cre_Positive_D14_1


title: CH22_DTAG_T_G177D_HA_BRACHYURY_REP1

description: Chromatin IP against HA (brachyury) in CH22 HA-dTAG-T(G177D), T(-/-)

value: HA-Tag (C29F4) Rabbit mAb #3724, lot8


title: singleCopy - H3 WT - Replicate 2

description:
total RNA depleted for rRNA
singleCopy - H3 WT - Replicate 2
singleCopy.counts.txt


title: Cal27_KO17_Input

source_name: Cal-27 cells & S2 cells (spiked-in)


title: Det562_RNA

source_name: Detroit-562 cells

value: NSD1 wild-type


title: MDA-231ba429D (miRNA-seq)

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

data_processing:
the Solexa CHASTITY quanlity filtered reads were harvested as Clean Reads
adapter sequences were trimmed with cutadapt and the adaptor-trimmed-reads (>= 15nt) were left
miRDeep2 software was used to quantify known miRNA and predict the novel miRNAs
The CPM value for miRNA were calculated with R package edgeR and differentially expressed miRNAs were filtered using edgeR
Genome_build: GRCh38/miRBase22

source_name: human mammary tumor cell line

growth_protocol: cells were grown in DMEM media supplemented with 10% FBS, 1 mM sodium pyruvate, 4 mM glutamine, 1% antibiotic/antimycotic and 300ug/ml puromycin (InvivoGen, San Diego, CA). RNA was extracted from sub-confluent cells

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) RiboZero Magnetic Gold Kit (Human/Mouse/Rat), NEB multiplex small RNA library Prep set for Illumina

value: human mammary tumor cell line

value: stably transfected with a vector containing the miR-200b/200a/429 cluster


title: CH22_DTAG_T_G177D_HA_BRACHYURY_INPUT_REP1

description: Input for CH22_DTAG_T_G177D_HA_BRACHYURY_REP1

value: Enginered cell line derived from CH22 parental chordoma cell line


title: ScxLinDTR_Cre_Negative_D28_1

value: ScxCre negative; DTR F/+

value: Day 28 post-repair


title: ScxLinDTR_Cre_Negative_D28_3


title: Det562_H3K27ac

description: dba.rda

extract_protocol:
About 10 million cells per cell line were grown and directly crosslinked on the plate with 1% formaldehyde (Sigma) for 10 minutes at room temperature and the reaction was stopped using 125nM Glycine for 5 minutes. Fixed cell preparations were washed with ice-cold PBS, scraped off the plate, pelleted, washed twice again in ice-cold PBS and flash frozen pellets stored at -80°C. Thawed pellets were resuspended in 500ul cell lysis buffer (5 mM PIPES-pH 8.5, 85 mM KCl, 1% (v/v) IGEPAL CA-630, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate, EDTA-free Protease Inhibitor tablet) and incubated 30 minutes on ice. Samples were centrifugated and pellets resuspended in 500ul of nuclei lysis buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 50 mM NaF, 1 mM PMSF, 1 mM Phenylarsine Oxide, 5 mM Sodium Orthovanadate and EDTA-free protease inhibitor tablet) and incubated 30 minutes on ice. Sonication of lysed nuclei was performed on a BioRuptor UCD-300 at max intensity for 60 cycles, 10s on 20s off, centrifuged every 15 cycles, chilled by 4°C water cooler. Samples were checked for sonication efficiency using the criteria of 150-500bp by gel electrophoresis of a reversed cross-linked and purified aliquot. After the sonication, the chromatin was diluted to reduce SDS level to 0.1% and concentrated using Nanosep 10k OMEGA (Pall). Before ChIP reaction 2% of sonicated drosophila S2 cell chromatin was spiked-in the samples for quantification of total levels of histone mark after the sequencing.
ChIP reaction for histone modifications was performed on a Diagenode SX-8G IP-Star Compact using Diagenode automated Ideal ChIP-seq Kit. Dynabeads Protein A (Invitrogen) were washed, then incubated with specific antibodies, 1.5 million cells of sonicated cell lysate, and protease inhibitors for 10 hr, followed by 20 min wash cycle using the provided wash buffers (DIAGENODE Immunoprecipitation Buffers, iDeal ChIP-seq kit for Histone). Reverse cross linking took place on a heat block at 65°C for 4 hr. ChIP samples were then treated with 2ul RNase Cocktail at 65°C for 30 min followed by 2ul Proteinase K at 65°C for 30 min. Samples were then purified with QIAGEN MiniElute PCR purification kit as per manufacturers’ protocol. In parallel, input samples (chromatin from about 50,000 cells) were reverse crosslinked and DNA was isolated following the same protocol. Library preparation was carried out using KAPA Hyper Prep library preparation reagents, following the manufacturer’s protocol.

value: H3K27ac (Cell Signaling, 8173)

value: Patient-derived head and neck squamous cell carcinoma cell line


title: ScxLinDTR_Cre_Negative_D28_2


title: MDA-231ba429C (miRNA-seq)


title: Cal27_KO17_RNA

source_name: Cal-27 cells

extract_protocol:
Total RNA was extracted from cell pellets of approximatively 1 million cells, washed with PBS, spun down and preserved at -80, using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions including DNAse treatment option.
Library preparation was performed with ribosomal RNA depletion according to the manufacturer’s instructions (NEB) to achieve greater coverage of mRNA and other long non-coding transcripts.

value: NSD1 knock-out


title: Cal27_KO17_H3K27ac

description: dba.rda


title: CH22_DTAG_T_G177D_K27AC_REP2

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6


title: Cal27_KO1_Input


title: ScxLinDTR_Cre_Negative_D14_3

value: Day 14 post-repair


title: singleCopy - H3 WT - Replicate 3

description:
total RNA depleted for rRNA
singleCopy - H3 WT - Replicate 3
singleCopy.counts.txt


title: ScxLinDTR_Cre_Negative_D14_2


title: CH22_DTAG_T_G177D_HA_BRACHYURY_REP2


title: LE12_Pselt+MPP

city: BETHESDA

first: abdel

middle: G

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Clariom_S_Human microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

label: Biotin

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Clariom_S_Human GeneChips (Affymetrix, Inc).   Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling.  300 ng of total RNA was used for labeling with the Affymetrix kit (Cat # 900652). After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

growth_protocol: The human SH-SY5Y neuroblastoma cell line (ATCC, Manassas, USA) was maintained in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, Saint-Quentin Fallavier, France), supplemented with 10% fetal bovine serum (Lonza, Levallois, France), 1% L-glutamine, 50 units/ml of penicillin and 50 units/ml of streptomycin (Thermo Fisher Scientific, Villebon-sur-Yvette , France), at 37°C in 5% CO2 humidified atmosphere. The medium was renewed every 2-3 days.

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Twenty-four hours after plating, cells were treated or not with 500 μM or 1 mM MPP+(Sigma-Aldrich) for 36 h in the presence or absence of PSELT (10 μM). For the microarray gene expression analysis, cells were treated with PSELT for 6 h only.

value: SH-SY5Y neuroblastoma cell line

value: WT

tag: diet

value: Pselt+MPP


title: Cal27_KO1_H3K27ac

description: dba.rda

data_processing:
Sequences were all aligned to the GRCh38 analysis set.
Reads from ChIP-seq and targeted sequencing for knock-out validation were mapped using BWA v0.7.17 with default settings of the BWA-MEM algorithm.
WGBS/RNA-seq reads were adapter and quality (Q10) trimmed using BBDuk from BBTools v38.73 (https://sourceforge.net/projects/bbmap/) (t=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=rl trimq=10 minlen=2)
Trimmed WGBS reads were aligned as well as deduplicated using BISCUIT  v0.3.12 (https://github.com/zhou-lab/biscuit) with default options
Per-base methylation calling was performed with MethylDackel  v0.4.0 (https://github.com/dpryan79/MethylDackel) after excluding biased ends
Trimmed RNA-seq reads were aligned using STAR v2.7.3a based on GENCODE Release 33 annotations with the ENCODE standard options
ENCODE blacklisted regions were excluded from all analyses.
Variants were identified with GATK v4.1.5.0 using HaplotypeCaller.
Genome_build: hg38
Supplementary_files_format_and_content: Salmon quantification files were obtained using Salmon v1.1.0 with default settings of the gentrome-based option
Supplementary_files_format_and_content: ChIP-seq bigWig files were obtained through first binning raw tag counts into 10 kb windows using bedtools76 v2.29.0 with intersectBed (-c) in combination with the makewindows command. Next, library size normalization consisted of dividing binned tag counts by the total number of mapped reads after filtering, while input normalization involved taking the log2 ratio of ChIP signals by those of the input (i.e., without immunoprecipitation) with the addition of pseudocount (1) to avoid division by 0. Additionally, quantitative normalization entailed the multiplication of original signal (either in CPM or as log2 ratio over input) by the genome-wide modification percentage information obtained from mass spectrometry.
Supplementary_files_format_and_content: narrowPeak of H3K27ac peaks were called using MACS v2.2.6 (-g hs -q 0.01)
Supplementary_files_format_and_content: WGBS bigWig files in 1 kb bins were calculated by taking per-base methylation calls and dividing the number of methylated base-calls divided by the total number of calls per window.
Supplementary_files_format_and_content: RNA-seq bigWig files were created through deepTools v3.3.1 with bamCoverage --normalizeUsing CPM
Supplementary_files_format_and_content: RData file containing the H3K27ac consensus peakset count matrix (dba.rda) was produced with DiffBind v2.14.0.
Supplementary_files_format_and_content: RData file containing a subsetted beta value matrix (mCG.450k.rda) was generated by filtering the genome-wide CpG matrix to include only CpG sites also covered by the Illumina 450k array.


title: MDA-231c141F (miRNA-seq)

value: stably transfected with a vector containing the miR-200c/141 cluster


title: MDA-231ba429A (miRNA-seq)


title: singleCopy - H3 WT - Replicate 1

description:
total RNA depleted for rRNA
singleCopy - H3 WT - Replicate 1
singleCopy.counts.txt


title: ScxLinDTR_Cre_Negative_D14_1

value: Flexor digitorum longus tendon

value: Acute flexor tendon injury and repair

value: 10-12 weeks


title: LE10_Pselt+MPP


title: RJ423c141C (RNA-seq)

data_processing:
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
aligned reads are summarized to gene-level counts by the featureCounts tool
Genome_build: GRCm38_ens92_ercc_sirv
Supplementary_files_format_and_content: counts

source_name: murine mammary tumor cell line

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
KAPA stranded Illumina kits for the RNA-seq library preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Library prep performed by Arraystar Inc (Rockville, MD)

value: murine mammary tumor cell line

value: stably transfected with vector containing miR-200c and miR-141


title: LE11_Pselt+MPP


title: MDA-231ba429B (miRNA-seq)

value: human mammary tumor cell line

value: stably transfected with a vector containing the miR-200b/200a/429 cluster


title: MDA-231c141E (miRNA-seq)


title: RJ423c141B (RNA-seq)


title: RJ423c141A (RNA-seq)


title: LE08_Pselt

value: Pselt


title: MDA-231c141D (miRNA-seq)


title: LE09_Pselt


title: HeLa_DMSO-b

city: Higashi-Osaka

first: Kei

last: IIDA

state: Osaka

address: Kowakae 3-4-1

country: Japan

institute: Kindai University

data_processing:
Basecalling was performed with NovaSeq Control Software  v1.4.0
The seuqence data was mapped to the genome sequence with STAR ver. 2.4.1d .
Genome_build: hg19
Supplementary_files_format_and_content: Expression values of refseq gene models were calculated with RSEM ver. 1.3.0.

source_name: HeLa

growth_protocol: HeLa cells were expanded in MEM containing 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from HeLa cells using the RNeasy mini kit (QIAGEN).
TruSeq Stranded mRNA Library Prep Kit
Oligo-dT beads capture polyA tails

treatment_protocol: Incubated with 10 μM ALESIA racemate in MEM containing 5% fetal bovine serum and 1% penicillin-streptomycin for 6 hours, and then harvested for extraction of RNA

value: HeLa

value: DMSO


title: HeLa_DMSO-c


title: MDA-231c141C (miRNA-seq)


title: HeLa_DMSO-a


title: RJ423EV3C (RNA-seq)

value: stably transfected with empty vector


title: MDA-231EV3 (miRNA-seq)


title: RJ423EV2C (RNA-seq)


title: LE07_Pselt


title: HeLa_ALESIA-c

value: ALESIA racemate


title: RJ423EV1C (RNA-seq)


title: HeLa_ALESIA-b


title: LE06_MPP

value: MPP


title: MDA-231EV2 (miRNA-seq)


title: LE05_MPP

value: SH-SY5Y neuroblastoma cell line


title: Cal27_H3K27ac

description: dba.rda

value: H3K27ac (Cell Signaling, 8173)

value: Patient-derived head and neck squamous cell carcinoma cell line

value: NSD1 wild-type


title: LE04_MPP

value: WT


title: H8

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Data were analyzed using Cell Ranger™ v2.0.2 pipelines which is available in 10xGenomics website.
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

extract_protocol:
Blood was rinsed with PBS containing heparin; brains were dissected, collected in ice‐cold PBS, and cut into small pieces. Tissue was digested in 1 ml Accutase (Merck) per brain at 37 °C for 30 min and triturated through 100 μm cell strainers which were rinsed with 10% FCS in PBS. Cells were purified by a linear 40% Percoll (GE Healthcare) centrifugation step at 650 xg without brakes for 25 min and the myelin top layer and supernatant were discarded. Mononuclear cells were resuspended in FACS buffer (1% BSA and 0.1% sodium azide in PBS) and counted. For scRNA-seq cells from brains of 5 12-month-old and 4 24-month-old mice were pooled into 2 separate samples.
Around 15,000 CD45highCD8+ single-cells were sorted per sample and encapsulated in droplets using 10X Genomics GemCode Technology kit v2 and processed following manufacturer’s specifications.
Chromium single cell 3´ v2 (10XGenomics)

tag: sorting antibodies


title: HeLa_ALESIA-a


title: MDA-231EV1 (miRNA-seq)


title: MDA-231EV (miRNA-seq)


title: H7


title: S034

status: Public on Feb 07 2021

city: Bethesda

first: Xin

middle: Wei

last: Wang

state: MARYLAND

address: 37 Convent Drive

department: Laboratory of Human Carcinogenesis

institute: National Cancer Institute

data_processing:
Basecalling perormed by RTA.
Demultiplexing performed by Bcl2fastq.
Alignment, tagging, gene and transcript counting performed CellRanger.
Aggregation performed by CellRanger.
Genome_build: GRCh38
Supplementary_files_format_and_content: 1) cell barcodes (barcodes.tsv) 2) genes (genes.tsv), 3) count matrix (matrix.mtx), and 4) cell information (Info.txt)

source_name: Primary liver cancer single-cell

extract_protocol: Single cells prepared from biopsies were captured following the 10x Genomics Single Cell 3’ Reagent Kit v2 user guide. Briefly, single cells were washed and re-suspended in PBS supplemented with 0.04% BSA. Cell numbers was adjusted to 1,200 cells/ul based on cell concentration and viability. Cell suspension was then partitioned into Gel Beads-in-emulsion (GEMs) together with a pool of ~3,500,000 10x Barcodes to index each cell’s transcriptome when they are dissolved during reverse transcription (GEM-RT). First-strand cDNA was purified from the post GEM-RT reaction mixture after GEM generation and barcoding. Purified first-strand cDNA was used as template of 14 cycles of PCR, and PCR products were cleaned up using SPRIselect size selection beads. The cDNA concentration was assessed with a Bioanalyzer (Agilent Technologies). cDNA libraries were prepared following the 10x Genomics Single Cell 3’ Reagent Kit v2 user guide with necessary modifications to the PCR cycles according to the recovered cDNA concentration.

tag: cancer type

value: Intrahepatic cholangiocarcinoma


title: LE02_Ctrl

value: Control


title: LE03_Ctrl


title: S033

value: Hepatocellular carcinoma


title: S032


title: S031


title: LE01_Ctrl


title: S030


title: S029


title: S027


title: S026


title: S028


title: S023


title: S021


title: S019


title: S018


title: S025


title: S024


title: S022


title: Whole Embryo - Solvent Yellow 33 - 10.5µM - R1

city: Vicksburg

first: Natalia

last: Garcia-Reyero

state: MS

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: U.S. Army Corps of Engineers

description:
1637-NV-1_93-TCTCGCGC-TATAGCCT_S359
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt

data_processing:
fastq files were trimmed with Trim Galore v.0.6.5
trimmedreads were quantified using Salmon v.1.1.0 with default settings for paired-end reads in selective alignment mode and aligned against version 97 of the danio rerio reference genome GRCz11
Salmon output was summarized to genes using tximport v.1.1.4.2 in R. Ensembl gene ids were called from the org.Dr.eg.db v. 3.10.0 package in R.
Normalization factors were calculated using calcNormFactors in edgeR
Differentially expressed genes (>=1.5 fold and < 0.05 FDR) were identified by quasi-likelihood negative binomial generalized linear model with edgeR v.3.28.1.
Genome_build: version 97 of zebrafish reference genome GRCz11
Supplementary_files_format_and_content: raw counts for all samples from tximport are in rawcounts.txt. Dye-specific txt files contain log2 counts per million (CPM) values for each sample
rawcounts.txt: raw counts from salmon, read by tximport
DisperseRed9_log2cpm.txt: log2 cpms for disperse red 9 samples
DisperseBlue14_log2cpm.txt: log2 cpms for disperse blue 14 samples
SolventViolet47_log2cpm.txt: log2 cpms for solvent violet 47 samples
SolventRed169_log2cpm.txt: log2 cpms for solvent red 169 samples
SolventYellow33_log2cpm.txt: log2 cpms for solvent yellow 33 samples

organism: Danio rerio

growth_protocol: Adult 5D zebrafish begin spawning at 7am, and embryos are collected within the first two hours of spawning. The most healthy, fertilized embryos are selected for dechorionation. They were then loaded into 96-well round bottom plates filled with 100uL of embryo media, and the Bioprinter was used to add chemicals to make their final concentrations

extract_protocol:
Direct-zol RNA miniprep kit (Zymo research)
RNASeq libraries were prepared using 200 ng of total RNA and the NEBNext® Ultra™ II RNA Library Prep  (NEB, Cat: E7765S) per manufacturer’s instructions, with mRNA enriched via poly-A-selection using oligoDT beads.

treatment_protocol: Embryos were collected for RNA isolation at 48hpf to and to evade the eventual death of the embryos and to assess embryos during a time when significant gene changes may be occurring due to chemical exposure

value: SPF 5-D

value: Solvent Yellow 33

tag: concentration


title: S020


title: S017


title: Whole Embryo - Disperse Red 9 - 25µM - R3

description:
1637-NV-1_89-TCTCGCGC-CAGGACGT_S355
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 25µM

value: Disperse Red 9


title: Whole Embryo - Disperse Blue 14 - 261.5µM - R4

description:
1637-NV-1_90-TCTCGCGC-CCTATCCT_S356
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

value: Disperse Blue 14


title: Whole Embryo - Solvent Red 169 - Control - R4

description:
1637-NV-1_87-TCTCGCGC-AGGCGAAG_S353
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 23µM - R1

description:
1637-NV-1_91-TCTCGCGC-GGCTCTGA_S357
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

source_name: Whole Embryo - Solvent Violet 47 - 23µM

value: Solvent Violet 47


title: S014


title: Whole Embryo - Solvent Red 169 - 35.6µM - R4

description:
1637-NV-1_92-TCTCGCGC-TAATCTTA_S358
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 35.6µM

value: Solvent Red 169


title: S015


title: Whole Embryo - Solvent Yellow 33 - Control - R2

description:
1637-NV-1_86-TCCGGAGA-TATAGCCT_S352
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Blue 14 - Control - R4

description:
1637-NV-1_88-TCTCGCGC-ATAGAGGC_S354
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 35µM - R3

description:
1637-NV-1_84-TCCGGAGA-GTACTGAC_S350
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 35µM


title: Whole Embryo - Disperse Blue 14 - 314µM - R4

description:
1637-NV-1_83-TCCGGAGA-GGCTCTGA_S349
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 314µM


title: Whole Embryo - Solvent Violet 47 - 31.5µM - R1

description:
1637-NV-1_79-TCCGGAGA-AGGCGAAG_S345
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - 50µM - R4

description:
1637-NV-1_81-TCCGGAGA-CAGGACGT_S347
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 50µM


title: Whole Embryo - Solvent Yellow 33 - 12µM - R1

description:
1637-NV-1_80-TCCGGAGA-ATAGAGGC_S346
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt

source_name: Whole Embryo - Solvent Yellow 33 - 12µM


title: Whole Embryo - Disperse Blue 14 - 133µM - R4

description:
1637-NV-1_82-TCCGGAGA-CCTATCCT_S348
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 133µM


title: Whole Embryo - Solvent Red 169 - 1µM - R4

description:
1637-NV-1_85-TCCGGAGA-TAATCTTA_S351
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 1µM


title: S016


title: Whole Embryo - Solvent Red 169 - 35.6µM - R3

description:
1637-NV-1_77-TCCGCGAA-TAATCTTA_S343
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 25µM - R2

description:
1637-NV-1_74-TCCGCGAA-CAGGACGT_S340
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 17.5µM - R4

description:
1637-NV-1_76-TCCGCGAA-GGCTCTGA_S342
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 9µM - R4

description:
1637-NV-1_78-TCCGCGAA-TATAGCCT_S344
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt

source_name: Whole Embryo - Solvent Yellow 33 - 9µM


title: Whole Embryo - Disperse Blue 14 - 261.5µM - R3

description:
1637-NV-1_75-TCCGCGAA-CCTATCCT_S341
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - Control - R3

description:
1637-NV-1_72-TCCGCGAA-AGGCGAAG_S338
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 9µM - R1

description:
1637-NV-1_71-TAATGCGC-TATAGCCT_S337
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 55µM - R2

description:
1637-NV-1_69-TAATGCGC-GTACTGAC_S335
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 55µM


title: Whole Embryo - Solvent Red 169 - 11.2µM - R4

description:
1637-NV-1_70-TAATGCGC-TAATCTTA_S336
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 11.2µM


title: Whole Embryo - Disperse Blue 14 - 209µM - R4

description:
1637-NV-1_67-TAATGCGC-CCTATCCT_S333
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 209µM


title: Whole Embryo - Disperse Blue 14 - Control - R1

description:
1637-NV-1_65-TAATGCGC-ATAGAGGC_S331
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 45µM - R1

description:
1637-NV-1_61-GAGATTCC-GTACTGAC_S327
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 45µM


title: Whole Embryo - Solvent Red 169 - 5µM - R2

description:
1637-NV-1_62-GAGATTCC-TAATCTTA_S328
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 5µM


title: Whole Embryo - Solvent Red 169 - Control - R1

description:
1637-NV-1_64-TAATGCGC-AGGCGAAG_S330
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - Control - R2

description:
1637-NV-1_58-GAGATTCC-CAGGACGT_S324
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - Control


title: Whole Embryo - Disperse Blue 14 - 171µM - R2

description:
1637-NV-1_59-GAGATTCC-CCTATCCT_S325
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 171µM


title: Whole Embryo - Solvent Violet 47 - Control - R4

description:
1637-NV-1_60-GAGATTCC-GGCTCTGA_S326
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Disperse Blue 14 - Control - R3

description:
1637-NV-1_73-TCCGCGAA-ATAGAGGC_S339
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 12µM - R4

description:
1637-NV-1_57-GAGATTCC-ATAGAGGC_S323
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - Control - R4

description:
1637-NV-1_63-GAGATTCC-TATAGCCT_S329
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Blue 14 - 209µM - R1

description:
1637-NV-1_51-GAATTCGT-CCTATCCT_S317
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 40µM - R3

description:
1637-NV-1_48-GAATTCGT-AGGCGAAG_S314
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

source_name: Whole Embryo - Solvent Violet 47 - 40µM


title: Whole Embryo - Disperse Red 9 - 10µM - R3

description:
1637-NV-1_66-TAATGCGC-CAGGACGT_S332
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 10µM


title: Whole Embryo - Disperse Red 9 - Control - R4

description:
1637-NV-1_50-GAATTCGT-CAGGACGT_S316
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 55µM - R1

description:
1637-NV-1_45-CTGAAGCT-GTACTGAC_S311
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 7.5µM - R3

description:
1637-NV-1_47-CTGAAGCT-TATAGCCT_S313
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 12µM - R3

description:
1637-NV-1_44-CTGAAGCT-GGCTCTGA_S310
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

source_name: Whole Embryo - Solvent Violet 47 - 12µM


title: Whole Embryo - Solvent Yellow 33 - 7.5µM - R2

description:
1637-NV-1_55-GAATTCGT-TATAGCCT_S321
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - 11.2µM - R1

description:
1637-NV-1_54-GAATTCGT-TAATCTTA_S320
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 13.5µM - R2

description:
1637-NV-1_49-GAATTCGT-ATAGAGGC_S315
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 17.5µM - R2

description:
1637-NV-1_68-TAATGCGC-GGCTCTGA_S334
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 12µM - R2

description:
1637-NV-1_52-GAATTCGT-GGCTCTGA_S318
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 45µM - R3

description:
1637-NV-1_53-GAATTCGT-GTACTGAC_S319
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - 11.2µM - R3

description:
1637-NV-1_46-CTGAAGCT-TAATCTTA_S312
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: Whole Embryo - Disperse Blue 14 - 209µM - R2

description:
1637-NV-1_43-CTGAAGCT-CCTATCCT_S309
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: S045

source_name: Primary liver cancer single-cell


title: Whole Embryo - Disperse Red 9 - 10µM - R2

description:
1637-NV-1_42-CTGAAGCT-CAGGACGT_S308
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 31.5µM - R4

description:
1637-NV-1_56-GAGATTCC-AGGCGAAG_S322
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: S043


title: Whole Embryo - Solvent Yellow 33 - 13.5µM - R4

description:
1637-NV-1_41-CTGAAGCT-ATAGAGGC_S307
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 40µM - R4

description:
1637-NV-1_40-CTGAAGCT-AGGCGAAG_S306
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: S041


title: S044


title: S042


title: S046


title: S038


title: Whole Embryo - Disperse Red 9 - 55µM - R4

description:
1637-NV-1_37-CGGCTATG-GTACTGAC_S303
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 9µM - R2

description:
1637-NV-1_39-CGGCTATG-TATAGCCT_S305
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - 35.6µM - R1

description:
1637-NV-1_38-CGGCTATG-TAATCTTA_S304
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 35.6µM


title: Whole Embryo - Disperse Blue 14 - Control - R2

description:
1637-NV-1_33-CGGCTATG-ATAGAGGC_S299
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - Control - R2

description:
1637-NV-1_32-CGGCTATG-AGGCGAAG_S298
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: S040


title: Whole Embryo - Disperse Red 9 - 10µM - R4

description:
1637-NV-1_34-CGGCTATG-CAGGACGT_S300
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - 17.5µM - R3

description:
1637-NV-1_36-CGGCTATG-GGCTCTGA_S302
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: S035


title: LSC isolated from BL/6 CML mice treated with Veh_rep2

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Department for BioMedical Research

country: Switzerland

institute: University of Bern

data_processing:
Primary data analysis was performed with the Illumina RTA v2.4.11 .
The  sequence assembly and alignment was performed using the SeqMan NGen software v.15 and analyzed using ArrayStar software v.15 (DNASTAR, USA).
The level of gene expression was assessed after Reads Per Kilobase Million (RPKM) normalization and log2 transformation.
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: Tab-delimited text file includes linear total RPKM  normalized values.

source_name: LSK cells  treated with Veh

extract_protocol:
Total RNA was extracted from FACS-purified bone marrow BL/6 LSCs treated with MCP or Veh, using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified BL/6 LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 recipients. Upon CML development, mice were treated with MCP (10mg/kg) or Veh in vivo. LSCs from treated BL/6 mice of either group were then isolated for RNA extraction.

tag: tissue

value: Bone marrow derived LSCs

tag: age

value: post natal week 8

value: BL/6 (WT)


title: S036


title: LSC isolated from BL/6 CML mice treated with Veh_rep3


title: S037


title: Whole Embryo - Solvent Yellow 33 - Control - R3

description:
1637-NV-1_31-CGCTCATT-TATAGCCT_S297
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - 35µM - R4

description:
1637-NV-1_29-CGCTCATT-GTACTGAC_S295
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 35µM


title: Whole Embryo - Solvent Red 169 - 5µM - R1

description:
1637-NV-1_30-CGCTCATT-TAATCTTA_S296
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: LSC isolated from BL/6 CML mice treated with Veh_rep1


title: Whole Embryo - Solvent Violet 47 - 31.5µM - R3

description:
1637-NV-1_24-CGCTCATT-AGGCGAAG_S290
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: Whole Embryo - Solvent Yellow 33 - 12µM - R3

description:
1637-NV-1_25-CGCTCATT-ATAGAGGC_S291
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt

source_name: Whole Embryo - Solvent Yellow 33 - 12µM


title: Whole Embryo - Disperse Blue 14 - 171µM - R1

description:
1637-NV-1_27-CGCTCATT-CCTATCCT_S293
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: Whole Embryo - Solvent Violet 47 - Control - R3

description:
1637-NV-1_28-CGCTCATT-GGCTCTGA_S294
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: S039


title: Whole Embryo - Solvent Yellow 33 - 7.5µM - R1

description:
1637-NV-1_23-ATTCAGAA-TATAGCCT_S289
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Red 9 - Control - R1

description:
1637-NV-1_26-CGCTCATT-CAGGACGT_S292
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt


title: LSC isolated from BL/6 CML mice treated with MCP_rep2

source_name: LSK cells  treated with MCP


title: Whole Embryo - Disperse Blue 14 - 261.5µM - R1

description:
1637-NV-1_35-CGGCTATG-CCTATCCT_S301
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt


title: KPPF PDAC tumor 3

city: Houston

first: Yang

last: Chen

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: UT-MD Anderson Cancer Center

description:
KPPF-3
Each biological sample includes 8 Fastq files named starting with "Sample name".
KPPF_tumors_all_matrix.csv

data_processing:
Raw sequencing data from the Illumina platform were converted into Fastq files and aligned to the reference genome mm10 using the 10X Genomics Cell Ranger Pipeline.
After the alignment, a matrix file containing the cell barcode identity and gene values was exported by the 10X Genomics Cell Ranger Pipeline.
Matrix files for the samples were then processed and analyzed by Seurat R software 3.5.3.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Processed data are in the CSV (comma-separated values) matrix format. Each group, either KPPF tumors or KPPF;Col1smaKO tumors, has one combined matrix CSV file as processed data (KPPF_tumors_all_matrix.csv or KPPF_Col1smaKO_combined_matrix.csv).

source_name: Mouse pancreatic tumor single-cell RNA-seq

growth_protocol: KPPF (FSF-KrasG12D/+;Trp53frt/frt;Pdx1-Flp) and KPPF;Col1smaKO (FSF-KrasG12D/+;Trp53frt/frt;Pdx1-Flp;αSMA-Cre;Col1a1loxP/loxP) mice were housed under standard housing conditions and allowed to grow until they developed palpable tumors with 1 cm in diameter.

extract_protocol:
Single-cell barcoding and library preparation were performed using the 10X Genomics’ Chromium controller and Single Cell 3’ Reagent Kits v2 according to the manufacturer’s instructions.
Following capture and lysis, cDNA was synthesized and amplified to construct Illumina sequencing libraries using the 10X Chromium v2 according to the manufacturer’s instructions.

treatment_protocol: All mice were housed under standard housing conditions at MDACC animal facilities, without any treatment.

value: KPPF

tag: detailed genotype

value: Pancreatic tumor


title: KPPF PDAC tumor 1

description:
KPPF-1
Each biological sample includes 8 Fastq files named starting with "Sample name".
KPPF_tumors_all_matrix.csv


title: KPPF PDAC tumor 2

description:
KPPF-2
Each biological sample includes 8 Fastq files named starting with "Sample name".
KPPF_tumors_all_matrix.csv


title: KPPF;Col1smaKO PDAC combined

description:
KPPF;Col1smaKO-combined
Each biological sample includes 2 Fastq files named starting with "Sample name".
KPPF_Col1smaKO_combined_matrix.csv


title: Whole Embryo - Solvent Red 169 - 5µM - R3

description:
1637-NV-1_22-ATTCAGAA-TAATCTTA_S288
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt


title: LSC isolated from BL/6 CML mice treated with MCP_rep1


title: LSC isolated from BL/6 CML mice treated with MCP_rep3


title: MM2_3

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Adapter and quality trimming with Trimmomatic 0.32: ILLUMINACLIP:nextera.fa:2:40:15 MINLEN:25
Align to mm9 genome bwa mem version 0.7.5a-r405
Filter alignments for q>20
Remove mitochondrial and Encode blacklist reads
Get cut site position = 5' end of read +4
Convert to bigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigWig cut-site position

source_name: Hypothalamus

growth_protocol: They were maintained on a 12-h light/dark cycle and given ad libitum access to food and water. Mutant mice were caged with their wild-type littermates

extract_protocol: Libraries were prepared for sequencing using standard Illumina protocols

value: MM2 (this manuscript)


title: MM2_1


title: MM2_2


title: Whole Embryo - Solvent Violet 47 - 12µM - R1

description:
1637-NV-1_20-ATTCAGAA-GGCTCTGA_S286
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt


title: WT_4

value: Mecp2tm2Bird, RRID:IMSR_JAX:006849, wild-type control


title: WT_3

value: MM2 (this manuscript), wild-type control


title: WT_2


title: WT_1


title: KO_3

value: Mecp2tm2Bird, RRID:IMSR_JAX:006849


title: miRNA_EVT9

city: Tokyo

first: Manabu

last: Ogoyama

address: 1-1-5, Sendagi

department: Molecular Medicine and Anatomy

institute: Nippon Medical School

data_processing:
mRNA/lncRNA-sequencing analysis and miRNA-sequencing analysis were carried out on an Illumina MiSeq v2 Reagent Kit 300cycle (cat. no. MS-102-2002; Illumina), and MiSeq v2 Reagent Kit 50cycle (cat. no. MS-102-2001; Illumina), respectively.
The paired-end raw reads of 151 bp length for mRNA/lncRNA-sequencing and single reads of 26 bp length for miRNA-sequencing were obtained as fastq files which were imported into CLC genomics workbench (version 8.0.1; Qiagen) for analysis of the raw data included the trimming, filtering, and cleaning up the contaminated reads with the default parameters [a minimum quality score of 0.05 (equivalent to Phred quality score of 30)].
Clean 151 bp reads 26 bp reads were aligned to the human genome sequence retrieved from the Ensembl database (Assembly GRCh38.p13, database version 82.38 and 101.38) and microRNA database miRbase (release 21), respectively, using CLC Genomics Workbench Map Reads to Reference tool (length fraction = 0.95 and similarity fraction = 0.9).
Normalization of gene expression data was performed by the TMM method of edgeR package (version 3.3.8; Bioconductor, https://www.bioconductor.org/). Statistically differentially expressed transcripts were conducted using edgeR. Genes that had a false discovery rate (FDR)-corrected p-value (q-value) of < 0.05 and an absolute log2 fold change (log FC) ≥ 1 were judged to be significantly differentially expressed (i.e., differentially expressed genes, DEGs).
Genome_build: Ensembl, miRbase
Supplementary_files_format_and_content: Abundance measurements (normalized values) obtained from raw gene counts for every gene and every sample using TMM methods of edgeR

source_name: Extravillous trophoblast cells

growth_protocol: Minced chorionic villi of first-trimester human placental tissues were placed in collagen type 1-coated dish. Outgrowth cells from adherent villous tips were dispersed, passed through a nylon strainer of pore diameter 40 μm and replaced in collagen type 1-coated dish. After removal of nonadherent cells and debris by washing with PBS, residual cells were isolated EVT cells. Minced chorionic villous tips were defined as first-trimester chorionic CVT cells.

extract_protocol:
The total RNA was extracted from each sample using RNAiso Plus (cat. no. 9109; Takara Bio, Shiga, Tokyo).
TruSeq Stranded Total RNA Library Prep Kit (cat. no. RS-122-2301; Illumina) was used with 1 µg of total RNA for the preparations of mRNA/lncRNA-seq libraries according to the manufacturer’s instructions.

value: Extravillous trophoblast cells

tag: gestational week

tag: rna population

value: miRNA


title: miRNA_VT14

source_name: Chorionic villous trophoblast cells

value: Chorionic villous trophoblast cells


title: KO_2


title: Whole Embryo - Disperse Red 9 - 45µM - R2

description:
1637-NV-1_21-ATTCAGAA-GTACTGAC_S287
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - 45µM

value: SPF 5-D


title: miRNA_EVT14


title: miRNA_VT9


title: miRNA_VT16


title: EVT16

value: mRNA


title: EVT9


title: EVT14


title: VT16


title: VT14


title: CML LSC from CD93-/- (KO) rep3

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep3

source_name: CML LSC cells

extract_protocol:
Total RNA was extracted from FACS-purified bone marrow BL/6 (WT) or CD93-/- (KO) LSKs and BL/6 (WT) or CD93-/- (KO) LSCs using the RNeasy Micro Kit (QIAGEN AG, Switzerland).
Libraries were generated from  total RNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio, Japan).

treatment_protocol: FACS-purified BL/6 and CD93-/- LSKs were harvested and transduced twice with BCR-ABL1-GFP. Cells were injected intravenously (i.v.) into the non-irradiated syngeneic BL/6 recipients (BL/6 and CD93-/- CML). Upon CML development, LSCs from BL/6 and CD93-/- CML mice were isolated. Naïve LSKs from BL/6 (WT) or CD93-/- (KO) mice were used as controls.

value: Bone marrow

tag: cell type

tag: disease state

value: CML


title: VT9


title: CML LSC from CD93-/- (KO) rep2

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep2


title: KO_1


title: CML LSC from BL/6 (WT) rep3

description: CML LSC isolated from bone marrow of BL/6 (WT) rep3

value: WT


title: CML LSC from CD93-/- (KO) rep1

description: CML LSC isolated from bone marrow of CD93-/- (KO) rep1

value: Bone marrow derived LSCs


title: miRNA_EVT16


title: HMC3 replicate 3

city: Boston

first: Songlei

last: Liu

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard University

data_processing:
A human genome reference index was built by STAR 2.5.2b using genome primary assembly (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/GRCh38.primary_assembly.genome.fa.gz) and annotation file (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/gencode.v27.primary_assembly.annotation.gtf.gz) from GENCODE.
Read alignment and quantification were performed using STAR -quantMode GeneCounts.
Genome_build: GRCh38 GENCODE release 27
Supplementary_files_format_and_content: Text file with reads per gene counts from STAR -quantMode GeneCounts

source_name: HMC3 cells

extract_protocol:
Cells cultured in 6-well plates were treated with 600 µl TRIzol (ThermoFisher, 15596018) directly on plate. The solution was used for total RNA extraction using Direct-zol RNA MiniPrep Kit (Zymo Research, R2050). RNA amount was quantified using Qubit RNA HS Assay Kit (ThermoFisher, Q32852) and RNA integrity was checked by the presence of 18S and 28S bands on a 2% E-Gel EX Agarose Gel (ThermoFisher, G402002).
1 µg RNA was used for library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (NEB, E7760S) following manufacturer’s instruction on combined usage with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Library QC and sequencing was performed by the Biopolymers Facility at Harvard Medical School.
Stranded poly(A) RNA-seq

value: Brain

tag: cell line

value: HMC3 cells

value: Microglia


title: HMC3 replicate 1


title: Whole Embryo - Solvent Red 169 - 1µM - R2

description:
1637-NV-1_14-ATTACTCG-TAATCTTA_S280
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 1µM

value: Solvent Red 169


title: Whole Embryo - Solvent Violet 47 - 40µM - R1

description:
1637-NV-1_16-ATTCAGAA-AGGCGAAG_S282
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

source_name: Whole Embryo - Solvent Violet 47 - 40µM

value: Solvent Violet 47


title: Whole Embryo - Disperse Red 9 - 35µM - R1

description:
1637-NV-1_13-ATTACTCG-GTACTGAC_S279
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

value: Disperse Red 9


title: HMC3 replicate 2


title: Whole Embryo - Solvent Yellow 33 - 13.5µM - R1

description:
1637-NV-1_17-ATTCAGAA-ATAGAGGC_S283
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt

value: Solvent Yellow 33


title: Whole Embryo - Disperse Blue 14 - 171µM - R3

description:
1637-NV-1_19-ATTCAGAA-CCTATCCT_S285
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 171µM

value: Disperse Blue 14


title: Whole Embryo - Disperse Red 9 - Control - R3

description:
1637-NV-1_18-ATTCAGAA-CAGGACGT_S284
processed data file: rawcounts.txt, DisperseRed9_log2cpm.txt

source_name: Whole Embryo - Disperse Red 9 - Control


title: Whole Embryo - Solvent Violet 47 - 23µM - R3

description:
1637-NV-1_8-ATTACTCG-AGGCGAAG_S274
processed data file: rawcounts.txt, SolventViolet47_log2cpm.txt

source_name: Whole Embryo - Solvent Violet 47 - 23µM


title: Whole Embryo - Solvent Yellow 33 - Control - R1

description:
1637-NV-1_15-ATTACTCG-TATAGCCT_S281
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Solvent Red 169 - 50µM - R3

description:
1637-NV-1_10-ATTACTCG-CAGGACGT_S276
processed data file: rawcounts.txt, SolventRed169_log2cpm.txt

source_name: Whole Embryo - Solvent Red 169 - 50µM


title: Whole Embryo - Solvent Yellow 33 - 10.5µM - R4

description:
1637-NV-1_9-ATTACTCG-ATAGAGGC_S275
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt


title: Whole Embryo - Disperse Blue 14 - 314µM - R3

description:
1637-NV-1_12-ATTACTCG-GGCTCTGA_S278
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 314µM


title: Whole Embryo - Disperse Blue 14 - 133µM - R3

description:
1637-NV-1_11-ATTACTCG-CCTATCCT_S277
processed data file: rawcounts.txt, DisperseBlue14_log2cpm.txt

source_name: Whole Embryo - Disperse Blue 14 - 133µM


title: Whole Embryo - Solvent Yellow 33 - 10.5µM - R3

description:
1637-NV-1_7-AGCGATAG-TATAGCCT_S273
processed data file: rawcounts.txt, SolventYellow33_log2cpm.txt