title: Leukemic evolution

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: Time 3

data_processing:
Raw base call (BCL) files generated by NextSeq 550 sequencer were demultiplexed using Cell Ranger software to obtain FASTQ files
The FASTQ files obtained were then processed using Partek® Flow® software (version 9.0) following manufacturer guidelines. Reads were trimmed, aligned to the human reference genome hg38 (GRCh38) than deduplicated, to obtain one alignment per unique molecular identifier (UMI), choosing Ensembl Transcripts release 91 for the annotation.
After filtering out barcodes associated to droplets containing no cells, aligned reads were quantified generating a single cell count matrix. Cells meeting the following quality control (QC) parameters were included in the analysis: total reads between 6.500 to 52.000; expressed genes between 1.000 and the maximum detected number; mitochondrial reads percentage less than 15%.
features were filtered in order to include only genes expressed in more than 0.1% of cells
UMI counts were then normalized following Partek® Flow® recommendations: for each UMI in each sample the number of raw reads was divided by the number of total mapped reads in that sample and multiplied by 1.000.000, obtaining a count per million value (CPM), 1.0 was added to CPM and the normalized expression value was log transformed.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data files in .txt format contain normalized expression matrix. Column header correspond to cell barcodes while features (gene ID) are on rows.

source_name: Peripheral blood

extract_protocol:
Frozen PBMC’s were thawed following 10X Genomics “Sample Preparation Demostrated Protocol”. Immunomagnetic selection of CD34+ cell population was then performed by means of “CD34 Microbead kit, human” (Miltenyi Biotec) following the protocol provided by the manufacturer.
10000 unfixed CD34+ cells were resuspended in PBS/0.05% BSA and loaded in the 10X Chromium Controller as recommended in manufacturer protocol. Samples were processed using the Chromium Single Cell 3ʹ Reagent Kits v3 (10X Genomics, Pleasanton, California, USA) and the libraries were multiplexed and sequenced on a NextSeq 550 using High Output Kit v2.5 chemistry (Illumina, San Diego, California, USA).

value: CD34+ HSPCs from PBMNCs

value: Peripheral blood

tag: disease

value: sAML

value: Ruxolitinib


title: Treatment

status: Public on Feb 16 2021

type: SRA

description: Time 2

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue

value: primary myelofibrosis

tag: treatment


title: Sox10+_48-50hpf

city: Houston

first: Rosa

last: Uribe

state: Texas

address: 6100 Main St.

department: BioSciences

country: USA

institute: Rice University

data_processing:
Illumina NextSeq 500 used for basecalling
CellRanger (v2.1.0) software facilitated genomic alignment, filtering, barcode reading, and exportation for further analysis
Genome_build: DanioGRCz10
Supplementary_files_format_and_content: 10X Genomics Chromim Filtered Gene BC Cellular Barcodes (barcodes.tsv) and genes (genes.tsv); 10X Genomics Chromium Raw Gene BC Cellular Matrix (matrix.mtx)

molecule: polyA RNA

organism: Danio rerio

source_name: Derivative Sox10+ Neural Crest

growth_protocol: Embryos were collected synchronously, batched by stage. All embryos were raised according to standard practices in E3 embryonic media for the first 24 hours and then transfered to 1X 1-phenyl 2-thiourea (PTU)/E3 solution. At 24 hours post fertilization, embryos were sorted manually for GFP expression. Developmentally delayed or malformed embryos were removed. All work was conducted under protocols approved by and in accordance with  Rice University Institutional Animal Care and Use Committee (IACUC).

extract_protocol:
Posterior tissue (Vagal and trunk domains) were harvested; Single cell suspension was prepared via digestion in 37°C 1X Accumax buffer (Sigma-Aldrich, A7089) for 30-45 minutes. Suspension was washed in Hank's Buffer (1x HBSS; 2.5 mg/mL BSA; 10μM pH8 HEPES), concentrated via centrifugation (200 rcf for 10 minutes at 4°C) in a small volume of Hank's buffer, and sorted for GFP+ cells via FACS. GFP+ cells were used as input for the 10X Genomics Chromium platform using the 10X Single Cell 3’ V2 chemistry kit for 10,000 cells.
RNA libraries were prepared for sequencing using standard Illumina protocols following the 10x Genomics pipeline

tag: genotype/variation

value: -4.9sox10:EGFP ba2Tg

tag: developmental stage

value: FACS isolated -4.9sox10:EGFP+ cells


title: MEF_WT_Pol II_ChIPseq

city: Illkirch

first: Fang

last: WANG

address: Parc d'Innovation 1, Rue Laurent Fries Illkirch, 67404

country: France

institute: INSTITUT DE GENETIQUE DE BIOLOGIE MOLECULAIRE ET CELLURAIRE (IGBMC)

description: Chromatin IP against RNA Pol II and H2Bub

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peak calling was performed using MACS2 v2.1.1.20160309 with default parameters, except ‘narrow’ for pol II peaks and ‘broad’ for H2Bub peaks.
Genome_build: mm10
Supplementary_files_format_and_content: .narrowPeak or .broadPeak generated by MACS2

molecule: genomic DNA

organism: Mus musculus

source_name: MEF_WT_Pol II

growth_protocol: mESCs were first cultured with feeders for two passages, then removed feeders and continued culturing in the presence of leukaemia inhibitory factor (LIF) in medium containing 15% foetal calf serum (FCS) containing PD0325901 (1uM) and CH99021 (3uM); MEF cells were generated from E10.5 mice embryos and cultured in MEF medium (DMEM with 10% FCS plus penicillin and streptomycin).

extract_protocol:
Chromatin was fixed in 1% Paraformaldehyde (PFA), sheared to 200-700bp using the Covaris E220 sonicator, then immunoprecipitated using the indicated antibody.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 7 to 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: No specific treatments

value: Mouse embryonic fibroblasts (MEFs)

tag: genotype

tag: strain

value: DBA/2 x C57BL/6

tag: chip antibody

value: anti-RPB1 antibody (generated in-house, catalog# PB-7G5)


title: MEF_WT_H2Bub_ChIPseq

value: anti-H2Bub1 (MediMabs, catalog# #MM-0029-P, batch/lot#2991404010-P-09)


title: MEF_KO_H2Bub_ChIPseq


title: MEF_KO_input_ChIPseq


title: Sox10+_68-70hpf


title: mESC_KO_H2Bub_ChIPseq

value: Mouse embryonic stem cell (mESC)


title: MEF_KO_Pol II_ChIPseq

source_name: MEF_KO_Pol II


title: MEF_WT_input_ChIPseq


title: SAP rep3

city: Chengdu

first: bing

last: wang

state: Sichuan

address: No. 270, Tianhuan Road, Rongdu Avenue, Jinniu District, Chengdu City, Sichuan Province

department: General Surgery

country: China

institute: The General Hospital of Western Theater Command

data_processing:
Basecalls performed using CASAVA version 1.8
The high quality reads of circRNA were aligned to the reference genome/transcriptome with STAR software and circRNAs were detected and identified with DCC software.
Use the circBase database and Circ2Traits to annotate the identified circRNA.
The high quality reads of lncRNA and mRNA were aligned to the mouse reference genome (UCSC MM10) with hisat2 software.
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the FPKM as the expression profiles of lncRNA and mRNA
Genome_build: MM10
Supplementary_files_format_and_content: excel
Supplementary_files_format_and_content: The lncRNA expression profile file include FPKM Values, Counts and Annotations. The circRNA expression profile file include junction reads, Normalized Intensity and Annotations.

source_name: pancreatic tissues

extract_protocol:
According to the manufacturer's instructions, total RNA was extracted from frozen samples using Trizol reagent (Ambion), and the RNA concentration of each sample was measured using a NanoDrop ND-1000 instrument (Thermo Fisher Scientific, Waltham, MA, USA), with OD260/OD280 values as an indicator of RNA purity.
Ribo-Zero rRNA Removal Kits (Illumina, USA) was used to remove rRNAs from total RNA. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, USA).

treatment_protocol: The mice were randomly divided into control group and SAP group (3 mice per group). Before the operation, 5% isoflurane was given for inhalation anesthesia, and then 4% sodium taurocholate salt was slowly retrogradely injected into the biliopancreatic duct with a micro infusion pump to induce SAP.

value: Pancreas


title: mESC_WT_H2Bub_ChIPseq


title: mESC_KO_input_ChIPseq


title: mESC_WT_Pol II_ChIPseq

source_name: mESC_WT_Pol II


title: mESC_WT_input_ChIPseq


title: Chronic phase

description: Time 1

value: No


title: acute myocardial infarction 8

city: Beijing

first: Chenxi

last: Song

address: No 167 Beilishi Road

institute: Fuwai Hospital Chinese Academy of Medical Sciences

data_processing:
Illumina bcl2fastq (version 2.20.0.422) used for base-calling.
The original sequences were filtered by Cutadapt software (http: //pypi.python.org/pypi/cutadapt) to obtain the high quality sequences (clean reads)
The human genome sequences and annotations were downloaded from the genome sequence database ENSEMBL (version Homo_sapiens.GRCh38.91.chr)（ http://www.ensembl.org ）
The clean reads were mapped to the human reference genome using HISAT2 software (version 2.1.0)
HTSeq software (version 0.6.0) was used to calculate the gene count, and Fragments per Kilobase per Million Mapped Fragments (FPKM) was carried out to convert the count number to eliminate the influence of gene expression caused by gene length and sequencing quantity
The DESeq2 (version 1.20.0) package was used to analyze the differential expression of genes and to calculate P-valve between each pair of groups
Genome_build: the genome sequence database ENSEMBL (version Homo_sapiens.GRCh38.91.chr)（ http://www.ensembl.org ）
Supplementary_files_format_and_content: FPKM values for each sample

source_name: peripheral blood monocyte

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols PE150

tag: gender

value: female

tag: age

tag: disease state

value: acute myocardial infarction


title: acute myocardial infarction 7

value: male


title: MEF_KO3_RNASeq

description:
Sequencing total RNA from MEF cells
MEF_RNAseq.tsv

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover
Reads were preprocessed in order to remove adapter, polyA and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Then, reads were mapped onto the mm10 assembly of Mus musculus genome using STAR (version 2.5.3a). Gene expression quantification was performed from uniquely aligned reads using htseq-count (version 0.6.1p1), with annotations from Ensembl version 90 and “union” mode.
Read counts have been normalized across samples with the median-of-ratios method, to make these counts comparable between samples. Differential expression genes were implemented in the Bioconductor package DESeq2 (version 1.16.1).
Genome_build: mm10
Supplementary_files_format_and_content: mESC_RNAseq.tsv; MEF_RNAseq.tsv

extract_protocol:
RNA was extracted from MEFs using the MN kit, according to manufacturer's instructions, including a DNase digestion step to eliminate DNA from the sample. RNA was eluted in H2O.
Total RNA was extracted from mESCs and MEFs using the Macherey-Nagel NucleoSpin RNA isolation kit, according to manufacturer's instructions.
RNA-Seq libraries were generated from 700 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94 ? for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following the addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.


title: acute myocardial infarction 6


title: acute myocardial infarction 5


title: acute myocardial infarction 4


title: mESC_KO_Pol II_ChIPseq

source_name: mESC_KO_Pol II


title: acute myocardial infarction 2


title: acute myocardial infarction 1


title: Breast cancer patient_4_after chemotherapy

type: RNA

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: This sample is isolated from breast cancer after chemotherapy

hyb_protocol: Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN). Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies) in Hybridization Oven (Cat.# G2545A, Agilent technologies), according to the manufacturer’s instructions for 17 hours

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies).

source_name: TAMs from breast cancer patient after chemotherapy

label_protocol: RNA amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies), following the manufacturer’s instructions.

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions, RNA quantity and quality were measured by Qubit 4 (Invitrogen). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: TAMs isolationed from fresh tumor samples collected from biopsy (before chemotherapy) or surgical resection (after chemotherapy) by magnetic-activated cell sorting using direct CD14 Isolation Kit (Miltenyi Biotec, 130-050-201) for CD14+ cells

tag: diagnosis

value: breast cancer

value: tumor-associated macrophages (TAMs)


title: intermediate coronary lesion 8

value: intermediate coronary lesion


title: Breast cancer patient_4_before chemotherapy

description: This sample is isolated from breast cancer before chemotherapy

source_name: TAMs from breast cancer patient before chemotherapy


title: Breast cancer patient_3_before chemotherapy


title: Breast cancer patient_2_before chemotherapy


title: Breast cancer patient_1_after chemotherapy


title: MEF_WT3_RNASeq


title: MEF_KO1_RNASeq


title: mESC_KO2_RNASeq

description:
Sequencing total RNA from mESCs
mESC_RNAseq.tsv

extract_protocol:
RNA was extracted from mESC using the MN kit, according to manufacturer's instructions, including a DNase digestion step to eliminate DNA from the sample. RNA was eluted in H2O.
Total RNA was extracted from mESCs and MEFs using the Macherey-Nagel NucleoSpin RNA isolation kit, according to manufacturer's instructions.
RNA-Seq libraries were generated from 700 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94 ? for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following the addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.


title: Breast cancer patient_1_before chemotherapy


title: Breast cancer patient_3_after chemotherapy


title: mESC_KO1_RNASeq


title: mESC_WT1_RNASeq


title: MEF_WT2_RNASeq


title: mESC_KO3_RNASeq


title: intermediate coronary lesion 6


title: Pax2-GFP_Cl-2

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Raw BCL files from the Illumina HiSeq were demultiplexed into paired-end, gzip-compressed FASTQ files for each channel using Cell Ranger’s mkfastq.
Using Cell Ranger’s count, reads were aligned to the mouse reference transcriptome (mm10), and transcript counts quantified for each annotated gene within every cell.
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 binary data format

source_name: trunk of mouse embryo 21 somite stage

growth_protocol: dissected embryos

extract_protocol:
Dissociated cells and FACS
10X Chromium Single Cell 3'

value: C57BL6 xC3H background

value: trunk of mouse embryo

value: 21 somite stage

tag: genotype/group

value: Pax2-GFP Clump


title: intermediate coronary lesion 2


title: MEF_WT1_RNASeq

value: Mouse embryonic fibroblasts (MEFs)


title: MEF_KO2_RNASeq

value: DBA/2 x C57BL/6


title: Breast cancer patient_2_after chemotherapy


title: intermediate coronary lesion 3


title: intermediate coronary lesion 5


title: intermediate coronary lesion 7


title: intermediate coronary lesion 4


title: Pax2-GFP_SC-3

source_name: trunk of mouse embryo 18 somite stage

value: 18 somite stage

value: Pax2-GFP Single cell


title: acute myocardial infarction 3


title: mESC_WT2_RNASeq

value: Mouse embryonic stem cell (mESC)


title: Pax2-GFP_Gata3KO_SC-3

value: Pax2-GFP; Gata3KO Single-cell


title: Pax2-GFP_SC-2

value: Pax2-GFP Single-cell


title: intermediate coronary lesion 1


title: normal coronary artery 8

value: normal coronary artery


title: normal coronary artery 6


title: vagina_SM-A9HOS

city: San Diego

first: Bing

last: Ren

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

data_processing:
For each sequenced single nucleus ATAC-Seq library, we obtained four FASTQ files, two for paired end DNA reads and two for the combinatorial indexes for i5 and T7 (768 and 364 indices, respectively). We selected all reads with up to 2 mismatches per i5 and T7 index (Hamming distance between each pair of indices is 4) and integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ files.
snATAC-seq reads were aligned to the GRCh38 genome assembly using BWA version 0.7.17-r1188 with the following parameters: "mem -M -k 32 -t 8".
Aligned reads were name sorted and filtered using Samtools version 1.9 with the following parameters: "-f 2 -F 0x70c -q 30".
Duplicated paired-end fragments were removed for each nucleic and nucleic were filtered based on stringent quality control criteria including an enrichment of reads at transcription start sites (TSS enrichment; TSSe) greater than 7-fold, and a minimum of > 1,000 mapped paired-end fragments per nucleus.
Nuclei were further filtered for potential doublets using a version of Scrublet modified for single cell ATAC-seq.
For each sample, we generated a cell by bin (5kb) count matrix and used it for the initial clustering analysis.
Nuclei from all samples were pooled and subjected to clustering analysis using the Taiji pipeline (https://taiji-pipeline.github.io/).
Genome_build: GRCh38
Supplementary_files_format_and_content: *.mtx.gz: Bin (row) by cell (column) count matrix in Matrix Market format; *.barcodes.txt.gz: column names for the matrix representing cell barcodes; *.features.txt.gz: row names for the matrix representing genomic regions (features); clustering_results.txt: tab-delimited text files containing final clustering result of nucleic from all samples

source_name: vagina

extract_protocol:
Nuclei were extracted from flash frozen tissue either by manual pulverization via mortar and pestle while submerged in liquid nitrogen, or homogenization in a gentleMACS M-tube (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf).
Extracted nuclei were permeabilized either in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor), or 1 mL OMNI Buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water). After resuspension in permeabilization buffer, nuclei were rotated at 4 ˚C for 5 minutes before being pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 or HiSeq4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).

tag: sample type

value: normal

tag: sample preparation

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: female

tag: race

value: asian

tag: Cause of death

value: cerebral vascular accident


title: uterus_SM-IOBHX

source_name: uterus


title: normal coronary artery 5


title: thyroid_SM-IOBHW

source_name: thyroid


title: thyroid_SM-JF1O4


title: thyroid_SM-C1MKY

value: male

value: white

value: anoxia


title: uterus_SM-A87A2


title: normal coronary artery 1


title: normal coronary artery 2


title: GY2-8_1A

city: Tianjin

first: Ping

last: Zhu

address: 288, Nanjing Road, Heping District

department: State Key Laboratory of Experimental Hematology

institute: Institute of Hematology and Blood Disease Hospital

data_processing:
demultiplexing of single cell data by unique barcodes
R2 contains the cell barcode (bp 1-8) and UMI (bp 9-16), R1 is the biological read.
The file cell label and barcodes.xls includes the cell barcode sequence for each cell ID and is available on the series record.
quality control by romving template switching oligonucleotide (TSO), polyA tail, and low quality reads using Trimmomatic (v0.36)
UMI determination and read alignment using hisat2 (v2.1.0)
gene expression counting using HTSeq (v0.9.1)
Genome_build: hg38
Supplementary_files_format_and_content: counts of sequencing reads per gene by cell

source_name: Irradiation of ATM knock down

growth_protocol: Cells were cultured in DMEM medium with 10% fetal bovine serum and 100 units/mL penicillin-streptomycin solution at 37℃ with 5% CO2.

extract_protocol:
Single cells were isolated by mouth pipetting and lysed in 2.5ul lysis buffer containing Triton X-100 and RNase inhibitor.
Single cell whole transcriptome amplification was performed using modified Smart-seq2 and 3' mRNA libraries were constructed by KAPA Hper Prep Kit and NEBNext Multiplex Oligos for Illumina.

treatment_protocol: The cells from the IR and ATM-KD-IR groups were treated by 5Gy IR and continued culturing for 4 hours after that.

tag: cell line

value: ATM knockdown

tag: radiation treatment

value: irradiated


title: normal coronary artery 3


title: stomach_SM-IOBHV

source_name: stomach


title: stomach_SM-JF1O3


title: stomach_SM-JF1NP


title: GY2-7_1A


title: stomach_SM-CHLWL


title: GY2-6_1A

source_name: ATM knock down

value: untreated


title: GY2-5_1A


title: small_intestine_SM-JF1O2

source_name: small intestine terminal ileum


title: small_intestine_SM-ADA5F


title: GY2-4_TKR

source_name: Irradiation of Wild type

value: WT


title: small_intestine_SM-A62GO


title: skin_sun_exposed_SM-JF1NT

source_name: skin sun exposed


title: normal coronary artery 7


title: GY2-3_TKR

source_name: Wild type


title: skin_sun_exposed_SM-IQYCP


title: GY2-2_TKR


title: GY2-1_TKR


title: pancreas_SM-JF1O6

source_name: pancreas


title: normal coronary artery 4

source_name: peripheral blood monocyte


title: skin_SM-JF1O1

source_name: skin non sun exposed


title: pancreas_SM-IOBHS


title: OD37_Negative

city: Birmingham

first: Paul

last: Moss

state: West Midlands

address: Vincent Drive

department: Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

data_processing:
Sequenced reads were mapped to hg19 whole genome using STAR with default parameters and raw feature counts were generated using HTSeq with paramters HTSeq.scripts.count -f bam -r name -m union -s reverse
hg19
Counts matrix with raw counts for each feature in each sample

source_name: Peripheral Blood

extract_protocol:
Fresh peripheral blood T cells were enriched for CD4+ T cells using the Easysep human CD4+ enrichment kit. Enriched CD4+ T cells were then stained with CMV Class II tetramer, and subsequently surface antibodies for 15 minutes at 4oC. Using the MoFlo™ sorter, CD3+, CD4+, tetramer+ cells were sorted into 2 populations; PD1+  and PD1-. Sorting was performed within 4 hours of blood sampling.  After sorting, cells were immediately pelletted,  3500g for 10 minutes, and RLT plus lysis buffer added and vortexed for 1 minute. RNA extraction was then performed according to manufacturer’s instructions. (RNEasy Plus micro kit, Qiagen).
RNA libraries were prepared using a TruSeq Stranded Total RNA Library preparation kit
RNA-Seq - Illumina HiSeq2000 platform using TruSeq version 3 chemistry, over 100 cycles (Oxford Gene Technologies).

tag: cell type

value: CMV-specific CD4 T cell

tag: pd1 expression

value: PD1 negative

tag: tcr sequencing protocol


title: SN234_Negative


title: OD12_Positive

value: PD1 positive


title: OD37_Positive


title: OD12_Negative


title: DL_Positive


title: pancreas_SM-ADRUQ


title: skin_sun_exposed_SM-ADYHK


title: 84PS_Positive


title: DL_Negative


title: 84PS_Negative


title: 112DF_Negative


title: skin_sun_exposed_SM-IOBHT


title: nerve_tibial_SM-IOBHQ

source_name: tibial nerve


title: Human ESC (naïve) PANDORA-seq rep 2

city: Riverside

first: Junchao

last: Shi

state: CA

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
For each RNA library, around 10 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13. 2) The reads with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The reads with ploy A. 5) The reads shorter than 15nt. The clean reads were obtained after data filtration.
Genome_build: mm10 (for mouse), hg19 (for human)
Supplementary_files_format_and_content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Naïve embryonic stem cells

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

tag: tissue

value: Naive embryonic stem cells

tag: treatment

value: RNAs were treated with T4PNK, then AlkB before cDNA library construction.

tag: molecule type

value: 15-50 nt RNA


title: muscle_SM-JF1O9

source_name: gastrocnemius muscle

value: normal

value: flash-frozen tissue


title: SN234_Positive


title: muscle_SM-IOBHP

value: female

value: asian


title: nerve_tibial_SM-CHLWU

value: male


title: 112DF_Positive


title: ovary_SM-IOBHR

source_name: ovary

value: cerebral vascular accident


title: pancreas_SM-JF1NS

value: white

value: anoxia


title: Human ESC (naïve) PANDORA-seq rep 1


title: skin_SM-IOBHU


title: Human ESC (naïve) traditional rep 2

value: RNAs were sequenced with standard protocols.


title: Human ESC (primed) PANDORA-seq rep 3

source_name: Primed embryonic stem cells

value: Primed embryonic stem cells


title: Human ESC (naïve) traditional rep 1


title: muscle_SM-ADA6L


title: lung_SM-JF1NZ

source_name: lung


title: Human ESC (primed) PANDORA-seq rep 1


title: Human ESC (primed) PANDORA-seq rep 2


title: mammary_tissue_SM-JF1NV

source_name: breast mammary tissue


title: mammary_tissue_SM-IOBHL


title: Human ESC (primed) +T4PNK rep 3

value: RNAs were treated with T4PNK before cDNA library construction.


title: lung_SM-ACCPU


title: lung_SM-A8WNH


title: muscle_SM-C1PWV


title: Human ESC (primed) +T4PNK rep 2


title: heart_lv_SM-JF1NY

source_name: heart left ventricle


title: Human ESC (primed) +T4PNK rep 1


title: Human ESC (primed) +AlkB rep 3

value: RNAs were treated with AlkB before cDNA library construction.


title: liver_SM-A8WNZ

source_name: liver


title: Human ESC (primed) +AlkB rep 2


title: Human ESC (primed) +AlkB rep 1


title: Human ESC (primed) traditional rep 3


title: heart_lv_SM-IOBHO


title: Human ESC (primed) traditional rep 2


title: esophagus_muscularis_SM-IOBHM

source_name: esophagus muscularis


title: heart_atrial_appendage_SM-IOBHN

source_name: heart right atrial appendage


title: Human ESC (primed) traditional rep 1


title: esophagus_muscularis_SM-CSSCV


title: Human hela cell PANDORA-seq (+T4PNK, +AlkB) rep 3

source_name: HeLa cells

value: HeLa cells


title: esophagus_mucosa_SM-AZPYJ

source_name: esophagus mucosa


title: esophagus_muscularis_SM-A8CPH


title: esophagus_mucosa_SM-A9VPA


title: Human hela cell PANDORA-seq (+T4PNK, +AlkB) rep 2


title: Human hela cell PANDORA-seq (+AlKB, +T4PNK) rep 2

value: RNAs were treated with AlkB, then T4PNK before cDNA library construction.


title: Human hela cell PANDORA-seq (+T4PNK, +AlkB) rep 1


title: esophagus_mucosa_SM-A9HOR


title: nerve_tibial_SM-CP2V6


title: esophagus_ge_junction_SM-IOERG

source_name: esophagus gastroesophageal junction


title: esophagus_ge_junction_SM-CTD24


title: Human hela cell +T4PNK rep 3


title: colon_transverse_SM-BZ2ZS

source_name: transverse colon


title: colon_transverse_SM-ACCQ1


title: colon_transverse_SM-A9VP4


title: Human hela cell +T4PNK rep 1


title: colon_transverse_SM-A9HOW


title: Human hela cell +AlkB rep 3


title: Human hela cell +AlkB rep 1


title: colon_sigmoid_SM-JF1O8

source_name: sigmoid colon


title: Human hela cell traditional rep 3


title: colon_sigmoid_SM-AZPYO


title: Human hela cell +T4PNK rep 2


title: artery_tibial_SM-IOBHK

source_name: tibial artery


title: Human hela cell PANDORA-seq (+AlKB, +T4PNK) rep 3


title: Human hela cell traditional rep 1


title: artery_aorta_SM-JF1NU

source_name: aorta


title: artery_tibial_SM-CHLWW


title: artery_aorta_SM-C1PX3


title: Human hela cell traditional rep 2


title: Human hela cell PANDORA-seq (+AlKB, +T4PNK) rep 1


title: esophagus_muscularis_SM-IQYD1


title: Uhrf1 cKO rep3 [FLS-KO8_S6]

city: Toon

first: Noritaka

last: Saeki

state: Ehime

address: Shitsukawa

department: Advanced Research Support Center

country: Japan

institute: Ehime university

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and analyzed by Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks output

source_name: Primary synovial fibroblasts

growth_protocol: Swollen ankles obtained from  K/BxN serum transfer arthritis model were dislocated and digested by Collagenase TypeⅣ. To obtain synovial fibroblasts with high purity, obtained synovial cells were seeded to typeⅠcollagen-coated culture dish and cultured for 1 hour. Then, non-adherent cells were removed. After 16 hours, adherent cells were used as synovial fibroblasts.

extract_protocol:
Total RNA was extracted with Isogen (Nippon gene, Japan) and RNeasy spin column kit (Qiagen, USA). 1 µg of RNA samples with RNA integrity number (RIN) greater than 9 were used for library prepairation.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego CA)  according to the manufacturer's instructions and subsequently validated for an average size of about 311-328bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit for the construction of sequencing libraries.

treatment_protocol: Synovial fibroblasts were cultured in DMEM Glutamax supplemented with 10%FBS and 1% antibiotics for 16 hours

tag: strain background

tag: genotype/variation

value: Uhrf1 cKO

value: Fibroblasts derived from ankle tissue of K/BxN serum transfer arthritis

tag: disease state

value: Arthritis on day 4

tag: passage

value: cultured cells (passage 0)


title: Control

data_processing:
MDB-seq was performed twice against one sample. Sequence data were mapped on the mouse genome (mm10) using CLC Genomics Workbench v8. Then duplicate data were combined.
Peaks were called using MACS version 1.4.2 with the following setting: band width = 100, pvalue cutoff = 1.00e-2, control
Genome_build: mm10
Supplementary_files_format_and_content: peak

extract_protocol:
Genomic DNA was extracted with DNeasy spin column kit (Qiagen, USA). Extracted DNA was sonicated with a Covaris sonicator (Covaris Inc.) to obtain ~300 bp fragments. MBD2-mediated enrichment of methylated DNA was performed using the methylated DNA enrichment kit, EpiXplore (TAKARA, Japan) according to the manufacturer’s instructions.
MBD-Seq libraries were prepared using DNA SMART ChIP-Seq Kit (TAKARA, Japan) according to the manufacturer’s instructions and validated for an average size of about 300-700 bp using a TapeStation and the Agilent High Sensitivity D1000 ScreenTape kit.

value: Control

tag: time point


title: artery_aorta_SM-CR89M

tag: sample type

value: normal

tag: sample preparation

value: flash-frozen tissue

tag: donor age (years)


title: artery_aorta_SM-C1MLC

tag: donor sex

value: female

tag: race

value: asian

tag: Cause of death


title: adrenal_gland_SM-A8WNO

source_name: adrenal gland

value: cerebral vascular accident


title: Control rep3 [FLS-C10_S3]

tag: cell type


title: heart_atrial_appendage_SM-JF1NX


title: Uhrf1 cKO rep1 [FLS-KO3_S4]


title: adipose_omentum_SM-CSSD4

source_name: adipose omentum

value: male

value: white

value: anoxia


title: Control rep1 [FLS-C6_S1]


title: adipose_omentum_SM-IOBHJ


title: adipose_omentum_SM-ADYHB


title: MM10_ChIP_Input

city: Singapore

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: bone marrow of newly diagnosed patients with MM

data_processing:
ChIP-seq reads were mapped to human hg19 reference genome using bowtie2 program with default parameters.
Aligned ChIP-seq reads were remove duplicate with samtools rmdup package.
ChIP-Seq peaks were called with MACS2 software, version 2.1.1.2016030. Threshold for the peaks called is q-value < 0.01, keep-dup=1
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files called with MACS2

growth_protocol: Plasma cells were isolated by CD138 immunomagnetic bead selection from bone marrow aspirates of newly diagnosed patients with MM, which were obtained from the National University Hospital after approval by the institutional ethical committee.

extract_protocol:
Library construction from the H3K27ac ChIP-seq samples and sequencing of single-end 50bps long reads by the Illumina HiSeq 4000 were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Single end ChIP-Seq sequencing

treatment_protocol: TL-Om1 cells were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.

tag: subject status

value: newly diagnosed patients with MM

tag: subject id

value: Plasma cells from bone marrow aspirates

tag: chip antibody

value: none (WCE)


title: MM10_H3K27ac_ChIP-seq

value: anti-H3K27ac (Abcam, ab4729)


title: aSMA periosteum 2 days and 13 weeks (mixed samples)

city: Farmington

first: William

middle: F

last: Flynn

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

data_processing:
Paired-end fastqs were generated using BCL2Fastq v2.18.0.12 (Illumina)
Digital expression matrices were constructed for each pair of fastqs using Drop-seq_tools v1.13 (http://mccarrolllab.com/dropseq/) in the following manner: bam creation with Picard (v2.9.3) FastqToSam;
cell and umi tagging, filtering, trimming with Drop-seq_tools TagBamWithReadSequenceExtended, FilterBAM, TrimStartingSequence, PolyATrimmer;
alignment with STAR (v2.5.4a) to GRCm38_74 genome and picard (v2.9.3) SortSam; merging and tagging with picard (v2.9.3) MergeBamAlignment and Drop-seq_tools (v1.13) TagReadWithGeneExon;
expression matrix creation with Drop-seq_tools (v1.13) DigitalExpression was used to produce expression matrices for the 3 samples.
Genome_build: GRCm38_74
Supplementary_files_format_and_content: TSV, gene by cell matrix of read and deduplicated read (umi) counts

source_name: Tibia and femur periosteum with 30 min collagenase/hyaloronidase digest

extract_protocol:
Custom designed Drop-Seq barcodes from Integrated DNA Technologies (IDT) were delivered into each well of each 384 well plate. All primers in one well shared the same unique cell barcode and billions of different unique molecular identifiers (UMIs). An Echo 525 liquid handler was used to sequentially dispense lysis buffer, primers (custom designed Drop-Seq barcodes from Integrated DNA Technologies), and reaction reagents totaling 1 microliter into each well in the plate for the cell lysis and cDNA synthesis using a modified Drop-Seq protocol. Following cDNA synthesis, the contents of each well were collected and pooled into one tube using a Caliper SciClone Liquid Handler. After treatment with exonuclease to remove unextended primers, the cDNA was PCR amplified for 13 cycles and the cDNA was fragmented and amplified for sequencing using a Nextera XT DNA sample prep kit (Illumina) using custom primers (see below) that enabled the specific amplification of only the 3′ ends.
scRNA-seq

treatment_protocol: Tamoxifen, 75mg/kg in corn oil given ip, 2 injections one day apart, then mice euthanized at indicated time points

tag: strain

value: aSMACreER/Ai9/Col2.3GFP (2 days sample) and aSMACreER/Ai9/R26-M2rtTA/TetOP-H2B-GFPH2B (13 weeks sample)

tag: tissue

value: periosteum

tag: time

value: 2 d of chase (2 days sample) and 96 d of chase (13 weeks sample)

tag: age at isolation

value: 10.3 wk (2 days sample) and 20.1 wk (13 weeks sample)


title: aSMA periosteum 6 weeks

description: aSMA cells

value: 43 d of chase


title: Uhrf1 cKO

tag: strain background

tag: genotype/variation

value: Uhrf1 cKO

value: Fibroblasts derived from ankle tissue of K/BxN serum transfer arthritis

value: Arthritis on day 4


title: MM9_H3K27ac_ChIP-seq


title: MM8_ChIP_Input


title: MM8_H3K27ac_ChIP-seq


title: VEH-5

city: Boston

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

data_processing:
The quality of the fastq files was checked using the FastQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). An estimation of ribosomal RNA in the raw data was obtained with riboPicker. Reads were aligned with the STAR mapper (version 2.5.2a) to the GENCODE release M14 of the Mus musculus genome (GRCm38 assembly). A raw count of reads per gene was also obtained with STAR (--quantMode TranscriptomeSAM GeneCounts option; ). The R/Bioconductor package DESeq2 was used to assess differential expression between experimental groups (Wald statistical test + False Discovery Rate correction). Prior to processing the differential expression analysis, genes for which sum of raw counts across all samples were less than 2 were discarded. Gene ontology enrichments were performed using DAVID functional annotation tool. Cell-type enrichment analysis was calculated using chi-square test. Cell-type specific genes were obtained from previously published data .
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV file with normalized gene expression.

source_name: brain

extract_protocol:
Total RNA (500 ng) from the striatum of injected mice was extracted using the RNeasy Mini Kit (QIAGEN; 74104) and underwent DNase treatment to prevent genomic DNA contamination. RNA integrity was assessed using RNA 6000 Nano Chips on a 2100 Bioanalyser (Agilent; 5067-1511). Samples with non-degraded RNA (RIN ≥ 8.5) were used for sequencing.
Preparation of indexed cDNA sequencing libraries was carried out using the TruSeq poly-A mRNA method (Illumina; 20020594). Briefly, poly-A mRNA transcripts were captured from total RNA using poly-T beads and cDNA was generated using random hexamer priming.
Paired-end sequencing (2 × 50 cycles) of indexed cDNA libraries was then carried out on a HiSeq 2500 machine (Illumina), generating at least 50 million reads per sample. Sequencing was performed using v4 SBS and Cluster Kits (Illumina; FC-401-4002).

value: striatum

tag: age

value: adult , 8 weeks

tag: genotype

value: wild type

tag: treatment

value: VEHICLE


title: VEH-3


title: VEH-4


title: VEH-2


title: VEH-1


title: Control rep2 [FLS-C7_S2]

value: Control

tag: disease state

tag: passage

value: cultured cells (passage 0)


title: MM7_H3K27ac_ChIP-seq

value: newly diagnosed patients with MM

value: Plasma cells from bone marrow aspirates


title: MM6_H3K27ac_ChIP-seq

value: anti-H3K27ac (Abcam, ab4729)


title: Uhrf1 cKO rep2 [FLS-KO4_S5]


title: HD-sRNAs + LNA-SCB-7

value: human HD-sRNAs + LNA-SCB


title: MM5_H3K27ac_ChIP-seq


title: MM7_ChIP_Input

value: none (WCE)


title: adipose_omentum_SM-CHZRM

tag: sample type

value: normal

tag: sample preparation

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: male

tag: race

value: white

value: anoxia


title: HD-sRNAs + LNA-SCB-5


title: VEH-8


title: HD-sRNAs + LNA-SCB-4


title: MM9_ChIP_Input

tag: subject status

tag: subject id

tag: cell type

tag: chip antibody


title: MM4_ChIP_Input


title: HD-sRNAs + LNA-SCB-6

tag: tissue

tag: strain


title: MM5_ChIP_Input


title: MM4_H3K27ac_ChIP-seq


title: HD-sRNAs + LNA-SCB-3


title: VEH-6


title: MM3_ChIP_Input


title: HD-sRNAs + LNA-SCB-2


title: HD-sRNAs + LNA-CTG-6

value: human HD-sRNAs + LNA-CTG


title: HD-sRNAs + LNA-CTG-5

value: striatum


title: MM3_H3K27ac_ChIP-seq


title: MM6_ChIP_Input


title: HD-sRNAs + LNA-CTG-4

value: adult , 8 weeks


title: MM2_H3K27ac_ChIP-seq


title: HD-sRNAs + LNA-CTG-3

value: wild type


title: MM1_ChIP_Input


title: MM1_H3K27ac_ChIP-seq


title: U266_ChIP_Input

growth_protocol: Daudi, RAJI, H929, JJN3, KMS11, KMS12, KMS28BM, RPMI-8226 and U266 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

treatment_protocol: Multiple myeloma cell lines were cross-linked with formaldehyde for 10 min. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody.  A sample of whole cell extract (WCE) was sequenced and used as the background to determine enrichment.

tag: cell line

value: Multiple Myeloma cell line


title: U266_H3K27ac_ChIP-Seq


title: Human hela cell +AlkB rep 2

value: HeLa cells

value: RNAs were treated with AlkB before cDNA library construction.

tag: molecule type

value: 15-50 nt RNA


title: HD-sRNAs-10

tag: age

tag: genotype

value: human HD-sRNAs


title: HD-sRNAs-11

tag: treatment


title: HD-sRNAs-8


title: HD-sRNAs + LNA-CTG-1


title: RPMI_8226_H3K27ac_ChIP-Seq

value: RPMI

value: anti-H3K27ac (Abcam, ab4729)


title: HD-sRNAs-9


title: HD-sRNAs-7


title: HD-sRNAs-6


title: NP_ChIP_Input

source_name: NP (normal plasma cell)

value: NP

value: normal plasma cell

value: none (WCE)


title: RAJI_ChIP_Input

source_name: RAJI

value: RAJI

value: B-lymphoma cell line


title: NP_H3K27ac_ChIP-Seq


title: KMS28BM_ChIP_Input


title: HD-sRNAs-5


title: MM2_ChIP_Input

value: newly diagnosed patients with MM

value: Plasma cells from bone marrow aspirates


title: HD-sRNAs-4

value: striatum


title: HD-sRNAs-3

value: adult , 8 weeks


title: KMS28BM_H3K27ac_ChIP-Seq


title: HD-sRNAs-2

value: wild type


title: KMS12_ChIP_Input

value: Multiple Myeloma cell line


title: HD-sRNAs + LNA-CTG-2

value: human HD-sRNAs + LNA-CTG


title: lung_SM-A62E9

source_name: lung

value: normal

value: flash-frozen tissue

value: male

value: white

tag: Cause of death

value: anoxia


title: CTL-sRNAs-8

value: human CTL-sRNAs


title: KMS11_ChIP_Input


title: CTL-sRNAs-7


title: CTL-sRNAs-5


title: RAJI_H3K27ac_ChIP-Seq

value: anti-H3K27ac (Abcam, ab4729)


title: JJN3_H3K27ac_ChIP-Seq


title: JJN3_ChIP_Input

value: none (WCE)


title: H929_ChIP_Input


title: CTL-sRNAs-4


title: CTL-sRNAs-3


title: KMS12_H3K27ac_ChIP-Seq


title: H929_H3K27ac_ChIP-Seq


title: Daudi_ChIP_Input

source_name: Daudi

value: Daudi


title: CTL-sRNAs-1


title: JJN3 THZ1 treated sample #2 [JJN3_T3]

data_processing:
RNA-seq datasets of control samples, THZ1 treated samples for JJN3 and H929 were aligned to the hg19 human genome using STAR 2.5.2a with the parameter outFilterMultimapNmax set to 1.
featureCount was used for the mapped reads in .bam files to generate count tables based on the Ensembl gene annotation
Bioconductor package DESeq2 v1.12.4 was used to analyze differential gene expression using 2 control vs 2 treated samples (2 DMSO vs 2 THZ1 treatment samples).
Genome_build: hg19
Supplementary_files_format_and_content: txt file for differentially expressed genes; featureCount output

source_name: JJN3 THZ1 treated

growth_protocol: JJN3 and H929 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Library construction and sequencing of single-end 50bps long reads by the Illumina Hiseq4000 were performed at the BGI Biotech Solutions (Hong Kong) Co Ltd (Hong Kong).

treatment_protocol: JJN3 and H929 cells were treated with DMSO or THZ1 50 nM. At 24 hours post treatment , after which total RNA were harvested.

value: multiple myeloma (MM) cell line


title: Daudi_H3K27ac_ChIP-Seq

value: B-lymphoma cell line


title: JJN3 THZ1 treated sample #1 [JJN3_T2]


title: JJN3 DMSO sample #2 [JJN3_D3]

source_name: JJN3 DMSO

value: DMSO


title: RPMI_8226_ChIP_Input

value: RPMI


title: HD-sRNAs-1

value: striatum

value: adult , 8 weeks

value: human HD-sRNAs


title: JJN3 DMSO sample #1 [JJN3_D2]


title: UV2 isotype rep3

city: Charlestown

first: Jennifer

middle: A

last: Lo

address: 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital/Harvard Medical School

description:
N5
Lo_rsem_genes_tpm.txt

data_processing:
Reads were mapped to the UCSC mouse transcriptome using Bowtie 2.
Gene expression was quantified using RSEM. On average 79.8% of the reads mapped to the transcriptome in each sample (range 78.4-81.6%).
RSEM yielded an expression matrix (genes x samples) of inferred gene counts, which was converted to TPM (transcripts per million).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Lo_rsem_genes_tpm.txt: Tab-delimited text file includes TPM values for each sample and gene.

source_name: syngeneic melanoma graft - bulk tumor

growth_protocol: Syngeneic mouse melanoma grafts were generated by inoculating 1E6 parental (D4M.3A.3) or UV2 (D3UV2) mouse melanoma cells in PBS into each flank of 8-week-old female C57BL/6 mice.

extract_protocol:
Total RNA was isolated and purified using the TissueLyser II and RNeasy extraction kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Syngeneic mouse melanoma grafts on the left flanks of each mouse were treated with isotype control antibody, anti-PD-1, or triple therapy (isotype antibody + imiquimod + ablative fractional photothermolysis) on days 8, 10, and 12 after tumor cell inoculation (antibodies and imiquimod or lotion on days 8, 10, and 12; ablative fractional photothermolysis on days 8 and 12). Tumors were extracted and sequenced 13 days of growth in vivo (1 day after completion of therapy).

value: D3UV2 (UV2) melanoma

value: isotype control antibody


title: UV2 anti-PD-1 rep3

description:
NP6
Lo_rsem_genes_tpm.txt


title: UV2 isotype rep2

description:
N4
Lo_rsem_genes_tpm.txt


title: H929 THZ1 treated sample #2 [H929_T2]

source_name: H929 THZ1 treated


title: UV2 anti-PD-1 rep1

description:
NP3
Lo_rsem_genes_tpm.txt


title: H929 THZ1 treated sample #1 [H929_T1]


title: KMS11_H3K27ac_ChIP-Seq

value: Multiple Myeloma cell line


title: CTL-sRNAs-6

value: wild type


title: H929 DMSO sample #1 [H929_D1]

source_name: H929 DMSO


title: UV2 anti-PD-1 rep2

description:
NP5
Lo_rsem_genes_tpm.txt


title: Parental triple therapy rep1

description:
DT1
Lo_rsem_genes_tpm.txt

value: D4M.3A.3 (parental) melanoma

value: anti-PD-1 + ablative fractional photothermolysis + imiquimod


title: Parental triple therapy rep3

description:
DT5
Lo_rsem_genes_tpm.txt


title: Parental anti-PD-1 rep3

description:
DP5
Lo_rsem_genes_tpm.txt


title: PC9_DAC_ATAC

city: Taipei

first: Rueyhung

middle: Roc

last: Weng

address: No. 1, Roosevelt Rd., Sec. 4

department: Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Adaptor and low-quality sequences were trimmed from sequenced reads. For mRNA-seq, the processed reads were mapped to hg19 genome reference using TopHat v2.1.1 with parameters -very-sensitive --segment-length 30 --segment-mismatches 2. For ATAC-seq, the the processed reads were also aligned to hg19 genome reference using BWA mem (v0.7.17-r1188) with default -M parameter and a maximum fragment length of 2,000.
For mRNA-seq, mapped reads were counted for each gene using the R packages GenomicFeatures (v1.36.4) and GenomicAlignments (v1.20.1), according to the GENCODE human GRCh37 annotation. FPKM normalization of the raw-counts and differentially expressed genes analysis were performed using DESeq2 (v1.24.0).
For ATAC-seq, the PCR duplicated alignments were marked using Picard (v2.21.4). Further quality filtering was performed using SAMtools (v1.9) to remove unmapped reads, unmapped mates, PCR duplicated reads, unpaired alignments, and reads mapped to mitochondrial DNA. The broad peak regions were called using MACS2 v2.2.5 with parameters: --nomodel --shift -75 --extsize 150 --keep-dup all --broad --broad-cutoff 0.1. Annotation of the peaks was reported using ChIPseeker v1.20.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files including DESeq2-analyzed mRNA-seq data and MACS2-called broad peaks with ChIPseeker-annotation of ATAC-seq data.

source_name: cell line_PC9

growth_protocol: Lung cancer cell lines were cultured in RPMI-1640 medium with 10% FBS and 1% antibiotics.

extract_protocol:
For mRNA-seq analysis, total RNA were extracted from lung cancer cell lines using Trizol reagent and Invitrogen PureLink RNA Mini Kit according to the manufacturer's procedures. For ATAC-seq analysis, DNA sample preparation was performed as described in Corces et al., 2017.
mRNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocol and Omni-ATAC protocol as described previously (Corces et al., 2017), respectively.

treatment_protocol: Lung cancer cell lines were treated with 100 nM decitabine (DAC) for 72 hours followed by growing in drug-free medium for three days

value: Decitabine-treated


title: H929 DMSO sample #2 [H929_D2]


title: UV2 isotype rep1

description:
N3
Lo_rsem_genes_tpm.txt


title: Parental anti-PD-1 rep2

description:
DP4
Lo_rsem_genes_tpm.txt


title: CL1-5_DAC_ATAC

source_name: cell line_CL1-5


title: Parental anti-PD-1 rep1

description:
DP2
Lo_rsem_genes_tpm.txt


title: H1299_DAC_ATAC

source_name: cell line_H1299


title: Parental isotype rep3

description:
D5
Lo_rsem_genes_tpm.txt


title: PC9_Mock_ATAC

value: PBS-treated


title: CL1-5_Mock_ATAC


title: Parental isotype rep2

description:
D4
Lo_rsem_genes_tpm.txt


title: H1299_Mock_ATAC


title: PLc_9_Ket

city: London

first: Sanjay

middle: Padmakar

last: Khadayate

address: Du Cane Road

institute: MRC London Institute of Medical Sciences

description: processed data file: NormalizedCounts.csv

data_processing:
Primary analysis RTA 1.18.64 and Secondary analysis CASAVA- 1.8.4.
Sequencing was conducted on an Illumina HiSeq 2500 system with 100 base pair paired-end reads.
Gene based counting was performed using the HTSeq counts module.
Gene expression analysis was performed using the DESeq2 Bioconductor package.
Sequencing reads were mapped to mm9 genome using tophat 2.0.11 with parameter --library-type fr-firststrand.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: NormalizedCounts.csv: Comma-delimited text file includes normalized counts for each Sample generated by DESeq2 package.

source_name: Pre-limbic cortex

extract_protocol:
Two days following 5 days of ketamine or saline injections, brains were rapidly removed and the PLc was dissected and frozen in isopentane on dry ice. Total RNA was isolated using the TriZol reagent (Invitrogen) and purified using RNeasy micro kits from Qiagen. RNA integrity was assessed using the Agilent Bioanalyser and all RNA Integrity number (RIN) values were above 8.
The cDNA library was prepared using the NEB Next Ultra II Library Prep kit (New England Biolabs, USA).

treatment_protocol: Ketamine at a dose of 30mg/kg (i.p) or saline vehicle (i.p) were administered once daily for 5 consecutive days.

value: 9 weeks

value: Pre-limbic cortex

value: Ketamine


title: Parental isotype rep1

description:
D2
Lo_rsem_genes_tpm.txt


title: A549_DAC_ATAC

source_name: cell line_A549


title: PLc_5_Ket


title: PC9_DAC_mRNA


title: A549_Mock_ATAC


title: PLc_6_Sal

value: Saline


title: H1792_DAC_mRNA

source_name: cell line_H1792


title: PLc_10_Sal


title: H1792_Mock_mRNA


title: PLc_1_Sal


title: CL1-5_DAC_mRNA


title: CL1-0_DAC_mRNA

source_name: cell line_CL1-0


title: H1299_DAC_mRNA


title: CL1-5_Mock_mRNA


title: H1299_Mock_mRNA


title: PLc_3_Ket


title: A549_DAC_mRNA


title: A549_Mock_mRNA


title: CL1-0_Mock_mRNA


title: Parental triple therapy rep2

description:
DT3
Lo_rsem_genes_tpm.txt


title: PC9_Mock_mRNA


title: HS_atcyp18-2_rep3

city: Daejeon

first: Areum

last: Lee

address: 125 Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
The transcriptome short reads (<25 bp) were filtered out using DynamicTrim and LengthSort of solexaQA package
The read counts were calculated by mapping the filtered reads that passed the pre-processing using HTSeq
The filtered reads were normalised using the DESeq library
he IR ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons
The intron retention (IR) ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons. AS occurred outside of IRs requiring junction reads, junction information was extracted using regtools
Genome_build: Araport 11
Supplementary_files_format_and_content: Xlsx was processed data

organism: Arabidopsis thaliana

source_name: Arabidopsis

growth_protocol: Arabidopsis seeds were sown on sterilized soil and grown for 3 weeks in culture room conditions (23℃, light/dart 16h/8h)

extract_protocol:
Total RNA was prepared from leaf using WizPrepTM Plant RNA Mini Kit (WIZBIOsolutions, Seongnam, South Korea)
Total RNA was extracted from the leaves, and cDNA was synthesized using PrimeScript™ RT reagent Kit (TaKara, Japan). The resultant cDNA fragments were purifed, end-reparided, polyA-tailed, and ligated to index adapters following the Illumina protocol.

treatment_protocol: The 3-week-old plant was transferred to the chamber and exposed to a temperature of 47℃ for 1 hour.

value: Rosette leaf

tag: ecotype

value: heat stress


title: HS_atcyp18-2_rep1


title: HD-sRNAs-CTX

description: Pool obtained from at least 10 samples

data_processing:
We used cutadapt  to remove 3’ adapter sequence from CTL-sRNA and HD-sRNA samples. Sequences that had the adapter were analyzed with bcbio-nextgen smallRNA-seq pipeline (https://bcbio-nextgen.readthedocs.io/en/latest/, 1.0.2a0-a003647) that uses a series of tools to characterize small RNA sequences (seqbuster , seqcluster, STAR , multiqc ).
Genome_build: hg19
Supplementary_files_format_and_content: TSV with normalized counts for miRNA.

source_name: brain

extract_protocol:
small RNA (sRNA) fractions were purified from total RNA with the RNA Clean & Concentrator-5 Kit (Zymo Research; R1015) according to the manufacturer’s instructions.
CTL-sRNA-PT, HD-sRNA-PT, CTL-sRNA-CTX, HD-sRNA-CTX, CTL-sRNA-CB and HD-sRNA-CB pools (200 ng) were processed with NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs; E7330S), size selection was performed by Novex® Pre-Cast 6% TBE PAGE gel (Thermo Fisher Scientific; EC62652BOX) and the bands of interest cut as follows: a) 145-160 bp band (corresponding to adapter-ligated constructs derived from the 21 and 30 nt RNA fragments, respectively), b) 160-180 bp band, c) 180-200 bp band, d) 200-300 bp band, e) 300-500 bp.
Paired-end sequencing (2 × 50 cycles, CTL-sRNA-PT, HD-sRNA-PT) or single-end sequencing (1 x 50 nt, CTL-sRNA-CTX, HD-sRNA-CTX, CTL-sRNA-CB, HD-sRNA-CB) of indexed cDNA libraries were then carried out on a HiSeq 2500 machine (Illumina), generating at least 50 million reads per sample. Sequencing was performed using v4 SBS and Cluster Kits (Illumina; FC-401-4002).

value: Frontal cortex

value: adult

tag: genotype/variation

value: mutant huntingtin


title: HD-sRNAs-CB

description: Pool obtained from at least 10 samples

value: Cerebellum


title: HS_atcyp18-2_rep2


title: HS_WT_rep3

value: WT


title: HD-sRNAs-PT

description: Pool obtained from at least 10 samples

value: Putamen


title: CTL-sRNAs-CTX

description: Pool obtained from at least 10 samples

value: wild type-huntingtin


title: HS_WT_rep2


title: PEGASEMP-treated tumor, biological rep 4

city: Coimbra

first: João

middle: Nuno

last: Moreira

address: Faculty of Medicine, Polo 1, Rua Larga

country: Portugal

institute: Center for Neuroscience and Cell Biology

description: Gene expression data of PEGASEMP-treated biphasic mesothelioma tumors

hyb_protocol: 5 ug of fragmented/labeled ss-cDNA were hybridized for 16 hr at 45°C on GeneChip HTA 2.0 in the GeneChip Hybridization oven 640. Chips were then washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Processing and downstream analysis of the experimental data was performed with R (version 3.5.0), using Bioconductor Oligo package (version 1.44.0) for the oligonucleotide microarray-preprocessing. All samples were preprocessed with the RMA algorithm.

label: biotin

source_name: PEGASEMP-treated tumor

label_protocol: 5.5 ug of single strand-cDNA (ss-cDNA) were prepared and biotinylated according to the standard Affymetrix protocol, from 200 ng of total RNA (GeneChip WT PLUS Reagent Kit Manual Target Preparation for Gene Chip Whole Transcript (WT) Expression Assay, Thermo Fisher Sci. 23 January 2017)

growth_protocol: One million mesothelioma cells were orthotopically injected intrapleurally (i.pl.) in 4-5 weeks-old female CD-1 nude mice [Crl:CD1-Foxn1nu], under deep isoflurane anesthesia.

extract_protocol: RNA was extracted using TriFast Gold Reagent (Euroclone) in combination with the TissueLyser (20hz x 3minutes) (QIAGEN).

treatment_protocol: Female CD-1 nude mice [Crl:CD1-Foxn1nu] bearing the MM487:Luc biphasic mesothelioma tumors, were treated twice, intravenously, with PEGASEMP at 7 mg/Kg/week. Saline was used as control following the same schedule.

value: Human mesothelioma MM487 cells-derived tumor

value: Biphasic mesothelioma

value: Tumors growing for 5 weeks

value: PEGASEMP-treated


title: PEGASEMP-treated tumor, biological rep 1


title: PEGASEMP-treated tumor, biological rep 3


title: Non-treated tumor, biological rep3

description: Gene expression data of non-treated biphasic mesothelioma tumors

source_name: Non-treated tumor

value: non-treated


title: Non-treated tumor, biological rep2


title: PEGASEMP-treated tumor, biological rep 2


title: CTL-sRNAs-PT

description: Pool obtained from at least 10 samples


title: HS_WT_rep1


title: C_atcyp18-2_rep3

value: control


title: CTL-sRNAs-CB

description: Pool obtained from at least 10 samples


title: C_atcyp18-2_rep2


title: C_WT_rep3


title: C_WT_rep2


title: Lymphocytes_SCZ_19

city: Chicago

first: Eleonora

last: Gatta

state: IL

address: 1601 W Taylor St

department: Psychiatry

institute: University of Illinois at Chicago

description: S111.3 (column name in supplementary files)

data_processing:
Fastq files were processed and demultiplexed with bcltofastq 1.8.4 for pools 1 and 2 and bcltofastq 2.17.1.14 for pool 3.
Raw reads were then checked for quality using FASTQC (v 0.11.2), trimmed and filtered using Trimmomatic (v 0.33) to remove residual adapter content and low-quality bases (Phred quality score < 28). Trimmed/filtered reads were aligned to UCSC‐hg38 genome and gene models using STAR (v 3.5.0a) using --quantMode GeneCounts to generate gene-level counts; reverse-stranded counts were used.
12,290 genes without logCPM > log2 (1) in at least 3 samples were filtered out, leaving 14,154 genes to be analyzed for differential expression. TMM-values were re-calculated and expression values were normalized using the limma-voom + TMM method,42 then analyzed using a statistical model that accounted for processing batch, sex and age.
Multiple hypothesis testing adjustments for the schizophrenic vs. control comparison were done using the False Discovery Rate method.43
Genome_build: UCSC‐hg38
Supplementary_files_format_and_content: Guidotti_RawCounts_3combined.xlsx contains raw gene-level counts, some gene annotation information and a column indicating which genes passed the filtering thresholds. Guidotti_VoomNormalizedValues_3combined.xlsx contains voom-normalized log2 count per million expression values for genes that passed filtering thresholds. Guidotti_VoomWeights_3combined.xlsx contains voom's weights per-gene and per-sample to adjust for the relationship between mean and variance in expression values.

source_name: Lymphocytes

extract_protocol:
Subject’s blood was collected in 4-8 lavender top collection tubes (EDTA) (~8 ml blood per tube), and processed using Balance Salt Solution (BSS, see Ficoll-Paque Plus instructions for reagent preparation). Blood samples were then layered over cold Ficoll-Paque Plus, and centrifuged using a swinging bucket rotor at 400 g for 45 min at 4°C. The lymphocyte layer was removed into sterile collection tubes, centrifuged at 100 g for 10 min at 4°C and loose lymphocyte pellet washed with BSS.
RNA-seq libraries were constructed using the Illumina TruSeq Stranded RNA sample Prep kit (Illumina, CA) following manufacturer’s instructions. A single library was prepared from each sample. All libraries were then quantitated by qPCR, combined in equimolar concentration into three pools of 11-16 individual (half C and half S), and each pool was sequenced on two lanes of a HiSeq2500.

tag: diagnosis

value: Schizophrenia

tag: batch

tag: Sex

value: M

value: Hispanic

tag: cigarette smoked per week

tag: cigarettes pack per day

tag: number of years smoking

value: Clozapine

value: haloperidol

tag: mood medications

tag: benzodiazepines

tag: panss

tag: matrics


title: C_WT_rep1

tag: tissue

value: Rosette leaf


title: Lymphocytes_SCZ_18

description: S108.3 (column name in supplementary files)

tag: age

tag: race

value: White


title: Lymphocytes_SCZ_15

description: S104.3 (column name in supplementary files)

value: Casucasian

value: quit

value: Quit

value: Fluphenazine


title: Lymphocytes_SCZ_14

description: S103.3 (column name in supplementary files)

value: African American

value: Olanzapine

value: Lorazepam,Clonazepam


title: Lymphocytes_SCZ_17

description: S107.3 (column name in supplementary files)

value: Trazadone


title: Lymphocytes_SCZ_13

description: S96.2 (column name in supplementary files)


title: C_atcyp18-2_rep1

tag: genotype

tag: treatment


title: Lymphocytes_SCZ_12

description: S95.2 (column name in supplementary files)

value: Perphenazine

value: Valproic acid


title: Lymphocytes_SCZ_16

description: S106.3 (column name in supplementary files)

value: Schizophrenia

value: F

value: aripiprazole

value: citalopram, Bupropion


title: Lymphocytes_SCZ_11

description: S91.2 (column name in supplementary files)

value: M

value: Hispanic

value: Abilify


title: Lymphocytes_SCZ_10

description: S90.2 (column name in supplementary files)

value: White


title: Non-treated tumor, biological rep4

value: Human mesothelioma MM487 cells-derived tumor

tag: cell type

value: Biphasic mesothelioma

value: Tumors growing for 5 weeks

value: non-treated


title: Liver_WH-5_T6_Fish94_X547_M12

city: St. John's

first: Anne

last: Beemelmanns

address: 0 Marine Drive

department: Ocean Science

institute: Memorial University

hyb_protocol: Equal quantities (825 ng) of each labeled aRNA (refer to label protocol) from one experimental sample and the common reference were pooled, fragmented following the manufacturer's instructions and co-hybridized to a cGRASP-designed Agilent 44K salmonid oligonucleotide microarray as per the manufacturer’s instructions (Agilent, Mississauga, ON). The arrays were hybridized at 65°C for 17 h with 10 rpm rotation in an Agilent hybridization oven. The array slides were washed immediately following hybridization as per the manufacturer's instructions.

scan_protocol: Each microarray was scanned at 5 µm resolution and 90% of laser power using a ScanArray Gx Plus scanner and ScanArray Express software (v4.0; Perkin Elmer, Woodbridge, ON) with photomultiplier tube (PMT) set to balance fluorescence signal between channels.

data_processing: Signal intensity data was extracted from tiff images using Imagene v9.0 (BioDiscovery). In addition to automated quality flagging, spots affected by dust particles, scratches and other local artefacts were flagged manually. Raw data was read into Bioconductor package 'marray', base 2 logratios were calculated from background-corrected median signals and control spots were removed. Data was normalized using printtip loess. Logratio data for a particular spot was removed when the raw signal value in one of the channels of that spot was lower than the threshold, which was calculated as (median background + 2 * SD) for each channel on each array. Logratio data for a particular spot was also removed if the spot was flagged in Imagene.

organism: Salmo salar

source_name: Liver tissue

label_protocol: Six individual fish from each of the CT, WN and WH treatment groups (n=6,N=18) were used in the microarray analysis using a common reference design. An equal quantity of each DNase I-treated, column-purified liver total RNA sample involved in the microarray experiment was pooled to make a common reference for the microarray hybridizations. Anti-sense amplified RNA (aRNA) was in vitro transcribed from 1 µg of each experimental RNA or reference pooled RNA using Ambion's Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies), following the manufacturers' instructions. The quality and quantity of aRNA were assessed using UV spectrophotometry and agarose gel electrophoresis. Twenty µg of aRNA was precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer; the resulting solution was used in a labeling reaction following the manufacturer's protocol. Resulting aRNA was labeled with either Cy3 (for the common reference) or Cy5 (for the experimental individuals) fluor (GE HealthCare, Mississauga, ON) through a dye-coupling reaction, following the manufacturer's instructions. The labeling efficiency was measured using the microarray function of the NanoDrop spectrophotometer.

extract_protocol: Liver samples (100 mg) were homogenized in 0.8 ml of TRIzol reagent (Invitrogen/Life Technologies, Burlington, ON) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON) using a TissueLyser (QIAGEN), frozen on dry ice and stored at -80°C. Frozen homogenates were slowly thawed on wet ice and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions. To separate TRIzol-extracted RNA from organic materials, Crude RNA samples were diluted with nuclease-free water (Life Technologies) to an equal concentration of 100 µg, mixed with an equal volume of Acid-Phenol:Chloroform (5:1 solution, PH 4.5, Ambion, Life Technologies) and centrifugation was carried out at 17,000 g and 4°C for 20 min. Then, 190 µl of aqueous phase was precipitated with 0.1 volume of 3 M sodium acetate (pH 5.5; Invitrogen, Life Technologies) and 2.2 volumes of ice-cold 100% ethanol (Commercial Alcohols, Greenfield) at −80°C for 12 h, followed by a centrifugation at 17,000 g and 4°C for 30 min. The RNA pellets were washed in 5x volumes of 70 % ethanol and centrifuged at 17,000 g and 4°C for 20 min, air-dried at room temperature for 10 min and dissolved in 100 µl nuclease-free water (Life Technologies) at 55°C for 5 min. To remove remaining genomic DNA, 40 µg of precipitated RNA was incubated for 10 min with 6.8 Kunitz units of DNase I (RNase-Free DNase Set, QIAGEN) and 1x manufacturer’s buffer. DNase-treated RNA samples were column-purified from salts, proteins and nucleotides using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s guidelines. RNA integrity was tested with gel electrophoresis (1% agarose) and RNA extraction purity and yields were measured by A260/280 and A260/230 NanoDrop UV spectrophotometry.

treatment_protocol: Atlantic salmon post-smolts 138.1 ± 1.1 g (mean ± S.E.) were randomly distributed among 6 tanks (1.5m^3,  60 fish tank-1) with flow-through seawater (32 ppt salinity), and all fish were kept on a photoperiod of 14 hours light / 10 hours dark. In two tank duplicates we applied the following treatments: (1) Control (CT) constant temperature of 12°C and 100 % air saturation; (2) Warm & Normoxic (WN) incremental temperature increase (1°C per week from 12 - 20°C at 100% air saturation); and (3) Warm & Hypoxic (WH) decrease in oxygen content of 70% air saturation over one week, followed by two weeks of acclimation to this oxygen level, and then incremental temperature increase (1°C per week from 12 - 20°C at 70% air saturation). During the experiment, salmon were carefully fed by hand to satiation twice daily with commercial pellets (EWOS, Cargill Innovation Center, Dirdal, Norway). At the end of trial, 8 fish from each tank (8 fish per treatment, 4 per tank replicate; n = 8, N = 24) were euthanized with 400 mg L^-1 of tricaine-methane-sulfonate (TMS; Syndel Laboratories, Vancouver, BC) after 24 h of fasting. Body weight, fork length, liver mass, spleen mass and ventricle mass of fish were measured and recorded. Liver tissues (200-300 mg sample-1) were rapidly dissected from fish, placed in RNase-free 1.5 mL tubes, flash-frozen in liquid nitrogen, and stored at -80°C until RNA extractions were performed. For this microarray study we selected the liver / RNA samples from 6 individual fish per treatment (3 per tank replicate; n = 6, N = 18).

value: Liver

tag: life stage

value: Juvenile

value: WH

source_name: pool of RNAs from liver tissues invovled in the microarray experiment (i.e. CN,WN,WH)


title: Liver_WH-6_T6_Fish95_X526_M18


title: Lymphocytes_SCZ_9

description: S88.2 (column name in supplementary files)

tag: diagnosis

value: Indian


title: Liver_WH-4_T6_Fish93_X525_M6


title: Lymphocytes_SCZ_8

description: S80.2 (column name in supplementary files)

tag: batch

value: Lurasidone


title: V2-1-a BSseq

city: Los Angeles

first: Colette

middle: L

last: Picard

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

data_processing:
For BS-PCR samples (V1-1, V1-2, V1-5, V1-9), reads were first compared to the primer sequences used to amplify the desired regions and only reads containing these primer sequences were kept. Reads were then truncated to exclude the primer sequences. Pre-processed reads were mapped to TAIR10 using Bismark and processed into per-position methylation count data.
For BS-seq samples (V2 and V3 samples), reads were aligned to TAIR10 using Bismark and processed into per-position methylation count data. Whole genome metaplots and overall genome-wide methylation were generated using ViewBS.
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq (V2, V3 samples), text files containing all per-position methylation data are provided for each sample (*cxfile), with 7 fields: chromosome, position (1-based), strand of C, number of methylated reads, number unmethylated reads, sequence context, and specific 3 bp sequence context. Separate bigWig tracks of methylation levels for CG, CHG and CHH methylation are also provided; only positions with 5+ coverage were used to generate the bigWig files. In .bw files, values of -10 indicate positions where there was 5+ coverage, but the methylation level was zero (to distinguish from positions with less than 5 coverage). For BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions. These files have 6 fields: chromosome, start (0-based index), end, number of unmethylated reads, number of methylated reads, and percent methylated reads.

source_name: rosette leaf

growth_protocol: Plants were grown under long-day conditions (16h light/8h dark) at 23°C in controlled growth chambers.

extract_protocol:
Libraries were prepared from approximately 75-150 ng genomic DNA using the Ovation Ultralow Methyl-seq kit (NuGEN) and sequenced on Illumina HiSeq 2500.
DNA was extracted using the CTAB-based method.

treatment_protocol: For agroinoculation of Arabidopsis plants, the protocol from Burch-Smith et al. 2006 (Plant Physiol.) was followed. Briefly, GV3101 strains containing either TRV RNA1 and RNA2(no guide RNA)/g4/g4.g10.g18 were mixed in 1:1 proportion at an OD 600 =1.5 and was agro-inoculated onto the lowest two leaves of 12-14 days old Arabidopsis plants.

value: rosette leaf

tag: cultivar

value: SunTag-TET1, no guide

tag: v1 parent

tag: developmental stage

value: rosette stage


title: V1-9 BSPCR

extract_protocol:
Genomic DNA was bisulfite-converted using the Qiagen EpiTect bisulfite kit and amplified using primers described in Gallego-Bartolomé et al. 2019. Libraries were constructed from the converted PCR products using the Ovation Ultralow V2 kit (NuGEN) and sequenced on Illumina HiSeq 2500.
DNA was extracted using the CTAB-based method.

value: TRV +gRNA (g4, g10, g18)


title: Non-treated tumor, biological rep1


title: V2-9-a BSseq


title: V2-2-d BSseq


title: V2-5-a BSseq


title: Liver_WH-3_T1_Fish75_X547_M13


title: Lymphocytes_SCZ_7

description: S79.2 (column name in supplementary files)

value: Schizophrenia

tag: Sex

value: M

value: African American

tag: cigarette smoked per week

tag: cigarettes pack per day

tag: number of years smoking

value: Fluphenazine

value: Clozapine

value: Quetiapine

value: Lithium

value: Clonazepam


title: Liver_WN-5_T5_Fish90_X547_M11

value: Liver

value: WN


title: Liver_WN-6_T5_Fish91_X526_M17

value: Juvenile


title: V1-2 BSPCR

value: TRV +gRNA (g4)


title: Liver_WH-1_T1_Fish73_X528_M1

value: WH


title: Liver_WN-4_T5_Fish89_X528_M5


title: Lymphocytes_SCZ_6

description: S72.2 (column name in supplementary files)

value: Pimozide

value: haloperidol

tag: mood medications

tag: benzodiazepines

tag: panss


title: Liver_WN-1_T2_Fish77_X524_M2

tag: tissue


title: Liver_WN-3_T2_Fish79_X547_M14


title: V1-5 BSPCR

value: rosette leaf

tag: genotype

value: SunTag-TET1, no guide

value: rosette stage

value: TRV -gRNA


title: Liver_WH-2_T1_Fish74_X525_M7

tag: treatment


title: Liver_CT-5_T4_Fish86_X525_M10

value: CT


title: normal

city: La Jolla

first: Kuniaki

last: Sato

address: 3855 Health Sciences Dr Room 2345

department: Moores Cancer Center

data_processing:
The in-house pipeline Genomon 2.5.0  (https://genomon-project.github.io/GenomonPagesR)  was used for quality control and mapping.
The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the sequencing reads were aligned to the human reference GRCh38 genome with Gencode v22 annotations by STAR v2.5.2a with following parameters; --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --alignSJstitchMismatchNmax -1 -1 -1 -1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12.
Read counts per gene were quantified using the HTSeq Python package.
Genome_build: GRCh38 with Gencode v22 annotations
Supplementary_files_format_and_content: tab-delimited text files of read counts per gene from HTSeq

source_name: Non-cancerous tonsil tissue

extract_protocol:
Total RNA was extracted from the cells using ISOGEN (Nippon Gene).
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. The suitable fragments are selected for the PCR amplification as templates. During the quality checking steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

value: Non-cancerous tonsil tissule


title: sqcc

source_name: Carcinoma tissue

value: Oropharyngeal squamous cell carcinoma


title: smcc

value: Oropharyngeal small cell carcinoma


title: Lymphocytes_SCZ_5

description: S54.1 (column name in supplementary files)

value: Schizophrenia

tag: age

value: M

tag: race

value: African American

value: Clozapine

tag: matrics


title: V1-1 BSPCR


title: P14 Ileum WT + rmIl22 rep 3

city: Gothenburg

first: Thaher

last: Pelaseyed

address: Box 440

department: Medical Biochemistry and Cell Biology

country: Sweden

institute: University of Gothenburg

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt

data_processing:
Quality of raw data was assessed using FastQC (version 0.11.2) looking at per base sequence quality and adapter contamination.
If required, Fastq files were quality filtered using prinseq (version 0.20.3) (Schmieder and Edwards, 2011).
The number of mapped reads was calculated using HTseq (version 0.6.1p1) (Anders et al., 2015) with the stranded reverse protocol.
Normalization for transcripts per million (TPM) was performed using “biomaRt” library in R (Durinck et al., 2005).
Normalization for differential gene expression was performed using DESeq2 (version 1.14) in R (Love et al., 2014).
Genome_build: The reads were mapped against the mouse reference genome mm10 from Ensembl using STAR (version 2.4.0f for the DC and 2.5.2b for the Si8).
Supplementary_files_format_and_content: tab-delimited text files include gene name, log2FoldChange and padj for each gene
Supplementary_files_format_and_content: tab-delimited text files include Transcripts Per Million (TPM) for each gene in every sample

source_name: Mouse whole ileum

extract_protocol:
Ileum samples for mRNA analysis were collected in RNAlater (#76104, Qiagen) and kept at -80°C until RNA extraction. Total RNA was isolated using RNeasy Plus Mini Kit (#74134, Qiagen) and DNase Max Kit (#15200-50, Qiagen), followed by storage at -80°C.
The quality of isolated RNA was determined using a Bioanalyzer (Agilent) with RIN values greater than 8. cDNA libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo Zero Gold (Rev. E; Illumina) according to manufacturer´s protocol.

treatment_protocol: C57BL/6N mice were injected with 0.1 μg/g bodyweight of rmIl22 in 100 µL PBS or PBS alone at P14 and P15 and sacrificed at P16.

tag: strain

value: Ileum

value: Postnatal day 24


title: Liver_CT-3_T3_Fish83_X526_M15

value: Liver

tag: life stage

value: Juvenile


title: Liver_CT-6_T4_Fish87_X526_M16


title: Liver_WN-2_T2_Fish78_X528_M8

value: WN


title: Liver_CT-1_T3_Fish81_X524_M3


title: Liver_CT-4_T4_Fish85_X524_M4


title: Lymphocytes_SCZ_3

description: S52.1 (column name in supplementary files)

tag: diagnosis

tag: batch

value: F

value: Olanzapine

value: Quetiapine

value: Valproic acid


title: P14 Ileum WT + rmIl22 rep 2

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt

value: 0.1 μg/g bodyweight of rmIl22 in 100 µL PBS


title: Lymphocytes_SCZ_4

description: S53.1 (column name in supplementary files)

tag: Sex

value: haloperidol


title: P14 Ileum WT + rmIl22 rep 1

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt


title: P14 Ileum WT + PBS rep 3

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt

value: Postnatal day 14

value: 100 µL PBS


title: Lymphocytes_SCZ_2

description: S51.1 (column name in supplementary files)

value: Schizophrenia

tag: cigarette smoked per week

value: Lorazepam


title: Lymphocytes_SCZ_1

description: S48.1 (column name in supplementary files)

value: African American

tag: cigarettes pack per day


title: Liver_CT-2_T3_Fish82_X528_M9

value: CT


title: P14 Ileum WT + PBS rep 2

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt

value: Ileum


title: Lymphocytes_Cont_18

description: C117.3 (column name in supplementary files)

value: Control

value: M

value: Asian

tag: number of years smoking


title: CTL-sRNAs-2

value: striatum

value: adult , 8 weeks

value: wild type

value: human CTL-sRNAs


title: P14 Ileum WT + PBS rep 1

description:
TPM.txt
DEG_P14 rmIl22vsPBS.txt


title: Lymphocytes_Cont_17

description: C116.3 (column name in supplementary files)

value: White

tag: mood medications


title: NHA, biological rep3

first: Hye Jin

last: Nam

email: nhj0120@gmail.com, hjnam@krict.re.kr

state: Not US or Canada

address: 141 Gajeongro, Yuseong

institute: Korea Research Institute of Chemical Technology

description: Gene expression data from NHA cells

hyb_protocol: After fragmentation, the biotin-labeled cRNAs were hybridized for 16 h at 45 °C, according to the standard Affymetrix protocols.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the GeneChips

data_processing: The data were analyzed using Affymetrix Expression Console and summarized using the probe logarithmic intensity error algorithm. Background correction and normalization was conducted using Perfect Match and Sketch-Quantile, respectively

source_name: NHA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA

growth_protocol: 559T and 592T: Cells were maintained in spheroidal suspension in Neurobasal-A medium (Gibco, 10888-022) supplemented with 0.5X B-27 (Gibco, 17504-001), 0.5X N2 (Gibco, 17502-001), L-glutamine (2 mM, Gibco, 25030-081), EGF (100 ng/ml, R&D systems, 236-EG), FGF (100 ng/ml, R&D systems, 3718-FB) and ZellShield (Minerva Biolabs GmbH). NHA: NHA cells were purchased from Lonza (CC-2563) and cultured in ABM medium (Lonza, CC-3187) supplemented with AGM SingleQuots (CC-4123) and ZellShield (Minerva Biolabs GmbH).

extract_protocol: TRIzol (Invitrogen)

treatment_protocol: No treatment

tag: gbm subtype

value: normal human astrocyte


title: NHA, biological rep2

description: Gene expression data from NHA cells


title: 592T, biological rep1

description: Gene expression data from 592T cells

value: mesenchymal subtype of glioblastoma


title: P24 Ileum WT rep 4

description:
TPM.txt
DEG_P24vsP14.txt

value: Postnatal day 24


title: P24 Ileum WT rep 3

description:
TPM.txt
DEG_P24vsP14.txt


title: Lymphocytes_Cont_16

description: C115.3 (column name in supplementary files)

value: Hispanic

tag: benzodiazepines


title: Lymphocytes_Cont_15

description: C113.3 (column name in supplementary files)

value: F


title: P24 Ileum WT rep 2

description:
TPM.txt
DEG_P24vsP14.txt

tag: tissue


title: P24 Ileum WT rep 1

description:
TPM.txt
DEG_P24vsP14.txt


title: Lymphocytes_Cont_14

description: C112.3 (column name in supplementary files)


title: 592T, biological rep2

description: Gene expression data from 592T cells


title: E9.5c5+CsA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

data_processing:
library strategy: Post-bisulfite adaptor tagging (PBAT)
All reads were processed with Trim_galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove 4 bases from 5’-ends, 1 base from 3’-ends, adaptor sequences, and low-quality reads (quality score < 20).
The processed reads were mapped onto mouse genome (mm10) with bismark program from Bismark (v0.17.0) with “--pbat” option (Krueger and Andrews, 2011).
Mapped data (BAM format) were converted to methylation levels using bismark_methylation_extractor program from Bismark.
Samtools (v1.3) (Li et al, 2009) and IGVTools (v2.3.52) (James et al., 2011) were used to manipulate BAM files and create wig files. Only CpGs, whose read depth are between 4 and 200, are included in the bigWig files.
Genome_build: mm10
Supplementary_files_format_and_content: bismark report file
Supplementary_files_format_and_content: bigwig file containg %mC of all CpGs

source_name: Mouse E9.5 PGC

growth_protocol:
ESCs were cultured and maintained in N2B27 medium with 2i (PD0325901,0.4 mM: Stemgent; CHIR99021, 3 mM: Stemgent) and LIF (1,000 U/ml; Merck Millipore) on a dish coated with poly-L-ornithine (0.01%; Sigma) and laminin (10 ng/ml; BD Biosciences)
Induction of EpiLCs and PGCLCs was performed as reported previously.  Briefly, the EpiLCs were induced by plating 1 × 105 ESCs on a well of a 12-well plate coated with human plasma fibronectin (16.7 mg/ml: Merck Millipore) in N2B27 medium containing activin A (20 ng/ml: Peprotech), FGF2 (12 ng/ml: Thermo Fisher Scientific), and KSR (1%: Thermo Fisher Scientific). The PGCLCs were induced from d2 EpiLCs under a floating condition in a well of a low-cell-binding U-bottom 96-well plate (Thermo Scientific) in serum-free medium [GK15; GMEM (Thermo Fisher Scientific) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine] in the presence of the cytokines BMP4 (500 ng/ml; R&D Systems), LIF (1,000 U/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).
Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV-positive-d4 PGCLCs or EGFP-positive-E9.5 PGCs (B6D2F1×Stella–EGFP).  m220-5 cells were used as the feeder cells for PGCLCs or E9.5 PGCs as described previously.  Briefly, m220-5 cells were cultured for three passages with 10 µM of both forskolin and rolipram (FR10) to permit adaptation to these compounds prior to mitomycin C (MMC) treatment (1–2 µg/ml, 2 h).  Purified d4 PGCLCs or E9.5 PGCs were plated on m220-5 cells in GMEM containing 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine, 2.5% FCS, 100 ng/ml SCF, 10 µM forskolin, and 10 mM rolipram.  Half of the culture medium was changed every 2 days.  Following chemicals and cytokine were used in this study: cyclosporin A (Sigma), FK506 (Sigma), FGF2 (Thermo Fisher Scientific), FGF7 (R&D Systems), FGF10 (R&D Systems), and WNT5A (R&D Systems).

extract_protocol:
WGBS was performed as described previously [Shirane et.al.,2016, Dev Cell,39,87].  Briefly, purified BV-positive d4c7 PGCLCs and Stella-EGFP positive E9.5c5 each cultured with CsA were lysed with 10 mM Tris–Cl (pH 8.0) containing 150 mM NaCl, 10 mM EDTA, 0.5% SDS, and 1 mg/mL proteinase K at 55°C overnight with shaking.  The lysate was incubated with 1.32 µg/ml RNase A at 37°C for 1 h, and extracted once with TE-saturated phenol, twice with phenol–chloroform, and once with chloroform.  Genomic DNA was precipitated with an equal volume of isopropanol, washed twice with 70% ethanol, air-dried, and then dissolved in 10 mM Tris–Cl (pH 8.0).
The purified genomic DNA (50 ng) was spiked with 0.5 ng unmethylated lambda phage DNA (Promega) and subjected to bisulfite conversion and library construction using the post-bisulfite adaptor tagging (PBAT) method [28] for deep sequencing on an Illumina HiSeq 1500/2500 system as described previously[Shirane et.al.,2016, Dev Cell,39,87].

value: B6D2F1 x C57BL/6

tag: transgene

value: Stella-EGFP reporter

tag: cell sorting

value: EGFP sort


title: Mouse ESC PANDORA-seq rep 3

first: Junchao

last: Shi

address: 900 University Ave

data_processing:
For each RNA library, around 10 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13. 2) The reads with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The reads with ploy A. 5) The reads shorter than 15nt. The clean reads were obtained after data filtration.
Genome_build: mm10 (for mouse), hg19 (for human)
Supplementary_files_format_and_content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Embryonic stem cells

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

value: Embryonic stem cells

tag: treatment

value: RNAs were treated with T4PNK, then AlkB before cDNA library construction.

tag: molecule type

value: 15-50 nt RNA


title: P14 Ileum WT rep 4

description:
TPM.txt
DEG_P24vsP14.txt

value: Ileum

tag: age

value: Postnatal day 14


title: Mouse ESC PANDORA-seq rep 1


title: Lymphocytes_Cont_12

description: C94.2 (column name in supplementary files)

value: Control

tag: race

value: African American

tag: matrics


title: Lymphocytes_Cont_13

description: C97.2 (column name in supplementary files)

tag: diagnosis

value: M


title: Mouse ESC PANDORA-seq rep 2


title: 592T, biological rep3

description: Gene expression data from 592T cells


title: 559T, biological rep3

description: Gene expression data from 559T cells

value: proneural subtype of glioblastoma


title: NHA, biological rep1

description: Gene expression data from NHA cells

value: normal human astrocyte


title: P14 Ileum WT rep 3

description:
TPM.txt
DEG_P24vsP14.txt

tag: strain


title: 559T, biological rep1

description: Gene expression data from 559T cells


title: IRENA_3: Macrophages transfected with Lentivirus packaged IRENA

city: Guangzhou

first: Jiang

last: Liu

address: 107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: This sample is prepared by ovexpressing IRENA in macrophages

hyb_protocol: Labeled cRNA were purified by RNeasy mini kit (QIAGEN). Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies) in Hybridization Oven (Cat.# G2545A, Agilent technologies), according to the manufacturer’s instructions for 17 hours

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies). Raw data were normalized by Quantile algorithm, GeneSpring Software 11.0 (Agilent technologies).

source_name: IRENA overexpressed macrophages

label_protocol: RNA amplified and labeled by Low Input Quick Amp WT Labeling Kit (Agilent technologies), following the manufacturer’s instructions.

growth_protocol: Primary peripheral blood mononuclear cells (PBMC) were isolated from peripheral blood of healthy donors and cultured in DMEM supplemented with 10ng/ml M-CSF and 10% FBS for 6 days to obtain macrophages.

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions, RNA quantity and quality were measured by Qubit 4 (Invitrogen). RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: PMBC derived macrophages were transfected with Lentivirus packaged IRENA or vector.

value: macrophages

tag: genotype/variation

value: overexpressing IRENA


title: vector_3: Macrophages transfected with Lentivirus packaged vector

description: This sample is prepared as control group by transfected vector in macrophages

source_name: control macrophages

value: vector control


title: vector_2: Macrophages transfected with Lentivirus packaged vector


title: IRENA_1: Macrophages transfected with Lentivirus packaged IRENA


title: Mouse ESC +T4PNK rep 3

city: Riverside

institute: University of California, Riverside

value: RNAs were treated with T4PNK before cDNA library construction.


title: 559T, biological rep2

description: Gene expression data from 559T cells


title: Lymphocytes_Cont_11

description: C93.2 (column name in supplementary files)

tag: batch

tag: Sex

value: F

tag: cigarette smoked per week


title: IRENA_2: Macrophages transfected with Lentivirus packaged IRENA


title: P14 Ileum WT rep 2

description:
TPM.txt
DEG_P24vsP14.txt


title: Lymphocytes_Cont_10

description: C92.2 (column name in supplementary files)

tag: cigarettes pack per day

tag: number of years smoking

tag: mood medications


title: Mouse ESC +T4PNK rep 1

tag: tissue


title: Mouse ESC +T4PNK rep 2


title: vector_1: Macrophages transfected with Lentivirus packaged vector