title: Set22

status: Public on Jul 31 2021

type: SRA

city: Philadelphia

first: Song-Jun

last: Xu

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

description: processed data file: Set2_RNA_seq_SE_junction_counts.txt

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned against mouse reference genome (mm9 or mm10 ensemble annotation) using STAR (Version 2.4.1d)
ChIP-seq reads were aligned mouse reference genome (mm9, ensemble annotation) using Bowtie2
Cut&Run-seq reads were aligned mouse reference genome (mm9, ensemble annotation) using Bowtie2 with specifics --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Alternative splicing was analyzed by rMATS V3.2.4
Genome_build: mm9/mm10
Supplementary_files_format_and_content: bigwig; text file with exon skipping coordiates and their junction counts
Supplementary_files_format_and_content: IgG_1.bw: Merged bigwig files for dCas9-SET2-sgRNA-T1-C-1,dCas9-SET2-sgRNA-T1-C-2, and dCas9-SET2-sgRNA-T1-C-3
Supplementary_files_format_and_content: IgG_2.bw: Merged bigwig files for dCas9-SET2-sgRNA-NT-C-1,dCas9-SET2-sgRNA-NT-C-2, and dCas9-SET2-sgRNA-NT-C-3

molecule: total RNA

organism: Mus musculus

source_name: Nucleus Accumbens

extract_protocol:
For tissue collection, mice were euthanized by cervical dislocation and the brain was placed in ice-cold phosphate buffered saline with protease inhibitor cocktail (Roche cOmplete Protease inhibitor). 1 mm thick sections of prefrontal cortex, nucleus accumbens and ventral tegmental area, brain regions were prepared using a cold tissue matrix and regions were micro-dissected with a 2- or 1.2-mm diameter micro-punch (Harris)
ChIP and RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: cell type

value: Brain

tag: age

value: 8 weeks

tag: genotype

value: wild type

tag: treatment


title: R195G3


title: R195G2


title: Set23


title: Set21


title: R195G1


title: GFP3

value: HSV-GFP


title: GFP2


title: GFP1


title: Set2_H3K36me3_3

library_source: genomic

molecule: genomic DNA

tag: chip antibody

value: Rabbit polyclonal anti-H3K36me3 antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: Set2_H3K36me3_2


title: R195G_H3K36me3_2


title: R195G_H3K36me3_1


title: R195G_H3K36me3_3


title: InputSet2


title: InputR195G


title: GFP_H3K36me3_3


title: GFP_H3K36me3_1


title: Saline_Input_3

value: 1-day Abstinence

value: saline SA


title: Saline_Input_2


title: Saline_Input_1


title: Cocaine_Input_2

value: cocaine SA


title: Cocaine_Input_3


title: Cocaine_Input_1


title: Saline_H3K36me3_3


title: Set2_H3K36me3_1


title: Cocaine_H3K36me3_3


title: dCas9-SET2-sgRNA-N3-3

source_name: Neuro-2a cells

value: neuroblast


title: dCas9-SET2-sgRNA-N3-2


title: Cocaine_H3K36me3_2


title: dCas9-SET2-sgRNA-N2-3


title: dCas9-SET2-sgRNA-N3-1


title: dCas9-SET2-sgRNA-N2-2


title: dCas9-SET2-sgRNA-N2-1


title: dCas9-SET2-sgRNA-NT-C-3

description: processed data file: IgG_2.bw


title: dCas9-SET2-sgRNA-NT-C-2

description: processed data file: IgG_2.bw


title: Cocaine_H3K36me3_1


title: InputGFP


title: dCas9-SET2-sgRNA-T1-C-2

description: processed data file: IgG_1.bw


title: dCas9-SET2-sgRNA-T1-C-1

description: processed data file: IgG_1.bw


title: dCas9-SET2-sgRNA-NT-C-1

description: processed data file: IgG_2.bw


title: GFP_H3K36me3_2


title: Saline_H3K36me3_1


title: Saline_H3K36me3_2


title: dCas9-SET2-sgRNA-T1-5


title: dCas9-SET2-sgRNA-T1-1


title: dCas9-SET2-sgRNA-T1-3


title: dCas9-SET2-sgRNA-T1-4


title: dCas9-SET2-sgRNA-T1-2


title: dCas9-SET2-sgRNA-NT-6


title: dCas9-SET2-sgRNA-NT-4


title: dCas9-SET2-sgRNA-NT-5


title: dCas9-SET2-sgRNA-NT-2


title: dCas9-SET2-sgRNA-T1-C-3

description: processed data file: IgG_1.bw


title: Batch5

city: Guangzhou

first: Yanjuan

last: Chen

state: Guangdong

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

country: China

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For modified STRT-seq data, raw reads were first split for each cell by specific barcode sequence attached in Read 2. The TSO sequence and polyA tail sequence were trimmed for the corresponding Read 1 after UMI information was aligned to it. Reads with adapter contaminants or low-quality bases (N > 10%) were discarded. Subsequently, we aligned the stripped Read 1 sequences to mm10 mouse transcriptome (UCSC) using tophat2 (version 2.0.12). Uniquely mapped reads were counted by HTSeq package and grouped by the cell-specific barcodes. Duplicated transcripts were removed based on the UMI information for each gene. Finally, for each individual cell, the copy number of transcripts of a given gene was the number of the distinct UMIs of that gene.
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts values for each cell

molecule: polyA RNA

source_name: E10_non-hematopoietic circulating cells

extract_protocol:
modified STRT-seq
A modified STRT-seq protocol was applied for single-cell RNA-seq. Briefly, sorted single cells in good condition were picked into lysis by mouth pipetting, and the scRNA-seq libraries were constructed based on STRT-seq with some modifications. cDNAs were synthesized using sample-specific 25-nt oligo-dT primer containing 8-nt barcode (TCAGACGTGTGCTCTTCCGATCT-XXXXXXXX-DDDDDDDD-T25, X representing sample-specific barcode while D standing for unique molecular identifiers (UMI). After reverse transcription and second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR using ISPCR primer and 3’ Anchor primer. Samples were pooled and purified using Agencourt AMPure XP beads . 4 cycles of PCR were performed to introduce index sequence  and subsequently, 400 ng cDNAs were fragmented to around 300 bp by Covaris S2. After being incubated with Dynabeads MyOneTM Streptavidin C1 beads (Thermo Fisher, 65002) for 1 hour at room temperature, cDNA Libraries were generated using KAPA Hyper Prep Kit (Kapa Biosystems, kk8505). After adaptor ligation, the libraries were amplified by 8 cycles of PCR using QP2 primer and short universal primer. The libraries were sequenced on Illumina Hiseq 4000 platform in 150 bp pair-ended manner

tag: development stage

tag: tissue

value: Blood circulates in the heart

value: Non-hematopoietic circulating cells

tag: sorting marker


title: feto-placental endothelial cells from Tek x JJ 39-2 Mutant

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

data_processing:
Mapping of the reads and gene-level count was performed using STAR (2.5.0a) using the GRCm38 genome and Ensembl V99 gene model
Genome_build: Grcm38
Supplementary_files_format_and_content: Raw gene-level counts in tab-delimited text format

source_name: feto-placental endothelial cells

growth_protocol: Feto-placental endothelial cells (FPEC - defined as CD31+/CD41- cells) were isolated by FACS from E16 labyrinthine zone placentae, using an Aria-Fusion cell sorter (BD Bioscience), with exclusion of cell duplets and dying cells (7AAD+).

extract_protocol:
Total RNA was extracted from sorted FPEC using RNeasy Plus Micro Kits (Qiagen – 74034). Quantity and quality were verified using the RNA 6000 Pico Kit (Agilent – 5067-1513) and an Agilent 2100 Bioanalyzer. Only RNA samples with RNA integrity numbers (RIN) >9.0 were used.
Total RNA (5 ng) was whole-transcriptome amplified using the Ovation RNA–Seq System V2 (NuGEN). To prepare the RNA–seq libraries the amplified cDNA (1μg per sample) was fragmented to 200bp using a Bioruptor Sonicator (Diagenode), end repaired and barcoded using the Ovation Rapid DR Library System (NuGEN).

tag: replicate

value: Mutant

tag: sample

value: Tek x JJ 39-2


title: feto-placental endothelial cells from Tek x JJ 45-1 Wild-type

value: Wild-type

value: Tek x JJ 45-1


title: feto-placental endothelial cells from Tek x JJ 41-5 Wild-type

value: Tek x JJ 41-5


title: feto-placental endothelial cells from Tek x JJ 39-5 Mutant

value: Tek x JJ 39-5


title: feto-placental endothelial cells from Tek x JJ 45-5 Mutant

value: Tek x JJ 45-5


title: feto-placental endothelial cells from Tek x JJ 45-4 Wild-type

value: Tek x JJ 45-4


title: dCas9-SET2-sgRNA-T1-6

value: 8 weeks

value: wild type


title: feto-placental endothelial cells from Tek x JJ 643-3 Wild-type

value: Tek x JJ 643-3


title: Batch4


title: Batch3


title: Batch2


title: Batch1


title: LC3: Mutant

city: Winnipeg

first: Dr. Vernon

last: Dolinsky

state: Manitoba

address: 601 John Buhler Research Centre, 715 McDermot Avenue

department: Department of Pharmacology and Therapeutics

country: Canada

institute: University of Manitoba

data_processing:
The base calls are made by the RTA software on the computer that runs the instrument. The RTA for the Hiseq 4000 is v .2.7.7. Using default parameters.
After quality check the reads were aligned to mm10 genome assembly  using STAR v2.5.1b using default parameters .
All those reads that were not mapped or do not have proper mate pairs were removed using tool jvarkit (GRADLE_VERSION=5.1.1) from the aligned files.
For differential analysis software HOMER (v4.9) was used. First using homer script makeTagDirectory, the tag directories were made, which contains basic configuration information, such as the total number of reads, the total number of unique positions with aligned reads. Then homer script analyzeRepeats.pl was used to generate raw read counts based on exons and the counts were not adjusted and were condensed to genes. Further, the raw reads were subjected to homer script getDiffExpression.pl where we used edgeR to obtain the differentially regulated genes.  We used a cutoff of ≥1.5 fold and FDR of ≤0.05 to find the significant genes.
Genome_build: Mus musculus mm10 genome assembly

source_name: pancreas

extract_protocol:
Total RNA from the islets was extracted using RNAeasy Micro kit (Qiagen, Valencia CA, USA) as per manufacturer instructions. Subsequently, ribosomal RNA was removed from two micrograms total RNA by using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Illumina).  Total RNA and mRNA purity and integrity was assessed using Bioanalyzer 2000 Total RNA Pico and mRNA Pico, respectively (Agilent Technologies, Santa Clara CA, USA).
The library was prepared according to NEBNext Ultra II Directional RNA Library Prep for Illumina (NEB, Ipswich, MA, USA).  Ribosomal RNA depleted RNA (10-100 ng) was fragmented and random primed, converted to cDNA and ligated to sequencing adaptors.  PCR enrichment of adaptor-ligated libraries was performed and libraries were analyzed and measured using Bioanalyzer 2000 2100 Expert DNA 1000 chip (Agilent Technologies, Santa Clara CA, USA).

treatment_protocol: At 3-4 months of age islets were isolated from male Tafazzin knock-down and non-transgenic control mice that consumed a low-fat chow diet. Approximately 300 Islets were used for each sample pooled from 2-3 mice to provide sufficient RNA for analysis.

tag: Sex

value: male

value: islets

tag: genotype/variation

value: Tafazzin-knockdown


title: LC2: Control

value: non-transgenic control


title: LC4: Mutant


title: dCas9-SET2-sgRNA-NT-1

value: neuroblast

value: Rabbit polyclonal anti-H3K36me3 antibody

value: Abcam


title: dCas9-SET2-sgRNA-NT-3


title: Schizont_Rep1

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

country: Germany

institute: Univeritätsklinikum Erlangen

data_processing:
Quality control of samples using FastQC version 0.11.8
Read trimming and alignment using STAR version 2.7.3
Expression analysis using Cufflinks version 2.2.1
Differential expression analysis using Cuffdiff (included in Cufflinks version 2.2.1)
Genome_build: PlasmoDB-28_Pfalciparum3D7_Genome.fasta / PlasmoDB-28_Pfalciparum3D7.gff (available on PlasmoDB)
Supplementary_files_format_and_content: Output generated by cufflinks showing the rpkm value per gene

organism: Plasmodium falciparum

source_name: P. falciparum in vitro culture

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.25% Albumax (Gibco) and 5% human serum (AB+). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions and subsequently purified using RNeasy columns (QIAGEN).
Libraries marked with [1] were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina Kit (E7420), libraries marked with [2] were generated using the NEB Next Ultra II directional RNA Library Prep Kit for Illumina (E7760); in both cases mRNA was purified using NEBNext Poly(A) mRNA Magnetic Isolation module for isolation of mRNA; Library amplification was performed using the KAPA Hifi PCR kit (KK2101) according to published procedures (PMID: 26067602).

treatment_protocol: For induction of gametocytogenesis, parasites were stressed by lowering the hematocrit and cultivation in partially spent medium. Asexual parasites were selectively inhibuited by addition of N-acetyl-D-glucosamine on day 0 of gametocyte differentiation (ring stage). Gametocytes were enriched magnetically on a MACS CS column on day 3 and FACS sorted using GFP only or GFP and Mitrotracker Deep Red (as defined below) on days 4, 6, and 10 of gametocyte differentiation.

tag: parasite line

tag: facs-sort criteria

tag: Stage

value: schizont stage

tag: library kit


title: Ring_Rep1

value: ring stage


title: Ring_Rep2


title: D10F_Rep4

value: GPF high, Mitotracker positive

value: day 11 mature female gametocytes


title: D10F_Rep3

value: GPF high

value: day 10 mature female gametocytes


title: D10M_Rep1

value: GPF low, Mitotracker positive

value: day 10 mature male gametocytes


title: feto-placental endothelial cells from Tek x JJ 39-6 Mutant

tag: strain

tag: age

tag: genotype

value: Mutant

value: Tek x JJ 39-6


title: D10F_Rep1


title: D10F_Rep2


title: D6M_Rep2

value: day 6 immature male gametocytes


title: D6F_Rep3

value: day 6 immature female gametocytes


title: D4F_Rep2

value: day 4 immature female gametocytes


title: D6F_Rep1


title: D4M_Rep2

value: GPF low

value: day 4 immature male gametocytes


title: D6F_Rep2


title: D6M_Rep1


title: LC1: Control

value: male

value: islets

value: non-transgenic control


title: D6F_Rep4


title: D4M_Rep3


title: uninj_MAML_HS_MG2

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
deseq2_raw_counts.txt
128297

data_processing:
Alignment with STAR v2.6.1b
Count estimates with RSEM v1.3.1
Genome_build: danRer11
Supplementary_files_format_and_content: tab-delimited text of raw counts

organism: Danio rerio

source_name: Mueller glia cells

growth_protocol: Zebrafish were maintained in aquaria at 28 degrees centrigrade

extract_protocol:
One day after treatment, retinas were isolated, dissociated, and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol.
RNA libraries prepared using standard Illumina  protocols

treatment_protocol: Fish received a 1 hour heat shock at 37 degrees centrigrade, every 6 hours for a 24 hour period.


title: uninj_MAML_HS_MG3

description:
deseq2_raw_counts.txt
128298


title: D4F_Rep1


title: uninj_HS_MG2

description:
deseq2_raw_counts.txt
128294

value: gfap:GFP transgenic


title: uninj_HS_MG3

description:
deseq2_raw_counts.txt
128295


title: uninj_HS_MG1

description:
deseq2_raw_counts.txt
128293


title: uninj_MAML_HS_MG1

description:
deseq2_raw_counts.txt
128296


title: 3M_Dup_clone_6_rep_2

city: La Jolla

first: Lilia

middle: M

last: Iakoucheva

state: California

address: 9500 Gilman Drive, MC0603

department: Psychiatry

institute: University of California San Diego

data_processing:
Illumina RTA version 2.7.6 software used for basecalling.
All fastqs were trimmed for adapter sequence and low base call quality (Phred score < 30 at ends) using Cutadapt (v1.14).
Trimmed reads were then aligned to the GRCH37.p13 (hg19) reference genome via STAR (2.5.3a) using comprehensive gene annotations from Gencode (v19).
Gene-level quantifications were calculated using RSEM (v1.3).
Genome_build: Human GRCH37.p13 (hg19) reference genome
Supplementary_files_format_and_content: count matrix with rows as genes (EnsembIDs) and columns as samples

organism: Homo sapiens

source_name: 3M cerebral organoids

growth_protocol:
iPSCs: To generate induced pluripotent stem cells (iPSCs), skin fibroblasts were infected with Sendai virus vectors containing coding sequences of human OCT4, SOX2, KLF4 and c-MYC (Cytotune reprogramming kit, Thermo Fisher). Four days post infection, fibroblasts were trypsinized to single cells, plated on the inactivated mouse embryonic fibroblast feeders, and cultured using human embryonic stem cell medium (vendor?). After 3–4 weeks, iPSC clones were manually picked and propagated clonally on feeders. After 8-10 passages, iPSCs were transferred to a feeder-free system and grown on matrigel-coated dishes (Corning) in mTeSR1 media (StemCell Technologies). The cells were passaged by manually picking colonies.
Cerebral organoids: Feeder-free iPSCs at passage 15 or later were fed daily with mTeSR1 for at least 7 days before differentiation. Colonies were dissociated using Accutase (Life Technologies) in PBS (1:1) for 10 minutes at 37°C and centrifuged for 3 minutes at 100xg. The cell pellet was resuspended in mTeSR1 supplemented with 10 μM SB431542 (SB, Tocris) and 1 μM Dorsomorphin (Dorso, R&D Systems). Approximately 5 × 106 cells were transferred to each well of a 6-well plate and kept in suspension under rotation (95 rpm) in the presence of 5 μM ROCK inhibitor (StemCell Technologies) for 24 hours to form free-floating spheres. Then, the media was replaced with mTeSR1 for additional 48 hours. After 72 hours, Media1 [Neurobasal (Life Technologies) supplemented with Glutamax, 2% Gem21 NeuroPlex (Gemini Bio-Products), 1% N2 NeuroPlex (Gemini Bio-Products), 1% MEM nonessential amino acids (NEAA, Life Technologies), 1% penicillin/streptomycin (PS; LifeTechnologies), 10 μM SB and 1 μM Dorso] was used for maintenance for 7 days, with media changes every other day. Subsequently, Media1 was replaced with Media2 [Neurobasal with Glutamax, 2% Gem21 NeuroPlex, 1% NEAA and 1% PS] supplemented with 20 ng/mL FGF2 (Life Technologies) for additional 7 days. Then, Media2 was supplemented with both 20 ng/mL FGF2 and 20 ng/mL EGF (Life Technologies) and spheres were cultured for additional 7 days with media changes every other day. Next, organoids were transferred into Media3 [Media2 supplemented with 10 ng/mL BDNF, 10 ng/mL GDNF, 10 ng/mL NT-3 (all from Life Technologies), 200 μM L-ascorbic acid (Tocris) and 1 mM dibutyryl-cAMP (StemCell Technologies)] for another 7 days with media changes every other day. After 28 days, cortical organoids were maintained in Media2 for as long as needed, with media changes every 3-4 days. All organoids were generated, grown and used for all experiments in the same plate with one DEL, one DUP and one CTRL (called a “batch” thereafter) to reduce batch effect from genotypes.

extract_protocol: RNA-seq libraries were prepared using standard Illumina protocols

value: 3M cerebral organoids

value: DUPLICATION

tag: disease state

value: autism


title: 3M_Dup_clone_5_rep_1


title: 3M_Dup_clone_5_rep_2


title: 3M_Dup_clone_4_rep_1


title: 3M_Dup_clone_6_rep_1


title: 3M_Dup_clone_2_rep_2


title: 3M_Dup_clone_3_rep_2


title: 3M_Dup_clone_4_rep_2


title: 3M_Dup_clone_3_rep_1


title: D4M_Rep1


title: 3M_Dup_clone_1_rep_2


title: 3M_Dup_clone_1_rep_1


title: 3M_Del_clone_5_rep_2

value: DELETION


title: 3M_Del_clone_5_rep_1


title: 3M_Dup_clone_2_rep_1


title: 3M_Del_clone_4_rep_1


title: 3M_Del_clone_2_rep_1


title: 3M_Del_clone_1_rep_2


title: 3M_Del_clone_3_rep_2


title: 3M_Del_clone_3_rep_1


title: 3M_Del_clone_2_rep_2


title: 3M_control_clone_6_rep_2

value: CONTROL


title: 3M_Del_clone_1_rep_1


title: 3M_control_clone_6_rep_1


title: 3M_control_clone_5_rep_1


title: 3M_control_clone_5_rep_2


title: 3M_Del_clone_6_rep_2


title: 3M_control_clone_4_rep_1


title: 3M_control_clone_2_rep_2


title: 3M_control_clone_3_rep_1


title: 3M_control_clone_2_rep_1


title: 3M_control_clone_1_rep_2


title: 3M_control_clone_4_rep_2


title: 3M_Del_clone_4_rep_2


title: 3M_Del_clone_6_rep_1


title: 1M_Dup_clone_6_rep_2

source_name: 1M cerebral organoids

value: 1M cerebral organoids


title: 3M_control_clone_1_rep_1


title: 1M_Dup_clone_6_rep_1


title: 1M_Dup_clone_5_rep_2


title: 1M_Dup_clone_5_rep_1


title: 1M_Dup_clone_4_rep_2


title: 1M_Dup_clone_4_rep_1


title: 1M_Dup_clone_2_rep_2


title: 1M_Dup_clone_3_rep_1


title: 1M_Dup_clone_1_rep_2


title: 1M_Del_clone_6_rep_1


title: 1M_Dup_clone_1_rep_1


title: 1M_Del_clone_5_rep_2


title: 1M_Del_clone_6_rep_2


title: 3M_control_clone_3_rep_2


title: 1M_Del_clone_4_rep_2


title: 1M_Del_clone_3_rep_1


title: 1M_Del_clone_3_rep_2


title: 1M_Del_clone_1_rep_2


title: 1M_Del_clone_2_rep_2


title: 1M_Del_clone_4_rep_1


title: 1M_Del_clone_1_rep_1


title: 1M_Del_clone_5_rep_1


title: 1M_Del_clone_2_rep_1


title: 1M_control_clone_6_rep_2


title: 1M_control_clone_6_rep_1


title: 1M_control_clone_4_rep_2


title: 1M_Dup_clone_3_rep_2


title: 1M_control_clone_5_rep_2


title: 1M_control_clone_3_rep_2


title: 1M_control_clone_4_rep_1


title: 1M_control_clone_3_rep_1


title: 1M_Dup_clone_2_rep_1


title: 1M_control_clone_1_rep_2


title: Ipsc_Dup_clone_6_rep_2

source_name: iPSCs

value: iPSCs


title: 1M_control_clone_5_rep_1


title: Ipsc_Dup_clone_5_rep_2


title: Ipsc_Dup_clone_5_rep_1


title: Ipsc_Dup_clone_4_rep_2


title: Ipsc_Dup_clone_6_rep_1


title: Ipsc_Dup_clone_4_rep_1


title: Ipsc_Dup_clone_3_rep_1


title: Ipsc_Del_clone_6_rep_2


title: Ipsc_Dup_clone_1_rep_2


title: Ipsc_Dup_clone_2_rep_1


title: Ipsc_Dup_clone_1_rep_1


title: Ipsc_Del_clone_5_rep_2


title: Ipsc_Del_clone_3_rep_1


title: Ipsc_Dup_clone_3_rep_2


title: Ipsc_Dup_clone_2_rep_2


title: Ipsc_Del_clone_5_rep_1


title: Ipsc_Del_clone_4_rep_2


title: Ipsc_Del_clone_2_rep_1


title: Ipsc_Del_clone_2_rep_2


title: Ipsc_Del_clone_4_rep_1


title: Ipsc_Del_clone_6_rep_1


title: Ipsc_control_clone_6_rep_1


title: 1M_control_clone_2_rep_1


title: 1M_control_clone_2_rep_2


title: Ipsc_Del_clone_1_rep_2


title: Ipsc_Del_clone_1_rep_1


title: Ipsc_control_clone_6_rep_2


title: Ipsc_control_clone_5_rep_2


title: Ipsc_control_clone_4_rep_2


title: Ipsc_control_clone_5_rep_1


title: Ipsc_control_clone_3_rep_1


title: Ipsc_control_clone_3_rep_2


title: Ipsc_Del_clone_3_rep_2


title: CD28_PMA

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

data_processing:
Sequence reads were aligned using STAR aligner with hg38 reference genome.
HTSeq-count was used to generate count files.
For each individual, the fold change (FC) between unstimulated and stimulated conditions were calculated. Genes with fold change higher than 2 fold in 3 out of 4 controls were used to filter the residual responsive genes to generate heatmaps.
HTSeq-count is used to get the count files, followed by DESeq2 package in R for normalization and log2 transformation.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: normalized and log2 transformed counts

source_name: naïve CD4+ T cells

growth_protocol: Thawed and negatively sorted CD4+ naive T-cells were rested overnight in x-vivo20 prior stimulation

extract_protocol:
RNeasy plus micro kit (Qiagen)
cDNA was prepared with the SMART-Seq RNA kit (Takara Bio) for low-input RNA and DNA library preparation and used the Nextera XT DNA Library Preparation Kit (Illumina) and the Nextera XT Index Kit v2 set A (Illumina), respectively

treatment_protocol: Stimulation for two hours with the indicated combination of mAb coated beads (miltenyi)

value: Tree-man syndrome patient

tag: treatment

value: PMA stimulation

tag: cell type

value: naive CD4+ T cells


title: CD28_CD2

value: CD2 stimulation


title: CD28_CD3+CD2

value: CD3+CD2 co stimulation


title: CD28_NS

value: unstimulated


title: CD28_CD3

value: CD3 stimulation


title: CD28_CD28

value: CD28 stimulation


title: Ctl5_PMA

value: control 5


title: CD28_CD3+CD28

value: CD3+Cd28 co stimulation


title: Ctl5_CD3


title: Ctl3_PMA

value: control 3


title: Ctl5_NS


title: Ctl5_CD2


title: Ctl3_CD3+CD28


title: Ctl3_CD3+CD2


title: Ctl3_CD28


title: Ctl5_CD3+CD28


title: Ctl5_CD28


title: Ctl3_CD2


title: 1M_control_clone_1_rep_1


title: Ctl3_NS


title: Ctl2_PMA

value: control 2


title: Ipsc_control_clone_4_rep_1

value: autism


title: Ctl3_CD3


title: Ctl2_CD3+CD28


title: Ctl5_CD3+CD2


title: Ctl2_CD3+CD2


title: Ctl2_CD28


title: Ipsc_control_clone_2_rep_1


title: Ipsc_control_clone_1_rep_1


title: Ipsc_control_clone_1_rep_2


title: Ipsc_control_clone_2_rep_2


title: Ctl2_NS


title: Ctl2_CD3


title: Ctl2_CD2


title: Ctl1_PMA

value: control 1


title: Ctl1_CD3+CD28


title: Ctl1_CD3+CD2


title: Ctl1_CD28


title: Ctl1_CD2


title: Ctl1_CD3


title: Macaque_Placenta_ChIP-Seq_H3K4me3_rep2

city: Bethesda

first: Mingan

last: Sun

state: Maryland

address: Building 6B, 6 Center Drive

department: Eunice Kennedy Shriver National Institute of Child Health and Human Development

institute: National Institute of Health

data_processing:
ChIP-Seq reads were trimmed with TrimGalore v0.6.4 and then aligned to the corresponding reference genome using Bowtie v2.3.5 with default settings. PCR duplicates were removed using the rmdup function of samtools v1.10. The data reproducibility between biological replicates was confirmed, then reads from replicates were pooled together for further analysis.
Peak calling was performed with MACS v2.2.5 with default settings. H3K4me1 was called as broad peaks, while H3K4me3, H3K27ac and SRF were called as narrow peaks. The peaks for human and mouse were further cleaned by removing those overlapped with ENCODE Blacklist V2 regions.
Genome_build: Mmul_10
Supplementary_files_format_and_content: The peak files are of BED format

organism: Macaca mulatta

source_name: Rhesus monkey placenta

extract_protocol:
Placenta samples for Rhesus monkey were collected following previous study (Dunn-Fletcher, et al. 2018). Two placenta samples were collected by cesarean section, and frozen at -80 degree for use.
ChIP-Seq for placenta samples was performed using the MAGnifyTM Chromatin Immunoprecipitation System (ThermoFisher, 492024). Chromatin fragmentation was performed using Diagenode Bioruptor Plus Sonicator. The antibodies used include H3K4me1 (Abcam, ab8895), H3K4me3 (Abcam, ab8580), H3K27ac (Abcam, ab4729).
ChIP-Seq libraries were constructed using Takara SMARTer ThruPLEX DNA-Seq Kit (Takara, R400674), and then sequenced as 50 bp single-end reads with HiSeq2500 (Illumina).

value: Placenta

tag: chip antibody

value: H3K4me3 (Abcam, ab8580)


title: Macaque_Placenta_ChIP-Seq_H3K4me1_rep2

tag: tissue

value: H3K4me1 (Abcam, ab8895)


title: Ctl1_NS


title: Macaque_Placenta_ChIP-Seq_H3K27ac_rep1

value: H3K27ac (Abcam, ab4729)


title: Macaque_Placenta_ChIP-Seq_H3K27ac_rep2


title: Macaque_Placenta_ChIP-Seq_H3K4me1_rep1


title: Macaque_Placenta_RNA-Seq_rep2

data_processing:
RNA-Seq reads were trimmed with Trim Galore v0.6.4.
Transcripts per Million (TPM) value for each gene was calculated using RSEM v1.3.2 with reference genome and gene annotation downloaded from ENSEMBL database.
Genome_build: Mmul_10
Supplementary_files_format_and_content: The gene expression files are of tab-delimited txt format

extract_protocol:
Placenta samples for Rhesus monkey were collected following previous study (Dunn-Fletcher, et al. 2018). Two placenta samples were collected by cesarean section, and frozen at -80 degree for use.
Total RNA for placenta samples was extracted using RNeasy Micro kit (Qiagen, 74004) with on-column DNase digestion. RNA samples were submitted for library construction by TruSeq stranded mRNA sample preparation kit (Illumina) and sequencing as 75 bp paired-end reads with HiSeq2500 (Illumina).


title: Macaque_Placenta_ChIP-Seq_Input


title: Macaque_Placenta_RNA-Seq_rep1


title: Macaque_Placenta_ChIP-Seq_H3K4me3_rep1


title: WT anthers control-3

city: Taipei

first: Der-Fen

last: Suen

address: No. 128, Sec. 2, Academia Road, Nankang

department: Agricultural Biotechnology Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
Trimmomatic: Adapter removal was done using Trimmomatic 0.35 software in single end mode with parameters ILLUMINACLIP:adapter_file.fa:2:30:4 SLIDINGWINDOW:4:30 HEADCROP:15 LEADING:25 TRAILING:30 MINLEN:80
Salmon: To perform mapping and quantify transcript abundance, quasi-alignment was adopted using Salmon (version 0.12.0).
Genome_build: TAIR10
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include transcripts per million (TPM) values and number of reads for each transcript.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown at 22 ℃ under ~110 μmol/m2.s light intensity and 16h light/8h dark cycle. Seeds were surface sterilized and grown on agar plates with half strength modified Hoagland's medium (P. D. Millner, 1992) containing 250 mM KH2PO4, 1% sucrose and 1% bactoagar for 10 days and transferred to hydroponic system using the half strength modified Hoagland’s medium without sucrose for 18 days and followed by the treatment.

extract_protocol:
Total RNA was extracted using a RNeasy Mini kit (Qiagen) following manufacturer's instruction and processed by RNase free DNase I (Qiagen).
The cDNA libraries were built using the Illumina TruSeq RNA Sample Preparation v2 kit (Illumina) and sequenced in single-end using the Illumina Miseq System (Miseq 150 cycles v3, SR150).

treatment_protocol: After plants were grown for 28 days (10+18 days) under Fe-sufficient condition, plants were transferred to the Fe-sufficient condition (50mM NaFe-EDTA) or Fe-deficient condition without adding NaFe-EDTA and grew for 18 days, and then samples were collected for further analysis.

tag: ecotype

value: WT

value: Whole anthers at stage PMC-TC

value: Control 1/2 Hoagland media


title: WT anthers Fe-deficient-2

value: Fe-deficient media


title: WT anthers control-2


title: WT anthers control-1


title: WT anthers Fe-deficient-3


title: WT anthers Fe-deficient-1


title: 4310479167_H_severe asthma non-smoker

type: RNA

city: New Lambton Heights

first: Stephany

last: Sanchez

state: NSW

address: Lot 1 Kookaburra Circuit

department: Respiratory and Sleep Medicine

country: Australia

institute: University of Newcastle

hyb_protocol: 750 ng of cRNA was hybridized to Illumina HumanRef‐8 V2 Beadchips

scan_protocol: BeadChips were scanned using the Illumina Bead Station and data was captured using BeadScan 3.5.11 (Illumina, San Diego, USA).

data_processing: Array raw data were processed using GenomeStudio software, Illumina and analysed using R Bioconductor lumi and limma packages. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and data passed quality control in R during analysis. Data was log2‐transformed and quantile‐normalised.

label: biotin

source_name: induced sputum

label_protocol: biotin

growth_protocol: Induced sputum were placed in RNA-later (Qiagen, Hilden, Germany) for storage at -20 °C prior to RNA extraction.

extract_protocol: RNA extraction was perfomed using (RNeasy Mini Kit and RNAse-free DNAse, Qiagen, Hilden, Germany). RNA was quantified (Quant-iT RiboGreen RNA Quantitation Assay Kit, Life Technologies Corporation, USA)

treatment_protocol: Samples were lysed (RNeasy Lysis Buffer, Qiagen, Hilden, Germany) and homogenised (TissueLyser II, Qiagen, Hilden, Germany) prior to RNA extraction.

value: sputum

tag: disease status

value: severe asthma

tag: gender

value: male

tag: atopy

value: atopic

tag: smoking history

value: former smoker

tag: packyear

tag: daily oral corticosteroid

value: no


title: 4310479167_A_healthy control

value: healthy control

value: female

value: non-smoker


title: 4147931029_D_mild/moderate asthma

value: mild/moderate asthma


title: 4310479166_G_severe asthma non-smoker


title: 4135447194_H_mild/moderate asthma

value: non-atopic


title: 4310479168_E_healthy control


title: 4147931029_C_mild/moderate asthma


title: 4147931008_A_mild/moderate asthma


title: 4310479166_A_mild/moderate asthma


title: 4147931034_G_mild/moderate asthma


title: 4310479173_H_healthy control


title: 4310479163_E_severe asthma smoker/ex-smoker


title: 4310479156_D_severe asthma smoker/ex-smoker


title: 4310479173_E_severe asthma smoker/ex-smoker


title: 4310479168_B_severe asthma non-smoker


title: 4310479156_C_severe asthma smoker/ex-smoker


title: 4310479166_E_mild/moderate asthma


title: 4310479167_D_mild/moderate asthma


title: 4310479167_B_healthy control


title: 4147931029_F_severe asthma smoker/ex-smoker


title: 4310479167_E_severe asthma smoker/ex-smoker


title: 4147931029_H_mild/moderate asthma


title: 4310479166_D_mild/moderate asthma


title: 4310479156_G_severe asthma smoker/ex-smoker


title: 4310479168_H_mild/moderate asthma


title: 4147931008_C_mild/moderate asthma


title: 4147931008_E_mild/moderate asthma


title: 4147931034_E_severe asthma smoker/ex-smoker


title: 4135447179_G_severe asthma non-smoker


title: 4135447179_H_severe asthma non-smoker


title: 4135447179_E_mild/moderate asthma


title: 4135447179_D_mild/moderate asthma


title: 4135447178_H_mild/moderate asthma


title: 4135447179_B_severe asthma non-smoker


title: 4135447175_D_healthy control


title: 4135447178_G_healthy control


title: 4135447178_D_severe asthma non-smoker


title: 4135447175_C_healthy control


title: TNBC_120

city: Halle (Saale)

first: Martina

last: Vetter

address: Ernst-Grube-Str. 40

department: Dept. of Gynaecology

description: Gene expression data from tumor tissue of primary breast cancer

hyb_protocol: Following fragmentation, 6.6µg of ds-cDNA were hybridized for 16 hr at 45°C on GeneChip HG-U133_Plus_2.0 Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450 by Thermo Fisher Scientific.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G by Thermo Fisher Scientific.

data_processing: The data was analyzed in the R prgramming environment with the RMA-algorithm of the simpleaffy package.

source_name: breast cancer

label_protocol: Biotinylated ds-cDNA were prepared according to the standard GeneChip 3'IVT PICO Kit protocol from 25 ng total RNA (protocol P/N 703308 Rev.4; by Thermo Fisher Scientific)

growth_protocol: primary tumor

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy FFPE Kit - Qiagen)

treatment_protocol: no treatment

value: primary tumor

value: Triple-negative breast cancer


title: 4135447179_C_mild/moderate asthma


title: 4135447175_B_healthy control


title: 4135447178_E_healthy control


title: TNBC_124


title: 4135447160_A_mild/moderate asthma


title: 4135447175_A_healthy control


title: 4135447160_H_severe asthma non-smoker


title: TNBC_122


title: 8-EV-A71+ER-DRI in mice

city: Wuhan

first: Yang

last: Qiu

state: Hubei

address: No. 44 Xiaohongshan Central District, Wuchang District,

institute: Wuhan institue of virology, CAS

description: small RNA

data_processing:
The deep sequencing and data analysis have been described in detail previously (Qiu et al., 2017). In brief, libraries of small RNAs from cells with different treatments were constructed using TruSeq Small RNA Library Preparation Kits (Illumina) according to manufacturer’s instructions. The libraries were sequenced by Illumina HiSeq 2000 at RiboBio (Guangzhou, China). The sequencing reads were mapped to the human genome (release hg19) and mouse genome (release GRCm38) by using Bowite 2.2.5 and miRNA reads were determined on the basis of the number of reads, which were identical to the annotated miRNA sequences in miRBase version 18, only allowing +2 or -2 nt to be templated by the corresponding genomic sequence at the 3’ end. Viral small RNA (vsRNA) reads that cannot be mapped to human genome were then mapped to EV-A71 genome with 100% identity. The subsequent analysis of distribution and length of these vsRNAs were calculated using in-house Perl scripts.
Genome_build: hg19, GRCm38, KC954664.1
Supplementary_files_format_and_content: read counts

organism: Enterovirus A71

source_name: ICR mice

tag: host

value: Mus musculus

tag: host strain

value: ICR

tag: host tissue

value: muscles (the hind legs)

value: +ER-DRI


title: TNBC_116


title: TNBC_121


title: TNBC_113


title: TNBC_117


title: 7-EV-A71+Vehicle in mice

description: small RNA

extract_protocol: TruSeq Small RNA Library Preparation Kits (Illumina)

value: +Vehicle


title: 5-EV-A71+TAT-NoDice

description: small RNA

source_name: Human  HEK293T cells

value: Homo sapiens

tag: host cell line

value: +TAT-NoDice


title: 4-EV-A71-NoDice

description: small RNA

value: -NoDice


title: TNBC_118


title: 3-EV-A71+ER-DRI

description: small RNA


title: TNBC_114


title: TNBC_115


title: 2-EV-A71+TAT

description: small RNA

value: +TAT


title: HSC2 cells treated with Elental for 12 hr

city: Ube

first: Koji

last: Harada

address: 1-1-1 minami-kogushi

department: Oral & maxillofacial surgery

country: Japan

institute: Yamaguchi university

data_processing:
The raw data of the sequences were converted to sequence reads, and adaptor sequences and low quality bases were removed using Torrent suite software (ver. 4.2.1).
The trimmed reads were mapped to the hg19 Ampliseq Transcriptome ERCC v1 using a Torrent mapping alignment program with default setting.
Read counts for each gene were caluculated using Ampliseq RNA plugin software.
Genome_build: Custamized hg19, hg19 Ampliseq Transcriptome ERCC v1 spplied by Thermo Fisher Scientific as the reference sequences
Supplementary_files_format_and_content: Tab-delimited text files include raw gene counts for each amplicon annotated with gene symbol and each sample.

source_name: human oral squamous cell carcinoma cells

growth_protocol: HOK cells were cultured in Oral Keratinocyte Medium- New Zealand Origin BPE medium (OKM-NZ, #2611-NZ; ScienCell Research Laboratories) which contains OKM basal medium supplemented with 1% oral keratinocyte growth supplement- New Zealand Origin BPE (OKGS-NZ, #2652NZ; ScienCell Research Laboratories) and 1% penicillin/streptomycin solution (#0503; ScienCell Research Laboratories), and will be referred to complete OKM-NZ medium. HSC2 cells were cultured in Dulbecco’s modified Eagle’s medium (D-MEM)/Ham’s F-12 (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher scientific, MA, USA) and 100 μg/ml streptomycin/ 100 units/ml penicillin (Thermo Fisher scientific). All cells were cultured and maintained in a humidified atmosphere containing 5% CO2 at 37˚C.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Invitrogen). Ion Ampliseq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific) was used with 70 ng of total RNA for the construction of sequencing libraries.
Seventy ng of total RNAs were reverse-transcribed to cDNAs using Ion Ampliseq Transcriptome Human Gene Expression kit. Synthesized cDNA were amplified with the primer set of Ion Ampliseq Transcriptome Human Gene Expression Core Panel (Thermo Fisher Scientific). Amplified cDNA were ligated to adaptors and barcoded using Ion Barcode Adaptors 17-32 Kit (Thermo Fisher Scientific), and then amplified by PCR. Libraries were amplified on beads by emulsion PCR and enriched, and then loaded to Ion PI Chip Kit v3 BC using Ion Chef system (Thermo Fisher Scientific). Libraries on the chip were sequenced by Ion Proton using protocols of Hi-Q Chef kit.

treatment_protocol: HOK cells and HSC2 cells treated with 5 μg/ml of Elental® for 0 hr, 0.5 hr, 3 hr and 12 hr.

value: oral squamous cell carcinoma cells

tag: agent

value: 5 microg/ml of Elental

tag: time point

value: 12 hours


title: TNBC_123

tag: disease state


title: TNBC_119


title: 1-EV-A71

description: small RNA

tag: treatment


title: HSC2 cells treated with Elental for 3 hr

tag: cell type

value: 3 hours


title: HSC2 cells treated with Elental for 0.5 hr

value: 0.5 hours


title: HSC2 cells treated with Elental for 0 hr

value: 0 hours


title: TNBC_111

tag: tissue

value: primary tumor


title: TNBC_112

value: Triple-negative breast cancer


title: 6-EV-A71+ER-DRI-NoDice

description: small RNA

value: +ER-DRI-NoDice


title: TNBC_109


title: TNBC_105


title: TNBC_110


title: TNBC_107


title: TNBC_108


title: HOK cells treated with Elental for 12 hr

source_name: human oral keratinocyte cells

value: human oral keratinocyte cells


title: TNBC_103


title: TNBC_102


title: TNBC_101


title: HOK cells treated with Elental for 3 hr


title: TNBC_106


title: HOK cells treated with Elental for 0.5 hr


title: HOK cells treated with Elental for 0 hr


title: TNBC_104


title: TNBC_100


title: MSUS cauda epididymosomes_sample_8_run2

city: Zürich

first: Deepak

last: Tanwar

state: ZH

address: Winterthurerstrasse 190

country: Switzerland

institute: ETH Zürich

data_processing:
Small RNA-sequencing FASTQ files were processed using the ExceRpt pipeline, a previously established pipeline for extracellular vesicle small RNA data analysis [Rozowsky et al., Cell Syst 2019]. Briefly, ExceRpt first automatically identifies and removes known 3? adapter sequences. Afterwards the pipeline aligns against known spike-in sequences used for library construction, filters low-quality reads and aligns them to annotated sequences in the UniVec database and endogenous ribosomal RNAs. Reads that were not filtered out in the pre-processing steps are then aligned to the mouse genome and transcriptome using STAR aligner [Dobin et al., Bioinformatics 2013].
The annotations were performed in the following order: miRbase, tRNAscan, piRNA, GENCODE and circRNA. Reads mapped to miRNAs were combined from sequencing obtained before and after size-selection and were corrected for batch effect using RUVSeq [Leek, Nucleic Acids Res. 2014]. Normalization factors were calculated using the TMM [Robinson et al., Genome Biology 2010] method and differential expression was performed using the edgeR package [Robinson et al., Bioinformatics 2010] in R.
Genome_build: GRCm38
Supplementary_files_format_and_content: Gene count matrices and, for short RNA biotypes

source_name: MSUS cauda epididymosomes

extract_protocol:
Cauda epididymosomes were extracted by ultracentrifugation. Briefly, after pelleting sperm following the sperm swim-up protocol in M2 medium (Sigma, M7167), the supernatant was centrifuged at 2'000 rcf for 10 min, 10'000 rcf for 30 min and then ultracentrifuged at 120'000 rcf at 4C for 2 h (TH 64.1 rotor, Thermo Fisher Scientific). The epididymosomal pellet was then washed in PBS at 4C and ultracentrifuged at 120'000 rcf at 4C for 2 h. The resulting pellet was resuspended in 60 ?l of PBS for all downstream analysis.
The library was prepared following the Manufacturer's protocol for the NEB Next Small RNA-seq kit. Same libraries were sequenced twice - with and without size-selection to enrich for miRNAs among all small RNAs.

treatment_protocol: Cauda epididymosomes were extracted from adult males subjected to MSUS and Control males. The MSUS treatment corresponds to unpredictable maternal separation for 3-hours daily during the first 2 weeks after birth, combined with maternal stress (dums are subjected to forced swim or restraint daily during the 2 week period) at unpredictable times.

tag: condition

value: MSUS

tag: time from last injection

value: 9 months-old males

value: cauda epididymosomes

tag: molecule subtype

value: small RNA

tag: library preparation kit

value: NEB NEXT Small RNA-seq


title: Control cauda epididymosomes_sample_11_run2

source_name: Control cauda epididymosomes

value: Control


title: MSUS cauda epididymosomes_sample_14_run2


title: Control cauda epididymosomes_sample_7_run2


title: TNBC_98


title: TNBC_99


title: MSUS cauda epididymosomes_sample_6_run2


title: Control cauda epididymosomes_sample_5_run2


title: Control cauda epididymosomes_sample_9_run2


title: TNBC_97


title: MSUS cauda epididymosomes_sample_4_run2


title: MSUS cauda epididymosomes_sample_2_run2


title: MSUS cauda epididymosomes_sample_14_run1


title: TNBC_96


title: TNBC_95


title: TNBC_90


title: TNBC_94


title: TNBC_93


title: Control cauda epididymosomes_sample_9_run1


title: TNBC_91


title: Control cauda epididymosomes_sample_7_run1


title: TNBC_87


title: Control cauda epididymosomes_sample_3_run2


title: MSUS cauda epididymosomes_sample_8_run1


title: TNBC_88


title: MSUS cauda epididymosomes_sample_6_run1


title: Control cauda epididymosomes_sample_5_run1


title: TNBC_86


title: TNBC_92


title: TNBC_84


title: Control cauda epididymosomes_sample_11_run1


title: TNBC_89


title: Control cauda epididymosomes_sample_3_run1


title: TNBC_81


title: TNBC_85


title: TNBC_82


title: TNBC_79


title: KO 3t3 embryo fibroblasts Mnt IP_Exp2

city: Seattle

last: Freie

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq v1.8.4
Alignment was to mm10 with Bowtie 2,  reads >700bp filtered out
Alignment for RNASeq was done using TopHat
RNA Seq data was processed using DESeq2
Peakcalls were done using MACS at pvalue 1x10-5
Genome_build: mm10
Supplementary_files_format_and_content: BigWigs were created using bedtools (genomecov) and WigToBigWig scripts. Normalization was to library size

source_name: mouse embryo fibroblasts

growth_protocol: Testes tissue was harvested from mice. 3T3 cells were grown in DMEM with 10% FBS and Pen/Strep.

extract_protocol:
For RNA-Seq Trizol extraction was used. For ChIP-Seq formaldehyde cross-linking was used. Micrococcal nuclease was included for the 3T3 ChIP-Seq experiments.
For RNA-Seq 50x50 paired-end and for ChIP-Seq 25x25 paired-end sequencing was performed on an Illumina HiSeq 2500 instrument at the Fred Hutchinson Cancer Research Center Genomics Shared Resource.

treatment_protocol: No Treatment

tag: age

value: embryonic

tag: genotype

value: Mlx knockout

value: embryonic fibroblasts


title: MSUS cauda epididymosomes_sample_4_run1


title: TNBC_78


title: KO 3t3 embryo fibroblasts GFP non-specific control_Exp2


title: TNBC_83


title: TNBC_77


title: TNBC_80


title: WT 3t3 embryo fibroblasts Mnt IP_Exp2

value: Wildtype


title: WT 3t3 embryo fibroblasts GFP non-specific control_Exp2


title: KO 3t3 embryo fibroblasts Mlx IP_Exp1


title: KO 3t3 embryo fibroblasts Max IP_Exp1


title: 200598770001_L_severe asthma non-smoker

hyb_protocol: 750 ng of cRNA was hybridized to Illumina’s HT-12 V4 Beadchips

data_processing: Array raw data were processed using GenomeStudio software, Illumina and analysed using R Bioconductor lumi and limma packages. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and data passed quality control criteria in R during analysis. Data was log2‐transformed and quantile‐normalised.

source_name: endobronchial biopsy

growth_protocol: Endobronchial biopsy samples were placed in RNA-later (Qiagen, Hilden, Germany) for storage at -20 °C prior to RNA extraction.

value: endobronchial biopsy

tag: disease status

value: severe asthma

tag: gender

value: female

tag: atopy

value: atopic

tag: smoking history

value: non-smoker

tag: daily oral corticosteroid

value: no


title: TNBC_74

value: primary tumor

value: Triple-negative breast cancer


title: 200598770001_I_mild/moderate asthma

value: mild/moderate asthma

value: non-atopic

value: former smoker

tag: packyear


title: 200598770001_F_healthy control

value: healthy


title: 200598770001_J_severe asthma non-smoker

value: male


title: 200598770001_B_healthy control


title: 200598770001_G_healthy control


title: 200598770001_D_healthy control


title: TNBC_73


title: TNBC_70


title: TNBC_71


title: TNBC_72


title: 200598770046_J_healthy control


title: 200598770046_L_healthy control


title: KO 3t3 embryo fibroblasts GFP non-specific control_Exp1

value: embryonic


title: WT 3t3 embryo fibroblasts Mlx IP_Exp1


title: WT 3t3 embryo fibroblasts Max IP_Exp1


title: TNBC_69


title: TNBC_68


title: TNBC_67


title: 200598770046_G_healthy control


title: 200598770046_B_healthy control


title: 200598770046_E_healthy control


title: TNBC_75


title: 200598770046_A_healthy control


title: 200598770012_K_mild/moderate asthma


title: 200598770046_I_healthy control


title: WT 3t3 embryo fibroblasts GFP non-specific control_Exp1


title: TNBC_66


title: TNBC_65


title: 200598770046_C_healthy control


title: 200598770012_L_severe asthma non-smoker

value: yes

tag: mg prednisone/day


title: 200598770012_J_severe asthma non-smoker


title: KO testes ChIPSeq Max IP

source_name: mouse testes

value: 7 months

value: Mlx knockout

value: testes


title: KO testes ChIPSeq input control


title: TNBC_64

tag: disease state


title: 200598770012_I_severe asthma non-smoker

value: endobronchial biopsy

value: severe asthma


title: WT testes ChIPSeq Mlx IP

value: Wildtype


title: WT testes ChIPSeq Max IP


title: WT testes ChIPSeq input control


title: KO testes RNASeq biological paired replicate 3


title: TNBC_63


title: TNBC_62


title: 200598770012_G_mild/moderate asthma

value: female

value: atopic

value: non-smoker


title: KO testes RNASeq biological paired replicate 1


title: 200598770012_E_mild/moderate asthma

value: no


title: 200598770014_F_severe asthma smoker/ex-smoker


title: 200598770012_H_mild/moderate asthma

value: mild/moderate asthma


title: TNBC_61

value: primary tumor

value: Triple-negative breast cancer


title: 200598770012_F_mild/moderate asthma

value: non-atopic


title: 200598770014_D_severe asthma non-smoker


title: 200598770012_B_mild/moderate asthma


title: 200598770014_H_healthy control

value: healthy

value: male

value: former smoker


title: 200598770014_E_severe asthma non-smoker

value: yes


title: 200598770012_D_severe asthma non-smoker


title: 200598770014_B_mild/moderate asthma


title: TNBC_58


title: 200598770012_A_severe asthma non-smoker


title: TNBC_56


title: TNBC_57


title: 200598770014_A_severe asthma non-smoker


title: KO testes RNASeq biological paired replicate 2

value: 7 months

value: Mlx knockout


title: 200598770012_C_severe asthma non-smoker

value: endobronchial biopsy


title: WT testes RNASeq biological paired replicate 2

value: testes


title: TNBC_60


title: MSUS cauda epididymosomes_sample_2_run1

value: MSUS

value: 9 months-old males

value: cauda epididymosomes

value: small RNA

value: NEB NEXT Small RNA-seq


title: WT testes RNASeq biological paired replicate 1

value: Wildtype


title: WT testes RNASeq biological paired replicate 3


title: 200598770014_C_severe asthma smoker/ex-smoker

value: severe asthma

value: female

value: no


title: KO testes ChIPSeq Mlx IP


title: TNBC_76

value: primary tumor

value: Triple-negative breast cancer


title: 200598770022_L_mild/moderate asthma

value: mild/moderate asthma

value: atopic

value: non-smoker


title: TNBC_53


title: 200598770022_J_severe asthma smoker/ex-smoker

value: non-atopic

value: former smoker

value: yes


title: 200598770022_H_severe asthma non-smoker

value: endobronchial biopsy


title: TNBC_55


title: 200598770022_I_mild/moderate asthma


title: TNBC_52


title: TNBC_54


title: 200598770022_F_severe asthma non-smoker

value: male


title: TNBC_59


title: 200598770022_D_severe asthma non-smoker


title: 200598770022_G_mild/moderate asthma


title: 200598770022_K_severe asthma non-smoker


title: TNBC_50


title: 200598770022_E_mild/moderate asthma


title: 200598770022_C_severe asthma non-smoker


title: TNBC_51


title: 200598770017_G_severe asthma non-smoker


title: HeLa P 2D-DMEM

city: Singapore

first: Dawn

middle: Sijin

last: Nin

address: 8 Medical Drive, Blk MD7, level 4

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: #1 HeLa P 2D-DMEM

hyb_protocol: Standard Illumina hybridization protocol  Standard Illumina scanning protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: Biotin

source_name: HeLa Parental

growth_protocol: 2.5 million cells were mixed with an equal volume of Matrigel matrix (Corning®) and subcutaneously injected into the left flank of recipient mice

extract_protocol: Total RNA was extracted using TRIzol reagent (ThermoFisher Scientific, Cat. #15596018), following the manufacturer’s protocol.

treatment_protocol: Palpable tumour size of 1500 mm3 were sacrificed by CO2 euthanasia and tumour excised.

tag: host strain

value: BALB/C-nude

tag: Sex

tag: tissue/cell type

value: HeLa Prental Xenograft tumour


title: 200598770017_I_severe asthma non-smoker

tag: tissue


title: 200598770017_E_severe asthma non-smoker


title: HeLa C5 2D-DMEM

description: #2 HeLa C5 2D-DMEM

source_name: HeLa Radio-resistant cultured in 2D conditions in DMEM

value: HeLa radio-resistant Xenograft tumour

tag: culture condition

value: 2D conditions in DMEM


title: HeLa C5 3D-B27

description: #3 HeLa C5 3D-B27

source_name: HeLa Radio-resistant cultured in 3D conditions in B27 media

value: 3D conditions in B27 media


title: 200598770017_C_severe asthma non-smoker

value: severe asthma

value: female


title: TNBC_48

value: primary tumor


title: HeLa C5 3D-DMEM

description: #4 HeLa C5 3D-DMEM

source_name: HeLa Radio-resistant cultured in 3D conditions in DMEM

value: 3D conditions in DMEM


title: 200598770017_F_severe asthma non-smoker


title: RNA-seq of nicotine mice sperm2

city: Shanghai

first: Dong

last: Zhang

address: dongchuan road

institute: shanghaijiaotong university

description: mice treated with nicotine2

data_processing:
The “OLB” and “CASAVA” software programs allowed the retrieval of the original fastq sequence data.
Using the fastx package, clean reads were attained.
“TOPHAT” was used after the reads and junction reads were mapped to the reference sequence.
The gene expression data estimated from the RPKM values were obtained using “Cuffinks”.
Genome_build: mm8
Supplementary_files_format_and_content: Excel files include read, RPKM values for each Sample

source_name: spermatozoa

extract_protocol:
RNA was extracted using Trizol reagent. TruSeqTM DNA Sample Prep Kit-Set A  was used with 20 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After an adult male mouse (approximately 11 weeks of age) was sacrificed, the cauda of the epididymis was carefully isolated, and the spermatozoa were forced out after a nick was cut in the cauda epididymis. The isolated spermatozoa were suspended in HTF (Human Tube Fluid: 5.9 g/L NaCl, 0.35 g/L KCl, 0.049 g/L MgSO4.7H2O, 0.054 g/L KH2PO4, 0.57 g/L CaCl2, 2.1 g/L NaHCO3, 0.5 g/L Glucose, 3.4 ml/L sodium lactate, 0.037 g/L sodium pyruvate, 0.075 g/L ampicillin, 0.05 g/L streptomycin, 4 g/L BSA, 0.002g/L phenol red) for subsequent treatments.

tag: strain

tag: developmental stage

value: adult

value: spermatozoa

tag: agent

value: nicotine


title: 200569440013_K_severe asthma non-smoker

tag: age

value: non-atopic

value: no


title: TNBC_46

value: Triple-negative breast cancer


title: 200569440013_I_severe asthma smoker/ex-smoker

value: endobronchial biopsy

tag: disease status

value: atopic

value: former smoker

value: yes


title: 200598770017_D_severe asthma smoker/ex-smoker

tag: gender


title: TNBC_49


title: 200598770017_A_severe asthma non-smoker

tag: atopy

value: non-smoker


title: 200569440013_L_mild/moderate asthma

value: mild/moderate asthma

tag: smoking history


title: RNA-seq of nicotine mice sperm1

description: mice treated with nicotine1


title: 200569440013_E_severe asthma non-smoker

tag: daily oral corticosteroid


title: RNA-seq of control mice sperm2

description: mice treated with saline2

value: saline


title: TNBC_47


title: 200569440013_J_severe asthma non-smoker

value: severe asthma

value: male


title: 200569440013_D_mild/moderate asthma

value: female


title: 200598770017_B_severe asthma smoker/ex-smoker

tag: packyear


title: 200569440013_F_severe asthma non-smoker


title: 200569440013_B_mild/moderate asthma


title: RNA-seq of control mice sperm1

description: mice treated with saline1


title: 200569440013_H_severe asthma non-smoker


title: TNBC_45

value: primary tumor


title: TNBC_42


title: TNBC_43


title: 200569440006_J_severe asthma smoker/ex-smoker


title: 200569440013_A_severe asthma non-smoker


title: TNBC_40


title: TNBC_44


title: 200569440013_C_severe asthma non-smoker

tag: mg prednisone/day


title: 200569440006_H_severe asthma non-smoker


title: TNBC_37

tag: disease state


title: 200569440006_E_severe asthma non-smoker


title: 200569440006_L_mild/moderate asthma


title: 200569440006_K_severe asthma non-smoker


title: Healthy control [200598770046_G]

hyb_protocol: 750 ng of cRNA was hybridized to Illumina’s HT-12 V4 BeadChips.

data_processing: Array raw data were processed using GenomeStudio software, Illumina and analysed using GeneSpring GX14.9.1, Agilent Technologies. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (principle component analysis plots). Data was log2‐transformed and quantile‐normalised.

label_protocol: Biotin

extract_protocol: RNA extraction was performed (RNeasy Mini Kit and RNase-free DNase, Qiagen, Hilden, Germany). RNA was quantified (Quant-iT RiboGreen RNA Quantitation Assay Kit, Life Technologies Corporation, USA).

value: Endobronchial biopsy

value: healthy

tag: inflammatory phenotype

value: Healthy control

value: Male

tag: acqmean


title: Healthy control [200598770046_E]

value: non-atopic


title: Healthy control [200598770046_C]


title: TNBC_39

value: Triple-negative breast cancer


title: DKO cells expressing the Q84E mutant ATP11A

city: Bunkyou-ku

first: Katsumori

last: Segawa

state: Tokyo

address: 1-5-45, Yushima

department: Medical Research Institute

institute: Tokyo Medical and Dental University

description:
Gene expression data from mouse DKO cells that stably express the mutant ATP11A.
DKO-Q84E

hyb_protocol: After the fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: mouse T-lymphoma cell line WR19L

label_protocol: Biotinylated cRNA were prepared by GeneChip 3' IVT PLUS Reagent Kit (Thermo Fisher Scientific) from 250 ng total RNA according to the manufacturer's instructions.

growth_protocol: Cells were grown in RPMI1640-10% FCS with standard antibiotics.

extract_protocol: Acid guanidinium thiocyanate-phenol-chloroform extraction coupled with RNeasy spin-column purification of total RNA was performed.

treatment_protocol: No treatment

value: BALB/c

tag: cell line

tag: cell type

value: T-lymphoma cells

tag: genotype


title: TNBC_32

tag: tissue


title: Healthy control [200598770046_I]


title: DKO cells expressing human ATP11A

description:
Gene expression data from mouse DKO cells that stably express human ATP11A.
DKO-hATP11A-WT

tag: strain


title: TNBC_33


title: Healthy control [200598770046_L]

value: Female

value: atopic


title: 200569440006_I_severe asthma smoker/ex-smoker

value: endobronchial biopsy

value: former smoker

value: no


title: Healthy control [200598770046_A]

value: non-smoker


title: TNBC_35


title: Healthy control [200598770046_B]


title: 200569440006_A_mild/moderate asthma

value: mild/moderate asthma


title: Severe eosinophilic asthma [200598770012_H]

data_processing: Array raw data were processed using GenomeStudio software, Illumina and analysed suing GeneSpring GX14.9.1, Agilent Technologies. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (principle component analysis plots). Data was log2‐transformed and quantile‐normalised.

value: Severe asthma

value: Eosinophilic asthma


title: 200569440006_G_severe asthma non-smoker

value: severe asthma

value: male


title: Healthy control [200598770046_J]

value: Endobronchial biopsy

value: healthy

value: Healthy control


title: TNBC_38

value: primary tumor

value: Triple-negative breast cancer


title: TNBC_41


title: Parental WR19L cells

description:
Gene expression data from mouse T-lymphoma cells, WR19L.
W3

value: BALB/c

value: T-lymphoma cells

value: Parental cells


title: 200569440006_D_severe asthma non-smoker

value: endobronchial biopsy

value: atopic


title: 200569440006_C_mild/moderate asthma

value: female

value: no


title: flippase-deficient WR19L (DKO) cells

description:
Gene expression data from mouse WR19L cells deficient for plasma membrane phospholipid flippases (ATP11A and ATP11C) (DKO).
DKO


title: TNBC_34


title: TNBC_36


title: TNBC_29


title: TNBC_31


title: Severe eosinophilic asthma [200598770022_J]

value: Female

value: non-atopic

value: former smoker


title: Severe eosinophilic asthma [200598770022_G]

value: Severe asthma

value: Eosinophilic asthma

value: non-smoker


title: Severe eosinophilic asthma [200598770022_D]

value: Endobronchial biopsy


title: Severe eosinophilic asthma [200598770022_B]

value: Male


title: Severe paucigranulocytic asthma [200598770022_F]

value: Paucigranulocytic asthma


title: TNBC_30

value: primary tumor

value: Triple-negative breast cancer


title: Severe paucigranulocytic asthma [200598770022_C]


title: Severe eosinophilic asthma [200598770017_G]


title: Severe neutrophilic asthma [200598770017_L]

value: Neutrophilic asthma


title: Severe paucigranulocytic asthma [200598770014_D]


title: Severe neutrophilic asthma [200598770017_I]


title: Healthy control [200598770014_H]

value: healthy

value: Healthy control


title: TNBC_27


title: TNBC_24


title: Severe paucigranulocytic asthma [200598770017_A]


title: Severe eosinophilic asthma [200598770012_L]


title: Severe paucigranulocytic asthma [200598770014_B]


title: Severe paucigranulocytic asthma [200598770014_C]


title: TNBC_20


title: TNBC_25


title: Severe paucigranulocytic asthma [200598770014_A]


title: TNBC_22


title: TNBC_28


title: TNBC_23


title: Severe eosinophilic asthma [200598770017_C]


title: Severe eosinophilic asthma [200598770022_K]

value: atopic


title: Severe eosinophilic asthma [200598770022_A]


title: Severe eosinophilic asthma [200598770022_H]


title: Severe neutrophilic asthma [200598770012_J]


title: Severe paucigranulocytic asthma [200598770017_E]


title: Severe paucigranulocytic asthma [200598770012_K]


title: Severe eosinophilic asthma [200598770012_G]


title: Severe paucigranulocytic asthma [200598770017_H]


title: TNBC_18


title: Severe eosinophilic asthma [200598770012_D]


title: TNBC_26


title: TNBC_17


title: TNBC_16


title: TNBC_19


title: Severe eosinophilic asthma [200598770012_F]


title: Severe eosinophilic asthma [200569440013_L]


title: Severe neutrophilic asthma [200598770017_K]


title: Severe neutrophilic asthma [200569440013_J]


title: TNBC_21


title: Healthy control [200598770001_B]


title: Severe eosinophilic asthma [200569440013_K]


title: Severe eosinophilic asthma [200598770012_C]


title: Healthy control [200598770001_F]


title: Healthy control [200598770001_G]


title: TNBC_15


title: TNBC_12


title: Severe paucigranulocytic asthma [200598770012_A]


title: TNBC_14


title: Severe neutrophilic asthma [200569440013_F]


title: Severe eosinophilic asthma [200569440013_I]


title: Severe eosinophilic asthma [200569440013_C]


title: Severe eosinophilic asthma [200569440013_E]


title: Severe paucigranulocytic asthma [200569440013_H]


title: Severe paucigranulocytic asthma [200569440013_B]


title: TNBC_9


title: Severe paucigranulocytic asthma [200569440006_I]


title: TNBC_10


title: Severe neutrophilic asthma [200569440006_J]


title: Severe eosinophilic asthma [200569440006_E]


title: Severe eosinophilic asthma [200569440006_G]


title: Severe paucigranulocytic asthma [200569440006_H]


title: TNBC_11


title: TNBC_7


title: Liver_HF_rep2_Ribo

city: chengdu

first: Tengda

last: Huang

state: Sichuan

address: gaopeng road

department: West China Hospital

institute: Sichuan University

description: total Ribosome protected fiagments

data_processing:
Library strategy: Ribo-Seq
Illumina HiSeq-2000 software used for basecalling.
For both mRNA and RPF sequencing data sets, high quality reads were mapped to the RefSeq mRNA reference sequence (mm10) through the FANSe2 algorithm, with the parameters -L80 -E5 -I0 -S14 -B1 -U0.  Reads that mapped to alternative splice variants of one gene were merged.
The mRNA and RPFs in each sample were normalized by reads per kilo base per million reads (RPKM). Differentially expressed genes (DEGs) were identified with the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Liver

growth_protocol: Mice at 8 weeks of age were used. Eighteen mice were randomly selected into two groups: a high-fat model group (HF group, n = 6), and a betaine treated group (HB group, n = 6).

extract_protocol:
RNA-seq: Total RNA samples were prepared from two independent experiments (HF and HB groups). Total RNA was isolated using TRIzol® RNA extraction reagent (Ambion, Austin, Texas, USA), following the manufacturer’s instructions. Equal amounts of total RNA from each preparation were pooled for subsequent library construction and RNA-seq. Ribo-seq: A total of 90 mg of liver tissue was pre-treated with 100 mg/ml cycloheximide for 15 min, followed by three washes with pre-chilled PBS prior to the addition of 2 ml of cell lysis buffer [1% Triton X-100 in ribosome buffer (RB buffer, 20 mM HEPES-KOH (pH 7.4), 15 mM MgCl2, 200 mM KCl, 100 μg/ml cycloheximide, and 2mM dithiothreitol)] to T-75 flasks. After 30-min in an ice-bath, cell lysates were split into two pre-chilled 1.5 ml tubes. Cell debris was removed by centrifugation at 16,200 × g for 10 min at 4 °C. Supernatants were transferred into new pre-chilled 1.5 ml tubes with 2 μl of Ribolock RNase Inhibitor (40 U/μl, Fermentas) in each tube. RNase I (10 U/μl, Fermentas) was then added at 0.2 μl per tube, followed by incubation for 15 min at 37 °C, and the reaction terminated with 1% SDS (1/10 volume per tube). The digested samples were pooled and layered onto the surface of 15 ml of sucrose buffer (30% sucrose in RB buffer). The ribosomes were pelleted by ultracentrifugation at 185,000 × g for 5 h at 4 °C. RNA extraction was then performed by the Trizol method and ribosomal RNA (rRNA) depleted with a Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat) (Epicenter) by the manufacturer’s instructions. The fraction with an insertion size ~28 nt was excised and purified from a gel.
RNA-seq: The sequencing libraries were constructed following the TruSeqTM RNA Sample Preparation Guide (Illumina, San Diego, California, USA).   Briefly, the polyA+ mRNA was selected with RNA Purification Beads (Illumina).   The library was constructed by using the Illumina TruSeq RNA sample Prep Kit v2 and sequenced with an Illumina HiSeq-2000 for 50 cycles.   High quality reads that passed the Illumina quality filters were kept for sequence analysis.  Ribo-seq:RPFs were sequenced with an Illumina HiSeq-2000 sequencer for 36 or 50 cycles.

treatment_protocol: The mice in the HF and HB groups were fed a high-fat diet (45% kcal fat) for 25 weeks. Betaine was dissolved in water at a concentration of 2% w/v.

value: Liver

value: post natal week 25

tag: treatment

value: high fat diet from week 8


title: Liver_HB_rep2_RNA

data_processing:
Illumina HiSeq-2000 software used for basecalling.
For both mRNA and RPF sequencing data sets, high quality reads were mapped to the RefSeq mRNA reference sequence (mm10) through the FANSe2 algorithm, with the parameters -L80 -E5 -I0 -S14 -B1 -U0.  Reads that mapped to alternative splice variants of one gene were merged.
The mRNA and RPFs in each sample were normalized by reads per kilo base per million reads (RPKM). Differentially expressed genes (DEGs) were identified with the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

tag: age

value: high fat diet adding betaine (2percent w/v) from week 8


title: Liver_HF_rep1_Ribo

description: total Ribosome protected fiagments


title: Liver_HF_rep2_RNA


title: Liver_HB_rep2_Ribo

description: total Ribosome protected fiagments


title: Severe neutrophilic asthma [200569440013_A]

tag: disease status

value: Female


title: Liver_HF_rep1_RNA


title: Liver_HB_rep1_Ribo

description: total Ribosome protected fiagments


title: Liver_HB_rep1_RNA


title: TNBC_4

source_name: breast cancer


title: MEFs, wt_input (control for wt_h3k9 ChIP)

city: Baton Rouge

first: Joomyeong

last: Kim

state: LA

address: 202 Life Sciences Bldg

department: Biological Sciences

institute: Louisiana State University

description:
Same raw file as for wt_input (control for wt_peg3 ChIP).
Even though processed control (*_control.bigwig) files are different, the same raw input fastq file was used to generate them.

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with the following configurations: bowtie2 -p <> -x <mm10_index> input.fastq -S output.sam
Data were filtered and converted to bam using the following script: sed '/chrM/d;/random/d;/chrUn/d' $1.sam > $1_filtered.sam | samtools view -S -b $1_filtered.sam > $1.bam | samtools view -c $1.bam
Peaks were called using MACS2 with the following setting: macs2 callpeak -t treatment.bam -c input.bam -f BAM -g mm -n <output> --bdg -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using custom script
Supplementary_files_format_and_content: peak text files

source_name: Mouse Embryonic Fibroblast

growth_protocol: MEF cells extracted from age-matched 14.5 days post coitum embryos from Peg3-WT and Peg3-KO sample

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Mouse Embryonic Fibroblast (MEF)

tag: chip antibody

value: none (input)

value: wildtype


title: MEFs, ko_input (control for ko_h3k9 ChIP)

description:
Same raw file as for ko_input (control for ko_peg3 ChIP).
Even though processed control (*_control.bigwig) files are different, the same raw input fastq file was used to generate them.

value: Peg3 knockout


title: MEFs, ko_input (control for ko_peg3 ChIP)

description:
Same raw file as for ko_input (control for ko_h3k9 ChIP).
Even though processed control (*_control.bigwig) files are different, the same raw input fastq file was used to generate them.


title: MEFs, wt_input (control for wt_peg3 ChIP)

description:
Same raw file as for wt_input (control for wt_h3k9 ChIP).
Even though processed control (*_control.bigwig) files are different, the same raw input fastq file was used to generate them.


title: MEFs, ko_h3k9 ChIP

value: H3K9me3 antibody


title: MEFs, wt_h3k9 ChIP


title: TNBC_5


title: Severe paucigranulocytic asthma [200569440006_D]

value: Endobronchial biopsy

value: Severe asthma

value: Paucigranulocytic asthma

tag: gender

value: Male

tag: atopy

value: non-smoker


title: TNBC_6

value: primary tumor

value: Triple-negative breast cancer


title: Severe neutrophilic asthma [200569440006_F]

value: Neutrophilic asthma

value: atopic

tag: smoking history


title: TNBC_3


title: TNBC_2


title: TNBC_1


title: MEFs, ko_peg3 ChIP

value: PEG3 antibody


title: C. elegans linc4-2

city: Jerusalem

first: Yonatan

last: Tzur

address: Givat-Ram

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Low quality bases, poly-G, adapters, and poly-A sequences were removed with cutadapt, v2.10, with parameters -q32,32, -O 1, -m 15 and --match-read-wildcards.
Low quality reads were filtered out with fastq_quality_filter of the FASTX package, v0.0.14, with parameters -q 20 and -p 90.
Processed reads were aligned with tophat, v2.1.1, with parameters -G genes.gtf, -N 5, --read-gap-length 5, --read-edit-dist 10, --segment-length 19, --read-realign-edit-dist 3, --no-coverage-search and --library-type fr-unstranded.
Raw counts were obtained with htseq-count, v0.12.4, with parameter -s 'no'.
Normalization and differential expression were done with DESeq2, v1.22.2, with independentFiltering=F and otherwise default parameters, after removing genes with less than 10 raw counts. Significant genes were further filtered, taking ones with baseMean>5 and |log2FoldChange| > 5/sqrt(baseMean) + 0.4.
Genome_build: WBcel235
Supplementary_files_format_and_content: Excel file with the analysis results. First line is a header row, followed by data for each gene. Columns A-K have general gene details; L-Q have raw counts; R-W have normalized counts; X is the baseMean; Y-AC have the differential expression results (linc-4 / WT); AD indicates passing further filtering, 'FALSE' for non-significant, 'TRUE' for significant without passing filtering, and 'THR' for significant and passing further filtering. Missing values are marked with '?'.

organism: Caenorhabditis elegans

source_name: linc-4 Adult worms

growth_protocol: Solid media

extract_protocol:
TRIzol  + Zymo Research Direct-zol RNA miniprep plus kit
mRNA enrichment, Fragmentation, RT, second-strand cDNA synthesis, ligation of Adapters

tag: background strain


title: C. elegans linc4-1


title: C. elegans N2-3 (WT-3)

source_name: N2 Wild type Adult worms

value: Wild type


title: C. elegans N2-2 (WT-1)


title: C. elegans linc4-3


title: C. elegans N2-12 (WT-2)


title: SRN39_3_S_CTR_REP2

city: Davis

first: Dorota

last: Kawa

state: CA

address: 451 Health Sciences Dr.

department: Plant Biology and Genome Center

institute: University of California

description:
3'mRNA-Seq library
SRN39_3_S_CTR_REP2

data_processing:
Technical replicates of the libraries were pooled before reads were processed
Barcodes were trimmed from raw reads with fastx-trimmer with parameters: -v -f 12 -Q33
Adaptor trimming and quality filtering was performed with reaper from Kraken Suite  with options: -geom no-bc -tabu $tabu -3pa $seqAdapt -noqc -dust-suffix 6/ACTG -dust-suffix-late 6/ACTG -nnn-check 1/1 -qqq-check 35/10 -clean-length 30 -polya 5.
Trimmed reads were mapped to the reference genome of Sorghum bicolor BTx623 (McCormick et al., 2018) using STAR (Dobin et al., 2013) with options: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignIntronMin 20 --alignIntronMax 10000 --outFilterMismatchNmax 5 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts.
Genome_build: Sorghum bicolor v3.1.1 (https://phytozome.jgi.doe.gov/pz/portal.html)
Supplementary_files_format_and_content: Table with raw gene counts for every gene and every sample

organism: Sorghum bicolor

growth_protocol: Four day old seedlings of approximately the same radicle length were transferred to a soil plug, that is, a 50 mL falcon tube filled with sterile soil (soil collected from the Clue Field in the Netherlands; 52° 03’ 37.91’’ N and 5° 45’ 7.074’’ E, which was further dried, sieved through 4 mm mesh and sterilized by gamma irradiation) mixed with 5% sterile water (w/v). Seedlings were watered with autoclaved water every second day. On day ten, seedlings together with the soil plug were transferred to 40 cm long cones (Greenhouse Megastore, catalog number CN-SS-DP) filled with 700 mL of 0.5-1.0 mm filter sand (filcom.nl/). Plants were organized in a randomized manner in a greenhouse compartment with a temperature of 28°C during the day (11 hours) and 25°C at night (13 hours), with 70% relative humidity and light intensity of 450mmol/m2/s. At days zero, seven and 14, plants were watered with 50 mL of modified half-strength Hoagland solution with 0.05 mM KH2PO4. On days one, four, ten, 13 and 17, plants were watered with 50 mL deionized sterile water. Two and three weeks after transfer to the cones (corresponding to 28 and 35 day old plants) root material was harvested two hours after the light turned on. Each sorghum plant was gently taken from the cone and the whole root system was cleaned from the sand and soil by washing in water, dried with paper towel and snap frozen in liquid nitrogen (taking approximately 3 minutes per plant).

extract_protocol:
Root tissue was manually ground and RNA was extracted with RNaesy Plus Mini kit (Qiagen) with application of QIAshredder columns (Qiagen) and on-column Dnase I (Qiagen) treatment. Total RNA obtained was precipitated with 3M NaOAc pH 5.2 (Thermo Scientific) in 100% ethanol and washed with 70% (v/v) ethanol
RNA‑seq libraries were synthesized with QuantSeq 3’ mRNA‑Seq Library Prep Kit (Lexogen) according to manufacturer protocol.

tag: plant age

value: 35 day old

value: whole root


title: SRN39_2_S_CTR_REP4

description:
3'mRNA-Seq library
SRN39_2_S_CTR_REP4

value: 28 day old


title: SRN39_3_S_CTR_REP3

description:
3'mRNA-Seq library
SRN39_3_S_CTR_REP3


title: SRN39_3_S_CTR_REP4

description:
3'mRNA-Seq library
SRN39_3_S_CTR_REP4


title: SRN39_2_S_CTR_REP3

description:
3'mRNA-Seq library
SRN39_2_S_CTR_REP3


title: SRN39_2_S_CTR_REP2

description:
3'mRNA-Seq library
SRN39_2_S_CTR_REP2


title: SRN39_2_S_CTR_REP1

description:
3'mRNA-Seq library
SRN39_2_S_CTR_REP1


title: KI.clone.58_rep3

city: Basel

first: Anton

last: Glück

institute: Novartis Institutes for BioMedical Research

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol, using an Agilent Technologies GeneChip Scanner 3000

data_processing: MAS5 normalization to a trimmed mean of 150 (trimming off the top 2 and bottom 2 percent)

source_name: A549 KI clone 58

label_protocol: NuGEN Ovation protocol

extract_protocol: RNeasy Mini Kit (Qiagen, 74104)

value: CARD10 R587A knock-in cells


title: KI.clone.20_rep1

source_name: A549 KI clone 20


title: KI.clone.20_rep2


title: MEFs, wt_peg3 ChIP

value: Mouse Embryonic Fibroblast (MEF)

value: wildtype


title: KI.clone.58_rep1


title: KI.clone.20_rep3


title: SQR_3_S_CTR_REP3

description:
3'mRNA-Seq library
SQR_3_S_CTR_REP3

value: Shanqui Red


title: KI.clone.58_rep2


title: WT.clone.10_rep3

source_name: A549 WT clone 10

value: wild-type


title: WT.clone.11_rep2

source_name: A549 WT clone 11


title: WT.clone.11_rep1


title: SQR_3_S_CTR_REP2

description:
3'mRNA-Seq library
SQR_3_S_CTR_REP2


title: SRN39_3_S_CTR_REP1

description:
3'mRNA-Seq library
SRN39_3_S_CTR_REP1


title: SQR_2_S_CTR_REP4

description:
3'mRNA-Seq library
SQR_2_S_CTR_REP4


title: SQR_2_S_CTR_REP2

description:
3'mRNA-Seq library
SQR_2_S_CTR_REP2


title: SQR_3_S_CTR_REP1

description:
3'mRNA-Seq library
SQR_3_S_CTR_REP1


title: IPSC_LNCRNA02

city: Shreveport

first: Tarek Magdy

last: Mohamed

address: 1501 Kings Highway, BRI F3-15/22

department: Pathology

institute: LSU Health Shreveport

data_processing: Reads were mapped to the GRCh38 reference human genome using HISAT2 (Kim et al., 2019). Gene expression levels and exon usage were estimated using featureCounts function in the Subread software (Liao et al., 2013). Differential gene expression analysis was done using DEseq2 package (Love et al., 2014) and R (v3.3.3).

source_name: hiPSCs

growth_protocol: Cardiomyocytes were diffrentiated and maintained according to our establisshed protocol (Burridge et al., 2014)

extract_protocol:
RNA was extracted using TRI Reagent and Direct–zol RNA microprep kit (both Zymo) including on-column DNase digestion to remove genomic DNA. Samples were quantified using an Agilent 2100 Bioanalyzer and passed QC.
Forward stranded library preparation was done after ribosomal RNA depletion and sequencing with DNBseq platform sequencing (BGI), generating ~90 million paired-end 100 bp reads for each sample.

treatment_protocol: Day 30 hiPSC–CMs from 6 patients (3 Control and 3 S427L) were treated with 1 mM doxorubicin or vehicle for 24 h

tag: nodicr over-expression

value: NO


title: IPSC_WT02

value: YES


title: IPSC_WT01


title: WT.clone.11_rep3


title: IPSC_LNCRNA01


title: SQR_2_S_CTR_REP3

description:
3'mRNA-Seq library
SQR_2_S_CTR_REP3


title: si-DDX23#3

city: Jinan

first: Chen

last: Zhao

state: China

address: 107 Wenhua Xi Road

department: Department of Obstetrics and Gynecology

institute: Qilu Hospital, Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Raw reads were first filtered to obtain clean reads using FASTX-Toolkit
High-quality reads were mapped to the human reference genome hg19 using TopHat software with default parameters
Alignment was independently performed for reads from each sample, and reads mapping to more than three genomic sites were discarded
Based on the value of reads per kilobase per million mapped reads, gene expression levels were determined using Cufflinks software
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements

extract_protocol:
Total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovarian cancer cell

tag: sirna


title: SQR_2_S_CTR_REP1

description:
3'mRNA-Seq library
SQR_2_S_CTR_REP1


title: si-DDX23#2


title: TNBC_8

data_processing: The data was analyzed in the R prgramming environment with the RMA-algorithm of the simpleaffy package.

value: primary tumor

tag: disease state


title: si-DDX23#1

tag: cell line


title: si-NC#3

tag: cell type

value: si-NC


title: DAPT_3

city: Ann Arbor

first: Bioinformatics

last: Core

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

description:
121570
raw_counts.txt

data_processing:
Alignment with TopHat v2.0.13 and bowtie2 v2.2.1 with --b2-very-sensitive
htseq-count v0.6.1
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited text of raw counts

source_name: Mueller Glia cells

extract_protocol:
One day after treatment, retinas were isolated, dissociated, and GFP+ Muller glia purified by FACS. RNA was isolated with Trizol.
RNA libraries prepared using standard Illumina  protocols

treatment_protocol: Fish were immersed in fish water containing DMSO or DAPT

value: DAPT


title: DAPT_2

description:
121569
raw_counts.txt


title: si-NC#1


title: PBMC RV NA high 24

city: Woolloongabba

first: Gayathri

last: Thillaiyampalam

state: QLD

address: 37 Kent Street

department: UQDI

institute: University of Queensland

data_processing:
Sequence reads (fastq files) were trimmed for adapter sequences usingCutadapt (version 1.11) and aligned using STAR (version 2.5.2a) to theGRCh37 assembly with the gene, transcript, and exon features of Ensembl (release 89) gene model. Qualitycontrol metrics were computed using RNA-SeQC (version 1.1.8) and expression was estimated using RSEM (version 1.2.30)
In normalising we corrected for library size by dividing each samples gene count by million reads mapped.This procedure is a common approach known as counts per million (CPM). We further corrected for differencesin RNA composition using a method proposed by Robinson and Oshlack (2010a) called trimmed mean of M-values (TMM). We used the function calcNormFactors()from the edgeR package to obtain TMM factors and used these to correct for differences in RNA composition.
Genes with less than 2 CPM were filtered out.
Function glmQLFit() from edgeR package fits a quasi-likelihood negative binomial generalised log-linear model to count data to identify differentially expressed genes. Significant genes were filtered with multiple testing corrected false discovery rate (FDR) < 0.05 and log fold-change > 1.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts, normalised counts matrix

source_name: PBMC

growth_protocol: Primary PBMC were isolated from whole blood and cultured for 24h

extract_protocol: Truseq mRNA kit

treatment_protocol: Rhinovirus stimulated cells were cultured with RV16 for 24h and unstimulated with media

value: Peripheral blood morphonuclear cell

tag: culture

value: rhinovirus stimulated

tag: asthma status

value: No

tag: ifn-α producer

value: high


title: DAPT_1

description:
121568
raw_counts.txt

growth_protocol: Zebrafish were maintained in aquaria at 28 degrees centrigrade

tag: treatment


title: si-NC#2


title: EGFP::ASH1DBAH mutAT1 Rep 1

city: Berlin

first: Leonie

last: Ringrose

address: Philippstr. 13

department: IRI Lifesciences

institute: Humboldt University Berlin

data_processing:
Base calling was done following the HiSeq2000 instrument manufacturer's base calling software.
Reads were aligned against the Drosophila melanogaster reference genome (UCSC dm3 release) using TopHat version 2.0.9
After alignment reads were associated with known genes based on annotations derived from UCSC and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.0.1, Bioconductor version 2.12)
For statistical testing data were log transformed using voom approach in the limma package.
Genome_build: UCSC dm3 release
Supplementary_files_format_and_content: tab delimited text file including count values for each sample

organism: Drosophila melanogaster

source_name: wing disc

growth_protocol: Larvae raised at 25 degrees.

extract_protocol:
Total RNA was extracted from dissected 3rd instar larval wing discs using Trizol Reagent (Ambion). RNA was additionally treated with DNase (Turbo DNase, Ambion). cDNA was synthesized using the SuperScript II kit (Invitrogen) according to the manufacturer's instructions. Priming was performed with equal amounts of oligo(dT) and random decamer primers (Ambion). RNA was removed by treatment with RNase H (NEB) before PCR analysis or mRNA purification and sequencing.
mRNA was purified from total RNA using Oligo (dT)25 Dynabeads (Invitrogen), fragmented by heat treatment and converted to cDNA using Superscript III (Invitrogen). Sequencing libraries were prepared with the KAPA Library Preparation Kit Illumina series (KK8201). Libraries were sequenced on an Illumina HiSeq 2000.

tag: genotype

value: w[1118]; P{pTub - EGFP::ASH1 DBAH mut AT1, w+}; ash1[10]/ash1[22]

tag: internal sample id


title: DMSO_3

description:
121567
raw_counts.txt

value: DMSO


title: EGFP::ASH1DBAH mutAT1 Rep 2


title: EGFP::ASH1DBAH Rep 3


title: EGFP::ASH1DBAH mutAT1 Rep 3


title: WT.clone.15_rep3

source_name: A549 WT clone 15


title: WT.clone.10_rep1


title: DMSO_2

description:
121566
raw_counts.txt


title: WT.clone.15_rep1


title: EGFP::ASH1DBAH Rep 2


title: EGFP::ASH1DBAH Rep 1


title: WT.clone.10_rep2


title: EGFP::ASH1 WT Rep 3


title: PBMC unst NA high 24

value: Unstimulated


title: DMSO_1

description:
121565
raw_counts.txt


title: uninj_DMSO_MG_3

data_processing:
Adapter trimming with Trim Galore v0.4.5 and cutadapt v1.15
Alignment with bowtie2 v2.3.4.1 with -X 2000 --no-mixed --no-discordant
Deduplicate with picard v2.20.2
Filter alignments for MAPQ > 10
Peak calling with macs2 v2.1.2 with -f BAM --nomodel --shift -100 --extsize 200
Genome_build: danRer11
Supplementary_files_format_and_content: narrowPeak peak calls

growth_protocol: gfap:GFP transgenic zebrafish were maintained in aquaria at 28 degrees centrigrade

extract_protocol:
One day after treatment, retinas were isolated, dissociated, and GFP+ Muller glia purified by FACS.  Nuclei were isolated for ATACseq analysis.
ATACseq libraries prepared according to Buenrostro et al., Curr. Protoc. Mol. Biol. 109:21.29-1-21.29.9, 2015.

treatment_protocol: Fish were immersed in fish water containing either DMSO or DAPT


title: PBMC RV NA low 22

value: low


title: PBMC unst NA low 22


title: WT.clone.15_rep2


title: EGFP::ASH1 WT Rep 1


title: WT Rep 3


title: PBMC RV NA low 23


title: EGFP::ASH1 WT Rep 2


title: uninj_DMSO_MG_1


title: WT Rep 2


title: WT Rep 1


title: uninj_DAPT_MG_2


title: PBMC RV NA high 20


title: PBMC unst NA high 21


title: uninj_MG_3

extract_protocol:
Two days post injury, control uninjured and injured retinas were isolated, dissociated, and GFP+ Muller glia purified by FACS. Nuclei were isolated for ATACseq analysis.
ATACseq libraries prepared according to Buenrostro et al., Curr. Protoc. Mol. Biol. 109:21.29-1-21.29.9, 2015.

treatment_protocol: gfap:GFP transgenic zebrafish retinas were either left uninjured (control) or received 8 needle poke injuries (experimental).

value: uninjured

tag: day


title: uninj_DAPT_MG_3


title: PBMC unst NA low 23


title: PDX E39 m 3 (Niraparib)

city: San Francisoc

first: Mehdi

last: Nosrati

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

data_processing:
All single-cell libraries were pseudo-aligned to the human Ensembl version 72 transcriptome using the Kallisto through AltAnalyze version 2.1.3. as described in our previous publication [40]. To ensure quality control, libraries with less than 300,000 paired-end reads or estimated read percentage alignment <20% were excluded. Unsupervised population discovery was performed using the software ICGS version 2 (Venkatasubramanian et al. 2019, bioRxiv) and PCA-loading gene analysis and HOPACH clustering in AltAnalyze. PCA-loading genes were selected as the top-100 correlated and top-100 anti-correlated genes associated with the first 4 principal components. Initial identified predominant gene clusters from the PCA-loading analysis were excluded prior to ICGS2, by identifying genes correlated to the centroid of the gene clusters with a Pearson rho > 0.1 (21,719 genes remaining after exclusion). ICGS2 was run using the default program parameters. To expand the cell-cluster identified from the ICGS2 analysis of SJIA with donor BM macrophages, an aggerate score (sum of the TRIM8 cluster maker genes), was used to identify additional SJIA patient cells (n=12, total) enriched in TRIM8-associated genes prior to differential expression analyses. For the identification of TRIM8-cluster specific genes, we applied empirical Bayes moderated (eBayes) t-test comparing TRIM8-cluster SJIA cells to all donor macrophage cells (AltAnalyze). Only genes with a minimum average TPM >1 in the two compared populations, eBayes t-test p<0.05 (following Benjamini-Hochberg correction) and fold > 1.5 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file

source_name: PDX melanoma tumor

extract_protocol: Total RNA was extracted from PDX tumor tissues using the RNeasy tissue kit (Qiagen) after tissue disruption using ruptor disposable probes and the concentration measured by Qubit RNA HS Assay Kit (ThermoFisher Scientific)

value: metastatic melanoma

tag: tissue

value: PDX melanoma tumor

value: Niraparib


title: PBMC RV NA high 21


title: PBMC unst NA low 19


title: PBMC RV NA low 19


title: PDX E39 m 12 (Niraparib)


title: PBMC RV NA high 18


title: PDX E39 m 24 (Vehicle)

value: Vehicle


title: PDX E39 m 21 (Vehicle)


title: inj_4dpi_MG_3

value: injured


title: PBMC RV NA high 17


title: uninj_MG_1


title: PDX E39 m 7 (Vehicle)


title: TNBC_13

city: Halle (Saale)

first: Martina

last: Vetter

address: Ernst-Grube-Str. 40

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy FFPE Kit - Qiagen)

value: primary tumor

value: Triple-negative breast cancer


title: Healthy control [200598770001_D]

city: New Lambton Heights

first: Stephany

last: Sanchez

address: Lot 1 Kookaburra Circuit

institute: University of Newcastle

data_processing: Array raw data were processed using GenomeStudio software, Illumina and analysed using GeneSpring GX14.9.1, Agilent Technologies. Sample and gene profiling results were included in the analysis if the sample was successfully amplified (sufficient cRNA generated) and hybridized (95th percentile of fluorescence score>500) and the data passed quality control criteria in GeneSpring GX (principle component analysis plots). Data was log2‐transformed and quantile‐normalised.

source_name: endobronchial biopsy

value: Endobronchial biopsy

tag: disease status

value: healthy

tag: inflammatory phenotype

value: Healthy control

tag: age

tag: gender

value: Female

tag: atopy

value: non-atopic

value: non-smoker

tag: packyear

tag: acqmean


title: inj_4dpi_MG_2


title: PBMC unst NA high 17

value: Peripheral blood morphonuclear cell

value: No

value: high


title: uninj_DAPT_MG_1

value: DAPT


title: SKNO1-siAE

city: Shenzhen

first: De

middle: sheng

last: Gong

address: Xueyuan AVE 1098, Nanshan District

department: Department of Hematology and Oncology, International Cancer Center

institute: Shenzhen University General Hospital

data_processing:
Raw sequence reads were filtered to remove adaptor (cutadapt-1.4.2) contamination and poor-quality reads.
Clean sequences were mapped to human genome using BSMAP v2.73 (Parameters：-v 0.1 -g 1 -p 8 -R -u).
Finally, the unique aligned sequence was applied for the subsequent methylation analysis.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include methylated values for each Sample

source_name: Acute myeloid leukemia cell line

growth_protocol: The SKNO-1, SKNO1-siAE cell lines were maintained in RPMI 1640 medium supplemented with 10% fetal calf serum (Hyclone, Logan, UT, USA), penicillin (107 U/L) and streptomycin (10 mg/L) at 37°C in a 5% CO2 atmosphere.

extract_protocol:
Genomic DNA isolation from the cell lines was performed using the Wizard® Genomic DNA Puriﬁcation Kit (Promega Corp., Madison, WI, USA).
Bisulfite DNA conversion was performed using the Epi-Tect-Bisulﬁte Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: SKNO-1 cells infected with the pRRLcPPT.hPGK, a lentiviral vector encoding the previously described 12siAGF1 oligonucleotides, which were designed against the AML1-ETO mRNA fusion site, allowing the silencing of AML1-ETO in SKNO-1 cells12, 13 to produce the SKNO1-siAE cell lines.

tag: cell line


title: PBMC RV NA low 16

tag: cell type

value: rhinovirus stimulated

value: low


title: SKNO-1


title: PDX E39 m 1 (Niraparib)

tag: disease state

value: metastatic melanoma

value: PDX melanoma tumor

value: Niraparib


title: MPP_TFEB_2

city: Toronto

first: Laura

last: Garcia Prat

address: 101 College street

department: Princess Margaret Cancer Centre

institute: University Health Network

data_processing:
Equimolar quantities of libraries were pooled and sequenced with 4 cDNA libraries per lane on a High Throughput Run Mode Flowcell with v4 sequencing chemistry on the Illumina 30 HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length to reach depth of 55-75 million reads per sample
Reads were then aligned with STAR v2.5.2b(49) against hg38 and annotated with ensembl v90. Default parameters were used except for the following: chimSegmentMin 12; chimJunctionOverhangMin 12; alignSJDBoverhangMin 10; alignMatesGapMax 100000; alignIntronMax 100000; chimSegmentReadGapMax parameter 3; alignSJstitchMismatchNmax 5 -1 5 5.
Read counts were generated using HTSeq v0.7.2(50) and general statistics were obtained from picard v2.6.0.

source_name: Cord blood

growth_protocol: In vitro culture in X-Vivo 10, 1% BSA, L-Glutamine, Pen/Strep and cytokines SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL7 (IL-7; 10 ng/ml)

extract_protocol:
PicoPure RNA Isolation Kit (Thermo Fisher)
cDNA conversion was performed using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara) and libraries were prepared using Nextera XT DNA Library Preparation Kit (Illumina)
4 libraries were sequenced/lane on a HiSeq 2500 following manufacturer’s protocol generating paired-end reads of 125-bp in length

treatment_protocol: Lentiviral transduction, cells collected 3 days after transduction (4 days after sorting)

tag: group

value: TFEBWT

value: Short-term hematopoietic stem cells (ST-HSC)

value: 3 days post- transduction

tag: genotype/variation

value: TFEB overexpression


title: MPP_TFEB_1

tag: treatment


title: uninj_MG_2

value: uninjured


title: MPP_GP91_2

value: CTRL

value: GP91 overexpression (control)


title: PBMC unst A low 15

tag: culture

value: Unstimulated

tag: asthma status

value: Asthma

tag: ifn-α producer


title: PBMC unst NA low 16

value: Peripheral blood morphonuclear cell

value: No


title: inj_4dpi_MG_1

value: injured

tag: day


title: PBMC unst NA high 18

value: high


title: PBMC RV A low 15

value: rhinovirus stimulated

value: low


title: PBMC unst A low 14