title: small RNA-seq of total rep2

city: Wuhan

first: Yu

last: Zhou

state: Hubei

address: Luojia Hill

department: College of Life Sciences

country: China

institute: Wuhan University

data_processing:
Reads of small RNA-seq were trimmed using the cutadapt program and then mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)meters -n 0 -l 20 -k 1 -best. Reads counts of mature miRNAs were calculated using featureCounts program (Liao et al., 2014)fracOverlap 0.8 --fracOverlapFeature 0.8 -s 1 -M. The enrichment of miRNAs from RIP over input or pellet over total lysate were calculated with edgeR package (Robinson et al., 2010). We defRNAs as CPM >50, log2 fold-change >0.5 and p-value < 0.05. The motif analysis was per “clean” data for the following analysis.Reads were firstly mapped using Bowtie2 (Langmead and Salzberg, 2012) against repetitive elements derived from RepBase (version 23.09) (Bao et al., 2015), and also tRNA and rRNA ,which were derived from tRNAscan database (Lowe and Chan, 2016) and NCBI, respectively. Reads that were not mapped to those sequences were aligned to genome sequence using STAR (Dobin et al., 2013) with parameters --outFilterMultimapNmax 5 --outSAMmultNmax 1 --alignEndsType Local --alignIntronMax 1. For mapped reads with the same genomic position and same barcode, only one was retained to avoid PCR products. For processing RNA-seq data, reads counts of genes were calculated with featureCounts program. Differential expression was calculated using edgeR, in which we used a RPKM cutoff of 1, a log2 fold-change cutoff of 0.5 and a p-value cutoff of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for normalized coverage in genome. For paired-end RNA-seq data, we used only Read 2 to generate the bigWig file.

source_name: small RNA-seq of total

growth_protocol: N2a cells were cultured in DMEM (Gibco) medium supplemented with 10% FBS at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted by TRIZOL reagent.
For RIP-seq, N2a cells cultured in a 150 mm plate were washed twice with cold PBS followed by UV irradiation at 400mJ/cm2 under a HL-2000Hybrilinker. Scrapped cells were harvested by centrifugation at 500 g for 5 min at 4°C. Crosslinked cells were lysed in 1 ml lysis buffer (20mM Tris-Hcl pH 7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 0.1% SDS, 0.1% deoxycholate, 100U/ml RNasin Ribonuclease Inhibitors (Promega), 1 u/ml EDTA-free complete protease inhibitor cocktail (Roche)) on ice for 30 min. Lysates were centrifuged at 12,000 g at 4°C for 15 min to remove cell debris. An input of collected supernatant was set aside for subsequent analysis. Each sample was then divided and incubated with 5 μg of either anti-TDP-43 antibody (Proteintech) or rabbit IgG (Millipore) on a rotator overnight at 4°C. Complexes were pulled down by incubation with protein G Dynabeads on a rotator for 2 hours at 4°C. Beads were washed twice with lysis buffer, twice with wash buffer (add 300 mM NaCl), and boiled to reverse UV cross-linking. Co-precipitated RNAs were extracted from beads and used for construction of small RNA library or analysis by quantitative RT-PCR (qRT-PCR) using specific primers.To isolate cellular insoluble aggregates, two 10-cm dish N2a cells were extracted sequentially, as previously described (Guo et al., 2011; Hu et al., 2017). Briefly, cells were harvested, lysed in the moderate RIPA lysis buffer (50mM Tris (pH 7.4), 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, EDTA-free complete protease inhibitor cocktail (Roche), 100U/ml RNasin Ribonuclease Inhibitors (Promega)) on ice for 30 min, and centrifuged at 17000 g at 4°C for 30 min. The bottom cell debris (i.e. nuclear, mitochondria and stress granules) were depleted. The resultant supernatant fractions were incubated with 1% Sarkosyl for 30 min at room temperature with agitation, and then the detergent insoluble proteins were obtained by ultracentrifugation of the supernatants at 41600 rpm at 4°C for 30 min and washed twice by PBS buffer. The whole cell lysates and the detergent-insoluble pellets were separately collected, and the isolated protein and RNA were used for Western blotting analysis and small RNA-seq library construction.The small RNA library was constructed using sensitivity-improved method as described (Yang et al., 2016) or modifications. Briefly, isolated total RNA (~1 μg) was mixed with 25 pmol 3′ adapter, 1 × T4 ligase reaction buffer, 33% polyethylene glycol (molecular weight 8000), 40 U RNL2tr K227Q (NEB), and 20 U RiboLock RNase Inhibitor (Thermo Fisher). The samples were incubated at 22°C for 2 hours, then at 16°C for 1 hour, followed by addition of 1 μl of 10 μM RT primer before heat inactivation at 75°C for 5 min. 200 pmol of the 5′ adapter was added for ligation by T4 RNA ligase 1 (NEB) and incubated at 22°C for 1 hour. Linker-ligated RNAs were reverse transcribed with Superscript III (Invitrogen) at 50°C for 30 min, 55°C for 30 min, then at 95°C for 5 min and PCR-amplified with Q5 High-Fidelity 2× Master (NEB). The product was fractionated on a 4% agarose gel and extracted by QIAEX II Gel Extraction Kit (QIAGEN). The recovered DNA was quantified for deep sequencing.

treatment_protocol: All expression plasmids were cloned into pCMV-myc with PCR amplified sequences by using specific primers. Plasmids and siRNAs or miRNA mimics/inhibitors were respectively transfected into cells with Lipofectamine 2000 and RNAi Max (Invitrogen) according to the manufacturer’s protocols. Cells were harvested 36–48 hours post-transfection for subsequent analysis. For double transfection, cells were first transfected with siRNA for 12 h and then with plasmid for another 24-36 h.

value: N2A neuroblastoma cell line

tag: treatment


title: small RNA-seq of pellet rep1

status: Public on Oct 12 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: small RNA-seq of pellet

tag: cell line


title: small RNA-seq of pellet rep2


title: OB_15_0068_2

city: San Diego

first: Zhengyan

last: Kan

state: CA

address: 10770 Science Center Drive

department: Computational Biology, Oncology Research & Development

country: USA

institute: Pfizer

data_processing:
RNA-Seq data was analyzed using the RSEM42 pipeline with hg19 as the genome reference
Genome_build: hg19
Supplementary_files_format_and_content: expression matrix with gene expression by samples in TPM units

organism: Homo sapiens

source_name: Primary Tumor

extract_protocol: For RNA-Seq, sequencing libraries were prepared using TruSeq RNA Sample Preparation kit v2 (RS-122-2001 and RS-122-2002, Illumina). Sequencing of the RNA libraries was performed on an Illumina HiSeq2500 in 100-bp paired-end mode of the TruSeq Rapid PE Cluster kit and the TruSeq Rapid SBS kit.

tag: gender

value: Female

tag: age

value: Premenopausal

value: No

value: Invasive ductal carcinoma

value: AC+T

value: Negative

tag: bilaterality

tag: multiplicity

value: Basal

value: TN

tag: time


title: small RNA-seq of TDP-43-RIP rep2

source_name: small RNA-seq of TDP-43-RIP

tag: genotype/variation

value: WT

tag: rip antibody


title: OB_15_0190_2

value: Yes

value: Not Detected

value: Normal


title: OB_15_0190_1


title: small RNA-seq of TDP-43-RIP rep1


title: OB_15_0181_1

value: AC+T+Trastuzumab

value: Positive

value: LumA


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B1_ad002

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snm3C-seq
Reads were trimed with Cutadapt for adapters and low-quality bases (Phred score >= 20)
The trimmed fastq files were mapped to in-silico bisulfite converted mm10 reference genome using Bismark with bowtie1
The umapped reads were split into the first 40bp, middle segment, and the final 40bp, and split reads were mapped to the reference genome using Bismark with bowtie1
The BAM files were filtered using Samtools by MAPQ > 10 and PCR duplicates were removed using Picard
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls were generated with in-house developed package with the filtered BAM files
Two ends of reads from separated BAM files were paired, and chromosome contacts were extracted with in-house pipeline
Genome_build: mm10
Supplementary_files_format_and_content: ALLC files: tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column; HIC files: The single cell contact file contains eight columns, corresponding to the short format for Juicer tools pre (https://github.com/aidenlab/juicer/wiki/Pre). Specifically, each row represents a contact, including the columns of read1_strand, read1_chromosome, read1_position, read1_fragment, read2_strand, read2_chromosome, read2_position, read2_fragment. We did not use the information of restriction fragment, so read1_fragment and read2_fragment were set to be 0 and 1, respectively. The contact files for single cells could be merged by “sort -m -k2,2 -k6,6” to generate the contact file of a cell type, which could be used as the input to Juicer tools pre to generate .hic file of the cell type.

molecule: genomic DNA

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Lee, Dong-Sung, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, et al. 2019. “Simultaneous Profiling of 3D Genome Structure and DNA Methylation in Single Human Cells.” Nature Methods 16 (10): 999–1006.

tag: brain region

value: Hippocampus

tag: Sex

value: male

tag: strain


title: small RNA-seq of total rep1

value: N2A neuroblastoma cell line


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad006


title: OB_15_0157_3

value: Female

value: Premenopausal

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B11_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B11_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B12_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B11_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B11_ad002


title: small RNA-seq of Input rep2

source_name: small RNA-seq of Input


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad010


title: small RNA-seq of Input rep1


title: OB_15_0157_1

value: No

value: Invasive ductal carcinoma

value: AC+T


title: OB_15_0139_2

value: Negative

value: Basal

value: TN


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad004


title: OB_15_0139_3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B11_ad006


title: OB_15_0139_1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad002


title: Gut_E13.5_rep2

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Embryonic gut excluding the stomach was dissected.

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Clariom S type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: gut tissue_without stomach_E13.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA extraction was performed in accordance with the manufacturer’s instructions (Thermo Fisher Scientific, Waltham, USA).

treatment_protocol: Embryonic regions of interest were dissected in 1XPBS at 4°C and collected in 1mL of TRIzol reagent (Thermo Fisher Scientific, Waltham, USA).

tag: developmental stage

tag: genotype

value: wiltype

tag: tissue

value: embryonic tissue


title: Gut_E13.5_rep3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad007


title: OB_15_0107_3

value: Yes

value: Detected

value: Not Detected


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad007

value: Hippocampus


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad006

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad004


title: OB_15_0107_2

value: Positive


title: OB_15_0119_1

value: Female


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad001


title: OB_15_0080_2

value: Postmenopausal

value: LumB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A9_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad007


title: OB_15_0074_1

value: Premenopausal

value: No

value: Invasive carcinoma with lobular feature

value: ER+


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad010


title: MOLM_DMSO_RNA-seq

city: Cambridge

first: Muxin

last: Gu

email: muxingu@gmail.com, mg445@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre, Puddicombe Way

department: Haematology

country: United Kingdom

institute: University of Cambridge

description:
control sample
The A and B broadPeak files are obtained from WT_CLICK_A vs this sample and WT_CLICK_B vs this sample, respectively.

data_processing:
RNAseq data were mapped to the human genome assembly GRCh38 by STAR 2.7.1b,(3) using arguments “--outSAMunmapped Within KeepPairs --outFilterIntronMotifs RemoveNoncanonicalUnannotated   --chimSegmentMin 0   --chimJunctionOverhangMin 20”.
BigWig files were produced by deepTools 3.3.2 bamCoverage using RPKM normalization.
Exonic reads were removed using the intersect function in Bedtools v2.29.0, using exon regions derived from the Ensembl GRCh38 Version 93.
Reads on the forward strand were extracted using Samtools 1.9, with “view -f 128 -F 16” and “-f 80” and merged into one file. Reads on the reverse strand were extracted using “view -f 144” and “-f 64 -F 16” and merged.
Broad peaks were called by MACS2 2.1.4, using WT as treatment and METTL16/METTL3 as control, with arguments “callpeak --broad --extsize=300 --keep-dup 20 --nomodel -g hs --broad-cutoff 0.9 --max-gap 500”.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files for genomic tracks, text files for MACS2 peaks

source_name: Acute Myeloid Leukemia

growth_protocol: MOLM13 cells were cultured in RPMI1640 (Gibco) supplemented with 10% v/v FBS and 1% v/v penicillin/streptomycin/glutamine. 293T cells were cultured in DMEM (Gibco) supplemented with 10% v/v FBS and 1% v/v penicillin/streptomycin/glutamine.

extract_protocol:
Total RNA was extracted from pelleted cells using RNAeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNAseq data from all experiments were generated as the 75 bp paired-end Illumina reads.

treatment_protocol: MOLM-13 cells were transfected using Lipofectamine 2000 reagent (Invitrogen) according to the manufacturer’s instructions using PLKO-TETon-Puro lentiviral vectors expressing shRNAs against the coding sequence of human METTL3, METTL16 or a scrambled control. 24 h after spinfection, the cells were replated in fresh medium containing 1 μg ml−1 of puromycin and kept in selection medium for 7 days. Anti-METTL3 and scrambled shRNAs were induced by treating the cells with 200 ng mL-1 tetracycline for 3 days, anti-METTL16 – by identical treatment for 2 days. gRNA assays were performed using dual gRNA vectors as reported previously. Viral supernatants were collected 48h after transfection. All transfections and viral collections were performed in 15-cm plates was performed as mentioned below. For virus production, 5 μg of the above plasmids and 5 μg psi-Eco packaging vector were transfected dropwise into the 293T cells using 47.5μL TransIT LT1 (Mirus) and 600μL Opti-MEM (Invitrogen). The resulting viral supernatant was harvested and transduction of cells was performed in 6-well plates. After transduction, transduced cells were sorted for BFP (for gRNA).

tag: cell type

value: Acute Myeloid Leukemia

value: DMSO


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad012


title: Vagal NCCs_E8.75_rep2

description: Tissue region at the level of the first to seventh somite was dissected.

source_name: tissue region containing vagal NCCs_E8.75

value: wiltype


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-B10_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad001


title: Vagal NCCs_E8.75_rep1

value: embryonic tissue


title: Gut_E13.5_rep1


title: Vagal NCCs_E8.75_rep3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A7_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A8_ad008


title: control virus transduced CB rep2

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo Sapiens, Ensembl GRCh38 Patches Skipped
Supplementary_files_format_and_content: tab-delimited, raw counts

source_name: control virus transduced CB

growth_protocol: CB CD34+ cells were thawed and plated in X-VIVO 10 supplemented with 1% FBS, 100U/ml Penicillin/Streptomycin, 2mM L-Glutamine in the presence of 100ng/mL SCF, 100ng/mL Flt3-L and 15ng/mL TPO (maintenance medium). Lentiviral suspension was added to the cultures at a multiplicity of infection (MOI) of 1-10.

extract_protocol:
Total RNA was extracted from sorted cells using RNeasy mini kit (Qiagen). Extracted RNA was processed in order to produce Illumina sequencing libraries.
TruSeq RNA stranded; PolyA, TruSeq RNA Kit

value: CD34+ Cord Blood HSPCs

tag: viral transduction

value: control virus transduced CB


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A7_ad007


title: BRAF-V600E virus transduced CB rep2

source_name: BRAF-V600E virus transduced CB

value: BRAF-V600E virus transduced CB


title: Vagal NCCs_E9.5_rep1

source_name: tissue region containing vagal NCCs_E9.5


title: control virus transduced CB rep3


title: SAMPLE 24_wait-list T2

city: Nijmegen

first: Ivana

last: Buric

address: Montessorilaan 3

country: Netherlands

institute: Donders Institute for Brain, Cognition and Behaviour, Raboud University

data_processing: CFX manager generated raw data that was exported into 'non_normalized.txt' for the analyses

label: SYBR green

source_name: wait-list T2

label_protocol: RNA was then converted to fluorescent cRNA for hybridization to IL-1 signaling pathway plate H96 (Bio-Rad Labs Ltd, UK) with theromocycling.

growth_protocol: Venipuncture samples were collected into 10ml  EDTA tubes, lysed and frozen at -80°C until extraction

extract_protocol: Peripheral blood mononuclear cells were isolated by density gradient centrifugation. Ribonucleic acid (RNA) was extracted (QiaAmp RNA Blood Mini kit; Qiagen) and tested for suitable mass and integrity (NanoDrop One, Acclaro Sample Intelligence; Thermo  Scientific).

treatment_protocol: lysis

tag: participant id

tag: sample group

value: Control post-intervention

value: whole blood

value: peripheral blood mononuclear cells


title: Vagal NCCs_E9.5_rep2


title: Vagal NCCs_E9.5_rep3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad001

value: Hippocampus

value: male


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A7_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad002


title: SAMPLE 23_wait-list T2


title: control virus transduced CB rep1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad008


title: SAMPLE 22_wait-list T2


title: SAMPLE 21_wait-list T2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad004


title: BRAF-V600E virus transduced CB rep1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A7_ad004


title: SAMPLE 20_wait-list T2


title: SAMPLE 19_yoga T2

source_name: yoga T2

value: yoga post-intervention


title: BRAF-V600E virus transduced CB rep3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A6_ad007


title: SAMPLE 18_yoga T2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad001


title: SAMPLE 17_yoga T2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A5_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A4_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A4_ad010


title: SAMPLE 16_yoga T2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A4_ad004


title: 27_4

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

description:
IMS-M2 cells cultured without FA treated with OTX
LRPT20

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie2 v2.2.6
Peaks were called using MACS2
RPGC normalized bigwig files were generated using Deeptools 3.1.2
Genome_build: hg19
Supplementary_files_format_and_content: RPGC normalized bigwig files were generated using Deeptools 3.1.2, reads were elongated to 150bp

extract_protocol:
Cells were fixed in 1% formaldehyde, chromatine was sonicated using a Bioruptor Pico
Libraries were constructed using a custom protocol and NEXTFLEX adapters and barcodes

tag: cell line

value: hematopoietic cells

tag: disease state

value: AML

tag: treatment

value: ChIP using anti-H3K27me3 antibody (Diagenode, C15410069)


title: 27_6

description:
U937 cells cultured with FA treated with OTX
LRPT22


title: 27_5

description:
U937 cells cultured with FA treated with DMSO
LRPT21


title: 27_3

description:
IMS-M2 cells cultured without FA treated with DMSO
LRPT19


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad010

tag: age


title: 27_8

description:
U937 cells cultured without FA treated with OTX
LRPT24


title: SAMPLE 14_mindfulness T2

source_name: mindfulness T2

value: mindfulness post-intervention


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A4_ad007


title: 27_2

description:
IMS-M2 cells cultured with FA treated with OTX
LRPT18


title: SAMPLE 13_mindfulness T2


title: 27_1

description:
IMS-M2 cells cultured with FA treated with DMSO
LRPT17


title: 27_7

description:
U937 cells cultured without FA treated with DMSO
LRPT23


title: SAMPLE 12_wait-list T1

source_name: wait-list T1

value: Control pre-intervention


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad007


title: 9_8

description:
U937 cells cultured without FA treated with OTX
LRPT16

value: ChIP using anti-H3K9me2 antibody (Diagenode, C15200154)


title: SAMPLE 11_wait-list T1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A4_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad004


title: 9_7

description:
U937 cells cultured without FA treated with DMSO
LRPT15


title: SAMPLE 10_wait-list T1


title: SAMPLE 15_mindfulness T2


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad002


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A2_ad010


title: 9_6

description:
U937 cells cultured with FA treated with OTX
LRPT14


title: SAMPLE 9_wait-list T1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A2_ad006


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A2_ad008


title: 9_5

description:
U937 cells cultured with FA treated with DMSO
LRPT13


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A3_ad008


title: SAMPLE 7_yoga T1

source_name: yoga T1

value: yoga pre-intervention


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A2_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A2_ad002


title: 9_3

description:
IMS-M2 cells cultured without FA treated with DMSO
LRPT11


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad012


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad012


title: SAMPLE 6_yoga T1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad002


title: SAMPLE 5_yoga T1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad006


title: 9_1

description:
IMS-M2 cells cultured with FA treated with DMSO
LRPT9


title: SAMPLE 4_yoga T1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad002


title: I_8

description:
U937 cells cultured without FA treated with OTX
LRPT8

value: sonicated Input chromatin


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad010


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A1_ad007


title: SAMPLE 3_mindfulness T1

source_name: mindfulness T1

value: mindfulness pre-intervention


title: SAMPLE 8_wait-list T1


title: I_7

description:
U937 cells cultured without FA treated with DMSO
LRPT7


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad007


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad008


title: 9_4

description:
IMS-M2 cells cultured without FA treated with OTX
LRPT12


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A11_ad012


title: I_6

description:
U937 cells cultured with FA treated with OTX
LRPT6


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad006


title: SAMPLE 1_mindfulness T1


title: CWRU004275

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix in CSV format containing raw read counts

molecule: polyA RNA

source_name: Treatment: oxLDL, Donor: N058, Time: 24hrs

growth_protocol: in vivo

extract_protocol:
RNA was extracted from PBMCs using Rneasy Plus Micro Kit from QIAGEN
RNA libraries were prepared for sequencing using the Nextera XT Library Prep Kit and Nextera XT Index Kit v2 Set A.

value: CD8 T cells

value: oxLDL

tag: donor


title: I_5

description:
U937 cells cultured with FA treated with DMSO
LRPT5


title: 9_2

description:
IMS-M2 cells cultured with FA treated with OTX
LRPT10


title: I_4

description:
IMS-M2 cells cultured without FA treated with OTX
LRPT4


title: CWRU004274

source_name: Treatment: IL15, Donor: N058, Time: 24hrs


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A11_ad010


title: I_3

description:
IMS-M2 cells cultured without FA treated with DMSO
LRPT3


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A11_ad008


title: CWRU004272

source_name: Treatment: CD3.CD28, Donor: N058, Time: 24hrs


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A11_ad001

source_name: C57BL/6J Male P56 Mouse Brain


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad004


title: SAMPLE 2_mindfulness T1


title: CWRU004273

source_name: Treatment: CD2, Donor: N058, Time: 24hrs


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad008


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad007


title: CWRU004271

source_name: Treatment: Medium, Donor: N058, Time: 24hrs

value: Medium


title: I_1

description:
IMS-M2 cells cultured with FA treated with DMSO
LRPT1


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A12_ad001


title: I_2

description:
IMS-M2 cells cultured with FA treated with OTX
LRPT2


title: CWRU004270

source_name: Treatment: oxLDL, Donor: N058, Time: 6hrs


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A11_ad004


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad001


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad010


title: CWRU004268

source_name: Treatment: CD2, Donor: N058, Time: 6hrs


title: m6A_MOLM13_WT_C

data_processing:
Library strategy: miCLIP
M6A sites were analysed by first mapping Reads from the miCLIP experiments to the GRCh38 assembly using STAR 2.7.1a with arguments “--outFilterMismatchNoverReadLmax 0.05 --alignIntronMax 0”.
Forward and reverse genomic-coverage tracks were subsequently produced by the bamCoverage function in deepTools 3.3.2 with arguments “--normalizeUsing None –filterRNAstrand forward” and “--normalizeUsing None –filterRNAstrand reverse” respectively.
BigWig files were produced by deepTools 3.3.2 bamCoverage without normalization.
genome build: GRCh41
bigwig files for genomic tracks

source_name: Acute Myeloid Leukemia

extract_protocol: Total RNA was isolated from MOLM-13 eight days after doxycycline administration using the RNAeasy midi kit (Qiagen). Successively polyA enriched RNA was purified from 300 μg total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). 500 ng of polyA+ purified RNA were used for each immunoprecipitation reaction. m6A RNA immunoprecipitation was performed using the Magna MeRIP m6A kit (Millipore) according to the manufacturer’s instructions.

value: Acute Myeloid Leukemia


title: Duo_r1_InDrop

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

institute: Vanderbilt University Medical Center

data_processing:
[10x]  The sequencing output FASTQs were processed with CellRanger 3.0.2 and aligned to the reference transcriptome (intron+exon)
[inDrop]  For inDrop, reads were filtered, sorted by their designated barcode, and aligned to the reference transcriptome (intron + exon) using DropEST pipeline (STAR). Mapped reads were quantified into UMI-filtered counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: matrix (inDrop): contains a gene-barcode-count matrix
Supplementary_files_format_and_content: matrix (10x): contains a raw count matrix
Supplementary_files_format_and_content: features (10x): contains a list of detected genes with Ensembel IDs and gene symbols corresponding to the associated 10x matrix file
Supplementary_files_format_and_content: barcodes (10x): contains an ordered list of barcodes corresponding to the 10x matrix file

source_name: Duodenum

extract_protocol:
Nuclei were isolated using the NucleiEZ lysis buffer with modifications, as described. FACS was performed to isolate neuronal nuclei and glia, which were gated for 7AAD+ and high intensity of CFP from the Phox2b-CFP reporter and collected in Eppendorf LoBind protein plates coated with 1% BSA in 1X PBS.
[10x]  For generation of 10X libraries, nuclei were encapsulated using version 3 Chromium Single Cell 3’ library reagents.  Libraries were sequenced using a Nova-seq 6000 or Nextseq 500 and a paired-end 50 bp sequencing flow cell at a total depth of 3.6 Billion reads across all 10X runs
[inDrop]  inDrop utilizes CEL-Seq in preparation for sequencing and is summarized as follows: 1) Reverse transcription (RT) (supplemented with 30µM DTT), 2) ExoI nuclease digestion (no HinFI), 3) SPRI purification (SPRIP), 4) Second strand synthesis, 5) T7 in vitro transcription linear amplification, 6) SPRIP, 7) short RNA fragmentation, 8) SPRIP, 9) Primer annealing, 10) RT, 11) SPRIP and 12) library enrichment PCR (doubled reaction size), 13) SPRIP. Number of nuclei encapsulated was calculated by observing the single nuclei suspension loading rate multiplied by bead loading efficiency during the duration of encapsulation. The largest sample contained an estimated 5000 nuclei, while the smallest contained an estimated 100 nuclei.  Libraries were sequenced on a Nextseq 500 (Illumina) with a 150bp paired-end sequencing kit in a customized sequencing run.

tag: age (weeks)

value: Female

tag: fixation

value: Unfixed

tag: platform

value: inDrop


title: m6A_MOLM13_WT_D

data_processing:
Library strategy: miCLIP
M6A sites were analysed by first mapping Reads from the miCLIP experiments to the GRCh38 assembly using STAR 2.7.1a with arguments “--outFilterMismatchNoverReadLmax 0.05 --alignIntronMax 0”.
Forward and reverse genomic-coverage tracks were subsequently produced by the bamCoverage function in deepTools 3.3.2 with arguments “--normalizeUsing None –filterRNAstrand forward” and “--normalizeUsing None –filterRNAstrand reverse” respectively.
BigWig files were produced by deepTools 3.3.2 bamCoverage without normalization.
genome build: GRCh42
bigwig files for genomic tracks


title: m6A_MOLM13_WT_B

data_processing:
Library strategy: miCLIP
M6A sites were analysed by first mapping Reads from the miCLIP experiments to the GRCh38 assembly using STAR 2.7.1a with arguments “--outFilterMismatchNoverReadLmax 0.05 --alignIntronMax 0”.
Forward and reverse genomic-coverage tracks were subsequently produced by the bamCoverage function in deepTools 3.3.2 with arguments “--normalizeUsing None –filterRNAstrand forward” and “--normalizeUsing None –filterRNAstrand reverse” respectively.
BigWig files were produced by deepTools 3.3.2 bamCoverage without normalization.
genome build: GRCh40
bigwig files for genomic tracks


title: CWRU004267

source_name: Treatment: CD3.CD28, Donor: N058, Time: 6hrs


title: Ile_r6_10x

source_name: Ileum

tag: Sex

value: Fixed


title: Ile_r5_10x

tag: strain

value: Male


title: Ile_r4_10x


title: m6A_MOLM13_WT_A

data_processing:
Library strategy: miCLIP
M6A sites were analysed by first mapping Reads from the miCLIP experiments to the GRCh38 assembly using STAR 2.7.1a with arguments “--outFilterMismatchNoverReadLmax 0.05 --alignIntronMax 0”.
Forward and reverse genomic-coverage tracks were subsequently produced by the bamCoverage function in deepTools 3.3.2 with arguments “--normalizeUsing None –filterRNAstrand forward” and “--normalizeUsing None –filterRNAstrand reverse” respectively.
BigWig files were produced by deepTools 3.3.2 bamCoverage without normalization.
genome build: GRCh39
bigwig files for genomic tracks


title: Ile_r2_InDrop


title: CWRU004266

source_name: Treatment: Medium, Donor: N058, Time: 6hrs


title: Ile_r3_10x


title: Duo_r4_10x


title: CWRU004265

source_name: Treatment: oxLDL, Donor: N043, Time: 24hrs


title: 191216-CEMBA-mm-P56-CEMBA191126-9J-1-CEMBA191126-9J-2-A10_ad002

tag: brain region

value: Hippocampus

value: male


title: input_MOLM13_WT

data_processing:
Library strategy: miCLIP
M6A sites were analysed by first mapping Reads from the miCLIP experiments to the GRCh38 assembly using STAR 2.7.1a with arguments “--outFilterMismatchNoverReadLmax 0.05 --alignIntronMax 0”.
Forward and reverse genomic-coverage tracks were subsequently produced by the bamCoverage function in deepTools 3.3.2 with arguments “--normalizeUsing None –filterRNAstrand forward” and “--normalizeUsing None –filterRNAstrand reverse” respectively.
BigWig files were produced by deepTools 3.3.2 bamCoverage without normalization.
genome build: GRCh38
bigwig files for genomic tracks


title: CWRU004264

source_name: Treatment: IL15, Donor: N043, Time: 24hrs


title: Duo_r2_InDrop


title: METTL16-KD_Control_B

data_processing:
Library strategy: Slick-Seq (Surrogate-Click-Degradation-Sequencing)
RNAseq data were mapped to the human genome assembly GRCh38 by STAR 2.7.1b,(3) using arguments “--outSAMunmapped Within KeepPairs --outFilterIntronMotifs RemoveNoncanonicalUnannotated   --chimSegmentMin 0   --chimJunctionOverhangMin 20”.
BigWig files were produced by deepTools 3.3.2 bamCoverage using RPKM normalization.
Exonic reads were removed using the intersect function in Bedtools v2.29.0, using exon regions derived from the Ensembl GRCh38 Version 93.
Reads on the forward strand were extracted using Samtools 1.9, with “view -f 128 -F 16” and “-f 80” and merged into one file. Reads on the reverse strand were extracted using “view -f 144” and “-f 64 -F 16” and merged.
Broad peaks were called by MACS2 2.1.4, using WT as treatment and METTL16/METTL3 as control, with arguments “callpeak --broad --extsize=300 --keep-dup 20 --nomodel -g hs --broad-cutoff 0.9 --max-gap 500”.
genome build: GRCh38
processed data files format and content: bigwig files for genomic tracks, text files for MACS2 peaks

extract_protocol: RNAseq data from all experiments were generated as the 75 bp paired-end Illumina reads.


title: CWRU004269

source_name: Treatment: IL15, Donor: N058, Time: 6hrs


title: Duo_r3_10x


title: CWRU004263

source_name: Treatment: CD2, Donor: N043, Time: 24hrs


title: Col_r6_10x

source_name: Colon


title: Col_r5_10x


title: syd_flower_SYD

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

institute: IRHS

data_processing: ChIPseq analysis was carried out using MACS 1.4.2 (Yong Zhang et al., 2008) to normalize the immunoprecipitations with the input sequencing data.

organism: Arabidopsis thaliana

source_name: flowers

growth_protocol: Plants were grown at 22°C with 16h light and at 20°C at night

extract_protocol:
SYD-specific antiserum was raised in rabbits using a SYD-specific peptide (MKEERQRRIRERQKE-C, EZBiolab, Supplementary Figure S5A). Specificity of the antiserum was confirmed by Western blots on sonicated nuclei fractions using SYD antiserum (1:500) or H3 antibody (pAB-060-050, Diagenode, as a loading control), followed by probing with secondary anti-rabbit HRP (1:30 000). The detection was performed with CDP-star reagent (NEB #N7001).  Nuclei were sonicated during 15 min with a Covaris M220 (75W peak power/5% duty factor/200 cycles/burst) (Ikeuchi et al., 2015). Chromatin immuno-precipitation was performed as previously described (Engelhorn and Turck, 2017) and 12 µl of SYD-specific antiserum and 3µl of H3K27me3 (Diagenode, C15410069) were used per IP.
ChIP DNA was amplified using Microplex Library Preparation kit v2 (Diagenode, C05010012).

treatment_protocol: no treatment

value: complete inflorescence

tag: antibody

value: SYD antibody

tag: genotype/variation

value: syd


title: swn_flower_SYD

tag: tissue

value: swn


title: CWRU004262

source_name: Treatment: CD3.CD28, Donor: N043, Time: 24hrs

tag: cell type


title: Col_r3_InDrop


title: METTL16-KD_CLICK_B


title: lfy_flower_SYD

value: lfy


title: CWRU004261

source_name: Treatment: Medium, Donor: N043, Time: 24hrs


title: METTL3-KD_Control_B


title: clf_flower_SYD

value: clf


title: Col_r1_InDrop


title: METTL3-KD_Control_A


title: Ile_r1_part1_InDrop


title: Col_flower_SYD

value: Col


title: CWRU004260

source_name: Treatment: oxLDL, Donor: N043, Time: 6hrs

value: CD8 T cells

value: oxLDL


title: CWRU004259

source_name: Treatment: IL15, Donor: N043, Time: 6hrs


title: METTL3-KD_CLICK_B

value: Acute Myeloid Leukemia


title: Col_r4_10x

value: Female


title: METTL16-KD_Control_A


title: CWRU004258

source_name: Treatment: CD2, Donor: N043, Time: 6hrs


title: Neuronal nuclei Col_rep2

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 mouse assembly
Supplementary_files_format_and_content: counts matrix

extract_protocol:
Nuclei were isolated using the NucleiEZ lysis buffer with modifications, as described in May-Zhang et al. FACS was performed to isolate neuronal nuclei and glia, which were gated for 7AAD+ and high intensity of CFP from the Phox2b-CFP reporter and collected into a 1.5-mL RNAse-free tube filled with 350 uL of RNA lysis buffer RLT from the RNeasy Micro kit.
cDNA libraries were prepared using the Takara SMARTer kit according to llumina's instructions. Libraries were sequenced using the NovaSeq as 1x100bp single-end reads. Each sample had a mean depth of approximately 138 million reads and a mean alignment rate of 99.01%.

value: Colon


title: Col_flower_input


title: METTL3-KD_CLICK_A


title: CWRU004257

source_name: Treatment: CD3.CD28, Donor: N043, Time: 6hrs


title: Neuronal nuclei Col_rep1


title: WT_Control_B

source_name: Acute Myeloid Leukemia


title: Glial nuclei lle_rep2

value: Ileum


title: Glial nuclei Col_rep1


title: WT_Control_A


title: CWRU004256

source_name: Treatment: Medium, Donor: N043, Time: 6hrs

value: Medium


title: CWRU004255

source_name: Treatment: oxLDL, Donor: N009, Time: 24hrs


title: Glial nuclei lle_rep1

source_name: Ileum

value: Male


title: ctrl_siNC RNA-seq rep1

data_processing:
Reads of small RNA-seq were trimmed using the cutadapt program and then mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)meters -n 0 -l 20 -k 1 -best. Reads counts of mature miRNAs were calculated using featureCounts program (Liao et al., 2014) fracOverlap 0.8 --fracOverlapFeature 0.8 -s 1 -M. The enrichment of miRNAs from RIP over input or pellet over total lysate were calculated with edgeR package (Robinson et al., 2010). We defRNAs as CPM >50, log2 fold-change >0.5 and p-value < 0.05. The motif analysis was per “clean” data for the following analysis.Reads were firstly mapped using Bowtie2 (Langmead and Salzberg, 2012) against repetitive elements derived from RepBase (version 23.09) (Bao et al., 2015), and also tRNA and rRNA ,which were derived from tRNAscan database (Lowe and Chan, 2016) and NCBI, respectively. Reads that were not mapped to those sequences were aligned to genome sequence using STAR (Dobin et al., 2013) with parameters --outFilterMultimapNmax 5 --outSAMmultNmax 1 --alignEndsType Local --alignIntronMax 1. For mapped reads with the same genomic position and same barcode, only one was retained to avoid PCR products. For processing RNA-seq data, reads counts of genes were calculated with featureCounts program. Differential expression was calculated using edgeR, in which we used a RPKM cutoff of 1, a log2 fold-change cutoff of 0.5 and a p-value cutoff of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for normalized coverage in genome. For pair-end RNA-seq data, we used only Read 2 to generate the bigWig file.

source_name: neuroblastoma

value: N2A neuroblastoma cell line

value: siNC


title: ctrl_siNC RNA-seq rep2


title: ctrl_Mock RNA-seq rep2

value: Mock


title: WT_CLICK_B


title: ctrl_Mock RNA-seq rep1


title: Neuronal nuclei lle_rep2


title: WT_CLICK_A


title: Neuronal nuclei lle_rep1


title: TDP-43-CTF RNA-seq rep2

data_processing:
Reads of small RNA-seq were trimmed using the cutadapt program and then mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)meters -n 0 -l 20 -k 1 -best. Reads counts of mature miRNAs were calculated using featureCounts program (Liao et al., 2014)fracOverlap 0.8 --fracOverlapFeature 0.8 -s 1 -M. The enrichment of miRNAs from RIP over input or pellet over total lysate were calculated with edgeR package (Robinson et al., 2010). We defRNAs as CPM >50, log2 fold-change >0.5 and p-value < 0.05. The motif analysis was per “clean” data for the following analysis.Reads were firstly mapped using Bowtie2 (Langmead and Salzberg, 2012) against repetitive elements derived from RepBase (version 23.09) (Bao et al., 2015), and also tRNA and rRNA ,which were derived from tRNAscan database (Lowe and Chan, 2016) and NCBI, respectively. Reads that were not mapped to those sequences were aligned to genome sequence using STAR (Dobin et al., 2013) with parameters --outFilterMultimapNmax 5 --outSAMmultNmax 1 --alignEndsType Local --alignIntronMax 1. For mapped reads with the same genomic position and same barcode, only one was retained to avoid PCR products. For processing RNA-seq data, reads counts of genes were calculated with featureCounts program. Differential expression was calculated using edgeR, in which we used a RPKM cutoff of 1, a log2 fold-change cutoff of 0.5 and a p-value cutoff of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for normalized coverage in genome. For paired-end RNA-seq data, we used only Read 2 to generate the bigWig file.

source_name: TDP-43-CTF RNA-seq


title: CWRU004253

source_name: Treatment: CD2, Donor: N009, Time: 24hrs


title: CWRU004254

source_name: Treatment: IL15, Donor: N009, Time: 24hrs


title: Glial nuclei Duo_rep2

source_name: Duodenum

value: Duodenum


title: CWRU004251

source_name: Treatment: Medium, Donor: N009, Time: 24hrs


title: CWRU004252

source_name: Treatment: CD3.CD28, Donor: N009, Time: 24hrs


title: Glial nuclei Duo_rep1


title: TDP-43-CTF RNA-seq rep1


title: FL-TDP-43 RNA-seq rep1

source_name: FL-TDP-43 RNA-seq


title: FL-TDP-43 RNA-seq rep2


title: WT littermate control rep3

city: New York

first: Alvaro

last: Villarreal-Ponce

state: New York

address: Skirball Institute of Biomolecular Medicine Floor 2 Lab 3

department: Plastic Surgery

institute: NYU Langone Health

description: Lin- CD49f+

data_processing:
Paired-end reads were trimmed using Trimmomatic (version 0.35) with the following parameters HEADCROP:5, LEADING:20 TRAILING:20, SLIDINGWINDOW:4:17 MINLEN:25
Trimmed reads were aligned to the mouse genome (mm10/gencode.vM13) with STAR aligner (version 2.6.0c)
Aligned reads were quantified using the RNA-seq by Expectation-Maximization algorithm (RSEM) (version 1.2.31) with the following standard parameters: rsem-calculate-expression, --paired-end. Samples displaying >78% alignment were considered for downstream analyses
Samples were filtered using Python (Version 3.7.1) and only genes expressed at minimum 1 TPM in at least one sample in all biological replicates were kept and considered for downstream analyses. Only protein coding-, lncRNA, and miRNA genes were considered for downstream analyses. A pseudo-count of 0.1 was added to TPM values
Genome_build: mm10
Supplementary_files_format_and_content: raw counts of sequencing reads

source_name: Day 5 wound keratinocytes

extract_protocol:
Microdissection of a ~2.5mm concentric ring around the 10mm wound was carried out using a 15mm-diameter punch biopsy. Wounded skin was harvested at indicated time points and digested in 10u/mL Dispase (Thermo Fisher, 17105041) and 5ug/mL Accutase (Bio-Legend, 42301) before passing the suspension through a 70um pore cell trainer. Lineage-positive cells and dead cells/debris were excluded from the cell suspension utilizing the MACS Lineage Depletion Kit (Miltenyi, 130-090-858) and MACS Dead Cell Removal Kit (Miltenyi, 130-090-101), respectively, following the manufacturer’s instructions. Cell number and viability was assessed using trypan blue and a hemocytometer. Dissociated single cells were suspended in 5% FBS in 1x PBS and incubated with various antibody combinations for multi-parameter flow acquisition and analysis. Live keratinocytes were sorted using antibodies directed against the following surface makers: Lin- (CD5-, CD45R-, CD11b-, Cr-1-, 7-4-, Ter-119-) (Miltenyi, 130-090-858), CD49f+ (Bio-Legend, 313610) using a SY3200 4 laser/10 color cell sorter.
For RNA-seq, cDNA library preparation used optimal quality RNA (RIN>9). Full length cDNA library amplification was performed as previously described. Briefly, total RNA was reverse-transcribed and the resulting cDNA was pre-amplified using the Nugen Trio RNAseq Kit (Nugen Inc.). Paired-end 50 (PE50) sequencing was performed on the Illumina HiSeq 4000 (Illumina).

tag: genotype

value: K14Cre-ER; Nrf2 +/+

value: Sorted wound keratinocytes

value: 5 days post wounding


title: WT littermate control rep2

description: Lin- CD49f+


title: WT littermate control rep1

description: Lin- CD49f+


title: CWRU004250

source_name: Treatment: oxLDL, Donor: N009, Time: 6hrs


title: Nrf2 cKO rep3

description: Lin- CD49f+

value: K14Cre-ER; Nrf2 flox/flox


title: siTDP-43 RNA-seq rep2

source_name: siTDP-43 RNA-seq


title: Neuronal nuclei Duo_rep1


title: Nrf2 cKO rep2

description: Lin- CD49f+


title: CWRU004248

source_name: Treatment: CD2, Donor: N009, Time: 6hrs


title: siTDP-43 RNA-seq rep1


title: Susceptibility_Prefrontal_Cortex_16

description: Susceptible

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.7.1, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Mus Muscuslus, Ensembl, GRCm38.p5
Supplementary_files_format_and_content: tad-delimited, raw counts

source_name: Prefrontal cortex

extract_protocol:
Animals were decapitated, brains extracted and  micropunches of mPFC (including anterior cingulate, prelimbic and dorsal parts of the infralimbic cortices; bregma: +2.3 to +1.3 mm) and Amy (including major parts of the basolateral nuclei; bregma: -1.2 to -2.2 mm) regions  prepared. Total RNA was extracted from mPFC and Amy samples using the SPLIT RNA extraction kit (Lexogen, Austria) following the manufacture’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On GD 12, pregnant mice were randomly assigned to a single injection of poly(I:C) (potassium salt, P9582, Sigma–Aldrich, Buchs, St Gallen, Switzerland) or treatment with endotoxin-free 0.9% NaCl (B. Braun, Melsungen, Switzerland) vehicle solution at a dose of 5 mg/kg and injection volume of 5 ml/kg

value: male

value: Prefrontal cortex

tag: phenotype

value: Susceptible


title: siNC RNA-seq rep2

source_name: siNC RNA-seq

tag: cell line


title: CWRU004247

source_name: Treatment: CD3.CD28, Donor: N009, Time: 6hrs

value: CD8 T cells


title: RACM-RNA-seq-p0

city: San Francisco

first: Ravi

last: Mandla

address: 555 Mission Bay Blvd South

department: Medicine - Cardiology

institute: UC San Francisco

data_processing:
Reads were trimmed for polyA, polyT, and low quality reads using trimmomatic and aligned to mm10 using hisat2
Reads were counted per exon using featureCounts, then analyzed and normalized using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file containing raw read count output from featureCounts, along with renaming convention

source_name: Right Atrial Cardiomyocytes

extract_protocol:
Total RNA was isolated from sorted cells using the RNeasy Micro Kit (Qiagen 74004). cDNA was synthesized from RNA samples with the Ovation RNA-Seq System V2 kit (NuGEN) according to manufacturer’s instructions. RNA-seq libraries were analyzed by Bioanalyzer (Agilent) and quantified by qPCR (KAPA). Sequencing was carried out on an Illumina HiSeq 4000 using 100-bp paired end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To isolate pure populations of pacemaker cells (PCs) and right atrial cardiomyocytes (RACMs), Hcn4-GFP or Hcn4-GFP/Myh6-mCherry neonatal hearts were imaged under live fluorescence and the GFP+ SAN head was identified at the junction of the superior vena cava and right atrium. For each biological replicate, SAN-RA junctions from 8-10 neonatal hearts were pooled for digestion to a single cell suspension for flow sorting.

tag: developmental stage

value: neonatal

value: FACS-isolated Right atrial cardiomyocytes


title: CWRU004246

source_name: Treatment: Medium, Donor: N009, Time: 6hrs

tag: treatment


title: siNC RNA-seq rep1

extract_protocol:
Total RNA was extracted by TRIZOL reagent.
For RIP-seq, N2a cells cultured in a 150 mm plate were washed twice with cold PBS followed by UV irradiation at 400mJ/cm2 under a HL-2000Hybrilinker. Scrapped cells were harvested by centrifugation at 500 g for 5 min at 4°C. Crosslinked cells were lysed in 1 ml lysis buffer (20mM Tris-Hcl pH 7.6, 150mM NaCl, 1% NP-40, 1mM EDTA, 0.1% SDS, 0.1% deoxycholate, 100U/ml RNasin Ribonuclease Inhibitors (Promega), 1 u/ml EDTA-free complete protease inhibitor cocktail (Roche)) on ice for 30 min. Lysates were centrifuged at 12,000 g at 4°C for 15 min to remove cell debris. An input of collected supernatant was set aside for subsequent analysis. Each sample was then divided and incubated with 5 μg of either anti-TDP-43 antibody (Proteintech) or rabbit IgG (Millipore) on a rotator overnight at 4°C. Complexes were pulled down by incubation with protein G Dynabeads on a rotator for 2 hours at 4°C. Beads were washed twice with lysis buffer, twice with wash buffer (add 300 mM NaCl), and boiled to reverse UV cross-linking. Co-precipitated RNAs were extracted from beads and used for construction of small RNA library or analysis by quantitative RT-PCR (qRT-PCR) using specific primers.To isolate cellular insoluble aggregates, two 10-cm dish N2a cells were extracted sequentially, as previously described (Guo et al., 2011; Hu et al., 2017). Briefly, cells were harvested, lysed in the moderate RIPA lysis buffer (50mM Tris (pH 7.4), 150 mM NaCl, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS, EDTA-free complete protease inhibitor cocktail (Roche), 100U/ml RNasin Ribonuclease Inhibitors (Promega)) on ice for 30 min, and centrifuged at 17000 g at 4°C for 30 min. The bottom cell debris (i.e. nuclear, mitochondria and stress granules) were depleted. The resultant supernatant fractions were incubated with 1% Sarkosyl for 30 min at room temperature with agitation, and then the detergent insoluble proteins were obtained by ultracentrifugation of the supernatants at 41600 rpm at 4°C for 30 min and washed twice by PBS buffer. The whole cell lysates and the detergent-insoluble pellets were separately collected, and the isolated protein and RNA were used for Western blotting analysis and small RNA-seq library construction.The small RNA library was constructed using sensitivity-improved method as described (Yang et al., 2016) or modifications. Briefly, isolated total RNA (~1 μg) was mixed with 25 pmol 3′ adapter, 1 × T4 ligase reaction buffer, 33% polyethylene glycol (molecular weight 8000), 40 U RNL2tr K227Q (NEB), and 20 U RiboLock RNase Inhibitor (Thermo Fisher). The samples were incubated at 22°C for 2 hours, then at 16°C for 1 hour, followed by addition of 1 μl of 10 μM RT primer before heat inactivation at 75°C for 5 min. 200 pmol of the 5′ adapter was added for ligation by T4 RNA ligase 1 (NEB) and incubated at 22°C for 1 hour. Linker-ligated RNAs were reverse transcribed with Superscript III (Invitrogen) at 50°C for 30 min, 55°C for 30 min, then at 95°C for 5 min and PCR-amplified with Q5 High-Fidelity 2× Master (NEB). The product was fractionated on a 4% agarose gel and extracted by QIAEX II Gel Extraction Kit (QIAGEN). The recovered DNA was quantified for deep sequencing.


title: RACM-RNA-seq-p2


title: RACM-RNA-seq-p4


title: CWRU004245

source_name: Treatment: oxLDL, Donor: N005, Time: 24hrs

value: oxLDL


title: Susceptibility_Amygdala_35

description: Susceptible

source_name: Amygdala

value: Amygdala


title: Neuronal nuclei Duo_rep2

value: Male


title: VU24_Musc_R3

description: from VU14 donor

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 human assembly
Supplementary_files_format_and_content: counts matrix

source_name: Colon

extract_protocol:
Total RNA was extracted using the RNeasy Micro® kit (Ambion) as described in May-Zhang et al. Jove 2018. Briefly, 1-3 Arcturus XT laser capture caps were pooled for each sample after collecting sufficient quantities of enteric ganglia. Lysates were incubated at 26C for 30 min in 250uL of Buffer RLT with repeated brief vortexing. Lysates were frozen at -80C and stored for up to 2 months before isolating RNA.
cDNA libraries were prepared using the Takara SMARTer kit according to llumina's instructions. Libraries were sequenced using the NovaSeq as 1x100bp single-end reads. Each sample had a mean depth of approximately 138 million reads and a mean alignment rate of 99.01%.

value: Female

tag: race

value: Hispanic/Latino

tag: age

tag: sequencer

value: NovaSeq 6000


title: CWRU004249

source_name: Treatment: IL15, Donor: N009, Time: 6hrs

tag: donor


title: PC-RNA-seq-p4

source_name: SAN Pacemaker Cells

value: FACS-isolated SAN Pacemaker cells


title: VU24_Musc_R1

description: from VU14 donor


title: Susceptibility_Amygdala_34

description: Susceptible


title: CWRU004244

source_name: Treatment: IL15, Donor: N005, Time: 24hrs


title: VU24_Musc_R2

description: from VU14 donor


title: CWRU004243

source_name: Treatment: CD2, Donor: N005, Time: 24hrs


title: Susceptibility_Prefrontal_Cortex_14

description: Susceptible


title: METTL16-KD_CLICK_A

source_name: Acute Myeloid Leukemia

value: Acute Myeloid Leukemia


title: PC-RNA-seq-p0


title: PC-RNA-seq-p2


title: Susceptibility_Amygdala_32

description: Susceptible


title: Resilience_Prefrontal_Cortex_9

description: Resilient

value: Resilient


title: VU23_Musc_R3

description: from VU14 donor

source_name: Ileum


title: H3.3 K27R;L126A;I130A

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
H3K27me3 and EZH2 ChIP-Seq were normalized using ChIP-Rx (1000000/number of reads aligned to the exogenous refernce genome)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: H3.3K27M;L126A;I130A triple mutant

growth_protocol: MEFs were grown in Dulbecco's modified Eagle's medium with 10% FBS

extract_protocol:
Cells were crosslinked with 1% PFA for 5 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with Mnase to generate mono-nucleosomes. Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: Lentivurses for stable expression of H3.3K27M, H3.3K27R, H3.3K27M;L126A;I130A or H3.3K27R;L126A;I130A were transduced in the cells.

value: Mouse embryonic fibroblasts

value: Cells expressing H3.3K27M;L126A;I130A triple mutant

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)

tag: molecule subtype

value: Immunoprecipitated DNA


title: Susceptibility_Prefrontal_Cortex_15

description: Susceptible

tag: Sex

value: male

value: Prefrontal cortex

value: Susceptible


title: VU23_Musc_R2

description: from VU14 donor


title: CWRU004241

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix in CSV format containing raw read counts

source_name: Treatment: Medium, Donor: N005, Time: 24hrs

value: CD8 T cells

value: Medium


title: CWRU004242

source_name: Treatment: CD3.CD28, Donor: N005, Time: 24hrs


title: Resilience_Prefrontal_Cortex_8

description: Resilient

source_name: Prefrontal cortex


title: H3.3 K27M;L126A;I130A


title: VU23_Musc_R1

description: from VU14 donor


title: CWRU004240

source_name: Treatment: oxLDL, Donor: N005, Time: 6hrs

value: oxLDL


title: H3.3 K27R

value: Cells expressing H3.3K27M


title: Resilience_Prefrontal_Cortex_7

description: Resilient


title: CWRU004239

source_name: Treatment: IL15, Donor: N005, Time: 6hrs


title: Resilience_Amygdala_28

description: Resilient

value: Amygdala


title: H3.3 K27M


title: CWRU004238

source_name: Treatment: CD2, Donor: N005, Time: 6hrs


title: Resilience_Amygdala_27

description: Resilient


title: CWRU004237

source_name: Treatment: CD3.CD28, Donor: N005, Time: 6hrs


title: Resilience_Amygdala_25

description: Resilient


title: H3.1K27R_k27me3_mm9

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
H3K27me3 and EZH2 ChIP-Seq were normalized using ChIP-Rx (1000000/number of reads aligned to the exogenous refernce genome); reChIP-Seq were normalized by RPKM
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig [genome wide enrichment], bed (peaks)

treatment_protocol: Lentivurses for stable expression of H3.3K27M, H3.3K27R, H3.1K27M and H3.1K27R were transduced in the cells.

value: Cells expressing H3.1K27R


title: empty_reEZH2_FL400

source_name: Empty

value: control cells

value: FLAG (Sigma aldrich; Cat number:F3165; lot number:NA, monoclonal)  + EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: VU22_Musc_R2

description: from VU14 donor

source_name: Duodenum

value: Female

value: Hispanic/Latino

value: NovaSeq 6000


title: CWRU004236

source_name: Treatment: Medium, Donor: N005, Time: 6hrs


title: VU21_Musc_R3

description: from VU12 donor

source_name: Colon

value: Male

value: Black/African American


title: VU22_Musc_R1

description: from VU14 donor


title: Control_Prefrontal_Cortex__5

description: Control

value: Control


title: H3.3K27R_k27me3

value: Mouse embryonic fibroblasts

value: Cells expressing H3.3K27R

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)

value: Immunoprecipitated DNA


title: VU21_Musc_R2

description: from VU12 donor


title: Control_Prefrontal_Cortex__4

description: Control

value: male

value: Prefrontal cortex


title: H3.3K27R_EZH2_mm9

value: Cells expressing H3.1K27M

value: EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: H3.3K27M_EZH2_mm9

value: Cells expressing H3.3K27M


title: VU21_Musc_R1

description: from VU12 donor


title: CWRU004234

source_name: Treatment: IL15, Donor: N016, Time: 24hrs

value: CD8 T cells


title: Control_Prefrontal_Cortex__3

description: Control


title: VU22_Musc_R3

description: from VU14 donor


title: CWRU004233

source_name: Treatment: CD2, Donor: N016, Time: 24hrs


title: CWRU004232

source_name: Treatment: CD3.CD28, Donor: N016, Time: 24hrs


title: VU19_Musc_R2

description: from VU12 donor


title: VU19_Musc_R3

description: from VU12 donor


title: Ile_r1_part2_InDrop

data_processing:
[10x]  The sequencing output FASTQs were processed with CellRanger 3.0.2 and aligned to the reference transcriptome (intron+exon)
[inDrop]  For inDrop, reads were filtered, sorted by their designated barcode, and aligned to the reference transcriptome (intron + exon) using DropEST pipeline (STAR). Mapped reads were quantified into UMI-filtered counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: matrix (inDrop): contains a gene-barcode-count matrix
Supplementary_files_format_and_content: matrix (10x): contains a raw count matrix
Supplementary_files_format_and_content: features (10x): contains a list of detected genes with Ensembel IDs and gene symbols corresponding to the associated 10x matrix file
Supplementary_files_format_and_content: barcodes (10x): contains an ordered list of barcodes corresponding to the 10x matrix file

tag: age (weeks)

tag: strain

tag: fixation

value: Fixed

tag: platform

value: inDrop


title: H3.3K27M_K27me3_mm9_rep1

tag: genotype/variation

tag: antibody


title: Col_r2_InDrop

value: Unfixed


title: H3.3K27M_K27me3_mm9_rep2

description: processed data file: H33K27M_K27me3_Peaks1192.bed

tag: cell type


title: VU19_Musc_R1

description: from VU12 donor

value: NovaSeq 6000


title: H3.3K27M_reEZH2_subFLAG

value: FLAG (Sigma aldrich; Cat number:F3165; lot number:NA, monoclonal)  + EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: CWRU004231

source_name: Treatment: Medium, Donor: N016, Time: 24hrs

value: Medium


title: Control_Amygdala__20

description: Control

source_name: Amygdala

tag: tissue

value: Amygdala

tag: phenotype

value: Control


title: VU15_MuI_R3

description: from VU15 donor

source_name: Muscle-Ileum

value: Male

value: Asian (Nepali)


title: H3.1K27R_EZH2_mm9

value: Mouse embryonic fibroblasts

value: Immunoprecipitated DNA


title: Control_Amygdala__21

description: Control

value: male


title: CWRU004235

source_name: Treatment: oxLDL, Donor: N016, Time: 24hrs

value: oxLDL


title: VU20_Musc_R3b

description: from VU12 donor

source_name: Muscle (ileum)

value: Black/African American


title: VU15_MuI_R2

description: from VU15 donor


title: CWRU004230

source_name: Treatment: oxLDL, Donor: N016, Time: 6hrs


title: VU20_Musc_R2b

description: from VU12 donor


title: CWRU004229

source_name: Treatment: IL15, Donor: N016, Time: 6hrs


title: H3.1K27M_EZH2_mm9

value: Cells expressing H3.1K27M

value: EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: CWRU004228

source_name: Treatment: CD2, Donor: N016, Time: 6hrs

value: CD8 T cells


title: Control_Amygdala__24

description: Control


title: VU15_MuI_R1

description: from VU15 donor


title: VU15_MuC_R3

description: from VU15 donor

source_name: Muscle-Colon


title: H3.1K27M_k27me3_mm9_rep2

description: processed data file: H31K27M_K27me3_Peaks1053.bed

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)


title: CWRU004227

source_name: Treatment: CD3.CD28, Donor: N016, Time: 6hrs


title: VU9_Ile_R3

source_name: Ileum

value: Hispanic/Latino


title: H3.1K27M_K27me3_mm9_rep1


title: VU15_MuC_R2

description: from VU15 donor

value: NovaSeq 6000


title: CWRU004226

source_name: Treatment: Medium, Donor: N016, Time: 6hrs


title: VU15_MuC_R1

description: from VU15 donor


title: H3.1K27M_reEZH2_subFLAG

value: FLAG (Sigma aldrich; Cat number:F3165; lot number:NA, monoclonal)  + EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: VU9_Ile_R2


title: K562 rep2

first: Huang

last: Zhu

address: 2880 Torrey Pines Scenic Dr.

department: Medicine

institute: University of California-San Diego

description: Processed data_FPKM_all the samples_with annotation.xlsx

data_processing:
Raw image data file from high-throughput sequencing (illumina) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base calling)
Raw sequencing reads were filted as follow: (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N represents base that could not be determined);  (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Clean reads were mapped to human genome using STAR software. In order to avoid losing a lot of effective junction reads,  we use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely. Reads were mapped to exon, intron and intergenic.
Gene expression level was estimated by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008).
Genome_build: Homo_sapiens_hg38
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for all the samples

source_name: Leukemia cell line

growth_protocol: NK cells were harvested after they reached maturity and co-cultured with irradiated K562-mbIL-21-4-1BB artificial antigen presenting cells (aAPCs) for expansion with media containing RPMI 1640 and 10% FBS; supplemented with 50 units/mL of hIL-2 (Peprotech). K562, Raji and Jurkat were maintained in RPMI 1640+10% FBS.

extract_protocol:
Total RNA was isolated from cells using the miRNeasy Kit (Qiagen) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leukemia cell line

tag: passage

tag: expansion method

value: using K562-41BB-mbIL21


title: VU9_Ile_R1

tag: race


title: EEDflox_M406E_K27me3

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
H3K27me3 and EZH2 ChIP-Seq were normalized using ChIP-Rx (1000000/number of reads aligned to the exogenous refernce genome); FLAG ChIPs were normalized by RPKM.
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig [genome wide enrichment], bed (peaks)

source_name: Cells expression EZHIP M406E

extract_protocol:
Cells were crosslinked with 1% PFA for 5 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with Mnase to genrate mono-nucleosomes. Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: Lentivurses for stable expression of EZHIP WT or M406E were transduced in the cells. EED floxed cells were treated with cre-recombinanse hit-and-run lentivirus to generate EED knockout line and a single clone was selected for analyses.

value: Cells expression EZHIP M406E


title: VU9_Col_R3

source_name: Colon

value: Male

tag: age


title: Jurkat rep2

source_name: T cell line

value: T cell line


title: K562 rep1


title: VU9_Col_R2

tag: sequencer


title: EEDflox_M406E_FLAG

value: Mouse embryonic fibroblasts

value: FLAG (Sigma aldrich; Cat number:F3165; lot number:NA, monoclonal)


title: EEDflox_M406E_EZH2

value: Immunoprecipitated DNA


title: VU7_Ile_R4

value: Hisp/Latino/Black


title: VU8_Ile_R4

value: Female

value: Caucasian


title: VU9_Col_R1


title: Jurkat rep1


title: VU6_Col_4c

description: Cross-platform control (identical to sample VU6_Col_R1)

value: Black/African American


title: VU20_Musc_R1b

description: from VU12 donor


title: VU3_Ile_c4

description: Cross-platform control


title: VU2_Ile_R3


title: VU8_Ile_R3


title: Raji rep1

source_name: B cell lymphoma cell line

value: B cell lymphoma


title: EEDnull_wtORF_FLAG

source_name: EED knockout Cells expression EZHIP

value: EED knockout Cells expression EZHIP


title: EEDnull_wtORF_EZH2

value: EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: VU2_Ile_R2

value: NovaSeq 6000


title: NK92 rep2

source_name: NK cell line

value: Natural killer cell line


title: VU8_Duo_R3

source_name: Duodenum


title: VU8_Duo_R2


title: EEDflox_wtORF_FLAG

source_name: Cells expression EZHIP

value: Cells expression EZHIP


title: VU15_MuD_R2

description: from VU15 donor

source_name: Muscle-Duod

value: Asian (Nepali)


title: EEDflox_wtORF_K27me3

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)


title: EEDnull_wtORF_K27me3


title: H9NK rep2

source_name: NK cells derived from human ES cell line-H10

value: human embryo

value: using K562-41BB-mbIL21


title: VU15_MuD_R4

description: from VU15 donor

value: Male


title: VU2_Ile_R1


title: UiPSCNK rep2

source_name: NK cells derived from iPSC

value: ubilical cord blood


title: TAZ_wtORF_K27me3

source_name: Cells expression EZHIP treated with Tazemetostat

value: Mouse embryonic fibroblasts

tag: treatment

value: Tazemetostat

value: Immunoprecipitated DNA


title: VU15_MuD_R5

description: from VU15 donor


title: TAZ_wtORF_FLAG

value: FLAG (Sigma aldrich; Cat number:F3165; lot number:NA, monoclonal)

tag: molecule subtype


title: VU8_Col_R3

tag: Sex

value: Female

value: Caucasian


title: VU15_Ile_R5


title: VU8_Duo_R1


title: VU8_Col_R2


title: H9NK rep1

source_name: NK cells derived from human ES cell line-H9


title: VU8_Ile_R1


title: TAZ_wtORF_EZH2


title: VU15_Ile_R4


title: UiPSCNK rep1


title: UCBNK rep2

source_name: NK cells derived from CD34+ cells isolated from ubilical cord blood


title: VU7_Ile_R3

source_name: Ileum

value: Hisp/Latino/Black


title: DMSO_wtORF_K27me3

source_name: Cells expression EZHIP treated with DMSO

value: DMSO


title: NK92 rep1


title: UCBNK rep1


title: VU15_Ile_R2

value: NovaSeq 6000


title: VU7_Ile_R1


title: DMSO_wtORF_FLAG


title: DMSO_wtORF_EZH2

value: EZH2 (Cell signaling; Cat number:5246; lot number:NA, monoclonal)


title: VU15_Duo_R4


title: PBNK rep1

source_name: NK cells obtained from peripheral Blood

value: peripheral Blood


title: VU7_Col_R3


title: VU7_Col_R2


title: VU8_Col_R1


title: VU15_Col_R5

value: Asian (Nepali)


title: VU7_Col_R1


title: VU15_Duo_R2


title: R302S_rescue_H3K27me3

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
H3K27me3 and EZH2 ChIP-Seq were normalized using ChIP-Rx (1000000/number of reads aligned to the exogenous refernce genome)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig [genome wide enrichment], bed (peaks)

treatment_protocol: EED floxed cells were treated with cre-recombinanse hit-and-run lentivirus to generate EED knockout line and a single clone was selected for analyses. Lentivurses for stable expression of EED WT, R302S or Y365A were transduced in the cells

value: EED knockout Cells rescued with EED R302S

value: H3K27me3 (Cell signaling; Cat number:9733; lot number:NA, monoclonal)


title: Y365A_rescue_EZH2

value: EED knockout Cells rescued with EED Y365A


title: VU6_Ile_R3

value: Male

value: Black/African American


title: VU15_Col_R4


title: VU15_Col_R3


title: VU6_Ile_R1


title: VU6_Ile_R2


title: R302S_rescue_EZH2

value: Mouse embryonic fibroblasts


title: VU15_Duo_R5


title: VU14_Ile_R3


title: PBNK rep2

value: using K562-41BB-mbIL21


title: VU6_Col_R3


title: EEDwt_rescue_H3K27me3

value: EED knockout Cells rescued with EED wt

value: Immunoprecipitated DNA


title: Y365A_rescue_H3K27me3


title: EEDflox_wtORF_EZH2

value: Cells expression EZHIP


title: EEDwt_rescue_EZH2


title: RACM-ATAC-seq-rep3

data_processing:
Reads were trimmed and aligned to mm9 using TopHat
Peaks were called for each sample using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Non-normalized BigWig files were constructed using bamCoverage from deeptools.

source_name: Right Atrial Cardiomyocytes

extract_protocol:
ATAC-seq was performed as described in the original protocol {Buenrostro, 2015 #3087} with the following modifications. Sorted cells were washed in ice-cold PBS and spun at 350 rcf for 3 minutes. To isolate nuclei, cells were resuspended in 200 ml lysis buffer (in mM: 20 Tris-HCl pH 8.0, 85 KCl, 0.5% Triton X-100, EDTA-free protease inhibitors, PBS) and spun down at 500 rcf for 5 minutes in the cold. The isolated nuclei was incubated for 30 minutes at 37°C in a 50-ml Tn5 transposase reaction mix (Illumina FC-121-1031). The transposed chromatin was purified with Qiagen MinElute Reaction Cleanup Kit (Qiagen 28204).
Libraries were generated and amplified usingNEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs M0541S) for 15 cycles. Libraries were cleaned up with Qiagen kit and quantified using BioAnalyzer (Agilent) and Qubit (Thermo Fisher). Sequencing was carried out on an Illumina HiSeq 4000 using 100-bp paired end reads, yielding approximately 40 million mapped reads per sample.

tag: developmental stage

value: FACS-isolated Right atrial cardiomyocytes


title: VU6_Col_R2

source_name: Colon


title: RACM-ATAC-seq-rep2


title: VU14_Ile_R1

value: Female

value: Hisp/Latino/Black


title: VU14_Ile_R2

value: NovaSeq 6000


title: VU14_Duo_R3


title: gWAT- B6.Cg-Mir146atm1.1Bal/J HFD- #5

city: Ulm

first: Julian

last: Roos

department: Department of Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

source_name: gWAT of B6.Cg-Mir146atm1.1Bal/J ND mice after 10 weeks of high fat diet

growth_protocol: Female C57BL/6J and B6.Cg-Mir146atm1.1Bal/J were obtained from the Jackson Laboratory (Bar Harbor, USA). Mice were housed at 22–24 °C with a 14/10 h light/dark cycle and ad libitum access to food and water.

extract_protocol: Whole tissues were minced in liquid nitrogen. Total RNA isolation was performed with the Direct-zol RNA mini Prep Kit (Zymo Research, Freiburg, Deutschland).

treatment_protocol: At an age of 10 weeks, chow diet was changed to either control diet (normal diet, ND, D12450B mod. LS 13 kJ% fat from vegetable oil) or high fat diet (HFD, D12492n(I) mod. 60kJ% fat from lard) (Ssniff Spezialdiäten, Soest, Germany).

tag: diet

value: mice 10 weeks on high fat diet

value: gonadal white adipose tissue (gWAT)

tag: gender

value: female

tag: genotype/strain

value: B6.Cg-Mir146atm1.1Bal/J ND


title: gWAT- B6.Cg-Mir146atm1.1Bal/J HFD- #1

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay


title: gWAT- B6.Cg-Mir146atm1.1Bal/J HFD- #2


title: gWAT- B6.Cg-Mir146atm1.1Bal/J HFD- #4


title: VU5_Ile_R3

value: Caucasian


title: VU14_Duo_R2


title: VU5_Ile_R2


title: RACM-ATAC-seq-rep1


title: VU14_Duo_R1


title: PC-ATAC-seq-rep4

source_name: SAN Pacemaker Cells

value: FACS-isolated Pacemaker Cells from Sinus Node


title: gWAT- B6.Cg-Mir146atm1.1Bal/J HFD- #3


title: PC-ATAC-seq-rep3


title: VU5_Col_R3

value: Male


title: gWAT- C57BL/6J HFD- #5

source_name: gWAT of C57BL/6J mice after 10 weeks of high fat diet


title: VU5_Ile_R1


title: gWAT- C57BL/6J HFD- #3


title: VU14_Col_R3


title: PC-ATAC-seq-rep2


title: VU6_Col_R1

value: Black/African American


title: VU14_Col_R2


title: VU5_Col_R2


title: PC-ATAC-seq-rep1


title: gWAT- C57BL/6J HFD- #2


title: VU5_Col_R1


title: gWAT- C57BL/6J HFD- #1


title: gWAT- B6.Cg-Mir146atm1.1Bal/J ND- #5

source_name: gWAT of B6.Cg-Mir146atm1.1Bal/J ND mice after 10 weeks of normal diet

value: mice 10 weeks on normal diet


title: VU13_Ile_R3


title: C3H10T1/2, H3.3G34W_BRD4 (ChIP-seq)

description: Immunoprecipitated DNA

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using RPKM (1000000/aligned reads) or RX (1000000/reads aligned to drosophila genome)
Deeptools was used to generate bigwig files for visuallization
mosaics was used to identify enriched regions of the genome.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig, bed (peaks)

source_name: mMSC C3H10T1/2

growth_protocol: Cells were grown in Dulbecco's modified Eagle's medium with 10% FBS

extract_protocol:
Cells were crosslinked with 1% PFA for 5 min. Lysed in (15 mM Tris, 1 mM CaCl2, 0.25% TritonX-100), treated with MNase to genrate mono-nucleosomes and sonicated using covaris (PIP 140, DF 5%, CPB 200 for 45 sec for 3 times). Chromatin was dialyzed against RIPA buffer (10mM Tris, 1% TritonX-100, 0.1% SDS, 0.1% Na-DOC) and supernatant was incubated with antibody overnight. Antibody was caputred using dynabeads for 3 hours. IPed material was eluted by boiling the beads in 1% SDS buffer at 65 degree C, after washing 5 times.
Libraries were constructed according to NEB Next Ultra protocol

treatment_protocol: Lentivurses for stable expression of H3.3WT or H3.3G34W were transduced in the cells.

tag: cell line

tag: genotype

value: cells overexpressing H3.3G34W

tag: chip antibody

value: BRD4 (Bethyl Laboratories, Cat# A301-985A50, Lot 6)


title: VU4_Ile_R2


title: C3H10T1/2, H3.3G34W_FLAG-H3.3 (ChIP-seq)

description: Immunoprecipitated DNA

value: M2 (Sigma Aldrich, Cat# F1804-50UG)


title: VU13_Ile_R1


title: VU13_Col_R3


title: C3H10T1/2, H3.3G34W_FLAG-H3K36me3_reChIP (ChIP-seq)

description: Immunoprecipitated DNA

value: M2 (Sigma Aldrich, Cat# F1804-50UG) + H3K36me3 (Active Motif, pAb Cat# 61101, Lot 32412003)


title: VU4_Duo_R3

source_name: Duodenum


title: gWAT- B6.Cg-Mir146atm1.1Bal/J ND- #3

tag: tissue


title: VU13_Col_R2


title: VU4_Duo_R2


title: gWAT- B6.Cg-Mir146atm1.1Bal/J ND- #1


title: VU14_Col_R1


title: C3H10T1/2, H3.3G34W_MED1 (ChIP-seq)

description: Immunoprecipitated DNA

value: MED1 (Bethyl Laboratories, Cat# A300-793A, Lot 6)


title: VU4_Ile_R3

value: Female


title: C3H10T1/2, H3.3WT_MED1 (ChIP-seq)

description: Immunoprecipitated DNA

value: cells overexpressing H3.3WT


title: VU4_Duo_R1


title: VU13_Col_R1

value: NovaSeq 6000


title: gWAT- B6.Cg-Mir146atm1.1Bal/J ND- #4


title: VU13_Ile_R2


title: gWAT- C57BL/6J ND- #4

source_name: gWAT of C57BL/6J mice after 10 weeks of normal diet


title: C3H10T1/2, H3.3WT_BRD4 (ChIP-seq)

description: Immunoprecipitated DNA


title: gWAT- B6.Cg-Mir146atm1.1Bal/J ND- #2


title: gWAT- C57BL/6J HFD- #4

value: mice 10 weeks on high fat diet


title: VU4_Ile_R1


title: VU4_Col_R4


title: C3H10T1/2, H3.3WT_FLAG-H3.3 (ChIP-seq)

description: Immunoprecipitated DNA


title: C3H10T1/2, H3.3G34W_FLAG-H3K27me3_reChIP (ChIP-seq)

description: Immunoprecipitated DNA

value: M2 (Sigma Aldrich, Cat# F1804-50UG) + H3K27me3 (Cell Signaling C36B11, Cat# 9733)


title: VU4_Col_R3


title: VU11_Ile_R2


title: VU11_Ile_R3


title: C3H10T1/2, H3.3WT_H3.3FLAG-H3K36me3_reChIP (ChIP-seq)

description: Immunoprecipitated DNA


title: H3.3G34W_input

description: genomic input DNA for ChIPs

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using RPKM (1000000/aligned reads)
Genome_build: mm9

value: cells overexprssing H3.3G34W


title: gWAT- C57BL/6J ND- #1

value: gonadal white adipose tissue (gWAT)

value: female


title: H3.3WT_input

description: genomic input DNA for ChIPs

value: cells overexprssing H3.3WT


title: gWAT- C57BL/6J ND- #5


title: VU4_Col_R2

value: Caucasian


title: VU3_Ile_R3

value: Male


title: C3H10T1/2, H3.3WT_H3.3FLAG-H3K27me3_reChIP (ChIP-seq)

description: Immunoprecipitated DNA


title: H3.3G34W_K27me3_reChIP-validation

description:
Immunoprecipitated DNA
RPKM_K36me3Peaks_reChIPvalidation.txt

data_processing:
Reads were aligned using Bowtie 1.0.0 using default parameters
Data was normalized using RPKM (1000000/aligned reads) or RX (1000000/reads aligned to drosophila genome)
Normalized read density at H3K36me3 peaks were determined for validation of H3K27me3 reChIP-Seq
Genome_build: mm9
Supplementary_files_format_and_content: RPKM_K36me3Peaks_reChIPvalidation.txt (RPKM enrichment at peaks. Bed file.)

treatment_protocol: Lentiviruruses for stable expression of H3.3WT or H3.3G34W were transduced in the cells.


title: VU11_Ile_R1


title: VU12_Ile_R4

description: Cross-platform control

value: Black/African American


title: gWAT- C57BL/6J ND- #3

value: mice 10 weeks on normal diet


title: Mut6: HSCs from Ramp1 Mut rep3

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

data_processing:
Original image data file from high-throughput sequencing (like Illumina) is transformed into sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Raw reads filtering is as follows: 1. Remove reads with adaptor contamination; 2. Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); 3. Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
Sequencing reads were aligned to the mouse genome (mm10) using Spliced Transcripts Alignment to a Reference (STAR).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene and then FPKM (Fragments Per Kilobase of exon model per Million mapped reads) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: Xin MutvsWT_DEG statistics (xls format) contains normalised read counts, read counts and all statistical results by DESeq2 R package ; Xin Gene Description_all fpkm (txt) contails all gene description and fpkm values

source_name: bone marrow

extract_protocol: Total RNA from ~2000 sorted HSCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).

value: adult

value: bone marrow

tag: cell type

value: haematopoietic stem cell (HSC)

value: Ramp-/-


title: VU3_Ile_R1


title: VU11_Duo_R2

value: Female


title: VU3_Ile_R2


title: H3.3WT_K27me3_reChIP-validation

value: cells overexpressing H3.3WT


title: VU11_Duo_R1

value: NovaSeq 6000


title: VU3_Duo_R3


title: gWAT- C57BL/6J ND- #2


title: PY6_CK22_1

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

institute: Guangxi University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated. In short, the number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: MSU RGAP release 7.0
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Oryza sativa

source_name: Untreated seedlings

growth_protocol: The seedlings were grew under normal condition in green house for 21 days

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
cDNA library

treatment_protocol: 21-day old seedlings were drought-treated to soil moisture of 20%.

value: penultimate leaves

value: 21 days

tag: line

tag: phenotype

value: Drought sensitive

tag: stress

value: Untreated


title: PY6_CK22_3

tag: age


title: PY6_CK22_2


title: PY6_CK20_3


title: VU11_Col_R3

tag: race

tag: sequencer


title: PY6_CK20_2


title: Mut4: HSCs from Ramp1 Mut rep1


title: Mut5: HSCs from Ramp1 Mut rep2


title: PY6_CK20_1


title: VU3_Duo_R1


title: WT3: HSCs from Ramp1 WT rep3


title: VU11_Col_R2


title: VU11_Col_R1


title: VU11_Duo_R3


title: WT2: HSCs from Ramp1 WT rep2


title: VU3_Col_R2


title: WT1: HSCs from Ramp1 WT rep1


title: VU3_Col_R3


title: U937-FA_OTX_3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
reads were aligned using Tophat v2.1.1
differential expression was assessed using Cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: Tab separated file containing FPKM values of each genes of the hg19 UCSC reference annotation

source_name: U937 cells cultured without FA treated with OTX

extract_protocol:
Total RNA was extracted using Qiagen RNAEasy plus mini kit
Stranded RNA-seq libraries done with barcoded TruSeq Stranded mRNA LT Sample Prep Kit

value: hematopoietic cells

tag: disease state

value: AML


title: PY6_22_3

source_name: Drought treated seedlings

value: Drought treated


title: PY6_22_2


title: U937-FA_OTX_2


title: H3.3G34W_EZH2

description: Immunoprecipitated DNA

value: cells overexpressing H3.3G34W

value: EZH2 (Cell Signaling, mAb #5246)


title: VU3_Col_R1

tag: Sex

value: Male

value: Caucasian


title: U937-FA_OTX_1


title: PY6_22_1


title: H3.3WT_EZH2

description: Immunoprecipitated DNA


title: VU12_Ile_R3

value: Black/African American


title: VU3_Duo_R2


title: PY6_20_3


title: U937-FA_DMSO_3

source_name: U937 cells cultured without FA treated with DMSO


title: H3.3G34W_FLAG-K36me3

description: Immunoprecipitated DNA

value: M2 (Sigma Aldrich, Cat# F1804-50UG) + H3K36me3 (Active Motif, pAb Cat# 61101, Lot 32412003)


title: PY6_20_2


title: VU12_Ile_R2

source_name: Ileum


title: PY6_20_1


title: VU12_Ile_R1


title: H3.3WT_FLAG-k36me3

description: Immunoprecipitated DNA


title: SETD2KO_H3.3G34W_K27ac

description: Immunoprecipitated DNA

value: SETD2 knockout cells overexpressing H3.3G34W

value: H3K27ac (Active Motif; pAb Cat# 39133)


title: U937-FA_DMSO_1


title: VU12_Duo_R3


title: PR403_CK20_3

value: Drought tolerant


title: U937+FA_OTX_3

source_name: U937 cells cultured with FA treated with OTX


title: SETD2KO_H3.3WT_K27ac

description: Immunoprecipitated DNA

value: SETD2 knockout cells overexpressing H3.3WT


title: VU12_Duo_R2


title: U937+FA_OTX_2


title: VU12_Duo_R1


title: H3.3G34W_K27ac

description: Immunoprecipitated DNA

value: control cells overexpressing H3.3G34W


title: PR403_CK20_2

value: penultimate leaves

value: 21 days


title: U937+FA_OTX_1


title: U937+FA_DMSO_3

source_name: U937 cells cultured with FA treated with DMSO


title: PR403_CK22_3

value: Untreated


title: PR403_CK20_1


title: VU12_Col_R3


title: H3.3WT_K27ac

description: Immunoprecipitated DNA

value: control cells overexpressing H3.3WT


title: VU12_Col_R2


title: PR403_CK22_2


title: U937+FA_DMSO_2

value: hematopoietic cells

value: AML


title: U937-FA_DMSO_2


title: VU12_Col_R1


title: PR403_CK22_1


title: U937+FA_DMSO_1


title: PR403_20_3

value: Drought treated


title: SH_SNA rep3

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

data_processing:
Sequence reads were aligned to the mm10 mouse reference genome sequence using tophat version 2.0.12 running Bowtie2-2.2.3.
Gene structure annotations corresponding to the Ensembl annotation of the mm10 genome sequence were used to build a transcriptome index and provided to tophat during the alignment step
The aligned reads were sorted using samtools-0.1.19, then read counts per gene were obtained from mapped reads using HTSeq-0.6.0
EdgeR version 3.8.6 (using limma-3.22.7) in R-3.1.1 was used to identify differentially expressed genes.
Read-level quality checking was performed using fastqc-0.10.1 and the fastqc-aggregator (https://github.com/staciaw/fastqc_aggregator) and gene-level quality checking was performed using RSeQC-2.6.1 (Wang et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited txt file of sequencing read counts per gene
Supplementary_files_format_and_content: tab-delimited txt file represents the normalized expression data as FPKM, produced by EdgeR

source_name: sciatic L4-L6 dorsal root ganglion

extract_protocol:
For whole DRG, RNA was extracted using RNeasy kit (Qiagen), according to manufacturer’s guidelines. Residual DNA contamination was removed by treating the spin column with 40 units of RNase-free DNase I (Qiagen) for 15 min at room temperature prior to RNA elution. RNA concentrations and purity were verified for each sample following elution with Agilent 2100 Bioanalyzer (Agilent). RNA with RIN factor above 7.5 was used for library preparation.
Libraries were generated using the TruSeq mRNA Sample Preparation Kit  (Illumina, San Diego CA) at Ospedale San Raffaele according to the Sample Preparation Guide protocol. Ligation and library integrity was verified using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent). Sample libraries ligated with unique adapter sequences were multiplexed and were sequenced using Illumina HiSeq 2500 100-cycle, pair end sequencing.

treatment_protocol: Mice (5-8 weeks old)  were housed for 10 days in EE vs SH and underwent either sciatic nerve axotomy or sham injury

value: sciatic L4-L6 dorsal root ganglion

tag: strain

tag: treatment

value: 10 days Standard Housing plus SNA

value: 5-8 weeks old


title: EE_Sham rep3

value: 10 days Environmental Enrichment plus Sham


title: SH_Sham rep3

value: 10 days Standard Housing plus Sham


title: VU10_Ile_R3

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software
RNA-Seq reads were then aligned to their respective Ensembl release 76 human or mouse top-level assemblies with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned, unambiguous reads by Subread:featureCount version 1.4.5
Isoform expression of known Ensembl transcripts were estimated with Sailfish version 0.6.13.
Sequencing performance was then assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.3.
Genome_build: Ensembl release 76 human assembly
Supplementary_files_format_and_content: counts matrix

value: Male

value: Black/African American


title: IMS-M2-FA_OTX_3

source_name: IMS-M2 cells cultured without FA treated with OTX


title: VU10_Ile_R2


title: PR403_20_2

value: Drought tolerant


title: Raji Rep2

source_name: B cell lymphoma cell line

value: B cell lymphoma

tag: passage

tag: expansion method

value: using K562-41BB-mbIL21


title: IMS-M2-FA_OTX_2

tag: cell line


title: PR403_20_1

value: penultimate leaves


title: VU10_Ile_R1