title: PB3M

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
27 mRNA-Seq samples were pooled and sequenced on a NovaSeq 6000 SP using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.33).
First pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMtype BAM Unsorted
Second pass alignment of reads to the hg38 reference genome was performed using STAR (version 2.5.2b) with parameters: STAR --genomeDir /path/to/genomeDir --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --clip3pAdapterSeq - --readFilesIn /path/to/read1.fastq.gz /path/to/read2.fastq.gz --readFilesCommand zcat --runThreadN 32 --outFileNamePrefix <prefix> --outSAMunmapped Within --outWigType None --outWigStrand Stranded --sjdbFileChrStartEnd /path/to/sjdbFile.txt --sjdbGTFfile /path/to/annotations.gtf --limitSjdbInsertNsj 4000000 --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.3.0) and the hg38 v28 gene annotation.
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file contains limma-voom normalized differential expression output.

source_name: Mutant fallopian tube cell line

growth_protocol: 2.5 x 10^5 cells were seeded into Primaria® T25 tissue culture flasks and cultured for three days. FOMI medium (5 ml) was replenished every day. Cells were maintained at 37 degrees Celsius, 5% CO2 and 5% O2 in a humidified environment.

extract_protocol:
RNeasy Plus Mini kit (Qiagen, Germany)
Illumina TruSeq® Stranded mRNA Library Prep (Illumina Inc., CA)

treatment_protocol: For generation of cell lines see Bronder et al. (2021) https://doi.org/10.1101/2021.03.12.435079

value: Mutant fallopian tube cell line

tag: gfp expression

value: to generate/immortalize the parental FNE1 cell line

value: TP53/BRCA1 double-mutant, MYC overexpressing

tag: subclone

value: mutant subclone PB3M


title: Acceptors_TW_0min DE67NGSUKBR114203

status: Public on Sep 28 2021

type: SRA

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

country: Germany

institute: University Hospital Bonn

library_source: transcriptomic

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Batch correction
Flooring
Genome_build: mm10

molecule: total RNA

organism: Mus musculus

source_name: Microglia

growth_protocol: Primary mouse microglia were routinely isolated from neonatal mice. Cells of two brains were plated into T75 flasks and cultured for 7-10 days in DMEM supplemented with 10% FCS, 1% P/S and 1% L929 cell supernatant. Loosely attached mature microglia were shaken off the astrocytic layer and used for experiments.

extract_protocol:
RNA was isolated via Qiagen miRNeasy (micro)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 100bp single reads, 15mio reads deep per sample, NovaSeq 6000

treatment_protocol: Donors (typically 0.25 Mio. per Well in a 24 Well plate) and Acceptors (typically 6 Mio. in a T25 flask) were seed and allowed to adhere overnight. Donors were treated with 1 µM Atto-488-labeled alpha-synuclein for 14 hrs. Acceptors were labelled with CellTracer Violet for 15 min. Following labelling donor and acceptor populations were co-cultured for 15, 30, 60, 150 and 300 min without direct cell-cell contact. RNA of "donor" and "acceptor" cell populations was collected using 700 µl Trizol.

tag: cell type

value: primary mouse microglia

tag: passages

tag: strain


title: 15065X7

city: Salt Lake City

first: Vedran

last: Radojcic

state: UT

address: 2000 Cir of Hope Dr

department: Huntsman Cancer Institute

country: USA

institute: University of Utah

description: Bulk RNA sequencing

data_processing:
The human GRCh38 FASTA and GTF files were downloaded from Ensembl release 92.
The reference database was created using STAR version 2.5.4a with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: FeatureCounts output files combined into a single tab-delimited matrix

organism: Homo sapiens

source_name: Sorted CD8-positive T cells

extract_protocol:
Trizol, followed by GeneJet Micro kit
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)

tag: disease state

value: No GVHD


title: ST88 cell, BRD3  ChIP, sh HuR#1, number 3

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and  their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and  only are retained those  with at least 20 phred quality score.
The sequencing data were mapped to the hg38 genome assembly via Bowtie.
Biological replicates merged and peak calling was performed using Model-based analysis of ChIP-seq (MACS) 2 (Zhang et al., 2008) to identify regions of ChIP-Seq enrichment over background (input) with an enrichment threshold of adjusted p-value < 0.01.
Genome_build: hg38
Supplementary_files_format_and_content: Peaks called from merged biological replicates by MACS2 are submitted as tab separated text files with ".broadPeak" extension.

molecule: genomic DNA

source_name: Cancer cell line

growth_protocol: Human MPNST cell line were maintained in Dulbecco’s modified Eagle Medium (DMEM) (Thermo Fisher Scientific) supplemented with 10% (v/v) fetal bovine serum (FBS) (Thermo Fisher Scientific) and 1% (v/v) antibiotic/antimycotic (Thermo Fisher Scientific) under standard conditions of 37 ºC and 5% CO2.

extract_protocol:
PCR purification kit (Qiagen).
Sequencing libraries were prepared following TruSeq® ChIP Sample Preparation Guide with the corresponding kit (Illumina Inc.).  ChIPseq libraries were single-read sequenced for 51 nucleotides in a HiSeq2500 (Illumina Inc.)

treatment_protocol: Chromatin immunoprecipitation was performed essentially as described (Fontanals-Cirera et al., 2017). In brief, ST88-14 cells were infected with shControl or shHuR#1 lentivirus, selected with puromycin for 2 days, replated and then 2 days later cross-linked with 1% formaldehyde for 10 min at RT and reaction quenched with 125 mM glycine for 5 min. The isolated nuclei were resuspended in nuclei lysis buffer and sonicated using a Bioruptor Sonicator (Diagenode). The samples were immunoprecipitated with the appropriate antibodies overnight at 4 ºC. Protein G beads (Thermo Fisher Scientific) were added and incubated for 1 h, and the immunoprecipitates were washed twice, each with low-salt, high-salt and LiCl buffer. The eluted DNA was reverse-crosslinked and purified using PCR purification kit (Qiagen).

value: NF1-derived MPNST

tag: cell line

tag: chip antibody

value: Anti-BRD3  Rabbit polyclonal, Bethyl, Cat# A302-367A

tag: treatment

value: sh HuR


title: ST88 cell, BRD3  ChIP, sh Ctr, number 2

value: sh Ctr


title: aSyn_Donor_3 [DE04NGSUKBR108935_S226]

data_processing:
Alignment with STAR against the mm10 reference genome
quantification of gene counts via Partek's E/M algorithm
DEseq2 normalization
Batch correction
Flooring
Genome_build: mm10
Supplementary_files_format_and_content: normalized and raw counts

extract_protocol:
RNA was isolated via Qiagen miRNeasy (micro)
performed by the NGS Core Facility University Hospital Bonn according to the maufacturers' user guide for the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (https://www.lexogen.com/quantseq-3mrna-sequencing/#quantseqdownloads/)
1x 50bp single reads, 15mio reads deep per sample, Illumina HiSeq2500

treatment_protocol: Donors (typically 10 Mio. per petri dish) and Acceptors (typically 2 Mio. per T25 flask) were seed and allowed to adhere overnight. Donors were treated with 1 µM Atto-488-labeled alpha-synuclein for 14 hrs. Acceptors were labelled with CellTracer Violet for 15 min. Following labelling donor and acceptor populations were co-cultured for 15, 30, 60, 150 and 300 min. Co-cultures were sorted back into their original “donor” and “acceptor” cell populations by flow cytometrical cell sorting and RNA was collected using 700 µl Trizol.

tag: group


title: Untreated_Ctrl_3 [DE31NGSUKBR108934_S225]


title: 15065X4

description: Bulk RNA sequencing

value: GVHD


title: Acceptors_150min_3 [DE52NGSUKBR108944_S235]


title: PB3E

tag: genotype

value: TP53/BRCA1 double-mutant, empty vector

value: mutant subclone PB3E


title: 15065X8

description: Bulk RNA sequencing


title: Acceptors_TW_15min DE57NGSUKBR114189


title: Acceptors_300min_4 [DE06NGSUKBR110063_S82]


title: Ctrl_0min DE40NGSUKBR114204


title: ST88 cell, BRD4  ChIP, sh Ctr, number 2

value: Anti-BRD4 Antibody  Rabbit polyclonal, Bethyl, Cat# A301-985A50


title: Donors_30min_3 [DE90NGSUKBR108939_S230]


title: 15065X9

description: Bulk RNA sequencing


title: Acceptors_30min_3 [DE63NGSUKBR108940_S231]


title: PB2E

value: mutant subclone PB2E


title: Acceptors_150min_4 [DE60NGSUKBR110061_S80]


title: Donors_TW_300min DE36NGSUKBR114179


title: ST88 cell, BRD4  ChIP, sh HuR#1, number 2


title: 15065X6

description: Bulk RNA sequencing


title: Donors_150min_4 [DE87NGSUKBR110060_S79]


title: Acceptors_60min_4 [DE17NGSUKBR110059_S78]


title: Acceptors_15min_3 [DE20NGSUKBR108938_S229]


title: PB3

value: TP53/BRCA1 double-mutant

value: mutant subclone PB3


title: Acceptors_TW_0min DE30NGSUKBR114190


title: Donors_60min_4 [DE44NGSUKBR110058_S77]


title: PB1

value: Mutant fallopian tube cell line

value: mutant subclone PB1


title: Acceptors_TW_60min DE51NGSUKBR114200


title: Donors_TW_0min DE35NGSUKBR114197


title: Acceptors_30min_4 [DE71NGSUKBR110057_S76]


title: Donors_TW_60min DE42NGSUKBR114168


title: Donors_15min_3 [DE47NGSUKBR108937_S228]


title: 15065X2

description: Bulk RNA sequencing


title: P3M

value: to generate/immortalize the parental FNE1 cell line

value: TP53 mutant, MYC overexpressing

value: mutant subclone P3M


title: ST88 cell, H3K27Ac  ChIP, sh Ctr, number 2

value: Anti-H3K27Ac-human antibody  Rabbit polyclonal, Abcam, Cat# ab4729


title: Donors_TW_150min DE46NGSUKBR114193

value: primary mouse microglia


title: Acceptors_TW_150min DE41NGSUKBR114186


title: Donors_300min_4 [DE33NGSUKBR110062_S81]


title: Donors_TW_60min DE19NGSUKBR114194


title: ST88 cell, H3K27Ac  ChIP, sh HuR#1, number 1

value: NF1-derived MPNST


title: P1M_2

value: mutant subclone P1M


title: ST88 cell, BRD4  ChIP, sh Ctr, number 3

value: sh Ctr


title: ST88 cell, BRD4  ChIP, sh HuR#1, number 3

value: sh HuR


title: P1M_1


title: PB2

value: mutant subclone PB2


title: Untreated_Ctrl_4 [DE39NGSUKBR110051_S70]


title: PB2M

value: TP53/BRCA1 double-mutant, MYC overexpressing

value: mutant subclone PB2M


title: PB1E

value: TP53/BRCA1 double-mutant, empty vector

value: mutant subclone PB1E


title: ST88 cell, BRD4  ChIP, sh Ctr, number 1

value: Anti-BRD4 Antibody  Rabbit polyclonal, Bethyl, Cat# A301-985A50


title: ST88 cell, H3K4me1 ChIP, sh Ctr, number 1

value: Anti-Histone H3, monomethyl (Lys4)  Rabbit polyclonal, Abcam, Cat# ab8895


title: Acceptors_TW_30min DE24NGSUKBR114201


title: PB1M

value: Mutant fallopian tube cell line

value: mutant subclone PB1M


title: Acceptors_TW_300min DE31NGSUKBR114172


title: Donors_TW_15min DE25NGSUKBR114183


title: ST88 cell, H3K27Ac  ChIP, sh Ctr, number 1


title: ST88 cell, BRD4  ChIP, sh HuR#1, number 1


title: Donors_30min_4 [DE98NGSUKBR110056_S75]


title: Donors_TW_150min DE09NGSUKBR114180


title: Acceptors_TW_15min DE20NGSUKBR114176


title: ST88 cell, H3K4me1 ChIP, sh Ctr, number 3


title: ST88 cell, H3K4me1 ChIP, sh HuR#1, number 2


title: P2M

value: to generate/immortalize the parental FNE1 cell line

value: TP53 mutant, MYC overexpressing

value: mutant subclone P2M


title: P1M_3


title: RNA-seq_LSK-G12D_E2-KO-shGem_rep1

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to mouse reference genome (GRCm38) by STAR 2.7.3a in the 2-pass mode
Gene counts were quantified with HTSeq
Differential gene-repeat expression analyses were performed using DEseq2.
Genome_build: mm10
Supplementary_files_format_and_content: text file of gene read count values

growth_protocol: Mouse lineage negative cells were cultured  in Prime-XV Mouse Hematopoietic Cell Medium (Irvine Scientific) supplemented with 50 μmol/L β-Mercaptoethanol, 1% FBS, 50 ng/mL stem cell factor (SCF) and 50 ng/mL TPO. All cultures were incubated at 37°C in 5% CO2.

extract_protocol: For RNA-seq analysis using the illumina NextSeq500, RNA was extracted from sorted GFP positve LSK cells (~10, 000) using RNeasy plus Micro Kit (Qiagen). Total RNA was processed for library generation using the SMARTer stranded pico input total RNA-seq kit v2 (Takara).

treatment_protocol: Lineage negative cells were transduced with shRNA virus against luciferase (shLuc) or GEM (shGem) by two rounds of spin infection (1200g, 90 min, 32℃) with shRNA viruses within 48 hours

tag: tissue

value: bone marrow

value: bone marrow LSK cells

value: shGem


title: Acceptors_15min_4 [DE28NGSUKBR110055_S74]

value: primary mouse microglia


title: aSyn_Donor_4 [DE12NGSUKBR110052_S71]


title: ST88 cell, H3K27Ac  ChIP, sh HuR#1, number 3

value: NF1-derived MPNST

value: Anti-H3K27Ac-human antibody  Rabbit polyclonal, Abcam, Cat# ab4729

value: sh HuR


title: Donors_15min_4 [DE55NGSUKBR110054_S73]


title: ST88 cell, H3K27Ac  ChIP, sh HuR#1, number 2


title: Donors_TW_30min DE15NGSUKBR114169


title: RNA-seq_LSK-G12D_E2-KO-shLuc_rep2

value: shLuc


title: ST88 cell, H3K4me1 ChIP, sh HuR#1, number 3


title: Acceptors_TW_60min DE14NGSUKBR114187


title: ST88 cell, H3K27Ac  ChIP, sh Ctr, number 3

value: sh Ctr


title: P1E_1

value: TP53 single-mutant, empty vector

value: mutant subclone P1E


title: Acceptors_TW_300min DE08NGSUKBR114198


title: P1E_2


title: P3

value: TP53 single-mutant

value: mutant subclone P3


title: ST88 cell, H3K4me1 ChIP, sh Ctr, number 2

value: Anti-Histone H3, monomethyl (Lys4)  Rabbit polyclonal, Abcam, Cat# ab8895


title: Untreated_Ctrl_4 [DE66NGSUKBR110050_S69]


title: P3E

value: Mutant fallopian tube cell line

value: to generate/immortalize the parental FNE1 cell line

value: mutant subclone P3E


title: RNA-seq_LSK-WT-shGem_rep2

source_name: LSK-WT-shGem

value: bone marrow

value: WT


title: CM-RevDKO.Rep1

city: Philadelphia

first: Chunjie

last: Jiang

state: PA

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: ExpressionProfile.txt

data_processing:
RNA-seq reads were aligned to mm10 using Hisat2 with default parameters. Only unique mapped reads were considered for further analysis. Normalized expression value, FPKM, was calculated for each gene using StringTie
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HORMER V4.9; Normalized abundance measurement was generated using StringTie.

source_name: Heart

growth_protocol: Hearts from 2-months-old mice were harvested at ZT10 and atria were trimmed.

extract_protocol:
Total RNA was extracted by using TRIZOL
RNA libraries were prepared for sequencing using the NEBNext Ultra II kit

tag: age

value: heart

value: CM-RevDKO


title: CM-RevDKO.Rep3

description: ExpressionProfile.txt


title: P2E

value: mutant subclone P2E


title: RevFloxed_Control.Rep3

description: ExpressionProfile.txt

value: control


title: P1_3

value: mutant subclone P1


title: RNA-seq_LSK-WT-shGem_rep1

value: bone marrow LSK cells

value: shGem


title: ST88 cell, H3K4me3 ChIP, sh HuR#1, number 1

value: NF1-derived MPNST

value: Anti-Histone H3 (tri methyl K4) Rabbit polyclonal, Abcam, Cat# ab8580

value: sh HuR


title: RevFloxed_Control.Rep2

description: ExpressionProfile.txt


title: RNA-seq_LSK-WT-shLuc_rep2

source_name: LSK-WT-shLuc

value: shLuc


title: Acceptors_TW_150min DE04NGSUKBR114173

value: primary mouse microglia


title: RNA-seq_LSK-G12D_E2-KO-shLuc_rep1


title: P1E_3

value: Mutant fallopian tube cell line

value: TP53 single-mutant, empty vector

value: mutant subclone P1E


title: RNA-seq_LSK-G12D_E2-KO-shGem_rep2

value: bone marrow


title: G12D_E2-KO_T2

data_processing:
Raw data were pre-processed with 10x Genomics Cell Ranger Single Cell Software Suite 2.0.2.  bcl files were fdemultiplexed into fastq files using "cellranger mkfastq". Reads alignment to mm10 reference genome and single cell 3' gene counting were performed using "cellranger count".
Genome_build: mm10
Supplementary_files_format_and_content: count matrix as genes as columns and cells as rows

molecule: polyA RNA

source_name: G12D/E2-KO HSPCs

growth_protocol: All mice were be maintained under specific pathogen free core facility. Age mathced (8-12 weeks) mice were Intraperitoneally injected with pIpC for five times at 20 mg/ml every other day. Bone marrow cells were harvest  at T1 (2 weeks after pIpC), T2 (2 months post-pIpC) and T3 (4 months post-pIpC) by flushing femurs and tibias with a 25G needle. Bone marrow cells were stained with c-kit anitbody in Ca2+- and Mg2+-free Hank’s buffered salt solution plus 2% heat-inactivated bovine serum. C-kit+ cells were enriched by magnetic seperation and then subjected to scRNA-seq with 10x genomics platform.

extract_protocol:
10x Genomics Chromium Single Cell 3′ Reagent Kit
3' mRNA sequencing

value: Bone marrow Kit+ cells

tag: time point

value: T2 (2 months post-pIpC)


title: FNE1_2

source_name: Fallopian tube cell line

value: Fallopian tube cell line

value: to generate/immortalize the parental FNE1 cell line

value: Wildtype

value: parental FNE1


title: G12D_E2-KO_T3

value: T3 (4 months post-pIpC)


title: RNA-seq_MPNST cell ST88-14 number 2  shHuR#1

description:
shHuR3_2
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed for adapters using cutadapt (Martin, 2011) and aligned to hg38 genome using STAR(Dobin et al., 2013).
Quantification in expected counts from genes and isoforms were computed by RSEM (Li and Dewey, 2011) using genecode annotation v.26 [https://www.gencodegenes.org/].
We use TMM method to estimate scale factors between samples followed by the voom function in limma to convert them into log2counts per million (logCPM).
Finally, differential expression between shControl and shHUR-infected cells were evaluated by LIMMA bioconductor package (Ritchie et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: Tables of raw gene and isoform counts, obtained from the BAM files of the samples in each comparative. These tables are in tab separated plain text format.

extract_protocol:
RNA isolated 2 days later with TRIzol Reagent (Thermo Fisher Scientific) following manufacturer’s instructions.
TruSeq® RNA Sample Preparation v2 (Illumina Inc.)

treatment_protocol: ST88-14 MPNST cells were infected with shControl or shHuR#1 lentivirus, selected with puromycin for 2 days, replated and then RNA isolated 2 days later

tag: genotype/variation


title: RNA-seq_MPNST cell ST88-14 number 1 shHuR#1

description:
shHuR3_1
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt


title: G12D_E2-KO_T1

value: T1 (2 weeks after pIpC)


title: ST88 cell, Input, sh Ctr, number 3

value: NF1-derived MPNST

value: none (input)

value: sh Ctr


title: ST88 cell, Input, sh HuR#1, number 1

value: sh HuR


title: ST88 cell, H3K4me3 ChIP, sh HuR#1, number 3

value: Anti-Histone H3 (tri methyl K4) Rabbit polyclonal, Abcam, Cat# ab8580


title: Ctrl_0min DE03NGSUKBR114191

value: primary mouse microglia


title: CM-RevDKO.Rep2

description: ExpressionProfile.txt

value: heart

value: CM-RevDKO


title: ST88 cell, Input, sh Ctr, number 1


title: RNA-seq_MPNST cell ST88-14 number 2 sh Ctr

description:
shCtr_2
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt


title: G12D_T2

source_name: G12D HSPCs

value: bone marrow


title: ST88 cell, H3K4me3 ChIP, sh Ctr, number 1


title: ST88 cell, H3K4me3 ChIP, sh Ctr, number 3


title: THP-1 Derived Macrophages - PW rep2

city: Tianjin

first: Rui

last: Wang

address: No. 22, Meteorological Station Road, Heping District, Tianjin

country: China

institute: Tianjin Medical Univercity

data_processing:
Quality control.The data of the sequenced fragments measured by the high-throughput sequencer is converted into sequence data (reads) by CASAVA base recognition, and the file is in fastq format. In order to ensure the quality and reliability of data analysis,clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome.Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level.featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: hg19, GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: THP-1 Derived Macrophages

growth_protocol: The THP-1 cells were cultured in the complete RPMI 1640 medium containing 10% FBS, 2 mM L-glutamine and 1 mM sodium pyruvate with 5% CO2 at 37 C. These cells were seeded into culture plates with the addition of PMA (50 ng/mL)for 24 h to differentiate into macrophages.They were then washed twice with PBS and rested for 48 h prior to further experiments.

extract_protocol:
The total RNA was extracted using RNeasy mini kit and assessed by a Nanodrop Lite Spectrophotometer for the purity.
RNA libraries were prepared for sequencing using standard Illumina protocols.A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase,Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The seeded macrophages were treated with the hybrids-PW, TLR ligands LPS or both the hybrid-PW and TLR ligands LPS stimulus for various time periods.

value: THP-1 Derived Macrophages

value: peripheral blood

value: treated with PW for 4 hours


title: G12D_T1

value: Bone marrow Kit+ cells


title: ST88 cell, Input, sh HuR#1, number 3


title: ST88 cell, H3K4me3 ChIP, sh HuR#1, number 2


title: P1_2

value: Mutant fallopian tube cell line

value: to generate/immortalize the parental FNE1 cell line

value: TP53 single-mutant

value: mutant subclone P1


title: E2-KO_T3

source_name: E2-KO HSPCs

value: T3 (4 months post-pIpC)


title: THP-1 Derived Macrophages - LPS-PW rep3

value: treated with PW and LPS cosimulation for 4 hours


title: RevFloxed_Control.Rep1

description: ExpressionProfile.txt

value: control


title: P2

value: mutant subclone P2


title: L3_2

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

data_processing:
Quality score trimming and filtering were performed with Trimmomatic (v0.32).
Trimmed reads were aligned to the annotated Dm genome (build BDGP5, Ensembl release 70) using Hisat2 (v2.1.0)
Per gene read counts were calculated from the TopHat output using htseq-count (v0.5.4p5)
RPKM (Reads Per Kilobase of exon per Megabase of library size)  were caclulated using Cufflinks (2.2.1)
Differential gene expression was analyzed using the R package DESeq2 (v1.2.8)
Genome_build: BDGP dm6
Supplementary_files_format_and_content: tab-delimited text files include FBGN number and RPKM values for each sample.

organism: Drosophila melanogaster

source_name: third instar larvae peripheral hemocytes

extract_protocol:
RNA were extracted with Qiagen RNeasy Plus Micro kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Library preparation was performed using Kapa Biosystems library preparation kit.

treatment_protocol: Adults were bleed by perfusing PBS. Third instar larval lymph glands were dissected in ice cold PBS.

value: Blood

value: third instar larvae


title: P1_1


title: RNA-seq_LSK-WT-shLuc_rep1

value: bone marrow LSK cells

value: WT

value: shLuc


title: FNE1_3

value: Fallopian tube cell line

value: Wildtype

value: parental FNE1


title: RNA-seq_MPNST cell ST88-14 number 3  shHuR#1

description:
shHuR3_3
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt

value: NF1-derived MPNST

value: sh HuR


title: RNA-seq_MPNST cell ST88-14 number 3 sh Ctr

description:
shCtr_3
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt

value: sh Ctr


title: ST88 cell, Input, sh Ctr, number 2

value: none (input)


title: CD8 T cells activated with Trans beads from Donor 3

type: RNA

city: Pamplona

first: Itziar

last: Otano

address: Avda Pio XII, 55

institute: CIMA-University of Navarra

hyb_protocol: A total of 2.3μg of biotinylated cRNA was fragmented and hybridized to Affymetrix hukman Clariom S Assay  (ThermoFisher Scientific Inc.)

scan_protocol: Arrays were scanned with  Affymetrix GeneChip Command Console (AGCC) Software at the Molecular Biology Department (Murcia University)

data_processing: The microarray data were analyzed using the Affymetrix Transcriptome Analysis Console. The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters.

label: biotin

source_name: Purified human CD8 T cells activated for 32 hours

label_protocol: RNA (100ng) was used for generating biotinylated cRNA through single-round amplification using the MessageAmpIII RNA Amplification kit following the manufacturer’s recommendations (Ambion, ThermoFisher Scientific Inc.).

growth_protocol: Human CD8 T cells were purified from peripheral blood of 3 healthy donors.

extract_protocol: RNA from  activated  CD8 T cells was extracted using Trizol and RNeasy Micro kit (Qiagen) per the manufacturer’s instructions.

treatment_protocol: mAb coated beads were used to stimulate CD8 T cells for 32 hours. Microbeads were covalently coated with either anti-CD3 mAb, anti-CD137 mAb, or a mixture of both antibodies to mimic antigen-presenting cells. Coated microbeads with anti-CD3 and anti-CD137 mAbs are named  cis beads, whereas a mixture of 1:1 microbeads coated with anti-CD3 or anti-CD137 are named trans beads.

tag: activation time

value: 32 hours

tag: disease

value: healthy


title: WT_T2

source_name: WT HSPCs

value: bone marrow

value: Bone marrow Kit+ cells

value: T2 (2 months post-pIpC)


title: L3_3

value: Blood


title: THP-1 Derived Macrophages - LPS-PW rep2

value: THP-1 Derived Macrophages

value: peripheral blood

value: treated with PW and LPS cosimulation for 4 hours


title: THP-1 Derived Macrophages - PW rep3

value: treated with PW for 4 hours


title: ST88 cell, Input, sh HuR#1, number 2


title: RNA-seq_MPNST cell ST88-14 number 1 sh Ctr

description:
shCtr_1
shHuR3_vs_shCtrl_CountsxGene.txt
shHuR3_vs_shCtrl_CountsxIsoform.txt


title: WT_T1

value: WT

value: T1 (2 weeks after pIpC)


title: LG_1

source_name: third instar larvae lymph gland

value: third instar larvae


title: FNE1_1

value: Fallopian tube cell line

tag: gfp expression

value: to generate/immortalize the parental FNE1 cell line

value: Wildtype

value: parental FNE1


title: G12D_T3

value: T3 (4 months post-pIpC)


title: THP-1 Derived Macrophages - LPS rep1

value: treated with LPS for 4 hours


title: H3K27ac.IgG

data_processing:
Library strategy: Cut&Run
ChIP-seq reads were aligned to the mm10 using Bowtie2. Only unique mapped reads were considered for further analysis. Peak calling was performed by HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using HORMER V4.9; Normalized abundance measurement was generated using StringTie.

source_name: Heart (Isolated adult cardiomyocytes)

growth_protocol: Cardiomyocytes from hearts from 2-months-old mice were harvested via Langendorff perfusion.

extract_protocol:
H3K27ac (Cell Signaling Technology #8173) or Rabbit IgG (Cell Signaling Technology #3900) at 1:100 was incubated with cardiomyocytes which were attached to Concanavalin A coated magnetics beads (Bangs Laboratories #BP531) overnight at 4 degrees. Next day, 2.5ul of pA-MNase from 1:10 dilution of the original stock provided by the Henikoff lab was applied to cell-beads mixture and incubated at room temperature for 10min. Pull-down DNA was extracted in phase-lock tubes using phenol-chloroform method.
DNA library was prepared using Hyper-prep kit (KAPA Biosystems KK8502).

value: Rabbit IgG CST#3900

value: heart


title: CD8 T cells activated with Cis beads from Donor 2

value: 32 hours

value: healthy


title: THP-1 Derived Macrophages - PW rep1

value: THP-1 Derived Macrophages


title: E2-KO_T2

value: bone marrow

value: Bone marrow Kit+ cells

value: T2 (2 months post-pIpC)


title: THP-1 Derived Macrophages - Unstim rep3

value: peripheral blood

value: untreated


title: E2-KO_T1

value: T1 (2 weeks after pIpC)


title: LG_2

value: Blood

value: third instar larvae


title: CD8 T cells activated with Cis beads from Donor 3


title: THP-1 Derived Macrophages - LPS-PW rep1

value: treated with PW and LPS cosimulation for 4 hours


title: CD8 T cells activated with aCD3  beads from Donor 2


title: THP-1 Derived Macrophages - LPS rep2


title: WT_T3

value: WT


title: L3_1


title: CD8 T cells activated with Trans beads from Donor 1


title: CD8 T cells activated with Trans beads from Donor 2


title: AD_3

source_name: Adult hemocytes

value: Adult


title: THP-1 Derived Macrophages - Unstim rep2


title: CD8 T cells activated with aCD3  beads from Donor 3


title: THP-1 Derived Macrophages - LPS rep3

value: treated with LPS for 4 hours


title: LG_3


title: H3K27ac_RevFloxed_Control

value: control


title: H3K27ac_CM-RevDKO

value: heart

value: CM-RevDKO


title: AD_2


title: THP-1 Derived Macrophages - Unstim rep1


title: CD8 T cells activated with aCD3  beads from Donor 1

value: 32 hours

value: healthy


title: RUN_13_10_NC

status: Public on Sep 27 2021

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: Probes were hybridized to 60 ng of total RNA for 20 hours at 65°C and applied to the nCounter preparation station for automated removal of excess probe and immobilization of probe-transcript complexes on a streptavidin-coated cartridge.

scan_protocol: Data were collected with the nCounter digital analyzer by counting the individual barcodes. Readout of the cartridges was performed in the Institute for Pathology, Hannover Medical School.

data_processing: For normalization of RNA-expression data the trimmed mean of M-values (TMM) method was used for composition bias and to estimate the relative RNA expression. TMM normalization was performed using the calcNormFactor und voom function in R (v3.5.3), which calculated a normalization factor for each sample. The product of these factors and the library sizes defined the effective library size in all downstream analyses.

label_protocol: We assessed the expression of 770 genes by using the nCounter PanCancer Immune Profiling Panel of the nanoString technology (nanoString Technologies, Seattle WA, U.S.A). Each biotinylated capture probe in the panel was manufactured with specificity to a 100-base region of the target mRNA. A complementary reporter probe tagged with a specific fluorescent barcode was also included, thus resulting in two sequence-specific probes for each target transcript.

extract_protocol: Primary lung adenocarcinoma patients with  available Formalin-fixed paraffin-embedded (FFPE) tissue derived from resectates suitable for the proposed analysis.were collected from 2001 to 2017.   Tumors were graded according to the 2015 World Health Organization Classification of Lung Tumors and for determination of tumor state. The cohort included LUADS with no history of previous malignancies or history of receiving chemotherapy or radiotherapy. 138 patients whose FFPE material exclusively deriving from resectates was used in downstream itranscriptomic analysis of which 58 (42.0%) were of female and 80 (58.0%) of male human origin. Lung adenocarcinomas were classified into four different groups, depending on their PD-L1 expression status determined by IHC and total immune infiltration determined by H&E. Cases with tumors expressing PD-L1 and high total immune cell infiltration were designated as PH (n=23), cases with tumors expressing PD-L1 and low total immune cell infiltration were designated as PC (n=7), cases with no PD-L1 expression and high total immune cell infiltration were designated as NH (n=53) and cases with no PD-L1 expression and low total immune cell infiltration were designated as NC (n=55). For each sample tissue areas with preferably high tumor cell content were selected for nucleic acid extractions using microdissection. For the PH group with a slightly heterogeneous PD-L1 expression pattern, only areas with PD-L1 positive tumor cells were chosen. mRNA isolation and quantification were performed using the Maxwell RSC RNA FFPE Kit together with the Maxwell RSC instrument (Promega, Fitchburg WI, U.S.A.) and the Qubit fluorimeter (ThermoFisher, Waltham MA, U.S.A.), respectively.

value: primary lung cancer

value: NC

tag: run

tag: patient id

value: lung adenocarcinoma


title: RUN_13_08_NC


title: RUN_13_09_NC


title: RUN_13_07_NC


title: RUN_13_04_NC


title: RUN_13_05_NC


title: RUN_13_03_NC


title: RUN_13_02_NC


title: RUN_13_11_NC


title: AD_1


title: RUN_12_11_PH

value: PH


title: RUN_12_06_PC

value: PC


title: RUN_13_06_NC


title: RUN_12_07_PC


title: RUN_12_05_PC


title: RUN_12_12_PH


title: RUN_12_09_PC


title: RUN_13_01_NC


title: RUN_12_04_PC


title: RUN_12_10_NC


title: RUN_12_02_NH

value: NH


title: RUN_12_03_PC


title: RUN_12_08_PC


title: RUN_11_09_PH


title: RUN_11_11_PH


title: RUN_13_12_NC


title: RUN_12_01_NH


title: CD8 T cells activated with Cis beads from Donor 1


title: RUN_11_06_PH


title: RUN_11_05_PH


title: RUN_11_07_PH


title: RUN_11_04_PH


title: Cal_2

city: Beijing

first: Xiaoping

state: Beijing

address: No. 5, Dongdan Santiao, Dongcheng District, Beijing

institute: Peking Union Medical College

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

organism: Rattus norvegicus

source_name: heart

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

tag: strain background

value: Sprague Dawley

value: Cal


title: Cal_3


title: RUN_11_10_PH


title: Control1_3

value: Control


title: Cal_1


title: RUN_11_08_PH


title: RUN_11_03_PH


title: RUN_11_01_PH


title: RUN_11_02_PH


title: Model_3

value: Model


title: Model_2


title: RPE.KDM4A-OE.S4.rep2

city: Boston

first: Fei

last: Ji

address: 185 Cambridge St

institute: Massachusetts General Hospital

description: RPE KDM4A 2

data_processing:
Library strategy: Repli-Seq
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 reference genome hg19 using BWA
Coverage over 50 kbp genomic bins were count across the genome, followed by the Loess smoothing of bin counts as described in (C. Marchal et al., Nat Protoc, 2018)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, smoothen genome coverage over 50Kb

source_name: Retinal Pigmented Epithelial

growth_protocol: 15 cm plates of 2 million RPE cells were seeded for 48 hours, in order to be harvested at ~70% confluency

extract_protocol:
Cells were washed and resuspended in 2.5 ml cold 1X PBS – 1% FBS. 7.5 ml cold 70% EtOH was added drop by drop while vortexing the samples. Fixed cells were stored at -20 degrees. Cells were pelleted at 4 degrees, resuspended in 3 ml 1X PBS – 1% FBS – 1/100 Propidium Iodide – 250 g/ml RNAse A, and incubated 1 hour RT in the dark.  After FACS sort DNA was extracted and replicating DNA immunoprecipitated with anti-BrdU.
Libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences 30024) following supplier’s protocol, starting with 15 ml of immunoprecipitated DNA and following the recommendation for <10 ng, using 7 cycles of PCR amplification. Library length distribution were assessed by TapeStation (Agilent) and quantified with Qubit (ThermoFisher). Libraries were single-end sequenced (75 cycles) using a NextSeq500 (Illumina).

treatment_protocol: 100 mM BrdU for 2 hours

tag: cell type

value: Retinal Pigmented Epithelial

tag: cell cycle phase

tag: ip antibody

value: BrdU


title: RUN_11_12_PH

tag: disease state


title: RUN_9_11_NH


title: RUN_9_08_NH


title: RPE.KDM4A-OE.S2.rep2

description: RPE KDM4A 2


title: RUN_9_10_NH


title: Control1_1


title: RUN_9_12_NH


title: RPE.KDM4A-OE.S3.rep2

description: RPE KDM4A 2


title: RUN_9_09_NH


title: RPE.KDM4A-OE.S4.rep1

description: RPE KDM4A 1


title: Model_1


title: RUN_9_05_NH


title: Control1_2


title: RPE.Ctrl.S4.rep2

description: RPE Control 2

value: Ctrl


title: RUN_9_04_NH


title: RUN_9_07_NH


title: RPE.KDM4A-OE.S3.rep1

description: RPE KDM4A 1


title: RUN_9_03_NH


title: RPE.Ctrl.S3.rep2

description: RPE Control 2


title: RUN_9_02_NH


title: RPE.KDM4A-OE.S2.rep1

description: RPE KDM4A 1


title: RUN_9_01_NH


title: RPE.Ctrl.S1.rep2

description: RPE Control 2


title: RUN_9_06_NH


title: RPE.Ctrl.S2.rep2

description: RPE Control 2


title: RPE.Ctrl.S3.rep1

description: RPE Control 1


title: RPE.KDM4A-OE.S1.rep2

description: RPE KDM4A 2


title: RUN_8_11_NH


title: RUN_8_12_NH


title: RUN_8_10_NH


title: RPE.KDM4A-OE.G2.rep1

description: RPE KDM4A 1


title: RPE.KDM4A-OE.ES.rep2

description: RPE KDM4A 2

value: early S


title: RPE.KDM4A-OE.S1.rep1

description: RPE KDM4A 1


title: RUN_8_05_NH


title: RUN_8_03_NH


title: RPE.Ctrl.S1.rep1

description: RPE Control 1


title: RUN_8_02_NH


title: RPE.Ctrl.S4.rep1

description: RPE Control 1


title: RUN_7_12_NH


title: RUN_8_07_NH


title: RPE.Ctrl.G2.rep2

description: RPE Control 2


title: RUN_8_08_NH


title: RUN_8_06_NH


title: RPE.Ctrl.S2.rep1

description: RPE Control 1


title: RPE.KDM4A-OE.ES.rep1

description: RPE KDM4A 1


title: RPE.KDM4A-OE.G2.rep2

description: RPE KDM4A 2


title: RUN_8_09_NH


title: RUN_8_01_NH


title: RPE.Ctrl.G2.rep1

description: RPE Control 1


title: RUN_7_07_NH


title: RPE.KDM4A-OE.LS.rep2

description: RPE KDM4A 2

value: late S


title: RUN_8_04_NH


title: RPE.Ctrl.LS.rep2

description: RPE Control 2


title: RUN_7_11_NH


title: RUN_7_06_NH


title: RUN_7_10_NH


title: RPE.Ctrl.ES.rep2

description: RPE Control 2


title: RPE.KDM4A-OE.input.LS.rep2

data_processing:
Reads were aligned to hg19 using BWA, and PCR duplicates were removed using samtools rmdup.
Peak calling was performed using the Homer package (HOMER v4.8) with matched inputs.
Coverage over 50 kbp genomic bins were count across the genome and count per million reads (CPM) was normalizaed in each library.
Genome_build: hg19
Supplementary_files_format_and_content: peak files (bed) generated by findpeaks (Homer)
Supplementary_files_format_and_content: bigWig, CPM genome coverage over 50Kb

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP sequencing libraries were prepped using the TruSeq ChIP Sample Preparation kit (Illumina) following the supplier’s protocol with slight modifications. 1 ng or 35 ml of DNA was used for library preparation. After ligating the adapters, fragments were amplified with 13 cycles of PCR (“Purify Ligation Products” section was skipped). The PCR products were purified using a Double-Sided SPRI approach: AMPure was added to 0.6X SPRI concentration (30 ml of AMPure is added to 50 ml of PCR reaction) and incubated for 10 minutes at RT before being placed on the magnet. Beads were discarded and supernatant was incubated with 0.85X SPRI concentration (12 ml of AMPure is added) and incubated for 10 minutes at RT before being placed on the magnet. Liquid was removed before performing two washes with 450 ml fresh 70% EtOH. DNA was eluted with 15 ml H2O. Library length distribution were assessed by TapeStation (Agilent) and quantified with Qubit (ThermoFisher). Libraries were single-end sequenced (75 cycles) using a NextSeq500 (Illumina).

tag: chip antibody

value: input


title: RPE.Ctrl.LS.rep1

description: RPE Control 1


title: RPE.KDM4A-OE.LS.rep1

description: RPE KDM4A 1


title: RPE.KDM4A-OE.input.G2.rep2


title: RUN_7_08_NH

tag: group


title: RUN_7_03_NH


title: RUN_6_12_NH


title: RPE.Ctrl.ES.rep1

description: RPE Control 1


title: RPE.KDM4A-OE.input.ES.rep2


title: RUN_7_05_NH


title: RPE.KDM4A-OE.input.G1.rep2


title: RPE.KDM4A-OE.input.G2.rep1


title: RUN_6_11_NH


title: RUN_6_10_NH


title: RUN_7_02_NH


title: RUN_7_04_NH


title: RUN_7_01_NH


title: RPE.Ctrl.input.LS.rep2


title: RUN_6_08_NH


title: RPE.KDM4A-OE.input.G1.rep1


title: RUN_7_09_NH


title: RPE.KDM4A-OE.input.LS.rep1


title: RPE.KDM4A-OE.input.ES.rep1


title: RPE.Ctrl.input.G2.rep2


title: RUN_6_07_NH


title: RPE.Ctrl.input.ES.rep1


title: RPE.Ctrl.input.G2.rep1


title: RUN_6_04_NH


title: RPE.Ctrl.input.LS.rep1


title: RPE.KDM4A-OE.H3K27ac.LS.rep2


title: RUN_6_01_NH


title: RUN_6_06_NH


title: RPE.KDM4A-OE.H3K27ac.G2.rep2


title: RPE.Ctrl.input.G1.rep1


title: RPE.KDM4A-OE.H3K27ac.ES.rep2


title: RUN_6_09_NH


title: RUN_6_02_NH


title: RPE.Ctrl.input.ES.rep2


title: RUN_5_12_NH


title: RPE.KDM4A-OE.H3K27ac.LS.rep1


title: RUN_5_11_NH


title: RUN_5_10_NH


title: RUN_5_08_NH


title: RPE.Ctrl.input.G1.rep2


title: RPE.KDM4A-OE.H3K27ac.G1.rep2


title: RPE.KDM4A-OE.H3K27ac.G1.rep1


title: RPE.KDM4A-OE.H3K27ac.G2.rep1


title: RUN_6_03_NH


title: RPE.KDM4A-OE.H3K27ac.ES.rep1


title: RUN_5_07_NH


title: RPE.Ctrl.H3K27ac.G2.rep2


title: RPE.Ctrl.H3K27ac.ES.rep2


title: RUN_5_05_NH


title: RUN_5_09_NH


title: RUN_5_06_NH


title: RUN_5_04_NC


title: RPE.Ctrl.H3K27ac.LS.rep2


title: RUN_5_03_NC


title: RUN_5_02_NC


title: RPE.Ctrl.H3K27ac.G2.rep1


title: RPE.Ctrl.H3K27ac.G1.rep2


title: RUN_10_12_PH


title: RPE.Ctrl.H3K27ac.ES.rep1


title: RUN_10_11_PH


title: RUN_10_10_PH


title: RUN_10_08_PH


title: RPE.KDM4A-OE.H3K27me3.LS.rep2


title: RPE.KDM4A-OE.H3K27me3.G2.rep2


title: RUN_10_07_PH


title: RUN_10_06_PH


title: RUN_10_09_PH


title: RPE.KDM4A-OE.H3K27me3.LS.rep1


title: RPE.KDM4A-OE.H3K27me3.ES.rep2


title: RUN_10_05_PH


title: RPE.KDM4A-OE.H3K27me3.G2.rep1


title: RPE.KDM4A-OE.H3K27me3.ES.rep1


title: RUN_10_04_PH


title: RUN_5_01_NC


title: RUN_10_03_PH


title: RUN_6_05_NH


title: RPE.KDM4A-OE.H3K27me3.G1.rep2


title: RPE.Ctrl.H3K27ac.LS.rep1


title: RPE.Ctrl.H3K27ac.G1.rep1


title: RPE.Ctrl.H3K27me3.ES.rep2


title: RPE.Ctrl.H3K27me3.LS.rep2


title: RUN_10_01_PH


title: RPE.Ctrl.H3K27me3.G1.rep2


title: RPE.KDM4A-OE.H3K27me3.G1.rep1


title: RUN_3_11_NC


title: RPE.Ctrl.H3K27me3.G2.rep1


title: RUN_3_12_NC


title: RPE.Ctrl.H3K27me3.G2.rep2


title: RUN_10_02_PH


title: RPE.Ctrl.H3K27me3.LS.rep1


title: RPE.KDM4A-OE.H3K9ac.G2.rep1


title: RPE.KDM4A-OE.H3K9ac.ES.rep2


title: RPE.Ctrl.H3K27me3.ES.rep1


title: RUN_3_05_NC


title: RUN_3_10_NC


title: RUN_3_08_NC


title: RPE.KDM4A-OE.H3K9ac.LS.rep2


title: RUN_3_09_NC


title: RUN_3_06_NC


title: RPE.KDM4A-OE.H3K9ac.G2.rep2


title: RUN_3_02_NC


title: RUN_3_01_NC


title: RUN_3_03_NC


title: RPE.Ctrl.H3K27me3.G1.rep1


title: RUN_2_12_NC


title: RUN_3_04_NC


title: RPE.KDM4A-OE.H3K9ac.LS.rep1


title: RPE.KDM4A-OE.H3K9ac.G1.rep2


title: RPE.Ctrl.H3K9ac.LS.rep2


title: RPE.Ctrl.H3K9ac.G2.rep2


title: RUN_2_09_NC


title: RUN_3_07_NC


title: RUN_2_10_NC


title: RUN_2_11_NC


title: RPE.KDM4A-OE.H3K9ac.G1.rep1


title: RPE.Ctrl.H3K9ac.G2.rep1


title: RUN_2_07_NC


title: RUN_2_03_NC


title: RUN_2_08_NC


title: RPE.Ctrl.H3K9ac.ES.rep2


title: RUN_2_04_NC


title: RUN_2_06_NC


title: RPE.Ctrl.H3K9ac.LS.rep1


title: RUN_2_01_NC


title: RPE.KDM4A-OE.H3K9ac.ES.rep1


title: RPE.Ctrl.H3K9ac.G1.rep2


title: RUN_1_12_NC


title: RPE.Ctrl.H3K9ac.ES.rep1


title: RPE.KDM4A-OE.H3K9me3.LS.rep2


title: RPE.KDM4A-OE.H3K9me3.G2.rep1


title: RPE.KDM4A-OE.H3K9me3.G2.rep2


title: RPE.KDM4A-OE.H3K9me3.ES.rep2


title: RPE.KDM4A-OE.H3K9me3.G1.rep2


title: RUN_1_09_NC


title: RPE.Ctrl.H3K9ac.G1.rep1


title: RUN_2_02_NC


title: RPE.KDM4A-OE.H3K9me3.LS.rep1


title: RUN_1_11_NC


title: RPE.KDM4A-OE.H3K9me3.ES.rep1


title: RPE.KDM4A-OE.H3K9me3.G1.rep1


title: RPE.Ctrl.H3K9me3.G1.rep2


title: RPE.Ctrl.H3K9me3.G2.rep2


title: RUN_2_05_NC


title: RUN_1_10_NC


title: RPE.Ctrl.H3K9me3.ES.rep1


title: RPE.Ctrl.H3K9me3.ES.rep2


title: RUN_1_07_NC


title: RUN_1_05_NC


title: RUN_1_04_NC


title: RUN_1_03_NC


title: RPE.Ctrl.H3K9me3.LS.rep2


title: RUN_1_06_NC


title: RPE.Ctrl.H3K9me3.G1.rep1


title: Control Sample 4

city: Aas

first: Erik

middle: Magne Koscielniak

last: Rasmussen

address: Universitetstunet 3

country: Norway

institute: Norwegian University of Life Sciences

data_processing:
Basecalling was performed using Illumina CASAVA v. 1.8.2
Intital qulity control using FastQC v0.11.5
Trimming of low quality bases using Trimmomatic! v0.33
Bisulfite conversion efficiency was calculated by mapping the samples to the lambda phage genome
Trimmed reads were aligned to the Amel 4.5 reference genome (Elsik et al. 2014) using Bismark v. 0.16.3 (Krueger et al. 2011) and Bowtie 1.0.0 (Langmead et al. 2009)
Mapped reads were then deduplicated to remove PCR bias and cytosine repoprt files were generated using bismark
Cytosine report files where then imported into R v. 3.5.3 (R Core Team, 2019) using bsseq v. 1.18.0 (Hansen et al. 2012)
Assigning DMRs was done using a custom script (Herb et al. 2018) using bumphunter v. 1.25.5 and comb-p v0.v48
Genome_build: Amel_45
Supplementary_files_format_and_content: txt file in BED format with regions depicting the DMRs with FDR < 0.05

organism: Apis mellifera

source_name: Abdominal tissue extract

growth_protocol: Honey bees were collected from two separate donor hives on January 15th, 2014. In total,18 cages with approximately 50 bees were collected from both hives resulting in approximately 900 bees. For the entire, subsequent test period bees remained in the plastic cages, which had the following dimensions: width/depth/height: 19x18x23 cm and were lined with patches of mesh for ventilation. After collection, cages were transferred into a climate chamber, set to temperature of 26°C with approximately 60% relative humidity.

extract_protocol:
Phenol:Chloroform extraction (Rasmussen et al. 2016) Briefly, abdomen carcasses with adhering fat body were homogenized in ATL buffer (QIAGEN 19076) containing 0.4 mg Proteinase K (Sigma Aldrich P8044). Samples were then incubated at 56 °C with shaking at 400 rpm for 16 h in a Thermomixer (Eppendorf 5355 000.011). The lysate (500 µl) was extracted once in phenol:chloroform:isoamylalcohol (25:24:1) before the aqueous phase  was RNAse treated by incubating the sample with 5 µl of RNAse A (20 mg/ml) at 37 °C with shaking at 550 rpm for 30 min. The aqueous phase was extracted again using phenol:chloroform:isoamylalcohol (25:24:1)  before genomic DNA was precipitated by adding 1/10 volume equivalents of 3 M sodium acetate (pH 5.3),  10 µl of linear acrylamide (ThermoFisher Scientific AM9520) and 2.5 vol of ethanol, washed twice in 70 % ethanol, air dried, and dissolved in nuclease free water
MethylC (Urich et al. 2015) Briefly, 2 µg of genomic DNA spiked with 10 ng of λ-phage DNA which is devoid of DNA methylation was fragmented using a Sartorius Labsonic M sonicator, with cycle settings at 0.5 and power/amplitude set to 30 %. Average fragment length was assessed on an Agilent Bioanalyzer DNA High Sense chip. Lower and upper size cut-offs were performed using Agencourt AMPure XP beads at a volume of 0.6x and 1.4x to DNA solution respectively. Sticky ends were repaired using Epicentre End-it DNA end repair kit according to the manufacturer’s recommendations. Poly-Adenylated tails were added to blunt end fragments using New England Biolabs (NEB) Klenow Fragment (3'-->5' exo-) and NEBNext® dA-Tailing Reaction Buffer according to the manufacturer’s recommendations. The reactions were cleaned up using Agencourt AMPure XP beads at a volume of 1.4x to DNA solution. Methylated adapters were ligated to eluted DNA using NEB T4 DNA ligase according to manufacturer’s recommendations. Ligation reactions were purified twice using Agencourt AMPure XP beads at a volume of 1.0x to DNA solution. Eluted DNA was bisulfite converted using Human Genetic Signatures MethylEasy™ Xceed kit according to the manufacturer’s recommendations. A low cycle PCR was performed to increase sequencing depth. To estimate the number of cycles needed, PCR reactions were quantified using KAPA Library Quantification Kit using the manufacturer’s recommendations. Completed PCR products were cleaned up using Agencourt AMPure XP beads at a volume of 1.0x to DNA solution

treatment_protocol: All treatment diets were made based on the same stock feed solution, which also served as the control diet. The stock feed solution contained 50 % Bifor® (Nordic Sugar; 37 % sucrose, 19 % glucose, 19 % fructose in water), 2% Grace’s amino acid mix for insect cell culture (Sigma-Aldrich cat no G0148) or RPMI 1640 (Sigma-Aldrich cat no R7131), 1% lipid mix for insect cell culture (Sigma-Aldrich cat no L5146) and 47% dH2O. In treatment diets the dH2O fraction of the stock feed was partly substituted by the respective supplement

tag: strain

value: carnica

value: abdominal

tag: treatment

value: control

tag: cage

value: BG


title: Curcumin Sample 1

tag: tissue

value: curcumin & ethanol

value: C


title: RUN_1_02_NC

value: primary lung cancer

value: NC

value: lung adenocarcinoma


title: RPE.Ctrl.H3K9me3.LS.rep1

tag: genotype/variation


title: Control Sample 3


title: Curcumin Sample 3

value: D


title: RPE.Ctrl.H3K9me3.G2.rep1


title: Control Sample 5


title: Ethanol Sample 4

value: ethanol

value: B


title: Ethanol Sample 5


title: Curcumin Sample 2


title: RUN_1_08_NC


title: RPE.KDM4A-OE.H3K9me2.G2.rep2

value: Retinal Pigmented Epithelial


title: RPE.KDM4A-OE.H3K9me2.LS.rep2


title: Ethanol Sample 1

value: A


title: RPE.Ctrl.H3K9me2.LS.rep2

value: Ctrl


title: Ethanol Sample 2


title: RPE.Ctrl.H3K9me2.G2.rep2


title: RPE.Ctrl.H3K9me2.G2.rep1


title: RPE.KDM4A-OE.H3K9me2.G1.rep2


title: RPE.KDM4A-OE.H3K9me2.ES.rep2

value: early S


title: Ethanol Sample 3


title: End_IgG_EC1

city: London

first: Athina

last: Dritsoula

address: UCL Institute of Ophthalmology 11-43 Bat

country: United Kingdom

institute: University College London

data_processing:
Sequencing was performs on an Illumina NextSeq 500 with a 75bp single read and 8bp Unique Molecular Identifier.
~20M sequencing reads were generated for each sample. Read headers were marked with the UMI using UMI tools and then adaptor and quality trimmed (fastp) before aligning to the mouse genome (UCSC mm10) using STAR v2.5b
Reads were then PCR deduplicated (Je-Suite) before counting (FeatureCounts).
Differential expression and clustering was performed from the count data using the BioConductor package SARTools, a DESeq2 wrapper.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalised abundance measurements for  each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: IgG-treated EC sample 1

growth_protocol: B16F0 cells were sub-cut injected (day 0), and the tumours were grown for 17 days.

extract_protocol:
FACS sorted cells were collected in RLT RNA extraction buffer (Qiagen)
Libraries were made following the Illumina's instuctions. First strand cDNA synthesis was followed by PCR-amplification. Amplified cDNA was purified using beads and the cDNA libraries were made using the Nextera XT kit.

treatment_protocol: IgG and 15C4 injected at 50mg/kg every 3 days.

value: IgG

tag: tumour model

value: B16F0 melanoma


title: RPE.KDM4A-OE.H3K9me2.G1.rep1


title: Control Sample 1

value: carnica

value: abdominal

value: AG


title: End_IgG_EC3

source_name: IgG-treated EC sample 3


title: RPE.Ctrl.H3K9me2.ES.rep1


title: RPE.Ctrl.H3K9me2.ES.rep2


title: End_IgG_EC2

source_name: IgG-treated EC sample 2


title: Control Sample 2

value: control


title: RPE.Ctrl.H3K9me2.G1.rep1


title: End_15C4_EC2

source_name: 15C4-treated EC sample 2


title: End_15C4_EC3

source_name: 15C4-treated EC sample 3


title: RUN_1_01_NC


title: RPE.Ctrl.H3K9me2.G1.rep2


title: RPE.KDM4A-OE.H3K9me2.LS.rep1

value: late S


title: RPE.Ctrl.H3K9me2.LS.rep1


title: 23_S23_Striatum

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

description:
GSM4605381
THNO-all75-raw.csv

data_processing:
Base calling software: RTA v2
Reads were quasi-mapped to the mouse genome and quantified at the transcript level using Salmon v0.11.2 ( settings: -p 20 --seqBias --validateMappings --gcBias --biasSpeedSamp 5 -i GRCm38_index -l A -1) followed by summary to the gene level using tximport v1.10.1.
Multiple regression was performed with DESeq2 v1.3.1. Over-representation analysis was performed with the GO: Biological Processes gene sets using clusterProfiler v3.18.1.
Genome_build: mm10
Supplementary_files_format_and_content: The processed csv file contained raw (not normalized) gene level counts for all samples.

source_name: Striatum

growth_protocol: C57BL/6 mice were purchased from Charles River and maintained on a 12/12 hour light/dark cycle. Mice used in the experiments weighed between 22 and 28 g and were given food and water ad libitum. All animal experiments were approved by the Animal Care and Use Committee at the University of Virginia and conformed to the National Institutes of Health regulations for the use of animals in research.

extract_protocol:
Immediately following euthanasia, the mouse brains were harvested and the front right or left quadrants were excised, placed in RNAlater (Qiagen), and stored at -80 °C. RNA extraction was performed using the RNeasy Mini Kit (Qiagen). mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, Massachusetts).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs). Sequencing was performed using a NextSeq 500 (Illumina, San Diego, California) at a target depth of 25 million 2 x 75 bp paired end reads per sample.

treatment_protocol: Mice in groups designated “KA” received Ketamine with Dexmedetomidine or Xylazine via intraperitoneal injection. Once anesthetized, a tail vein catheter was inserted to permit intravenous injections of MBs and the MRI contrast agent. The heads of the mice were shaved and depilated, and the animals were then placed in a supine position over a degassed water bath coupled to an MR-compatible small animal FUS system (RK-100; FUS Instruments, Toronto, Canada). The entire system was then placed in a 3T MR scanner (Magnetom Trio; Siemens Medical Solutions, Malvern, Pennsylvania). A 2 inch cylindrical transmit-receive RF coil, designed and built in-house, was placed around the head to maximize imaging SNR. Baseline T1-weighted MR images were acquired and used to select 4 FUS target locations in and around the right or left striatum. Mice received an injection of albumin-shelled MBs , formulated as previously described. Sonication began immediately after clearance of the catheter. Sonications were performed at 0.4 MPa peak-negative pressure (PNP) using a 1.1 MHz single element focused transducer (FUS Instruments, Toronto, Canada) operating in 10 ms bursts, 0.5 Hz pulse repetition frequency and 2 minutes total duration. Immediately following the FUS treatment, mice received an intravenous injection of Gd-DPTA contrast agent (0.5 ul/g body weight; Magnevist; Bayer Health Care, Indianola, Pennsylvania), and T1-weighted contrast-enhanced images were acquired to assess BBBD. Naive mice received no anesthesia, MB, or FUS. "An" mice received just KA anesthesia, without MB or FUS. "Contralateral01" mice recieved KA anesthesia, MB, and 0.1 MPA FUS, with tissue harvested from the untreated hemisphere.

value: Striatum

tag: Sex

value: F

tag: anesthesia

tag: timepoint

tag: sequencing batch

tag: condition

value: naive


title: 21_S21_Striatum

description:
GSM4605379
THNO-all75-raw.csv


title: End_15C4_EC1

source_name: 15C4-treated EC sample 1


title: RPE.KDM4A-OE.H3K9me2.G2.rep1

tag: cell type


title: RPE.KDM4A-OE.H3K9me1.ES.rep2

tag: cell cycle phase


title: 22_S22_Striatum

description:
GSM4605380
THNO-all75-raw.csv


title: 13_S13_Striatum

description:
GSM4605378
THNO-all75-raw.csv

value: KA


title: RPE.KDM4A-OE.H3K9me1.LS.rep1


title: 12_S12_Striatum

description:
GSM4605377
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K9me1.G1.rep2


title: 17_S17_Striatum

description:
GSM4605374
THNO-all75-raw.csv

value: AnMB


title: RPE.KDM4A-OE.H3K9me2.ES.rep1


title: RPE.KDM4A-OE.H3K9me1.G2.rep2


title: 18_S18_Striatum

description:
GSM4605375
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K9me1.G2.rep1


title: RPE.KDM4A-OE.H3K9me1.ES.rep1


title: RPE.KDM4A-OE.H3K9me1.LS.rep2


title: 15_S15_Striatum

description:
GSM4605370
THNO-all75-raw.csv

value: An


title: RPE.Ctrl.H3K9me1.G1.rep2

value: Retinal Pigmented Epithelial


title: RPE.Ctrl.H3K9me1.LS.rep2


title: 19_S19_Striatum

description:
GSM4605371
THNO-all75-raw.csv


title: 16_S16_Striatum

description:
GSM4605373
THNO-all75-raw.csv


title: 5_S5_Striatum

description:
GSM4605369
THNO-all75-raw.csv

value: iso


title: 11_S11_Striatum

description:
GSM4605376
THNO-all75-raw.csv


title: RPE.Ctrl.H3K9me1.G2.rep2

value: Ctrl


title: 20_S20_Striatum

description:
GSM4605372
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K9me1.G1.rep1


title: 4_S4_Striatum

description:
GSM4605368
THNO-all75-raw.csv


title: RPE.Ctrl.H3K9me1.ES.rep2

value: early S


title: RPE.Ctrl.H3K9me1.G2.rep1


title: RPE.Ctrl.H3K9me1.LS.rep1


title: 7_S7_Striatum

description:
GSM4605366
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me3.G2.rep2


title: RPE.Ctrl.H3K9me1.G1.rep1


title: 9_S9_Striatum

description:
GSM4605363
THNO-all75-raw.csv


title: 6_S6_Striatum

description:
GSM4605365
THNO-all75-raw.csv


title: RPE.Ctrl.H3K9me1.ES.rep1


title: RPE.KDM4A-OE.H3K36me3.G1.rep2


title: RPE.KDM4A-OE.H3K36me3.ES.rep2


title: 10_S10_Striatum

description:
GSM4605361
THNO-all75-raw.csv


title: 2_S2_Striatum

description:
GSM4605364
THNO-all75-raw.csv


title: S161R_Striatum

description:
GSM4212535
THNO-all75-raw.csv

value: M


title: RPE.KDM4A-OE.H3K36me3.LS.rep1


title: RPE.KDM4A-OE.H3K36me3.G1.rep1


title: RPE.Ctrl.H3K36me3.LS.rep2


title: S162R_Striatum

description:
GSM4212536
THNO-all75-raw.csv


title: S165R_Striatum

description:
GSM4212533
THNO-all75-raw.csv


title: 8_S8_Striatum

description:
GSM4605362
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me3.ES.rep1


title: 1_S1_Striatum

description:
GSM4605367
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me3.G2.rep2


title: S164R_Striatum

description:
GSM4212532
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me3.LS.rep2


title: S163R_Striatum

description:
GSM4212531
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me3.G1.rep2


title: S167R_Striatum

description:
GSM4212528
THNO-all75-raw.csv


title: S169R_Striatum

description:
GSM4212530
THNO-all75-raw.csv


title: S168R_Striatum

description:
GSM4212529
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me3.G2.rep1


title: RPE.Ctrl.H3K36me3.LS.rep1


title: S166R_Striatum

description:
GSM4212527
THNO-all75-raw.csv


title: S160R_Striatum

description:
GSM4212534
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me3.G1.rep1


title: 228R_Striatum

description:
GSM4212525
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me3.ES.rep2


title: S197R_Striatum

description:
GSM4212523
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me2.ES.rep2


title: RPE.Ctrl.H3K36me3.G2.rep1


title: RPE.KDM4A-OE.H3K36me2.G1.rep2


title: RPE.KDM4A-OE.H3K36me2.LS.rep2


title: 229R_Striatum

description:
GSM4212526
THNO-all75-raw.csv


title: RPE.KDM4A-OE.H3K36me2.G2.rep1


title: RPE.KDM4A-OE.H3K36me2.LS.rep1


title: S195R_Striatum

description:
GSM4212521
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me3.ES.rep1


title: S196R_Striatum

description:
GSM4212522
THNO-all75-raw.csv


title: S205R_Striatum

description:
GSM4212520
THNO-all75-raw.csv


title: S200R_Striatum

description:
GSM4212519
THNO-all75-raw.csv


title: S199R_Striatum

description:
GSM4212518
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.G2.rep2


title: RPE.KDM4A-OE.H3K36me2.ES.rep1


title: RPE.KDM4A-OE.H3K36me2.G1.rep1


title: S204R_Striatum

description:
GSM4212517
THNO-all75-raw.csv


title: 227R_Striatum

description:
GSM4212524
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.ES.rep2


title: RPE.Ctrl.H3K36me2.LS.rep2


title: RPE.KDM4A-OE.H3K36me2.G2.rep2


title: S203R_Striatum

description:
GSM4212516
THNO-all75-raw.csv


title: S202R_Striatum

description:
GSM4212515
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.LS.rep1


title: RPE.Ctrl.H3K36me2.G1.rep2


title: 218R_Striatum

description:
GSM4212512
THNO-all75-raw.csv


title: 219R_Striatum

description:
GSM4212513
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.G2.rep1


title: S201R_Striatum

description:
GSM4212514
THNO-all75-raw.csv


title: 216R_Striatum

description:
GSM4212510
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.ES.rep1


title: 233R_S26_Striatum


title: 217R_Striatum

description:
GSM4212511
THNO-all75-raw.csv


title: RPE.Ctrl.H3K36me2.G1.rep1


title: 230R_S24_Striatum


title: RPE.KDM4A-OE.H3K36me1.G2.rep2


title: RPE.KDM4A-OE.H3K36me1.LS.rep2


title: RPE.KDM4A-OE.H3K36me1.ES.rep2


title: RPE.KDM4A-OE.H3K36me1.G1.rep2


title: 232R_S25_Striatum


title: RPE.KDM4A-OE.H3K36me1.G2.rep1


title: 233R_Striatum


title: 210R_S27_Striatum


title: 232R_Striatum


title: 230R_Striatum


title: 211R_S28_Striatum


title: RPE.Ctrl.H3K36me1.G2.rep2


title: RPE.Ctrl.H3K36me1.LS.rep2


title: 224R_Striatum


title: RPE.Ctrl.H3K36me1.G1.rep2


title: RPE.KDM4A-OE.H3K36me1.G1.rep1


title: RPE.Ctrl.H3K36me1.G2.rep1


title: 212R_S29_Striatum


title: 222R_Striatum


title: 211R_Striatum


title: 212R_Striatum


title: RPE.Ctrl.H3K36me1.ES.rep1


title: RPE.Ctrl.H3K36me1.ES.rep2


title: RPE.Ctrl.H3K36me1.G1.rep1


title: S207R_Striatum


title: RPE.KDM4A-OE.H3K4me3.G2.rep2


title: S208R_Striatum


title: RPE.Ctrl.H3K36me1.LS.rep1


title: 221R_Striatum


title: 210R_Striatum


title: S204L_Striatum


title: RPE.KDM4A-OE.H3K4me3.ES.rep2


title: RPE.KDM4A-OE.H3K4me3.LS.rep2


title: RPE.KDM4A-OE.H3K36me1.LS.rep1


title: S206R_Striatum


title: S202L_Striatum


title: S171R_Striatum


title: RPE.KDM4A-OE.H3K36me1.ES.rep1


title: S172R_Striatum


title: RPE.KDM4A-OE.H3K4me3.G1.rep2


title: RPE.KDM4A-OE.H3K4me3.G2.rep1


title: RPE.KDM4A-OE.H3K4me3.LS.rep1


title: RPE.KDM4A-OE.H3K4me3.ES.rep1


title: RPE.Ctrl.H3K4me3.LS.rep2


title: RPE.Ctrl.H3K4me3.G2.rep2


title: S203L_Striatum


title: RPE.Ctrl.H3K4me3.G1.rep2


title: Cas9-KR-rep1-stimulated

city: Cambridge

first: Ang

last: Cui

state: MA

address: 415 Main St.

institute: Broad Institute

data_processing:
Short sequencing reads were aligned to the mm10 reference genome using STAR
Transcript abundance was quantified using RSEM
Downstream analysis was performed using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: transcript counts txt file

source_name: Bone marrow derived macrophages

growth_protocol: BM derived macrophages (BMMs) were generated by growing cells in presence of M-CSF (10ng/ml, R&D Systems: 216-MC-025). BMMs were collected and reseeded on assay plates after 5-6 days of differentiation. All experiments were performed at 6-7 days of differentiation.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen: 74104 ) following the instruction of the manufacturer and quantified.
1ng of RNA was used in triplicates for the synthesis of cDNA using the Superscript III reverse transcription system (ThermoFisher: 18080093). cDNA quality was checked using High sensitivity DNA Bioanalyzer chip (Agilent) and 0.15ng cDNA was subjected to the process of making an amplified library and sequenced on  HiSeq 2500 (Illumina) to generate Smart-Seq2 sequencing data

treatment_protocol: BMMs were stimulated with/without Lipopolysaccharide (LPS) for 2h

value: Cas9 expressing mouse:Cas9-KR Jax Stock: 028555

value: Bone marrow

tag: age

value: 6-12 weeks

value: 2hr after LPS treatment


title: Cas9-KR-rep3-unstimulated

value: untreated


title: RPE.Ctrl.H3K4me3.ES.rep1


title: RPE.KDM4A-OE.H3K4me2.LS.rep2

value: late S


title: S170R_Striatum

value: Striatum


title: RPE.KDM4A-OE.H3K4me2.G1.rep2


title: RPE.KDM4A-OE.H3K4me3.G1.rep1


title: Cas9-FZ-rep3-unstimulated

value: Cas9 expressing mouse:Cas9-FZ :Jax Stock:026179


title: Cas9-FZ-rep1-stimulated


title: Cas9-FZ-rep1-unstimulated


title: S167L_Striatum


title: RPE.KDM4A-OE.H3K4me2.LS.rep1


title: RPE.KDM4A-OE.H3K4me2.G2.rep1


title: Cas9-KR-rep2-unstimulated


title: RPE.KDM4A-OE.H3K4me2.ES.rep1


title: RPE.Ctrl.H3K4me3.G2.rep1


title: S166L_Striatum


title: RPE.Ctrl.H3K4me3.LS.rep1


title: B6-rep3-stimulated

value: C57BL/6J, Jax Stock:000664


title: RPE.KDM4A-OE.H3K4me2.G2.rep2


title: Cas9-KR-rep2-stimulated


title: Cas9-FZ-rep3-stimulated


title: RPE.Ctrl.H3K4me3.G1.rep1


title: RPE.Ctrl.H3K4me2.LS.rep2


title: B6-rep2-unstimulated


title: S169L_Striatum

value: KA


title: Cas9-FZ-rep2-stimulated


title: B6-rep1-unstimulated


title: RPE.Ctrl.H3K4me2.G1.rep2


title: RPE.KDM4A-OE.H3K4me2.ES.rep2


title: RPE.Ctrl.H3K4me2.G2.rep1


title: Cas9-KR-rep1-unstimulated


title: Cas9-KR-rep3-stimulated


title: RPE.Ctrl.H3K4me2.LS.rep1


title: KO5: Cited2 KO 5

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

institute: Queen Mary University of London

data_processing:
sequenced on a NextSeq system
reads were aligned to the mm10 genome using hisat-2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: a counts table is provided for RNA-seq data

source_name: sorted haematopoietic stem cells

extract_protocol:
sorted Lin-Sca1+Kit+ (LSK) CD48−CD150+ haematopoietic stem cells
RNA-seq from bulk cells

treatment_protocol: deletion of a floxed Cited2 was induced in haematopoietic lineages by a cell type specific Cre

value: sorted haematopoietic stem cells

tag: genotype

value: Cited2 KO


title: KO3: Cited2 KO 3


title: Cas9-FZ-rep2-unstimulated


title: RPE.KDM4A-OE.H3K4me2.G1.rep1

value: Retinal Pigmented Epithelial

tag: chip antibody


title: RPE.Ctrl.H3K4me3.ES.rep2


title: RPE.Ctrl.H3K4me2.ES.rep2


title: WT5: wildtype 5

value: wildtype


title: RPE.KDM4A-OE.H3K4me1.LS.rep2


title: KO1: Cited2 KO 1


title: RPE.KDM4A-OE.H3K4me1.G2.rep2


title: B6-rep1-stimulated


title: B6-rep2-stimulated


title: RPE.KDM4A-OE.H3K4me1.ES.rep2


title: RPE.Ctrl.H3K4me2.G1.rep1

value: Ctrl


title: KO2: Cited2 KO 2


title: B6-rep3-unstimulated


title: RPE.Ctrl.H3K4me2.ES.rep1

value: early S


title: RPE.Ctrl.H3K4me2.G2.rep2


title: RPE.KDM4A-OE.H3K4me1.G1.rep2


title: RPE.KDM4A-OE.H3K4me1.G2.rep1


title: WT2: wildtype 2


title: WT4: wildtype 4


title: KO4: Cited2 KO 4


title: WT3: wildtype 3


title: RPE.KDM4A-OE.H3K4me1.G1.rep1


title: RPE.Ctrl.H3K4me1.G2.rep2


title: WT1: wildtype 1


title: RPE.KDM4A-OE.H3K4me1.ES.rep1


title: RPE.KDM4A-OE.H3K4me1.LS.rep1


title: CtBP2 mutant overexpression TEN-002-19

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: CtBP2 mutant overexpression

data_processing:
Sequencing was performed using NextSeq500 (Illumina) with paired-end 36-base read option.
Sequencing reads were mapped to mm10 mouse reference genome and quantified using CLC Genomics Workbench version 9.5.1 (Qiagen)
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) values were estimated for each gene and filtered.
For pairwise analysis, edgeR analysis (Empirical Analysis of DGE in CLC) was performed.
Filter genes by FDR p-value and fold change.
Genome_build: mm10

source_name: liver

extract_protocol:
livers were excised and RNA was purified with Sepasol-RNA reagent (Nakarai).
sequencing libraries were constructed from 500 ng total RNA using TruSeq RNA Sample Prep Kit v2 (Illumina) following manufacturer's instruction
Libraries were validated with Bioanalyzer (Agilent Technologies) to determine size distribution and concentration.

tag: diet

value: diet induced obesity

tag: virus

value: adenovirus mediated overexpression


title: CtBP2 mutant overexpression TEN-002-21

description: CtBP2 mutant overexpression

tag: strain


title: CtBP2 mutant overexpression TEN-002-20

description: CtBP2 mutant overexpression


title: CtBP2 mutant overexpression TEN-002-18

description: CtBP2 mutant overexpression


title: CtBP2 mutant overexpression TEN-002-17

description: CtBP2 mutant overexpression


title: RPE.Ctrl.H3K4me1.LS.rep2


title: CtBP2 wild-type overexpression TEN-002-14

description: CtBP2 wild-type overexpression


title: RPE.Ctrl.H3K4me1.ES.rep2


title: RPE.Ctrl.H3K4me1.G1.rep2


title: RPE.Ctrl.H3K4me1.G2.rep1


title: RPE.Ctrl.H3K4me1.LS.rep1


title: CtBP2 wild-type overexpression TEN-002-13

description: CtBP2 wild-type overexpression


title: CtBP2 wild-type overexpression TEN-002-12

description: CtBP2 wild-type overexpression


title: CtBP2 wild-type overexpression TEN-002-9

description: CtBP2 wild-type overexpression


title: RPE.Ctrl.H3K4me1.G1.rep1


title: CtBP2 wild-type overexpression TEN-002-10

description: CtBP2 wild-type overexpression


title: CtBP2 wild-type overexpression TEN-002-8

description: CtBP2 wild-type overexpression


title: GUS overexpression TEN-002-7

description: GUS overexpression


title: GUS overexpression TEN-002-6

description: GUS overexpression


title: CtBP2 mutant overexpression TEN-002-15

description: CtBP2 mutant overexpression


title: GUS overexpression TEN-002-5

description: GUS overexpression


title: CtBP2 mutant overexpression TEN-002-16

description: CtBP2 mutant overexpression


title: R689_29Weeks_Rectal_Biopsy

city: Atlanta

first: Rafick-Pierre

last: Sekaly

state: GA

address: 1750 Haygood Drive

institute: Emory University

data_processing:
The sequencing FASTQ files were aligned using the rapid Spliced Transcripts Alignment to a Reference (STAR) Aligner. Exonic transcript abundance of mapped reads was determined using HTSeq and the final counts were normalized by TMM (Trimmed Mean of M-values) by correcting for library size.
Genome_build: Macca Mulatta (Refseq Mmul_10)
Supplementary_files_format_and_content: xlsx data matrix files with normalized transcript/gene read counts

organism: Macaca mulatta

extract_protocol:
10mL of whole peripheral blood (collected in PAXgene tubes) and Rectal biopsies were collected at weeks 20 and 29, and cryopreserved at -80C. The PreAnalytix PAXgene Blood RNA or Qiagen's RNeasy kits were used to eextract RNA and an RNA-integrity number of 8 or above (measured using a bioanalyzer) was ensured prior to library preparation.
Library preparation was performed using the TruSeq Stranded Total RNA Library Prep Kit after rRNA and globin mRNA removal using the Globin-Zero Gold rRNA removal kit. ~30 million paired-end reads obtained per sample

tag: donor id

tag: weeks post-siv infection

tag: treated

value: anti-IFNa


title: R696_29Weeks_Rectal_Biopsy

value: control


title: R693_29Weeks_Rectal_Biopsy


title: R690_29Weeks_Rectal_Biopsy


title: R692_29Weeks_Rectal_Biopsy


title: R688_29Weeks_Rectal_Biopsy


title: R695_29Weeks_Rectal_Biopsy


title: R694_29Weeks_Rectal_Biopsy


title: R691_29Weeks_Rectal_Biopsy


title: GUS overexpression TEN-002-3

description: GUS overexpression


title: R687_29Weeks_Rectal_Biopsy


title: RPE.Ctrl.H3K4me1.ES.rep1

tag: genotype/variation


title: GUS overexpression TEN-002-4

description: GUS overexpression


title: R685_29Weeks_Rectal_Biopsy


title: GUS overexpression TEN-002-1

description: GUS overexpression


title: GUS overexpression TEN-002-2

description: GUS overexpression


title: R686_29Weeks_Rectal_Biopsy


title: CtBP2 wild-type overexpression TEN-002-11

description: CtBP2 wild-type overexpression


title: R695_20Weeks_Rectal_Biopsy


title: Input DNA

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm10
Supplementary_files_format_and_content: BW = signal map in bigWIG format (UCSC)

extract_protocol:
Liver samples were collected from mice fed normal chow diet after 6-h food withdrawal (n=4).Mouse liver tissue was submersed in PBS + 1% formaldehyde, cut into small pieces and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield.An aliquot of chromatin (30 ug) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against CtBP2 (Active Motif, cat# 61261, lot# 1). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

value: 16 weeks

tag: tissue

value: liver


title: R694_20Weeks_Rectal_Biopsy


title: R693_20Weeks_Rectal_Biopsy


title: R692_20Weeks_Rectal_Biopsy


title: R691_20Weeks_Rectal_Biopsy


title: R689_20Weeks_Rectal_Biopsy


title: R696_20Weeks_Rectal_Biopsy


title: R690_20Weeks_Rectal_Biopsy


title: R685_20Weeks_Rectal_Biopsy


title: R687_20Weeks_Rectal_Biopsy


title: R694_29Weeks_Blood

source_name: Blood


title: R696_29Weeks_Blood


title: R688_20Weeks_Rectal_Biopsy


title: CtBP2 ChIP-seq

value: CtBP2 (Active Motif, cat# 61261, lot# 1)


title: R686_20Weeks_Rectal_Biopsy


title: R695_29Weeks_Blood


title: R693_29Weeks_Blood


title: R692_29Weeks_Blood


title: Lung, 2500 ppm permethrin for 7 days, biological rep1

city: Osaka

first: Takako

last: Fukuda

address: 1-98, Kasugadenaka 3-chome, Konohana-ku

institute: Sumitomo Chimical Co., Ltd

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes using the Gene Expression Hybridization Kit (Agilent) following the manufacturers instructions. On completion of the fragmentation reaction, mixtures were hybridized to SurePrint G3 Rat Gene Expression 8x60K Microarrays for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%). The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

data_processing: The processed signal intensities were log2-transformed and normalized to the 75th percentile using GeneSpring GX software (version 14.8) (Agilent).

source_name: lung of mice fed diets containing 2500 ppm permethrin for 7 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Crlj:CD1(ICR) female mice aged 9 weeks were purchased, quarantined for 7 days and maintained at 22 - 26°C and a relative humidity range of 40 - 70% with frequent ventilation. A powdered diet and water were provided ad libitum.

extract_protocol: The lungs were stored in RNA stabilization solution (Ambion, Austin, TX) at –80°C. Total RNA samples were extracted from lung using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Animals were fed diets containing 0 (control), 20, 500, 2500 and 5000 ppm permethrin for periods of 7 days.

tag: gender

value: female

value: lung

value: 11 weeks


title: Lung, 20 ppm permethrin for 7 days, biological rep3

source_name: lung of mice fed diets containing 20 ppm permethrin for 7 days

value: containing 20 ppm permethrin for 7 days


title: R691_29Weeks_Blood


title: Lung, 500 ppm permethrin for 7 days, biological rep1

source_name: lung of mice fed diets containing 500 ppm permethrin for 7 days


title: Lung, 2500 ppm permethrin for 7 days, biological rep3

value: containing 2500 ppm permethrin for 7 days


title: Lung, 2500 ppm permethrin for 7 days, biological rep2


title: Lung, 500 ppm permethrin for 7 days, biological rep3

value: containing 500 ppm permethrin for 7 days


title: Lung, 20 ppm permethrin for 7 days, biological rep2


title: Lung, 5000 ppm permethrin for 7 days, biological rep3

source_name: lung of mice fed diets containing 5000 ppm permethrin for 7 days


title: KU812_shANP32B_2

city: Shanghai

first: Wei

last: Yusheng

state: New York

address: 227,South Road of Chongqian,Shanghai,China

institute: Shanghai Jiao Tong University of Medicine

data_processing:
The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina HiSeqXTen.
The clean reads were then aligned to  genome (mouse version:GRCm38 NCBI; human version:GRCh38 NCBI) using the hisat2. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.HTseqwas used to count gene and lncRNA counts and RPKM method was used to determine the gene expression.
We applied DESeq algorithm to filter the differentially expressed genes, after the protocol significant analysis
Genome_build: GRCm38 NCBI;GRCh38 NCBI
Supplementary_files_format_and_content: text files include FPKM values for each Sample

source_name: Peripheral blood

extract_protocol:
RNA was harvested using Trizol reagent. 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: chronic myelogenous leukemia cell line

tag: transfection


title: Lung, 5000 ppm permethrin for 7 days, biological rep2

value: containing 5000 ppm permethrin for 7 days


title: Lung, 20 ppm permethrin for 7 days, biological rep1


title: Lung, 500 ppm permethrin for 7 days, biological rep2


title: Lung, 5000 ppm permethrin for 7 days, biological rep1


title: KU812_shANP32B_1


title: Lung, 0 (control) for 7 days, biological rep3

source_name: lung of mice fed diets containing 0 (control) ppm chemical for 7 days


title: Lung, 0 (control) for 7 days, biological rep2

value: containing 0 (control) ppm chemical for 7 days


title: R689_29Weeks_Blood


title: R690_29Weeks_Blood


title: DAPT5 6h rep5

city: Planegg-Martinsried

first: Jasmin

last: Moneer

state: Munich

address: Grosshadernerstrasse

department: Biologie II

institute: LMU

description: The reads were demultiplexed. Illumina adapters and polyA sequences were trimmed and splice leader sequences (Stover and Steele, 2001) were removed from both forward and reverse reads. The tool ‘fastqfilter’ was used to ensure the paired nature of the filtered dataset, to filter out reads with a quality score lower than 20 and to exclude reads with a read length shorter than 30bp . Reads that contained ‘N’s were also removed from the dataset. Uploaded are the final reads.

data_processing:
Illumina adapters and polyA sequences were trimmed and splice leader sequences (Stover and Steele, 2001) were removed from both forward and reverse reads. The tool ‘fastqfilter’ was used to ensure the paired nature of the filtered dataset, to filter out reads with a quality score lower than 20 and to exclude reads with a  read length shorter than 30bp . Reads that contained ‘N’s were also removed from the dataset.
All forward and all reverse reads from all sequencing libraries were concatenated. The two resulting files were then used as input to the Trinity (version 2.8.4; Grabherr et al., 2011) de novo transcriptome assembler.
The assembly was run with the following parameters: -strand-specific library, in silico normalisation, -min_contig_length 300, -min_kmer_cov 1, no genome guided mode and no Jaccard Clip options.
The processed reads of the 36 RNA-seq libraries (timepoints 0, 3 and 6 h, DAPT and control samples, six replicates) were separately mapped to the de novo assembled transcriptome reference, within the Galaxy platform. The reads were mapped as strand-specific and with a maximum insert size of 800. RSEM (Li and Dewey, 2011) - with Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) as alignment method- was used as the abundance estimation method.
The raw counts were used as input for differential expression (DE) analysis by DESeq2 (version 1.18.1).

organism: Hydra vulgaris

source_name: whole animals

growth_protocol: Animals of the strain Hydra vulgaris (Basel) were grown in Hydra medium (0.1 mM KCl, 1 mM NaCl, 0.1 mM MgSO4, 1 mM Tris and 1

extract_protocol: RNA-seq libraries were prepared for six biological replicates for each experimental condition. cDNA libraries were synthesized from total RNA using the strand specific SENSE mRNA-Seq Library Prep Kit V2 for Illumina (Lexogen) and the Purification Module with Magnetic Beads (Lexogen). The samples were multiplexed and sequenced on three lanes on Illumina Hiseq2000 with a 100 bpsequencing strategy.

treatment_protocol: Regularly fed animals were starved for 24 h and incubated in either 20 μM DAPT with 1% DMSO in Hydra medium or in only 1% DMSO in Hydra medium (control sample) for 48 h. DAPT and DMSO were renewed every 12 h. Animals were collected, and total RNA was isolated at three different time points: directly at the end of 48 h (0 h), 3 h after DAPT removal (3 h) and 6 h after DAPT removal (6 h). After 48 h incubation, DAPT was removed and replaced with 1% DMSO in Hydra medium for the samples 3 h and 6 h. About 25 animals were collected per sample

tag: treatment

value: DAPT

tag: replicate

value: basel

tag: time point


title: DAPT6 6h rep6


title: R685_29Weeks_Blood


title: KU812_shNC_1

value: shNC


title: R688_29Weeks_Blood

value: anti-IFNa


title: R687_29Weeks_Blood


title: R686_29Weeks_Blood


title: DAPT4 6h rep4


title: DAPT3 6h rep3


title: R696_20Weeks_Blood

value: control


title: R695_20Weeks_Blood


title: DAPT1 6h rep1


title: DAPT2 6h rep2


title: DMSO6 6h rep6

value: DMSO (control)


title: R692_20Weeks_Blood


title: R693_20Weeks_Blood


title: DMSO5 6h rep5


title: DMSO3 6h rep3


title: DMSO4 6h rep4


title: R691_20Weeks_Blood


title: R690_20Weeks_Blood


title: R688_20Weeks_Blood


title: DMSO2 6h rep2


title: DAPT5 3h rep5


title: R686_20Weeks_Blood


title: DAPT6 3h rep6


title: DMSO1 6h rep1


title: R689_20Weeks_Blood


title: DAPT3 3h rep3


title: DAPT4 3h rep4


title: R687_20Weeks_Blood


title: DAPT2 3h rep2


title: R685_20Weeks_Blood


title: R694_20Weeks_Blood


title: DAPT1 3h rep1


title: L4_1_KT-P43

city: Xianyang

first: Young

last: Tang

state: Shaanxi

address: #22 Xinong Road, Yangling District

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
Sequencing adapters and reads with low quality were trimmed using Cutadapt before mapping. The quality of reads after filtering was examined using fastQC.
For mapping, bovine genomic sequence and RefSeq gene coordinate (ARS-UCD1.2/bosTau9) were downloaded from the UCSC genome browser. All filtered reads were aligned to bovine reference genome by RNA STAR (Galaxy Version 2.7.8a) with default parameters.
The number of reads per gene was counted by featureCounts (Galaxy Version 2.0.1). Differentially expressed genes between different samples were identified using default parameters in DESeq2 (Galaxy Version 2.11.40.6+galaxy1), which generated a principal component analysis plot and the heatmap of the sample-to-sample distance matrix.
The most differentially expressed genes (adjusted p-value < 0.05) were extracted from DESeq2 results with an absolute fold change > 5. The normalized counts for those dif-ferentially expressed genes and the Z-score of the counts were calculated on the galaxy platform and exhibited as heatmaps by Heatmap2 (Galaxy Version 3.0.1).
Genome_build: ARS-UCD1.2/bosTau9
Supplementary_files_format_and_content: Tabular files include Log(FC) values for every gene and normalized counts for all samples.
Supplementary_files_format_and_content: Tabular file for heatmap2 including normalized gene counts for all samples with absolute expression fold change > 5 compared with bMSCs

organism: Bos taurus

source_name: biPSCs

growth_protocol: bMSCs were maintained with ATCC low serum MSC medium; biPSCs were maintained in either KT medium or TiF medium.

extract_protocol:
Total RNA was isolated from bovine cells with different treatments using RNeasy Mini kit (Qiagen). The quality of total RNA was examined by Nanodrop, Agarose Gel Electrophoresis and the Aglient 2100 bioanalyzer. rRNA was then removed by using Ribo-Zero-rRNA Removal kit (Epicentre, Madison, WI, USA).
First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment. Finally, sequencing libraries were quantified by using Agilent 2100 bioanalyzer and then fed into Illumina sequencers.

treatment_protocol: Cells were grown in their respective media until 80% confluence before RNA extraction

tag: cell type

value: biPSCs

value: holstein

value: reprogrammed and maintained in KT medium


title: L3-2_KT-P10


title: L4-6_KT-P17


title: L4-1_KT-P17


title: DMSO2 3h rep2


title: DAPT5 0h rep5


title: L4_6_KT-P25


title: DMSO1 3h rep1


title: DAPT6 0h rep6


title: DMSO6 3h rep6


title: DAPT3 0h rep3


title: spt4del_Sua7-FLAG_rep2_Input

city: Oxford

first: Ulku

last: Uzun

address: South Parks Rd

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Paired FASTQ files were processed using usegalaxy.org. Illumina adapters were trimmed using Trim Galore!. Reads were aligned to SacCer3 and Pombe  genome using Bowtie2. Aligned reads were filtered to remove PCR duplicates using RmDp and filtered for quality reads MAPQ > 20 using Filter SAM or BAM.
To normalise reads to Pombe spike-ins, normalisation ratio was calculated to obtain the same amount of filtered Pombe BAM reads in each sample, and SacCer3 BAM reads were calibrated using Downsample SAM/BAM accordingly.
ChIP-seq peaks were obtained using MACS2 callpeak and the background signal was subtracted using MACS2 bdgcmp.
genome build: SacCer3 (R64) and ASM294v2
processed data file: bigwig files from MACS2 analysis

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in YPD (30°C, 160 rpm) from OD600 0.2 to 0.6-0.8.

extract_protocol:
Cells were crosslinked as described in (Brown, Howe et al., 2018). Crosslinked cells were resuspended in cold FA‐150 buffer (10 mM HEPES pH 7.9, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X‐100) and mixed with pre-crosslinked with S.pombe in 5:1 ratio (final S.pombe percentage being 16.7 %). The cell suspension was lysed with glass beads using the MagnaLyser (Roche; 6 x 45 s runs, 2500 g, 4°C). The lysate was sheared 30-40 min with a bioruptor sonicator 30 sec ON/30 sec OFF at high setting. The sheared lysate was cleared by centrifuge (10,000 g, 15 min, 4°C). Input DNA was taken from the supernatant. Following protein and RNA digestion, Input DNA was eluted with Zymoclean ChIP concentrator kit according to the manufacturer’s instructions.
standard NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: genotype

value: BY4741 spt4<delta>;SUA7-3xFLAG

value: no treatment

tag: extracted molecule

value: Total DNA


title: WT_Sua7-FLAG_rep1_Input

value: BY4741 SUA7-3xFLAG


title: DMSO5 3h rep5


title: DMSO3 3h rep3


title: DAPT2 0h rep2


title: WT_Sua7-FLAG_rep2_Input


title: DMSO4 3h rep4


title: spt4del_Sua7-FLAG_rep1_Input


title: DMSO4 0h rep4


title: DAPT4 0h rep4


title: DMSO5 0h rep5


title: spt4del_Sua7-FLAG_rep2

extract_protocol:
Cells were crosslinked as described in (Brown, Howe et al., 2018). Crosslinked cells were resuspended in cold FA‐150 buffer (10 mM HEPES pH 7.9, 150 mM NaCl, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X‐100) and mixed with pre-crosslinked with S.pombe in 5:1 ratio (final S.pombe percentage being 16.7 %). The cell suspension was lysed with glass beads using the MagnaLyser (Roche; 6 x 45 s runs, 2500 g, 4°C). The lysate was sheared 30-40 min with a bioruptor sonicator 30 sec ON/30 sec OFF at high setting. The sheared lysate was cleared by centrifuge (10,000 g, 15 min, 4°C) and the supernatant was incubated with anti-FLAG (M2) antibody for 15–20 h rotating at 4°C. Bound chromatin was immunoprecipitated for 90 min at 22°C with pre‐blocked Dynabeads protein G. Beads and attached chromatin were pelleted, washed, and immunoprecipitated chromatin was eluted from the beads as described in (Brown, Howe et al., 2018). DNA was eluted with Zymoclean ChIP concentrator kit according to the manufacturer’s instructions.
standard NEBNext Ultra II DNA Library Prep Kit for Illumina

value: DNA


title: DMSO6 0h rep6


title: spt4del_Sua7-FLAG_rep1


title: Lung, 0 (control) for 7 days, biological rep1

value: female

value: lung

tag: age

value: 11 weeks

tag: diet


title: WT_Sua7-FLAG_rep2


title: DMSO1 0h rep1