title: L5, BS-seq, rep1

data_processing:
For all libraries except BS-seq: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with default parameters.
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.2b (Dobin et al 2013) retaining multi-mapped reads mapping up to 10 positions. Subsequent read counting was performed with featureCounts version 2.0.0 (Liao, Smyth, and Shi 2014) on the TAIR10 TE and PCG annotations. Normalization and differential analyses were done using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) with default parameters. Only loci with Benjamini-Hochberg adjusted p-values < 0.05 and with a log2-fold change ≥ 0.585 or ≤ − 0.585 were considered differentially expressed.
BS-seq datasets : data analysis was done using the Methylpy analysis pipeline v1.4.6 (Schultz et al. 2015). Reads were filtered to remove PCR duplicates using Picard v2.23.3 and mapped to TAIR10 using Bowtie2 v2.4.1 (Langmead and Salzberg 2012). Only cytosines with a minimum coverage of 6 reads were retained.
ATAC-seq datasets : Reads were mapped to the Arabidopsis TAIR10 reference genome using STAR version 2.7.2b (--outFilterMultimapNmax 1 --outFilterMatchNmin 10 --alignIntronMax 10000, all other parameters default).Probable PCR duplicates were removed using MarkDuplicates from the Picard Tools suite v2.23.3.
Genome_build: TAIR10
Supplementary_files_format_and_content: BS-seq: bigWig format files with methylation levels for CG, CHG and CHH methylation. Only positions with 6+ coverage were used to generate the bigWig files. RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins. ATAC-seq: bigWig format files with normailzed read densities (Reads Per Genomic Content) calculated in 1 bp bins.


title: YPD_18°C replicate 1

status: Public on Jul 04 2023

type: SRA

city: Palaiseau

first: Nicolas

last: Lapalu

address: 22 place de l'agronomie

department: SPE

country: France

institute: INRAE

description: all_transcripts_counts_filter.sort.ggb.gff.gz

library_source: transcriptomic

data_processing:
Iso-Seq raw data were processed with the Iso-Seq V3.2 pipeline from PacBio providing polished Circular Consensus Sequences (CCS). CCS were then mapped to the Z. tritici IPO323 genome with Gmap (2019-01- 31) and unmapped, low mapping quality (≤0) or multi-mapped CCS were filtered out.
RNA-Seq data were cleaned and trimmed with Trimomatic (v 0.36). The cleaned sequences were then mapped to Z.tritici IPO323 genome using STAR (v 2.5.1b, --alignIntronMin 4 --alignIntronMax 5000 -- alignMatesGapMax 5000). Wig files of uniquely mapped reads were converted in BigWig files with wigToBigWig (v4). StringTie (v2.1.1) were then used to assemble the mapped RNA-Seq reads into transcripts with different parameters depending of the depth sequencing of libraries and type (-m 150 --rf --g 0 -f 0.1 -a 10 -j 2 or -j 4). Trinity script inchworm_transcript_splitter.pl (version 2.8.5) was used to split the transcripts with non-uniform coverage based on the jaccard clip method. Clipped transcripts were extracted with home-made script and clustered with Stringtie and associated bam files to obtain TPM counts. All libraries were concatenated into one gff file without merge to avoid loss of information by fusion of small transcripts into larger ones due to the large number of genes in Z.tritici with overlapping UTRs.
The CupCake package (v10.0.0, https://github.com/Magdoll/cDNA_Cupcake) filtered the isoforms, removing the less expressed and degraded ones using the following tools: collapse_isoforms_by_sam.py, get_abundance_post_collapse.py, filter_by_count.py, filter_away_subset.py. Readthrough transcripts were removed using the previous annotation (MPI, JGI, CURTIN, RRES) with BEDTools intersect with an overlap 100% full CDS (-F 1.0) and same strand (-s)) of at least 2 CDS. Mitochondrial transcripts were filtered out as well. Then, all libraries were processed with chain_samples.py from CupCake and clustered for stringent selection. Splicing junctions obtained by STAR (SJ.out.tab files) from Illumina RNA-Seq libraries were used to filter out isoform transcripts with unsupported junctions. Finally, long-read transcripts fully spanning Transposable Element were removed with BEDTools, giving the final set of transcript evidence.
Assembly: Z.tritici IPO323
Supplementary files format and content: gff format file with isoforms from Iso-Seq data
Supplementary files format and content: gff format file with all transcripts assembles from RNA-Seq data

molecule: total RNA

organism: Zymoseptoria tritici

source_name: mycelium

growth_protocol: The reference isolate of Z. tritici IPO323 was stored at -80°C as a yeast-like cell suspension (10e7-8 cells/mL in 30% glycerol). Z. tritici was grown at 18°C in the dark on Yeast extract Peptone Dextrose (YPD) agar, Potato Dextrose Broth (PDB). For RNA production, Z. tritici IPO323 isolate (4 days old yeast-like cells diluted to 10-5 cells/mL final) was cultivated in 75 mL agitated liquid cultures (500 mL Erlen flasks, 150 rpm) at 18°C in the dark for 4 days. Different media were used including Glucose-NO3 synthetic medium defined as MM-Zt (E. Marchegiani et al, 2015). MM-Zt was modified by replacing glucose (10 g/L) by different carbon sources (Xylose, Mannitol, Galactose, Sucrose at 10 g/L)). Histone Deacetylase inhibitors such as trichostatin (TSA, Sigma ref, 1 microM final) and SAHA (SAHA, Sigma ref, 1 mM final) were added to MM-Zt. The composition of complex media (YPD, PDB, AE) was already described (G. Scalliet et al, 2012). Cultures of IPO323 in YPD and PDB were performed at 18°C and 25°C, while AE cultures were performed only at 18°C. A total of 14 culture conditions were used for RNA production. All cultures for RNA-Seq were performed in triplicates.

extract_protocol:
Cultures were centrifuged at 3000 rpm for 10 minutes and mycelium pellet washed with water was frozen with liquid nitrogen. Frozen mycelium was lyophilized and kept at -80°C until extraction. RNAs were extracted using Quiagen Plant RNAeasy Kit according to manufacturer protocol (Ref. 74904, Quiagen France SAS, Courtaboeuf, France).
PacBio Iso-Seq libraries preparation and sequencing was performed by the INRAE platform Gentyane (http://gentyane.clermont.inrae.fr). SMARTer PCR cDNA Synthesis Kit (ref 634926, Clontech, Mountain View, CA, USA) was used for polyA primed first cDNA strand synthesis followed by optimized PCR amplification and library preparation using SMRTbell Template Prep Kit (ref 101-357-000, Pacific Bioscience, Menlo Park, CA, USA) according to manufacturer protocols. The cDNA libraries were prepared without size selection and bar-coded for multiplexing. Sequencing was performed on a PacBio SEQUEL (version 1). Illumina RNA-seq single stranded libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490, New England BioLabs, Ipswich, Massachusetts, USA) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7765, New England BioLabs, Ipswich, Massachusetts, USA). Custom 8 bp barcode was added to each library during the preparation process. Sample were pooled and cleaned with magnetic beads included in the library preparation kit. The pool was run on a lane of Illumina HiSeqX (Illumina, San Diego, California, USA) using a 150-cycle paired end run

tag: tissue

value: mycelium

tag: strain

tag: growth media

value: YPD


title: C. elegans, etoh D1, rep1

city: Nanjing

first: Xiao

last: Zang

address: 12 Xuefu Rd, Pukou

country: China

institute: Nanjing University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Read quality was checked for each sample by using FastQC v 0.11.5.
Reads were aligned to the C.elegans genome (version Wbcel235) using TopHat2 with parameters -r 30 -G -p 8 --microexon-search --library-type fr-unstranded.
Raw counts of sequencing reads were generated by using the python script HTSeq.
Differential expression and dataset normalization were performed using the Bioconductor package DESeq2.
Assembly: Wbcel235
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms are fed on NGM plates with OP50 till L4, extracted on D1.

extract_protocol:
RNA samples were extracted by  Trizol reagent (Takara#9108Q) and Direct-zol RNA MiniPrep Kit (Zymo#R2052). 3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme #NR605-01).

treatment_protocol: L4 worms are treated with etoh or 5-Ph-IAA for 24 hours.

value: whole worm

tag: genotype

value: neuronal DAF-15 AID worm

tag: treatment

value: etoh


title: lung MHCIIlow, rep1

city: Chengdu

first: Teng

last: Ma

address: No.17 People's South Road

institute: sichuan university

data_processing:
Before applying any data filtering criteria, RNA-Seq reads were adapter trimmed using Trim Galore (v0.6.7) for removing low-quality data, and FastQC (v0.11.9) software was used to assess data quality.
Reads were mapped to the mouse reference genome (mm10) using HISAT2 software (v2.2.1).
The mapped reads were assembled into transcripts or genes by featureCounts (v2.0.2) software and genome annotation (mm10.gtf).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mapped reads for each Sample

organism: Mus musculus

source_name: Lung

extract_protocol:
For RNA extraction, a 1% agarose gel was used to detect RNA degradation and contamination.
Sequencing libraries were generated using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, E7530L) and index codes were added to the attribute sequences of each sample and sequenced using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, PE-401-3001) on the cBot Cluster Generation System to cluster the index-coded samples.

value: Lung

tag: cell line

value: cells

tag: cell type

value: primary cells

value: WT

tag: neutrophils

value: MHCIIlow

value: tumor-bearing


title: YPD_25°C_Iso-Seq

description: isoforms.ranking.gff.gz

molecule: polyA RNA


title: MMZt N+TSA replicate 3

value: MMZt N+TSA


title: Differentiated organoidsNiemannPickTypeB, biol rep 2

city: Madrid

first: GEMA

last: GOMEZ-MARIANO

address: Carretera de Majadahonda Pozuelo

country: Spain

institute: ISCIII

data_processing:
RNASeq pipeline written in Nextflow
Fastq files were analyze for quality control using FastQC, v0.11.8
Raw reads were trimmed using Trimmomatic v.0.38 (4-base wide sliding window; removed reads with less than 50 nucleotides)
Read aligment was done with STAR v2.6.1d and quality control performed using RseQC v3.0.0
Gene quatification was calculated using Subread´s featurecounts package v1.6.4
Assembly: Ensembl GRCh38
Supplementary files format and content: tab-delimited text files include "normalized count" values for all Sample
Supplementary files format and content: 1 file with all samples

organism: Homo sapiens

source_name: Liver

extract_protocol:
RNA was isolated using TriReagent (Sigma) followed by DNAseI digestion. 1.2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using TruSeq Stranded mRNA Kit (Illumina) following manufacturer's protocols.

value: Liver

value: organoid

value: hepatocyte differentiation


title: Differentiated organoidsNiemannPickTypeB, biol rep 3


title: SY12 mitosis biorep 3

city: Tokyo

first: Yasutaka

last: Kakui

address: 1-21-1 Nishiwaseda, Shinjuku-ku

country: Japan

institute: Waseda Institute for Advanced Study

library_source: genomic

data_processing:
basecalling with bcl2fastq v2.20.0
alignment using BWA 0.7.17
processing using Juicer 1.5.6
Genome_build: Saccharomyces cerevisiae BY4742
Supplementary_files_format_and_content: Juicer inter_30.hic file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: SY12 mitosis_cell culture

growth_protocol: Cells were grown in YP containing 2 % glucose. Cells were arrested in G1 phase by the addition of 0.02 µg/mL a-factor. Then, cells were released into YPD containing 15 µg/mL nocodazole to arrest in M phase.

extract_protocol:
Crosslinked chromatin was digested by DpnII. The sticky ends were filled in by Biotin-14-dATP and the other dNTPs. Proximal ligation was performed, followed by DNA recovery by Biotin-Streptavidin interaction.
NEBNext Ultra DNA Library Prep kit for Illumina and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) were used for adapter ligation and indexing. Indexed Hi-C library was purified by double selection of SPRI selection beads.

treatment_protocol: Cells were crosslinked with 1 % formaldehyde for 30 minutes at 25 ºC.

tag: cell cycle

value: mitosis arrested cells

tag: restriction enzyme

value: DpnII

tag: biological replicate


title: YPD_18°C_Iso-Seq

description: isoforms.ranking.gff.gz

value: mycelium


title: Differentiated organoidsControl, biol rep 3

value: Normal


title: SY12 mitosis biorep 2


title: Bulk_PDB_YPD_MM_18°C_Iso-Seq

description:
bulk of RNA from mycelium grown in PDB, YPD and MM at 18 degrees C
isoforms.ranking.gff.gz

value: PDB and YPD


title: Differentiated organoidsControl, biol rep 2


title: L5, BS-seq, rep2

city: Clermont-Ferrand

first: Olivier

last: Mathieu

state: Auvergne

address: 28 Place Henri Dunant

department: UMR 6293 - iGReD

institute: CNRS

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Plants were grown in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol:
DNA was extracted from 16-day-old seedlings using the Wizard Genomic DNA Purification kit (Promega).
Bisulfite conversion, library preparation and sequencing were performed at the Beijing Genomics Institute (Hong Kong). Methylated adapters were ligated prior to bisulfite treatment using the ZYMO EZ DNA methylation Gold kit. Libraries were sequenced PE 100 bp on HiSeq X Ten (Illumina)

treatment_protocol: no treatment

tag: developmental stage

value: 16-day-old seedlings

value: seedling


title: MMZt N+TSA replicate 1


title: MMZt N+SAHA replicate 3

value: MMZt N+SAHA


title: SY12 mitosis biorep 1


title: Differentiated organoidsControl, biol rep 1


title: PDB_25°C_Iso-Seq

description: isoforms.ranking.gff.gz

value: PDB


title: SY12 G1 biorep 3

source_name: SY12 G1_cell culture

value: G1 arrested cells


title: PDB_18°C_Iso-Seq

description: isoforms.ranking.gff.gz


title: MMZt N+SAHA replicate 2


title: MMZt N+SAHA replicate 1


title: Y Amplicon-NGS on treated cells (without transplantation)

city: Freiburg

first: Gianni

last: Monaco

address: Breisacher Straße

country: Germany

institute: Freiburg Medical Center

data_processing:
The raw Illumina reads were checked for adapters and quality via FastQC. The raw Illumina sequence reads were trimmed of their adapters using Trimmomatic v. 0.36. Raw sequence data (.bcl files) generated from Illumina MiSeq were converted into fastq files and de-multiplexed using Illumina bsl2fastq v. 2.17 program.
Indels were detected using CRISPResso2 (https://github.com/pinellolab/CRISPResso2)
Assembly: TACATGAACACCAACCTGGTCCAGGAGAACTTCAGCAGgtacccagcagcccccgatctgccctcggccgccatgtctccaaggctcacgagtaagtggcatgttgggattccctttggttgggattccctttggtgacttccttggaggatgtaaccagcttcggggacagggagctcactgcttcccttaaaggtccttttttcttctgcccagctctaagcacggcaagcctttccctgtatccctccaggcctgggcccatcattaatggcccctaactgcatctccttcctct
Supplementary files format and content: Excel file containing the indels In comparison to the reference amplicon
Library strategy: Amplicon-seq

source_name: HSPCs from bone marrow

growth_protocol: Cells were cultured at 37°C and 5% CO2. Lineage-negative (Lin-) HSCs (Miltenyi Biotec, 130-090-858) from femur and tibia-derived BM were stimulated for 3h in StemSpan SFEM II medium (StemCell Technologies) supplemented with L-glutamine (20 mM, Gibco), mSCF, mTPO and hIGF2 (20 ng/ml each) plus hIGF2 and mIL-3 (10 ng/ml each, Peprotech) before nucleofection. After 20h of culture without mIL-3, 10E6 cells were infused via tail vein to recipients conditioned with 5 cycles of busulfan (20 mg/kg, Fresenius Kabi) over 5 consecutive days. Animals were kept in a dedicated facility.

extract_protocol:
Genomic DNA was isolated from cells using theNucleoSpin Tissue Mini kit for DNA from cells and tissue (Macherey-Nagel) according to the manufacturer’s instructions.
DNA library preparations, sequencing reactions, and initial bioinformatics analysis were conducted at AZENTA, Inc. (Leipzig, Germany). DNA Library Preparation, clustering, and sequencing reagents were used throughout the process using NEBNext Ultra DNA Library Prep kit following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). End repaired adapters were ligated after adenylation of the 3’ends followed by enrichment by limited cycle PCR. DNA libraries were quantified using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and multiplexed in equal molar mass.
The pooled DNA libraries were loaded on the Illumina instrument according to manufacturer’s instructions. The samples were sequenced using a 2x250 paired-end (PE) configuration. Image analysis and base calling were conducted by the Illumina Control Software on the Illumina instrument.

treatment_protocol: Lineage-negative (Lin-) HSCs (Miltenyi Biotec, 130-090-858) from femur and tibia-derived BM were stimulated for 3h in StemSpan SFEM II medium (StemCell Technologies) supplemented with L-glutamine (20 mM, Gibco), mSCF, mTPO and hIGF2 (20 ng/ml each) plus hIGF2 and mIL-3 (10 ng/ml each, Peprotech) before nucleofection (Lonza 4D nucleofector, P4 kit, program CA137) with two times 3µg Cas9 (IDT) complexed at a 1:3 molar ratio with sgRNAs (BioLegio). After 20h of culture without mIL-3, 10E6 cells were infused via tail vein to recipients conditioned with 5 cycles of busulfan (20 mg/kg, Fresenius Kabi) over 5 consecutive days. Cells were harvested from peripheral blood through tail vain bleeding or extracted from the indicated source upon sacrifice of the mice.

value: HSPCs

tag: sample type

value: Amplicons from gDNA

value: Jinx; C57BL/6J-Unc13dJinx/Mmucd

value: Cas9+sgRNAs u3 and d4-treated


title: SY12 G1 biorep 1


title: SY12 G1 biorep 2


title: SAHA_Iso-Seq

description: isoforms.ranking.gff.gz

value: SAHA


title: MMZt N+TSA replicate 2

value: MMZt N+TSA


title: Z Amplicon-NGS on treated cells (without transplantation)


title: Galactose replicate 3

value: Galactose


title: X Amplicon-NGS on treated cells (without transplantation)


title: SY7 mitosis biorep 3

source_name: SY7 mitosis_cell culture

value: mitosis arrested cells


title: Man_Iso-Seq

description: isoforms.ranking.gff.gz

value: Mannitol


title: Galactose replicate 2

value: mycelium


title: TSA_Iso-Seq

description: isoforms.ranking.gff.gz

value: TSA


title: 6R Amplicon-NGS on treated cells (post transplantation)

source_name: Lin+ HSPCs from bone marrow


title: SY7 mitosis biorep 2

value: DpnII


title: Differentiated organoidsNiemannPickTypeB, biol rep 1

value: Liver

value: organoid

value: hepatocyte differentiation


title: Xyl_Iso-Seq

description: isoforms.ranking.gff.gz

value: Xylose


title: 5R Amplicon-NGS on treated cells (post transplantation)


title: rtel1-3-NT-r1

data_processing:
For all libraries: reads were trimmed and quality-filtered using trim-galore v.0.5.0 with default parameters.
RNA-seq datasets: reads were mapped to TAIR10 using STAR v.2.7.2b (Dobin et al 2013) retaining multi-mapped reads mapping up to 10 positions. Subsequent read counting was performed with featureCounts version 2.0.0 (Liao, Smyth, and Shi 2014) on the TAIR10 TE and PCG annotations. Normalization and differential analyses were done using DESeq2 version 1.26.0 (Love, Huber, and Anders 2014) with default parameters. Only loci with Benjamini-Hochberg adjusted p-values < 0.05 and with a log2-fold change ≥ 1 or ≤ − 1 were considered differentially expressed.
Assembly: TAIR10 (Araport11 annotation)
Supplementary files format and content: RNA-seq: bigWig format files with normalized read densities (reads per million of mapped reads) calculated in 1 bp bins. ChIP-seq: bigWig format files with normailzed read densities (Reads Per Genomic Content) calculated in 1 bp bins.

source_name: 14-day-old seedlings

growth_protocol: Plants were grown on soil in long-day conditions (16h light, 8h dark) at 23°C with 50% relative humidity.

extract_protocol: Total RNA was extracted from 14-day-old seedlings using NucleoSpin RNA Plus kit (MACHEREY-NAGEL)

treatment_protocol: Plants were grown on Murashige and Skoog medium supplemented with 2.5mg/l mitomycin C (M0503; Sigma-Aldrich)  in long-day conditions (16h light, 8h dark) at 23°C

value: 14-day-old seedlings


title: Galactose replicate 1


title: Glu_Iso-Seq

description: isoforms.ranking.gff.gz

value: Glucose


title: SY7 mitosis biorep 1


title: Mannitol replicate 3


title: 4R Amplicon-NGS on treated cells (post transplantation)

value: HSPCs

value: Amplicons from gDNA


title: 6L Amplicon-NGS on treated cells (post transplantation)

source_name: Lin- HSPCs from bone marrow

value: Jinx; C57BL/6J-Unc13dJinx/Mmucd

value: Cas9+sgRNAs u3 and d4-treated


title: SY7 G1 biorep 2

source_name: SY7 G1_cell culture

value: G1 arrested cells


title: 5L Amplicon-NGS on treated cells (post transplantation)


title: Mannitol replicate 1


title: Rehydrated Male 07

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

data_processing:
BBDuk v38.22, read trimming, arguments=tpe tbo
FastQC v0.11.5, read quality control
Rsubread v2.0.1, Alignment to JacJac1.0 genome (GCA_00028075.1)
FeatureCounts (Subread v1.6.2) Read summarisation
DESeq2 v1.36.0, Differential Expression Analysis
Assembly: GCA_00028075.1
Supplementary files format and content: FeatureCount output file JacJacKidneyCountsRsubread99.gene.txt

organism: Jaculus jaculus

source_name: Kidney

growth_protocol: All animals were kept single housed at 25°C constant temperature, 12-hour light cycle, with free access to dry food pellets throughout.

extract_protocol:
Whole left kidney was dissected after sacrifice and frozen using dry ice. A pestle and mortar with liquid nitrogen was used to break up the sample. Powdered tissue was lysed using no more than 100ml/mg of Trizol. Chloroform phase separation was used to isolate RNA then cleaned up using Zymo Direct-Zol RNA miniprep kit as per manufacturer's instructions. All storage was at -80C.
polyA selection

treatment_protocol: Animals were randomly assigned to three experimental groups: Control (access to water ad libitum), Dehydrated (water restriction 11 days), and Rehydration (water restriction 7 days followed by access to water ad libitum 3 days).

value: Kidney

tag: Sex

value: Male

value: Rehydrated


title: Rehydrated Male 08


title: AE_Iso-Seq

description: isoforms.ranking.gff.gz

value: mycelium

value: Yeast extract Glycerol


title: BY4742 mitosis biorep 3

source_name: BY4742 mitosis_cell culture

value: mitosis arrested cells

value: DpnII


title: Xylose replicate 3


title: 4L Amplicon-NGS on treated cells (post transplantation)


title: Rehydrated Male 04


title: Xylose replicate 2


title: Rehydrated Male 02


title: BY4742 mitosis biorep 2


title: f Amplicon-NGS on treated cells (post transplantation)


title: e Amplicon-NGS on treated cells (post transplantation)


title: Xylose replicate 1


title: BY4742 mitosis biorep 1


title: SY7 G1 biorep 3


title: Mannitol replicate 2

value: Mannitol


title: Sucrose replicate 3

value: Sucrose


title: Dehydrated Male 06

value: Dehydrated


title: Rehydrated Male 01


title: d Amplicon-NGS on treated cells (post transplantation)

source_name: Peripheral blood

value: Peripheral blood


title: Sucrose replicate 2


title: c Amplicon-NGS on treated cells (post transplantation)


title: BY4742 G1 biorep 2

source_name: BY4742 G1_cell culture


title: Dehydrated Male 05


title: SY7 G1 biorep 1


title: Sucrose replicate 1

source_name: mycelium


title: b Amplicon-NGS on treated cells (post transplantation)


title: BY4742 G1 biorep 1


title: Dehydrated Male 03


title: Dehydrated Male 02


title: M34 Amplicon-NGS on treated cells (post transplantation)


title: a Amplicon-NGS on treated cells (post transplantation)


title: Glucose replicate 3

value: Glucose


title: Glucose replicate 2


title: M33 Amplicon-NGS on treated cells (post transplantation)

value: HSPCs


title: BY4742 G1 biorep 3


title: lung MHCIIlow, CI, rep2

value: Lung

value: cells

value: primary cells

value: WT

value: tumor-bearing


title: Control Male 04

value: Kidney

value: Male

value: Control


title: M32 Amplicon-NGS on treated cells (post transplantation)

value: Amplicons from gDNA

value: Jinx; C57BL/6J-Unc13dJinx/Mmucd

value: Cas9+sgRNAs u3 and d4-treated


title: AE (Yeast extract Glycerol) replicate 2

value: mycelium

value: Yeast extract Glycerol


title: AE (Yeast extract Glycerol) replicate 3


title: Control Male 03


title: M31 Amplicon-NGS on treated cells (post transplantation)


title: AE (Yeast extract Glycerol) replicate 1


title: HemSC-EVs-miRNA

city: Shanghai

first: Enhao

last: Lu

address: 826 Zhangheng Road

institute: Fudan University

data_processing:
miRNA-seq:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer.
Firstly, Q30 was used to perform quality control.  The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 15nt) were left by cutadapt software (v1.9.3).
Then, trimmed reads from all samples were pooled, and miRDeep2 software (v2.0.0.5) was used to predict novel miRNAs.
The trimmed reads were aligned to the merged human pre-miRNA databases (known pre-miRNA from miRBase plus the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch.
The numbers of mature miRNA mapped tags were defined as the raw expression levels of that miRNA.  The read counts were normalized by TPM (tag counts per million aligned miRNAs) approach.
RNA-seq:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).  The high quality trimmed reads were used to analyse circRNAs and LncRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4).   edgeR software (v3.16.5) was used to normalized the data
LncRNA: The high quality reads were aligned to the reference genome with hisat2 software (v2.0.4).   Then, HTSeq software (v0.9.1) was used to get the gene level (mRNA) and transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization
Assembly: hg19
Supplementary files format and content: Raw count and normalized count of miRNAs
Supplementary files format and content: Raw count and normalized count of CircRNAs
Supplementary files format and content: Raw count and normalized count of LncRNAs

source_name: infantile hemangioma

extract_protocol:
miRNA-seq: Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
miRNA-seq: The small RNA libraries were constructed with GenSeq® Small RNA Library Prep Kit (GenSeq, Inc.) by following the manufacturer’s instructions.
RNA-seq: Samples were flash frozen on dry ice, and RNA was harvested using Trizol reagent.  Illumina TruSeq RNA Sample Prep Kit was used with 1.5 ug of total RNA for the construction of sequencing libraries.
RNA-seq: Total RNA was used for removing the rRNAs with GenSeq® rRNA Removal Kit (GenSeq, Inc.). Then, the rRNA-depleted samples were subjected to library construction with GenSeq® Low Input RNA Library Prep Kit (GenSeq, Inc.) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Novaseq instrument with 150bp paired end reads.

value: infantile hemangioma

value: Hemangioma stem cells (HemSC)


title: Glucose replicate 1

value: Glucose


title: Control Male 06


title: miR-574-5p-knockdown_2

type: RNA

city: Xiamen

first: James

middle: Yunqing

last: Yang

state: Fujian

address: Xiang'an South Road

department: School of Life Sciences

institute: Xiamen University

description: miR-574-5p knockdown HeLa cells

hyb_protocol: Hybridization was performed in NimbleGen Hybridization System.

scan_protocol: After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 software.

data_processing: Further Data analysis was performed using Agilent GeneSpring GX v11.5.1 software.

source_name: HeLa cells

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.

growth_protocol: Normal HeLa medium.

extract_protocol: 96 h after viral infection, cells were harvested and total RNAs were prepared by stardard protocols.

treatment_protocol: HeLa cells were seeded on plates at the density of 20-30% confluency and incubated overnight. HeLa cells infected with control or  lentiviruses carrying shRNA against miR-574-5p   at multiplicity of infection of 1:1 and in the presence of Polyberene.

value: HeLa

value: miR-574-5p knockdown


title: WT_early-1

status: Public on Jul 03 2023

city: Wuhan

first: Liang

last: Hu

address: 1 Nanhu Yaoyuante, Hongshan District

institute: Hubei Academy of Agricultural Sciences

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: IRGSP-1.0
Supplementary files format and content: TXT file contain counts for each sample

organism: Oryza sativa

source_name: Leaf sheaths of rice

growth_protocol: The near isogenic lines (NILs) contain the BPH14 (B14), BPH15 (B15) or both BPH14/BPH15 (B1415) genes were developed by H.B.W. using‘Wushansimiao’, an indica inbred rice cultivar, as the recurrent parent (RP) (Wang et al., 2019). The aforementioned four types of seeds were grown in plastic cups (9 cm in diameter and 15 cm in height) with 15 plants per cup, and maintained in a greenhouse with cycles of 32 ± 2 °C/14 h light and 26 ± 2 °C/10 h dark periods.

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: The endpoint method was used for BPH treatments and sample collection (Wu et al., 2017). All time points of treatments began at different times, and they were stopped at the same time. The seedlings of B14, B15, B1415 and RP were infested with 8 third instar BPH nymphs per seedling at the four-leaf stage after 0, 3, 12, 24, 48, 60, and 72 h. For analysis, three biological replicates per treatment with 15 seedlings per replicate were used. Leaf sheaths were mixed as non-infested group (0 h), infested early group (3, 6 and 12 h) and infested late group (24, 48 and 72 h). Samples were referred to as B14_0, B14_early, and B14_late for the B14 lines, and B15_0, B15_early, and B15_late for the B15 lines, and B1415_0, B1415_early, and B1415_late for the B1415 lines, and RP_0, RP_early, and RP_late for the RP lines. Leaf sheathes were collected and frozen in liquid nitrogen, and stored at -80 °C until use.

value: Leaf sheaths of rice

value: The recurrent parent (RP) 'Wushansimiao', an indica inbred rice cultivar

value: Early feeding stage


title: WT_late-2

value: Late feeding stage


title: WT_late-1


title: WT_early-2


title: WT_early-3


title: WT_0-1

value: Non-infested by BPH


title: WT_0-2


title: B15_late-3

value: The near isogenic lines (NILs) contain the BPH15


title: WT_0-3


title: miR-574-5p-knockdown_1

description: miR-574-5p knockdown HeLa cells


title: Control_2

description: Normal HeLa cells

value: Wild-type


title: Control Male 01

value: Kidney

value: Male

value: Control


title: Control_3

description: miR-574-5p knockdown HeLa cells


title: WT_late-3


title: B15_late-1


title: B15_early-3


title: miR-574-5p-knockdown_3

description: miR-574-5p knockdown HeLa cells


title: B15_late-2


title: Control_1

description: Normal HeLa cells


title: B15_early-2


title: L5_k27m3-1

extract_protocol: none provided

value: 14-day-old seedlings

tag: antibody

value: anti-H3K27me3 (C15410069, Diagenode)


title: B1415_late-3

value: The near isogenic lines (NILs) contain both the BPH14 and BPH15


title: B1415_late-2


title: B15_early-1


title: B15_0-3


title: B15_0-1


title: B15_0-2


title: B1415_late-1


title: B1415_early-2


title: B1415_early-1


title: B1415_0-3


title: B1415_0-1


title: B14_0-1

value: The near isogenic lines (NILs) contain the BPH14


title: B14_0-2


title: B14_0-3


title: B1415_early-3


title: B14_late-3


title: B14_late-1


title: B14_early-3


title: B14_early-2


title: N3767_delta-cdp2_ChIPseq_H3K9me3_rep2

city: Colorado Springs

first: Andrew

middle: David

last: Klocko

state: Colorado

address: 278 Centennial Hall, 1420 Austin Bluffs Pkwy

department: Chemistry and Biochemistry

country: USA

institute: University of Colorado Colorado Springs

description: immunopreciptated DNA

data_processing:
Raw ChIP-seq data files, as fastq files, were mapped to version 14 of the Neurospora crassa genome (nc14) [Rodriguez et al., 2022 [Pubmed ID: ] with bowtie2 (version 2.4.2), and output sam files were converted to sorted bam files using samtools (version 1.14), which were used by Deeptools (version 3.5.0) to produce bigwig files with 25 basepair bin resolution, normalized by Reads per Kilobase Per Million Reads (RPKM), for display on the Integrative Genomics Viewer (IGV)
Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156])
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts, Knight-Ruiz corrected contact counts, or the calculated log2 difference in contacts between a wild type strain (wild type data from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and one of the three mutant strains presented here.
Supplementary files format and content: the bigwig files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin.

organism: Neurospora crassa

source_name: germinated conidia

growth_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and was disrupted by sonication, which simultaneously sheared chromatin, using a Bioruptor Pico (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and histone modification antibody was added (typically 1uL) and samples were nutated overnight at 4oC. The next day, equilibrated protein A/G magnetic agarose beads (Pierce/Thermo Scientific; cat # PI78609) was added to bind the antibody, incubated for 2 hours at 4oC, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl was buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65oC. Samples (IP and input) were decrosslinked at 65oC overnight. The next day, samples were RNaseA treated for two hours at 50oC, then proteinase K treated for 2 hours at 50oC, the DNA was extracted with phenol:chloroform:IAA (25:24:1), and DNA was precipitated with ethanol, sodium acetate, and glycogen, and allowed to precipitate overnight at -80oC. The next day, samples were precipitated by centrifugation, washed, dried in a Speedvac and resuspended in 30uL TE. ChIP DNA was quantified with a Qubit 3.0 using the HS method.
Approximately 10 ng of DNA was used to generate ChIP-Seq libraries. Each library was prepared using the NEB Next Ultra II Library Preparation Kit (New England Biolabs, #E7645L) with the adapters from the NEBNext® Multiplex Oligos for Illumina®(Index Primers Set 1 [E7335L] or 2 [E7500L]) according to the manufacturer’s instructions, except that final libraries were only PCR-amplified using eight cycles for amplification.

treatment_protocol: Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 15 min in 0.5% formaldehyde at room temperature, with shaking at 100 rpm, and then quenched with 0.125M glycine for histone modification ChIP.

value: germinated conidia

value: asexual, unsynchronized cells

value: Active Motif H3K9me3 pAb cat# 39161, Lot #30220003

value: mat a his-3 delta cdp-2::hph


title: N3613_delta-chap_ChIPseq_H4K16ac_rep1

description: immunopreciptated DNA

value: Active Motif H4K16ac pAb cat# 39167, Lot #08719003

value: mat A; delta chap::hph


title: B1415_0-2

value: Leaf sheaths of rice


title: N3767_delta-cdp2_ChIPseq_H4K16ac_rep2

description: immunopreciptated DNA


title: B14_late-2

value: Late feeding stage


title: B14_early-1

value: Early feeding stage


title: N150_WT_ChIPseq-H3K9ac_rep1

description: immunopreciptated DNA

value: Active Motif H3K9ac pAb cat# 39137, Lot #28720002


title: N150_WT_ChIPseq-H3K9ac_rep2

description: immunopreciptated DNA


title: N3767_delta-cdp2_ChIPseq_H3K9ac_rep2

description: immunopreciptated DNA


title: N3767_delta-cdp-2_HiC_DpnII_rep6

description: Hi-C ligation products

data_processing:
All in situ Hi-C contact maps and other analyses presented in this manuscript were generated using the program suite HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/index.html) (Ramírez et al. 2018), using version 3.5 for all analyses. Briefly, raw fastq files were mapped to the Neurospora genome (version 14 [Rodriguez et al., 2022 [Pubmed ID: 35244156]) using bowtie2 (version 2.3), with the --local and --reorder flags, and the Hi-C contact matrix was built with hicBuildMatrix using the default settings (with both DpnII [GATC] and MseI [TTAA] restriction sites used for quality control), and resulting images of the contact matrix images were made with hicPlotMatrix; (total) merged matrices were constructed by first merging all replicates using the cat command and processing them in an identical manner. Contact map images are either presented as raw or Knight-Ruiz corrected (Knight and Ruiz 2012), performed with the hicCorrectMatrix program, to account for differences in restriction enzyme site distribution or sequencing bias of underlying DNA. Differences between wild type datasets (from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and mutant datasets were performed with hicCompareMatrices in which the experimental (mutant) matrix was listed first and the control (wild type) matrix was listed second; all compare matrices used the --log2diff flag to obtain the log2 difference in contact strength. Wild type matrices with approximately the same number of valid reads as the mutant dataset were generated by selecting the appropriate number of total reads from fastq files of the wild type datasets (Rodriguez et al., 2022) using the sed command, reads were mapped to the nc14 genome, and the contact matrix built with hicBuildMatrix as above.
Assembly: nc14_genome-seq-name.fasta (version 14; Rodriguez et al., [Pubmed ID: 35244156])
Supplementary files format and content: the .h5 files are contact matrices generated by hicExplorer; briefly, this 3D matrix is divided into bins, and the interactions between the bins is reported - either raw contact counts, Knight-Ruiz corrected contact counts, or the calculated log2 difference in contacts between a wild type strain (wild type data from Rodriguez et al., 2022 [Pubmed ID: 35244156]) and one of the three mutant strains presented here.
Supplementary files format and content: the bigwig files are generated by Deeptools; briefly, these files divide the genome into bins and the number (count) of sequencing reads per bin is reported for each bin.

growth_protocol: To grow WT Neurospora culture, 25 mL cultures containing 1x Vogel’s medium + 1.5% sucrose were inoculated with 1.25x10^8 conidia, (harvested from ~six baby slants by vortexing with water; conidia were washed twice prior to use) and grown at 32 °C with shaking at 200 revolutions per minute (RPM) for ~four hours until ~90% of conidia had germinated, and growth tubes were ~4x the length of the initial conidia.

extract_protocol:
First, the concentration of genomic DNA per spheroplast aliquot was determined by resuspending one aliquot per culture replicate in 200 μL decrosslinking buffer (50 mM Tris-HCl [pH 8], 5 mM sodium ethylenediaminetetraacetic acid [Na EDTA], 0.5% [w/v] sodium dodecyl sulfate [SDS]) plus 100 mg proteinase K (Invitrogen) and incubated at 65°C for 16 hours. The volume was then increased to a total of 500 μL using TE buffer (10 mM Tris-HCl [pH 8], 1 mM Na-EDTA), and 40 mg RNase A (Invitrogen) was added. Aliquots were incubated at 37 °C for 30 min, and genomic DNA was extracted with twice 25:24:1 phenol:chloroform:isoamyl alcohol (25:24:1; ThermoFisher cat# AC327115000), once with chloroform, and precipitated with 0.1 volume sodium acetate (pH 5.2) and 1 volume isopropanol, centrifuged (10 minutes, 13k rpm), and the resulting DNA pellet was washed once with 70% (v/v) ethanol, dried for 10 min in a Savant SpeedVac (ThermoFisher, Model # DNA120-115), and resuspended in 50 μL TE. The total DNA concentration per pellet was determined by quantifying 2 μL of the total resuspension of genomic DNA (50 μL) using a Qubit 3.0 HS DNA quantification kit (ThermoFisher cat# Q33217). Spheroplasts containing 3.5 μg of genomic DNA were resuspended in 270 μL of 1x restriction enzyme buffer (either DpnII, above) and 50 μL hydrated glass beads were added (Sigma-Aldrich #G1145, Acid washed, 150-212 μm). Spheroplasts were lysed by vortexing tubes for 30 seconds followed by 30 seconds on ice; five total cycles were performed. Following the settling of the beads, 270 μL of supernatant (and cell debris, if possible) were moved to a new tube. SDS was added to 0.625% final concentration (30 μL of 6.25% stock), tubes incubated at 62 °C for 7 minutes, and immediately placed on ice. Triton X-100 was added to a final concentration of 1% [33 μL of 10% (v/v)] and 10x DpnII or MseI buffer was added to account for added volumes of SDS, Triton and enzymes. Genomic DNA in chromatin was then digested with 200 U DpnII and MseI (double digest) for 16 hours at 37°C while nutating. Samples were then centrifuged for 3000 rpm for 10 minutes, the supernatant was removed, and the pellets, which contained permeabilized nuclei and chromatin, were resuspended in 83 μL of 1x DpnII buffer. Sticky ends were blunted in a 100 μL reaction with 30 μM each of dCTP, dGTP, dTTP, Biotin-14-dATP (Invitrogen cat# 19524-016), and 25 U of Klenow (large fragment). Reactions were mixed by pipetting and incubated at 37°C for 60 minutes with nutating. An additional 110 μL of 1x DpnII or MseI buffer was added to the samples (210 μL total chromatin volume), and ligation reactions with 1x T4 Ligation buffer, 1% Triton X-100, 100 μg/mL BSA, and 1675 U of T4 DNA ligase were immediately prepared and incubated at 16 °C for 4 hours. Proteinase K (250 μg total; Gold Biotechnology cat# 97062-238) was added and reactions were decrosslinked at 65°C once overnight (~16 hours) and following the addition of another 250 μg of proteinase K, reactions were decrosslinked a second time for 2 hours. Cooled samples were extracted twice with phenol:chloroform:isoamyl alcohol, the aqueous fraction was transferred to a 2.0 mL microcentrifuge tube, and the volume increased to 500 μL with additional TE buffer. Ligated DNA circles were precipitated by addition of 0.1x volume 3M sodium acetate pH 6.0, 2.5x volumes 100% ethanol, 40 μg glycogen (ThermoFisher cat# R0561), incubation at -80 °C for 30 minutes followed by centrifugation at 13,000 rpm for 15 minutes. Pellets were washed once with 70% ethanol, dried at RT for 10 minutes in a speedvac, and resuspended in 50 μL TE. RNaseA (20 μg; SigmaAldrich cat# R4875) was added and samples were incubated at 37 °C for 30 minutes. An additional 450 μL TE was added, and ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform. The aqueous fraction was transferred to a new 2.0 mL microcentrifuge tube, and ligation products were precipitated (0.1x 3M sodium acetate pH 6.0 and 2.5x 100% ethanol were added, and tubes were incubated at -80 °C for 20 minutes and centrifuged at 13,000 rpm for 10 minutes), washed, dried, resuspended in 25 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA) and stored at -20 °C. To remove biotin-dATP from unligated DNA ends, 50 μL reactions consisting of 1x NEB buffer 2.1, 100 μM each of dATP and dGTP, and 5 U of T4 DNA polymerase were incubated at 12 °C for 2 hours and quenched with EDTA (final concentration 10 mM), and the reaction volume was increased to 500 μL with TE/10. DNA ligation products were extracted once with 25:24:1 phenol:chloroform:isoamyl alcohol and once with chloroform, transferred to a 2.0 mL microcentrifuge tube, and ethanol precipitated (0.1x volume 3M sodium acetate, pH 6.0 and 2.5x volume 100% ethanol were added, tubes were incubated at -80 °C for 20 minutes, centrifuged at 13,000 rpm for 10 minutes, washed, dried, and DNA pellets were resuspended in 500 μL TE/10). Ligation products were sheared by sonication (Qsonica, Model Q55; amplitude = 30%, 30 seconds sonication, 30 second incubation on ice between pulses). Sheared, biotinylated ligation products were captured on streptavidin magnetic beads (Dynabeads M280, Invitrogen cat# 11205D) equilibrated with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) at RT for 30 minutes, with pipetting every 10 minutes. Beads were washed on a magnetic rack three times with 1x BW buffer, twice with TE/10, and resuspended in 25 uL TE/10 buffer.
Hi-C libraries for Illumina sequencing were prepared using a NEBNext Ultra II kit (New England Biolabs cat# E7645) with corresponding Multiplex Barcode sets (NEB cat# E7335 and E7500) according to the manufacturer’s protocol, with the following exceptions, as all steps were performed using the Hi-C library attached to the magnetic streptavidin beads: following the adapter ligation and USER enzyme digestion, magnetic beads were washed five times with 1x BW buffer (5 mM Tris-HCl [pH 8 at 25°C], 0.5 mM Na-EDTA, 1 M NaCl, 0.05% [v/v] Tween-20) and once with TE/10, and resuspended in 15 μL TE/10 (10 mM Tris-HCl [pH 8 at 25 °C], 0.1 mM sodium EDTA); PCR enrichment of the barcoded Hi-C library off streptavidin beads used either eight or 15 cycles (or an initial fifteen PCR cycles, whereupon the beads were washed three times with TE/10, and were re-amplified by an additional 8 cycles, for a total of 23 cycles) and following the separation of the aqueous PCR product from the magnetic beads, the PCR product was cleaned with a 1:1 ratio of Ampure XP beads (Agencourt, Beckman-Coulter) per the manufacturer’s protocol, resuspended in 25 μL TE/10, and quantified by a Qubit HS reaction. Prior to sequencing, all libraries were assessed for quality via Fragment Analyzer and qPCR (Genomics and Cell Characterization Core Facility [GC3F], University of Oregon). Indexed in situ Hi-C libraries were pooled and sequenced on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 at the Genomics and Cell Characterization Core Facility [GC3F] at the University of Oregon as 100 nucleotide (nt) paired-end (PE100) sequencing runs. Hi-C dataset fastq files are provided in table S1.

treatment_protocol: Methanol-free formaldehyde was added to a final concentration of 1% and cultures were incubated 10 minutes at room temperature (RT; ~25°C) with shaking at 100 RPM for crosslinking; 1 M Tris-HCl [pH 8 at 25°C] (Hoffman et al. 2015) was added to a final concentration of 125 mM and cultures were incubated at RT for 10 minutes, shaking at 100 RPM, to quench the reaction. Conidia were harvested by centrifugation (4000 RPM, 3 min) and resuspended gently in 20 mL spheroplasting buffer (1 M sorbitol, 100 mM KPO4 [pH 7.5]) with b-mercaptoethanol added to 30mM. Conidia were pelleted again and resuspended in 20 mL spheroplasting buffer with b-mercaptoethanol added to 1mM. VinoTaste (Novozymes; powder dissolved in water to a stock solution of 50 mg/mL) was added to 50mg and strains were digested at 30°C, shaking at 100 RPM, for 60 min. Spheroplasts were harvested by centrifugation (3500 RPM, 2 min) and pellets were washed twice with 20 mL Spheroplasting buffer, followed by three washes of the buffer of the 1x restriction enzyme to be used for digestion, here DpnII buffer (100 mM NaCl, 50 mM Tris-HCl [pH 7.9 at 25°C], 10 mM MgCl2, 100 μg/mL BSA). Washed pellets were resuspended in 3.5 mL of the same restriction enzyme buffer, split into four – 1 mL aliquots in 1.7 mL Eppendorf tubes, pelleted (10,000 rpm, 5 min), whereupon the supernatant was removed, and spheroplast pellets were stored at -80°C.


title: N3752_WT_ChIPseq-H4K16ac_rep2

description: immunopreciptated DNA


title: N3613_delta-chap_ChIPseq_H3K9me3_rep2

description: immunopreciptated DNA


title: N6144_delta-cdp-2+delta-dim2_ChIPseq_H4K16ac_rep2

description: immunopreciptated DNA

value: mat A delta cdp-2::hph; delta dim-2::hph


title: sk19

city: Balice

first: Ewelina

last: Semik-Gurgul

address: Krakowska 1

department: Department of Animal Molecular Biology

country: Poland

institute: National Research Institute of Animal Production

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-quality set to 20 and a minimum read length of 36 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The aligned to the horse reference genome (EquCab3.0) using BSMAP (Yuanxin and Wei, 2009) with default options recommended for RRBS data, specifying the enzyme cleavage site (MspI) and mapping only to two forward strands.
The percentage of methylation of individual CpG sites with coverage higher than 5 reads was determined using Methylation Caller software provided in BSMAP package. Then, the files were processed in R to obtain input files for Methylkit software.
Assembly: EquCab3.0
Supplementary files format and content: Files containing the percentage of methylation of individual CpG sites determined using Methylation Caller software followed by the conversion in R to be viable as input files for Methylkit software

organism: Equus caballus

source_name: skin tissue

extract_protocol:
DNA was isolated from tissue using a Sherlock AX (A&A Biotechnology) kit
To quantify DNA methylation levels across the genome RRBS methodology was used following the Ovation RRBS Methyl-Seq System (NuGEN) protocol. 24 DNA libraries were pooled in two pools and sequenced on the NexSeq 500 platform (Illumina) using a 75-bp single-end read and High-Output Flow Cell. The sequencing was performed along with a balanced control library obtained from the viral DNA (PhiX, Illumina).

treatment_protocol: The collected material was transferred into tubes and stored at -20°C.

value: skin tissue


title: N6144_delta-cdp-2+delta-dim2_ChIPseq_H4K16ac_rep1

description: immunopreciptated DNA


title: N6144_delta-cdp-2+delta-dim2_ChIPseq_H3K9me3_rep1

description: immunopreciptated DNA


title: N6144_delta-cdp-2+delta-dim2_ChIPseq_H3K9me3_rep2

description: immunopreciptated DNA


title: sk16


title: N3613_delta-chap_ChIPseq_H3K9me3_rep1

description: immunopreciptated DNA


title: N3767_delta-cdp2_ChIPseq_H3K9me3_rep1

description: immunopreciptated DNA


title: N3767_delta-cdp2_ChIPseq_H3K9ac_rep1

description: immunopreciptated DNA


title: sk11


title: N3767_delta-cdp2_ChIPseq_H4K16ac_rep1

description: immunopreciptated DNA


title: N150_WT_ChIPseq-H3K9me3_rep1

description: immunopreciptated DNA


title: sk2


title: sk17


title: N150_WT_ChIPseq-H4K16ac_rep1

description: immunopreciptated DNA


title: N3613_delta-chap_ChIPseq_H4K16ac_rep2

description: immunopreciptated DNA


title: sk14


title: sc10

source_name: tumour tissue

value: tumour tissue


title: sk9


title: sk6


title: sc6


title: sk1


title: sk3


title: sc74L


title: sk15


title: sc67L


title: sc2


title: sk19

data_processing:
Raw sequencing reads were first subjected to quality control using FastQC software (Babraham Bioinformatics, UK)
Low quality reads (phred-quality set to 20 and a minimum read length of 36 was required to pass the filter) and fragments containing adapter sequences were filtered with the use of FlexBar software (Dodt et al., 2012)
The mapping procedure was utilized using Tophat2 software (Trapnell et al., 2009), followed by counting of the reads to the gtf annotation file of Equus Caballus 3.0 assemble release v. 97 with the use of htseq-count software (Anders et al., 2015).
The differential expression analysis was performed with the use of Deseq2 software with the log transformation method (Love et al., 2014)
Assembly: EquCab3.0
Supplementary files format and content: Files containing gene counts for every gene and every sample created with htseq-count software

extract_protocol:
RNA was isolated from tissue using using TRIzol reagent (Invitrogen, Carlsbad, California) in combination with a Direct-zol RNA kit (Zymo Research)
The RNA-seq was performed using Swift Rapid RNA Library Kit (Biosciences) with deplete rRNA (Ribo-off rRNA Depletion Kit (Vazyme)), according to the protocol. The libraries were ligated with different indexes,  pooled in one pool and sequenced in the 150 pair-end cycles on Illumina NovaSeq.

treatment_protocol: The collected material was transferred into tubes with RNAlater and stored at -80°C.


title: sc3


title: sc9


title: sc4


title: sk15


title: sk13


title: sc71L


title: sc12


title: sk9


title: sk3


title: sk6


title: sc11


title: sc65L


title: sc10


title: sk17


title: sk11


title: sk2


title: sk16


title: sc11


title: sc6


title: sc2


title: sc3


title: sc9


title: sc74L


title: sc4


title: sk14


title: sc67L


title: sc65L


title: TBI 3 dpi mouse brain

city: Spring Hill

first: Duy

middle: Truong

last: Pham

state: Queensland

address: 391 Wichkham Terrace

country: Australia

institute: The University of Queensland

description:
TBI_3dpi_Mouse_Brain_C_Visium
10x Genomics

data_processing:
Raw BCL files were processed by bcl2fastq V2.7.0, and the fastq reads mapped to the mouse reference genome GRCm38 by SpaceRanger V1.0.0 with default settings
Assembly: GRCm38
Supplementary files format and content: spatial/aligned_fiducials.jpg: Aligned fiducials QC image
Supplementary files format and content: spatial/detected_tissue_image.jpg: Detected tissue QC image
Supplementary files format and content: spatial/scalefactors_json.json: Scale conversion factors for spot diameter and coordinates at various image resolutions
Supplementary files format and content: spatial/tissue_hires_image.png: Downsampled full resolution image
Supplementary files format and content: spatial/tissue_lowres_image.png: Full resolution image downsampled to 600 pixels on the longest dimension
Supplementary files format and content: spatial/tissue_positions_list.csv: CSV containing spot barcode
Supplementary files format and content: filtered_feature_bc_matrix.h5: Contains only tissue-associated barcodes in in HDF5 format.
Supplementary files format and content: filtered_feature_bc_matrix/barcodes.tsv.gz: List of barcodes
Supplementary files format and content: filtered_feature_bc_matrix/features.tsv.gz: List of feature
Supplementary files format and content: filtered_feature_bc_matrix/matrix.mtx.gz: Ciount matrix
Library strategy: Spatial transcriptomics Visium platform

source_name: Brain

extract_protocol:
Mice were subjected to controlled cortical impact injury or sham surgery (i.e., craniotomy only) as described previously. Injury parameters were: impact speed, 3.5 m/s; deformation depth, 1.0 mm; duration, 400 ms. Mice were sacrificed three days after TBI or sham surgery, their brains dissected in an RNase-free environment and immediately transferred into refrigerated O.C.T. compound (Sakura Tissue-Tek O.C.T. compound, Nagano, Japan) for flash-freezing in chilled isopentane. Samples were stored at -80°C until further processing. Library preparation of mouse brain samples was performed according to the Visium Spatial Gene Expression Reagent Kits User Guide (CG000239 Rev C, 10x Genomics, USA). Briefly, brain samples were cryosectioned until the dorsal hippocampus and dentate gyrus region were visible. Next, 10 μm sections were collected onto a pre-chilled Visium slide. All sections were dried onto the slides at 37°C for 1 minute, fixed in pre-chilled 100% methanol at -20°C for 30 minutes, and stained in Mayer's Haematoxylin for 5 minutes and Eosin for 2 minutes. Slides were then mounted in 85% glycerol for coverslipping and brightfield imaging (Axio Z1 slide scanner, Zeiss)
For Visium samples, permeabilisation of mouse brain samples was carried out for 18 minutes, resulting in a cDNA library size of 470 bp post-fragmentation. Library quantification was carried out using the KAPA Library Quantification kit (Roche), followed by in-house sequencing using a high output reagent kit and NextSeq500 instrument (Illumina) at the Institute for Molecular Bioscience Sequencing Facility. Sequencing was performed using the following protocol: Read1 - 28 bp, Index1 - 10 bp, Index2 - 10 bp, Read2 - 120 bp. . For Legacy samples,  ST sequencing libraries were prepared as per the manufacturer's instructions, with pre-permeabilisation and permeabilisation performed at 20 minutes and 7 minutes, respectively. On-slide cDNA synthesis, tissue removal, probe cleavage, and final library preparation were all performed as per the manual. High-quality cDNA libraries with sizes ranging between 660-780 bp were obtained and sequenced on the Illumina Nextseq500, using a 150 cycles kit with a read configuration of read 1 (26 bp) and read 2 (124 bp).

value: Brain

value: multiple cell types


title: Naive control mouse brain

description:
Naive_Control_Mouse_Brain_A_Visium
10x Genomics


title: sc12


title: sk1


title: sk13


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_6h_bioRep2

city: New York

first: Zhen

last: Sun

state: NY

address: 408 E 69th street, Z619

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Single-end sequencing reads were aligned to both the mouse genome (GRCm38.p6/mm10) and the drosophila genome (dm6) using STAR (v2.6.0a) with “--outFilterMismatchNoverLmax 0.03” and default parameters. The number of reads mapped to each gene was counted using STAR with “--quantMode GeneCounts”. For cell number based normalization, a drosophila gene-level count matrix was generated and passed to the estimateSizeFactors function of DESeq2 to calculate scale factors. Scaled bigwig pileup files of mouse alignments were generated using the bamCoverage program from DeepTools with “-bs 10 --normalizeUsing CPM --scaleFactor 1/(DESeq2 size factors calculated using drosophila spike-in alignments) --exactScaling --minMappingQuality 255 --skipNonCoveredRegions”.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: TT-seq

growth_protocol: E14 mESCs were cultured on 0.1% gelatin-coated dishes in 2i/LIF medium (50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, 50 μM b-mercaptoethanol, 1 μM MEKi (PD0325901), 3 μM GSK3i (CHIR99021), and 1x Leukemia Inhibitory Factor (LIF, produced in the Helin lab)).

extract_protocol:
Total RNA was extracted using TRIzol/chloroform extraction followed by isopropanol precipitation. 4sU-labelled Drosophila S2 cell RNA was spiked in. RNA was fragmented using NaOH and biotinylated with MTSEA biotin-XX linker. Biotinylated 4sU-RNA was pulled down using uMACS streptavidin MicroBeads and cleaned up using RNeasy MinElute Cleanup Kit (Qiagen) while retaining <200-nt RNA fragments.
Purified 4sU-RNA was used for strand-specific RNA sequencing library preparation with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for indicated amount of time followed by 15min co-treatment of 500 nM dTAG-13 and 1 mM 4sU. For control groups (dTAG-13 0h), cells were treated with 1 mM 4sU for 15min.

value: mouse embryonic stem cells

value: NSD1-dTAG knockin

value: dTAG-13 for 6h followed by dTAG-13 and 4sU for 15min


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_0h_bioRep1

value: 4sU for 15min


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_0h_bioRep2


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_1h_bioRep2

value: dTAG-13 for 1h followed by dTAG-13 and 4sU for 15min


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_6h_bioRep1


title: TT-seq_mESC_NSD1-dTAG_dTAG-13_1h_bioRep1


title: RRBS_mESC_Nsd1_WT_batch2_bioRep2

data_processing:
Raw sequencing reads were 3' trimmed for quality (<20) and adapter content using Trim Galore (v0.6.4). The trimmed sequence reads were C(G) to T(A) converted and mapped using Bismark (v0.19.0) to similarly converted reference mouse genome mm10 using default Bowtie2 settings. Uniquely aligned reads were retained and duplicated reads were discarded. The remaining alignments were then used for cytosine methylation calling by Bismark methylation extractor. CHG and CHH were discarded to focus on CpG methylation. CpGs were further filtered by C coverage >= 5 reads in all samples and 1kb windows with >= 3 CpGs were selected for further analysis.
Assembly: mm10
Supplementary files format and content: bigwig (%methylation and coverage)

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue Kit (Qiagen) with RNase A treatment according to manufacturer's protocol. Genomic DNA was digested with Msp I (NEB) and purified using MinElute PCR Purification Kit (Qiagen).
1 μg of Msp I-digested DNA was subjected to end repair, clean-up, 3’ adenylation, adapter ligation, and size selection clean-up using the NEXTFLEX Bisulfite Library Prep Kit (PerkinElmer) according to manufacturer’s protocol. Bisulfite conversion of DNA was then performed using the EZ DNA Methylation-Lightning Kit (Zymo Research) according to manufacturer’s protocol. DNA was amplified using the KAPA HiFi HotStart Uracil+ ReadyMix Kit (Roche) according to manufacturer’s protocol and cleaned up using Agencourt AMPure XP magnetic beads (Beckman Coulter).

treatment_protocol: Cells were treated with 500 nM dTAG-13 for indicated amount of time.

value: wild type

value: no treatment


title: RRBS_mESC_Nsd1_KO2_batch2_bioRep2

value: Nsd1 knockout 2


title: RRBS_mESC_Nsd1_KO2_batch2_bioRep1


title: RRBS_mESC_Nsd1_WT_batch2_bioRep1


title: sc71L


title: RRBS_mESC_NSD1-dTAG_dTAG-13_24h_batch1_bioRep1

value: dTAG-13 for 24h


title: RRBS_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep2

value: dTAG-13 for 6h


title: RRBS_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep2


title: RRBS_mESC_NSD1-dTAG_dTAG-13_24h_batch1_bioRep2


title: RRBS_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1


title: RRBS_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_1h_batch4_bioRep3

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). 3' UTR annotations of the GRCm38.p6/mm10 assembly were obtained from the UCSC table browser. 3’ UTR annotations were assigned to Ensembl gene IDs and collapsed using the mergeBed program from bedtools (v2.27.1). For alignment to the mouse genome (GRCm38.p6/mm10) and ERCC spike-in sequences and read counting at 3’ UTRs, single-end sequencing reads were processed using the slamdunk all program from SlamDunk (v0.4.3) with “-n 100 -m” and default parameters. For gene-level analysis, reads mapped to different 3’ UTRs of the same gene were summed up using the alleyoop collapse program from SlamDunk. Differential gene expression analysis was performed using DESeq2 (v1.30.0) with reads that contain more than one T>C conversions (nascent RNA reads). Size factors were calculated using corresponding total RNA reads for global normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing raw read counts (total read counts and T>C conversion read counts) at 3' UTR of genes
Library strategy: SLAM-seq

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) with DTT supplemented to all buffers. Total RNA was spiked in with ERCC RNA Mix 1 and subjected to thiol-linked alkylation by iodoacetamide. RNA was re-purified by ethanol precipitation.
Alkylated RNA was used for 3’-end polyA RNA sequencing library preparation with the QuantSeq 3’ mRNA-Seq Library Prep FWD Kit for Illumina (Lexogen) according to the manufacturer’s protocol.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for indicated amount of time followed by 2h co-treatment of 500 nM dTAG-13 and 100 uM 4sU. For control groups (dTAG-13 0h), cells were treated with 100 uM 4sU for 2h.

value: NSD1-dTAG knockin; piggyBac NSD1-FL N1751Q

value: dTAG-13 for 1h followed by dTAG-13 and 4sU for 2h


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_1h_batch4_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch4_bioRep1

value: 4sU for 2h


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch4_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch4_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_1h_batch4_bioRep3

value: NSD1-dTAG knockin; piggyBac NSD1-FL


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch4_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_1h_batch4_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch4_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_1h_batch4_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_6h_batch3_bioRep3

value: dTAG-13 for 6h followed by dTAG-13 and 4sU for 2h


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch4_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_6h_batch3_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch3_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_6h_batch3_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_6h_batch3_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_6h_batch3_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch3_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_1h_batch4_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_6h_batch3_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch3_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_24h_batch1_bioRep2

value: dTAG-13 for 24h followed by dTAG-13 and 4sU for 2h


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_24h_batch1_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_24h_batch1_bioRep3


title: CUT&RUN_H3K36me2_mESC_Nsd1_KO2_NSD1-FL

data_processing:
Bcl files containing raw sequencing data were converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422, Illumina). Paired-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) using Bowtie2 (v2.3.4.1) with “--local --very-sensitive-local --phred33 --no-unal --no-mixed --no-discordant -I 10 -X 700 -S”. Reads were also aligned to the drosophila (dm6) genome with additional “--no-overlap” to map spike-in reads. Number of mapped reads to each genome was used to generate scaling factors for downstream spike-in normalization. Sam files were converted to bam files, sorted and indexed using samtools (v1.9). Peaks were called using MACS2 (v2.2.6) callpeak program with “-f BAMPE --keep-dup 1 -q 0.05”. Peaks from NSD1 CUT&RUN using NSD1-dTAG mESCs were additionally filtered for q < 0.000001. For peak calling, datasets generated using NSD1 degraded (72h) cells, Nsd1 KO cells or IgG was used as controls. Bigwig pileup files were generated using the bamCoverage program from DeepTools (v3.2.1) with “-bs 10 --extendReads --normalizeUsing RPKM --exactScaling --skipNonCoveredRegions” and filtered for mouseENCODE blacklisted genomic regions (v2). For NSD1/H3K36me2 and SETD2/H3K36me3 CUT&RUN in NSD1-dTAG and SETD2-dTAG cells, respectively, as well as for NSD1 CUT&RUN in rescue cells expressing NSD1 C series, scaling factors calculated using the percentage of spike-in reads were applied to the “--scaleFactor” option for cell number based normalization. In other cases, the spike-in read percentage was very close and a scaling factor of 1 was applied.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&RUN

growth_protocol: E14 mESCs were cultured on 0.1% gelatin-coated dishes in 2i/LIF medium (50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, 50 μM b-mercaptoethanol, 1 μM MEKi (PD0325901), 3 μM GSK3i (CHIR99021), and 1x Leukemia Inhibitory Factor (LIF, produced in the Helin lab)). EpiSCs were cultured on 16.7 μg/mL fibronectin-coated dishes in medium containing 50% DMEM/F12, 50% Neurobasal, 0.5% N2 supplement, 1% B27 supplement, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 50 μM b-mercaptoethanol, 12.5 ng/mL recombinant human basic FGF (FGF2), 20 ng/mL Activin A, and 175 nM Wnt inhibitor NVP-TNKS656.

extract_protocol:
Dessociated cells were bound to Concanavalin A beads and permeabilized with Digitonin, followed by binding of antibodies and pAG-MNase to targets on native chromatin in situ. MNase cleavage of target occupied DNA was activated by addition of CaCl2 at 4C. Cleaved DNA was released by incubation at 37C and purified using Monarch DNA Cleanup Kit (NEB).
Libraries were prepared with less than 10 ng CUT&RUN DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol with modifications: end prep was performed for 30 min at 20C followed by 1 h at 50C to prevent melting of small fragments, adaptor-ligated DNA was cleaned up without size selection, and the anneal/extension step of PCR amplification was performed for 10s at 65C to favor exponential amplification of the desired CUT&RUN fragments.

treatment_protocol: Cells were treated with 500 nM dTAG-13 for indicated amount of time. For EB differentiation, mESCs were grown in suspension in non-TC-treated culture dishes in medium containing GMEM, 10% heat-inactivated FBS, 1% Penicillin/Streptomycin, 2 mM L-Glutamine, 0.1 mM Non-essential amino acids, 1 mM Sodium Pyruvate, and 100 μM β-Mercaptoethanol.

value: Nsd1 knockout 2; piggyBac NSD1-FL

tag: cut&run antibody

value: H3K36me2 (Thermo Fisher, MA5-14867)


title: CUT&RUN_H3K36me2_mESC_Nsd1_KO2_NSD2-FL

value: mouse embryonic stem cells

value: Nsd1 knockout 2; piggyBac NSD2-FL


title: CUT&RUN_H3K36me2_mESC_Nsd1_KO2


title: CUT&RUN_H3K4me3_mESC_NSD1-dTAG_dTAG-13_24h

value: NSD1-dTAG knockin

value: H3K4me3 (Thermo Fisher, PA5-27029)


title: CUT&RUN_H3K4me3_mESC_NSD1-dTAG_dTAG-13_6h


title: CUT&RUN_H3K4me3_mESC_NSD1-dTAG_dTAG-13_0h


title: CUT&RUN_H3K4me3_mESC_NSD1-dTAG_dTAG-13_1h

value: dTAG-13 for 1h


title: CUT&RUN_H3K4me1_mESC_NSD1-dTAG_dTAG-13_24h

value: H3K4me1 (Cell Signaling, 5326)


title: CUT&RUN_H3K4me1_mESC_NSD1-dTAG_dTAG-13_6h


title: CUT&RUN_H3K4me1_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: CUT&RUN_H3K4me1_mESC_NSD1-dTAG_dTAG-13_1h


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_N1751Q_dTAG-13_0h_batch3_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch3_bioRep2


title: CUT&RUN_BRD4_mESC_NSD1-dTAG_dTAG-13_24h

value: dTAG-13 for 24h

value: BRD4 (Abcam, ab128874)


title: gRNA readout in lentiguide puro plasmid library

city: TAMPA

last: Wang

state: FL

address: 14059 Riveredge Drove

institute: Moffitt Cancer Center

description: Amplicon of gRNA integration

library_source: other

data_processing:
count_spacers.py (https://github.com/fengzhanglab/Screening_Protocols_manuscript/blob/master/count_spacers.py) was used to quantify gRNA count from Read1 file
Supplementary files format and content: Raw count matrix of gRNA, rows as gRNA design name, column as each sample
Library strategy: Amplicon-seq

molecule: other

organism: Expression vector lentiGuide-Puro

source_name: plasmid

growth_protocol: All cells were screened in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Genomic DNA was extracted with a midi-prep kit with Rnase treatment.
gRNA integration was amplified from the gDNA of each sample. The gDNA amount was equivalent to at least 5 million cells.

treatment_protocol: Cells were passaged with a minimal number of 5 million (equivalent to 500-fold library size) after confirming single guide RNA integration (MOI ~ 0.3)

value: plasmid

tag: time point

value: Screening library


title: SLAM-seq_mESC_NSD1-dTAG_NSD1-FL_dTAG-13_0h_batch3_bioRep3

value: 4sU for 2h


title: PH-LHD_14

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with BaseCaller Illumina software to BCL files and demultiplexed to fastq files with bcl2fastq v2.20.0.422.
Sequencing quality was determined using FastQC v. 0.11.5 software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequences were aligned to the reference genome Homo sapiens (hg38 version 96, https://www.ensembl.org/Homo_sapiens/Info/Index) using STAR aligner v. 2.5.2a, allowing for 2 mismatches within 50 bases.
Read counting was performed using featureCounts v. 1.5.0-p1.
Read counts were analyzed in the R/Bioconductor environment v. 3.6.1 (www.bioconductor.org) using the DESeq2 package v. 1.24.0.
Genes were annotated using the Homo sapiens GTF file hg38 version 96 (https://www.ensembl.org/Homo_sapiens/Info/Index) to quantify the reads within genes.
Supplementary files format and content: Tab-delimited gene counts

source_name: pulmonary artery trunk

extract_protocol:
Snap-frozen PA specimens were subjected to TRIzol-RNA extraction. RNA quality was assessed by measuring the RNA integrity number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.).
Library preparation for total RNA-Seq was performed using TruSeq™ Stranded Total RNA with Ribo-Zero Gold (Illumina, Cat. Nr. RS-122-2301) starting from 1000 ng of total RNA. The size range of the final cDNA libraries was determined by applying the SS NGS Fragment 1- to 6000-bp Kit on the Fragment Analyzer (average 340 bp). Accurate quantification of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega).

tag: tissue

value: pulmonary artery trunk

tag: disease

value: pulmonary hypertension due to left heart disease

tag: age

value: M


title: CUT&RUN_p300_mESC_NSD1-dTAG_nontreated

tag: genotype

value: p300 (Cell Signaling, 86377)


title: CUT&RUN_H3K27ac_mESC_NSD1-dTAG_nontreated

tag: treatment

value: H3K27ac (Thermo Fisher, MA5-23516)


title: PH-LHD_15


title: CUT&RUN_HA_NSD1_mESC_NSD1-dTAG_dTAG-13_6h

tag: cell line

value: mouse embryonic stem cells

value: dTAG-13 for 6h

value: HA (Cell Signaling, 3724)


title: CUT&RUN_H3K9me3_mESC_NSD1-dTAG_nontreated

tag: cell type

value: NSD1-dTAG knockin


title: ChIP-seq_SPT6_mESC_NSD1-dTAG_dTAG-13_6h

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Paired-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) using Bowtie2 (v2.3.4.1) with “--local --very-sensitive-local --phred33 --no-unal --no-mixed --no-discordant -I 10 -X 700 -S”. Reads were also aligned to the drosophila (dm6) genome with additional “--no-overlap” to map spike-in reads when applicable. Sam files were converted to bam files, sorted and indexed using samtools (v1.9). Peaks were called using MACS2 (v2.2.6) callpeak program with “-f BAMPE --keep-dup 1 -q 0.05” using input as control. Bigwig pileup files were generated using the bamCoverage program from DeepTools (v3.2.1) with “-bs 10 --extendReads --normalizeUsing RPKM --exactScaling --skipNonCoveredRegions” and filtered for mouseENCODE blacklisted genomic regions (v2). The spike-in read percentage was very close and a scaling factor of 1 was applied.
Assembly: mm10
Supplementary files format and content: bigwig, narrowPeak

extract_protocol:
Cells were dissociated and crosslinked with 1% formaldehyde. Nuclei were isolated and chromatin was fragmented using a bioruptor sonicator. Drosophila chromatin was spiked in for Pol II ChIPs. Immunoprecipitation was performed using indicated antibodies and immunocomplexes were further pulled down using Protein G beads. Beads were washed and eluted followed by reverse crosslinking and DNA purification.
Libraries were prepared with 3 ng ChIP or input DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s protocol. Bead based sized selection was performed to enrich for DNA with ~250 bp inserts

tag: chip antibody

value: SPT6 (Cell Signaling, 15616)


title: CUT&RUN_H3K36me2_mESC_Nsd1_KO2_NSD1-FL_N1751Q

value: Nsd1 knockout 2; piggyBac NSD1-FL N1751Q

value: H3K36me2 (Thermo Fisher, MA5-14867)


title: ChIP-seq_SPT6_mESC_NSD1-dTAG_dTAG-13_0h

value: no treatment


title: PH-LHD_12


title: PH-LHD_10


title: PH-LHD_11


title: ChIP-seq_PAF1_mESC_NSD1-dTAG_dTAG-13_6h

value: PAF1 (Cell Signaling, 12883)


title: PH-LHD_8


title: PH-LHD_9


title: ChIP-seq_PAF1_mESC_NSD1-dTAG_dTAG-13_0h


title: CUT&RUN_BRD4_mESC_NSD1-dTAG_dTAG-13_1h

value: dTAG-13 for 1h

value: BRD4 (Abcam, ab128874)


title: PH-LHD_7


title: ChIP-seq_SPT5_mESC_NSD1-dTAG_dTAG-13_6h_batch2_bioRep2

value: SPT5 (BD Biosciences, 611107)


title: PH-LHD_6

value: pulmonary artery trunk


title: PH-LHD_4

value: pulmonary hypertension due to left heart disease


title: ChIP-seq_SPT5_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1


title: PH-LHD_5

value: F


title: PH-LHD_3


title: ChIP-seq_SPT5_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2


title: PH-LHD_13

value: M


title: ChIP-seq_SPT5_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1


title: PH-LHD_2


title: ChIP-seq_NELF-E_mESC_NSD1-dTAG_dTAG-13_6h

value: NELF-E (Abcam, ab170104)


title: ChIP-seq_NELF-C_mESC_NSD1-dTAG_dTAG-13_6h

value: mouse embryonic stem cells

value: NELF-C (Cell Signaling, 12265)


title: LHD w/o PH_5

value: left heart disease without pulmonary hypertension


title: LHD w/o PH_4


title: ChIP-seq_NELF-C_mESC_NSD1-dTAG_dTAG-13_0h

value: NSD1-dTAG knockin


title: PH-LHD_1


title: ChIP-seq_NELF-E_mESC_NSD1-dTAG_dTAG-13_0h


title: LHD w/o PH_3


title: ChIP-seq_H3K18acyl_mESC_NSD1-dTAG_nontreated

value: H3K18acyl (EpiCypher, 13-0050)


title: ChIP-seq_H3K18ac_EpiSC_NSD1-dTAG_nontreated

value: mouse epiblast stem cells

value: H3K18ac (Thermo Fisher, 703896)


title: LHD w/o PH_1


title: ChIP-seq_H3K18ac_mESC_NSD1-dTAG_nontreated

value: no treatment


title: Donor_8

value: healthy heart


title: Donor_7


title: WT2

city: Bethesda

first: Kai

last: Yu

state: Maryland

address: 50 South Drive, Bldg 50, Room 5151

institute: NHGRI

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequences from the Chromium platform were de-multiplexed and aligned using CellRanger ver. 3.1.0 from 10x Genomics
Assembly: mm10
Supplementary files format and content: The file "filtered_feature_bc_matrix.h5" is the aggregated data, read-depth normalized. This file was used for all downstream analyses.

source_name: bone marrow

extract_protocol:
Single cell: dissociation protocol: DOI: 10.1016/j.mex.2018.10.009. Single cells were captured using 10x Genomics Chromium.
Single-cell RNA-seq libraries were prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3. Cell lysis, cDNA preparation and library construction was prepared following the manufacturers protocol.

value: bone marrow

value: sorted c-Kit+ cells


title: LEU2

description: 10x Genomics


title: PRE2

description: 10x Genomics


title: Donor_6


title: Donor_5


title: Donor_4


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_24h_bioRep3

value: SETD2-dTAG knockin

value: dTAG-13 for 24h followed by dTAG-13 and 4sU for 2h


title: Donor_3

value: pulmonary artery trunk


title: ChIP-seq_H3K18acyl_EpiSC_NSD1-dTAG_nontreated


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_24h_bioRep2


title: Donor_1


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_24h_bioRep1


title: Donor_2

value: F


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_6h_bioRep3

value: dTAG-13 for 6h followed by dTAG-13 and 4sU for 2h


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_6h_bioRep1


title: LHD w/o PH_2


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_0h_bioRep3

value: 4sU for 2h


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_0h_bioRep1

value: mouse embryonic stem cells


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_6h_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_1h_batch2_bioRep2

value: dTAG-13 for 1h followed by dTAG-13 and 4sU for 2h


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_1h_batch2_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch2_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep3


title: SLAM-seq_mESC_SETD2-dTAG_dTAG-13_0h_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_6h_batch1_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep3


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep2


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_0h_batch1_bioRep1


title: SLAM-seq_mESC_NSD1-dTAG_dTAG-13_1h_batch2_bioRep1


title: RNA-seq_EB_d6_NSD1-dTAG_dTAG-13_bioRep3

data_processing:
Bcl files containing raw sequencing data was converted to fastq format, adaptor trimmed and demultiplexed using bcl2fastq2 (v2.20.0.422). Single-end sequencing reads were aligned to the mouse genome (GRCm38.p6/mm10) with default parameters. The number of reads mapped to each gene was counted using STAR with “--quantMode GeneCounts”. Differential gene expression analysis was performed using DESeq2 (v1.30.0) with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files containing raw read counts at genes

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and ERCC RNA Mix 1 was spiked in. Poly(A) RNA was selected using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Strand-specific RNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

value: EB differentiation for 6 days; dTAG-13 for 6 days


title: Ctrl.IOMM-Lee.rep4

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

institute: INSERM

description: human anaplastic meningioma cell line IOMM-Lee

hyb_protocol: One hundred ng of total RNA were used as the starting amount for microarrays experiments. 3.5 µg of labeled DNA were hybridized onto Affymetrix cartridges for 16 hours at 45°C under continuous rotation at 60 rpm. The arrays were washed and scanned according to the protocol GeneChip® Expression Wash, Stain and Scan for Cartridge Arrays (P/N 702731 Rev. 4).

scan_protocol: GeneShips were scanned using a GeneChip Scanner 3000

data_processing: Fluorescence values corresponding to raw expression data for each sample were extracted as a whole from each Affymetrix CEL files (one file per sample) using the R oligo package with the corresponding platform definitions (pd.hugene.2.0.st). The extraction method included no normalization or background correction with the RMA algorithm. Positive and negative control probes were removed.

label: biotin

source_name: mirVana miR Mimic Negative Control biological replicate 4

label_protocol: Gene expression experiments were performed using Affymetrix Human Genechip v.2.0 and ST Arrays using GeneChip® WT PLUS Reagent Kit, according to the standard protocol for Target Preparation for GeneChip® Whole Transcript (WT) Expression Arrays (P/N 703174 Rev.2).

growth_protocol: A human malignant meningioma cell line, IOMM-Lee cells, (intraosseous malignant meningioma; a generous gift from Dr Gillespie and Dr Jensen, University of Utah, USA),  was immortalized by retroviral transduction with human telomerase reverse transcriptase, (Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Germany). In order to perform anchorage-dependent cell growth assay, 25,000 cells were incubated per well in 24-well plates. Cells were transfected with 17 nM of miRs. The number of cells per microliter was counted at 2, 4, and 6 days after transfection using LUNA Automated Cell Counter (Logos Biosystems, Annandale, USA).

extract_protocol: Seventy-two hours after transfection independently with miR-16 (n=6, miR Mimic hsa-miR-16-5p), mir-519 (n=6, miR Mimic hsa-miR-519a-3p) and miR negative controls (n=6, mirVana miR Mimic Negative Control), the transfected IOMM-Lee cells were used for total RNA extractions using the TRIzol protocol (Invitrogen, Life Technologies, Carlsbad, CA, USA)

treatment_protocol: The overexpression of miR-16 and miR-519 was achieved by transfection of mirVana miR Mimic hsa-miR-16-5p (Ambion, Life Technologies) and mirVana miR Mimic hsa-miR-519a-3p (Ambion, Life Technologies), respectively. MirVana miR Mimic Negative Control (Ambion, Life Technologies) was used as a control. Cells transfections using Lipofectamine RNAiMAX Transfection Reagent were performed followinginhe manufacturer’s instructions.  Transfection efficacy was chrified at 4after using qRT-PCR technique.

value: IOMM-Lee cells


title: miR16.IOMM-Lee.rep6

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 6


title: Ctrl.IOMM-Lee.rep2

source_name: mirVana miR Mimic Negative Control biological replicate 2


title: miR519.IOMM-Lee.rep5

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 5


title: miR519.IOMM-Lee.rep6

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 6


title: Ctrl.IOMM-Lee.rep3

source_name: mirVana miR Mimic Negative Control biological replicate 3


title: miR16.IOMM-Lee.rep4

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 4


title: miR519.IOMM-Lee.rep2

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 2


title: RNA-seq_EB_d6_NSD1-dTAG_dTAG-13_bioRep2

value: NSD1-dTAG knockin


title: Ctrl.IOMM-Lee.rep5

source_name: mirVana miR Mimic Negative Control biological replicate 5


title: RNA-seq_EB_d6_NSD1-dTAG_dTAG-13_bioRep1


title: RNA-seq_EB_d6_NSD1-dTAG_nontreated_bioRep3

value: EB differentiation for 6 days


title: miR519.IOMM-Lee.rep1

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 1


title: Ctrl.IOMM-Lee.rep6

source_name: mirVana miR Mimic Negative Control biological replicate 6


title: Alzheimer's disease Sample 4

city: Gainesville

first: Curtis

middle: A

last: Nutter

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

description:
rRNA depleted
AD_4

data_processing:
aligned using STAR
alignment analyzed using rMATS
alignment analyzed using DESEQ2
alignment analyzed using HOMER
Assembly: GRCh38/hg38
Supplementary files format and content: DataFileS2_Nutter_Final is an excel file which contains tabs with paired group comparisons of alternative splicing changes from rMATS or differential expression from DESeq2. There are also tabs with gene counts for all expressed genes for all sample groups.

source_name: choroid plexus, lateral

extract_protocol:
Human ChP tissues (Alzheimer’s disease and neurologically unaffected controls) were obtained from the NIH NeuroBioBank. Myotonic dystrophy type 1 ChP tissues were obtained both from the University of Florida (UF) Center for NeuroGenetics and the Stanford University Neuromuscular BioBanks. All human ChP tissues used in this study were pre-existing and deidentified.
For RNA isolation, tissue samples were homogenized in 300 μL TRI Reagent (Zymo R2050-1-200) and incubated at 25C for 10 min. Total RNA was isolated using the Direct-zol RNA miniprep kit (Zymo), following the manufacturer’s instructions, including an on-column DNase I digestion step. RNA concentration was determined using the Qubit 4 Fluorometer with a broad range RNA quantification broad range kit (Invitrogen). RNA quality was checked using a Fragment Analyzer (Agilent) and depleted of rRNA (rRNA Depletion Kit v2 Human/Mouse/Rat, NEB).
cDNA libraries prepared using the Ultra II Directional RNA Library, NEB. Human ChP libraries were generated using 500 ng of total RNA input and sequenced on Illumina NextSeq500 and/or NextSeq2000 platforms.

value: choroid plexus, lateral

value: male

tag: disease group

value: Alzheimer's disease

tag: age of_death


title: miR519.IOMM-Lee.rep3

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 3


title: GATA2_HA-IP

city: Cambridge

first: Richard

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Raw CLIP-seq reads were trimmed using Cutadapt. The adapter sequence AGATCGGAAGAGCACACGTCTGAA was trimmed from the 5’ end of the reads,  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT adapter sequence from the 3’ end, and a universal four nucleotide UMI from the 3’ end. Prior to mapping, UMIs were extracted from the 5’ end of the reads using UMI-tools version 1.0.0 with the argument --bc-pattern=NNNNNNNN.  Bowtie2 was used to map all trimmed reads to the hg19 human genome using parameters -p 40 –end-to-end –no-discordant86,87. Trimmed, mapped, and unique reads were then sorted using the samtools sort function and indexed using the bedtools index function. Lastly, reads were collapsed to account for PCR duplicates using the extracted UMIs with the UMI-tools dedup function. These trimmed, mapped, and collapsed reads were then used for downstream analysis. To call CLIP-seq peaks, .bed files were generated using MACS with parameters -g hs --keep-dup auto –-nomodel.
Assembly: hg19
Supplementary files format and content: bed file containing called CLIP peaks

growth_protocol: K562 cells were cultured in suspension flasks containing RPMI-1640 medium with GlutaMAX™ supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 μg/mL streptomycin

extract_protocol:
Cells were washed in 1X PBS and cell pellets were lysed in eCLIP lysis buffer [20 mM HEPES-NaOH pH 7.4, 1 mM EDTA, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1x cOmplete EDTA-free protease inhibitor cocktail (Roche 4693132001)]. Samples were sonicated in a Diagenode Bioruptor (30 s ON/OFF) on medium for 5 minutes. RNase I (ThermoFisher AM2294) was added to lysates for a final concentration of 0.4 U/µL and incubated at 37 C at 1200 rpm for 5 min. EDTA was immediately added at a final concentration of 21 mM. Lysates were clarified at 15,000g for 10 minutes at 4˚C and supernatant was transferred to fresh tubes. Protein concentration was measured using Protein Assay Dye Reagent (Bio-Rad 5000006). Dynabeads were washed in eCLIP binding buffer (20 mM HEPES-NaOH pH 7.4, 20 mM EDTA, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate). Antibody was added to bead mixture and incubated, rotating at room temperature for 45 min. Antibody-bead mixture was washed in eCLIP binding buffer and mixed with calculated amount of lysate. Tubes were incubated overnight rotating at 4˚C. 2% of lysate-bead mixture was transferred to a new tube to serve as input sample. IP samples were washed with CLIP wash buffer (20 mM HEPES-NaOH pH 7.4, 20 mM EDTA, 5 mM NaCl, 0.2% Tween-20) and IP50 (20 mM Tris pH 7.3RT, 0.2 mM EDTA, 50 mM KCl, 0.05% NP-40). Samples were treated with TURBO DNase (ThermoFisher AM2238) and 0.1 U/µL final concentration of RNase I (in some cases, 1 U/µL final concentration was used for better visualization of bands, e.g. Fig. S2A). IP samples were washed in CLIP wash buffer and FastAP buffer (10 mM Tris-Cl pH 7.5RT, 5 mM MgCl2, 100 mM KCl, 0.02% Triton X-100). IP RNA was dephosphorylated using FastAP phosphatase reaction FastAP Thermosensitive Alkaline Phosphotase (ThermoFisher EF0652), and T4 PNK (NEB M0201S).     IP samples were washed in CLIP wash buffer and 1X RNA Ligase buffer (50 mM Tris-Cl pH 7.5RT, 10 mM MgCl2]. A 3’ IR-800 fluorescent adaptor was ligated using T4 RNA Ligase 1 high concentration (NEB M0437M). Samples were washed in eCLIP high-salt wash buffer (50 mM Tris-HCl pH 7.4RT, 1M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and CLIP wash buffer. IP and input samples were eluted with 4X LDS Sample Buffer (ThermoFisher NP0007), run on an 8% bis-tris gel, and transferred overnight to a nitrocellulose membrane.
The transferred membrane was cut ~0–50 kDa above protein size and incubated with Proteinase K (ThermoFisher AM2548) to isolate crosslinked RNA. Remaining steps were performed as per the seCLIP protocol83, with some modifications. RNA was purified and concentrated with phenol:chloroform:IAA (ThermoFisher AM9732) and ethanol precipitation. 3’ and 5’ adapters were designed to include an IR800 fluorophore and an 8-nt UMI for cDNA ligation, respectively. We did not include 5’ deadenylase enzyme in our 5’ ligation reactions and we used the AffinityScript RT (Agilent 600107) for crosslinking-induced truncation.

treatment_protocol:
GATA2 transgenic K562 cells were treated for 5 hours with 1 µg/mL doxycycline and 24 hours with 100 µM 4-thiouridine.
Cells were UV crosslinked at 365 nm at 0.3 J/cm^2

value: chronic myelogenous leukemia cell line

value: GATA2 transgene


title: miR16.IOMM-Lee.rep2

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 2


title: GATA2_Input


title: miR519.IOMM-Lee.rep4

source_name: miR Mimic hsa-miR-519a-3p miR519 biological replicate 4


title: RNA-seq_EB_d6_NSD1-dTAG_nontreated_bioRep1


title: RNA-seq_EB_d6_NSD1-dTAG_nontreated_bioRep2


title: Ctrl.IOMM-Lee.rep1

source_name: mirVana miR Mimic Negative Control biological replicate 1


title: miR16.IOMM-Lee.rep3

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 3


title: Alzheimer's disease Sample 2

description:
rRNA depleted
AD_2

value: female

tag: (co-)morbidities

value: Breast Cancer


title: Alzheimer's disease Sample 1

description:
rRNA depleted
AD_1

value: Hypertension, Vascular disease


title: RNA-seq_mESC_NSD1-dTAG_nontreated_bioRep3

value: no treatment


title: miR16.IOMM-Lee.rep1

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 1


title: miR16.IOMM-Lee.rep5

source_name: miR Mimic hsa-miR-16-5p miR16 biological replicate 5


title: RNA-seq_mESC_NSD1-dTAG_nontreated_bioRep2


title: Alzheimer's disease Sample 3

description:
rRNA depleted
AD_3


title: myotonic dystrophy type 1 Sample 4

description:
rRNA depleted
DM1_4

value: myotonic dystrophy type 1


title: myotonic dystrophy type 1 Sample 3

description:
rRNA depleted
DM1_3


title: RNA-seq_mESC_WT_dTAG-13_72h_bioRep3

value: WT

value: dTAG-13 for 72h


title: RNA-seq_mESC_NSD1-dTAG_nontreated_bioRep1

value: mouse embryonic stem cells


title: RNA-seq_mESC_WT_dTAG-13_72h_bioRep2


title: Neurologically unaffected control Sample 5

description:
rRNA depleted
CTL_5

value: Neurologically unaffected control

value: Diabetes, Lung Cancer, Hypertension, Atherosclerosis, Cardiovascular disease


title: RNA-seq_mESC_WT_dTAG-13_72h_bioRep1


title: Neurologically unaffected control Sample 3

description:
rRNA depleted
CTL_3

value: Atherosclerosis, Cardiovascular disease


title: myotonic dystrophy type 1 Sample 1

description:
rRNA depleted
DM1_1


title: RNA-seq_mESC_WT_nontreated_bioRep1


title: Neurologically unaffected control Sample 4

description:
rRNA depleted
CTL_4

value: Hypertension, Atherosclerosis, Cardiovascular disease


title: Neurologically unaffected control Sample 2

description:
rRNA depleted
CTL_2

value: choroid plexus, lateral


title: CUT&RUN_HA_NSD1_mESC_Nsd1_KO2_NSD1-FL

value: Nsd1 knockout 2; piggyBac NSD1-FL

value: HA (Cell Signaling, 3724)


title: SMA patient after six months of  Nusinersen treatment  [17_T6]

city: Pavia

first: Maria

last: Garofalo

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

data_processing:
FastQ files were generated via llumina bcl2fastq2 Version 2.17.1.14
Trimmed reads were aligned through Bluebee Corall platform. Differential expression analysis was performed using R package DESeq2.
Assembly: hg38
Supplementary files format and content: DESeq2 output

source_name: CSF

extract_protocol:
RNA was extracted using miRNeasy Serum/Plasma (Qiagen)
Libraries were prepared starting from 500 ng of total RNA. RNA was fractioned for rRNA depletion using RiboCop V1.3 (Lexogen) and libraries were prepared with the CORALL Total RNA-Seq Library Prep Kit (Lexogen) following manufacturer's intructions. The quality of libraries was analyzed using 4200 Tape Station with a “DNA High sensitivity” assay (Agilent) and quantified using High Sensitivity dsDNA assay with a Qubit device (Life Technologies). Sequencing was performed using Illumina NextSeq 500.

value: CSF

tag: disease state

value: SMA

tag: treatment/time point