title: Fezf2Control_Upper

first: Paola

last: Arlotta

address: 7 Divinity Ave

department: Stem Cell and Regenerative Biology

institute: Harvard University

description: single cell

data_processing:
For scRNA-seq, sequencing and basecalling were performed with NextSeq 500 instrument (Illumina). For snRNA-seq, sequencing and basecalling were performed with NovaSeq instrument (Illumina).
Cellranger mkfastq (10x Genomics v2.1.0) was used to demultiplex bcl files to fastq files using standard parameters
Cellranger count (10x Genomics v2.1.0) was used to produce an aligned single cell feature count matrix, using mm10 genome as a reference.
Seurat (v3.1.1) pipeline including SCTransform was used to normalize and scale the single cell data. Default parameters were used. The following parameters were used for regression: percent.mt, nCount_RNA, and replicate.
PCA and t-SNE were used to for dimensionality reduction and visualization of single cells data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts
Supplementary_files_format_and_content: tab-delimited file with the metadata for each sample in the matrix

source_name: P14 Fezf2Control S1 cortex Layers 1-4

growth_protocol: Standard mouse housing conditions

extract_protocol:
Samples were maintained at 4C. S1 cortex was micro-dissected, homogenized and sorted for all nuclei in nuclei solubilization buffer. For scRNA-seq, S1 cortex layers were micro-dissected, homogenized in PBS with DNAse and RNAse-inhibitor, followed by FACS in BSA-containing PBS.
Libraries were produced using 10x genomics technology.

treatment_protocol: Fezf2 WT and KO mice were equally housed and treated. Genotypes were obtained through standard breeding.

value: S1 cortex


title: LY1_H3K27Ac-Diagenode

status: Public on Apr 26 2022

type: SRA

city: New York

first: Laura

last: Pasqualucci

state: NY

address: 1130 St Nicholas Avenue

department: Institute for Cancer Genetics

country: USA

institute: Columbia University

library_source: genomic

data_processing:
Sequencing data were acquired through the default Illumina pipeline using Casava V1.8.
Reads were aligned to the human genome (UCSC hg19) using the Bowtie2 aligner v2.1.0, allowing up to two mismatches. Duplicate reads (i.e. reads of identical length mapping to exactly the same genomic locations) were removed with samtools v0.1.19 using the rmdup option.
Reads were normalized to total reads aligned (counts per million). Peak detection was done using ChIPseeqer v2.0, enforcing a minimum fold change of 2 between ChIP and input reads, a minimum peak width of 100 bp, and a minimum distance of 100 bp between peaks.
The threshold for statistical significance of peaks was set at 10^-15
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain peak locations. Columns 1, 2, and 3 contain the chromosome, start, and end position of the peak respectively.

molecule: genomic DNA

organism: Homo sapiens

source_name: DLBCL cell line

growth_protocol: Cells were grown in IMDM medium supplemented with 10% FBS and 1% Penicillin/Streptomicin at 37C and 5% CO2. Cells in log phase of growth were harversted and used for H3K27Ac ChIP-Seq experiments.

extract_protocol:
Cell lysis and nuclei isolation was performed using the TruChIP Chromatin Shearing Kit High Cell SDS (Covaris). Nuclei were sonicated using the S220 Ultrasonicator (Covaris) in order to obtain chromatin fragments of 200-500bp.
ChIP-seq libraries were constructed starting from 3ng of ChIP or Input DNA as reported in Blecher-Gonen et al., 2013, Nature protocol. Libraries were quantified using the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems), normalized to 15nM, pooled and sequenced in an Illumina HiSeq 4000 instrument as paired-end 150 bp reads, obtaining on average 25x10^6 reads/sample.

treatment_protocol: Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, quenched by the addition of glycine to a final concentration of 0.125 M, and frozen.

tag: tissue

value: DLBCL cell line

tag: cell line

tag: antibody

value: H3K27Ac Diagenode #A1723-0041D


title: Rad21KO primary dissociated cortical neuron treated with TTX/D-AP5 and 1h KCl Rep1 5C

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Library strategy: 5C-seq
5C analysis steps were performed as described (Gilgenast et al., 2019; Beagan et al., 2020; Fernandez et al., 2020). Briefly, paired-end reads were aligned to the 5C primer pseudo-genome using Bowtie, allowing only reads with one unique alignment to pass filtering. Only reads for which one paired end mapped to a forward/left-forward primer and the other end mapped to a reverse/left-reverse primer were tallied as true counts. Primer-primer pairs with outlier count totals, resulting primarily from PCR bias, were identified as those with a count at least 8-fold higher (100-fold for the lower-quality Arc region) than the median count of the 5x5 subset of the counts matrix centered at the primer-primer pair in question; outlier counts were removed.  Primer-primer pair counts were then converted to fragment-fragment interaction counts by averaging the primer-primer counts that mapped to each fragment-fragment pair (max of 2 if both a forward/left-forward and a reverse/left-reverse primer were able to be designed to both fragments and were not trimmed during outlier removal). We then divided our 5C regions into adjacent 4 kb bins and computed the relative interaction frequency of two bins (i,j) by summing the counts of all fragment-fragment interactions for which the coordinates of one of the constituent fragments overlapped (at least partially) a 12 kb window surrounding the center of the 4 kb ith bin and the other constituent fragment overlapped the 12 kb window surrounding the center if the jth bin. Binned count matrices were then matrix balanced using the ICE algorithm69,71 and quantile normalized across all 8 replicates (2 per condition) within each experimental set (neuronal activation and cohesin-rescue experimental datasets were quantile normalized separately) as previously described (Beagan et al., 2020), at which point we considered each entry (i,j) to represent the Observed Interaction Frequency of the 4 kb bins i and j. Finally, the background contact domain ‘expected’ signal was calculated using the donut background mode (Su et al., 2017) and used to normalize the relative interaction frequency data for the background interaction frequency present at each bin-bin pair. The resulting background-normalized interaction frequency (“observed over expected”) counts were fit with a logistic distribution from which p-values were computed for each bin-bin pair and converted into ‘Background-corrected Interaction Scores’ (interaction score = -10*log2(p-value)), which have previously shown to be informatively comparable across replicates and conditions (Beagan et al., 2020).
Genome_build: mm9 5C primer psuedogenome
Supplementary_files_format_and_content: BED_6715-mm9-ERneuro.bed' is the bed file containing the coordinates for each 5C primer used in the neuronal activity experiments. 'BED_6718-mm9-synapt.bed' is the bed file containing the coordinates for each 5C primer used in the cohesin rescue experiments.   '[Rep_name].counts.txt' contains the number of reads mapped to each pair of 5C primers (see 5C processing) for each replicate.

organism: Mus musculus

source_name: Primary neuron

extract_protocol:
Neuronal cultures were fixed in 1% formaldehyde for 10 minutes (room temp) via the addition (1:10 vol/vol) of the following fixation solution: 50 mM Hepes-KOH (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 11% Formaldehyde. Fixation was quenched via the addition of 2.5 M glycine (1:20 vol/vol) and scraped into pellets. Each pellet was washed once with cold PBS, flash frozen, and stored at -80oC. For each condition, in situ 3C was performed on 2 replicates of 4-5 million cells as described (Beagan et al., 2020). Briefly, cells were thawed on ice and resuspended (gently) in 250 L of lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630) with 50 L protease inhibitors (Sigma P8340). Cell suspension was incubated on ice for 15 minutes and pelleted. Pelleted nuclei were washed once in lysis buffer (resuspension and spin), then resuspended and incubated in 50 L of 0.5% SDS at 62oC for 10 min. SDS was inactivated via the addition of 145L H2O, 25 uL 10% Triton X-100, and incubation at 37oC for 15 min. Subsequently, chromatin was digested overnight at 37oC with the addition of 25 L 10X NEBuffer2 and 100U (5 L) of HindIII (NEB, R0104S), followed by 20 min incubation at 62oC to inactivate the HindIII. Chromatin was re-ligated via the addition of 100 L 10% Triton X-100, 120 L NEB T4 DNA Ligation buffer (NEB B0202S), 12L 10 mg/mL BSA, 718 L H2O, and 2000 U (5 L) of T4 DNA Ligase (NEB M0202S) and incubation at 16oC for 2 hours. Following ligation nuclei were pelleted, resuspended in 300 L of 10 mM Tris-HCl (pH 8.0), 0.5 M NaCl, 1% SDS, plus 25 L of 20 mg/mL proteinase K (NEB P8107), and incubated at 65oC for 4 hours at which point an additional 25 L of proteinase K was added and incubated overnight. 3C templates were isolated next day via RNaseA treatment, phenol-chloroform extraction, ethanol precipitation, and Amicon filtration (Millipore MFC5030BKS). Template size distribution and quantity were assessed with a 0.8% agarose gel.
5C primers were designed according to the double-alternating design scheme using the My5C primer design software (http://my5c.umassmed.edu/my5Cprimers/5C.php)10 with universal “Emulsion” primer tails. Regions were designed to capture TAD structures immediately surrounding the genes of interest (Bdnf, Fos, Arc, Neurexin-1, Neuroligin-3, Synaptotagmin-1) in published mouse cortex HiC data. 5C reactions were carried out as previously described. 600 ng (~200,000 genome copies) of 3C template for each replicate was mixed with 1 fmole of each 5C primer and 0.9 ug of salmon sperm DNA in 1x NEB4 buffer, denatured at 95oC for 5 min, then incubated at 55oc for 16 hours. Primers which had then annealed in adjacent positions were ligated through the addition of 10 U (20 uL) Taq ligase (NEB M0208L) and incubation at 55oC for 1 hour then 75oC for 10 min. Successfully ligated primer-primer pairs were amplified using primers designed to the universal tails (FOR = CCTCTC TATGGGCAGTCGGTGAT, REV = CTGCCCCGGGTTCCTCATTCTCT) across 30 PCR cycles using Phusion High-Fidelity Polymerase. Presence of a single PCR product at 100 bp was confirmed via agarose gel, then residual DNA <100 bp was removed through AmpureXP bead cleanup at a ratio of 2:1 beads:DNA (vol/vol). 100 ng of the resulting 5C product was prepared for sequencing on the Illumina NextSeq 500 using the NEBNext Ultra DNA Library Prep Kit (NEB E7370) following the manufacturer’s instructions with the following parameter selections: during size selection, 70 uL of AMPure beads was added at the first step and 25 at the second step; linkered fragments were amplified using 8 PCR cycles. A single band at 220 bp in each final library was confirmed using an Agilent DNA 1000 Bioanalyzer chip, and library concentration was determined using the KAPA Illumina Library Quantification Kit (#KK4835). Finally, libraries were evenly pooled and sequenced on the Illumina NextSeq 500 using 37 bp paired-end reads.

tag: genotype

tag: treatment

value: TTX


title: E7

city: Carlsbad

first: Sagar

middle: S

last: Damle

state: CA

address: 2855 Gazelle Ct

department: Functional Genomics

institute: Ionis Pharmaceuticals

library_source: transcriptomic

data_processing:
Raw reads were mapped against the human genome Grch38 using STAR version 0.7.2
Mapped reads were annotated with overlapping genes using FeatureCounts
PCR duplicates were then discarded on a per-gene basis using UMI_Tools
Gene Counts were then computed using Salmon version 0.7.2 and human gene models from Ensembl build 96
Assembly: hg38
Supplementary files format and content: quant.sf files are default salmon output (tab-deliminited, indexed by ensembl transcript ID)

molecule: total RNA

growth_protocol: K562 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was harvested using the Zymo direct-zol RNA kits
Libraries constructed using Lexogen 3' QuantSeq kit (cat# XXXXXXX) using modified oligo-dT primers containing 12bp UMIs

treatment_protocol: K562 were electroporated with CRISPR plasmids, followed by ASO treatment, and processed on Day 6 for DGE analysis

tag: cell type

value: lymphoblasts

tag: plasmids


title: LY8-H3K27Ac-Diagenode


title: Fezf2Control_Middle

city: Cambridge

state: MA

description: single cell

source_name: P14 Fezf2Control S1 cortex Layer 5

tag: strain

tag: age


title: 55

type: genomic

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Genome Studio

source_name: Placenta

label_protocol: Standard Illumina Protocol

extract_protocol: Placental genomic DNA was extracted using Invitrogen PureLinkTM Genomic DNA kit. The genomic DNA was converted to bisulfite DNA using Zymo EZ DNA methylation kit.

treatment_protocol: Placentas were collected at delivery and then stored at −80 °C until DNA extractions were performed.

value: Placenta

tag: gender

value: Female

tag: sample type

value: Frozen autologous


title: Fezf2Control_Lower

description: single cell

source_name: P14 Fezf2Control S1 cortex Layer 6


title: 20-ARSF


title: LAPTM4B 2


title: T8 IRF4 rep2

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

country: Germany

institute: University Medical Center - Mainz

data_processing:
Quality control on the sequencing data was performed with the FastQC tool (version 0.11.2, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Sequenced reads were mapped to the mouse genome reference sequence with STAR (version 2.4.0j)
The ENSEMBL Mus_musculus.GRCm38 was chosen as reference genome, alignments were processed with the featureCounts function of the Rsubread package. The corresponding gtf annotation for the reference (ENSEMBL v76) was used.
Exploratory data analysis was performed with the pcaExplorer package (Marini et al., 2019)
Differential expression analysis was performed with DESeq2 (version 1.22.1), setting the False Discovery Rate to 0.1, using the ideal package [Marini et al. 2020].
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts as input matrix to DESeq2

source_name: single cell suspension of B progenitor cells

growth_protocol: 2,5 x 10^5 T11 cells were cultured in 500 µL RPMI medium in 48 well plates

extract_protocol:
RNAeasy Mini kit Qiagen
Library preparation was performed at the Institute for Immunology, University Medical Center of the Johannes Gutenberg-University Mainz using the NEBNext Ultra II Library Prep kit (New England Biolabs)

treatment_protocol: For viral transduction, 5 x 105 T11 cells were resuspended in 400 µL DMEM medium (D5030, Sigma-Aldrich) with 600 µL viral supernatant plus 1.5 µL polybrene and spun in culture plates at 2700 RPM for 90 min at 37 °C.

tag: condition

value: IRF4-RV transduced

value: pB-ALL cell line T8


title: Karpas422--INPUT

value: INPUT no Antibody


title: Rad21tev+DOX24h_primary_neuron_culture Rep1 Synaptic 5C


title: 24

value: Male


title: Karpas422-H3K27Ac-Diagenode


title: T8 IRF4 rep1


title: LY1_H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: RFP

value: RFP


title: T8 GFP rep2

value: EV transduced


title: 94


title: Cx3cr1_GFP_P60_Lower_rep2

description: single cell

source_name: P60 Cx3cr1 GFP S1 cortex Layer 6

extract_protocol:
Samples were maintained at 4C. S1 cortex layers were micro-dissected, homogenized in PBS with DNAse and RNAse-inhibitor, followed by FACS in BSA-containing PBS.
Libraries were produced using 10x genomics technology.

treatment_protocol: Cx3cr1-GFP heterozgous mice were used to genetically label microglia. Fezf2 WT and KO mice were equally housed and treated. Genotypes for all lines were obtained through standard breeding.

value: Cx3cr1 GFP tg/+


title: 23-GOLGA8N


title: Cx3cr1_GFP_P60_Middle_rep2

description: single cell

source_name: P60 Cx3cr1 GFP S1 cortex Layer 5


title: LAPTM4B 1


title: HT-INPUT

value: HT


title: TRPC5OS


title: T8 GFP rep1


title: Cx3cr1_GFP_P60_Upper

description: single cell

source_name: P60 Cx3cr1 GFP S1 cortex Layer 1-4

value: S1 cortex


title: H4K20me3_WT_rescue_rep2

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

data_processing:
Library strategy: CUT&Tag
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq

source_name: Embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). All cells were grown at 37 °C and 5% CO2.

extract_protocol:
Lysates are clarified from sonicated nuclei and histone-DNA complexes are isolated with antibody for ChIP-seq.  RNA is harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) is used with 1 ug of total RNA for libraries of RNA-seq. GRO-seq library is constructed by pull-down of BrU labelled nascent RNA which is then subjected to strand specifice library construction. CUT&Tag libraries are constructed from nuclei extraction and antibody binding, transposome tagmentation.
ChIP-seq, RNA-seq libraries were prepared for sequencing using standard Illumina protocols. CUT&Tag libraries are prepared from directely PCR. GRO-seq library is prepared by strand-specific library construction.

tag: chip antibody

value: Rabbit polyclonal anti-Histone H4K20me3 (Abcam, Cat. #ab9053)

value: WT


title: Cx3cr1_GFP_P60_Middle

description: single cell


title: Karpas422-H3K27Ac-Active Motif

value: DLBCL cell line


title: HT-H3K27Ac-Diagenode

value: H3K27Ac Diagenode #A1723-0041D


title: TTR

value: lymphoblasts

value: TTR


title: HLY1-INPUT


title: HT-H3K27Ac-Active Motif


title: Cx3cr1_GFP_P60_Lower

description: single cell


title: 21-CTPS2


title: H4K20me3_WT_rescue_rep1


title: H4K20me3_Smyd5_KO_rep2

value: Smyd5 KO


title: MN_T0_CRISPR

city: Melbourne

first: Joan

last: So

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
The RNA sequencing reads were trimmed using cutadapt (v1.16.5) to remove poor quality ends.
The resulting reads were aligned and statistical significance was calculated using MAGeCK algorithm (v0.5.8.1).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: AG636_CRISPRscreenCounts_normalised.txt: Normalized count file representing number of reads per guide scored in T0, T10 and T24 samples.

source_name: MLL-AF9; KrasG12D cell line

growth_protocol: MN cells tumor cells were cultured in Anne-Kelso DMEM supplemented with 20% foetal calf serum, 0.1mM L-asparagine, 100 U/mL penicillin, 100 mg/mL streptomycin, at 37°C and 10% CO2.

extract_protocol:
Genomic DNA was extracted from cells using DNeasy Blood & Tissue Kit (Qiagen).
Sequencing libraries were prepared by nested PCR method to amplify integrated CRISPR guides.

treatment_protocol: AG636 was refreshed every 2-3 days. 2 x 10^6 live cells was harvested at every time point.

value: MN AML cells

value: Untreated

tag: time point

value: 0 day


title: HLY1-H3K27Ac-Diagenode


title: 22-LAPTM4B


title: H4K20me3_Smyd5_KO_rep1


title: Neg

value: Neg


title: H4K20me3_Smyd5_KO_Smyd5_delC_rep2

value: delC rescue


title: MN_DMSO_T10_CRISPR

value: DMSO

value: 10 days


title: 4571_MA_58

city: Nashville

first: Margaret

middle: L

last: Axelrod

state: TN

address: 2200 Pierce Ave, 777 PRB

department: Medicine

institute: Vanderbilt University

data_processing:
Quality control was evaluated at different levels, including RNA quality, raw read data, alignment, and gene expression
Raw RNA-seq paired-ends were mapped to the human reference genome hg19 using STAR 2.7.3.
Raw reads count matrix was calculated by featureCounts and used for downstream analysis.
Supplementary files format and content: Feature Counts, csv
Supplementary files format and content: TPM, csv

source_name: Blood

extract_protocol:
Promega Maxwell RSC simplyRNA Blood kit (AS1380, Promega)
 ribo-depletion total RNA library preparation kit

value: Blood

value: PBMC

tag: response

value: RD


title: HLY1-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: GFP

value: GFP


title: H4K20me3_Smyd5_KO_Smyd5_FL_rep2

value: FL rescue

value: Rabbit polyclonal anti-Histone H4K20me3 (Abcam, Cat. #ab9053)


title: H4K20me3_Smyd5_KO_Smyd5_FL_rep1


title: HBL1-H3K27Ac-Diagenode

value: DLBCL cell line

value: H3K27Ac Diagenode #A1723-0041D


title: FARAGE-INPUT

value: FARAGE

value: INPUT no Antibody


title: 4571_MA_55


title: MN_100nM_T24_CRISPR

value: MN AML cells

value: 24 days


title: 4571_MA_56


title: MN_DMSO_T24_CRISPR


title: MN_250nM_T10_CRISPR


title: Cx3cr1_GFP_P60_Upper_rep2

description: single cell

value: Cx3cr1 GFP tg/+

value: S1 cortex


title: Pol2_WT_rescue_rep1

value: Mouse monoclonal anti-RNA polymerase II (Millipore, Cat. #05-623)

value: WT


title: MN_250nM_T24_CRISPR


title: HBL1-H3K27Ac-Active Motif


title: FARAGE-H3K27Ac-Diagenode


title: Pol2_WT_rescue_rep2


title: MN_100nM_T10_CRISPR

value: 10 days


title: 4571_MA_57

value: Blood

value: PBMC

value: No NAC


title: 4571_MA_53


title: H4K20me3_Smyd5_KO_Smyd5_delC_rep1

value: delC rescue

value: Smyd5 KO


title: AG636_4_RNAseq_RUNX1

description:
AG372_S44
RUNX1counts.txt

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (GRCm38/mm10).
Read counting was performed with featureCounts from the subread package (v1.5.0-p3).
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: RUNX1counts.txt: Count file generated by featureCounts.

source_name: Acute myeloid leukemia

growth_protocol: AML cells were transplanted into sub-lethal irradiated Ptprca recipients.

extract_protocol:
Cells were isolated from bone marrow and spleen of experimental mice by fluorescence-based cell sorting and total RNA was extracted using the Direct-zol™ RNA miniprep kit (Zymo Research) according to manufacturer’s instructions.
cDNA libraries were prepared using QuantSeq 3' mRNA seq kit (Lexogen).

treatment_protocol: AG636 was administered b.i.d. by oral gavage at a dose of 100mg/kg body weight.

tag: background

value: AML cells


title: HBL1-INPUT

value: DLBCL cell line


title: AG636_3_RNAseq_RUNX1

description:
AG371_S43
RUNX1counts.txt


title: FARAGE-H3K27Ac-Active Motif

value: H3K27Ac Active Motif #39135


title: 4571_MA_52

value: RD


title: DOHH2-INPUT

value: INPUT no Antibody


title: 4571_MA_54


title: AG636_2_RNAseq_RUNX1

description:
AG355_S42
RUNX1counts.txt


title: Pol2_Smyd5_KO_rep1


title: Pol2_Smyd5_KO_Smyd5_delC_rep2


title: 4571_MA_51

value: pCR


title: AG636_1_RNAseq_RUNX1

description:
AG353_S41
RUNX1counts.txt


title: DOHH2-H3K27Ac-Active Motif


title: DB-INPUT

value: DB


title: DB-H3K27Ac-Diagenode

value: H3K27Ac Diagenode #A1723-0041D


title: 4571_MA_49


title: 4571_MA_47


title: Vehicle_4_RNAseq_RUNX1

description:
V441_S40
RUNX1counts.txt

value: Vehicle


title: Pol2_Smyd5_KO_Smyd5_delC_rep1

value: Mouse monoclonal anti-RNA polymerase II (Millipore, Cat. #05-623)


title: 4571_MA_50


title: H4K20me3_WT_rep2

value: Rabbit polyclonal anti-Histone H4K20me3 (Abcam, Cat. #ab9053)

value: WT


title: Pol2_Smyd5_KO_Smyd5_FL_rep2

value: FL rescue


title: Vehicle_1_RNAseq_RUNX1

description:
V432_S37
RUNX1counts.txt


title: DOHH2-H3K27Ac-Diagenode


title: 4571_MA_46

value: Blood

value: PBMC


title: BJAB--INPUT

value: BJAB


title: H4K20me3_WT_rep1


title: DB-H3K27Ac-Active Motif


title: Pol2_Smyd5_KO_rep2

value: Smyd5 KO


title: Rad21tev+VEH24h_primary_neuron_culture Rep1 Synaptic 5C


title: Vehicle_3_RNAseq_RUNX1

description:
V434_S39
RUNX1counts.txt

value: AML cells


title: AG636_3_RNAseq_I1DN

description:
AL-8_S22
I1DNcounts.txt

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (GRCm38/mm10).
Read counting was performed with featureCounts from the subread package(v1.5.0-p3).
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: I1DNcounts.txt: Count file generated by featureCounts.

value: IDH1R132H; DNMT3AR882H; NrasG12D


title: Vehicle_2_RNAseq_RUNX1

description:
V433_S38
RUNX1counts.txt


title: 4571_MA_48


title: BJAB-H3K27Ac-Active Motif

value: DLBCL cell line

value: H3K27Ac Active Motif #39135


title: BJAB-H3K27Ac-Diagenode


title: H4K20me3_Smyd5_OE_rep2

value: Smyd5 OE


title: AG636_2_RNAseq_I1DN

description:
AL-7_S21
I1DNcounts.txt


title: LY18-H3K27Ac-Active Motif


title: 4571_MA_44

value: RD


title: 4571_MA_42

value: No NAC


title: AG636_1_RNAseq_I1DN

description:
AL-6_S20
I1DNcounts.txt


title: 4571_MA_43


title: Vehicle_2_RNAseq_I1DN

description:
AL-2_S16
I1DNcounts.txt


title: K562_RBM17_eCLIP_rep3

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Raw sequencing reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using cutadapt. Trimmed reads were mapped against RepBase to remove reads mapping to repetitive sequences. Remaining reads were mapped to the appropriate genome build using STAR aligner
For eCLIP samples, read densities were calculated to identify eCLIP peaks.
eclip data processing pipeline can be requested from the following link : https://github.com/YeoLab/eclip
Supplementary_files_format_and_content: bigwig, bed

source_name: Homo sapiens K562 immortalized cell line

growth_protocol: Chronic myelogenous leukemic cell line K562 were cultured in RPMI-1640, supplemented with 10% fetal bovine serum.

extract_protocol:
RBM17 eCLIP studies were performed in duplicate according to the published eCLIP-seq experimental procedures. 20 million K562 cells were washed in PBS and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation on ice, pelleted and snap frozen. Cells were then lysed in iCLIP lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate, 1:100 Protease Inhibitor Cocktail) and treated with Turbo DNase and RNase I to fragment RNA, and supernatants from lysates were collected for immunoprecipitation. 10 μg of RBM17 antibody mixture (Bethyl A302- 497A and A302-498A) for each sample was then pre-coupled to 125ul of sheep anti-rabbit Dynabeads (LifeTech), added to lysate and incubate overnight at 4℃. Prior to washing, 2% of the sample (with beads-RBM17 antibody-cell lysate) was taken as the size match input sample, with the remainder magnetically separated and washed twice with cold High salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) and wash buffer (20 mM Tris- HCl pH 7.4, 10 mM MgCl2, 0.2% Tween-20). After RNA adapter ligation, IP-western, eCLIP was performed by excising the area from 50 kDa to 125 kDa for Input and IP samples. Reverse transcription, DNA adapter ligation, and PCR amplification were performed according to the standard eCLIP experimental procedure. Three libraries (Input and RBM17 eCLIP duplicates were prepared and sent for paired-end 75-bp Illumina sequencing.
eCLIP-Seq

value: chronic myelogenous leukemic cell

tag: rip antibody

value: cell line


title: Vehicle_3_RNAseq_I1DN

description:
AL-3_S17
I1DNcounts.txt

value: Vehicle


title: Pol2_WT_rep2

value: Mouse monoclonal anti-RNA polymerase II (Millipore, Cat. #05-623)


title: K562_RBM17_eCLIP_rep2


title: Pol2_WT_rep1

value: WT


title: 4571_MA_41

tag: tissue

value: pCR


title: 4571_MA_40

value: Blood


title: K562_eCLIP_input

tag: cell line


title: LY10-H3K27Ac-Active Motif

tag: antibody


title: Vehicle_1_RNAseq_I1DN

description:
AL-1_S15
I1DNcounts.txt

tag: genotype


title: Pol2_Smyd5_OE_rep2

tag: treatment


title: 4571_MA_45

tag: cell type

value: PBMC


title: AG636_2_RNAseq_MN2

description:
JS-AGI8_S60
MN_JS12counts.txt

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (GRCm38/mm10).
Read counting was performed with featureCounts from the subread package (v1.5.0-p3).
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: MN_JS12counts.txt: Count file generated by featureCounts.

value: MLL-AF9; KrasG12D

value: MN AML cells


title: 4571_MA_39


title: D20D_iPSCs_EBd20_5 [RBG6709]

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

data_processing:
QC perfomed with custom R script (available upon request). Samples were thresholded based on fraction of mapped reads (25%), minimal number of rads (100,000), maximal fraction of mitochondrial reads (20%) and number of expressed genes (2000 genes > 10 cpm)
Data aligned with GSNAP (parameters: -A sam -B 5 -t 24 -n 1 -Q -N 1 -D) onto hg19 genome.
For each gene, how many aligned reads overlap its exons counted using HTSeq and ENSEMBL release 81 exon data
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with counts for each gene (how many aligned reads overlap its exons) generated using HTSeq

source_name: iPSC-derived day 20 EB cells purified as CD43+CD45+CD11b+CD41-

growth_protocol: Human iPSCs maintained in EPSCM were differentiated when 50-90% confluent and with at least three passages after thawing. ESPCM was refreshed three hours before dissociation. Human PSCs were washed once with PBS and dissociated using Accutase for 5-10 minutes at 37°C. The dissociation was quenched by addition of 10X the Accutase volume of Basal Media (BM): DMEM/F12, 20% Knockout Serum Replacement, MEM Non-Essential Amino Acids, Pencillin-Streptmycin-Glutamine, 0.1 mM β-mercaptoethanol, and 10 μM Y27632. A single cell suspension was generated by gentle pipetting. To deplete SNL feeder cells, the cell suspension was transferred back onto plates/dishes and incubated at 37°C for 45 minutes. Unattached EPSCs were then gently removed from the plate and pelleted at 300 g for 3 minutes. EPSCs were resuspended at a concentration of 1x105 cells/ml and 3 ml plated into Ultra-Low Attachment 6-well plates (Corning) and allowed to form EBs at 37°C with 5% CO2 for 48 hours. EBs were collected into 50 ml tubes and allowed to settle by gravity before BM was removed. EBs were resuspended in the same volume of human differentiation media (HDM): KnockOut-DMEM supplemented with 20% Fetal bovine serum (Hyclone; batched tested for human EPSC differentiation), Pencillin-Streptmycin-Glutamine , 0.1 mM β-mercaptoethanol, 0.3 mg/ml human transferrin, and 0.3 mM ascorbic acid. EBs were replated back in the same Ultra-Low Attachment 6-well plates and incubated at 37°C with 5% CO2. Media was replaced every 3-4 days. EBs were dissociated using Collagenase type I (Stem Cell Technologies) followed by TypLE to generate a single cell suspension.

extract_protocol:
50 cells were directly sorted into lysis buffer using an Influx Cell Sorter (BD).
RNA-seq was performed using the SmartSeq2 protocol (Picelli et al. 2014)

treatment_protocol: No treatment

value: iPSC-derived EB cells at day 20

tag: cell phenotype

value: Definive-wave hematopoietic cell

tag: iPSc line

value: EC-EPSCM

tag: cell population


title: H4K20me3_Smyd5_OE_rep1

tag: strain

value: Rabbit polyclonal anti-Histone H4K20me3 (Abcam, Cat. #ab9053)

tag: age


title: Pol2_Smyd5_OE_rep1

value: Smyd5 OE


title: D20D_iPSCs_EBd20_4 [RBG6708]


title: 4571_MA_38

value: RD


title: Vehicle_2_RNAseq_MN2

description:
JS-V4_S56
MN_JS12counts.txt


title: D20D_iPSCs_EBd20_3 [RBG6707]


title: AG636_1_RNAseq_MN2

description:
JS-AGI6_S58
MN_JS12counts.txt


title: H3K36me3_WT_forSmyd5_OE_rep2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: 4571_MA_37

value: No NAC


title: 4571_MA_36


title: H3K36me3_Smyd5_OE_rep1


title: Vehicle_1_RNAseq_MN2

description:
JS-V1_S55
MN_JS12counts.txt


title: Dox 1 day_4_RNAseq_MN

description:
E70_S42
JS04counts.txt

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Hisat2 (2.0.4) to the mouse reference genome (GRCm38/mm10).
Read counting was performed with featureCounts from the subread package (v1.5.0-p3).
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: JS04counts.txt: Count file generated by featureCounts.

treatment_protocol: AG636 was administered b.i.d. by oral gavage at a dose of 100mg/kg body weight. Doxycycline was administered ad libitum via doxycycline-supplemented food and water.

value: Doxycycline for 1 day


title: D20D_iPSCs_EBd20_2 [RBG6706]


title: H3K36me3_Smyd5_OE_rep2


title: 4571_MA_34


title: FLAG_WT_High_Salt_rep1

value: Mouse monoclonal anti-FLAG M2 (Sigma, Cat. #F1804)


title: 4571_MA_33


title: D20P_iPSCs_EBd20_5 [RBG6699]

source_name: iPSC-derived day 20 EB cells purified as CD43+CD34+CD41+CD45+

value: Primitive-wave hematopoietic cell


title: H3K36me3_WT_forSmyd5_OE_rep1

value: WT


title: D20P_iPSCs_EBd20_4 [RBG6698]


title: Dox 1 day_2_RNAseq_MN

description:
E65_S40
JS04counts.txt


title: Dox 1 day_3_RNAseq_MN

description:
E69_S41
JS04counts.txt


title: D20P_iPSCs_EBd20_3 [RBG6697]


title: D20P_iPSCs_EBd20_2 [RBG6696]


title: 4571_MA_32


title: FLAG_Smyd5_OE_High_Salt_rep2


title: FLAG_Smyd5_OE_High_Salt_rep1


title: FLAG_WT_High_Salt_rep2


title: D20P_iPSCs_EBd20_1 [RBG6695]


title: Dox 1 day_1_RNAseq_MN

description:
E64_S39
JS04counts.txt


title: 4571_MA_31


title: D20D_iPSCs_EBd20_1 [RBG6705]


title: Pol2_Smyd5_KO_Smyd5_FL_rep1

value: FL rescue

value: Mouse monoclonal anti-RNA polymerase II (Millipore, Cat. #05-623)

value: Smyd5 KO


title: 4571_MA_35

value: Blood

value: PBMC

value: pCR


title: SMYD5_WT_3

value: Rabbit polyclonal anti-SMYD5


title: AG636 1 day_2_RNAseq_MN

description:
D62_S37
JS04counts.txt

value: MLL-AF9; KrasG12D

value: MN AML cells

value: AG636 for 1 day


title: 4571_MA_30


title: D14D_iPSCs_EBd14_5 [RBG6674]

source_name: iPSC-derived day 14 EB cells purified as CD43+CD34+CD41-CD45-

value: iPSC-derived EB cells at day 14

value: Definive-wave hematopoietic cell

value: EC-EPSCM


title: SMYD5_WT_2


title: 4571_MA_29


title: D14D_iPSCs_EBd14_4 [RBG6673]


title: D14D_iPSCs_EBd14_3 [RBG6672]


title: Dox 4 days_ 3_RNAseq_MN

description:
C73_S35
JS04counts.txt

value: Doxycycline for 4 days


title: Dox 4 days_2_RNAseq_MN

description:
C49_S34
JS04counts.txt


title: SMYD5_WT_1


title: SMYD5_Smyd5_KO_3


title: 4571_MA_28

value: No NAC


title: 4571_MA_27


title: D14D_iPSCs_EBd14_2 [RBG6671]


title: Dox 4 days_1_RNAseq_MN

description:
C48_S33
JS04counts.txt


title: AG636 1 day_3_RNAseq_MN

description:
D75_S38
JS04counts.txt


title: 4571_MA_26


title: SMYD5_Smyd5_KO_1


title: Vehicle_4_RNAseq_MN

description:
A92_S32
JS04counts.txt

value: Vehicle for 4 days


title: D14D_iPSCs_EBd14_1 [RBG6670]


title: 4571_MA_24


title: Vehicle_3_RNAseq_MN

description:
A85_S31
JS04counts.txt


title: H3K36me3_WT_AM_rep2

value: Rabbit polyclonal anti-Histone H3K36me3 (Active Motif, Cat. #61101)

value: WT


title: 4571_MA_25


title: 4571_MA_23

value: RD


title: D14P_iPSCs_EBd14_5 [RBG6664]

source_name: iPSC-derived day 14 EB cells purified as CD43+CD34+CD41+CD235a+CD45-

value: Primitive-wave hematopoietic cell


title: H3K36me3_WT_AM_rep1


title: Vehicle_ 2_RNAseq_MN

description:
A58_S29
JS04counts.txt


title: D14P_iPSCs_EBd14_3 [RBG6662]


title: AG636 1 day_1_RNAseq_MN

description:
D59_S36
JS04counts.txt


title: H3K36me3_Setd2_KO_AM_rep2

value: Setd2 KO


title: Vehicle_1_RNAseq_MN

description:
A52_S30
JS04counts.txt


title: SMYD5_Smyd5_KO_2

value: Smyd5 KO


title: Exp_WT_rep2

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq


title: AG636_2_ATACseq

description:
JS12-8_S12
drug_merged_bin50_smooth150_e200_CPM_rmBlacklist.bw

data_processing:
Sample QC was first performed and overrepresented sequences identified using FastQC (Babraham Bioinformatics, Babraham Institute).
The RNA sequencing reads were trimmed using cutadapt (v1.9.1) to remove poor quality ends.
Read data was then aligned using Bowtie2 to the mouse reference genome (GRCm38/mm10).
Bigwigs were generated and data was visualised with deeptools (v2.5.3).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cells were isolated from bone marrow and spleen of experimental mice by fluorescence-based cell sorting. ATAC-seq was performed as previously published (Buenrostro, 2015).
Chromatin was tagmented using TDE1 Enzyme (Illumina), then adapters ligated and library amplified with HotStart KAPA readymix.


title: D14P_iPSCs_EBd14_1 [RBG6660]


title: H3K36me3_Setd2_KO_AM_rep1


title: D14P_iPSCs_EBd14_4 [RBG6663]


title: 4571_MA_21

value: Blood

value: PBMC


title: D14P_iPSCs_EBd14_2 [RBG6661]


title: 4571_MA_20


title: Exp_WT_rep1


title: Vehicle_2_ATACseq

description:
JS12-4_S10
veh_merged_bin50_smooth150_e200_CPM_rmBlacklist.bw

value: MLL-AF9; KrasG12D

value: Vehicle


title: 4571_MA_19


title: mixed clones ko gene expression library

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

library_source: transcriptomic single cell

data_processing:
Fastq files were obtained with using "cellranger mkfastq" (Cell Ranger v3 from 10x Genomics).
Demultiplexing, mapping and gene counting were performed with "cellranger count", Cell Ranger 3.0.2 from 10x Genomics.
Assembly: GRCh38
Supplementary files format and content: filtered_gene_bc_matrices text output files from Cell Ranger count

source_name: HMLER

growth_protocol: Cells were cultured in 2:1:1 MEGM (Lonza Bullet kit), DMEM and F12 media, supplemented with insulin (10 μg/ml), EGF (10 ng/ml), hydrocortisone (1 μg/ml), and 1x Pen/Strep (50 I.U./mL penicillin and 50 μg/mL streptomycin, Sigma-Aldrich #P4333).

extract_protocol:
For single cell RNA-seq, libraries for isolated single cells were generated using 10X genomics Chromium Single Cell 3’ Library & Gel bead   Kit V2 according to the manufacturer’s protocol. C1-sgControl, C1-sgEED and C1-sgKMT2D cells were stained using anti-human Hashtag antibody associated with three distinct barcodes (BioLegend) before library preparation. The resulting DNA library was double-size purified (0.6-0.8X) with SPRI beads and sequenced on an Illumina NextSeq using HO-SE75 kit or on HiSeq2 500 platform using PE50 kit.
10x genomics

tag: target/sample (barcode)

value: HMLER

tag: biolegend hashtag no.


title: Vehicle_1_ATACseq

description:
JS12-1_S9
veh_merged_bin50_smooth150_e200_CPM_rmBlacklist.bw

value: MN AML cells


title: Exp_Smyd5_KO_rep2


title: 4571_MA_18


title: Exp_Smyd5_KO_rep1


title: 4571_MA_17


title: Cx3cr1_GFP_Upper_rep2

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L14_2

data_processing:
For scRNA-seq, sequencing and basecalling were performed with NextSeq 500 instrument (Illumina). For snRNA-seq, sequencing and basecalling were performed with NovaSeq instrument (Illumina).
Cellranger mkfastq (10x Genomics v2.1.0) was used to demultiplex bcl files to fastq files using standard parameters
Cellranger count (10x Genomics v2.1.0) was used to produce an aligned single cell feature count matrix, using mm10 genome as a reference.
Seurat (v3.1.1) pipeline including SCTransform was used to normalize and scale the single cell data. Default parameters were used. The following parameters were used for regression: percent.mt, nCount_RNA, and replicate.
PCA and t-SNE were used to for dimensionality reduction and visualization of single cells data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts
Supplementary_files_format_and_content: tab-delimited file with the metadata for each sample in the matrix

source_name: P14 Cx3cr1 GFP S1 cortex Layer 1-4

value: Cx3cr1 GFP tg/+

value: S1 cortex Layers 1-4


title: 4C_Control-2

city: Vellore

first: Saravanabhavan

last: Thangavel

state: Tamil Nadu

address: Lab-7, Centre for Stem Cell Research, Christian Medical College campus,Bagayam.

department: Centre for Stem Cell Research (an unit of InStem-Bengaluru)

country: India

institute: Christian Medical College

data_processing:
All the raw data in .FASTq format was analyzed using 4Cseqpipe (https://github.com/changegene/4Cseqpipe) using default parameters.
This pipeline produces only image data as output. These files have not been included on the GEO records.
Library strategy: 4C

source_name: umbilical cord blood

growth_protocol: Control HUDEP-2 cells and PRR-βE1 biallelic deletion harboring HUDEP-2 clone were cultured in StemSpan SFEM-II media containing SCF (50ng/ml), EPO (3U/ml), Dexamethasone (1µM), Doxycycline (1µg/ml), and Glutamine (1x). For erythroid differentiation, cells were cultured in IMDM GlutaMAX Supplement media containing 3% AB serum, 2% FBS, Insulin (10µg/ml), Heparin (3U/ml), EPO (3U/ml), Holotransferrin (200 µg/ml), SCF (100ng/ml), IL3 (10ng/ml) and Doxycycline (1µg/ml).

extract_protocol:
HUDEP-2 control and PRR-βE1 clone were fixed with 1.5% formaldehyde and quenched with glycine (125 mM) and lysed using Dounce homogenizer . The 3C digestion was performed with Csp6I and ligation was performed by the T4 DNA ligase in 7.61 ml ligation mix (745 μl 10% Triton X-100, 745 μl 10x ligation buffer (500 mM Tris-HCl pH7.5, 100 mM MgCl2, 100 mM DTT), 80 μl 10 mg/ml BSA, 80 μl 100 mM ATP and 5.96 ml water).
Ligated samples were de-crosslinked overnight followed by PCI purification to obtain the 3C library. The second 4C digestion was performed by DpnII (50 units, NEB) and the samples were ligated, purified and precipitated similar to the 3C library to obtain the 4C library. The 4C library was subjected to RNAseA treatment and purified by the QIAquick PCR purification kit. The concentration of the library was then measured by Nanodrop and subjected to PCRs using the oligos for the respective viewpoints. The oligos used for the  HBG2 viewpoint are mentioned in the (sup. table 6).

treatment_protocol: Nucleofection and sorting: For electroporation of HUDEP-2 cells for PRR-βE1 deletion, 100pmol of Cas9 RNP with sgRNA against PRR and 100pmol of Cas9 RNP with sgRNA against βE1 were used. 2x105 cells were electroporated using P3 primary cell solution and supplement and were electroporated using Lonza 4D nucleofector with CA137 pulse code. The gene edited cells were single cell sorted after two passages. The single cell sorted clones were validated for genotype using gap PCR. A clone harboring PRR-βE1 deletion was erythroid differentiated and subjected to 4C analysis. Un-edited HUDEP-2 cell line was used as control. The cells were collected for analysis on day 4 of erythroid differentiation.

value: human erythroid progenitor cell

value: HUDEP-2 unedited cells

value: HUDEP-2 unedited

tag: day

value: Erythrioid differentiation day 4


title: 4C_PRR-βE1-2

value: HUDEP-2 single cell sorted clone harboring PRR-BetaE1 deletion

value: treated with gRNA PRR-BetaE1


title: AG636_1_ATACseq

description:
JS12-6_S11
drug_merged_bin50_smooth150_e200_CPM_rmBlacklist.bw


title: 4571_MA_22

tag: response

value: No NAC


title: 4571_MA_16

value: RD


title: 4C_PRR-βE1-1


title: Exp_Smyd5_KO_Smyd5_delC_rep2

value: delC rescue

value: Smyd5 KO


title: Exp_Smyd5_KO_Smyd5_delC_rep1


title: mixed clones ko hashtag library

value: Hashtag1 C1-sgControl (GTCAACTCTTTAGCG); Hashtag3 C1-sgEED (TTCCGCCTCTCTTTG); Hashtag4 C1-sgKMT2D (AGTAAGTTCAGCGTA)

value: TotalSeq-A0251 anti-human Hashtag 1 Antibody; TotalSeq-A0253 anti-human Hashtag 3 Antibody; TotalSeq-A0254 anti-human Hashtag 4 Antibody


title: 4C_Control-1


title: Cx3cr1_GFP_Middle_rep2

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L5_2

source_name: P14 Cx3cr1 GFP S1 cortex Layer 5

value: S1 cortex Layer 5


title: 4571_MA_15

value: Blood

value: PBMC


title: Exp_Smyd5_KO_Smyd5_FL_rep2

value: FL rescue


title: Cx3cr1_GFP_Upper

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L14_1

value: Cx3cr1 GFP tg/+

value: S1 cortex Layers 1-4


title: Exp_Smyd5_KO_Smyd5_FL_rep1


title: 4571_MA_13


title: Cx3cr1_GFP_Lower

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L6_1

source_name: P14 Cx3cr1 GFP S1 cortex Layer 6

value: S1 cortex Layer 6


title: AGS cells, ctrl

city: Beijing

first: Xiaohong

last: Wang

address: Fucheng

institute: Peking university cancer hospital

data_processing:
The quality control of raw data were completed by removing low-quality reads, adaptor sequences, empty reads, reads with N sequences over 10% and rRNA reads.
aligned to the GRCh38 genome assembly using Hisat2（version:2.0.4）
Uniquely mapped reads with mapping quality >=20 were retrieved for downstream analysis.
The expression levels of the transcripts were expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values of mRNA and lncRNA using the Stringtie v1.3.0
Differentially expressed mRNAs and lncRNAs were calculated by edgeR
Assembly: GRCh38
Supplementary files format and content: Excel files include FPKM and count values for each Sample

source_name: AGS

growth_protocol: Cells were cultured in Dulbecco’ s modified Eagle’ s medium (Gibco BRL, supplemented with 10% fetal bovine serum (10% FBS DMEM)

extract_protocol:
Total RNA was harvested using Qiagen Kit.1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were stably transfected with negative control and GGT7 plasmid  respectively.

value: AGS

value: gastric cancer cells

value: WT

tag: time

value: 2 weeks


title: AGS cells, GGT7

value: GGT7 ectopic expression


title: Cx3cr1_GFP_Lower_rep2

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L6_2

extract_protocol:
Samples were maintained at 4C. S1 cortex was micro-dissected, homogenized and sorted for all nuclei in nuclei solubilization buffer. For scRNA-seq, S1 cortex layers were micro-dissected, homogenized in PBS with DNAse and RNAse-inhibitor, followed by FACS in BSA-containing PBS.
Libraries were produced using 10x genomics technology.


title: 4571_MA_14

value: RD


title: GRO_WT_rep2

description:
nascent RNA
GRO_matrix.txt

data_processing:
Library strategy: Gro-Seq
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq


title: PLC/PRF/5 Tigecycline-treated_rep2

city: Shanghai

first: Wenxin

last: Qin

address: No.25, Lane 2200 Xie-Tu Road.

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30-5 20-3 20-W 4-M 20-n 0. 3.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: GRCh38.p13(Genome Reference Consortium Human Build 38)
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

source_name: Liver cancer cells

growth_protocol: PLC/PRF/5 and MHCC97H cells were cultured in DMEM with 10% FBS, glutamine and penicillin-streptomycin (Gibco) at 37℃ and 5% CO2.

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were DMSO or tigecycline treated for 72 hours.

value: Tigecycline-treated


title: Cx3cr1_GFP_Middle

description:
single cell
scRNA_Cx3cr1_GFP_raw_counts.dge.txt.gz
scRNA_Cx3cr1_GFP_metadata.txt
L5_1


title: GRO_WT_rep1

description:
nascent RNA
GRO_matrix.txt


title: 4571_MA_12

value: No NAC


title: Fezf2KO_Upper

description:
single cell
scRNA_Fezf2KO_raw_counts.dge.txt
scRNA_Fezf2KO_metadata.txt

source_name: P14 Fezf2KO S1 cortex Layers 1-4


title: 4571_MA_11


title: GRO_Smyd5_KO2_rep2

description:
nascent RNA
GRO_matrix.txt

source_name: Embryonic stem cells

value: Smyd5 KO


title: 4571_MA_10

value: pCR


title: Fezf2KO_Middle

source_name: P14 Fezf2KO S1 cortex Layer 5

value: S1 cortex Layer 5


title: PLC/PRF/5 Tigecycline-treated_rep1


title: PLC/PRF/5 Con_rep2

value: control


title: GRO_Smyd5_KO2_rep1

description:
nascent RNA
GRO_matrix.txt


title: Fezf2KO_Lower

source_name: P14 Fezf2KO S1 cortex Layer 6


title: 4571_MA_07

source_name: Blood

value: Blood

value: PBMC


title: GRO_Smyd5_KO1_rep1

description:
nascent RNA
GRO_matrix.txt


title: MHCC97H Tigecycline-treated_rep2


title: PLC/PRF/5 Con_rep1


title: GRO_Smyd5_KO1_rep2

description:
nascent RNA
GRO_matrix.txt


title: MHCC97H Tigecycline-treated_rep1


title: H3K36me3_WT_rescue_rep1

tag: chip antibody

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: uhg4-208wt-M-2

city: Greenwood

first: Rebecca

middle: A

last: MacPherson

state: SC

address: 114 Gregor Mendel Circle, Dr. Trudy Mackay

department: Center for Human Genetics

institute: Clemson University

description:
rRNA depleted RNA
RAM-uhg4-208wt-M-2_S4_L001

data_processing:
Barcoded reads were demultiplexed using the NovaSeq Illumina BaseSpace sequencing pipeline and merged across S1 flow cell lanes.
Filtering: We used the AfterQC pipeline (version 0.9.7) (Chen et al., 2017) to filter out low quality, short, and adapter reads and the bbduk command within the BBTools package (Bushnell, 2014) to detect levels of rRNA contamination.
Alignment: We used GMAP-GSNAP (Wu et al., 2016) to align filtered reads to the D. melanogaster reference genome v6.13 and the Subread package (Liao et al., 2013) to map unique alignments to Drosophila genes.
Assembly: dm6 v6.13
Supplementary files format and content: raw_counts_GEO.xlsx

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Each sample contained 30 whole flies, flash frozen at 3-5 days of age, and was homogenized using a Fisherbrand™ Bead Mill (ThermoFisher Scientific, Waltham MA). RNA was extracted using the Direct-zol RNA Miniprep kit (Zymo Research, Irvine, CA), resuspended in RNase-free water, and kept at -80°C until further use.
We prepared libraries according to Universal RNA-Seq with NuQuant + UDI (Tecan Genomics, Inc., Redwood City, CA) manufacturer instructions. Specifically, 100ng of total RNA was converted into cDNA via integrated DNase treatment. Second strand cDNA was fragmented using a Covaris ME220 Focused-ultrasonicator (Covaris, Woburn, MA) to 350bp. Drosophila AnyDeplete probes were used to deplete remaining ribosomal RNA and final libraries were amplified using 17 PCR cycles. We used TapeStation High Sensitivity D1000 Screentape (Agilent Technologies, Inc., Santa Clara, CA) and a Qubit™ 1X dsDNA HS Assay kit (Invitrogen, Carlsbad, CA) to measure the final library insert sizes and concentration, respectively.

tag: tissue

value: Whole body

tag: Sex

value: Male

value: 3-5 days

tag: replicate


title: uhg4-208wt-F-1

description:
rRNA depleted RNA
RAM-uhg4-208wt-F-1_S1_L001

tag: genotype

value: Female


title: 4571_MA_06


title: H3K36me3_WT_rescue_rep2

tag: treatment

value: WT


title: uhg4-208wt-F-2

description:
rRNA depleted RNA
RAM-uhg4-208wt-F-2_S2_L001


title: 4571_MA_05

tag: cell type


title: MHCC97H Con_rep2

tag: cell line


title: MHCC97H Con_rep1


title: 4571_MA_09


title: H3K36me3_Smyd5_KO_Smyd5_delC_rep2

value: delC rescue


title: 4571_MA_08


title: uhg4-208wt-M-1

description:
rRNA depleted RNA
RAM-uhg4-208wt-M-1_S3_L001


title: uhg4-208G-M-2

description:
rRNA depleted RNA
208ΔG
RAM-uhg4-208G-M-2_S16_L001


title: 4571_MA_04


title: H3K36me3_Smyd5_KO_Smyd5_delC_rep1


title: chip-seq using HA tag-BZW2

city: Toronto

first: Boaz

last: Nachmias

state: Ontario

address: 101 College St.

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
Reads were aligned against hg19 (UCSC version) using Bowtie2 v2.3.2.
Secondary and supplementary alignments were removed, and only primary alignments were kept.
Alignment reads were deduplicated to remove duplicate reads and keep unique reads using picard v. 1.9.1.
Genome_build: hg19
Supplementary_files_format_and_content: Narrow peaks were identified from the alignment files using MACS2 v.2.1.1 with a cutoff score FDR 0.01

source_name: OCI-AML2 cells

growth_protocol: OCI-AML2 cells were grown in Iscove’s Modified Dulbecco’s Medium (IMDM).

extract_protocol: ChIP assays were performed in OCI-AML2 cells expressing either HA-tagged BZW1 or BZW1 as previously described (Drobic et al., 2010), with a minor modification that cross-liked chromatin was sheared to ~500 bp fragments by sonication. Antibody against anti-HA (Abcam) and BZW1 (info) were used. ChIP DNA was sequenced on Illumina Nextseq2500.

treatment_protocol: To perform lentiviral transductions, 1.0x106 OCI-AML2 cells were centrifuged and resuspended in 3 mL of medium containing 5 mg/mL of protamine sulfate. 1 mL of virus was added to these cells


title: H3K36me3_Smyd5_KO_Smyd5_FL_rep2

value: FL rescue


title: uhg4-208G-F-2

description:
rRNA depleted RNA
208ΔG
RAM-uhg4-208G-F-2_S14_L001


title: 4571_MA_03

data_processing:
Quality control was evaluated at different levels, including RNA quality, raw read data, alignment, and gene expression
Raw RNA-seq paired-ends were mapped to the human reference genome hg19 using STAR 2.7.3.
Raw reads count matrix was calculated by featureCounts and used for downstream analysis.
Supplementary files format and content: Feature Counts, csv
Supplementary files format and content: TPM, csv


title: 4571_MA_02

value: RD


title: uhg4-208G-M-1

description:
rRNA depleted RNA
208ΔG
RAM-uhg4-208G-M-1_S15_L001


title: 4571_MA_01


title: chip-seq using HA tag-BZW1


title: uhg4-208G-F-1

description:
rRNA depleted RNA
208ΔG
RAM-uhg4-208G-F-1_S13_L001


title: chip-seq using BZW2 HA-tag, replicate 3


title: H3K36me3_Smyd5_KO_Smyd5_FL_rep1


title: H3K36me3_SMYD5_KO_rescue_rep2

value: SMYD5 KO


title: uhg4-208F-M-2

description:
rRNA depleted RNA
208ΔF
RAM-uhg4-208F-M-2_S12_L001


title: uhg4-208F-M-1

description:
rRNA depleted RNA
208ΔF
RAM-uhg4-208F-M-1_S11_L001


title: H3K36me3_SMYD5_KO_rescue_rep1


title: Fibros, scRNAseq

city: Saint Louis

first: Lucia

last: Capano

state: MO

address: 660 South Euclid Avenue

department: Developmental Biology

institute: Washington University in Saint Louis

data_processing:
Raw 10x reads were processed with the Cell Ranger count pipeline using default parameters (Cell ranger v3.1.0, 10x Genomics).
Reads were aligned to the hg38 reference index provided by 10x Genomics (refdata-cellranger-GRCh38 v3.0.0).
Cell barcode and UMI (unique molecular identifier) were extracted and corrected from the feature library using the same methods as gene expression read processing.  Feature-barcode matrices were generated by counting distinct UMIs of each gene within a given individual cell (Zheng et al., 2017).
The R package, Seurat (v3.2.3) was used for quality control, analysis, and exploration of scRNA-seq data (Satija et al., 2015). We first removed cells where features less than 200 were detected and mitochondrial counts were high, then filtered features detected in cells less than 10. Seurat was used to remove unwanted variation from the gene expression by regressing out proportion of mitochondrial UMIs and overall UMIs.
Assembly: hg38
BAM, bigWig, Leafcutter BAM, JUNC, and differential gene expression tables provided
Barcodes detected, genes detected, and matrix files provided for each sample

source_name: Dermal Fibroblasts

extract_protocol:
On collection day, cells were washed once with sterile DPBS, detached using Trypsin, quenched with 10% FBS in DMEM, and collected via centrifugation. Pellet was washed once more with DPBS and cells were recollected with centrifugation. Cells were resuspended in 0.4% BSA in DPBS, counted on a hemocytometer, and diluted to 1000 cells/uL. Cells were placed on ice and processed immediately once all samples were prepared.
For single cell RNAseq, cells were processed using the Chromiam Single Cell 3' Reagent Kit according to manufactorers protocol, resulting cDNA libraries were quantified on an Agilent Bioanalyzer and then run on Illumina NovaSeq 6000.

value: Dermal Fibroblasts

value: MAPT Wildtype


title: uhg4-208F-F-2

description:
rRNA depleted RNA
208ΔF
RAM-uhg4-208F-F-2_S10_L001


title: FLAG_WT_rescue_rep1

value: Mouse monoclonal anti-FLAG M2 (Sigma, Cat. #F1804)


title: iPSCNs, scRNAseq

source_name: iPSC-derived Neurons

value: iPSC-derived Neurons

value: small molecule differentiation


title: uhg4-208F-F-1

description:
rRNA depleted RNA
208ΔF
RAM-uhg4-208F-F-1_S9_L001


title: chip-seq using BZW2 HA-tag, replicate 2


title: chip-seq using BZW2 HA-tag, replicate 1


title: miNs, scRNAseq

source_name: Reprogrammed neurons

value: Reprogrammed neurons

value: miR-9/9*-124 overexpression


title: IVS10+16 miN 2, rep3

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used to determine sequencing quality and identify adapter contamination and FastQ files were trimmed using cutadapt for adapter contamination (if needed). Sequencing reads were mapped to the human reference genome (GRCh38) using STAR (Dobin and Gingeras, 2015).
Raw gene counts were extracted using deepTools multiBamSummary option –outRawCounts ((Ramírez et al., 2016).
Differential gene expression analysis was performed using DESeq2 normalizing to sequencing depth (Love et al., 2014).
BigWigs were made using samtools.
For Leafcutter, BAM files generated using --outSAMstrandField intronMotif option were convered to JUNC files, then loaded into the Leafcutter path as published (Li et al., 2018).
BAM and bigWig files of biological replicates for RNA-seq and leafcutter experiments
Assembly: hg38
BAM, bigWig, Leafcutter BAM, JUNC, and differential gene expression tables provided
Barcodes detected, genes detected, and matrix files provided for each sample

extract_protocol:
On collection day, cells were washed once with sterile DPBS, detached using Trypsin, quenched with 10% FBS in DMEM, and collected via centrifugation. Pellet was then put through Qiagen RNeasy Micro Kit according to protocol.
For bulk RNAseq, a cDNA library was prepared using CloneTech SMARTer for Illumina sequencing using poly-A library preparation.

value: MAPT IVS10+16

tag: genome build


title: FLAG_Smyd5_KO_rep2

value: Smyd5 KO


title: chip-seq using BZW1 HA-tag, replicate 2


title: uhg4-208A-M-2

description:
rRNA depleted RNA
208ΔA
RAM-uhg4-208A-M-2_S8_L001

value: Whole body

value: Male


title: IVS10+16 miN 2, rep2


title: chip-seq using BZW1 HA-tag, replicate 3


title: uhg4-208A-M-1

description:
rRNA depleted RNA
208ΔA
RAM-uhg4-208A-M-1_S7_L001

value: 3-5 days


title: FLAG_Smyd5_KO_rep1


title: chip-seq using BZW1 HA-tag, replicate 1


title: chip-seq using BZW1 antibody, replicate 3


title: uhg4-208A-F-2

description:
rRNA depleted RNA
208ΔA
RAM-uhg4-208A-F-2_S6_L001

value: Female


title: chip-seq using BZW1 input


title: IVS10+16 miN 1, rep3


title: FLAG_Smyd5_KO_Smyd5_delC_rep2

value: delC rescue


title: chip-seq using BZW1 antibody, replicate 2


title: FLAG_Smyd5_KO_Smyd5_delC_rep1


title: FLAG_WT_rescue_rep2

value: WT


title: IVS10+16 miN 2, rep1


title: FLAG_Smyd5_KO_Smyd5_FL_rep2

value: FL rescue


title: IVS10+16 miN 1, rep2


title: IVS10+16 miN 1, rep1


title: FLAG_Smyd5_KO_Smyd5_FL_rep1


title: iPSC-Neurons 1, rep3

value: iPSCN


title: BZW1/2 KD rep 3

data_processing:
During analysis, read adapters were removed using TRIM Galore 0.4.0, and reads were aligned against UCSC hg19 using Tophat v.2.0.11.
Genome_build: hg19
Supplementary_files_format_and_content: Read counts per gene were obtained through htseq- count v.0.6.1p2.

extract_protocol: RNA was isolated from OCI-AML2 cells 7 days post-transduction with shRNA targeting IPO11 or dual BZW1/2 versus  control and was sequenced (Illumina Nextseq2500).

tag: transduction

value: BZW1/2 KD


title: MOLM13 [Ribo-seq]

city: Guangzhou

first: Tianyuan

last: Liu

address: Shatai South Road, Baiyun District

department: Bioinformatics Department

institute: Sourthern Medical University

description: Ribosome-seq

data_processing:
The raw sequence reads were trimmed for the 3-end adapter with trim_galore (v0.6.6) (with the parameters ‘--adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality 20’) and low-quality sequences were trimmed.
Then retained reads that mapped to reference human rRNAs or tRNAs were then removed with bowtie2 (v2.4.2), and the remaining reads were aligned to the human reference genome (GENCODE Release 28) using STAR (v2.7.8a).
Expression levels relative to transcripts were estimated using StringTie (Version 2.1.5).
Assembly: hg38
Supplementary files format and content: gtf file were generated with command stringtie followed by StringTie; abundance measurements.
Library strategy: Ribo-seq

growth_protocol: The following cell lines were purchased from the ATCC and cultured in the corresponding medium with 10% FBS (Hyclone, Logan, Utah) at 37 ºC, 5% CO2 in a cell culture incubator. MOLM13 (DMEM), THP-1 (RPMI1640, 2-mercaptoethanol to a final concentration of 0.05 mM), HL60 (IMDM), K562 (IMDM).

extract_protocol:
Cells were lysed using 1 ml of mammalian lysis buffer (200 µI of 5 × Mammalian Polysome Buffer, 100 µI of 10% Triton X-100, 10 µI of DTT (100 mM), 10 µI of DNase I (1 U/µI), 2 µI of cycloheximide (50 mg/ml), 10 µI of 10% NP-40 and 668 µI of nuclease-free water). After incubation for 20 min on ice, the lysates were cleared by centrifugation at 10,000 × g and 4℃ for 3 min. For the 300-µI aliquots of clarified lysates per cell line, 5 units of ARTseq Nuclease were added to each A260 lysate, and the mixtures were incubated for 45 min at room temperature. Nuclease digestion was stopped by the addition of 15 µI of SUPERase In RNase Inhibitor (Ambion). Subsequently, the lysates were applied to Sephacryl S-400 HR spin columns (GE Healthcare Life Sciences), and ribosome-protected fragments were purified using the Zymo RNA Clean & Concentrator-25 kit (Zymo Research). Ribosomal RNA was depleted using the Ribo-Zero magnetic kit (Epi-centre).
Sequencing libraries of ribosome-protected fragments (RPFs) were generated using the ARTseq™ Ribosome Profiling Kit (Epicentre, RPHMR12126), according to the manufacturer’s instructions. The libraries were sequenced using an Illumina HiSeq X Ten instrument in the 150bp paired-end mode.

value: leukemia cell line


title: HL60 [Ribo-seq]

description: Ribosome-seq


title: iPSC-Neurons 1, rep2

value: MAPT Wildtype


title: FLAG_WT_rep2

extract_protocol:
Lysates are clarified from sonicated nuclei and histone-DNA complexes are isolated with antibody for ChIP-seq.  RNA is harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) is used with 1 ug of total RNA for libraries of RNA-seq. GRO-seq library is constructed by pull-down of BrU labelled nascent RNA which is then subjected to strand specifice library construction. CUT&Tag libraries are constructed from nuclei extraction and antibody binding, transposome tagmentation.
ChIP-seq, RNA-seq libraries were prepared for sequencing using standard Illumina protocols. CUT&Tag libraries are prepared from directely PCR. GRO-seq library is prepared by strand-specific library construction.

tag: strain

value: Mouse monoclonal anti-FLAG M2 (Sigma, Cat. #F1804)


title: BZW1/2 KD rep 2


title: FLAG_WT_rep1

tag: age


title: BZW1/2 KD rep 1


title: THP_1 [Ribo-seq]

description: Ribosome-seq


title: K562 [Ribo-seq]

description: Ribosome-seq


title: iPSC-Neurons 1, rep1

value: small molecule differentiation


title: BZW1/2 Non target control rep 3

value: BZW1/2 Non target control


title: uhg4-208A-F-1

description:
rRNA depleted RNA
208ΔA
RAM-uhg4-208A-F-1_S5_L001


title: FLAG_Smyd5_OE_rep2


title: IVS10+16 miN 3, rep3

value: Reprogrammed neurons

value: miR-9/9*-124 overexpression


title: BZW1/2 Non target control rep 2


title: GFP_sorted_28hpf

city: Iowa City

first: Colin

last: Kenny

state: Iowa

address: 51 Newton Road 100 Bowen Science Building Iowa

department: Anatomy and Cell Biology

institute: University of Iowa

description: Output files from CellRanger and raw sequence files

data_processing:
10x Data was processed with the Cell Ranger pipeline, version 5.0.1
Assembly: GRCz11
Supplementary files format and content: Tab-delimited .tsv files for features and barcodes
Supplementary files format and content: matrix .mtx for single-cell expression

organism: Danio rerio

growth_protocol: 50 Tg(mitfa:GFP) transgeneic zebrafish embryos were collected at 28 hours post fertilization (hpf) and washed in PBS without Ca2+ or Mg2+ (Life technology). Embryos were manually dechorionated under a dissecting scope (Leica KL300 LED), washed twice in 1X PBS and then cell dissociated cells using a pestle and incubated in trypsin (0.25%)-EDTA (Life technology) at 33°C for 30 minutes (ensuring to pipette mixed every 5 minutes). Reactions were quenched by adding PBS supplemented with 5% fetal bovine serum (FBS, Life technologies). Dissociated cells were centrifuged at 500 g for 5 minutes and cell pellets were washed with PBS-5%FBS before passing thought a Bel Art™ SP Scienceware™ Flowmi™ 40 μm cell strainers (ThermoFisher Scientific). Dissociated cells were re-suspended into single-cell solution and analyzed at the University of Iowa Flow Cytometry Facility, using an Aria Fusion instrument (Becton Dickinson, Franklin Lakes, NJ).

extract_protocol: The sorted cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10,000 cells were loaded per channel. Single-cell RNA-Seq libraries were prepared using Single Cell 3′ Reagent Kits v2: Chromium™ Single Cell 3′ Library & Gel Bead Kit v2, PN-120237; Single Cell 3′ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262 (10x Genomics) following the Single Cell 3′ Reagent Kits v2 User Guide (Manual Part # CG00052 Rev A).


title: chip-seq using BZW1 antibody, replicate 1


title: Lrv_FLX_Str_whole_6

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_6_S55

data_processing:
Illumina bcl2fastq v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence with CutAdapt, then aligned with STAR v 2.5 with parameter --clip5pNbases 10 and --quantMode TranscriptomeSAM GeneCounts.
Tables of gene counts generated by STAR were imported into R and differential gene expression analysis was performed using DESeq2 to compare exposure groups.
Genome_build: GRCz11v92
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample.

extract_protocol:
Qiagene miliamp total RNA extraction- column based
Illumina TruSeq Stranded mRNA libraries were built following the manufacturer’s protocol using 250ng of starting material.

treatment_protocol: Exposing to Fluoxetine (54ug/L) as treatment or Ethanol (0.0053%) as vehicle from 0 to 6 days post fertilization in larvae

tag: genotype/variation

value: SR4G transgenic

tag: stress status

value: Str

tag: drug status

value: FLX

value: larvae head


title: FLAG_Smyd5_OE_rep1

data_processing:
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Filtered RNA-seq reads were mapped to the mouse reference genome mm9, which excluded mitochondria and random chromosomes, by STAR (version 2.5.4b)(Dobin et al., 2013)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Expression matrixes were counted by featureCounts(Liao et al., 2014) (version 2.0.0)
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample of RNA-seq


title: IVS10+16 miN 3, rep1

value: MAPT IVS10+16


title: FLAG_Smyd5_KI_rep1


title: Lrv_FLX_Str_whole_5

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_5_S59


title: Lrv_FLX_Str_whole_4

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_4_S50


title: IPO11 KD rep 3

value: IPO11 KD


title: Healthy control miN 3, rep3


title: IPO11 KD rep 2


title: Lrv_FLX_Str_whole_3

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_3_S62


title: FLAG_Smyd5_KI_rep2


title: H3K36me3_Smyd5_KO2_rep1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: Smyd5 KO


title: IPO11 KD rep 1


title: Lrv_FLX_Str_whole_1

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_1_S57


title: H3K36me3_Smyd5_KO1_rep2


title: Healthy control miN 3, rep1


title: IPO11 Non target control rep 2

value: IPO11 Non target control


title: H3K36me3_Smyd5_KO1_rep1


title: IVS10+16 miN 3, rep2


title: Healthy control miN 2, rep3


title: Lrv_FLX_Bsal_whole_6

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal_6_S64

value: Bsal


title: Lrv_FLX_Bsal_whole_4

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal_4_S69


title: Healthy control miN 2, rep2


title: Lrv_FLX_Str_whole_2

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Str_2_S70


title: Healthy control miN 2, rep1


title: batch9_H3K36me3_KMD4D_KO2

value: KMD4D KO


title: Healthy control miN 3, rep2

value: MAPT Wildtype


title: IPO11 Non target control rep 3


title: BZW1/2 Non target control rep 1


title: H3K36me3_Smyd5_KO2_rep2


title: Biotinylation-seq_293T-WT_LSM11_pulldown_Rep2_R1

city: Yokohama

first: Hidefumi

last: Suzuki

address: Fukuura 3-9

country: Japan

institute: Yokohama City University

data_processing:
Library strategy: Biotinylation-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For biotinylation-seq, adapter sequences were trimmed using Trim Galore (v 0.64_dev).
Biotinylation-seq reads were mapped to human genome GRCH38 and Drosophila melanogaster genome build5.41 using the Bowtie2 alignment tool (version 2.3.5.1) with the default settings.
The mapped biotinylation-seq reads were subjected to count per million (CPM) normalization and then used for downstream analysis. IP/input or IP-input enrichment per gene was calculated with R (v. 4.0.2) and its package rtracklayer (version:1.48.0) using Ensemble GRCH38.92 gene annotation model. (Spike-in normalization was not used)
Genome_build: GRCH38 and Drosophila melanogaster genome build5.41 from NCBI
Supplementary_files_format_and_content: BigWig files include normalized count data

growth_protocol: Cells were cultured in 1X DMEM (Nacalai tesque) supplemented with 10% fetal bovine serum and 1X penicillin/streptomycin (Nacalai tesque) in a CO2 incubator (5% CO2) at 37°C.

extract_protocol:
For antibody-based in situ biotinylation-seq, HEK293T cells cultured in 10 cm dish were fixed with 4% PFA and permeabilized with 0.5% Triton X-100. After blocking, cells were incubated with primary antibodies, and then incubated with HRP-labeled secondary antibodies. After washing, HRP-based in situ biotinylation was performed by incubating cells with biotinylation buffer. The cells were lysed in 1% SDS RIPA buffer and were sonicated for DNA fragmentation. The biotinylated chromatin was pulled-down using SoftLinkTM Soft Release Avidin Resin (Promega), and the chromatin DNA was purified.
Libraries for ChIP-seq and antibody-based in situ biotinylation-seq were prepared using TruSeq ChIP Library Prep Kit (Illumina) and IDT for illumina-TruSeq RNA UD Index (Illumina). Library purification and size selection were performed using Agencourt AMPure XP system. Libraries were checked for quality and quantity using Bioanalyzer. Equimolar concentrations of libraries were pooled, and sequenced as paired-end reads on the Illumina Novaseq 6000 platform (ChIP-seq) or Hiseq 2500 platform (antibody-based in situ biotinylation-seq). PRO-seq libraries were generated essentially as described in Mahat et al., 2016 (Nat Protoc, 11:1455-76; doi: 10.1038/nprot.2016.086). Primers RPI1, RPI2, RPI3 and RPI4 were used to barcode cDNAs from 293T-WT_Rep1 (Wild type, replicate 1), 293T-WT_Rep2 (Wild type, replicate 2), 293T-EAF1mut_Rep1 (Mutant EAF1, replicate 1), and 293T-EAF1mut_Rep2 (Mutant EAF1, replicate 2), respectively.

value: wildtype

tag: spike-in source

value: Drosophila melanogaster

tag: protocol/antibody

value: Antibody-based biotinylation-seq/LSM11, Sigma-Aldrich Corp cat HPA039587

tag: sequenced molecule

value: genomic DNA pulldown


title: Lrv_FLX_Bsal_whole_2

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal_2_S51

tag: tissue


title: Lrv_FLX_Bsal_whole_3

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal_3_S53


title: Biotinylation-seq_293T-WT_LSM11_pulldown_Rep1_R1


title: batch7_H3K36me3_ZMYND13_KO2

tag: chip antibody

value: ZMYND13 KO


title: Biotinylation-seq_293T-WT_LSM11_Input_R1

value: Input for antibody-based biotinylation-seq/LSM11, Sigma-Aldrich Corp cat HPA039587

value: genomic DNA Input


title: Lrv_FLX_Bsal_whole_1

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal_1_S58

value: SR4G transgenic

value: FLX


title: batch7_H3K36me3_PRDM1_KO2#2

value: PRDM1 KO


title: Lrv_FLX_Bsal_whole_5

description:
pool of 22 dissected 6 days old larvae
Lrv_FLX_Bsal__5_S65

value: larvae head


title: batch5_H3K36me3_ZMYND2_KO2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: ZMYND2 KO


title: Biotinylation-seq_293T-WT_Coilin_pulldown_Rep1_R1

value: Antibody-based biotinylation-seq/Coilin, Abcam cat ab11822


title: batch8_H3K36me3_ZMYND12_KO2#2

value: ZMYND12 KO


title: IPO11 Non target control rep 1

value: IPO11 Non target control


title: Healthy control miN 1, rep1

value: Reprogrammed neurons

value: MAPT Wildtype

value: miR-9/9*-124 overexpression


title: Healthy control miN 1, rep3


title: H3K36me3_K562_Smyd5OE_rep2

data_processing:
Library strategy: CUT&TAG
Sequencing reads adaptor and low-quality bases were removed by Trim Galore (version 0.6.4) (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore)
Trimmed epigenomic sequencing data were then mapped to the mouse reference genome mm9 using Bowtie2(Langmead and Salzberg, 2012).PCR duplicates were removed by GATK4 (version 4.1.4.0) (https://github.com/broadinstitute/gatk) with the parameter ‘--REMOVE_DUPLICATES =true’.
Bedtools(Quinlan, 2014) (version 2.92.2) and bedGraphToBigWig (https://www.encodeproject.org/software/bedgraphtobigwig/) (version 4) were used to normalize mapped reads and calculate the coverage of features among the genome with the following parameters ‘genomecov --scaleFactor 10,000,000/mapped_reads_number’.
Assembly: mm9, hg19
Supplementary files format and content: BigWig files

source_name: Erythroleukemic cell line

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated dishes in DMEM supplemented with 15% fetal bovine serum (FBS), 1% antibiotic solution (penicillin/streptomycin), 1% glutamax, 1% MEM nonessential amino acids, 1% sodium pyruvate, 0.1 mM-mercaptoethanol and 1000 U/ml recombinant leukemia inhibitory factor (LIF). K562 cells were cultured in RPMI1640 supplemented with 1% glutamax, 1% antibiotic solution (penicillin/streptomycin) and 10% FBS. All cells were grown at 37 °C and 5% CO2.

extract_protocol:
CUT&Tag libraries are constructed from nuclei extraction and antibody binding, transposome tagmentation. ATAC-seq libraries are constructed from nuclei extraction and transposome tagmentation.
CUT&Tag and ATAC-seq libraries are prepared from directely PCR.

value: native

value: overexpression Smyd5


title: batch7_H3K36me3_SET1B_KO2

value: SET1B KO


title: Healthy control miN 1, rep2


title: Adult Brain RNA, rep2

source_name: Adult Brain

value: Adult Brain


title: Biotinylation-seq_293T-WT_Coilin_pulldown_Rep2_R1

value: wildtype

value: Drosophila melanogaster

value: genomic DNA pulldown


title: Fetal Neurons RNA, rep1

source_name: Fetal Neurons

value: Fetal Neurons


title: Lrv_Ctl_Str_whole_4

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_4_S63

value: SR4G transgenic

value: Str

value: Ctl

value: larvae head


title: Fetal Neurons RNA, rep2


title: Lrv_Ctl_Str_whole_3

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_3_S61


title: Lrv_Ctl_Str_whole_6

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_6_S71


title: Biotinylation-seq_293T-EAF1mut_LSM11_pulldown_Rep1_R1

source_name: HEK293T EAF1-mutant

value: Antibody-based biotinylation-seq/LSM11, Sigma-Aldrich Corp cat HPA039587


title: Adult Brain RNA, rep1


title: Biotinylation-seq_293T-WT_Coilin_Input_R1

value: Input for antibody-based biotinylation-seq/Coilin, Abcam cat ab11822

value: genomic DNA Input


title: batch5_H3K36me3_PRDM10_KO2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: PRDM10 KO


title: batch5_H3K36me3_PRDM8_KO2

value: PRDM8 KO


title: Biotinylation-seq_293T-EAF1mut_LSM11_pulldown_Rep2_R1


title: batch5_H3K36me3_ZMYND12_KO2#1

value: ZMYND12 KO


title: batch5_H3K36me3_PHF2_KO2

value: PHF2 KO


title: Lrv_Ctl_Str_whole_2

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_2_S49


title: H3K36me3_K562_Smyd5OE_rep1

value: native

value: overexpression Smyd5


title: Biotinylation-seq_293T-EAF1mut_LSM11_Input_R1

value: Drosophila melanogaster

value: Input for antibody-based biotinylation-seq/LSM11, Sigma-Aldrich Corp cat HPA039587


title: Biotinylation-seq_293T-EAF1mut_Coilin_pulldown_Rep2_R1

value: Antibody-based biotinylation-seq/Coilin, Abcam cat ab11822

value: genomic DNA pulldown


title: Biotinylation-seq_293T-EAF1mut_Coilin_pulldown_Rep1_R1


title: Lrv_Ctl_Str_whole_1

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_1_S56

value: SR4G transgenic

value: Str


title: batch4_H3K36me3_ZMYND15_KO2

value: ZMYND15 KO


title: Lrv_Ctl_Str_whole_5

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Str_5_S68

value: Ctl

value: larvae head


title: Lrv_Ctl_Bsal_whole_6

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal_6_S67

value: Bsal


title: Lrv_Ctl_Bsal_whole_4

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal_4_S54


title: H3K36me3_K562_rep1

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: WT


title: batch4_H3K36me3_SUV420h2_KO2

value: SUV420h2 KO


title: batch4_H3K36me3_SETD1B_KO2

value: SETD1B KO


title: batch4_H3K36me3_ZMYND6_KO2

value: ZMYND6 KO


title: Lrv_Ctl_Bsal_whole_1

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal_1_S52


title: SKNAS_Taze2_Input

city: West Lafayette

first: Nathaniel

middle: Wesley

last: Mabe

state: Indiana

address: 201 S. University St.

department: Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

data_processing:
ChIP-Seq data analysis was performed in alignment with the ENCODE Consortium standards (https://www.encodeproject.org/chip-seq/). All of the ChIP-Seq data sets were aligned to the GRCh38/hg38 human genes and Drosophila Melanogaster dm6 genes using bowtie2-2.3.5 with the standard options. PCR duplicates were removed with the Picard v2.18.2 MarkDuplicates tool56. The Active Motif Spike-in Normalization protocol was then applied to each hg38 sample by multiplying the human tag counts with the normalization factors derived from the uniquely mapped Drosophila reads as ratios between the sample with the lowest dm6 counts vs. the dm6 counts for that sample.
Correlations for replicate samples were computed with the multiBamSummary and bamCorrelate tools available in deepTools v3.5.157 and visualized as dendrograms and in PCA plots. Replicate reads were merged for each condition. The mapped reads for individual replicates and for merged reads were normalized in units of Reads Per Kilobase per Million (RPKM or rpm/bp) and coverage tracks for the RPKM signal were created as bigwig files for bins of size 20 base pairs by using the bamCoverage tool available in deepTools.
Peak calling was performed against input control using the MACS2 software58, with the broad option and  FDR ≤ 0.01. Area under Curve (AUC) RPKM normalized signal across genomic regions was computed with the bwtool software59. Peaks with low area under curve coverage (< 300 RPKM)  were disregarded and the ENCODE black-listed regions for hg38 were removed from each set of peak regions. Quality control tests for the mapped reads were performed by using the ChIPQC library available from Bioconductor v3.1060. The peaks were annotated with the closest hg38 genes by using the chipseeker package available from Bioconductor61.
The binding sites identified by MACS2 on merged reads were aggregated into consensus peaks per condition by requiring AUC binding signal > 500 for each replicate. The consensus peaks for both conditions were merged into a high confidence union peak set. A peak by sample counts matrix was created by counting the reads overlapping each peak with the multiBamSummary tool available from deepTools. The counts matrix was used to perform differential peak analysis in DESeq2. Differential binding across conditions was assessed based on the significance cut-offs |Delta(log2(AUC+1))| ≥ 0.5 and adjP-value ≤ 0.10. Genome track files were created with the bamCoverage tool available in deepTools and visualized as heatmaps and metaplots created with the computeMatrix tool available in deepTools,  and with the Integrative Genomic Viewer (IGV).
Genome_build: hg38
Supplementary_files_format_and_content: differential peak analysis of union peaks

source_name: SK-N-AS

extract_protocol:
Histone ChIP-sequencing was performed on 2 x 107 cells per reaction. Cells were crosslinked for 10 minutes in 1% formaldehyde and quenched in 0.20 M glycine for 5 minutes. Cells were lysed with SDS buffer supplemented with protease/phosphatase inhibitor cocktail and cell nuclei were pelleted. Nuclei pellets were resuspended in IP buffer and sheared for 15 minutes on a E220 Covaris sonicator (5% duty cycle, Peak power 140W, Cycles/burst 200) at 4C. Input lysates were separated from IP lysates, and the IP lysates were incubated overnight at 4C with a previously prepared mixture of antibody loaded on protein A or G magnetic beads. For ChIP-sequencing, 5 uL of drosophilia spike-in chromatin (ActiveMotif #53083) was added to each IP. Magnetic beads were washed twice with low salt wash buffer, twice with high salt wash buffer, twice with LiCl wash buffer, and once with cold TE. Washed DNA was eluted from beads with ChIP elution buffer. Input and IP samples were reverse crosslinked in high salt at 65C overnight. Uncrosslinked DNA was purified with SPRI beads and eluted for downstream analysis. Real-time quantitative RT-PCR for ST8SIA1 was performed using SYBR green (Bio-Rad) in combination with primers listed in Supplemental Table 4 and represented as percentage of input DNA. A gene desert on Chromosome 12 (ActiveMotif) was included as a negative control for antibody enrichment.
DNA for ChIP-sequencing was submitted to the DFCI genomics core facility for library preparation and sequencing. DNA libraries were prepared with automated Swift S2 ligation chemistry and at least 80M 50 bp reads were sequenced on a NovaSeq platform.

tag: lineage

value: Neuroblastoma

tag: protocol

value: 14 days treatment with tazemetostat or vehicle

value: Tazemetostat


title: Biotinylation-seq_293T-EAF1mut_Coilin_Input_R1

tag: genotype

value: Drosophila melanogaster

value: Input for antibody-based biotinylation-seq/Coilin, Abcam cat ab11822

value: genomic DNA Input


title: batch4_H3K36me3_PRDM6_KO2

first: Dong

last: Fang

address: 866 Yuhangtang Road

institute: Zhejiang University

tag: cell type

tag: treatment

value: PRDM6 KO


title: Lrv_Ctl_Bsal_whole_2

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal_2_S66

value: SR4G transgenic


title: SKNAS_Veh2_Input

value: Vehicle


title: 4Cseq_293T-WT_HIST1H2BK-bait_Rep2_R1

data_processing:
Library strategy: 4C-seq
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
For 4C-seq, pipe4C was used with the default setting for the data analysis. R1 files of paired-end read files were used for 4C-seq data analysis.
Supplementary_files_format_and_content: BigWig files include normalized count data

extract_protocol:
For 4C-seq, HEK293T cells cultured in 10 cm dish were fixed with 4% formaldehyde for 10 min at room temperature. Cross-linked HEK293T cells were lysed, and the lysate was subjected to first restriction enzyme digestion using NlaIII (R0125S; NEB) followed by in situ ligation reaction using T4 DNA ligase (10799009001; Roche Diagnostics, Tokyo). After reverse-cross-linking, the ligated DNA templates were purified using P-beads (NucleoMag® NGS Clean-up and Size Select, 744970.5, Takara Bio Inc). Then, 2nd round of restriction enzyme digestion using DpnII (R0543S; NEB) and ligation was performed for trimming and circularization of template DNA. Resulting 4C-templates were purified by P-beads and subjected to sequencing library preparation.
4C-seq libraries werec generated essentially as described in Krijger et al., 2020 (Methods, 170: 17-32; doi: 10.1016/j.ymeth.2019.07.014). 4C-seq libralies were pooled and sequenced on Illumina Hiseq 2500 platform.

tag: cell line

value: wildtype

value: 4C-template DNA


title: 4Cseq_293T-WT_HIST2H2AB-bait_Rep1_R1


title: batch4_H3K36me3_PRDM5_KO2

value: PRDM5 KO


title: H3K36me3_K562_rep2

value: native

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)


title: Lrv_Ctl_Bsal_whole_5

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal__5_S60

value: Bsal

value: Ctl

value: larvae head


title: SKNAS_Taze1_Input

value: Neuroblastoma


title: batch4_H3K36me3_PRDM3_KO2

value: PRDM3 KO


title: 4Cseq_293T-EAF1mut_HIST2H2AB-bait_Rep2_R1


title: Adt_FLX_Str_Tel_6

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_6_S47

value: Str

value: FLX

value: telencephalon


title: 4Cseq_293T-EAF1mut_HIST2H2AB-bait_Rep1_R1


title: batch4_H3K36me3_PRDM2_KO2

value: PRDM2 KO


title: Lrv_Ctl_Bsal_whole_3

description:
pool of 22 dissected 6 days old larvae
Lrv_Ctl_Bsal_3_S72


title: 4Cseq_293T-EAF1mut_HIST1H2BK-bait_Rep2_R1


title: batch4_H3K36me3_PRDM4_KO2

value: PRDM4 KO


title: SKNAS_Taze1_H3K27me3

value: 14 days treatment with tazemetostat or vehicle

value: Tazemetostat


title: SKNAS_Taze2_H3K27me3


title: Adt_FLX_Str_Tel_5

description:
pool of 5 dissected telencephalon
Adt_FLX_Str_Tel_5_S44

value: SR4G transgenic


title: 4Cseq_293T-WT_HIST1H2BK-bait_Rep1_R1

value: wildtype

value: 4C-template DNA


title: batch4_H3K36me3_PRDM16_KO2

value: PRDM16 KO


title: batch4_H3K36me3_PRDM12_KO2

value: Rabbit polyclonal anti-Histone H3K36me3 (Abcam, Cat. #ab9050)

value: PRDM12 KO


title: SKNAS_Veh1_H3K27me3

value: Vehicle


title: 4Cseq_293T-EAF1mut_HIST1H2BK-bait_Rep1_R1


title: CCND2OEExos OE2

first: meng

last: zhao

address: 501 Buliding 1, 18 Shilongshan Road, Cloud Town, Xihu District, Hangzhou, P.R. China

department: Life Science school

institute: Westlake Universituy

data_processing:
Raw sequencing reads (40 nts) were obtained using Illumina’s Sequencing Control Studio software  version 2.8 (SCS v2.8) following real-time sequencing image analysis and base-calling by Illumina's  Real-Time Analysis version 1.8.70 (RTA v1.8.70).
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in  hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species  precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived  miRNA candidates.
After the raw sequence reads, or sequenced sequences (sequ seqs) were extracted from image data, a series of digital filters (LC Sciences) were employed to remove various un-mappable sequencing reads. In this step, the “impurity” sequences due to sample preparation, sequencing chemistry and processes, and the optical digital resolution of the sequencer detector were removed. Those remaining sequ seqs (filtered sequ seqs with lengths between 15 and 32 bases) were grouped by families (unique seqs), and stored in the file [Sample]_mappableReads.fq, and were used to map with the reference database files.
Normalization of sequence counts in each sample (or data set) is achieved by dividing the counts by a library size parameter of the corresponding sample. The library size parameter is a median value of the ratio between the counts a specific sample and a pseudo-reference sample. A count number in the pseudo-reference sample is the count geometric mean across all samples.
Genome_build: GRCh38
Supplementary_files_format_and_content: Summary of known and predicted miRNA in this study.

source_name: exosomes from CCND2OECMs

growth_protocol: hiPSCs were seeded in a 6-well plate that had been coated with Matrigel (Corning), and cultured in mTeSR1 (STEMCELL Technologies) with daily medium changes to 80-90% confluency. For differentiation, the medium was replaced with RPMI 1640 medium supplemented with 2% B27 minus insulin (RB-medium; ThermoFisher Scientific) and 10 μM GSK-3β inhibitor CHIR99021 (CHIR, STEMCELL Technologies) when the cells reached 80-90% confluence (Day 0); 24 hrs later, the medium was replaced with CHIR-free RB-medium for another 48 hrs until day 3, followed by replacing with an RB-medium containing 10 μM of the Wnt inhibitor IWR1 (STEMCELL Technologies) for 48 hrs, until day 5. The medium was then replaced with IWR1-free RB-medium for 48 hrs until day 7. Furthermore, the medium was replaced with RPMI/B27 medium (containing insulin) (ThermoFisher Scientific). Spontaneously and rhythmically beating CMs, usually appearing around day 7 after initiation of the differentiation protocol (Day 0), were purified via a selection on a modified glucose-free RPMI medium (Thermo Fisher Scientific) supplemented with 4 mM lactate (Sigma) and B27 for at least 5 days. Exosomes from hiPSC-CMs were isolated from the cell culture media using a Total Exosome Isolation Kit (ThermoFisher Scientific).

extract_protocol:
Total RNA was extracted with TRIzol™ Reagent (Fisher Scientific) from exosomes for small RNA sequencing.
A small RNA library was generated from the samples using the Illumina Truseq™ Small  RNA Preparation kit according to Illumina’s TruSeq™ Small RNA Sample Preparation Guide.

treatment_protocol: CCND2 was overexpressed in the hiPSC with the lentivirus method. Firstly, the lenti-α-MHC/CCND2 plasmid was generated. Briefly, a pair of oligonucleotides (forward: 5'AGAGCCACCGGTATGGAGCTGCTGTGCCACGAGGT 3', reverse: 5'CTGCAGGCGCGCCGAATTTTTTTTTTAAGTTT CACCCT 3’; Invitrogen) were used to amplify the CCND2 insert from a plasmid (Addgene # 8958) by PCR. The amplified product was digested with AscI and AgeI endonucleases, and separated by a 2% agarose gel for purification. The purified product was subcloned into a lentivirus-α-MHC (myosin heavy chain) vector (Addgene # 21230). The inserted sequence was confirmed by Sanger sequencing. The lentivirus-α-MHC/CCND2 plasmid and the MISSION lentivirus packaging mixture (Sigma-Aldrich) were co-transfected into HEK293 cells with Lipofectamine 2000 (Invitrogen). Forty-eight hours later, the virus-containing supernatant was collected, concentrated (Clontech), filtered with a 0.45-μm low protein binding membrane (Millipore), and immediately transfected into hiPSCs. Forty-eight hours after transfection, G418 (400 μg/mL) was added for 7 days, and then the cells were allowed to grow in a standard culture medium until the colonies reached the size suitable for selection and expansion. CCND2 overexpression was verified by PCR and western blot.

tag: hipsc source

value: human cardiac fibroblast

value: CCND2 overexpression in hiPSC-CMs


title: SKNAS_Veh1_Input

value: Neuroblastoma


title: SKNAS_Veh2_H3K27me3