title: delta lexA/delta sulA M9/rdm/glu IPOD replicate 1

description:
DlexA_m9_rdm_glu_rzlog10p_chipsub.gr.gz
DlexA_m9_rdm_glu_ipod_vs_inp_lograt.gr.gz

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
Illumina TruSeq Nano DNA prep kit, with spin column cleanups replaced with Zymo spin columns.


title: dH1f_DMSO_RNA_2

status: Public on Jun 15 2021

type: SRA

city: Istanbul

first: Ayse Derya

last: Cavga

address: Rumelifeneri Yolu, Sariyer

country: Turkey

institute: Koc University

library_source: transcriptomic

data_processing:
Quality check of reads for all samples was carried out using FastQC version 0.11.5.
Reads were mapped to hg19 using HISAT2 version 2.1.0.
Raw read counts were generated using feautureCounts version 1.6.0.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimeted text files with raw counts for all samples.

molecule: total RNA

organism: Homo sapiens

source_name: fibroblast cells

extract_protocol:
RNA from cells was harvested using Trizol reagent. Libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®.
RNA libraries were prepared for sequencing using standard NEB protocols.

tag: cell type

tag: transduced with

tag: treatment

value: DMSO


title: dH1f_DMSO_RNA_1


title: dH1f_BI7273_RNA_3


title: H3K36me2_NSD1_WT_rep1

city: Hangzhou

first: Dong

last: Fang

state: Zhejiang

address: 866 Yuhangtang Road

department: Life Sciences Institute

country: China

institute: Zhejiang University

library_source: genomic

data_processing:
Library strategy: CUT&RUN
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

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cells

growth_protocol: All J1 mESCs were cultured 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 β-Mercaptoethanol, and 1,000 U/ml recombinant leukemia inhibitory factor (LIF). Cells were cultured on 0.1% gelatin coated plates with fresh medium.

extract_protocol:
RNA-seq: Total RNA from 10^6 cells was purified by RNeasy plus mini kit (Qiagen, Cat.# 74134). ATAC-seq: 10^6 mESCs were collected and lysed by lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% NP-40) and separated into 50 µl with 50,000 cells. CUT&RUN/CUT&Tag: mESCs were harvested and washed with Wash buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, and 1X Roche Complete Protease Inhibitor EDTA-Free tablet), 10 μl pre-washed Concanavalin A coated beads in binding buffer (20 mM HEPES pH7.9, 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) were added per sample.
RNA-seq and ATAC-seq libraries were prepared for sequencing using standard Illumina protocols. Other libraries preparation was described previously(Kaya-Okur et al., 2019a).

tag: strain

value: untreated

tag: chip antibody

value: H3K36me2 (Cell Signaling Technology, Cat.# 2901)

tag: genotype

value: wild type


title: progenitors (gut organoid) 2

city: San Francisco

first: Todd

last: McDevitt

state: CA

address: 1650 Owens St

department: GICD

country: USA

institute: Gladstone Institutes

description: WTC11 human induced pluripotent stem cells (iPSCs) genetically modified with fast green fluorescent calcium indicator GCaMP6f.

data_processing:
Demultiplex with bcl2fastq v2.20.0.
Align with HiSat2 v2.1.0.
Count transcripts with featureCounts v1.6.2.
Generate final counts with GFOLD v1.1.4.
Genome_build: GRCh38
Supplementary_files_format_and_content: *.read_cnt.txt: Tab-separated text files of counts.

source_name: day 5 progenitors derived small molecule inhibitors of Wnt signaling (GiWi) cardiac differentiation protocol

growth_protocol: iPSCs were differentiated to mesendoderm-derived progenitor cells following a chemically-defined, serum-free protocol modulating Wnt/β-catenin signaling (Lian et al., 2012). Briefly, iPSCs were seeded at a density of 3x10e4 cells/cm2 and fed with mTeSR1 medium until 100% confluency was reached (~3 days; termed differentiation day 0). At day 0, cells were fed with RPMI1640 medium with B27 Supplement Minus insulin (denoted as RPMI/B27-; Life Technologies) supplemented with 12μM CHIR-99021 (Selleckchem). Exactly 24h later, the medium was changed to fresh RPMI/B27-. On day 3, cells were fed with RPMI/B27- supplemented with 5μM IWP2 (Sellekchem) for 48h. On day 5, cells were dissociated.

extract_protocol:
Mesendoderm progenitor cells were dissociated at differentiation day 5 with Accutase and cell pellet lysed with Trizol (Ambion) and RNA was extracted using the Direct-zol Miniprep kit (ZymoResearch).
RNA-seq libraries were created using the SMARTer Stranded Total RNA Sample Prep Kit (Takara Bio).
Libraries were sequenced using NextSeq500/550 High Output v2.5 kit (spiked with 10% PhiX; Illumina) to a minimum depth of 29 million reads per sample.

value: iPSC-derived mesendoderm progenitors

tag: time point

value: Day 5


title: CD15s.Neg_1

city: Singapore

first: Kaibo

last: Duan

address: 8A Biomedical Grove, Immunos Building, Level 4

country: Singapore

institute: Singapore Immunology Network

description:
CD15s Neg Basophils from donor 1
readCounts_genes.txt
RHO1215

data_processing:
Paired-end reads were mapped to GRCm38 reference genome using STAR version 2.5.2b
Mapped paired-end reads were summarized to gene level using featureCounts v1.6.0 and with GENCODE GRCh38 v27 gene annotation
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes gene-level read counts for all samples

source_name: PBMC

extract_protocol:
Total RNA was isolated from CD15s enriched cells using ARCTURUS PicoPure RNA Isolation Kit (Applied Biosystems™ Thermo Fisher Scientific).
Reverse transcription and amplification were performed using Smart-seq2 method (Picelli et al., 2014). Briefly, cDNA was synthesized from 2 ng of purified total RNA using modified oligo(dT) primers along with array control RNA spikes (Ambion® Thermo Fisher Scientific). To generate sufficient quantities of cDNA for downstream library preparation steps, 13 cycles of PCR amplification were performed.  Pooled cDNA libraries were prepared (250 pg of cDNA per sample) using Nextera XT Kit (Illumina, San Diego, CA, USA) with dual indices for de-multiplexing. The libraries were quantified by qPCR (Kapa Biosystems) to ascertain the loading concentration. Samples were subjected to an indexed PE sequencing run of 2x151 cycles on an Illumina HiSeq 4000.

value: Basophils

tag: cell subset

value: CD15s Neg


title: H3K36me2_NSD1_KO2_rep1


title: Mint-ChIP-seq from endothelial cell (ENCLB797BVN)

city: Stanford

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR084ODZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR084ODZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB797BVN
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens male adult (53 years) endothelial in vitro differentiated cells, preserved by cryopreservation

tag: antibody

value: endothelial cell

value: in vitro differentiated cells

tag: description

value: PGP1 derived endothelial cells

tag: biosample encode accession

tag: Sex

value: male

tag: dev stage

value: adult

tag: age

value: 53 year

tag: lab

value: Bradley Bernstein, Broad

tag: source

value: George Church

tag: link

value: ENCBS239VAD at ENCODE; https://www.encodeproject.org/ENCBS239VAD/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: H3K36me2_NSD1_KO1_rep1

value: untreated


title: H3K27me3_NSD1_KO2_rep1

value: H3K27me3 (Cell Signaling Technology, Cat.# 9733)


title: progenitors (gut organoid) 1

tag: cell type


title: H3K27me3_NSD1_KO1_rep2


title: w_wing_H3K4me2_4_(20201229_KA_DmEc_1856_239)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: CUT&Tag for H3K47me2 in dissected wing imaginal discs from w1118 larvae

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to dm6 Drosophila melanogaster genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file dm6_fragments.bed.gz).  3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

organism: Drosophila melanogaster

source_name: CUT&Tag

extract_protocol:
cut-tag-with-drosophila-tissues-bnx5mfq6.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

value: H3K4me2 Epicypher cat#13-0027

tag: tissue

value: dissected wing imaginal discs


title: w_wing_RNAPIIS2p_2_(20210223_KA_DmEc_1914_wing)

description: CUT&Tag for RNAPIIS2p in dissected wing imaginal discs from w1118 larvae

value: RNAPIIS2p Cell Signalling Technology cat#13499


title: w_wing_RNAPIIS2p_1_(20210223_KA_DmEc_1736_wing)


title: w_wing_RNAPIIS2p_4_(20210223_KA_DmEc_1916_wing)


title: H3K27me3_NSD1_WT_rep2

tag: treatment

value: wild type


title: progenitors (cardiac microtissues) 2

value: iPSC-derived mesendoderm progenitors

value: Day 5


title: H3K27me3_NSD1_WT_rep1

tag: strain


title: H3K27me3_NSD1_KO2_rep2

tag: chip antibody


title: H3K36me2_NSD1_KO1_rep2

value: H3K36me2 (Cell Signaling Technology, Cat.# 2901)

tag: genotype


title: w_wing_RNAPIIS2p_3_(20210223_KA_DmEc_1915_wing)


title: w_wing_H3K4me2_5_(20201229_KA_DmEc_1857_239)


title: H3K27me3_NSD1_KO1_rep1


title: Mint-ChIP-seq from endothelial cell (ENCLB998VDM)

description:
https://www.encodeproject.org/experiments/ENCSR084ODZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human PGP1 derived endothelial cell
experiment encode accession: ENCSR084ODZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR759ZAX
encode release date: 2021-05-18
lab: Bradley Bernstein, Broad
library encode accession: ENCLB998VDM
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: endothelial cell

value: in vitro differentiated cells

value: PGP1 derived endothelial cells


title: w_wing_H3K27me3_5_(20201229_KA_DmEc_1851_187)

description: CUT&Tag for H3K27me3 in dissected wing imaginal discs from w1118 larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: progenitors (cardiac microtissues) 1

tag: time point


title: progenitors (multilineage organoid)


title: w_wing_H3K4me2_3_(20201229_KA_DmEc_1854_239)


title: H3K27ac_NSD1_WT_rep2

value: H3K27ac (Abcam, Cat.# ab4729)


title: H3K27ac_NSD1_WT_rep1


title: w_wing_H3K27me3_4_(20201229_KA_DmEc_1850_187)


title: Mint-ChIP-seq from immature natural killer cell (ENCLB560OMZ)

description:
https://www.encodeproject.org/experiments/ENCSR277YKG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR277YKG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB560OMZ
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens immature natural killer primary cell

value: immature natural killer cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

tag: health state

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: WT M9/rdm/glu stationary phase, ChIP replicate 3

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description:
wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
Surviving DNA reads with proper paired-end alignments were quantified using an in-house pipeline in which each read contributes a total signal of weight 1, divided over the length of the read. Further processing is described in detail in the accompanying paper
RNA reads were subject to quantitation using kallisto v0.43
Genome_build: E. coli U0006.3
Supplementary_files_format_and_content: Important: For all summary/processed files, note that we provide one file per experimental condition, which represents a consolidation of all replicates for that condition, as described in the accompanying manuscript.  Ipod_vs_inp.gr files – Raw IPOD occupancy traces prior to ChIP subtraction, given as a log_2 ratio of extracted to input. The .gr file extension refers to a simple graph type, where the first column indicates a genomic position and the second a corresponding signal    chip_vs_inp.gr files – RNA polymerase occupancy given as a log_2 ratio of extracted to input     V6rzlog10p.gr files – ChIP-subtracted IPODHR occupancy, z-scored and then used to calculate enrichment p values as described in the text    Abundance.tsv files – kallisto output giving (among other information) gene names and tpm estimates. See the kallisto documentation for details of the file format

organism: Escherichia coli

source_name: Cultured cells

growth_protocol: Cells were grown to early stationary phase (3 hours after reaching OD600=0.2) in M9/rdm/glu rich defined medium

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the digested lysates were mixed 1:1 with 2x IP buffer (200 mM Tris, pH 8.0; 600 mM NaCl; 4% Triton X-100; 2x Roche Complete EDTA-free protease inhibitors), and then kept on ice for no more than a few hours prior to antibody addition. We added 10 microliters of purified anti-E. Coli RNA polymerase antibody (Neoclone WP023), and incubated overnight with rocking at 4 C. Near the end of the incubation period, we resuspended an aliquot of 50 microliters of protein G dynabeads (Invitrogen) and equilibrated the protein G beads with 1x IP buffer lacking protease inhibitors. The bead aliquot was added to the antibody-lysate mixture, and then incubated 2 hours with rocking at 4o C. The bead-antibody-target complexes were subsequently subjected to the following series of washes, with 1 mL used per wash. All washes were at room temperature, and involved manual resuspension of the beads in the new wash buffer followed by immediate re-separation: 1x Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% Triton X-100; 1 mM EDTA); 1x Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1 mM EDTA);  1x Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 1 mM EDTA); 1x TE (10 mM Tris, pH 8.0; 1 mM EDTA). The antigens were subsequently eluted by adding 500 microliters of elution buffer (composition described above) and incubating 30 minutes at 65 C, with vigorous vortexing every 5-10 minutes, the protein G beads removed, and the remaining supernatant reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup

treatment_protocol: Cells were treated for 10 minutes with rifampicin, then crosslinked for 5 minutes with 1% formaldehyde, prior to quenching with excess glycine. The resulting pellets are washed with PBS and frozen

tag: condition

value: Stationary phase in M9/rdm/glu rich defined medium

value: WT


title: w_wing_H3K27me3_2_(20200624_KA_DmEc_1530_wing_187)

tag: antibody

value: dissected wing imaginal discs


title: WT M9/rdm/glu stationary phase, ChIP replicate 1


title: WT M9/rdm/glu stationary phase, RNA

description:
Ribosome-depleted RNA
wt_m9_rdm_glu_statphase_rna_abundance.tsv

extract_protocol:
Samples for RNA isolation were preserved immediately prior to rifampicin addition by dilution in a 5x excess of DNA/RNA Shield (Zymo); the RNA samples were then stored at -80o C until purification. RNA was isolated using a Zymo QuickRNA microprep kit following the manufacturer’s instructions, including the on-column DNase digestion. Purified RNA was quantified using RiboGreen (Invitrogen), and then ribosome-depleted using the Illumina RiboZero Gram-negative bacteria kit according to the manufacturer’s instructions, with the input RNA amount and all reaction volumes cut in half. Final recovery of the ribo-depleted RNA was accomplished using the modified Zymo spin column protocol present in the RiboZero documentation.
Epicentre ScriptSeq v2 prep kit

treatment_protocol: Cells were preserved using Qiagen RNAprotect bacterial reagent according to the manufacturer’s instructions


title: H3K27ac_NSD1_KO1_rep2

value: untreated


title: H3K27ac_NSD1_KO2_rep2


title: w_eye_only_H3K27me3_1_(20201229_KA_DmEc_1848_187)

description: CUT&Tag for H3K27me3 in dissected eye portions of eye-antennal imaginal discs from w1118 larvae


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB735JNC)

description:
https://www.encodeproject.org/experiments/ENCSR274VSS/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K27ac Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR274VSS
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR996DNY
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB735JNC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500,Illumina NextSeq 500

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD8-positive, alpha-beta memory T cell

tag: description

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

tag: biosample encode accession

value: ENCBS274KKV at ENCODE; https://www.encodeproject.org/ENCBS274KKV/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: Mint-ChIP-seq from immature natural killer cell (ENCLB105VBD)

description:
https://www.encodeproject.org/experiments/ENCSR277YKG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR277YKG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR050UUC
encode release date: 2020-09-02
lab: Bradley Bernstein, Broad
library encode accession: ENCLB105VBD
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

value: primary cell

tag: Sex

tag: dev stage


title: w_wing_H3K27me3_3_(20200817_KA_DmEc_1641_187)

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: w_eyeg_RNAPIIS2p_7_(20210223_KA_DmEc_1738_eye)

description: CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from w1118 larvae

value: RNAPIIS2p Cell Signalling Technology cat#13499

value: dissected eye imaginal discs


title: w_eye_only_H3K27me3_2_(20201229_KA_DmEc_1849_187)

value: dissected eye portions of eye-antennal imaginal discs


title: H3K27ac_NSD1_KO1_rep1

value: H3K27ac (Abcam, Cat.# ab4729)


title: H3K4me3_NSD1_WT_rep1

value: H3K4me3 (Abcam, Ca.t# ab8580)

value: wild type


title: WT M9/rdm/glu stationary phase, IPOD replicate 1

description:
wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
Illumina TruSeq Nano DNA prep kit, with spin column cleanups replaced with Zymo spin columns

value: Stationary phase in M9/rdm/glu rich defined medium


title: w_eye_RNAPIIS2p_5_(20210223_KA_DmEc_1912_eye)


title: w_eye_RNAPIIS2p_6_(20210223_KA_DmEc_1913_eye)


title: H3K4me3_NSD1_WT_rep2


title: WT M9/rdm/glu stationary phase, IPOD replicate 3

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup

value: WT


title: WT M9/min/glu, ChIP replicate 2

description:
wt_m9_min_glu_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
wt_m9_min_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

growth_protocol: Cells were grown to exponential phase (OD600=0.2) in M9/glu minimal medium

value: Exponential growth in M9/glu defined minimal medium


title: WT M9/min/glu, RNA

description:
Ribosome-depleted RNA
wt_m9_min_glu_rna_abundance.tsv


title: w_eye_RNAPIIS2p_4_(20210225_KA_DmEc_1911_eye)


title: H3K4me1_NSD1_WT_rep2

value: untreated

value: H3K4me1 (Abcam, Cat.# ab8895)


title: WT M9/min/glu, ChIP replicate 1


title: H3K27ac_NSD1_KO2_rep1


title: WT M9/rdm/glu stationary phase, input replicate 3

description: wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext DNA kit, but with a spin column replacing the first bead cleanup


title: w_eye_RNAPIIS2p_3_(20210223_KA_DmEc_1815_eye)


title: H3K4me1_NSD1_WT_rep1


title: WT M9/min/glu, Input replicate 2

description: wt_m9_min_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: ATAC_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: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB764CWD)

description:
https://www.encodeproject.org/experiments/ENCSR079JAG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR079JAG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB764CWD
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens CD4-positive, alpha-beta memory T primary cell, preserved by cryopreservation

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: not collected

value: healthy

value: unknown

tag: age

tag: lab

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS802GRA at ENCODE; https://www.encodeproject.org/ENCBS802GRA/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: ATAC_WT_rep1


title: w_eye_RNAPIIS2p_1_(20201015_KA_DmEc_1794_E1Z3G)

value: RNAPIIS2p Cell Signalling Technology cat#13499

value: dissected eye imaginal discs


title: ATAC_NSD1_KO2_rep2


title: w_eye_H3K4me2_9_(20201229_KA_DmEc_1861_239)

description: CUT&Tag for H3K4me2 in dissected eye imaginal discs from w1118 larvae

value: H3K4me2 Epicypher cat#13-0027


title: ATAC_NSD1_KO1_rep2


title: ATAC_NSD1_KO2_rep1


title: WT M9/min/glu, IPOD replicate 1

description:
wt_m9_min_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
wt_m9_min_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: WT M9/rdm/glu, chip replicate 4

description:
wt_m9_rdm_glu_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

growth_protocol: Cells were grown to exponential phase (OD600=0.2) in M9/rdm/glu rich defined medium

value: Exponential growth in M9/rdm/glu rich defined medium


title: WT M9/rdm/glu, RNA

description:
Ribosome-depleted RNA
wt_m9_rdm_glu_rna_abundance.tsv

value: WT


title: WT M9/min/glu, IPOD replicate 2

value: Exponential growth in M9/glu defined minimal medium


title: ATAC_NSD1_KO1_rep1

value: untreated


title: WT M9/rdm/glu, chip replicate 3


title: w_eye_H3K4me2_6_(20201229_KA_DmEc_1858_239)


title: w_eye_H3K4me2_7_(20201229_KA_DmEc_1859_239)


title: w_eye_H3K27me3_3_(20201229_KA_DmEc_1853_187)

description: CUT&Tag for H3K27me3 in dissected eye imaginal discs from w1118 larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: eyGAL_Vg_eye_RNAPIIS2p_5_(20210225_KA_DmEc_1910_V)

description: CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from eyGAL>Vg larvae

value: eyGAL>Vg


title: WT M9/rdm/glu, input replicate 4

description: wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: eyGAL_Vg_eye_RNAPIIS2p_4_(20210223_KA_DmEc_1909_V)


title: w_eye_RNAPIIS2p_2_(20210223_KA_DmEc_1814_eye)


title: eyGAL_Vg_eye_RNAPIIS2p_3_(20210223_KA_DmEc_1908_V)


title: WT M9/rdm/glu, IPOD replicate 4

description:
wt_m9_rdm_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: w_eye_H3K27me3_2_(20201229_KA_DmEc_1852_187)


title: Mint-ChIP-seq from naive B cell (ENCLB113ALK)

description:
https://www.encodeproject.org/experiments/ENCSR264HUZ/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR264HUZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB113ALK
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens naive B primary cell, preserved by cryopreservation

value: naive B cell

value: primary cell

value: B naive CD3- CD14- CD19+ CD27- IgD+

tag: source

tag: link

value: ENCBS644KFM at ENCODE; https://www.encodeproject.org/ENCBS644KFM/


title: Mint-ChIP-seq from naive B cell (ENCLB222NSV)

description:
https://www.encodeproject.org/experiments/ENCSR264HUZ/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human naive B cell
experiment encode accession: ENCSR264HUZ
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR499CKV
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB222NSV
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: not collected

value: healthy

value: unknown

value: Bradley Bernstein, Broad


title: eyGAL_Vg_eye_RNAPIIS2p_2_(20201005_KA_DmEc_1753_E1Z3G)

value: RNAPIIS2p Cell Signalling Technology cat#13499

tag: tissue


title: eyGAL_Vg_eye_H3K4me2_8_(20201229_KA_DmEc_1883_239)

description: CUT&Tag for H3K4me2 in dissected eye imaginal discs from eyGAL>Vg larvae

value: dissected eye imaginal discs


title: w_eye_H3K4me2_8_(20201229_KA_DmEc_1860_239)

value: H3K4me2 Epicypher cat#13-0027


title: eyGAL_Vg_eye_H3K4me2_7_(20201229_KA_DmEc_1882_239)


title: RNA-seq WIBR3 a5i/L/A [hESC.38wt_n3.r]

city: St Louis

first: Thorold

last: Theunissen

state: MO

address: 4515 McKinley Ave, Room 3313

department: Developmental Biology

institute: Washington Unversity School of Medicine

data_processing:
RNA-seq reads were aligned to the human genome hg38 with HISAT2 version 2.2.0 (ref: https://www.nature.com/articles/s41587-019-0201-4).
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount (Liao et al., 2013), version 1.4.6, with hg38 annotation gencodeV31 (Harrow et al., 2012).
All gene-level transcript counts were then imported into the R/Bioconductor package DESeq2 (Love et al., 2014).
Transcripts with CPM >1.0 were converted into a DESeq2 dataset and then regularized log transformed using the rlog function from the DESeq2 package.
Adjusted p-values for DGE were determined by DESeq2 using the R stats function p.adjust using the Benjamini and Hochberg correction to determine the false discovery rate with a 1.5- fold expression change and FDR < 0.05 required to consider a gene differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: counts per ENSEMBL gene as generated by FeatureCounts

source_name: Naïve hESC

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the SMARTer Directional cDNA Library Construction Kit
Libraries were sequenced on an Illumina HiSeq3000 1X50 platform

tag: cell type

value: Naive hESC

tag: culture condition

tag: passage


title: RNA-seq WIBR3 AXGYU [hESC.38wt_n7.r]

value: AXGYU


title: RNA-seq WIBR3 5i/L/A [hESC.38wt_n1.r]


title: eyGAL_Vg_eye_RNAPIIS2p_1_(20201005_KA_DmEc_1752_E1Z3G)

tag: genotype


title: eyGAL_Vg_eye_H3K4me2_6_(20201229_KA_DmEc_1881_239)


title: RNA-seq WIBR3 mTeSR1 [hESC.38wt_p.r]

source_name: Primed hESC

value: Primed hESC


title: RNA-seq H9 AXGYU [hESC.h9_n7.r]


title: eyGAL_Vg_eye_H3K4me2_5_(20201229_KA_DmEc_1880_239)


title: eyGAL_Vg_eye_H3K4me2_4_(20201229_KA_DmEc_1875_239)


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB998HAD)

description:
https://www.encodeproject.org/experiments/ENCSR176CXH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR176CXH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB998HAD
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: CD4-positive, alpha-beta memory T cell

value: CD4+ memory CD3+ CD4+ CD8- CD45RA- CD45RO+ nonTreg

value: David Hafler

value: ENCBS802GRA at ENCODE; https://www.encodeproject.org/ENCBS802GRA/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: MAIT_16h_K12_stim_E

city: Leipzig

first: Jana

last: Schor

state: Saxony

address: Permoserstr. 15

department: Molecular Systems Biology

country: Germany

institute: Helmholtz Centre for Environmental Research

data_processing:
For demultiplexing we used bcl2fastq (release 2.20), which is provided by Illumina.  Sequencing adapters were trimmed using the cutadapt (release 1.5) software, and subsequent quality control was performed using the fastqc program (release 0.11.2) and the fastx-toolkit (release 0.013). Reads were aligned to the human genome (UCSC Human Dec. 2013 GRCh38/hg38 Assembly) using the hisat2 mapping tool (release 2.1.0) and subsequently sorted by name and genomic location using samtools (release 1.1).
Fastq files were merged followed by a quality control with FastQC and a quality filter using the FASTQ Quality Filter of the FASTX-toolkit
Trim Galore was employed for adapter trimming
The reads were mapped to the human genome (GRCh38) with HISAT2
htseq_count was used to generate counts of reads that overlap annotated genes
Genome_build: UCSC Human Dec. 2013 GRCh38/hg38 Assembly
Supplementary_files_format_and_content: .txt number of reads that overlap gene

source_name: MAITcells

extract_protocol:
MAITcells were FACS-sorted based on their TCR Valpha7.2 and CD161 expression, yielding in a purity of >95%. Cells were lysed in 1 mL TRIzol (Thermo Fisher), RNA was isolated using miRNeasy Mini Kit (Qiagen) and Maxtract High Density tubes (Qiagen), residual DNA was removed using Ambion TURBO DNA-free Kit (Thermo Fisher) and RNA cleaned up by ethanol-precipitation.
The RNA integrity for each sample was controlled with the RNA 6000 Nano Assay and the Agilent 2100 Bioanalyzer (Agilent Technologies). 100ng total RNA was used for rRNA depletion. Ribosomal RNAs were removed from total RNA. A strand-specific library using the Ribo-Zero Gold H/M/R Magnetic Kit (Illumina, San Diego, CA, USA). A strand-specific library was prepared using the ScripSeqv2 Kit (Illumina), was checked by Agilent 2100 Bioanalyzer system with a High Sensitivity DNA Kit (Agilent). Library concentration was determined by Qubit 2.0 instrument using the Quant-iT dsDNA High Sensitivity kit (Thermo Fisher Scientific).  size selected in a range of 200-600 bp using preparative agarose gel in combination with MinElute Gel Extraction Kit (Qiagen).

treatment_protocol: K12 teatment: MAITcells were loaded with fixed E.coli for 3h, followed by intense washing in PBS to remove E.coli; CD3-28 treatment: MAITcells were stimulated with 50ng/ml IL-12 and 50ng/ml IL-18, 10µg/ml plate-bound anti-CD3 and 1µg/ml soluble anti-CD28 (both from Biolegend, CA, USA) or a combination of both for 16h

tag: time point


title: MAIT_16h_unstim_E

value: unstim


title: Mint-ChIP-seq from CD4-positive, alpha-beta memory T cell (ENCLB039SKT)

description:
https://www.encodeproject.org/experiments/ENCSR176CXH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me1 Mint-ChIP-seq on human CD4-positive, alpha-beta memory T cell
experiment encode accession: ENCSR176CXH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR917PCR
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB039SKT
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: primary cell

tag: health state


title: RNA-seq H9 AXGY [hESC.h9_n6.r]

value: AXGY


title: eyGAL_Vg_eye_H3K27me3_5_(20201229_KA_DmEc_1846_187)

description: CUT&Tag for H3K27me3 in dissected eye portions of eye-antennal imaginal discs from eyGAL>Vg larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: MAIT_0h_E

tag: condition


title: RNA-seq H9 5i/L/A [hESC.h9_n1.r]


title: RNA-seq WIBR3 AXGY [hESC.38wt_n6.r]


title: MAIT_16h_unstim_C


title: eyGAL_Pc_RNAi_eye_RNAPIIS2p_3_(20210318_KA_DmEc_1930_E1Z3G_2)

description: CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from eyGAL >Pc_RNAi larvae

tag: antibody


title: eyGAL_Pc_RNAi_eye_RNAPIIS2p_4_(20210318_KA_DmEc_1931_E1Z3G_2)


title: RNA-seq H9 mTeSR1 [hESC.h9_p.r]


title: MAIT_16h_K12_stim_C


title: MAIT_16h_CD3-28_stim_C


title: delta argR M9/rdm/glu stationary phase, ChIP replicate 1

description:
DargR_m9_rdm_glu_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
DargR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

value: Exponential growth in M9/rdm/glu rich defined medium

value: delta argR


title: eyGAL_Pc_RNAi_eye_RNAPIIS2p_2_(20210318_KA_DmEc_1929_E1Z3G_2)

value: RNAPIIS2p Cell Signalling Technology cat#13499


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB512VON)

description:
https://www.encodeproject.org/experiments/ENCSR169WAD/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR169WAD
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-09-05
lab: Bradley Bernstein, Broad
library encode accession: ENCLB512VON
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens immature natural killer primary cell with multiple sclerosis

value: immature natural killer cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: ENCBS911UEN at ENCODE; https://www.encodeproject.org/ENCBS911UEN/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: delta argR M9/rdm/glu stationary phase, Input replicate 2

description: DargR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: eyGAL_Pc_RNAi_eye_RNAPIIS2p_1_(20210318_KA_DmEc_1928_E1Z3G_2)

value: dissected eye imaginal discs


title: MAIT_0h_C


title: MAIT_16h_CD3-28_stim_E


title: eyGAL_Pc_RNAi_eye_H3K4me2_5_(20201229_KA_DmEc_1891)

description: CUT&Tag for H3K4me2 in dissected eye imaginal discs from eyGAL >Pc_RNAi larvae

value: H3K4me2 Epicypher cat#13-0027


title: RNA-seq H9 a5i/L/A [hESC.h9_n3.r]

value: Naive hESC


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB301JZD)

description:
https://www.encodeproject.org/experiments/ENCSR167XYG/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K9me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR167XYG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB301JZD
fragmentation methods: none

source_name: Homo sapiens CD14-positive monocyte primary cell with multiple sclerosis, preserved by cryopreservation

value: CD14-positive monocyte

value: primary cell

value: Monocyte CD3- CD14+ CD19-

tag: biosample encode accession

value: David Hafler

value: ENCBS080GJD at ENCODE; https://www.encodeproject.org/ENCBS080GJD/


title: eyGAL_Vg_eye_H3K4me2_3_(20201229_KA_DmEc_1874_239)


title: delta argR M9/rdm/glu stationary phase, Input replicate 1

value: Exponential growth in M9/rdm/glu rich defined medium

value: delta argR


title: delta argR M9/rdm/glu stationary phase, IPOD replicate 2

description:
DargR_m9_rdm_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
DargR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: MAIT_16h_CD3-28_stim_B


title: delta argR M9/rdm/glu stationary phase, ChIP replicate 2


title: MAIT_16h_K12_stim_B


title: eyGAL_Pc_RNAi_eye_H3K4me2_2_(20201229_KA_DmEc_1888)


title: delta argR M9/rdm/glu stationary phase, IPOD replicate 1


title: MAIT_0h_B


title: eyGAL_Pc_RNAi_eye_H3K4me2_4_(20201229_KA_DmEc_1890)


title: eyGAL_Pc_RNAi_eye_H3K4me2_1_(20201229_KA_DmEc_1884)


title: delta purR M9/rdm/glu stationary phase, ChIP replicate 2

description:
DpurR_m9_rdm_glu_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
DpurR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

value: delta purR


title: eyGAL_Pc_RNAi_eye_H3K4me2_3_(20201229_KA_DmEc_1889)


title: delta purR M9/rdm/glu stationary phase, ChIP replicate 1


title: delta purR M9/rdm/glu stationary phase, Input replicate 2

description: DpurR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: MAIT_16h_unstim_B

value: unstim


title: Mint-ChIP-seq from GM23338 (ENCLB363YUG)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 2
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB363YUG
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

source_name: Homo sapiens GM23338 cell line

tag: line

value: cell line

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%

tag: Sex

value: male

value: adult

value: 53 year

value: Paola Arlotta

value: ENCBS299FWQ at ENCODE; https://www.encodeproject.org/ENCBS299FWQ/

value: Derived from ENCODE donor ENCDO336AAA; https://www.encodeproject.org/ENCDO336AAA/


title: Mint-ChIP-seq from CD14-positive monocyte (ENCLB454CKA)

description:
https://www.encodeproject.org/experiments/ENCSR167XYG/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K9me3 Mint-ChIP-seq on human CD14-positive monocyte
experiment encode accession: ENCSR167XYG
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR509FRR
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB454CKA
fragmentation methods: none

value: CD14-positive monocyte

value: not collected

value: multiple sclerosis

tag: dev stage

value: unknown

tag: age

value: Bradley Bernstein, Broad

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: delta purR M9/rdm/glu stationary phase, Input replicate 1

value: Exponential growth in M9/rdm/glu rich defined medium


title: Mint-ChIP-seq from GM23338 (ENCLB636GRH)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 3
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB636GRH
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

tag: lab

tag: source

value: ENCBS695QJS at ENCODE; https://www.encodeproject.org/ENCBS695QJS/


title: delta purR M9/rdm/glu stationary phase, IPOD replicate 2

description:
DpurR_m9_rdm_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
DpurR_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

value: delta purR


title: delta purR M9/rdm/glu stationary phase, IPOD replicate 1


title: Mint-ChIP-seq from GM23338 (ENCLB140AJD)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 3
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB140AJD
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: cell line

tag: link


title: Mint-ChIP-seq from GM23338 (ENCLB655XNC)

description:
https://www.encodeproject.org/experiments/ENCSR068ZVD/
***************
biological replicate number: 2
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human GM23338
experiment encode accession: ENCSR068ZVD
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR787HYA
encode release date: 2021-05-24
lab: Bradley Bernstein, Broad
library encode accession: ENCLB655XNC
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina NextSeq 500

value: PGP-1 iPSCs provided by the George Church lab at HMS. purity 100%


title: WT M9/min/glu, Input replicate 1

description: wt_m9_min_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

value: Exponential growth in M9/glu defined minimal medium

value: WT


title: MAIT_0h_A


title: eyGAL_Pc_RNAi_eye_H3K27me3_2_(20201229_KA_DmEc_1886)

description: CUT&Tag for H3K27me3 in dissected eye imaginal discs from eyGAL >Pc_RNAi larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14

tag: tissue

value: dissected eye imaginal discs


title: WT M9/rdm/glu, chip replicate 2

description:
wt_m9_rdm_glu_merged_truseqnano_nebnext_chip_vs_inp_lograt.gr
wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: eyGAL_Pc_RNAi_eye_H3K27me3_3_(20201229_KA_DmEc_1887)


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_4_(20210310_KA_DmEc_1905_M)

description: CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from eyGAL>H3.3K27M larvae

value: RNAPIIS2p Cell Signalling Technology cat#13499


title: WGS from whole organism (ENCLB984NXZ)

description:
https://www.encodeproject.org/experiments/ENCSR971VTI/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR971VTI
assay title: WGS
encode release date: 2018-01-22
lab: Andrew Z. Fire, Stanford
library encode accession: ENCLB984NXZ

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans strain glp-1 (glp-1(e2141ts)) adult using egg bleaching whole organism

extract_protocol: not provided

value: whole organism

value: whole organisms

value: Synchronized adults without germline

value: adult

value: Andrew Z. Fire, Stanford

value: CGC

tag: worm synchronization stage

value: egg bleaching

value: ENCBS001KNW at ENCODE; https://www.encodeproject.org/ENCBS001KNW/

value: Derived from ENCODE donor ENCDO744ZAW; https://www.encodeproject.org/ENCDO744ZAW/


title: eyGAL_Pc_RNAi_eye_H3K27me3_1_(20201229_KA_DmEc_1885)


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_6_(20210223_KA_DmEc_1907_M)


title: WT M9/rdm/glu, chip replicate 1

value: Exponential growth in M9/rdm/glu rich defined medium


title: WT M9/rdm/glu, input replicate 3

description: wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
Illumina TruSeq Nano DNA prep kit, with spin column cleanups replaced with Zymo spin columns


title: WGS from whole organism (ENCLB502LDS)

description:
https://www.encodeproject.org/experiments/ENCSR075IPW/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR075IPW
assay title: WGS
encode release date: 2018-01-22
lab: Andrew Z. Fire, Stanford
library encode accession: ENCLB502LDS

source_name: Caenorhabditis elegans strain VC2010 (WT) L1 larva whole organism

value: not collected

value: L1 larva

value: Andrew Z. Fire

value: ENCBS676FZP at ENCODE; https://www.encodeproject.org/ENCBS676FZP/

value: Derived from ENCODE donor ENCDO575LPL; https://www.encodeproject.org/ENCDO575LPL/


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_5_(20210129_KA_DmEc_1906_E1Z3G)

value: dissected eye imaginal discs


title: WT M9/rdm/glu, input replicate 2

value: WT


title: WT M9/rdm/glu stationary phase, inputreplicate 1

description: wt_m9_rdm_glu_statphase_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr

value: Stationary phase in M9/rdm/glu rich defined medium


title: WT M9/rdm/glu, input replicate 1


title: WT M9/rdm/glu, IPOD replicate 3

description:
wt_m9_rdm_glu_merged_truseqnano_nebnext_ipod_vs_inp_lograt.gr
wt_m9_rdm_glu_merged_truseqnano_nebnext_v6rzlog10p_chipsub.gr


title: MAIT_16h_CD3-28_stim_A


title: MAIT_16h_unstim_D

value: unstim


title: MAIT_16h_K12_stim_D


title: MAIT_0h_D


title: MAIT_16h_CD3-28_stim_D


title: MAIT_16h_unstim_A


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_2_(20210223_KA_DmEc_1779_M)

value: RNAPIIS2p Cell Signalling Technology cat#13499


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_1_(20210223_KA_DmEc_1778_M)


title: WGS from whole organism (ENCLB949QEF)

description:
https://www.encodeproject.org/experiments/ENCSR619ZIZ/
***************
biological replicate number: 1
technical replicate number: 1
description:
experiment encode accession: ENCSR619ZIZ
assay title: WGS
encode release date: 2018-01-22
lab: Andrew Z. Fire, Stanford
library encode accession: ENCLB949QEF

source_name: Caenorhabditis elegans strain VC2010 (WT) mixed stage (embryo) whole organism

value: whole organism

value: whole organisms

value: mixed stage (embryonic)

value: ENCBS693KEK at ENCODE; https://www.encodeproject.org/ENCBS693KEK/


title: eyGAL_H3.3K27M_eye_H3K4me2_8_(20201229_KA_DmEc_1867_239)

description: CUT&Tag for H3K4me2 in dissected eye imaginal discs from eyGAL>H3.3K27M larvae

value: H3K4me2 Epicypher cat#13-0027


title: eyGAL_H3.3K27M_eye_H3K4me2_5_(20201229_KA_DmEc_1864_239)


title: eyGAL_H3.3K27M_eye_RNAPIIS2p_3_(20210310_KA_DmEc_1904_M)


title: eyGAL_H3.3K27M_eye_H3K4me2_6_(20201229_KA_DmEc_1865_239)


title: eyGAL_H3.3K27M_eye_H3K4me2_3_(20201229_KA_DmEc_1862_239)


title: eyGAL_H3.3K27M_eye_H3K4me2_4_(20201229_KA_DmEc_1863_239)


title: eyGAL_H3.3K27M_eye_H3K27me3_6_(20201229_KA_DmEc_1845_187)

description: CUT&Tag for H3K27me3 in dissected eye portions of imaginal discs from eyGAL>H3.3K27M larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: WT M9/rdm/glu, no rifampicin, replicate 2, ChIP

description:
norif_m9_rdm_glu_v6rzlog10p_chipsub.gr
norif_m9_rdm_glu_chip_vs_inp_lograt.gr

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the digested lysates were mixed 1:1 with 2x IP buffer (200 mM Tris, pH 8.0; 600 mM NaCl; 4% Triton X-100; 2x Roche Complete EDTA-free protease inhibitors), and then kept on ice for no more than a few hours prior to antibody addition. We added 10 microliters of purified anti-E. Coli RNA polymerase antibody (Neoclone WP023), and incubated overnight with rocking at 4 C. Near the end of the incubation period, we resuspended an aliquot of 50 microliters of protein G dynabeads (Invitrogen) and equilibrated the protein G beads with 1x IP buffer lacking protease inhibitors. The bead aliquot was added to the antibody-lysate mixture, and then incubated 2 hours with rocking at 4o C. The bead-antibody-target complexes were subsequently subjected to the following series of washes, with 1 mL used per wash. All washes were at room temperature, and involved manual resuspension of the beads in the new wash buffer followed by immediate re-separation: 1x Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% Triton X-100; 1 mM EDTA); 1x Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1 mM EDTA);  1x Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 1 mM EDTA); 1x TE (10 mM Tris, pH 8.0; 1 mM EDTA). The antigens were subsequently eluted by adding 500 microliters of elution buffer (composition described above) and incubating 30 minutes at 65 C, with vigorous vortexing every 5-10 minutes, the protein G beads removed, and the remaining supernatant reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup

treatment_protocol: Cells were crosslinked for 5 minutes with 1% formaldehyde, prior to quenching with excess glycine. The resulting pellets are washed with PBS and frozen

value: Exponential growth in M9/rdm/glu rich defined medium


title: MAIT_16h_K12_stim_A


title: WT M9/rdm/glu, no rifampicin, replicate 1, ChIP

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the digested lysates were mixed 1:1 with 2x IP buffer (200 mM Tris, pH 8.0; 600 mM NaCl; 4% Triton X-100; 2x Roche Complete EDTA-free protease inhibitors), and then kept on ice for no more than a few hours prior to antibody addition. We added 10 microliters of purified anti-E. Coli RNA polymerase antibody ( ), and incubated overnight with rocking at 4 C. Near the end of the incubation period, we resuspended an aliquot of 50 microliters of protein G dynabeads (Invitrogen) and equilibrated the protein G beads with 1x IP buffer lacking protease inhibitors. The bead aliquot was added to the antibody-lysate mixture, and then incubated 2 hours with rocking at 4o C. The bead-antibody-target complexes were subsequently subjected to the following series of washes, with 1 mL used per wash. All washes were at room temperature, and involved manual resuspension of the beads in the new wash buffer followed by immediate re-separation: 1x Wash buffer A (100 mM Tris, pH 8.0; 250 mM LiCl; 2% Triton X-100; 1 mM EDTA); 1x Wash buffer B (100 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 0.1% sodium deoxycholate; 1 mM EDTA);  1x Wash buffer C (10 mM Tris, pH 8.0; 500 mM NaCl; 1% Triton X-100; 1 mM EDTA); 1x TE (10 mM Tris, pH 8.0; 1 mM EDTA). The antigens were subsequently eluted by adding 500 microliters of elution buffer (composition described above) and incubating 30 minutes at 65 C, with vigorous vortexing every 5-10 minutes, the protein G beads removed, and the remaining supernatant reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup


title: eyGAL_H3.3K27M_eye_H3K27me3_5_(20201229_KA_DmEc_1844_187)

value: dissected eye portions of imaginal discs


title: WT M9/rdm/glu, no rifampicin, replicate 2, input

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, a 50 microliter input sample was diluted 1:9 in elution buffer (50 mM Tris, pH 8.0; 10 mM EDTA; 1% SDS) and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50o C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup


title: eyGAL_H3.3K27M_Vg_eye_RNAPIIS2p_5_(20210223_KA_DmEc_1917_MV)

description: CUT&Tag for RNAPIIS2p in dissected eye imaginal discs from eyGAL >H3.3K27M >Vg larvae


title: WT M9/rdm/glu, no rifampicin, replicate 1, input


title: WT M9/rdm/glu, no rifampicin, replicate 1, IPOD

description:
norif_m9_rdm_glu_v6rzlog10p_chipsub.gr
norif_m9_rdm_glu_ipod_vs_inp_lograt.gr

extract_protocol:
Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA.
NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup


title: TTseq.b0112

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description:
nuclear RNA nascent
TTseq.read_count.txt

data_processing:
Library strategy: TT-seq
RNA-Seq data were aligned against reference genome (dm3) using STAR (v2.3.0e) with default parameters and maximum fragment size of 2kb ("--alignMatesGapMax 2000"). The resulting files were filtered for concordant, primary alignments using SAMtools (v1.1). The enrichment of different genomic regions were analyzed using RSeQC (v3.0.1). Reads were assigned to RefSeq genes using featureCounts (v1.6.2) and differential expression between groups were analyzed using DESeq2.
TT-seq data were pre-processed in similar ways as RNA-seq. Visualization tracks were also generated in the same way. When assigning reads to RefSeq genes, we included the whole gene body instead of only coding regions. Differential expression between groups were analyzed again using DESeq2.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: Tab-delimited text files include raw read counts for each sample.

source_name: S2 cells

growth_protocol: S2 cells were grown in Schneider’s medium supplemented with 10% heat-inactivated fetal bovine serum and antibiotics.

extract_protocol:
Total RNA was isolated using TRIzol (Ambion) from S2 cell pellets vortexed for 30 min, extracted with ethanol precipitation, and subsequently purified with PureLink RNA Kit columns (Invitrogen).
TT-seq libraries were constructed using the dUTP method (Parkhomchuk et al., 2009).

treatment_protocol: Cells were treated with corresponding dsRNA to induce RNAi for 120 hours.

tag: cell line

tag: genotype/variation

value: dsMOF


title: TTseq.b0109

value: dsWhite


title: eyGAL_H3.3K27M_Vg_eye_RNAPIIS2p_4_(20210310_KA_DmEc_1903_MV)

tag: genotype


title: eyGAL_H3.3K27M_Vg_eye_RNAPIIS2p_2_(20210223_KA_DmEc_1771_MV)


title: eyGAL_H3.3K27M_Vg_eye_RNAPIIS2p_3_(20210310_KA_DmEc_1902_MV)


title: TTseq.b0108


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_7_(20201229_KA_DmEc_1872_239)

description: CUT&Tag for H3K4me2 in dissected eye portions of eye-antennal imaginal discs from eyGAL >H3.3K27M >Vg larvae


title: WT M9/rdm/glu, no rifampicin, replicate 2, IPOD


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_6_(20201229_KA_DmEc_1871_239)

value: dissected eye portions of eye-antennal imaginal discs


title: TTseq.b0107

value: dsMtor


title: eyGAL_H3.3K27M_Vg_eye_RNAPIIS2p_1_(20210223_KA_DmEc_1770_MV)

value: dissected eye imaginal discs


title: TTseq.b0105


title: mMB_YZ2_B3

type: RNA

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from tumor specimens was isolated after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany), using TRIzol (Invitrogen, Carlsbad, USA) and subsequent purification with a RNeasy Mini Spin Column (Qiagen, Hilden, Germany). Integrity and quantitation of total extracted RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Wilmington, DE, USA).

treatment_protocol: Tumor samples were snap frozen upon resection and stored at -80 oC until DNA extraction. Tumor content was assessed from equivalent material fixed in formalin and used for histological diagnosis (all samples contained ≥70% tumor cells).

value: glioma

tag: p53 status

tag: genetic specifics

value: hGFAP-Cre::p53-/-; Rictor+/-


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_4_(20201229_KA_DmEc_1869_239)

tag: antibody


title: mMBc_YZ_D4_b

value: normal brain

value: hGFAP-Cre::p53-/-; Pten+/-


title: TTseq.b0104


title: mMBc_YZ_D1_b


title: mMBc_YZ_G3_b

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor-/-


title: Mint-ChIP-seq from immature natural killer cell (ENCLB571JEV)

description:
https://www.encodeproject.org/experiments/ENCSR056GJY/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR056GJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB571JEV
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

value: primary cell

tag: description

value: supplied by Hafler lab as part of Encode4 project starting July2017

value: not collected

tag: health state

value: healthy

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS497KWS at ENCODE; https://www.encodeproject.org/ENCBS497KWS/

value: Derived from ENCODE donor ENCDO922TOC; https://www.encodeproject.org/ENCDO922TOC/


title: mMB_YZ_D1

value: medulloblastoma


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_3_(20201229_KA_DmEc_1868_239)

value: H3K4me2 Epicypher cat#13-0027

value: dissected eye portions of eye-antennal imaginal discs


title: mMBc_YZ_E1_b

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor+/-


title: mMBc_YZ_F3_b

value: normal brain

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor+/fl


title: mMB_YZ_E1


title: mMB_YZ_F3


title: mMB_YZ_E3


title: eyGAL_H3.3K27M_Vg_eye_H3K27me3_5_(20201229_KA_DmEc_1843_187)

description: CUT&Tag for H3K27me3 in dissected eye imaginal discs from eyGAL>H3.3K27M>Vg larvae

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14

value: dissected eye imaginal discs


title: TTseq.b0103

value: dsMtor


title: mMB_YZ_G3

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor-/-


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_5_(20201229_KA_DmEc_1870_239)


title: mMB_YZ_D4

value: hGFAP-Cre::p53-/-; Pten+/-


title: mMB_YZ_A5


title: Mint-ChIP-seq from immature natural killer cell (ENCLB985DOA)

description:
https://www.encodeproject.org/experiments/ENCSR056GJY/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K36me3 Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR056GJY
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR314IFB
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB985DOA
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

value: primary cell

value: supplied by Hafler lab as part of Encode4 project starting July2017

tag: biosample encode accession

value: not collected

value: healthy


title: WT M9/rdm/glu, IPOD replicate 1

tag: condition

value: Exponential growth in M9/rdm/glu rich defined medium

value: WT


title: mMBc_YZ_G4_b


title: TTseq.b0101

value: dsWhite


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB535TRC)

description:
https://www.encodeproject.org/experiments/ENCSR050UUC/
***************
biological replicate number: 1
technical replicate number: 1
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR050UUC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB535TRC
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

tag: Sex

tag: dev stage

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS620QTW at ENCODE; https://www.encodeproject.org/ENCBS620QTW/

value: Derived from ENCODE donor ENCDO976NED; https://www.encodeproject.org/ENCDO976NED/


title: eyGAL_H3.3K27M_Vg_eye_H3K27me3_4_(20201229_KA_DmEc_1842_187)

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14

value: dissected eye imaginal discs


title: Iso_Short_3_S3_R1_001

city: New York

first: Wanhe

last: Li

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
bcl2fastq v2.20 was used for basecalling.
STAR v2.4.2a was used for alignment.
featureCounts was used for generate counts matrix.
Genome_build: FlyBase release 6.13 (May 2016)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each aligned gene for each sample

source_name: whole head

extract_protocol:
Total RNA was extracted using TRIzol reagents and homogenized using a BeadBug microtube homogenizer (Benchmark Scientific). Samples were further extracted using chloroform and the aqueous phase containing nucleic acid was acquired by the assistance of Phase Lock Gel, Heavy (QuantaBio). RNeasy Mini Kit (Qiagen) was then used to remove DNA with DNase and further purify the samples, following the manufacturer's protocol.
Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA LT kit

tag: treatment

value: isolation

tag: treatment days

value: wild type Canton-S w1118 (iso1CJ)


title: Control Mint-ChIP-seq from immature natural killer cell (ENCLB177TNM)

description:
https://www.encodeproject.org/experiments/ENCSR050UUC/
***************
biological replicate number: 1
technical replicate number: 2
description: Control Mint-ChIP-seq on human immature natural killer cell
experiment encode accession: ENCSR050UUC
assay title: Control Mint-ChIP-seq
assembly: GRCh38
encode release date: 2020-08-04
lab: Bradley Bernstein, Broad
library encode accession: ENCLB177TNM
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

value: immature natural killer cell

tag: age

tag: lab

tag: source

tag: link


title: Iso_Short_2_S2_R1_001


title: Iso_Short_1_S1_R1_001


title: Iso_Long_3_S9_R1_001


title: Iso_Long_2_S8_R1_001


title: Iso_Long_1_S7_R1_001


title: w_eye_H3K4me2_4_(20201026_KA_DmEc_1812_239)

description: CUT&Tag

data_processing:
Genome_build: UCSC dm6
1. We used Bowtie2 2.4.1 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to dm6 Drosophila melanogaster genomic sequence obtained from UCSC. 2. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> <strand> (Supplementary file dm6_fragments.bed.gz). 3. We used bedtools genomecov to make normalized count bedgraph files, which are the fraction of counts at each base pair scaled by the size of the reference sequence (137567484) so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).

source_name: CUT&Tag for H3K4me2 in 6 dissected eye imaginal discs from w larvae

extract_protocol:
cut-tag-with-drosophila-tissues-bnx5mfq6.pdf
CUT&Tag uses tagmentation in which the barcoded adapters are integrated on both sides of the insert, so that the DNA that is released is already a barcoded library. PMID:31036827

tag: tissue

value: 6 dissected eye imaginal discs

value: H3K4me2 Epicypher cat#13-0027

value: w


title: w_wing_H3K27me3_1_(20201005_KA_DmEc_1732_187)

description: CUT&Tag

source_name: CUT&Tag for H3K27me3 in 4 dissected wing imaginal discs from w larvae

value: 4 dissected wing imaginal discs

tag: genotype


title: w_eye_H3K4me2_5_(20201026_KA_DmEc_1813_239)

description: CUT&Tag


title: w_eye_H3K4me2_3_(20201015_KA_DmEc_1797_239)

description: CUT&Tag


title: w_eye_H3K4me2_2_(20201015_KA_DmEc_1796_239)

description: CUT&Tag


title: Group_Long_3_S6_R1_001

value: group


title: w_wing_H3K4me2_2_(20201026_KA_DmEc_1809_239)

description: CUT&Tag

source_name: CUT&Tag for H3K4me2 in 4 dissected wing imaginal discs from eyGAL>Vg larvae


title: w_wing_H3K4me2_1_(20201026_KA_DmEc_1808_239)

description: CUT&Tag


title: Group_Long_2_S5_R1_001


title: mMB_YZ_E2

value: medulloblastoma

tag: p53 status

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor+/-


title: mMBc_YZ_D2_b

value: normal brain

tag: genetic specifics

value: hGFAP-Cre::p53-/-; Pten+/-


title: mMBc_YZ_F2_b

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor+/fl


title: mMBc_YZ_C5_b

value: hGFAP-Cre::p53-/-; Rictor-/-


title: Group_Long_1_S4_R1_001


title: eyGAL_Vg_eye_H3K4me2_2_(20201005_KA_DmEc_1751_239)

description: CUT&Tag

source_name: CUT&Tag for H3K4me2 in 6 dissected eye imaginal discs from eyGAL>Vg larvae

tag: antibody

value: eyGAL>Vg


title: mMB_YZ_G4

value: hGFAP-Cre::p53-/-; Pten+/-; Rictor-/-


title: mMBc_YZ_E2_b


title: mMB_YZ_G1


title: mMBc_YZ_G1_b


title: eyGAL_H3.3K27M_eye_H3K4me2_7_(20201229_KA_DmEc_1866_239)

source_name: CUT&Tag

value: dissected eye imaginal discs


title: mMBc_YZ_C3_b


title: w_eye_H3K4me2_1_(20201005_KA_DmEc_1734_239)

description: CUT&Tag


title: w_eye_H3K27me3_1_(20200624_KA_DmEc_1534_eye_187)

description: CUT&Tag

source_name: CUT&Tag for H3K27me3 in 6 dissected eye-antennal imaginal discs from w larvae

value: 6 dissected eye-antennal imaginal discs

value: H3K27me3 Cell Signalling Technology cat#9733 lot# 14


title: mMB_YZ_C4


title: eyGAL_Vg_eye_H3K4me2_1_(20201005_KA_DmEc_1750_239)

description: CUT&Tag


title: eyGAL_Vg_eye_H3K27me3_3_(20201027_KA_DmEc_1830_187)

description: CUT&Tag

source_name: CUT&Tag for H3K27me3 in 8 dissected eye portions of eye-antennal imaginal discs from eyGAL >Vg larvae


title: eyGAL_Vg_eye_H3K27me3_4_(20201027_KA_DmEc_1831_187)

description: CUT&Tag

value: 8 dissected eye portions of eye-antennal imaginal discs


title: eyGAL_Vg_eye_H3K27me3_2_(20201026_KA_DmEc_1805_187)

description: CUT&Tag


title: CUT&Tag_Crotonate-IgG

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
Library strategy: CUT&Tag
Genome_build: GRCm38
CUT&Tag reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v.2.4.1) with parameters “--mm --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”. Samtools (v1.10) was then used to convert files to bam format and filter reads mapped with parameters “-F 1804 -q 30”. After removing PCR duplicates using Mark Duplicates function in Picard (v2.22.0) and mitochondrial reads. MACS2 (v2.2.7.1) was used to call peaks with parameters “-g mm -q 0.05 -f BAMPE” relative to IgG samples.

source_name: E13.5 Forebrain

growth_protocol: NSPCs isolated from the E13.5 mice forebrain were cultured with DMEM/F12 medium (Invitrogen) supplemented with 20 ng/ml epidermal growth factor and 20 ng/ml fibroblast growth factor (EGF/FGF, PeproTech), 1% penicillin/streptomycin (Invitrogen), 0.5× B27 (Invitrogen), and 0.5× N2 (Invitrogen).

extract_protocol:
CUT&Tag assays were performed according the instructions of HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (TD-901, Vazyme). Briefly, 1 × 105 NSPCs were washed with 500 μl Wash Buffer and entrifuged at 600 × g for 3 min at room temperature and then resuspend in 100 μL 1 × Wash Buffer. ConA beads were washed twice with Binding Buffer. Next, 10 μL of washed ConA beads were added into NSPCs and incubated at room temperature with slow rotation for 10 min. Bead-bound NSPCs were resuspended in 50 μL of Antibody Buffer. Then, 1 μg of primary antibody (H3K4me3 or H3K27me3) or normal rabbit IgG was added and incubated at room temperature with slow rotation for 2 h. The primary antibody was removed using a magnet stand. The secondary antibody (0.5 μL) (Goat anti-Rabbit IgG H&L (ab6702, abcam)) was diluted in 50 μL of Dig-wash Buffer and NSPCs were incubated at room temperature with slow rotation for 1 h. NSPCs were washed three times with Dig-wash Buffer to remove unbound antibodies. Next, NSPC were incubated with 0.44 μM The Hyperactive pG-Tn5 Transposon diluted in 100 uL Dig-300 Buffer at room temperature with slow rotation for 1 h, and subsequently washed three times with Dig-300 Buffer. NSPCs were then resuspended in 300 μl of Tagmentation Buffer at 37 °C without rotation for 1 h. To terminate tagmentation, 10 μL of 0.5 M EDTA, 3 μL of 10% SDS and 2.5 μL of 20 mg/mL Proteinase K were added to 300 μl of sample and incubated overnight at 50 °C without rotation. DNA was purified using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation. 1 × cOmpleteTM, EDTA-free Protease Inhibitor Cocktail (04693132001, Roche) was pre-added in all buffers mentioned above.
For library amplification, 24 μL of DNA was mixed with 1 μL of TAE of HyperactiveTM In-Situ ChIP Library Prep Kit for Illumina (TD-901, Vazyme), 10 μL of 5 × TAB and 5 μL of ddH2O, as well as 5 μL of uniquely barcoded i5 and i7 primers from TruePrep® Index Kit V2 for Illumina (TD-202, Vazyme). A total volume of 50 μL of sample was placed in a Thermocycler using the following program: 72 °C for 3 min; 98 °C for 30 s; 16 cycles of 98 °C for 15 s, 60 °C for 30 s and 72 °C for 30 s; 72 °C for 5 min and hold at 4 °C. To purify the PCR products, 1.2× volumes of VAHTS® DNA Clean Beads (N411, Vazyme) were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 22 μL of ddH2O, and were sequenced on an Illumina NovaSeq 6000 platform and 150-bp paired-end reads were generated.

treatment_protocol: Briefly, NSPCs (passage 2–3) were grown to 50–60% confluence in 10-cm plates, and were treated with water (control group) and 10 mM crotonate (crotonate group) for 24 h.

tag: cell type

value: Embryonic Neural Stem/Progenitor Cells (eNSPCs)

value: Crotonate

tag: chip antibody

value: IgG (Cell Signaling Technology, 2729S, 9)


title: mMB_YZ_C1


title: CUT&Tag_Crotonate-H3K27me3


title: eyGAL_Vg_eye_H3K27me3_1_(20201026_KA_DmEc_1804_187)

description: CUT&Tag


title: mMB_YZ_C3

value: glioma


title: CUT&Tag_Crotonate-H3K4me3


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_2_(20201015_KA_DmEc_1775_239)

description: CUT&Tag

source_name: CUT&Tag for H3K4me2 in 6 dissected eye imaginal discs from eyGAL>H3.3K27M>Vg larvae

value: 6 dissected eye imaginal discs

value: H3K4me2 Epicypher cat#13-0027


title: eyGAL_H3.3K27M_Vg_eye_H3K4me2_1_(20201015_KA_DmEc_1774_239)

description: CUT&Tag


title: CUT&Tag_Control-IgG

value: Control


title: mMBc_YZ_B2_b

value: normal brain

value: hGFAP-Cre::p53-/-; Rictor+/-


title: mMBc_YZ_B1_b


title: mMB_YZ_C5

value: medulloblastoma


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB152HBM)

description:
https://www.encodeproject.org/experiments/ENCSR231ZZH/
***************
biological replicate number: 1
technical replicate number: 1
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR231ZZH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR019FIH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB152HBM
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

source_name: Homo sapiens CD8-positive, alpha-beta memory T primary cell with multiple sclerosis, preserved by cryopreservation

value: CD8-positive, alpha-beta memory T cell

value: primary cell

tag: description

value: CD8+ memory CD3+ CD4- CD8+ CD45RA- CD45RO+

tag: biosample encode accession

value: not collected

tag: health state

value: multiple sclerosis

value: unknown

value: Bradley Bernstein, Broad

value: David Hafler

value: ENCBS229YZM at ENCODE; https://www.encodeproject.org/ENCBS229YZM/

value: Derived from ENCODE donor ENCDO187BUH; https://www.encodeproject.org/ENCDO187BUH/


title: mMBc_YZ_B4_b


title: mMB_YZ_B1

value: glioma


title: mMB_YZ_A6


title: mMB_YZ_B2


title: CUT&Tag_Control-H3K27me3

value: Embryonic Neural Stem/Progenitor Cells (eNSPCs)


title: Mint-ChIP-seq from CD8-positive, alpha-beta memory T cell (ENCLB417PAI)

description:
https://www.encodeproject.org/experiments/ENCSR231ZZH/
***************
biological replicate number: 1
technical replicate number: 2
description: H3K4me3 Mint-ChIP-seq on human CD8-positive, alpha-beta memory T cell
experiment encode accession: ENCSR231ZZH
assay title: Mint-ChIP-seq
assembly: GRCh38
possible controls: ENCSR019FIH
encode release date: 2020-09-06
lab: Bradley Bernstein, Broad
library encode accession: ENCLB417PAI
fragmentation methods: none
instrument models: Illumina NovaSeq 6000,Illumina HiSeq 2500

tag: Sex

tag: dev stage