title: siZC3H4 Replicate 3

description: Library name: Sample 11

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 50 bp per mate and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the dm6 version of the Drosophila genome using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mouse (mm10) using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.  Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.
DMSO and dTAG BedGraphs were depth normalized using the normalize_bedGraph custom script. siNT and siZC3H4 BedGraphs were depth normalized using the normalize_bedGraph custom script
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
RNAseq reads within exons were summed per gene using featurecounts. RNAseq reads were summed between uaTSS to +3kb for uaRNAs. DESeq2 was used to generate a list of differentially expressed genes after ZC3H4 inhibition. DESeq2 size factors were overwritten to match depth normalization.
Assembly: mm10
Supplementary files format and content: bedGraph

growth_protocol: mESCs (CAST/129 hybrid background, female) were cultured on gelatin. For DMSO and dTAG-13 experiments, KnockOut DMEM (ThermoFisher, 10829018) was used, supplemented with 15% KO serum replacement (ThermoFisher, 10828028), 1X penicillin-streptomycin (MP, TMS-005-C), 1X non-essential amino acids (MP, TMS-001-C), 1% B-ME (MP, ES-007-E), 1X GlutaMAX (ThermoFisher, 35050061), 1000 U/ml LIF (Cell Guidance Systems, GFM200), 1 µM MEK inhibitor (Stemgent, PD0325901), and 3 µM GSK3 inhibitor (Stemgent, CHIR99021). For siNT and siZC3H4 experiments, wild-type F121-9 cells were grown in serum-free embryonic stem cell (SFES) medium with the same concentrations of LIF and inhibitors. SFES was composed of 50/50 NeuroBasal medium (Gibco) and DMEM/F12 medium (Gibco), supplemented with 0.5x B-27 (Gibco), 0.5× N-2 (Gibco), 2 mM l-glutamine (Gibco), 0.05% bovine albumin fraction V (Gibco) and 1.5 × 10−4 M monothioglycerol (Sigma).mESCs were fed daily and passaged every two days. mESCs were cultured at 37°C with 5% CO2.

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded total RNA kit using the manufacturer's protocol.

treatment_protocol: See individual samples. To generate TT-seq libraries after rapid depletion of ZC3H4, ZC3H4-dTAG cells were treated with 500nM dTAG13 (Sigma-Aldrich) for 40 minutes total and 500 µM 4sU was added for the last 10 minutes. For siNT and siZC3H4 TT-seq libraries, cells were exposed to 500µM 4sU (SigmaAldrich, T4509) in fresh media for 20 minutes before harvesting at 47 hours post transfection.

value: CAST/129 hybrid background, female

value: mouse embryonic stem cells

value: WT mESC

value: 30 nM siZC3H4


title: 207735830002_R06C01

status: Public on May 23 2025

type: genomic

city: New York

first: Abhimanyu

last: Amarnani

state: NY

address: 435 E 30th Street. 4th floor

country: USA

institute: New York University

hyb_protocol: Illumina

scan_protocol: Illumina

data_processing: Illumina

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Genotyping testing

label_protocol: Illumina

extract_protocol: Genomic DNA extracted was assessed by standard Illumina Infinium ImmunoArray 24v2-0.

tag: gender

value: M

tag: tissue

value: B cells

tag: disease state

value: ER


title: HT_KO_PR2_RNA

type: SRA

city: Houston

first: Haopeng

last: Yang

state: TX

address: 7455 Fannin ST

department: Lymphoma and Myeloma

institute: The University of Texas MD Anderson Cancer Center

description:
HT_KO_PR2_RNA
HTPR_all_clones_counts_matrix.csv

library_source: transcriptomic

data_processing:
CUT&RUN: Sequencing quality control was evaluated by FastQC. Paired-end CUT&RUN raw reads were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using Bowtie2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were sorted by coordinates and tested for mapped fragment size distribution by Samtools. The final aligned and sorted Bam files were used for further processing. Visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools with option: --normalizeUsing RPKM -e -bs 50 and evaluated in IGV browser. CUT&RUN peaks were called by MACS2 callpeak with option: -g hs -B -f BAM -q 0.01. IgG controls were used for comparison. Each technical repeat and biological repeat were separately processed.
ATAC-seq: Technical duplicates of each ATAC-seq samples were combined and sequencing quality control was evaluated by FastQC. Fastq files of paired-end ATAC-seq data were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using BWA (Burrows-Wheeler Aligner). Aligned reads were sorted by coordinates and filtered out mitochondrial DNA and black-listed regions by Samtools. Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The final aligned, sorted and filtered Bam files were used for further analysis. ATAC-seq visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools and corrected for Tn5 insertion. ATAC-seq peaks were called from Tn-5 corrected insertions using MACS2 callpeak with option ‘-g hs -q 0.05 -f BAMPE and -B’.
ChIP-seq:The sequencing files were first demultiplexed and trimmed based on the eight-nucleotide barcode using previously described pipeline, allowing one mismatch on the first eight-nucleotide from read 121. The demultiplexed reads were then evaluated by FastQC then aligned to the hg19 genome using BWA (Burrows-Wheeler Aligner). Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The H3K27ac peaks were called using MACS2 callpeak with option ‘-g hs -B -f BAM -q 0.01’. Input controls were used for comparison during peak calling.
RNA-seq: Data was trimmed with Trimmomatic, and both pre- and post-trimming quality controls were evaluated by FastQC. The trimmed data were aligned to version 19 of the human reference genome (hg19) using STAR (2-pass). Samples with at least 20 million uniquely mapping reads were retained for further analysis. Reads count was performed with the ‘Htseq-count’ command in HTSeq with option: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. Reads count filtering was applied to the DESeqDataSet matrix to keep only rows that have at least 10 reads total.
Assembly: hg19
Supplementary files format and content: bigwig, bed (for CUT&RUN ATAC-seq and ChIP-seq)
Supplementary files format and content: csv files with normalized counts (For RNA-seq)

molecule: total RNA

source_name: HT

growth_protocol: Cell were cultured in RPMI medium with 10% FBS and 1X penicillin/streptomycin.

extract_protocol:
Cells were collected and washed by PBS. After final wash, nuclei were isolated using nuclei extraction buffer and then washed twice with wash buffer. Five-hundred thousand nuclei were counted and incubated with activated Concanavalin A coated beads and subsequently mixed with antibody in antibody buffer for overnight incubation on nutator in a cold room. IgG controls were set in parrel for antibody enrichment and specificity validation. Nuclei were then washed three times with digitonin buffer and incubated with PAG-MNase for 10 minutes at room temperature. After 10 minutes of incubation, nuclei were washed three times again with digitonin buffer and resuspended with prechilled low salt high Ca2+ buffer  to initiate 1-hour digestion at 0 °C. The reaction was terminated by switching into stop buffer and incubating at 37 °C for 10 minutes to release digested DNA from the nuclei. DNA was then purified with Ampure beads size selection (0.5X to remove large fragment and 2X to recover desired nucleosomal DNA fragments).
NGS libraries were generated with KAPA Hyper Prep Kits (Roche KK8502) using 14 cycles of PCR amplification. Libraires were validated on a Tapestation 4200 (Agilent G2991BA), quantified by Qubit High Sensitivity dsDNA Kit (Life Technologies Q32854), multiplexed and sequenced on a NovaSeq6000 using 100-10-10-100bp reads format.

treatment_protocol: For CD40 stimulation, stimulation medium were prepared by incubation of 40 uL of CD40 ligand and 40 uL of cross-linking antibody mixture at room temperature for 30 minutes and subsequently adding into 10 mL of RPMI+10%FBS and 2 uL of IL4. Cells were seeded at 0.5 million per mL of CD40 stimulation medium at 37 °C. Negative control group was set in the absence of CD40 ligand multimer and IL4. For bi-specific antibody experiment, B tumor cell lines were stained with CellTrace™ Far Red and CD4+ T cells were stained with CellTrace™ Violet. After mixing as desired ratio (1:1), cells were cultured in RPMI supplemented with 10% FBS in the presence of 100 ng/mL mosunetuzumab for 12-hour and 24-hour respectively, prior to sorting. Co-culture right after mixing without mosunetuzumab treatment was set as 0-hour treatment group.

tag: cell line

value: HT

tag: cell type

value: B cell Lymphoma

tag: genotype

value: CREBBP KO EP300 WT

tag: treatment

value: No treatment

tag: time

tag: antibody


title: 207735830002_R05C02

value: F


title: siZC3H4 Replicate 2

city: Boston

first: Claudia

middle: A

last: Mimoso

state: MA

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

description: Library name: Sample 10

molecule: nuclear RNA

organism: Mus musculus

source_name: mouse embryonic stem cells

tag: strain


title: 207735830002_R04C02

value: NR


title: siNT Replicate 3

description: Library name: Sample 9

value: 30 nM siNT


title: HT_KO_PR1_RNA

description:
HT_KO_PR1_RNA
HTPR_all_clones_counts_matrix.csv


title: siNT Replicate 2

description: Library name: Sample 8


title: 207735830002_R04C01


title: 207735830002_R03C02


title: HT_WT_PR2_RNA

description:
HT_WT_PR2_RNA
HTPR_all_clones_counts_matrix.csv

value: CREBBP WT EP300 WT


title: 207735830002_R01C02


title: 207735830002_R02C02


title: siNT Replicate 1

description: Library name: Sample 7


title: HT_R1446C_PR2_RNA

description:
HT_R1446C_PR2_RNA
HTPR_all_clones_counts_matrix.csv

value: CREBBP R1446C EP300 WT


title: HT_Y1503C_A7_RNA

description:
HT_Y1503C_A7_RNA
HT_all_clones_counts_matrix.csv

value: CREBBP Y1503C


title: Donor_4_untreated_rep4

city: Cambridge

first: Niek

last: Wit

state: Not US or Canada

address: Puddicombe Way

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description: Library name: Donor_4

data_processing:
Data was processed using https://github.com/niekwit/rna-seq-salmon-deseq2 workflow
Assembly: Gencode Release 47 (GRCh38.p14)
Supplementary files format and content: Salmon quant files
Supplementary files format and content: DESeq2 analysis of Salmon quant files

molecule: polyA RNA

source_name: CD8 positive T cells

growth_protocol: Activated CD8+ T cells were cultured in complete RPMI 1640 supplemented with 10% FBS and 30 U/ml IL-2.

extract_protocol:
RNeasy Mini Kit
Novogene non-directional RNA-seq library preparation (AB Clonal Fast RNA-seq Lib Prep Kit V2)

treatment_protocol: 11 days 1 uM ML226

value: CD8 positive T cells

value: untreated


title: Donor_4_ML226_rep4

description: Library name: Donor_4_ML226


title: 6363_PRN; CDK12 f/f

city: Ann Arbor

first: Arul

middle: M.

last: Chinnaiyan

state: MICHIGAN

address: 1500 E. Medical Center Dr

institute: University of Michigan

description: Library name: SI_38408

data_processing:
Transcripts were quantified by kallisto with mouse reference genome (mm10) and then summarized to obtain gene level counts and TPM.
Assembly: mm10
Supplementary files format and content: comma-delimited text file includes raw counts of each sample

source_name: mouse ovarian tumor

extract_protocol:
RNA was extracted from cell pellets  using Qiagen RNA extraction kit. RNA quality was determined using a Bioanalyzer RNA Nano Chip
Poly-A selection was performed with Sera-Mag Oligo(dT)-Coated Magnetic Particles (38152103010150; GE Healthcare Life Sciences), and libraries were generated using a KAPA RNA HyperPrep kit (KK8541; Roche Sequencing Solutions).

value: mouse ovarian tumor

value: Epithelial


title: 6140_PRN; CDK12 f/f

description: Library name: SI_38406


title: 6227_PRN; CDK12  f/f

description: Library name: SI_38407


title: HT_Y1482N_G25_RNA

description:
HT_Y1482N_G25_RNA
HT_all_clones_counts_matrix.csv

value: CREBBP Y1482N


title: Donor_1_untreated_rep1

description: Library name: Donor_1


title: 6137J_PRN; CDK12 f/+

description: Library name: SI_38405


title: HT_R1446C_C12_RNA

description:
HT_R1446C_C12_RNA
HT_all_clones_counts_matrix.csv

value: CREBBP R1446C


title: HT_WT_PR1_RNA

description:
HT_WT_PR1_RNA
HTPR_all_clones_counts_matrix.csv


title: HT_Y1482N_G3_RNA

description:
HT_Y1482N_G3_RNA
HT_all_clones_counts_matrix.csv


title: Donor_3_untreated_rep3

description: Library name: Donor_3


title: Donor_1_ML226_rep1

description: Library name: Donor_1_ML226


title: 15973_PRN; CDK12 +/+

description: Library name: SI_38403


title: HT_R1446C_A1_RNA

description:
HT_R1446C_A1_RNA
HT_all_clones_counts_matrix.csv


title: Donor_2_ML226_rep2

description: Library name: Donor_2_ML226


title: 12402_PRN; CDK12 +/+

description: Library name: SI_38402


title: Donor_2_untreated_rep2

description: Library name: Donor_2


title: HT_KO_D31_RNA

description:
HT_KO_D31_RNA
HT_all_clones_counts_matrix.csv

value: CREBBP KO


title: HT_KO_B36_RNA

description:
HT_KO_B36_RNA
HT_all_clones_counts_matrix.csv

value: HT


title: tumor_TJ004

city: Sydney

first: Chenkai

last: Ma

state: NSW

address: 11 Julius Avenue

country: Australia

institute: CSIRO

library_source: transcriptomic single cell

data_processing:
Gene counts were made by CellRanger 7.1.0
Assembly: mm10
Supplementary files format and content: matrix files

source_name: tumor

extract_protocol:
Tumor tissues were minced carefully using scissors 1-2 mm diameter pieces in cell staining buffer (Biolegend, Cat# 420201), and placed in digestion media (10ml HBSS, HEPES 100ul, Collagenase P 10mg, BSA 100mg, and DNase I 10mg per tumor) inside a 50ml tube and incubated on a rotator at 37°C for 25 minutes. The digestion was then stopped by adding 10 ml HBSS including 10% FBS. The cell suspension was passed through a 40μm cell strainer, and removed red blood cells by resuspending in 5 ml of ACK red blood lysis buffer (Gibco) for 5 minutes. Zombie NIR staining was performed using the Zombie NIR Fixable Viability kit (Biolegend, Cat# 423105) according to its instructions for 20 minutes at room temperature. After Zombie NIR staining, cells were incubated with TruStain FcX Plus (BioLegend, Cat# 156603) for 10 minutes on ice, followed by staining with the flow cytometry antibodies all at 1:200 dilution for 25 minutes on ice. Cells are then washed thoroughly and resuspended for flow cytometry analysis. Spleen was mashed through a 70 μm cell strainer with the plunger end of a 5 ml syringe into single cell suspension. Without digestion, spleen single-cell samples were then proceeded with red blood cell lysis and cell staining using the same protocol as tumors.
The 10x Genomics Single Cell Gene Expression 3’ and 5’ workflows are both high-throughput, scalable technologies that encapsulate thousands of individual cells (or nuclei) in droplets for lysis and reverse transcription from up to 8 samples in parallel. The droplets contain primers for cell- and and molecule-specific barcoding of cDNA. We can prepare libraries for CITE-Seq/feature barcoding, CRISPR, or cell hashing. Using our 5’ workflow, we can profile the full length V(D)J regions from T-cell or B-cell receptors from human and mouse samples. The resulting libraries are typically sequenced on an Illumina NovaSeq 6000. Users must deliver live cells (or nuclei) in suspension to the Core

value: tumor

value: immuno cells

value: combination therapy


title: Donor_3_ML226_rep3

description: Library name: Donor_3_ML226


title: tumor_TJ003


title: tumor_TJ002


title: HT_WT_A13_RNA

description:
HT_WT_A13_RNA
HT_all_clones_counts_matrix.csv

value: B cell Lymphoma

value: CREBBP WT

value: No treatment


title: RL_Y1503C_A21_RNA

description:
RL_Y1503C_A21_RNA
RL_all_clones_counts_matrix.csv

source_name: RL

value: RL


title: Spleen_TJ004

source_name: spleen

value: spleen

value: no tumor control


title: tumor_TJ001

value: vehicle


title: RL_Y1482N_F30_RNA

description:
RL_Y1482N_F30_RNA
RL_all_clones_counts_matrix.csv


title: RL_Y1503C_A18_RNA

description:
RL_Y1503C_A18_RNA
RL_all_clones_counts_matrix.csv

value: CREBBP Y1503C


title: Spleen_TJ003


title: HT_WT_B13_RNA

description:
HT_WT_B13_RNA
HT_all_clones_counts_matrix.csv


title: male quadriceps, mouse 784

type: RNA

city: Columbus

first: Kendall

last: King

state: OH

address: 370 West 9th Ave.

institute: The Ohio State University

description: RNA extracted from left quadriceps of fasted aged male mice

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Transcriptome Analysis Console 4.0.
probe group file: Clariom_S_Mouse.r1.pgf
meta-probeset file: Clariom_S_Mouse.r1.mps
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46
value definition: Log2 intensity values from TAC after RMA

label: biotin

source_name: quadriceps, left leg

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Muscles were pulverized in liquid nitrogen, homogenized in polysome buffer and RNA was extraced using TRIzol reagent

value: B6.Cg-Lepob/J x C57BL/6J;Tas1r2tm1Csz

value: quadriceps

tag: category

value: OB KO


title: Spleen_TJ002


title: male quadriceps, mouse 763


title: male quadriceps, mouse 791


title: RL_Y1482N_C5_RNA

description:
RL_Y1482N_C5_RNA
RL_all_clones_counts_matrix.csv

value: CREBBP Y1482N


title: male quadriceps, mouse 643

value: OB WT


title: Spleen_TJ001


title: RL_R1446C_G2C20_RNA

description:
RL_R1446C_G2C20_RNA
RL_all_clones_counts_matrix.csv

value: CREBBP R1446C


title: H3K27ac CUT&Tag for E14-E15 brain cortex, rep2

city: Beijing

first: Zhe

last: Zhao

state: Beijing

address: Tsinghua university, Beijing

department: The IDG/McGovern Institute for Brain Research

country: China

institute: Tsinghua university

library_source: genomic

data_processing:
Raw fastq reads were trimmed by Cutadapt (version 1.18) to remove adapter and low-quality sequences. Fastq files were aligned to the mm10 reference genome using Bowtie2 (version 2.3.3.1) with -X 2000 option. Reads that have alignment quality < Q30, improperly paired, or aligned to ENCODE blacklisted regions were discarded. Duplicates were removed using Picard (version 2.20.4) tools. ChIP-seq signal for each sample were normalized to Reads Per Kilobase per Million mapped reads (RPKM).
assembly: mm10
bigwig file
Library strategy: CUT&Tag

source_name: mouse brain cortex

extract_protocol:
Single cell suspension was prepared from E10 to E17 CD-1 mouse embryos. Four brains were collected for each time point. For E10 and E11 time points, ventricular zone was dissected from the tip of the brain. For E12 to E17 time points, brain tissues were first embedded in 4% low melting agarose at 35-37 °C and sectioned at 200 μm thickness with a vibratome (Leica) in ice-cold and oxygen-bubbling artificial cerebrospinal fluid (ACSF) containing: 125 mM NaCl, 5 mM KCl, 1.25 mM NaH2PO4, 1 mM MgSO4, 2 mM CaCl2, 25 mM NaHCO3, and 20 mM glucose (pH 7.4). The brain sections were transferred to a 3.5 cm dish containing ice-cold hibernate-E medium, and then ventricular zone was dissected and picked up under a stereoscope. The isolated VZ tissues were digested with papain using a commercial kit (Worthington, LK003150) at 37 °C for 30 min according to the manufacturer’s recommendations. Single cell suspension was generated by dissociating the digested tissues through pipetting, washed with DPBS to remove digesting enzymes, and stained with DAPI in ice-cold DPBS. To enrich RGPs at later time points, FlashTag labeling was performed as previously described (Govindan et al., 2018). Briefly, pregnant mice were anesthetized, injected with FlashTag into the lateral ventricle of the uterine horns, and housed for 30 min. Then, single cell suspensions were prepared as described above.
A total of 1 × 105 FlashTag+ cortical cells were FACS-purified and pelleted immediately after sorting for each experiment. CUT&Tag libraries were prepared using NovoNGS® CUT&Tag® 3.0 High-Sensitivity Kit (Novoprotein, N259-YH01), according to the manufacturer’s instructions.

value: brain cortex

tag: developmental stage

value: wild type


title: male quadriceps, mouse 761


title: RL_R1446C_2B3_RNA

description:
RL_R1446C_2B3_RNA
RL_all_clones_counts_matrix.csv


title: male soleus, mouse 18

description: RNA extracted from left soleus of fasted aged male mice

source_name: soleus, left leg

value: C57BL/6J;Tas1r2tm1Csz backcrossed

value: soleus

value: aged KO


title: male quadriceps, mouse 642


title: male soleus, mouse 13

value: aged WT


title: male soleus, mouse 15


title: male soleus, mouse 11


title: H3K27ac CUT&Tag for E12-E13 brain cortex, rep2


title: male soleus, mouse 16


title: male quadriceps, mouse 644


title: RL_KO_3B3_RNA

description:
RL_KO_3B3_RNA
RL_all_clones_counts_matrix.csv

value: RL

value: B cell Lymphoma

value: CREBBP KO

value: No treatment


title: male soleus, mouse 20


title: RL_KO_2A1_RNA

description:
RL_KO_2A1_RNA
RL_all_clones_counts_matrix.csv


title: male quadriceps, mouse 723


title: male soleus, mouse 17


title: H3K27me3 CUT&Tag for E12-E13 brain cortex, rep2


title: male quadriceps, mouse 641


title: male soleus, mouse 7

description: RNA extracted from left soleus of fasted male mice

value: KO


title: RNA-seq K562, HDAC6 KO, replicate 2

city: Düsseldorf

first: Julian

last: Schliehe-Diecks

address: Moorenstr. 5

country: Germany

institute: Uniklinik Düsseldorf

description: Library name: RNA-seq_HDAC6_knock_out_2

data_processing:
Adapters were trimmed with FASTQ Trimmer (11 bases of the 5' and 1 base of the 3')
Data quality was assesed via fastqc and aggregated with MultiQC
Reads were aligned to the hg38 reference genome via RNA STAR
Aligned reads were counted with featureCounts and aggregated into a count matrix
edgeR in combination with a gene annotation file was used to normalize the counts (log2 CPM) and to calculate the Fold Change and significance of the genes
Assembly: hg38
Supplementary files format and content: A tabular normalizied counts matrix and a tabular differentially expressed gene matrix

source_name: blood

growth_protocol: K562 were lentivirally transduced to express CAS9 and a guide RNA, sorted via a fluorescence marker & monoclonally selected

extract_protocol:
RNA was isolated utilizing the Maxwell® RSC simplyRNA Cells Kit (Promega, #AS1390).
Library preparation was carried out following supplier’s guidelines by using the VAHTs Stranded mRNA-Seq Library Prep Kit (Illumina Inc. San Diego, USA). Briefly, total RNA (500 ng) was used for capturing of mRNA, fragmentation, cDNA synthesis, ligation of the adapters and library amplification. Purified libraries were normalized and sequenced on the NextSeq550 (Illumina) with 1x76 bp read setup. Followed by using bcl2fastq2 tool to convert the bcl files to fastq files.

value: blood

value: chronic myeloid leukemia

value: HDAC6 KO


title: RNA-seq K562, HDAC6 KO, replicate 3

description: Library name: RNA-seq_HDAC6_knock_out_3


title: RNA-seq K562, HDAC6 KO, replicate 1

description: Library name: RNA-seq_HDAC6_knock_out_1


title: RL_WT_G2C24_RNA

description:
RL_WT_G2C24_RNA
RL_all_clones_counts_matrix.csv

value: CREBBP WT


title: HiC-seq for E14-E15 brain cortex, rep2

data_processing:
Raw sequencing reads were trimmed by Cutadapt (version 1.18) to remove adapter and lowquality sequences. Trimmed paired-end reads were aligned, processed and iteratively corrected using HiCPro (version 2.11.1; Servant et al., 2015) with default parameters. Sequencing reads were mapped to the mm10 reference genome. To recover chimeric fragments spanning ligation junctions, the ligation sequence (GATCGATC) was searched in unmapped fragments and was used as split site to separate Hi-C joined ends in the chimeric fragments.
assembly: mm10
The files including all the valid interaction pairs (described as Servant et al., 2015).

extract_protocol:
Single cell suspension was prepared from E10 to E17 CD-1 mouse embryos. Four brains were collected for each time point. For E10 and E11 time points, ventricular zone was dissected from the tip of the brain. For E12 to E17 time points, brain tissues were first embedded in 4% low melting agarose at 35-37 °C and sectioned at 200 μm thickness with a vibratome (Leica) in ice-cold and oxygen-bubbling artificial cerebrospinal fluid (ACSF) containing: 125 mM NaCl, 5 mM KCl, 1.25 mM NaH2PO4, 1 mM MgSO4, 2 mM CaCl2, 25 mM NaHCO3, and 20 mM glucose (pH 7.4). The brain sections were transferred to a 3.5 cm dish containing ice-cold hibernate-E medium, and then ventricular zone was dissected and picked up under a stereoscope. The isolated VZ tissues were digested with papain using a commercial kit (Worthington, LK003150) at 37 °C for 30 min according to the manufacturer’s recommendations. Single cell suspension was generated by dissociating the digested tissues through pipetting, washed with DPBS to remove digesting enzymes, and stained with DAPI in ice-cold DPBS. To enrich RGPs at later time points, FlashTag labeling was performed as previously described (Govindan et al., 2018). Briefly, pregnant mice were anesthetized, injected with FlashTag into the lateral ventricle of the uterine horns, and housed for 30 min. Then, single cell suspensions were prepared as described above.
Hi-C libraries were prepared as described previously (Díaz et al., 2018) with minor modifications: 1 × 105 FlashTag+ FACS-purified cortical cells were immediately fixed for 10 min in freshly prepared 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS (Thermo Fisher Scientific, AM9624) at room temperature with gentle rotation (300 rpm). Then the reaction was quenched in 0.2 M glycine (Sigma-Aldrich, 50046) solution for 5 min at room temperature with gentle rotation (300 rpm). The cells were washed twice with 1 ml cold 1 × PBS (centrifuged at 400 g for 5 min at 4 °C). To lyse cells, the cells were resuspended in ice-cold in situ Hi-C buffer and incubated on ice for 15 min. The lysed cells were frozen in liquid nitrogen and stored at -80 °C until further use. Chromatin was digested using 50 U of MboI (New England Biolabs, R0147S) overnight at 37 ℃ with gentle rotation. After biotin filling, proximity ligation was carried out using 17.5 U T4 DNA Ligase (Thermo Fisher Scientific, EL0012) for 4 hours at 20 °C with gentle rotation. DNA was sheared to 200-500 bp fragments using Covaris S220 sonicator with a duty factor of 10%, peak power of 140 W, and 200 cycles per burst. Each sample was sonicated for 2 cycles, 50 s/cycle. Ligation fragments containing biotin were immobilized on Dynabeads™ MyOne™ Streptavidin C1 beads (Thermo Fisher Scientific, 65001). Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit, according to the manufacturer’s instructions. Libraries were PCR amplified for 14-16 cycles using NEBNext® Multiplex Oligos. DNA was then purified using 2.2 × VAHTS DNA Clean Beads and eluted in ultrapure H2O.


title: RL_WT_2B5_RNA

description:
RL_WT_2B5_RNA
RL_all_clones_counts_matrix.csv


title: male soleus, mouse 5


title: male soleus, mouse 1

value: WT


title: male soleus, mouse 4


title: male soleus, mouse 10


title: male soleus, mouse 12


title: male soleus, mouse 9


title: male soleus, mouse 6


title: Brain 12

city: La Jolla

first: Maria

middle: L

last: Karkanitsa

state: CA

address: 9100 Regents Rd, Apt G

department: Shu Chien Gene Lay Department of Bioengineering

institute: University of California San Diego

description: Nanostring nCounter Mouse Immunology Panel

hyb_protocol: 2 μL of Capture ProbeSet was added to each vessel,  mixed and placed on a thermocycler at 65oC for 16-48 hours before being maintained at 4°C for less than 24 hours.

scan_protocol: Nanostring nCounter Prep Station performed automated fluidic sample processing to purify and immobilize hybridized sample to cartridge surface. Digital barcode reads were analyzed by Nanostring nCounter® Digital Analyzer.

data_processing: Data was analyzed by ROSALIND®, with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library (3). Abundance of various cell populations was calculated on ROSALIND using the Nanostring Cell Type Profiling Module. In ROSALIND, we performed a filtering of Cell Type Profiling results to include results that have scores with a p-value greater than or equal to 0.05. Fold changes and p-values were calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual.

label: Probe

source_name: murine brain tissue

label_protocol: RNA sample concentrations were measured on a Qubit 3.0 Fluorometer with a QubitTM RNA HS Assay kit. 70 μL of hybridization buffer was mixed with Immunology Panel Reporter CodeSet solution, and 8 μL of this master mix was mixed in a separate reaction vessel with 100 ng of RNA per tissue sample and RNA-free water up to 13 μL total.

extract_protocol: Animals treated with LPS and iECM or saline were sacrificed at hour 30 as previously described. A total of n = 6 animals were used per group for a total of 12 animals and whole blood, spleen, lung, heart, brain, and kidney were harvested and flash frozen. 250 μL of whole blood was collected in 2 mL of RNAlater and stored at -80 C until further processing. Flash frozen samples tissue samples were homogenized with either a Tissue Tearer rotator homogenizer (Cole-Parmer, Vernon Hills, IL) or a Beadbug bead homogenizer (Benchmark Scientific). For lung, brain, kidney, and spleen, RNA was isolated through a NucleoSpin® RNA/Protein kit (Takara Bio USA Inc. San Jose, CA) while heart issue was processed with a RNeasy Fibrous Mini kit (Qiagen, Germantown, MD). Blood samples were isolated using a Mouse Ribopure Blood RNA Isolation Kit (Invitrogen). RNA was extracted based on manufacturer instructions with an on-column DNase digestion for minimizing genomic DNA contamination.

treatment_protocol: To model systemic inflammation associated with severe sepsis, nine-week-old wild-type female C57BL/6J mice (Jackson Laboratories) were immobilized via scruff before receiving an intraperitoneal (IP) injection of 10 mg/kg lipopolysaccharide (LPS) diluted at 1 mg/mL concentration in sterile saline. After 6 hours, mice received a secondary 1 mg/kg IP LPS injection. At 10 hours following the initial LPS injection, mice were arbitrarily selected for receiving either 200 μL of sterile saline or 10 mg/mL iECM injected into the tail vein with a 29G needle insulin syringe (Exel International, Redondo Beach, CA). Temperature and weight were taken preceding each handling timepoint. Any animals with a temperature above 28°C were excluded prior to injection with iECM or saline based on previous model validation showing this temperature profile indicated an inadequate inflammatory response to LPS. Treated animals were followed up for up to 20 hours post iECM or saline treatment to assess effect of the iECM material.

value: murine brain tissue

value: Saline


title: male soleus, mouse 19


title: H3K27me3 CUT&Tag for E14-E15 brain cortex, rep2

value: brain cortex

value: wild type


title: Brain 11


title: HiC-seq for E12-E13 brain cortex, rep2


title: MDA231 nor

city: guangzhou

first: jingyi

last: long

address: The Third Affiliated Hospital of Southern Medical University

institute: The southern medical university

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
For RNA-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
For RNA-seq: The reads mapped the genome were calculated using featureCounts (v1.6.3).
Assembly: The sequenced reads were single-end mapped to reference genome sequences GRCh38

source_name: Breast cancer

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For RNA-seq: VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina v2 was used for library construction.

value: Breast cancer

value: basal-like

value: normoxia for 6 hours


title: H3K27ac CUT&Tag for E14-E15 brain cortex, rep1


title: male soleus, mouse 2

value: soleus


title: Brain 10


title: Brain 8

value: iECM


title: MDA231 hyp

value: hypoxia for 6 hours


title: Brain 9


title: H3K27ac CUT&Tag for E12-E13 brain cortex, rep1


title: MCF-7 nor

value: luminal A


title: Brain 6


title: Brain 7


title: MCF-7 hyp


title: H3K27me3 CUT&Tag for E14-E15 brain cortex, rep1


title: Brain 5


title: MDA231 hyp

library_source: other

data_processing:
Libraries were sequenced using 150×150 paired-end sequencing on the Illumina NovaSeq 6000 instrument.
Cutadapt (v2.5) was used to trim adapters and filter for sequences. Sequencing reads were aligned to the human genome build hg38 (mouse genome mm10) using bowtie2 (v2.3.5.1) using default parameters. Regions of enrichment of HIF1-α were calculated using MACS2 (v2.1.2) using parameters -m 5 50.
For peak annotation, we adopt ChIPSeeker R pack utility annotatePeaks.pl, associating peaks with their nearby genes.
Assembly: hg38
Library strategy: CUT&Tag

molecule: other

source_name: Homo sapiens

growth_protocol: MDA-MB-231 cells (1*106 cells/well) were suspended in high-glucose DMEM containing 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C, 5%CO2

extract_protocol:
The CUT&Tag assay and subsequent DNA library construction were performed by following the manufacturer’s instructions for the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-01). An anti-HIF1-a monoclonal antibody (Affinity, BF8002) is used as the primary antibody.
Libraries were sequenced using 150×150 paired-end sequencing on the Illumina NovaSeq 6000 instrument.

treatment_protocol: treated with CoCl2 100uM for 24 hours

value: Homo sapiens

value: TNB

value: breast cancer cells


title: Brain 3


title: HiC-seq for E14-E15 brain cortex, rep1


title: Brain 2


title: SND1_k562_IP_rep1

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
data processing was done using the Skipper pipeline, freelly available at https://github.com/yeolab/skipper.
Adapters trimming was done with Skewer
proccessed reads were mapped with STAR (2.7.10a_alpha_220314)
PCR bias was removed using UMIcollapse
Assembly: hg38
Supplementary files format and content: tab separated values files
Supplementary files format and content: Supplementary files - reproducible enriched window including p and q values, enrichment scores, and the annotated regions for the significantly bound transcriptome tiled windows.

growth_protocol: HEK293T, HepG2 and HeLa cells were cultured in DMEM with 10% FBS at 37C, while K562 were cultured  in RPMI1640 with 10% FBS at 37C.

extract_protocol:
cells were lysed with eCLIP buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate), and RNA was fragmented using RNAse I. Then, samples were subjected for overnight incubation at 4C with corresponding beads-conjugated antibodies.
RNA fragments 3' end were dephosphorylated with FastAP (Thermo) and PNK (NEB), followed by 3' barcoded linker ligation (T4 RNA ligase I, NEB). Then, samples were ran on protein gel for an hour on 150V, followed by overnight transfer on nitrocellulose membrane. protein kDa size and 75kDa above it were extracted for IP and size-matched input and extracted from membrane with proteinase K. the samples subjected to reverse transcription (SSIII Thermo Fisher), and subsequent ExoSAP-IP and EDTA, NaOH and HCl treatment for degradation of excess RT primers and rna template. Additional 3' end ligation and PCR amplification (Q5 2X mix NEB) generated the final library products.

treatment_protocol: cells in 10cm plates were washed once with PBS followed by crosslinking with UV (254 nm, 400 mJ/cm2)

value: lymphoblast


title: HiC-seq for E12-E13 brain cortex, rep1


title: SND1_k562_IP_rep2


title: SND1_k562_Input_rep2


title: Blood 10

source_name: murine blood tissue

value: murine blood tissue


title: Brain 1


title: KO_L2C_ULI-MNase-seq_r2

city: Shanghai

first: Xinyu

last: Wang

address: Siping Road 1239

institute: Tongji University

description:
Library name: Sample16
KO L2C ULI-MNase-seq replicate2

data_processing:
ULI-MNase-seq: For raw paired-end MNase-seq reads, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. Clean MNase-seq reads were aligned to the mouse reference genome (mm10) using the bwa v0.7.12 mem command. Reads with a mapping quality (MAPQ) less than 10 was removed for downstream analysis. To create nucleosome profiles, the aligned paired-end reads was extended to 146bp length based on each read center. All the nucleosome profiles was scaled to 500 million reads in total.
Assembly: mm10
Supplementary files format and content: MNase signal file

source_name: late 2-cell

growth_protocol: Specific pathogen-free (SPF) mice were housed in the animal facility at Tongji University,Shanghai, China, and they were fed a standard diet. The temperature and light were strictly controlled (24 °C; 12 h light and 12 h dark). Smarca4flox/flox mice are from previous study(Qi et al. 2021). All animal experiments were performed in accordance with the University of Health Guide for the Care and Use of Laboratory Animals and were approved by the Biological Research Ethics Committee of Tongji University. To get MII oocytes for ICSI, B6D2F1 or Smarca4flox/flox Gdf9 Cre C57BL/6 female mice (8–12-weeks old) were superovulated by injection with 7 IU each of pregnant mare serum gonadotropin (PMSG), followed by injection of 5 IU of human chorionic gonadotropin (hCG) (San-Sheng Pharmaceutical) 48 h later.

extract_protocol:
20-30 blastomere per replicate were isolated and washed before they were placed into 1.4 μL of lysis buffer (10 mM Tris-HCl, pH 8.5, 5 mM MgCl2, 0.6% NP-40) for individual reactions. Then, 1.8 μL of MNase master mix (MNase buffer, 0.125 U/μL MNase (NEB, M0247S), 2 mM DTT, and 5% PEG 6000) was added into each tube, and the reaction was incubated at 25 °C for 10 min for chromatin fragmentation. The reaction was stopped by the addition of 0.4 μL of 100 mM EDTA, and then 0.4 μL of 2% Triton X-100 was added to the reaction to release the fragmented chromatin. Then, 0.2 μL of 20 mg/mL protease (Qiagen) was added, and the reaction was incubated at 50 °C for 90 min for protein digestion followed by incubation at 75 °C for 30 min for protease inactivation. The sequencing libraries were prepared using the KAPA Hyper Prep kit for the Illumina platform (Roche, kk8504) following the manufacturer’s instructions. After standard procedures including end repair and A-tailing, adapter ligation, post-ligation cleanup, and library amplification, the resulting products were subjected to a second round of PCR amplification with the same provided primers to generate sufficient DNA materials for highthroughput sequencing.
For mouse embryos, the sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase(Kapa Biosystems, KK8483) and KAPA HyperPrep Kit for the Illumina platform (Roche, kk8504) following manufacturer’s protocol. Paired-end sequencing with 150-bp read length was performed on the HiSeq X Ten (Illumina) platform.

value: late 2-cell

value: Smarca4 KO


title: KO_L2C_ULI-MNase-seq_r1

description:
Library name: Sample15
KO L2C ULI-MNase-seq replicate1


title: Blood 5

value: Saline


title: SND1_k562_Input_rep1


title: Blood 9


title: Blood 6


title: Blood 7


title: WT_L2C_ULI-MNase-seq_r2

description:
Library name: Sample14
WT L2C ULI-MNase-seq replicate2


title: Blood 8


title: PRPF17_HeLa_IP_rep2

source_name: HeLa

value: HeLa

value: epithelial cell


title: Blood 4


title: Blood 3


title: H3K27me3 CUT&Tag for E12-E13 brain cortex, rep1

value: brain cortex

value: wild type


title: Blood 2


title: Brain 4

value: murine brain tissue


title: Kidney 12

source_name: murine kidney tissue

value: murine kidney tissue


title: KO_E2C_ULI-MNase-seq_r2

description:
Library name: Sample12
KO E2C ULI-MNase-seq replicate2

source_name: early 2-cell

value: early 2-cell


title: Jurkat target genes ONT

city: PHILADELPHIA

first: YUNTIAN

last: FU

state: PA

address: 265 S. 37th Street

institute: University of Pennsylvania

description:
Library name: sample5
10X genomics

data_processing:
The demultiplexing, barcode processing, isoform quantification for Nanopore sequencing is done by LongcellPre (https://github.com/yuntianf/LongcellPre)
The demultiplexing, barcode processing, isoform quantification for PavBio sequencing is done by IsoSeq (https://isoseq.how/)
Assembly: Human hg38
Supplementary files format and content: Tab-seperated value files
Supplementary files format and content: Sparse matrix files

source_name: T-Cell

growth_protocol: Jurkat (ATCC TIB-152) and Cas9-stable Jurkat (SL555, GeneCopoeia, Inc., Rockville, MD, USA) cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS.

extract_protocol:
Jurkat (ATCC TIB-152) and Cas9-stable Jurkat (SL555, GeneCopoeia, Inc., Rockville, MD, USA) cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium (A3160702, Gibco) supplemented with 10% FBS (A3160702, Gibco).
Single-cell cDNA and gene expression libraries of cell lines are generated by Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v2 (10X Genomics, Pleasanton, CA, USA) as per the manufacturer’s protocol.  The cDNA and gene expression libraries are amplified with 16 and 14 cycles of PCR respectively. The quality of gene expression libraries is confirmed using 2% E-Gel (Thermo Fisher Scientific, Waltham, MA, USA). The libraries are then quantified using Qubit (Invitrogen) and sequenced on Illumina sequencers (Illumina, San Diego, CA, USA).

treatment_protocol: The oligonucleotide pool for gRNA library targeting splicing factors were cloned to lentiGuide-Puro plasmid (Addgene plasmid #52963) and produced lentiviruses were transduced to Cas9 stable Jurkat cells using spinoculation at 800g for 30 min at 32 °Celsius.

value: T-Cell

value: Jurkat

value: wild


title: Stimulated Jurkat CRSIPR target genes

description:
Library name: sample4
10X genomics

value: mixed with wild and CRISPR knock-out


title: Kidney 11


title: KO_E2C_ULI-MNase-seq_r1

description:
Library name: Sample11
KO E2C ULI-MNase-seq replicate1


title: Kidney 10


title: WT_E2C_ULI-MNase-seq_r2

description:
Library name: Sample10
WT E2C ULI-MNase-seq replicate2


title: PRPF17_Hek293T_IP_rep2

value: human embryonic kidney


title: WT_E2C_ULI-MNase-seq_r1

description:
Library name: Sample9
WT E2C ULI-MNase-seq replicate1


title: PRPF17_Hek293T_Input_rep2


title: PRPF17_Hek293T_IP_rep1


title: Jurkat CRISPR full transcriptme

description:
Library name: sample1
10X genomics


title: PRPF17_HeLa_IP_rep1


title: Kidney 9

value: iECM


title: Kidney 8


title: PRPF17_Hek293T_Input_rep1


title: Jurkat CRIPSR target genes

description:
Library name: sample2
10X genomics


title: KO_PN3_ULI-MNase-seq_r2

description:
Library name: Sample8
KO PN3 ULI-MNase-seq replicate2

source_name: PN3 stage zygote

value: PN3 stage zygote


title: WT_L2C_ULI-MNase-seq_r1

description:
Library name: Sample13
WT L2C ULI-MNase-seq replicate1

value: late 2-cell


title: Kidney 7


title: SNF2L+IAA_2

city: wuhan

first: yuchao

last: zhu

address: No. 1 SHizishan St

institute: Huazhong Agricultural University

description: Library name: Sample 5

data_processing:
Raw sequencing data was initially filtered using cutadapt (version 2.5) to remove low quality reads and trim adapter-contaminated sequences.
Map clean readings to T. gondii reference genome (TGME49), using Bowtie 2 (version 2.3.4.1), with default parameters.
Library quality was assessed by calculating insert size using samtools (version 1.12) and analyzing read distribution around transcription start sites (TSS) using deepTools (version 3.5.1)
Peak identification was performed using MACS 2 version 2.1.1. Bigwig is generated using bigWigMerge and bedGraphToBigWig (version 4.11.1).
Peaks were annotated with ChIPseeker (version 1.32.1). Visualization of peaks in genomic regions was performed using IGV Genome Browser.
Assembly: Clean reads were aligned to the reference genome (ME49) using Bowtie2 software (Langmead and Salzberg 2012)(version 2.2.4)  ToxoDB-63_TgondiiME49(https://toxodb.org/common/downloads/Current_Release/TgondiiME49/fasta/data/ToxoDB-63_TgondiiME49_Genome.fasta)
Supplementary files format and content: bw
Library strategy: CUT&Tag

organism: Toxoplasma gondii

source_name: tachyzoites

growth_protocol: All Toxoplasma gondii used in this study were maintained in human foreskin fibroblasts cultured at 37 ℃ in 5% CO2 in complete Dulbecco’s Modified Eagle Medium supplemented with 10% heat-inactivated fetal bovine serum, 100 unit/mL penicillin, and 100 μg/mL streptomycin

extract_protocol:
CUT&Tag was used to identify SNF2L occupancy in the genome of SNF2L-mAID strain. Intracellular parasites are released through needle channels and purified by 3 µm pore size membrane filtration. Approximately 5 × 105 Toxoplasma gondii tachyzoites were collected and processed using Illumina's Hyperactive Universal CUT&Tag Assay Kit (Vazyme Biotech, China) according to the manufacturer's instructions. Mouse anti-HA was used as primary antibody for immunoprecipitation.
The resulting DNA was amplified using TD 202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China) for library construction. The libraries were enriched, quantified and sequenced using the PE150 model on a NovaSeq 6000 sequencer (Illumina).

value: tachyzoites


title: WT_PN3_ULI-MNase-seq_r2

description:
Library name: Sample6
WT PN3 ULI-MNase-seq replicate2


title: KO_PN3_ULI-MNase-seq_r1

description:
Library name: Sample7
KO PN3 ULI-MNase-seq replicate1

value: Smarca4 KO


title: SNF2L+IAA_3

description: Library name: Sample 6


title: Blood 1

value: murine blood tissue


title: PRPF17_HeLa_Input_rep2

value: HeLa

value: epithelial cell


title: hnRNPC_K562_IP_rep2

value: lymphoblast


title: SNF2L+IAA_1

description: Library name: Sample 4


title: PRPF17_HeLa_Input_rep1


title: Stimulated Jurkat CRISPR full transcriptme

description:
Library name: sample3
10X genomics


title: Kidney 5

value: Saline


title: WT_PN3_ULI-MNase-seq_r1

description:
Library name: Sample5
WT PN3 ULI-MNase-seq replicate1

value: wild type


title: Kidney 6

value: murine kidney tissue


title: hnRNPC_K562_IP_rep1


title: SNF2L-IAA_3

description: Library name: Sample 3


title: hnRNPC_K562_Input_rep2


title: SNF2L-IAA_2

description: Library name: Sample 2


title: KO_MII_ULI-MNase-seq_r1

description:
Library name: Sample3
KO MII ULI-MNase-seq replicate1

source_name: MII oocytes

value: MII oocytes


title: hnRNPC_K562_Input_rep1


title: SNF2L-IAA_1

description: Library name: Sample 1


title: WT_MII_ULI-MNase-seq_r2

description:
Library name: Sample2
WT MII ULI-MNase-seq replicate2


title: WT_MII_ULI-MNase-seq_r1

description:
Library name: Sample1
WT MII ULI-MNase-seq replicate1


title: Kidney 3


title: hnRNPA2B1_HepG2_IP_rep1

value: Epithelial-like cells


title: 3HA_2_IgG

description: Library name: Sample 5

extract_protocol:
CUT&Tag was used to identify SNF2L occupancy in the genome of SNF2L-3HA strain. Intracellular parasites are released through needle channels and purified by 3 µm pore size membrane filtration. Approximately 5 × 105 Toxoplasma gondii tachyzoites were collected and processed using Illumina's Hyperactive Universal CUT&Tag Assay Kit (Vazyme Biotech, China) according to the manufacturer's instructions. Mouse anti-HA was used as primary antibody for immunoprecipitation. Parallel experiments using untreated murine IgG were included as controls.
The resulting DNA was amplified using TD 202 TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China) for library construction. The libraries were enriched, quantified and sequenced using the PE150 model on a NovaSeq 6000 sequencer (Illumina).

value: Toxoplasma gondii


title: 3HA_3_IgG

description: Library name: Sample 6


title: 3HA_1_IgG

description: Library name: Sample 4


title: hnRNPA2B1_HepG2_Input_rep2


title: Kidney 2


title: MK_P0_Flcn_KO

city: Kuamomoto

first: Shunsuke

last: Tanigawa

state: Kumamoto

address: 2-2-1 Chuou-ku honjyo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

description:
Library name: Sample2
10x Genomics

data_processing:
10x library equencing was performed on Illumina HiSeq X. Sequencing data were analyzed using Illumina bcl2fastq software (version 2.20.0) and converted to FASTQ format files. Subsequently, alignment was performed using the cellranger count function of Cell Ranger Single Cell software (version 7.1.0, 10x Genomics) with using STAR aligner 2.7.2a. The GRCm38 mouse reference genome, mm10 r102  was used.
Assembly: GRCm38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Embryonic kidney

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium. Reverse transcription was performed in droplet.
library construction was performed by using Chromium Single Cell 3ʹ Reagent Kits v2.

value: Embryonic kidney

value: Flcn KO


title: MK_P0_Flcn_WT

description:
Library name: Sample1
10x Genomics

value: Flcn WT


title: hnRNPA2B1_HepG2_Input_rep1


title: Lung 12

source_name: murine lung tissue

value: murine lung tissue


title: Kidney 1

value: iECM


title: Input ChIP-seq for brain cortex, rep2

data_processing:
Raw fastq reads were trimmed by Cutadapt (version 1.18) to remove adapter and low-quality sequences. Fastq files were aligned to the mm10 reference genome using Bowtie2 (version 2.3.3.1) with -X 2000 option. Reads that have alignment quality < Q30, improperly paired, or aligned to ENCODE blacklisted regions were discarded. Duplicates were removed using Picard (version 2.20.4) tools. ChIP-seq signal for each sample were normalized to Reads Per Kilobase per Million mapped reads (RPKM).
assembly: mm10
bigwig file

source_name: mouse brain cortex

extract_protocol:
Single cell suspension was prepared from E10 to E17 CD-1 mouse embryos. Four brains were collected for each time point. For E10 and E11 time points, ventricular zone was dissected from the tip of the brain. For E12 to E17 time points, brain tissues were first embedded in 4% low melting agarose at 35-37 °C and sectioned at 200 μm thickness with a vibratome (Leica) in ice-cold and oxygen-bubbling artificial cerebrospinal fluid (ACSF) containing: 125 mM NaCl, 5 mM KCl, 1.25 mM NaH2PO4, 1 mM MgSO4, 2 mM CaCl2, 25 mM NaHCO3, and 20 mM glucose (pH 7.4). The brain sections were transferred to a 3.5 cm dish containing ice-cold hibernate-E medium, and then ventricular zone was dissected and picked up under a stereoscope. The isolated VZ tissues were digested with papain using a commercial kit (Worthington, LK003150) at 37 °C for 30 min according to the manufacturer’s recommendations. Single cell suspension was generated by dissociating the digested tissues through pipetting, washed with DPBS to remove digesting enzymes, and stained with DAPI in ice-cold DPBS. To enrich RGPs at later time points, FlashTag labeling was performed as previously described (Govindan et al., 2018). Briefly, pregnant mice were anesthetized, injected with FlashTag into the lateral ventricle of the uterine horns, and housed for 30 min. Then, single cell suspensions were prepared as described above.
ChIP-seq libraries were prepared as described previously (Brind’Amour et al., 2015) with minor modifications: A total of 1 × 105 FlashTag+ cortical cells were FACS-purified and pelleted immediately after sorting for each experiment. The pelleted cells were frozen in liquid nitrogen and stored at -80 °C until further use. Cells were resuspended in cold Nuclear Isolation Buffer (Sigma-Aldrich, NUC-101). Before immunoprecipitation (IP), cells were thawed and digested using 80 U MNase (New England Biolabs, M0247S) for 5 min at 37 °C. The digestion was stopped by adding 10% of the reaction volume of 100 mM EDTA (Invitrogen, AM9260G). Chromatin was precleared in complete immunoprecipitation buffer with 10 µL Protein A/G Dynabeads (Invitrogen, 10001D and 10003D) for 2 hours at 4 °C with rotation. Meanwhile, 10 µL Protein A/G Dynabeads were mixed with 2 µL H3K27me3 antibody (Cell Signaling Technology, 9733) or H3K27ac antibody (Abcam, ab4729) under rotation for 3 hours at 4 °C in 100 µL complete immunoprecipitation buffer. The precleared chromatin was mixed with the antibody-bound beads under overnight rotation at 4 °C. Beads were then washed twice with low salt wash buffer and twice with high salt wash buffer. DNA was then eluted for 1.5 hours at 65 °C in 30 µL ChIP elution buffer. DNA was purified using 2.2 × VAHTS DNA Clean Beads and eluted in ultrapure H2O (Thermo Fisher Scientific, 10977015). For H3K27ac IP, 10 mM sodium butyrate (Sigma-Aldrich, 303410) was added in cold Nuclear Isolation Buffer, complete immunoprecipitation buffer, low salt wash buffer, and high salt wash buffer. Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit (New England Biolabs, E7645S), according to the manufacturer’s instructions. Libraries were PCR amplified for 13-15 cycles using NEBNext® Multiplex Oligos (New England Biolabs, E7335S). The amplified libraries were purified using 2.2 × VAHTS DNA Clean Beads and eluted in ultrapure H2O.

value: brain cortex


title: 3HA_3_IP

description: Library name: Sample 3

value: tachyzoites


title: 3HA_2_IP

description: Library name: Sample 2


title: KO_MII_ULI-MNase-seq_r2

description:
Library name: Sample4
KO MII ULI-MNase-seq replicate2

value: Smarca4 KO


title: U2OS- AiD DiV A- AsiSI -ER - siMePCE + RNase H

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

data_processing:
The adapter sequences in each raw fastq file (fastq) were trimmed using Trim Galore. The quality of each processed fastq file was then assessed with FastQC. Subsequently, the reads were aligned to the reference human genome hg19 using the bwa mem alignment method. SAMtools was employed to remove low-quality mapped reads by filtering out reads with a mapping quality score of less than 10, as well as PCR duplicates. Each read was extended by 200 bp to account for the full ChIP or DRIP fragment length during further analysis using deepTools bamCoverage. Reads per million reads (rpm) of 10 kb upstream and downstream for each AsiSI location were calculated from each sample using  deepTools multiBigwigSummary .
Assembly: hg19
Supplementary files format and content: bw files
Library strategy: DRIP-seq

source_name: U2OS- AiD-DiVA AsiSI -ER

growth_protocol: Cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ) and supplemented with 400µg/mL G418.

extract_protocol:
ChIP-seq: After siRNA depletion and AsiSI-mediated DSB induction, cells were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched with 20 mM Glycine for 5 min. Post quenching, the cells were lysed and chromatin was sonicated using a Bioruptor (Diagenode) instrument.
DRIP-seq: After siRNA depletion and AsiSI-mediated DSB induction, cells were harvested and genomic DNA was isolated. Extracted genomic DNA was digested overnight at 37°C using a restriction enzyme cocktail (BsrGI, EcoRI, HindIII, and XbaI NEB), followed by treatment with mock or RNase H. For each DRIP, 8 µg of digested DNAs were subject to immunoprecipitation with 10 µg of S9.6 antibody and eluted. The eluates were sonicated using the bioruptor (Diagenode) and used for library preparation.
Libraries were constructed using the NEBNext Ultra II kit following manufacturer’s instructions.

treatment_protocol: SiNC (Control) and siMePCE cells were treated with 300 nM of 4-hydroxytamoxifen (4-OHT) for 4 hrs to induce sequence-specific double strand breaks at AsiSI sites in actively transcribed regions.

value: U2OS- AiD-DiVA AsiSI -ER

value: siMePCE + RNase H

tag: dsb induction

value: 300nM 4OHT for 4 hrs


title: Lung 10

description: Nanostring nCounter Mouse Immunology Panel

value: Saline


title: Kidney 4


title: Lung 9


title: H3K27ac ChIP-seq for E12 brain cortex, rep2

value: wild type


title: hnRNPA2B1_HepG2_IP_rep2


title: 3HA_1_IP

description: Library name: Sample 1


title: U2OS- AiD DiV A- AsiSI -ER - siMePCE

value: siMePCE


title: H3K27ac ChIP-seq for E10 brain cortex, rep2


title: U2OS- AiD DiV A- AsiSI -ER - siNC + RNase H

value: siNC + RNase H


title: iSNF2L +IAA 24h RNA-seq 2

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Toxoplasma gondii type II strain ME49
The library was sequenced using the llumina Novaseq 6000 sequencing platform and 150 bp double ended readers were generated
Fastp (0.20.1) software is used to process raw reads in fastq format, and clean reads are obtained after removing low-quality reads for subsequent data analysis. The HISAT2 (2.1.0) software was used for reference genome alignment and FPKM calculation.
Differentially expressed genes were analyzed using DESeq2 (1.22.2) software, and genes with q < 0.05 and foldchange > 2 or foldchange < 0.5 were defined as differentially expressed genes (DEGs). DEGs were subjected to hierarchical cluster analysis using R (v 3.2.0) to reveal patterns of gene expression in different groups and samples.
Assembly: Clean reads were aligned to the reference genome ToxoDB-63_TgondiiME49(https://toxodb.org/common/downloads/Current_Release/TgondiiME49/fasta/data/ToxoDB-63_TgondiiME49_Genome.fasta)
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol reagent, and 1 ug of total RNA was used for the construction of sequencing libraries
Transcriptome libraries were constructed using the VAHTS Universal V5 RNA-seq Library Prep kit according to the instructions.


title: Lung 11


title: iSNF2L +IAA 24h RNA-seq 3


title: U2OS- AiD DiV A- AsiSI -ER - siNC

value: siNC


title: H3K27me3 ChIP-seq for E10 brain cortex, rep2


title: Lung 7


title: iSNF2L +IAA 24h RNA-seq 1


title: Lung 6


title: Input ChIP-seq for brain cortex, rep1


title: iSNF2L +IAA 12h RNA-seq 3


title: U2OS- AiD DiV A- AsiSI -ER - siMePCE input

value: siMePCE input


title: U2OS- AiD DiV A- AsiSI -ER - siMePCE + RNase H input

value: siMePCE + RNase H input


title: U2OS- AiD DiV A- AsiSI -ER - siNC + RNase H input

value: siNC + RNase H input


title: iSNF2L +IAA 12h RNA-seq 2


title: Lung 4


title: Lung 5


title: Lung 3


title: H3K27ac ChIP-seq for E10 brain cortex, rep1


title: U2OS- AiD DiV A- AsiSI -ER - siNC input

value: siNC input


title: iSNF2L +IAA 12h RNA-seq 1


title: H3K27me3 ChIP-seq for E12 brain cortex, rep1


title: Lung 8

value: murine lung tissue


title: H3K27me3 ChIP-seq for E12 brain cortex, rep2


title: iSNF2L +IAA 0h RNA-seq 3

value: 0 h


title: H3K27me3 ChIP-seq for E10 brain cortex, rep1

value: brain cortex


title: Lung 1

value: iECM


title: iSNF2L +IAA 0h RNA-seq 2

value: tachyzoites


title: U2OS- AiD DiV A- AsiSI -ER siMePCE RAD51

data_processing:
The adapter sequences in each raw fastq file (fastq) were trimmed using Trim Galore. The quality of each processed fastq file was then assessed with FastQC. Subsequently, the reads were aligned to the reference human genome hg19 using the bwa mem alignment method. SAMtools was employed to remove low-quality mapped reads by filtering out reads with a mapping quality score of less than 10, as well as PCR duplicates. Each read was extended by 200 bp to account for the full ChIP or DRIP fragment length during further analysis using deepTools bamCoverage. Reads per million reads (rpm) of 10 kb upstream and downstream for each AsiSI location were calculated from each sample using  deepTools multiBigwigSummary .
Assembly: hg19
Supplementary files format and content: bw files

value: U2OS- AiD-DiVA AsiSI -ER

tag: chip antibody


title: HiC-seq for E12-E15 brain cortex, rep2

data_processing:
Raw sequencing reads were trimmed by Cutadapt (version 1.18) to remove adapter and low-quality sequence. Trimmed paired-end reads were aligned, processed and iteratively corrected using HiCPro (version 2.11.1; Servant et al., Genome Biology 2015) with default parameters. Sequencing reads were mapped to the mm10 reference genome. To recover chimeric fragments spanning ligation junctions, the ligation sequence (GATCGATC) was searched in unmapped fragments and was used as split site to separate Hi-C joined ends in the chimeric fragments. Biological replicates were pooled for each time point using HiCPro with ‘-s merge_persample’. Hi-C contact difference was calculated by using ‘hicCompareMatrices’ function in HiCExplorer with a 1-Mb or 10-kb bin size. Hi-C contact maps were visualized using ‘hicPlotMatrix’ function in HiCExplorer (version 3.6; Wolff et al., Nucleic Acids Research 2020) with a 1-Mb or 10-kb bin size. For CRE filtering (see section "CRE identification"), HiC data from all time points were merged using HiCPro with ‘-s merge_persample’. To call TADs from Hi-C contact matrix, R package spectralTAD (version 1.8.0; Cresswell et al., BMC Bioinformatics 2020) was used on 10-kb bin size with default parameters and kept level 1 TAD. Hi-C contact map with TAD was visualized using “hicPlotTADs” function in HiCExplorer with a 10-kb bin size.
Assembly: mm10
Supplementary files format and content: The files including all the valid interaction pairs (described as Servant et al., 2015).

extract_protocol:
Cell suspension was prepared from E10 to E17 CD-1 mouse embryos. Four brains were collected for each time point. For E10 and E11 time points, ventricular zone was dissected from the tip of the brain. For E12 to E17 time points, brain tissues were first embedded in 4% low melting agarose at 35-37 °C and sectioned at 200 μm thickness with a vibratome (Leica) in ice-cold and oxygen-bubbling artificial cerebrospinal fluid (ACSF) containing: 125 mM NaCl, 5 mM KCl, 1.25 mM NaH2PO4, 1 mM MgSO4, 2 mM CaCl2, 25 mM NaHCO3, and 20 mM glucose (pH 7.4). The brain sections were transferred to a 3.5 cm dish containing ice-cold hibernate-E medium, and then ventricular zone was dissected and picked up under a stereoscope. The isolated VZ tissues were digested with papain using a commercial kit (Worthington, LK003150) at 37 °C for 30 min according to the manufacturer’s recommendations. Single cell suspension was generated by dissociating the digested tissues through pipetting, washed with DPBS to remove digesting enzymes, and stained with DAPI in ice-cold DPBS. To enrich RGPs at later time points, FlashTag labeling was performed as previously described (Govindan et al., 2018). Briefly, pregnant mice were anesthetized, injected with FlashTag into the lateral ventricle of the uterine horns, and housed for 30 min. Then, single cell suspensions were prepared as described above.
Hi-C libraries were prepared as described previously (Díaz, N. et al. Nat Commun. 2018) with minor modifications: 1x105 FlashTag+ FACS-purified cortex cells were immediately fixed for 10 min in freshly prepared 1% formaldehyde (Thermo Fisher Scientific, 28906) in PBS (Thermo Fisher Scientific, AM9624) at room temperature with gentle rotation (300 rpm). Then the reaction was quenched in 0.2 M glycine (Sigma-Aldrich, 50046) solution for 5 min at room temperature with gentle rotation (300 rpm). The cells were washed twice with 1 ml cold 1x PBS (centrifuged at 400 g for 5 min at 4°C). To lyse cells, the cells were resuspended in ice-cold in situ Hi-C buffer and incubated on ice for 15 min. The lysed cells were frozen in liquid nitrogen and stored at -80 °C until further use. Chromatin was digested using 50 U of MboI (New England Biolabs, R0147S) overnight at 37 ℃ with gentle rotation. After biotin filling, proximity ligation was carried out using 17.5 U T4 DNA Ligase (Thermo Fisher Scientific, EL0012) for 4 h at 20 °C with gentle rotation. DNA was sheared to 200-500 bp fragments using Covaris S220 sonicator with a duty factor of 10%, peak power of 140 W, and 200 cycles per burst. Each sample was sonicated for 2 cycles, 50s/cycle. Ligation fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (Thermo Fisher Scientific, 65001). Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit, according to the manufacturer’s instructions. Libraries were PCR amplified for 14-16 cycles by using NEBNext® Multiplex Oligos. DNA was then purified using 2.2x VAHTS DNA Clean Beads and eluted in ultrapure H2O.


title: iSNF2L +IAA 0h RNA-seq 1


title: U2OS- AiD DiV A- AsiSI -ER siMePCE XRCC4


title: HiC-seq for E12-E15 brain cortex, rep1


title: Heart 12

source_name: murine heart tissue

value: murine heart tissue


title: H3K27ac ChIP-seq for E12 brain cortex, rep1


title: iSNF2L+IAA ATAC-seq 3

data_processing:
The cutadapt (V2.5) tool is used to perform quality control on the original sequencing data, including removing adapter sequences, sequences with low quality sequencing bases and high proportion of unknown sequencing bases (N) in the original sequencing data, and reads shorter than 5bp after the above quality control.
Quality control qualified high quality sequencing reads were aligned to the reference genome using Bowtie2 (V2.3.4.1). Sambamba (V0.6.6) was used to mark duplicate reads, and script programs were used to count alignment metrics (including overall alignment rate, unique alignment rate, mitochondrial reads proportion, etc.).
Based on the bam file after marking duplication, use samtools (V1.12, samtools view) to count insert length. According to the unique sequence aligned to the reference genome in this project, the enrichment near the gene TSS is analyzed by using deeptools (V 3.5.1). The quality of the library can be characterized by the enrichment degree of the sequence near the TSS.
The open chromatin regions of each sample were identified using MACS2 (V2.1.1) software.
Assembly: Clean reads were aligned with the reference genome (Tgon.ToxoDB-63) using Bowtie2 software (Langmead and Salzberg 2012) V2.3.4.1
Supplementary files format and content: bigwig

extract_protocol:
Nuclei were isolated using nuclear lysis buffer, added to transposition reaction mixture [TruePrep DNA Library Prep Kit V2 for Illumina], incubated at 37℃ for 1 h, and transposition products were recovered using DNA Purification and Concentration Kit-5.
PCR amplification of the recovered transposition products was carried out using a system containing NEBNext High-Fidelity 2X PCR Master Mix and adaptive sequencing adapter primers, and the amplified PCR products were purified and recovered and fragments sorted using KAPA Pure Beads


title: U2OS- AiD DiV A- AsiSI -ER siMePCE GFP

value: 300nM 4OHT for 4 hrs

value: GFP


title: HiC-seq for E10-E11 brain cortex, rep2

value: wild type


title: Heart 10

value: Saline


title: iSNF2L+IAA ATAC-seq 2


title: Lung 2


title: iSNF2L+IAA ATAC-seq 1


title: HiC-seq for E10-E11 brain cortex, rep1


title: U2OS- AiD DiV A- AsiSI -ER siMePCE input

value: siMePCE


title: U2OS- AiD DiV A- AsiSI -ER siNC XRCC4

value: siNC


title: Heart 9


title: U2OS- AiD DiV A- AsiSI -ER siNC MePCE

value: MePCE


title: FLC31_Input

data_processing:
CUT&RUN: Sequencing quality control was evaluated by FastQC. Paired-end CUT&RUN raw reads were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using Bowtie2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were sorted by coordinates and tested for mapped fragment size distribution by Samtools. The final aligned and sorted Bam files were used for further processing. Visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools with option: --normalizeUsing RPKM -e -bs 50 and evaluated in IGV browser. CUT&RUN peaks were called by MACS2 callpeak with option: -g hs -B -f BAM -q 0.01. IgG controls were used for comparison. Each technical repeat and biological repeat were separately processed.
ATAC-seq: Technical duplicates of each ATAC-seq samples were combined and sequencing quality control was evaluated by FastQC. Fastq files of paired-end ATAC-seq data were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using BWA (Burrows-Wheeler Aligner). Aligned reads were sorted by coordinates and filtered out mitochondrial DNA and black-listed regions by Samtools. Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The final aligned, sorted and filtered Bam files were used for further analysis. ATAC-seq visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools and corrected for Tn5 insertion. ATAC-seq peaks were called from Tn-5 corrected insertions using MACS2 callpeak with option ‘-g hs -q 0.05 -f BAMPE and -B’.
ChIP-seq:The sequencing files were first demultiplexed and trimmed based on the eight-nucleotide barcode using previously described pipeline, allowing one mismatch on the first eight-nucleotide from read 121. The demultiplexed reads were then evaluated by FastQC then aligned to the hg19 genome using BWA (Burrows-Wheeler Aligner). Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The H3K27ac peaks were called using MACS2 callpeak with option ‘-g hs -B -f BAM -q 0.01’. Input controls were used for comparison during peak calling.
RNA-seq: Data was trimmed with Trimmomatic, and both pre- and post-trimming quality controls were evaluated by FastQC. The trimmed data were aligned to version 19 of the human reference genome (hg19) using STAR (2-pass). Samples with at least 20 million uniquely mapping reads were retained for further analysis. Reads count was performed with the ‘Htseq-count’ command in HTSeq with option: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. Reads count filtering was applied to the DESeqDataSet matrix to keep only rows that have at least 10 reads total.
Assembly: hg19
Supplementary files format and content: bigwig, bed (for CUT&RUN ATAC-seq and ChIP-seq)
Supplementary files format and content: csv files with normalized counts (For RNA-seq)

source_name: Primary FL sample 31

extract_protocol:
Cells were collected and washed by PBS. After final wash, nuclei were isolated using nuclei extraction buffer and then washed twice with wash buffer. Five-hundred thousand nuclei were counted and incubated with activated Concanavalin A coated beads and subsequently mixed with antibody in antibody buffer for overnight incubation on nutator in a cold room. IgG controls were set in parrel for antibody enrichment and specificity validation. Nuclei were then washed three times with digitonin buffer and incubated with PAG-MNase for 10 minutes at room temperature. After 10 minutes of incubation, nuclei were washed three times again with digitonin buffer and resuspended with prechilled low salt high Ca2+ buffer  to initiate 1-hour digestion at 0 °C. The reaction was terminated by switching into stop buffer and incubating at 37 °C for 10 minutes to release digested DNA from the nuclei. DNA was then purified with Ampure beads size selection (0.5X to remove large fragment and 2X to recover desired nucleosomal DNA fragments).
NGS libraries were generated with KAPA Hyper Prep Kits (Roche KK8502) using 14 cycles of PCR amplification. Libraires were validated on a Tapestation 4200 (Agilent G2991BA), quantified by Qubit High Sensitivity dsDNA Kit (Life Technologies Q32854), multiplexed and sequenced on a NovaSeq6000 using 100-10-10-100bp reads format.

value: Primary FL sample 31

value: CREBBP point mutant

value: sort B cells


title: U2OS- AiD DiV A- AsiSI -ER siMePCE MePCE


title: Heart 8


title: Heart 11


title: FLC27_Input

source_name: Primary FL sample 27

value: Primary FL sample 27


title: iSNF2L -IAA ATAC-seq 3

value: 0 h


title: Heart 7


title: U2OS- AiD DiV A- AsiSI -ER siNC RAD51


title: iSNF2L -IAA ATAC-seq 2


title: iSNF2L -IAA ATAC-seq 1


title: FLC26_Input

source_name: Primary FL sample 26

value: Primary FL sample 26


title: U2OS- AiD DiV A- AsiSI -ER siNC GFP


title: FLC24_Input

source_name: Primary FL sample 24

value: Primary FL sample 24


title: MHCC-97H cells, si-CENPU, rep3

city: Wuhan

first: Yingyi

last: Liu

address: #169, East Lake Road, Wuchang District, Wuhan

department: Department of Hepatobiliary and Pancreatic Surgery

institute: Zhongnan Hospital of Wuhan University

data_processing:
Illumina Novaseq 6000 sequencing system was used.
Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, paired-end RNA-seq sequencing library was sequenced with the Illumina NovaSeq 6000 sequencer.
The raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: Homo_sapiens GRCh38.p13
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: hepatocellular carcinoma tissuses

growth_protocol: Huh-7 and MHCC-97H hepatoma cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using PureLink RNA mini kit (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

treatment_protocol: Huh7 and MHCC-97H cells were transfected with si-CENPU (small interfering RNA targeting CENPU) and control si-NC respectively.

value: hepatocellular carcinoma tissuses

value: hepatoma cells

value: CENPU knockdown

value: transfected with Si-CENPU


title: UT-03

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Toxoplasma gondii type II strain ME49
Assembly: GCA_000006565.2 Toxoplasma gondii ME49
Supplementary files format and content: raw counts, FPKM

value: tachyzoites

value: Transgenic parasite ME49 iKD TGME49_217480-3HA-mAID

value: IAA for 0 h


title: Heart 5

data_processing: Data was analyzed by ROSALIND®, with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization were selected based on the geNorm algorithm as implemented in the NormqPCR R library (3). Abundance of various cell populations was calculated on ROSALIND using the Nanostring Cell Type Profiling Module. In ROSALIND, we performed a filtering of Cell Type Profiling results to include results that have scores with a p-value greater than or equal to 0.05. Fold changes and p-values were calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual.

value: murine heart tissue

value: Saline


title: FLC23_Input

first: Haopeng

last: Yang

address: 7455 Fannin ST

institute: The University of Texas MD Anderson Cancer Center

source_name: Primary FL sample 23

value: Primary FL sample 23


title: Heart 4

value: iECM


title: U2OS- AiD DiV A- AsiSI -ER siNC input

value: U2OS- AiD-DiVA AsiSI -ER

value: siNC

value: 300nM 4OHT for 4 hrs


title: FLC20_Input

source_name: Primary FL sample 20

value: Primary FL sample 20

value: CREBBP point mutant

value: sort B cells


title: UT-01


title: MHCC-97H cells, si-CENPU, rep2

value: hepatocellular carcinoma tissuses


title: IAA-03

value: IAA for 12 h


title: FLC34_Input

source_name: Primary FL sample 34

value: Primary FL sample 34

value: CREBBP WT


title: FLC33_Input

source_name: Primary FL sample 33

value: Primary FL sample 33


title: IAA-02

value: tachyzoites

value: Transgenic parasite ME49 iKD TGME49_217480-3HA-mAID


title: FLC32_Input

source_name: Primary FL sample 32

value: Primary FL sample 32


title: MHCC-97H cells, si-NC, rep3

value: hepatoma cells

value: WT

value: transfected with Si-NC


title: Heart 2

value: murine heart tissue

value: Saline


title: Infiltrating mononucleated cells from muscles of Spp1 floxed mice crossed to Lyz2Cre

city: Los Angeles

first: Feiyang

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

description: Library name: 10X_Lyz2_CRE_Spp1_floxed_mdx

data_processing:
The demultiplexing, barcoded process was done using Cell Ranger (v7). Low-quality cells were removed when more than 20% of the UMIs were derived from mitochondrial genes, when less than 200 features and more than 1,800 unique features were detected.
Assembly: mm10
Supplementary files format and content: Raw count matrix in rds format and cell barcode metadata in csv format

source_name: Muscle

extract_protocol:
cell suspensions were filtered through a 40 µm flowmi cell strainer (SP BEL-ART) and the cell count, and viability were determined using 0.4% trypan blue dye (Gibco). Live PBMCs (viability > 95%) were then resuspended with 1 mL 1X PBS containing 1% UltraPure bovine serum albumin (Thermo Fisher Scientific).
The cells were loaded onto the Chromium Controller instrument (10x Genomics) to generate gel bead-in-emulsions (GEM) and indexed sequencing libraries according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 user guide.

value: Muscle

value: all mononucleated

value: Spp1 floxed mice crossed to Lyz2Cre


title: Infiltrating mononucleated cells from mdx muscles

description: Library name: 10X_mdx

value: control WT


title: Heart 6

extract_protocol: Animals treated with LPS and iECM or saline were sacrificed at hour 30 as previously described. A total of n = 6 animals were used per group for a total of 12 animals and whole blood, spleen, lung, heart, brain, and kidney were harvested and flash frozen. 250 μL of whole blood was collected in 2 mL of RNAlater and stored at -80 C until further processing. Flash frozen samples tissue samples were homogenized with either a Tissue Tearer rotator homogenizer (Cole-Parmer, Vernon Hills, IL) or a Beadbug bead homogenizer (Benchmark Scientific). For lung, brain, kidney, and spleen, RNA was isolated through a NucleoSpin® RNA/Protein kit (Takara Bio USA Inc. San Jose, CA) while heart issue was processed with a RNeasy Fibrous Mini kit (Qiagen, Germantown, MD). Blood samples were isolated using a Mouse Ribopure Blood RNA Isolation Kit (Invitrogen). RNA was extracted based on manufacturer instructions with an on-column DNase digestion for minimizing genomic DNA contamination.

value: iECM


title: IAA-01

value: IAA for 12 h


title: UT-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome of Toxoplasma gondii type II strain ME49
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

value: Transgenic parasite ME49 iKD TGME49_203980-3HA-mAID

value: IAA for 0 h


title: MHCC-97H cells, si-NC, rep1

value: hepatocellular carcinoma tissuses


title: FLC30_Input

city: Houston

source_name: Primary FL sample 30

value: Primary FL sample 30

value: CREBBP WT

value: sort B cells


title: FLC28_Input

source_name: Primary FL sample 28

value: Primary FL sample 28


title: BM-Neutrophil, G-CSF, rep3

city: Suwon

first: JungHyub

last: Hong

address: 2066 Seobu-ro

country: South Korea

institute: University of SungKyunKwan

description: Library name: Sample 6

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012). The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020) using Bioconductor (Gentleman et al.,2004).
Gene classification was based on searches done by DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Bone marrow

growth_protocol: The mouse bone marrow-derived neutrophils were suspended at 4.0 x 10^5/200 µL in complete RPMI containing 3% fetal bovine serum (FBS) and 100 U/ml penicillin/streptomycin. The cells were plated at 200 µL/well on 96-well plates and incubated at 37°C with 5% CO2 for 6 hours.

extract_protocol:
RNA was lysed using RNAiso Plus (Takara) and purified according to the protocol of the PicoPure™ RNA Isolation Kit (Thermo).
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-seq Library Prep Kit (Lexogen, Inc. Austria) according to the manufacturer's instructions.

treatment_protocol: Bone marrow-derived neutrophils were treated with medium or medium containing 10 ng/ml G-CSF for 6 hours.

value: Bone marrow

value: Ex vivo BM-Neutrophil

value: Neutrophil

value: WT

value: G-CSF (10ng/ml)


title: UT-02

value: tachyzoites

value: Transgenic parasite ME49 iKD TGME49_217480-3HA-mAID


title: Heart 3

value: murine heart tissue

value: Saline


title: BM-Neutrophil, G-CSF, rep2

description: Library name: Sample 5


title: UT-2


title: MHCC-97H cells, si-CENPU, rep1

value: hepatoma cells

value: CENPU knockdown

value: transfected with Si-CENPU


title: FLC25_Input

source_name: Primary FL sample 25

value: Primary FL sample 25


title: Huh-7 cells, si-CENPU, rep3

value: hepatocellular carcinoma tissuses


title: FLC31_H3K27Ac

value: Primary FL sample 31

value: CREBBP point mutant

value: Mouse recombinant anti-H3K27Ac Active Motif Cat#91193


title: BM-Neutrophil, G-CSF, rep1

description: Library name: Sample 4

value: Bone marrow


title: UT-1

value: Transgenic parasite ME49 iKD TGME49_203980-3HA-mAID

value: IAA for 0 h


title: BM-Neutrophil, Medium, rep3

description: Library name: Sample 3

value: Ex vivo BM-Neutrophil

value: Neutrophil

value: WT

value: Medium


title: MHCC-97H cells, si-NC, rep2

value: transfected with Si-NC


title: Heart 1

value: murine heart tissue

value: iECM


title: BM-Neutrophil, Medium, rep2

description: Library name: Sample 2


title: FLC27_H3K27Ac

value: Primary FL sample 27

value: sort B cells


title: IAA-2

value: tachyzoites

value: IAA for 12 h


title: Huh-7 cells, si-NC, rep3

value: hepatocellular carcinoma tissuses

value: hepatoma cells


title: BM-Neutrophil, Medium, rep1

description: Library name: Sample 1


title: IAA-3


title: Huh-7 cells, si-CENPU, rep1

value: CENPU knockdown

value: transfected with Si-CENPU


title: FLC26_H3K27Ac

value: Primary FL sample 26

value: CREBBP point mutant

value: Mouse recombinant anti-H3K27Ac Active Motif Cat#91193


title: Huh-7 cells, si-NC, rep2


title: FLC24_H3K27Ac

value: Primary FL sample 24


title: IAA-1

value: Transgenic parasite ME49 iKD TGME49_203980-3HA-mAID


title: Huh-7 cells, si-NC, rep1

value: WT


title: dTAG Clone D7

city: Boston

first: Claudia

last: Mimoso

address: 45 Shattuck St. LHRRB

institute: Harvard Medical School

description: Library name: Sample 6

data_processing:
Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 50 bp per mate and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
Reads were first mapped to the dm6 version of the Drosophila genome using STAR 2.7.31. Reads not mapping to the spike genome were then used for alignment to mouse (mm10) using parameters --quantMode TranscriptomeSAM GeneCounts --outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --outFilterMismatchNmax 4 --alignSJoverhangMin 8 --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0. Duplicates were also removed using STAR.  Stranded coverage bedGraph files were generated from deduplicated BAM files using STAR.
DMSO and dTAG BedGraphs were depth normalized using the normalize_bedGraph custom script. siNT and siZC3H4 BedGraphs were depth normalized using the normalize_bedGraph custom script
BedGraph files were converted to the bigWig format, and merged bedGraphs for each experimental condition were generated using bigWigMerge (UCSC tools).
RNAseq reads within exons were summed per gene using featurecounts. RNAseq reads were summed between uaTSS to +3kb for uaRNAs. DESeq2 was used to generate a list of differentially expressed genes after ZC3H4 inhibition. DESeq2 size factors were overwritten to match depth normalization.
Assembly: mm10
Supplementary files format and content: bedGraph

source_name: mouse embryonic stem cells

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse. RNA was then fragmented. 4sU-containing RNA was biotinylated, pulled down, and washed. RNA was then eluted and purified.
4sU-labeled RNA was used as input to the Illumina TruSeq stranded total RNA kit using the manufacturer's protocol.

value: CAST/129 hybrid background, female

value: mouse embryonic stem cells

value: 500nM dTAG13


title: Hep3B-KD3

city: Jinan

first: Yu-Chuan

last: Yan

state: Shandong

address: 107 West Wen Hua Road

institute: Qilu Hospital of Shandong University

description:
Library name: Sample12
HP3B_KD3_tpm

data_processing:
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional- enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferronicorrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: hg38
Supplementary files format and content: HUH7_NC_vs_HUH7_KD.deseq2.annot.txt
Supplementary files format and content: HEP3B_NC_vs_HEP3B_KD.deseq2.annot.xls

growth_protocol: Huh7 cells were maintained in high-glucose DMEM supplemented with 10% foetal bovine serum, penicillin (100 IU/ml) and streptomycin (100 μg/ml). Hep3B cells were maintained in MEM-alpha supplemented with 10% foetal bovine serum, penicillin (100 IU/ml) and streptomycin (100 μg/ml).  All the cells were cultured in 25 cm2 polystyrene culture flasks in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted  using an RNA Rapid Extraction Kit (RNAfast200, Fastagen, China) according to the manufacturer’s instructions.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

value: Hepatocellular carcinoma

value: FAM111B knockdown


title: Huh-7 cells, si-CENPU, rep2


title: dTAG Clone A9

description: Library name: Sample 5


title: Hep3B-KD2

description:
Library name: Sample11
HP3B_KD2_tpm


title: FLC23_H3K27Ac

value: Primary FL sample 23

value: sort B cells


title: dTAG Clone A6

description: Library name: Sample 4


title: Hep3B-KD1

description:
Library name: Sample10
HP3B_KD1_tpm


title: FLC34_H3K27Ac

value: Primary FL sample 34

value: CREBBP WT


title: Hep3B-NC3

description:
Library name: Sample9
HP3B_NC3_tpm

value: Control group


title: DMSO Clone D7

description: Library name: Sample 3

value: DMSO


title: Hep3B-NC2

description:
Library name: Sample8
HP3B_NC2_tpm


title: FLC30_H3K27Ac

value: Primary FL sample 30


title: Hep3B-NC1

description:
Library name: Sample7
HP3B_NC1_tpm


title: Ire cells-s

city: Tainan

first: Kuan-Chung

last: Hsiao

address: 367 shengli road

country: Taiwan

institute: NHRI

data_processing:
Differential expression analysis Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.
GO and KEGG enrichment analysis GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of enriched genes with a significant padj less than 0.05. And topGO was used to plot DAG. KEGG (Kyoto Encyclopedia of Genes and Genomes) is a collection of databases dealing with genomes, biological pathways, diseases, drugs, and chemical substances (http://en.wikipedia.org/wiki/KEGG). We used scripts in house to enrich significant differential expression gene in KEGG pathways.
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Supplementary files format and content: Group_Ire-VS-Ire-S_DE_anno.xlsx

source_name: NSCLC

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen)/RNeasy Mini Kit (Qiagen)/other kits. Total RNA of each sample was quantified and qualified by Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), NanoDrop (Thermo Fisher Scientific Inc.) and 1% agrose gel. 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol. The poly(A) mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit. The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer and Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic，Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

tag: agent

value: statin

value: NSCLC

value: epithelial cells


title: DMSO Clone A6

description: Library name: Sample 1


title: DMSO Clone A9

description: Library name: Sample 2


title: tga7_LN_root3

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

institute: The University of Tokyo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: WT and tga7 seedlings were grown on 1/2 MS plates for 5 days and then on nitrogen-sufficient and nitrogen-defficient agar plates for 5 days.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: shoot part and root part from 10 day-old wild-type and tga7 seedlings grown under nitrogen-sufficient and nitrogen-defficient conditions

value: deficient nitrogen

value: root


title: FLC32_H3K27Ac

value: Primary FL sample 32

value: Mouse recombinant anti-H3K27Ac Active Motif Cat#91193


title: tga7_LN_root1


title: Ire cells


title: FLC28_H3K27Ac

value: Primary FL sample 28


title: Huh7-KD3

description:
Library name: Sample6
HUH7_KD3_tpm

value: Hepatocellular carcinoma


title: tga7_LN_root2


title: WT_LN_root3


title: FLC20_H3K27Ac

value: Primary FL sample 20

value: CREBBP point mutant


title: WT_LN_root2


title: Huh7-KD2

description:
Library name: Sample5
HUH7_KD2_tpm

value: FAM111B knockdown