title: Sample 5_Transcriptome_npy1Δ_rep2

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_n_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'SC_n_merge_genome.wig' generated based on the multiple samples #4-6
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt
Stat_Transcriptome_rnVSn_5UTRv.txt


title: Sample 2_Transcriptome_WT_rep2

status: Public on Apr 28 2020

type: SRA

city: Heidelberg

first: Yaqing

last: Zhang

state: baden württemberg

address: Im Neuenheimer Feld 364

department: Institute of Pharmacy and Molecular Biotechnology

country: Germany

institute: Heidelberg University

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_wt_rep2
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'SC_wt_merge_genome.wig' generated based on the multiple samples #1-3
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_rVSwt_5UTRv.txt

library_source: transcriptomic

data_processing:
Illumina NextSeq basecalling.
NAD captureSeq Analysis: Standard Unfragmented NADcaptureSeq Analysis: Original reads were demultiplexed by the barcode without mismatch and quality controlled. Further 5’ end leading (G/N)n and 3’ end adapter (C NNNNNN AGATCG) were trimmed (minimum length 12 nt). Reads mapped to spiked-in internal standard (IS) RNAI sequence (bowtie -v 2, version 1.1.2) were counted. IS unmapped reads were classified as small RNA reads (12-17 nt) or normal RNA reads (>18nt). Normal RNA reads were mapped to the reference genome S. cerevisae BY4742 strain (BY4742_Toronto_2012, SGD) (bowtie -v 2). Reads mapped to either rRNAs or tRNAs were separated and counted individually. Remaining reads that cannot map to rRNAs were remapped to the reference genome (bowtie –best --strata -M 1 -m 20 -v 2). Sam files were converted to bam files then sorted (samtools, version 0.1.13). Bam files were used to generate wig file which normalized by RPM for single nucleotide polymorphism analysis. Sorted sam files were further filtered by strand-specific selection. the filter-passed reads also be counted (htseq-count -m intersection-nonempty, version 0.6.0) based on annotation gff3 file (BY4742_Toronto_2012, SGD, mRNA regions were annotated by their 5’ UTR region (-120 to +65, translation starting site (TLS) referred as ‘0’). Raw hits were analyzed by DESeq2 (version 1.4.5, relevant package from Bioconductor version 2.14) for NAD-RNA enrichment statistics.
Transcriptome Analysis: Raw reads were demultiplexed and quality controlled with same parameter as previous analysis. Reads with 5’-/3’- end adapters were properly trimmed then the raw sequences were reverse complemented. Mapped reads to the reference genome (bowtie, -v 2). For rRNAs and tRNAs independent mapping and counting as well as rRNAs-free reads counting (same annotation region on 5’ UTR of mRNA) was same as performing NAD captureSeq analysis. Same procedure to generate wig file and to differential expression statistics.
Genome_build: BY4742 Saccharomyces cerevisiae
Supplementary_files_format_and_content: tab-delimited text files include 1) the raw counts of RNA species("rawHits" label) and DESeq2 statistics for their normalized enrichment ("Stat" label)for both NAD captureSeq (UF, SF, LF) and Transcriptome (SC). WIG files were generated without rRNA reads and in standard format.

molecule: total RNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured with the standard condition, YPD medium, 30 degree, shaking. Cell pellets were harvest when OD590 was ~0.8.

extract_protocol:
Total RNAs from yeast BY4742 strains were isolated by hot phenol method (Collart and Oliviero, 2001) with minor change. Harvested cells (OD590 0.8) from 0.5 L YPD. Fast frozen by liquid nitrogen, stored at -80 °C until all samples ready. Cell pellets were defreezed on ice and washed with dH2O. Resuspend cell pellets in 8 mL TES solution (10mM Tris-HCl (pH 7.5), 10 mM EDTA, 0.5% SDS) and added 8 mL phenol (Carl ROTH). Vortexed thoroughly 1 min and incubated 60 min at 65 °C with occasional shaking (50 seconds/10 min, 550 rpm). Place on ice 15-20 min. Centrifugation with 14,000 g at 4 °C. Followed by phenol extraction, P/C/I purification, and chloroform purification. RNA was precipitated with 0.1 volume 3 M NaOAc (pH 5.5) and 2.5 volume ethanol at -20 °C overnight. Precipitated RNA was solved in 2 mL dH2O. Measured its concentration and determined the integrity by 1.2% formaldehyde denature agarose gel electrophoresis. Treated 1 mg RNA with 100U DNase I (Roche) in 1X DNase I buffer (Roche) at 37 °C, 40 min. Twice P/C/I purification. RNA was precipitated by ethanol at -20 °C overnight. Solve in 100 µL dH2O. Measured the RNA concentration and check its integrity as well as genome DNA (gDNA) residue by 1.2% formaldehyde denature agarose gel electrophoresis.
Standard unfragmented NAD captureSeq (UF): gDNA-free total RNA applied NAD-RNA capture protocol (Winz et al., 2017) with minor modification as followed. Biological triplicates of total RNA. 100 µg total RNA was treated with adenosine diphosphate-ribosylcyclase (ADPRC, self-prepared, 22.5 U), 10 µL 4-pentyn-1-ol (Sigma-Aldrich), 5 ng NAD-RNAI (self-prepared, spiked-in control, optional) in 100 µL reaction including 50 mM Na-HEPES (pH 7.0), 5 mM MgCl2 at 37 °C, 60 min. The reaction minus ADPRC was utilized as background (negative control). The reaction stopped by adding 100 µL dH2O and 200 µL P/C/I reagent. Performed twice P/C/I extraction with additional three times ether (Honeywell) extraction afterwards. Followed by copper-click reaction, streptavidin beads binding, preadenylated-3’-adaptor ligation, reverse transcription, CTP tailing, anchored-5’-adapotr ligation, cDNA PCR amplification with barcode are same as standard capture protocol. Quality control of libraries by sanger sequencing of spike-in RNAI amplicon as well as other cDNA amplicons which were amplified by adaptor-ligated sequence on cDNA library then cloned into plasmid(s). Size-selected PCR products within the range of 150-300 bp were purified by 10% native polyacrylamide gel eletrophoresis. Cleanness of primer-dimer was examined by Bioanalyzer 2100 (Agilent) using Agilent High Sensitivity DNA Kit. Concentration was measured by Qubit. Multiplexed primer-dimer-free library at final concentration ~20 nM accordingly. Based on to the size distribution of cDNA, either adding of 20% v3 Phix Control (Illumina) or using customer Illumina sequencing primer which has 3Gs at the end of standard Illumina sequencing primer to mitigate unbalance library before NextSeq 500/550 75bp SE sequencing. Fragmented NAD captureSeq: Biological triplicates of total RNA (gDNA-free). 100 µg total RNA with 5 ng NAD-RNAI (spiked-in control, optional) randomly sheared in 65 µL reaction containing 0.5 volume of alkaline fragmentation solution (2 mM EDTA, 10 mM Na2CO3, 90 mM NaHCO3, pH 9.3) at 94 °C (5 min for wild type strain, 20 min for npy1Δ strain). Checked the sheared fragments on 1.2% formaldehyde denature agarose gel. Additional add 200 µL dH2O and precipitate properly sheared RNA with 2.5 volume ethanol, 0.1 volume 3 M NaOAc (pH 5.5), 1 µL glycogen at -20 °C overnight. Precipitated RNA washed by 75% ethanol and solve in dH2O. Followed by treating each 100 µg RNA with 100 U T4 PNK (Thermo Scientific), along with 0.1 mM ATP, 100 mM imidazole-HCl (pH 6.0), 10 mM MgCl2, 10 mM β-mercaptoethanol, 10 µg BSA (Thermo Scientific) in a total volume 200 µL, 37 °C, 5.5 h. Twice P/C/I purification and triple ether extraction followed by ethanol precipitation. Precipitated RNA washed by 75% ethanol and solve in dH2O as library input for performing standard NAD captureSeq. Size-selected PCR products with the range of 150-300 bp (small fragmented NAD captureSeq library, SF) and 300-500 bp (large fragmented NAD captureSeq library, LF) were purified from 10% native polyacrylamide gel. Bioanalyzer quality control, library multiplex and sequence strategy are same as unfragmented NAD captureSeq. Sequenced by NextSeq 500/550 75bp SE.Transcriptome libraries: Biological triplicates of total RNA (gRNA-free). 1 µg total RNA was performed ribosome RNA deletion by Ribo-Zero rRNA Removal Kit (yeast, Illumina). rRNA-depleted RNAs were randomly sheared at 94 °C 10 min. Fragmented RNAs were processed by NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). Barcoded PCR-amplified cDNA by NEBNext Multiplex Oligo for Illumina (NEB). Further cDNA size-selection in the range of 300-500 bp was performed by Agencourt RNAClean XP (Beckman Coulter). Samples were checked by Bioanalyzer and measured by Qubit. Multiplexed library was sequenced by NextSeq 500/550 75bp SE.

treatment_protocol: "S" for ADPRC full-treated while "N" for ADPRC minus control. "UF" represents unfragmented total RNA for library input, while "SF" and "LF" for small fragmented RNA library and large fragmented RNA library, respectivily. Details could be find in library construction protocol.

tag: strain

tag: genotype/variation

value: Mat{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0

tag: growth phase

value: Log phase


title: Sample 3_Transcriptome_WT_rep3

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_wt_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'SC_wt_merge_genome.wig' generated based on the multiple samples #1-3
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_rVSwt_5UTRv.txt


title: DP-4287

city: Hefei

first: Bin

last: Li

address: NO. 96 Jinzhai Road

country: China

institute: University of Science and Technology of China

description: ftATAC-seq data of mouse thymoctyes

library_source: genomic

data_processing:
We used BOWTIE2 to map the trimmed sequencing data to the corresponding genome index and used PICARD for the sorting, duplicate removal, and fragment length counting of the aligned data.
We calls peaks from the merged single-cell profiles of all cells using MACS2 to ensure that the entire analysis is unsupervised. We then ranked and filtered out the low quality peaks based on the false discovery rate (Q-value).
Genomic locations of the peaks were annotated by HOMER, and motifs searched by FIMO.
We calculates the number of fragments and the percent of reads mapped to the TSS region (±2000 BP) for each cell, and filters out high quality cells for downstream analysis.
We integrate all processing steps as a pre-process script of APEC.
Genome_build: mm9
Supplementary_files_format_and_content: The cell.csv file is a CSV format file containing the information of filtered cells; the features.bed file is a BED format file containing the information of filtered peaks; the matrix.mtx file is the fragment count matrix stored in MTX format.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse thymoctyes

extract_protocol:
Thymus tissues isolated from 6- to 8-week-old male mice were gently ground in 1 mL of RPMI-1640. Thymocytes in a single-cell suspension were counted after passing through a 40 μm nylon mesh. A total of 1 × 106 thymocytes were stained with PerCP-Cy5.5-anti-CD45, PE-anti-CD8a and APC-Cy7-anti-CD4 antibodies (Biolegend) and then fixed in 1× PBS containing 1% methanal at room temperature for 5 min. After washing twice with 1× PBS, the cells were counted again. A total of 1 × 105 fixed cells were resuspended in 40 μL of 1× TD buffer (5 mM Tris-HCl, pH 8.0, 5 mM MgCl2 , and 10% DMF) containing 0.1% NP-40. Then, 10 μL of fluorescent transposomes were added and mixed gently. Fluorescent tagmentation was conducted at 55 °C for 30 min and stopped by adding 200 µL of 100 mM EDTA directly to the reaction mixture. The cells were loaded on a Sony SH800S sorter, and single cells of the CD45+/AF488-Tn5hi population were index-sorted into each well of 384-well plates. The 384-well plates used to acquire sorted cells were loaded with 2 µL of release buffer (50 mM EDTA, 0.02% SDS) before use. After sorting, the cells in the wells were incubated for 1 min. Plates that were not processed immediately were preserved at -80 °C.
To prepare a single-cell ATAC-seq library, plates containing fluorescently tagmented cells were incubated at 55 °C for 30 min. Then, 4.2 μL of PCR round 1 buffer (1 μL of 100 μM MgCl2, 3 μL of 2× I-5 PCR mix [MCLAB], and 0.1 μL each of 10 μM R1 and R2 primers) were added to each well, followed by PCR: 72 °C for 10 min; 98 °C for 3 min; 10 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Thereafter, each well received 4 µL of PCR round 2 buffer (2 μL of I-5 PCR Mix, 0.5 μL each of Ad1 and barcoded Ad2 primers, and 1 μL of ddH2O), and final PCR amplification was carried out: 98 °C for 3 min; 12 cycles of 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min; 72 °C for 3 min; and holding at 4 °C. Wells containing different Ad2 barcodes were collected together and purified with a QIAquick PCR purification kit (Qiagen).

tag: tissue

value: thymocytes

tag: age

value: 6-8 weeks


title: Sample 1_Transcriptome_WT_rep1

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_wt_rep1
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #7-9
File 'Stat_Transcriptome_rVSwt_5UTRv.txt' generated based on the multiple samples #1-3 and samples #10-12
File 'SC_wt_merge_genome.wig' generated based on the multiple samples #1-3
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dVSwt_5UTRv.txt
Stat_Transcriptome_rVSwt_5UTRv.txt


title: zebrafish_989s_B19

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing:
bcl2fastq - demultiplexing
sequenced reads were trimmed for adaptor sequence, and then mapped to the zebrafish reference genome (danRer11) using TapHat2, Bowtie2.
raw read counts per gene were calculated using featureCounts from subread
for analysis, all raw counts from all cells of each of the three sample-plates (plate_123, plate_989, plate_990) were combined into one expression matrix file
counts data was processed and analyzed using velocyto, SingleCellExperiment and pagoda2 packages in R-software
Genome_build: GRCz11 (danRer11)
Supplementary_files_format_and_content: tab-deliminated txt file as expression matrix including non-normalized counts of all samples

organism: Danio rerio

source_name: zebrafish

extract_protocol:
FACS into 384well plate of single cells from partial dissociation of embryo trunks with 0.5% trypsin-EDTA and 10U Dnase I for 30min at 30°C
RNA libraries were prepared using standard SmartSeq2 protocol

value: embryo trunk

tag: starin

value: vegfc:Gal4FF;UASGFP; kdrl:mCherry

value: 48 hpf


title: DP-4286

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_B18


title: LNCaP TMW_24B

city: NEW YORK

first: Jennifer

last: Diaz

state: New York

address: 69 E 97TH ST, APT 17

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
aligned raw reads to hg19 reference genome (UCSC) using the STAR aligner (version 2.4.2a) (Dobin et al., 2013)
used the featureCounts (Liao, Smyth, & Shi, 2014) module from subread package (version 1.4.4) to map the aligned reads to genes in the hg19 reference genome
kept genes with at least one count in at least three control (DMSO) samples at any time point
normalized the resulting count matrix using Trimmed Mean of M-values (TMM) method (Robinson & Oshlack, 2010)
prouiced log base 2 of count per million (cpm) after adjusting plates as covariates
Genome_build: hg19
Supplementary_files_format_and_content: .csv files are matrices of logcpm for each gene (rows) and sample (columns)

molecule: polyA RNA

organism: Homo sapiens

source_name: LNCaP cells

growth_protocol:
MCF-7 (ATCC HTB-22) cells were obtained from ATCC. Cells were cultured according to manufacturer’s recommendations in ATCC-formulated Eagle's Minimum Essential Medium (Catalog No. 30-2003) with 10% heat-inactivated fetal bovine serum, and 0.01 mg/ml human recombinant insulin. LNCaP cells were purchased from ATCC (Cat No CRL-1740) and stored in liquid nitrogen until use. Frozen vial was quickly thawed in 37C bath, and then cells were washed from DMSO by spinning in 15ml vial filled with 10mls of PBS.  Cells were re-suspended in RPMI media (ATCC, Cat No 30-2001) supplemented with 10% Fetal Bovine Serum (ATCC, Cat No 30-2021) and plated into 75cm cell culture flask (Corning. Cat No 430641). Growth media was changed every 3-4 days. After reaching confluence, cells were split at a ratio 1:6.
To split, media was removed, cells were washed with PBS, and trypsin-EDTA mix was added for 5 min. After detachment, cells were washed with growth media, collected into 50ml vial, spin down at 1000RPM, suspended in fresh media and plated into 75cm flasks.

extract_protocol:
The cells were plated at a density of 8,000 cells per well in a 96 well plate (Greiner Cat. No. 655083) and placed in an incubator.  After 24 hours, the plates were removed from the incubator and treated with drugs using the HP D300 Digital Dispenser. The cells were then collected at the targeted time point by removing the media and pipetting 150uL of Qiagen Buffer RLT into each well.  The plates were then frozen and stored at -80C. For RNA extraction, the Qiagen RNeasy 96 kit (Cat. No. 74181) was used with the Hamilton ML STAR liquid handling machine equipped with a Vacuubrand 96 well plate vacuum manifold. A Sorvall HT 6 floor centrifuge was used to follow the vacuum/spin version of the RNeasy 96 kit protocol. The samples were treated with DNAse (Rnase-Free Dnase Set Qiagen Cat. No. 79254) during RNA isolation.  The RNA samples were then tested for yield and quality with the Bioanalyzer and the Agilent RNA 6000 Pico Kit.
The TruSeq Stranded mRNA Library Prep Kit (RS-122-2101/RS-122-2102) was then used to prepare the samples for 30 million reads of single end sequencing (100bp) with the Illumina HiSeq2500. Three replicates were used for the combination experiments and two replicates for the dose experiments.

treatment_protocol: Cells were treated with Withaferin A (Enzo Life Sciences BML-CT104-0010), Mefloquine hydrochloride (Sigma-Aldrich M2319-100MG) or Tamoxifen citrate (Tocris 0999) in 0.3% DMSO for the viability time courses (Figure 1C-H) or 0.4% DMSO for dose-response curves (Figure S1B).

tag: cell line

value: LNCaP cells

tag: cell line source

value: ATCC (Cat No CRL-1740)

tag: treatment

value: Tamoxifen, Mefloquine, and Withaferin

tag: treatment concentration (um)

value: 20 uM, 10 uM, and 5 uM, respectively

tag: solvent

value: DMSO

tag: hours of treatment

tag: replicate

value: B


title: LNCaP TMW_24A

value: A


title: LNCaP TMW_24C

value: C


title: DP-4284

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_12B


title: DP-4285

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_12A


title: LNCaP TMW_9C


title: zebrafish_989s_B16


title: LNCaP TMW_12C


title: zebrafish_989s_B17


title: zebrafish_989s_B15


title: T-5003

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_B14


title: Sample 6_Transcriptome_npy1Δ_rep3

description:
H3KVWBGX5_YZ_Nov17_17s005828-1-1_SC_n_rep3
File 'rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'rawHits_CDSforAllmRNA_transcriptome_all_strains.txt' generated based on the multiple samples #1-24
File 'Stat_Transcriptome_nVSwt_5UTRv.txt' generated based on the multiple samples #1-6
File 'Stat_Transcriptome_dnVSn_5UTRv.txt' generated based on the multiple samples #4-6 and samples #13-15
File 'Stat_Transcriptome_rnVSr_5UTRv.txt' generated based on the multiple samples #4-6 and samples #19-21
File 'SC_n_merge_genome.wig' generated based on the multiple samples #4-6
processed data file:
rawHits_5UTRforAllmRNA_transcriptome_all_strains.txt
rawHits_CDSforAllmRNA_transcriptome_all_strains.txt
Stat_Transcriptome_nVSwt_5UTRv.txt
Stat_Transcriptome_dnVSn_5UTRv.txt
Stat_Transcriptome_rnVSn_5UTRv.txt

value: BY4742 npy1::kanMX4


title: LNCaP TMW_9A


title: zebrafish_989s_B13


title: DP-4280

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_3B


title: LNCaP TMW_9B


title: LNCaP TMW_3A


title: DP-4281

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_6C


title: LNCaP TMW_6B


title: LNCaP TMW_6A


title: zebrafish_989s_B12


title: LNCaP TMW_0C


title: DP-4279

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_0B


title: DP-4283

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TMW_0A


title: LNCaP MW_24C

value: Mefloquine and Withaferin

value: 10 uM and 5 uM, respectively


title: LNCaP MW_24B


title: zebrafish_989s_B10


title: LNCaP MW_24A


title: LNCaP MW_12C


title: zebrafish_989s_B1


title: LNCaP TMW_3C


title: DP-4282

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP MW_12B


title: DP-4276

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A9


title: DP-4275

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP MW_9B


title: zebrafish_989s_A8


title: LNCaP MW_12A


title: LNCaP MW_9A


title: DP-4274

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A7


title: DP-4273

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_B11


title: zebrafish_989s_A6


title: LNCaP MW_6A


title: LNCaP MW_6B


title: LNCaP MW_6C


title: LNCaP MW_3B


title: LNCaP MW_3C


title: DP-4277

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A5


title: LNCaP MW_3A


title: DP-4278

description: ftATAC-seq data of mouse thymoctyes


title: DP-4271

description: ftATAC-seq data of mouse thymoctyes


title: DP-4272

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A4


title: LNCaP MW_0A


title: DP-4270

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP MW_0B


title: LNCaP MW_9C


title: zebrafish_989s_A3


title: LNCaP TW_24C

value: Tamoxifen  and Withaferin

value: 20 uM and 5 uM, respectively


title: DP-4269

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes

value: 6-8 weeks


title: zebrafish_989s_A24

value: embryo trunk

value: vegfc:Gal4FF;UASGFP; kdrl:mCherry


title: DP-4268

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TW_24A

value: LNCaP cells


title: LNCaP TW_24B

value: ATCC (Cat No CRL-1740)


title: LNCaP TW_12C


title: LNCaP TW_12B


title: LNCaP TW_12A


title: DP-4267

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A23

value: 48 hpf


title: zebrafish_989s_A22


title: zebrafish_989s_A21


title: LNCaP MW_0C


title: DP-4265

description: ftATAC-seq data of mouse thymoctyes


title: DP-4266

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TW_9A


title: LNCaP TW_9B


title: zebrafish_989s_A20


title: LNCaP TW_6C


title: zebrafish_989s_A19


title: LNCaP TW_6B


title: LNCaP TW_3C


title: DP-4264

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TW_6A


title: DP-4263

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A18


title: LNCaP TW_3A


title: LNCaP TW_0C


title: zebrafish_989s_A17


title: LNCaP TW_0A


title: DP-4262

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TW_9C


title: DP-4261

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_24C

value: Tamoxifen and Mefloquine

value: 20 uM and 10 uM, respectively


title: LNCaP TW_0B

value: DMSO

value: B


title: DP-4260

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_24B


title: zebrafish_989s_A15


title: LNCaP TM_12C

value: C


title: zebrafish_989s_A14


title: LNCaP TM_12A

value: A


title: zebrafish_989s_A13


title: LNCaP TM_12B


title: LNCaP TM_9C


title: LNCaP TW_3B


title: LNCaP TM_9B


title: zebrafish_989s_A12


title: DP-4256

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_9A


title: LNCaP TM_6C


title: zebrafish_989s_A11


title: LNCaP TM_6B


title: LNCaP TM_24A


title: DP-4255

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_P9


title: DP-4254

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_P8


title: DP-4259

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_989s_A16


title: LNCaP TM_3B


title: DP-4253

description: ftATAC-seq data of mouse thymoctyes


title: DP-4258

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_3A


title: LNCaP TM_0C


title: zebrafish_123s_P7


title: DP-4252

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_0A


title: DP-4257

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_0B


title: zebrafish_123s_P6


title: zebrafish_123s_P5


title: LNCaP W_24B

value: Withaferin A (Enzo Life Sciences BML-CT104-0010)


title: LNCaP W_24A


title: DP-4250

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_12C


title: LNCaP TM_6A


title: zebrafish_123s_P4


title: LNCaP W_12B


title: DP-4249

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP TM_3C


title: zebrafish_123s_P3


title: LNCaP W_9C


title: LNCaP W_9A


title: DP-4248

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_12A


title: LNCaP W_9B


title: LNCaP W_6C


title: DP-4247

description: ftATAC-seq data of mouse thymoctyes


title: DP-4246

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_P22


title: LNCaP W_6B


title: zebrafish_123s_P21


title: LNCaP W_6A


title: DP-4251

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_P19


title: DP-4244

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_3A


title: LNCaP W_3B


title: zebrafish_123s_P2


title: DP-4245

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_0C


title: LNCaP W_0B


title: zebrafish_123s_P18


title: DP-4243

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_0A


title: zebrafish_123s_P17


title: LNCaP M_24C

value: Mefloquine hydrochloride (Sigma-Aldrich M2319-100MG)


title: zebrafish_123s_P16


title: DP-4241

description: ftATAC-seq data of mouse thymoctyes


title: DP-4240

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP M_24A


title: LNCaP M_12C


title: zebrafish_123s_P15


title: LNCaP W_3C


title: DP-4242

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP M_12B


title: zebrafish_123s_P14


title: zebrafish_123s_P13


title: LNCaP M_24B


title: DP-4239

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP M_9B


title: LNCaP M_9A


title: zebrafish_123s_P11


title: LNCaP M_6C


title: LNCaP M_6B


title: zebrafish_123s_P1


title: LNCaP M_3C


title: DP-4237

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP M_6A


title: DP-4238

description: ftATAC-seq data of mouse thymoctyes


title: DP-4236

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O9


title: LNCaP M_3B


title: LNCaP M_3A


title: LNCaP M_12A


title: zebrafish_123s_O8


title: DP-4235

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP M_0C


title: LNCaP M_9C


title: LNCaP M_0A


title: DP-4234

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O7


title: LNCaP T_24C

value: Tamoxifen citrate (Tocris 0999)


title: zebrafish_123s_O5


title: LNCaP T_24B


title: zebrafish_123s_O4


title: DP-4233

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP T_24A


title: DP-4232

description: ftATAC-seq data of mouse thymoctyes


title: DP-4231

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP T_12B


title: DP-4230

description: ftATAC-seq data of mouse thymoctyes


title: ko_H3K27me2_rep4

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: ChIP-seq data of mouse developmental embryo

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Reads were trimmed with Trimmomatic.
The trimmed reads were aligned to the mouse reference genome mm10 with Bowtie2.
Sequencing tracks normalized by the mapped read counts were generated with deepTools.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: bigwig

source_name: embryonic trunk

extract_protocol:
The embryonic head and trunk were collected with microdissection. To prepare single cell suspension, the tissues were placed in 1 ml of phosphate-buffered saline, pipetted and passed through a 35-um cell strainer (Corning Japan, Tokyo, Japan). The cells were fixed for 10 min in a 1% formaldehyde solution at room temperature and then neutralized for 5 min in a 0.125 M glycine solution. Pooled tissue samples from two embryos were used in ChIP analysis. ChIP was performed as previously described 51,52. Briefly, fixed cells were re-suspended in 2 ml of sodium dodecyl sulfate lysis buffer, containing 10 mM Tris-HCl, pH 8.0 (Thermo Fisher Scientific), 150 mM NaCl (Thermo Fisher Scientific), 1% sodium dodecyl sulfate (Sigma-Aldrich, St. Louis, MO), 1 mM EDTA, pH 8.0 (Thermo Fisher Scientific), and cOmplete™ EDTA-free protease inhibitor cocktail (Sigma-Aldrich). The samples were then fragmented in a Picoruptor (40 cycles, 30 s on/30 s off; Diagenode, Liege Science Park, Belgium). The sonicated solution was diluted with ChIP dilution buffer [20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA, and 1% Triton X-100 (Sigma-Aldrich)] up to 10.3 ml; 10 ml were used for immunoprecipitation (10 ml) and the remaining 300 ul were saved as a non-immunoprecipitated chromatin (the input sample). Specific antibodies against H3K4me3, H3K9me2, and H3K27me3 (MAB Institute, Inc. Nagano, Japan), and H3K27me2 (Cell Signaling Technology, Danvers, MA), and total H3 (Abcam, Cambridge, MA) were bound to magnetic Dynabeads M-280 (Thermo Fisher Scientific) and mixed with the diluted, sonicated solution for immunoprecipitation. The prepared DNA was quantified using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific), and more than 10 ng of DNA were processed for sequence.
ChIP-Seq library was prepared using DNA sonicated to an average size of 0.5 kb. ChIP samples were processed for library preparation using a KAPA Hyper Prep kit (Kapa Biosystems Inc., Wilmington, MA), according to the manufacturer’s instructions.

tag: chip antibody

tag: genotype

value: Kdm7a mutant

tag: developmental stage


title: zebrafish_123s_O24


title: LNCaP T_9C


title: DP-4229

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: LNCaP T_12A


title: LNCaP M_0B


title: ko_H3K27me3_rep4


title: ko_H3K27_input_rep4


title: LNCaP T_9B


title: zebrafish_123s_O23


title: LNCaP T_12C


title: zebrafish_123s_O22


title: wt_H3K27_input_rep4

value: wild-type


title: wt_H3K27me2_rep4


title: LNCaP T_9A


title: DP-4226

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: DP-4227

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP W_24C


title: wt_H3K27me3_rep4


title: LNCaP T_6A


title: zebrafish_123s_O19

value: embryo trunk


title: zebrafish_123s_O21


title: LNCaP T_6C

value: LNCaP cells


title: DP-3032

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP T_6B

value: ATCC (Cat No CRL-1740)


title: DP-4225

description: ftATAC-seq data of mouse thymoctyes


title: ko_H3K27me3_rep3


title: zebrafish_123s_O3

value: 48 hpf


title: ko_H3K27_input_rep3


title: DP-4228

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP T_3B


title: ko_H3K27me2_rep3


title: LNCaP T_3C


title: DP-3030

description: ftATAC-seq data of mouse thymoctyes


title: DP-3031

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O18


title: LNCaP T_3A


title: zebrafish_123s_O15


title: zebrafish_123s_O17


title: wt_H3K27me2_rep3


title: LNCaP T_0C


title: DP-3029

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP T_0B


title: DP-3028

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O20


title: zebrafish_123s_O13


title: DP-3027

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O12


title: DP-3026

description: ftATAC-seq data of mouse thymoctyes


title: brain_H3K27me2_rep2

source_name: embryonic head


title: LNCaP T_0A


title: LNCaP DMSO_24C

value: 0.3% DMSO


title: brain_H3K27me3_rep2


title: zebrafish_123s_O10


title: DP-3025

description: ftATAC-seq data of mouse thymoctyes


title: DP-3024

description: ftATAC-seq data of mouse thymoctyes


title: wt_H3K27me3_rep3


title: somite_H3K27me3_rep2


title: zebrafish_123s_O1


title: somite_H3K27me2_rep2


title: LNCaP DMSO_24B


title: DP-3023

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP DMSO_24A


title: zebrafish_123s_O14


title: LNCaP DMSO_12C


title: DP-3022

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N9


title: wt_H3K27_input_rep3


title: brain_H3K27me2_rep1


title: LNCaP DMSO_12B


title: brain_H3K27me3_rep1


title: zebrafish_123s_N8


title: brain_H3K27_input_rep1


title: DP-3021

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_O11


title: LNCaP DMSO_12A


title: DP-3020

description: ftATAC-seq data of mouse thymoctyes


title: somite_H3K27me2_rep1


title: LNCaP DMSO_9C


title: DP-3019

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N6


title: somite_H3K27me3_rep1


title: zebrafish_123s_N5


title: LNCaP DMSO_9B


title: DP-3018

description: ftATAC-seq data of mouse thymoctyes


title: DP-3017

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N4


title: somite_H3K9me2_rep2


title: zebrafish_123s_N3


title: DP-3016

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP DMSO_6C


title: somite_H3K27_input_rep1


title: DP-3015

description: ftATAC-seq data of mouse thymoctyes


title: somite_H3K4me3_rep2


title: LNCaP DMSO_9A


title: zebrafish_123s_N24


title: LNCaP DMSO_6A


title: DP-3014

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N23


title: zebrafish_123s_N7


title: brain_H3K9me2_rep2


title: brain_H3K4me3_rep2


title: zebrafish_123s_N22


title: LNCaP DMSO_3C


title: DP-3013

description: ftATAC-seq data of mouse thymoctyes


title: ko_H3K9me2_rep2


title: zebrafish_123s_N21


title: DP-3012

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP DMSO_3B


title: zebrafish_123s_N20


title: LNCaP DMSO_3A


title: wt_H3K9me2_rep2


title: DP-3011

description: ftATAC-seq data of mouse thymoctyes


title: LNCaP DMSO_0C


title: zebrafish_123s_N19


title: LNCaP DMSO_6B


title: LNCaP DMSO_0B


title: somite_input_rep2


title: wt_H3K4me3_rep2


title: DP-3009

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N18


title: ko_H3K4me3_rep2


title: DMSO 48hr C

source_name: MCF7 cells

value: MCF7 cells

value: ATCC HTB-33


title: DP-3007

description: ftATAC-seq data of mouse thymoctyes


title: DP-3008

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N16


title: brain_input_rep2


title: DMSO 48hr B

value: ATCC HTB-32

value: B


title: ko_input_rep2


title: zebrafish_123s_N15


title: DP-3006

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_N17


title: DMSO 48hr A

value: ATCC HTB-31

value: A


title: wt_input_rep2


title: ko_H3K9me2_rep1


title: zebrafish_123s_N2


title: W 48hr C

value: ATCC HTB-30

value: Withaferin A (Enzo Life Sciences BML-CT104-0010)

value: DMSO

value: C


title: wt_H3K9me2_rep1

value: wild-type


title: DP-3010

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes

value: 6-8 weeks


title: zebrafish_123s_N12

value: embryo trunk


title: LNCaP DMSO_0A

value: LNCaP cells

value: ATCC (Cat No CRL-1740)


title: zebrafish_123s_N11

value: 48 hpf


title: T 48hr C

value: MCF7 cells

value: ATCC HTB-28

value: Tamoxifen citrate (Tocris 0999)


title: M 48hr C

value: ATCC HTB-29

value: Mefloquine hydrochloride (Sigma-Aldrich M2319-100MG)

value: B


title: zebrafish_123s_N10


title: DP-3002

description: ftATAC-seq data of mouse thymoctyes


title: W 48hr B

value: ATCC HTB-27


title: ko_input_rep1

value: Kdm7a mutant


title: zebrafish_123s_N1


title: wt_H3K4me3_rep1


title: zebrafish_123s_M9


title: zebrafish_123s_N13


title: DP-3001

description: ftATAC-seq data of mouse thymoctyes


title: wt_input_rep1


title: DN-4223

description: ftATAC-seq data of mouse thymoctyes


title: T 48hr B

value: ATCC HTB-25

value: DMSO

value: A


title: DN-4224

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: M 48hr B

value: ATCC HTB-26


title: somite_H3K9me2_rep1

value: wild-type


title: DP-3005

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: DP-3004

description: ftATAC-seq data of mouse thymoctyes


title: W 48hr A

value: ATCC HTB-24

value: Withaferin A (Enzo Life Sciences BML-CT104-0010)

value: C


title: M 48hr A

value: MCF7 cells

value: ATCC HTB-23


title: brain_H3K9me2_rep1


title: zebrafish_123s_M7

value: embryo trunk

value: 48 hpf


title: DN-4222

description: ftATAC-seq data of mouse thymoctyes


title: DN-4221

description: ftATAC-seq data of mouse thymoctyes


title: ko_H3K4me3_rep1


title: zebrafish_123s_M6


title: somite_H3K4me3_rep1


title: DN-4220

description: ftATAC-seq data of mouse thymoctyes


title: T 48hr A

value: ATCC HTB-22

value: Tamoxifen citrate (Tocris 0999)


title: zebrafish_123s_M5


title: zebrafish_123s_M4


title: somite_input_rep1


title: zebrafish_123s_M8


title: DN-4219

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M3


title: brain_H3K4me3_rep1


title: zebrafish_123s_M24


title: DN-4217

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 MW_12C

value: Mefloquine and Withaferin

value: 10 uM and 5 uM, respectively


title: DN-4218

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 MW_24B

value: DMSO

value: B


title: brain_input_rep1


title: MCF7 MW_12B


title: DN-4216

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: DN-4215

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M23


title: DN-4214

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M22


title: MCF7 MW_24C


title: MCF7 MW_12A

value: A


title: BMMERT-act-unstim2

city: Erlangen

first: Steffen

last: Uebe

address: Kussmaulallee 4

department: Humangenetisches Institut

institute: Uniklinikum Erlangen

description:
X210622
NGS2b_Normalized_Counts.txt

data_processing:
trimming with cutadapt
alignment with STAR v2.5.3a
read quantification with Salmon
normalization with limma
differential expression analysis with limma-trend
Samples  X197375, X197377, X197380 and X197381 were used for differential expression analysis in two setups: With samples X197378, X197379, X197382 and X197384 in one analysis and with samples X210618, X210619, X210621 and X210622 in another. Normalization with limma was performed over the entire dataset each time.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated text file with log-normalized counts

source_name: bone marrow macrophages

growth_protocol: Bone marrow cells were isolated and, after erythrocyte lysis, cultured in cDMEM supplemented with 10% FCS, 1% penicillin/streptomycin (Sigma Aldrich), 50 µM β-mercaptoethanol and 10% (v/v) M-CSF containing L cell conditioned medium (LCCM) for 7 days. After overnight depletion of adherent cells, non-adherent cells were re-plated at a density of 5 x 106 cells per 10 cm petri dish. On day 3, 5 ml cDMEM + 10 % LCCM were added, and differentiated bone marrow macrophages (BMM) were harvested on day 7. Tamoxifen treatment was started on day 1, 3 or 5 during macrophage differentiation at a final tamoxifen concentration of 0.1 or 1 µM in the culture medium.

extract_protocol:
For RNAseq analysis 0.5x10e6 BMM were stimulated with 2 µg/ml plate-coated TDM or evaporated isopropanol as solvent control for 24 hours. Total RNA was then isolated using the PeqGold RNA Micro Kit (Peqlab Biotechnology GmbH, Erlangen, Germany) according to the manufacturer’s guidelines.
RNAseq library preparation was done with pooled technical replicates using the TruSeq stranded mRNA Library Prep Kit (Illumina, Inc.)

treatment_protocol: BMM harvested on day 7 of differentiation in LCCM were plated at a density of 10e6 per well in 6-well plates, 0.5x10e6 in 24- or 48-well plates, and 0.2x106 per well in 96-well tissue culture plates (such that cell density was always 10e6/ml). Stimuli were added to cultures at the following final concentrations: IFNg (20 ng/ml), CpG ODN 1826 (0.5 µM), IFNb (100 U/ml). TDM was coated onto cell culture plastic, by first warming the stock solution (TDM 1 mg/ml in isopropanol) to 60 oC for 20’, followed by appropriate dilution in isopropanol and delivery to the culture plates to achieve a final TDM concentration of 2 µg/ml after addition of BMM. The plates were left open under the biosafety cabinet until the isopropanol was completely evaporated.

value: DGCR8wt/wt CreERT2+/-

tag: induction

value: Tamoxifen (active Cre)

tag: stimulus

value: Isopropanol (mock)

tag: cell type

value: bone marrow macrophages


title: BMMERT-act-unstim1

description:
X210619
NGS2b_Normalized_Counts.txt

tag: strain


title: BMMERT-wt-unstim2

description:
X210621
NGS2b_Normalized_Counts.txt

value: EtOH (wt)


title: BMMERT-wt-unstim1

description:
X210618
NGS2b_Normalized_Counts.txt


title: zebrafish_123s_M21

tag: tissue


title: MCF7 MW_9C

value: MCF7 cells

value: C


title: BMM-ko-stim2

description:
X197384
NGS2_Normalized_Counts.txt

value: DGCR8flox/flox Cre+/-

value: Tamoxifen (induced ko)

value: TDM (stimulated)


title: MCF7 MW_24A

value: ATCC HTB-22


title: MCF7 MW_9B

value: Mefloquine and Withaferin


title: zebrafish_123s_M20

value: embryo trunk

tag: age

value: 48 hpf


title: BMM-wt-stim2

description:
X197382
NGS2_Normalized_Counts.txt


title: DP-3003

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: zebrafish_123s_M2

tag: starin


title: DN-4212

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: DN-4211

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 MW_9A

tag: cell line

value: 10 uM and 5 uM, respectively

value: DMSO

value: A


title: BMM-ko-unstim2

description:
X197381
NGS2_Normalized_Counts.txt
NGS2b_Normalized_Counts.txt

value: Isopropanol (mock)


title: MCF7 MW_6C

tag: cell line source


title: zebrafish_123s_M18


title: BMM-wt-unstim2

description:
X197380
NGS2_Normalized_Counts.txt
NGS2b_Normalized_Counts.txt

value: bone marrow macrophages


title: MCF7 MW_6B

tag: treatment

value: B


title: DN-4210

description: ftATAC-seq data of mouse thymoctyes


title: BMM-ko-stim1

description:
X197379
NGS2_Normalized_Counts.txt


title: DN-4209

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M16


title: MCF7 MW_3C

value: MCF7 cells

tag: treatment concentration (um)


title: zebrafish_123s_M17


title: MCF7 MW_6A

tag: solvent


title: DN-4207

description: ftATAC-seq data of mouse thymoctyes


title: BMM-ko-unstim1

description:
X197377
NGS2_Normalized_Counts.txt
NGS2b_Normalized_Counts.txt


title: DN-4213

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M15


title: MCF7 MW_3B

tag: hours of treatment


title: BMM-wt-unstim1

description:
X197375
NGS2_Normalized_Counts.txt
NGS2b_Normalized_Counts.txt

value: EtOH (wt)


title: zebrafish_123s_M14


title: DN-4205

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M13


title: zebrafish_123s_M19


title: MCF7 MW_0C

tag: replicate

value: C


title: MCF7 MW_3A


title: Snai2-/- MSPC rep3

city: Bronx

first: Paul

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

data_processing:
Library adaptor sequences were trimmed using trim galore ( https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ )
single-ended sequencing reads were aligned to the mouse genome (mm10) and quantified using htseq-count. Next, we normalized for RNA composition by calculating scaling factors for each sample using calcNormFactors in edgeR (version 3.12.0). Nominal p-values were corrected using the Benjamini–Hochberg procedure to adjust for multiple hypothesis testing.
Differentially expressed gene sets were then identified using Ingenuity Pathways Analysis (GIAGEN Bioinformatics) and Gene Set Enrichment Analysis (GSEA) software (Broad Institute).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file contains individual gene counts and statistics for each group

source_name: bone marrow

extract_protocol:
Total RNA from 2,000-sorted CD45– Ter119– CD31–  Nes-GFP+ BM MSPCs was extracted using the RNAeasy Plus Micro kit (Qiagen), and assessed for integrity and purity using an Aligent 2100 Bioanalyzer (Agilent Technologies).
Complementary DNA libraries were then generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) and the Nextera XT DNA Sample preparation Kit (Illumina).

value: adult

value: bone marrow

value: mesenchymal stem and progenitor cells (MSPCs)


title: DN-4204

description: ftATAC-seq data of mouse thymoctyes


title: BMM-wt-stim1

description:
X197378
NGS2_Normalized_Counts.txt

value: DGCR8flox/flox Cre+/-

value: TDM (stimulated)


title: DN-4208

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 MW_0A

value: ATCC HTB-22

value: Mefloquine and Withaferin


title: Snai2-/- MSPC rep1


title: zebrafish_123s_M11

value: embryo trunk

value: 48 hpf


title: zebrafish_123s_M12


title: Control MSPC rep3

value: Control


title: MCF7 MW_0B

value: 10 uM and 5 uM, respectively

value: DMSO


title: MCF7 TW_24C

value: Tamoxifen  and Withaferin

value: 20 uM and 5 uM, respectively


title: Control MSPC rep2


title: DN-4203

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes

value: 6-8 weeks


title: zebrafish_123s_M1


title: MCF7 TW_24B

value: MCF7 cells

value: B


title: DN-4200

description: ftATAC-seq data of mouse thymoctyes


title: Control MSPC rep1

value: adult

value: bone marrow


title: DN-4201

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L9


title: DN-4206

description: ftATAC-seq data of mouse thymoctyes


title: Snai2-/- MSPC rep2

value: mesenchymal stem and progenitor cells (MSPCs)


title: DN-4199

description: ftATAC-seq data of mouse thymoctyes


title: MPten tumor 8

city: New York

first: Yu-Jui

last: Ho

address: 417 E 68th St

department: Cancer Biology & Genetics Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Genome_build: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary_files_format_and_content: Tab-delimited text file includes raw count table for each sample

source_name: Myc;Pten-/- prostate EPO-GEMM tumor

growth_protocol: 8-12 week old WT C57BL/6 male mice were anesthetized with isofluorane and the surgical site (pelvic region) scrubbed with a povidone-iodine scrub (Betadine) and rinsed with 70% alcohol. After opening the peritoneal cavity, the left seminal vesicle is used as a landmark and the anterior lobe of the prostate is pulled out. 50 μl of a plasmid mix (see table below) was injected into the right anterior lobe of the prostate using a 27.5 gauge syringe and tweezer electrodes were tightly placed around the injection bubble. Two pulses of electrical current (60V) given for 35 ms lengths at 500 ms intervals were then applied using an in vivo electroporator (NEPAGENE NEPA21 Type II electroporator). After electroporation, the peritoneal cavity was rinsed with 0.5ml of pre-warmed saline. After the procedure the peritoneal cavity was sutured and the skin closed with skin staples. The mice were kept at 37˚C until they awoke and post-surgery pain management was done with injections of buprenorphine for the three following days. Tumor formation was assessed by ultrasound imaging. Mice were sacrificed at end point, and RNA collected from whole prostate tissue. Genome editing in EPO-GEMM tumors was confirmed by Sanger sequencing.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition.

value: prostate tumors

value: Mpten

value: non-treated


title: zebrafish_123s_L8

value: embryo trunk


title: MCF7 TW_24A

value: ATCC HTB-22

value: A


title: MCF7 TW_12C

value: C


title: MPten tumor 7


title: DN-4202

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L7

value: 48 hpf


title: DN-4198

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_M10


title: MCF7 TW_12B

value: Tamoxifen  and Withaferin

value: DMSO


title: DN-4197

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: zebrafish_123s_L5


title: DN-4196

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: MCF7 TW_12A

value: MCF7 cells

value: 20 uM and 5 uM, respectively


title: zebrafish_123s_L4


title: MCF7 TW_9C


title: MPten tumor 5


title: DN-4193

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TW_9B

value: B


title: DN-4194

description: ftATAC-seq data of mouse thymoctyes


title: MPten tumor 2


title: MPten tumor 4


title: MPten tumor 6


title: MPten tumor 3


title: DN-4195

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TW_9A


title: zebrafish_123s_L3


title: zebrafish_123s_L24


title: MCF7 TW_6C


title: MPten tumor 1


title: zebrafish_123s_L23


title: MCF7 TW_6B


title: MP Wnt low tumor 5

source_name: Myc;p53-/- prostate EPO-GEMM tumor

value: MP Wnt low


title: zebrafish_123s_L6


title: zebrafish_123s_L22


title: MCF7 TW_6A


title: DN-2031

description: ftATAC-seq data of mouse thymoctyes


title: DN-2030

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L21


title: MCF7 TW_3C


title: DN-2029

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L20


title: MP Wnt low tumor 2


title: DN-2028

description: ftATAC-seq data of mouse thymoctyes


title: MP Wnt low tumor 3


title: MCF7 TW_3B


title: zebrafish_123s_L2


title: zebrafish_123s_L19


title: MP Wnt High tumor 5

value: MP Wnt High


title: DN-2032

description: ftATAC-seq data of mouse thymoctyes


title: DN-2026

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L18


title: MCF7 TW_3A


title: MCF7 TW_0C


title: MP Wnt low tumor 1

value: prostate tumors


title: DN-2025

description: ftATAC-seq data of mouse thymoctyes


title: DN-2027

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L17


title: MP Wnt low tumor 4


title: zebrafish_123s_L16


title: DN-2024

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TM_24C

value: Tamoxifen and Mefloquine

value: 20 uM and 10 uM, respectively


title: MCF7 TW_0B


title: MCF7 TW_0A


title: MP Wnt High tumor 3

value: non-treated


title: MP Wnt High tumor 2


title: zebrafish_123s_L15

value: embryo trunk


title: DN-2022

description: ftATAC-seq data of mouse thymoctyes


title: WT prostate 6

source_name: WT prostate

value: normal prostate

value: WT


title: MP Wnt High tumor 1


title: zebrafish_123s_L14

value: 48 hpf


title: DN-2021

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TM_24A

value: ATCC HTB-22

value: A


title: zebrafish_123s_L13


title: DN-2020

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: MP Wnt High tumor 4


title: WT prostate 5


title: MCF7 TM_12C

value: DMSO

value: C


title: MCF7 TM_12B

value: MCF7 cells


title: zebrafish_123s_L11


title: DN-2019

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: WT prostate 4


title: zebrafish_123s_L10


title: DN-2018

description: ftATAC-seq data of mouse thymoctyes


title: WT prostate 3


title: DN-2023

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TM_9B

value: B


title: zebrafish_123s_L1


title: MCF7 TM_9C


title: MCF7 TM_24B


title: WT prostate 1


title: DN-2017

description: ftATAC-seq data of mouse thymoctyes


title: WT prostate 2


title: DN-2016

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K9


title: MCF7 TM_6C


title: DN-2015

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_L12


title: MCF7 TM_9A


title: MCF7 TM_12A


title: zebrafish_123s_K6


title: zebrafish_123s_K5


title: DN-2014

description: ftATAC-seq data of mouse thymoctyes


title: ARID2_ChIPSeq_shPbrm1_2

city: Kolkata

first: Amitava

last: Sengupta

state: West Bengal

address: CN 6, Sector V, Salt Lake

department: Cancer Biology & Inflammatory Disorder Division

country: India

institute: CSIR - Indian Institute of Chemical Biology (Translational Research Unit of Excellence)

description: Sample 16

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using deeptools

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with specific antibody.
ChIP-seq library preparation was performed using TruSeqChIP Sample Prep Kit (Illumina) according to the manufacturer’s instructions.10ng of input ChIP-enriched DNA was used for ChIP-seq library preparation. Final libraries were checked using High Sensitivity chips in 2100 Bioanalyzer (Agilent). Average fragment size of final libraries was found to be 277 ± 13bp. Paired-end sequencing (2 x 100 bp) of these libraries were performed in HiSeq-2500 (Illumina) according to the manufacturer's protocols.

value: Stromal Cell line

tag: chip antibody

value: ARID2 (Bethyl Laboratories, Cat. A302-230A , Lot A302-230A-1)

tag: knockdown


title: H3K27ac_ChIPSeq_shPbrm1_1

description: Sample 17


title: MCF7 TM_6B

value: Tamoxifen and Mefloquine


title: MCF7 TM_6A

value: 20 uM and 10 uM, respectively


title: DN-2013

description: ftATAC-seq data of mouse thymoctyes


title: H3K27ac_ChIPSeq_shPbrm1_2

description: Sample 18


title: ARID2_ChIPSeq_shPbrm1_1

description: Sample 15


title: zebrafish_123s_K4


title: zebrafish_123s_K3


title: DN-2010

description: ftATAC-seq data of mouse thymoctyes


title: DN-2011

description: ftATAC-seq data of mouse thymoctyes


title: SMARCC1_ChIPSeq_shPbrm1_2

description: Sample 14

value: BAF155 (R-18) (Santa Cruz Biotechnology, Cat. sc-9746, Lot B1513)


title: MCF7 TM_3C


title: MCF7 TM_3B


title: SMARCC1_ChIPSeq_shPbrm1_1

description: Sample 13


title: MCF7 TM_3A


title: zebrafish_123s_K23

value: embryo trunk


title: zebrafish_123s_K7


title: 2% Input DNA_shPbrm1

description: Sample 10


title: zebrafish_123s_K24


title: MCF7 TM_0C


title: DN-2009

description: ftATAC-seq data of mouse thymoctyes


title: H3K27ac_ChIPSeq_shCtrl

description: Sample 9

source_name: shCtrl

value: shCtrl


title: DN-2012

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 TM_0A


title: ARID2_ChIPSeq_shCtrl

description: Sample 8


title: DN-2006

description: ftATAC-seq data of mouse thymoctyes


title: SMARCC1_ChIPSeq_shCtrl_2

description: Sample 7


title: MCF7 W_24C

value: Withaferin A (Enzo Life Sciences BML-CT104-0010)


title: DN-2005

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K20

value: 48 hpf


title: MCF7 TM_0B

value: ATCC HTB-22


title: MCF7 W_24B


title: SMARCC1_ChIPSeq_shCtrl_1

description: Sample 6


title: zebrafish_123s_K19


title: DN-2004

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K22


title: DN-2007

description: ftATAC-seq data of mouse thymoctyes


title: DN-2008

description: ftATAC-seq data of mouse thymoctyes


title: DN-2003

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K17


title: PBRM1_ChIPSeq_shCtrl_2

description: Sample 3

value: PBRM1 (Bethyl Laboratories, Cat. A301-591A , Lot A301-591A-2)


title: zebrafish_123s_K18


title: MCF7 W_24A

value: A


title: PBRM1_ChIPSeq_shCtrl_1

description: Sample 2


title: MCF7 W_12C

value: DMSO


title: DN-2002

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: DN-2001

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K16


title: zebrafish_123s_K21


title: 2% Input DNA_shCtrl

description: Sample 1


title: zebrafish_123s_K15


title: DKO Female_H3K4me1_3

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description: G158_H3K4me1_DKO_Female_MACS2_Peaks.bed.gz

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using Bowtie 2 (version 2.3.2)  (Langmead 2012 Nat Methods)
H3K27me3 regions were identified using SICER (version 1.1, window size 400 bp and gap size 2400 bp) (Xu, 2014 Methods Mol Biol). H3K27ac and H3K4me1 peaks were discovered using MACS2 (version 2.1.1) (Zhang 2008, Genome Biol) with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing the merged peaks/regions identified using MACS or SICER. Peaks identified in each of the individual samples were merged with all the samples in each of the 4 conditions (Male, Female, DKO_Male, DKO_Female) to generate one peak file per condition per histone mark. Each file contains the peak location and the peak ID

source_name: liver tissue

extract_protocol:
Chromatin was extracted from frozen liver tissue from each of 4 individual livers per group (exception: n=3 for DKO Female_H3K4me1). Crosslinking was achieved by adding formaldehyde to a final concentration of 1% for 5 min at room temperature. Samples were sonicated to a 100-300 bp size range. ChIP was performed using the following ChIP-validated antibodies: H3K27ac (Abcam Cat # ab4729, 3 μg antibody per 15 μg of sonicated chromatin),  H3K4me1 (Abcam Cat # ab8895, 1.2 μg antibody per 15 μg of sonicated chromatin), H3K27me3 (Abcam Cat # ab6002, 2 μg antibody per 10 μg of sonicated chromatin), and normal rabbit IgG (Santa Cruz, Cat # sc-2027, 3 μg antibody per 15 μg of sonicated chromatin).
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep kit for Illumina (NEB, catalog no. E7645) according to the manufacturer’s instructions. NEBNext Multiplex Oligos for Illumina (NEB, Set 1; catalog no. E7335, NEB, Set 2; catalog no. E7500) were used for multiplexing.

treatment_protocol: Ezh1-/- mice were generated by the lab of Thomas Jenuwein (Research Institute of Molecular Pathology, Vienna, Austria) and Ezh2-floxed mice (f/f) by the lab of Alexander Tarakhovsky (Rockefeller University, New York, NY, USA). Ezh2fl/fl mice were subsequently bred with Alb-Cre (AC) transgenic mice, and their offspring were bred with Ezh1-/- mice to generate the Ezh1/Ezh2 double knockouts (DKO) used in this study.

value: Ezh1-/-, EZH2f/f, AC+

tag: Sex

value: Female

value: 7 weeks

tag: antibody

value: H3K4me1 (Abcam #ab8895)


title: DN-1032

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: MCF7 W_12A

value: MCF7 cells


title: zebrafish_123s_K14


title: MCF7 W_9C

value: C


title: DKO Female_H3K4me1_2


title: DKO Female_H3K4me1_1


title: DN-1031

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K12


title: MCF7 W_9B

value: B


title: zebrafish_123s_K13

value: embryo trunk


title: Control Female_H3K4me1_4

value: Floxed control:Ezh2 f/f


title: MCF7 W_6C

value: Withaferin A (Enzo Life Sciences BML-CT104-0010)


title: Control Female_H3K4me1_3


title: MCF7 W_9A


title: zebrafish_123s_K11

value: 48 hpf


title: DN-1030

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 W_6B

value: ATCC HTB-22


title: DN-1028

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_K10


title: DN-1029

description: ftATAC-seq data of mouse thymoctyes


title: Control Female_H3K4me1_2


title: DN-1027

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 W_12B


title: MCF7 W_6A


title: Control Female_H3K4me1_1


title: zebrafish_123s_K1


title: DN-1026

description: ftATAC-seq data of mouse thymoctyes


title: DKO Male_H3K4me1_4

description: G158_H3K4me1_DKO_Male_MACS2_Peaks.bed.gz

value: Male


title: zebrafish_123s_J9


title: MCF7 W_3C


title: DKO Male_H3K4me1_3


title: zebrafish_123s_J8


title: DN-1024

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 W_3B


title: MCF7 W_3A

value: A


title: DN-1023

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 W_0C

value: DMSO


title: zebrafish_123s_J6


title: DKO Male_H3K4me1_1


title: MCF7 W_0B


title: Control Male_H3K4me1_4


title: zebrafish_123s_J5


title: DN-1021

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: Control Male_H3K4me1_3


title: zebrafish_123s_J4


title: MCF7 W_0A


title: DN-1022

description: ftATAC-seq data of mouse thymoctyes


title: Control Male_H3K4me1_2


title: zebrafish_123s_J3


title: DN-1020

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 M_24C

value: Mefloquine hydrochloride (Sigma-Aldrich M2319-100MG)


title: DN-1019

description: ftATAC-seq data of mouse thymoctyes


title: Control Male_H3K4me1_1


title: zebrafish_123s_J24


title: DN-1025

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 M_24B


title: DN-1018

description: ftATAC-seq data of mouse thymoctyes


title: DKO Female_H3K27me3_4

description: G157_H3K27me3_DKO_Female_SICER_Peaks.bed.gz

value: Ezh1-/-, EZH2f/f, AC+

value: Female

value: H3K27me3 (Abcam #ab6002)


title: zebrafish_123s_J7


title: DKO Male_H3K4me_2

value: 7 weeks

value: H3K4me1 (Abcam #ab8895)


title: MCF7 M_24A

value: MCF7 cells


title: DKO Female_H3K27me3_3


title: zebrafish_123s_J23


title: MCF7 M_12C

value: C


title: DKO Female_H3K27me3_2


title: DN-1016

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: zebrafish_123s_J21

value: embryo trunk


title: MCF7 M_12B

value: B


title: zebrafish_123s_J20

value: 48 hpf


title: MCF7 M_12A

value: ATCC HTB-22


title: DKO Female_H3K27me3_1


title: DN-1014

description: ftATAC-seq data of mouse thymoctyes


title: DN-1013

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 M_9C


title: Control Female_H3K27me3_3

value: Floxed control:Ezh2 f/f


title: zebrafish_123s_J19


title: MCF7 M_9B


title: zebrafish_123s_J18


title: MCF7 M_9A

value: A


title: DN-1011

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_J17


title: DN-1017

description: ftATAC-seq data of mouse thymoctyes


title: Control Female_H3K27me3_1


title: Control Female_H3K27me3_2


title: zebrafish_123s_J22


title: MCF7 M_6C

value: DMSO


title: DN-1010

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: DKO Male_H3K27me3_4

description: G157_H3K27me3_DKO_Male_SICER_Peaks.bed.gz

value: Male


title: DN-1015

description: ftATAC-seq data of mouse thymoctyes


title: DN-1009

description: ftATAC-seq data of mouse thymoctyes


title: DKO Male_H3K27me3_3

value: Ezh1-/-, EZH2f/f, AC+


title: Control Female_H3K27me3_4

value: Female


title: zebrafish_123s_J2


title: MCF7 M_6B

value: Mefloquine hydrochloride (Sigma-Aldrich M2319-100MG)


title: zebrafish_123s_J16


title: MCF7 M_6A


title: zebrafish_123s_J14


title: DN-1008

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 M_3C


title: DN-1012

description: ftATAC-seq data of mouse thymoctyes


title: DN-1007

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_J13


title: DKO Male_H3K27me3_1

value: 7 weeks

value: H3K27me3 (Abcam #ab6002)


title: DN-1006

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 M_3B

value: MCF7 cells


title: zebrafish_123s_J12


title: Control Male_H3K27me3_4


title: MCF7 M_3A


title: zebrafish_123s_J15


title: DN-1005

description: ftATAC-seq data of mouse thymoctyes


title: DN-1004

description: ftATAC-seq data of mouse thymoctyes


title: Control Male_H3K27me3_3


title: zebrafish_123s_J11


title: MCF7 M_0C

value: C


title: Control Male_H3K27me3_2


title: DKO Male_H3K27me3_2


title: zebrafish_123s_J10


title: Control Male_H3K27me3_1


title: DN-1003

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: MCF7 M_0B


title: MCF7 M_0A


title: zebrafish_123s_J1

value: embryo trunk


title: zebrafish_123s_I8


title: DN-1002

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_I9


title: DN-1001

description: ftATAC-seq data of mouse thymoctyes


title: DKO Female_H3K27ac_3

description: G156_H3K27ac_DKO_Female_MACS2_Peaks.bed.gz

value: H3K27ac (Abcam #ab4729)


title: zebrafish_123s_I6

value: 48 hpf


title: DKO Female_H3K27ac_1


title: MCF7 T_12C

value: ATCC HTB-22

value: Tamoxifen citrate (Tocris 0999)


title: CD8-4191

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4192

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 T_24B

value: B


title: DKO Female_H3K27ac_2


title: DKO Female_H3K27ac_4


title: CD8-4189

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 T_24A

value: DMSO

value: A


title: Control Female_H3K27ac_3

value: Floxed control:Ezh2 f/f


title: CD8-4190

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: Control Female_H3K27ac_4

value: Female


title: zebrafish_123s_I5


title: CD8-4187

description: ftATAC-seq data of mouse thymoctyes


title: Control Female_H3K27ac_2


title: MCF7 T_12B


title: MCF7 T_24C


title: MCF7 T_12A


title: zebrafish_123s_I23


title: CD8-4188

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4185

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_I3


title: MCF7 T_6C


title: MCF7 T_9C


title: zebrafish_123s_I7


title: MCF7 T_9B


title: zebrafish_123s_I20


title: MCF7 T_9A


title: Control Female_H3K27ac_1


title: DKO Male_H3K27ac_3

description: G156_H3K27ac_DKO_Male_MACS2_Peaks.bed.gz

value: Ezh1-/-, EZH2f/f, AC+

value: Male


title: MCF7 T_6A


title: CD8-4184

description: ftATAC-seq data of mouse thymoctyes


title: DKO Male_H3K27ac_2

value: 7 weeks


title: CD8-4186

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_I19


title: CD8-4183

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 T_3C

value: MCF7 cells


title: zebrafish_123s_I22


title: DKO Male_H3K27ac_1


title: MCF7 T_6B


title: DKO Male_H3K27ac_4


title: zebrafish_123s_I2


title: CD8-4181

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_I24


title: CD8-4182

description: ftATAC-seq data of mouse thymoctyes


title: Control Male_H3K27ac_2


title: MCF7 T_3B


title: MCF7 T_3A


title: CD8-4179

description: ftATAC-seq data of mouse thymoctyes


title: Control Male_H3K27ac_1


title: zebrafish_123s_I18


title: Control Male_H3K27ac_4


title: Control Male_H3K27ac_3


title: zebrafish_123s_I17


title: zebrafish_123s_I16


title: MCF7 T_0C

value: C


title: MCF7 T_0B


title: zebrafish_123s_I15


title: CD8-4178

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: CD8-4177

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 T_0A


title: zebrafish_123s_I4

value: embryo trunk


title: zebrafish_123s_I13


title: CD8-4176

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_24C

value: 0.3% DMSO


title: CD8-4175

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_24B


title: Ezh1/Ezh2-DKO Male_3

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and differential expression results comparing: Male controls to Female controls; Male-DKO to Male controls; Female-DKO to Female controls; and Male-DKO to Female-DKO.

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected and sequencing libraries were prepared using the Illumina TruSeq RNA library preparation kit (Illumina, cat# RS-122-2001), according to the manufacturer's instructions.


title: Ezh1/Ezh2-DKO Female_1


title: zebrafish_123s_I12

value: 48 hpf


title: Ezh1/Ezh2-DKO Female_3


title: CD8-4180

description: ftATAC-seq data of mouse thymoctyes


title: Ezh1/Ezh2-DKO Female_2


title: CD8-4174

description: ftATAC-seq data of mouse thymoctyes


title: Ezh1/Ezh2-DKO Male_2


title: zebrafish_123s_I10


title: CD8-4173

description: ftATAC-seq data of mouse thymoctyes


title: Ezh1/Ezh2-DKO Male_1


title: zebrafish_123s_I1


title: CD8-4172

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_12C

value: ATCC HTB-22


title: Control Female_3


title: zebrafish_123s_I14


title: zebrafish_123s_H9


title: MCF7 DMSO_12B


title: Control Female_2


title: zebrafish_123s_H8


title: CD8-4171

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4170

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_12A


title: zebrafish_123s_H7


title: Control Female_1


title: CD8-4169

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_H5


title: MCF7 DMSO_9B


title: MCF7 DMSO_9A


title: Control Male_3


title: Control Male_2


title: Control Male_1


title: MCF7 DMSO_24A


title: zebrafish_123s_H4


title: zebrafish_123s_H6


title: MCF7 DMSO_9C


title: CD8-4167

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4166

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4165

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_6B


title: CD8-4168

description: ftATAC-seq data of mouse thymoctyes


title: CGR8_LIM [I]

city: Rotterdam

first: Derk

last: ten Berge

address: Wytemaweg 80

department: Cell Biology

country: Netherlands

institute: ErasmusMC

data_processing:
Reads were mapped against the mouse GRCm38 reference genome (mm10) using HiSat2 (version 2.0.4). Gene expression values were called using htseq-count (version 0.6.1).
Reads were normalized using the DESeq2 package (version 1.10.1) counts function.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw count value table for each sample.
Supplementary_files_format_and_content: Matrices of normalized read counts.

source_name: Embryonic stem cells

growth_protocol: Cells were grown in serumfree N2B27 medium on tissue culture plastic plates coated with 0.1% gelatin and fetal calf serum (for time course samples) or (for the other samples) with 0.1% gelatin and 1:200 Cultrex Basement Membrane Extract, Type 2, reduced growth factor (BME 2 Organoid Matrix; AMSBIO).

extract_protocol:
Qiagen RNeasy mini kit.
Libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep Kit. The libraries were sequenced according to the Illumina TruSeq Rapid  v3 protocol (for time course samples) or v2 protocol (all other samples) on an Illumina HiSeq2500 sequencer.

treatment_protocol: Cells were cultured in the presence of LIF and the indicated supplements. 2i is CHIR99021+PD325901. Concentrations: CHIR99021 3 uM; PD325901 0.1 uM; IWP2 2 uM; FGF2 12 ng/ml; human Activin A 20 ng/ml.

tag: conditions

tag: passage number

tag: treatment duration

value: 5 passages in LIF+2i, then 6 passages in LIF+PD325901+IWP2


title: R1_LIM [I]

value: 5 passages in LIF+2i, then 4 passages in LIF+PD325901+IWP2


title: zebrafish_123s_H24

tag: tissue


title: CD8-4164

description: ftATAC-seq data of mouse thymoctyes

tag: strain

tag: age


title: CGR8_35hrs_LFAI [I]

tag: cell line

value: 35 hrs in Lif+FGF2+Activin A+IWP2

value: 7 passages in LIF+2i, then 35 hrs in LIF+FGF2+Activin A+IWP2


title: MCF7 DMSO_3C

tag: cell line source


title: zebrafish_123s_H23

tag: starin


title: MCF7 DMSO_6A

tag: treatment

value: A


title: CD8-4163

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: zebrafish_123s_H22


title: MCF7 DMSO_6C


title: zebrafish_123s_H3


title: MCF7 DMSO_3B

value: B


title: MCF7 DMSO_0C


title: CGR8_4d_LFAI [I]

value: 4 days in Lif+FGF2+Activin A+IWP2

value: 9 passages in LIF+2i, then 4 days in LIF+FGF2+Activin A+IWP2


title: CD8-4161

description: ftATAC-seq data of mouse thymoctyes


title: MCF7 DMSO_3A


title: CD8-4160

description: ftATAC-seq data of mouse thymoctyes


title: R1_4d_LFAI [I]

value: 3 passages in LIF+2i, then 4 days in LIF+FGF2+Activin A+IWP2


title: zebrafish_123s_H20


title: zebrafish_123s_H21


title: zebrafish_123s_H19


title: R1_2i [I]

value: 10 passages in LIF+2i


title: CGR8_2i [I]

value: 8 passages in LIF+2i


title: CD8-4159

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: zebrafish_123s_H2

value: embryo trunk


title: MCF7 DMSO_0B

value: MCF7 cells

value: 0.3% DMSO


title: MCF7 DMSO_0A

value: ATCC HTB-22


title: CD8-4158

description: ftATAC-seq data of mouse thymoctyes


title: R1_d4_LFAI [I]

value: 3 passages in LIF+2i, then 4 days in Lif+FGF2+Activin A+IWP2


title: R1_d3_LFAI [I]

value: 3 days in Lif+FGF2+Activin A+IWP2

value: 4 passages in LIF+2i, then 3 days in Lif+FGF2+Activin A+IWP2


title: zebrafish_123s_H17

value: 48 hpf


title: zebrafish_123s_H18


title: CD8-4157

description: ftATAC-seq data of mouse thymoctyes


title: R1_35hrs_LFAI [I]

value: 35 hrs in Lif+FGF2+Activin A+IWP2

value: 9 passages in LIF+2i, then 35 hrs in LIF+FGF2+Activin A+IWP2


title: CD8-4162

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: siARS2_Rep_3

city: Dallas

first: Nicholas

middle: K

last: Conrad

state: TX

address: 6000 Harry Hines Blvd

department: Microbiology

institute: UT Southwestern Medical Center

description:
3_25
Poly-A RNA
processed data file: countTable.fpkm.csv

data_processing:
The qualities of sequencing reads were evaluated using NGS QC Toolkit (v2.3.3) (Patel and Jain, 2012) and high-quality reads were extracted.
The human reference genome sequence and gene annotation data, hg19, were downloaded from Illumina iGenomes (https://support.illumina.com/sequencing/sequencing_software/igenome.html). The viral genome was downloaded from NCBI GenBank (https://www.ncbi.nlm.nih.gov/nuccore/GQ994935.1). The qualities of RNA-sequencing libraries were estimated by mapping the reads onto human transcript and ribosomal RNA sequences (Ensembl release 89) using Bowtie (v2.2.9) (Langmead and Salzberg, 2012).
STAR (v2.5.2b) (Dobin et al., 2013) was employed to align the reads onto the human and viral genomes, Picard (v1.140) (https://broadinstitute.github.io/picard/) was employed to sort the alignments, and HTSeq Python package (Anders et al., 2015) was employed to count reverse-stranded reads per gene. DESeq2 R Bioconductor package (Gentleman et al., 2004; Anders et al., 2010) was used to normalize read counts and identify differentially expressed (DE) genes.
Genome_build: hg19 (GRCh37) and GQ994935.1
Supplementary_files_format_and_content: countTable.fpkm.csv: Comma-separated text file of viral gene fpkm counts.

source_name: iSLK cells

growth_protocol: iSLK cells were grown at 37°C with 5% CO2 in DMEM (Sigma) supplemented with 10% Tet-Free fetal bovine serum (FBS, Atlanta Biologicals), 1x penicillin-streptomycin (Sigma), and 2 mM L-glutamine (Fisher). iSLK WT cells were grown in the presence of 0.1 mg/mL G418 (Fisher), 1 µg/mL puromycin (Sigma) and 50 µg/mL hygromycin.

extract_protocol:
RNA was harvested using TRI reagent (Molecular Research Center, Inc.) according to the manufacturer’s protocol. Total RNA was purified using Chloroform-isopropanol extraction. RNA samples were quantified using Nanodrop (Thermofisher) and RNA integrity was checked with Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA).
RNA sequencing libraries were prepared using the KAPA Biosystems Stranded mRNA-Seq kit as per manufacturer’s protocol. Briefly, mRNAs were first enriched with Oligod(T) beads. Enriched mRNAs were fragmented for 6 minutes at 94 °C in the presence of magnesium. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapter was ligated to cDNA fragments, followed by index addition (NEBNext multiplex Oligos for Illumina) and library enrichment with limited cycle PCR. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA).

treatment_protocol: iSLK cells were transfected with 20 or 40 nM siRNA (Silencer Select, ThermoFisher) using RNAiMAX transfection reagent (Invitrogen) per manufacturer’s instruction. Specifically, we used final concentrations of 20 nM siRNAs for ARS2. For PAPα/γ, we used 20 nM each of siRNAs that target PAPα or PAPγ for a total of 40 nM siRNA. Twenty-four hours after siRNA transfection, cells were split into new plates and allowed to grow for another 24 hours, after which doxycycline and NaB was added to induce lytic reactivation. Thus, total RNA was harvested 72 hours post siRNA transfection and 24 hours post lytic reactivation.

value: iSLK

tag: pabpn1 and papalpha/gamma-mediated rna decay (ppd)

value: no (pathway active)

tag: ars2-dependent decay

value: yes (pathway inactive)


title: siPAPα/γ_+_siARS2_Rep_3

description:
3_27
Poly-A RNA
processed data file: countTable.fpkm.csv


title: R1_d2_LFAI [I]

value: 2 days in Lif+FGF2+Activin A+IWP2

value: 4 passages in LIF+2i, then 2 days in Lif+FGF2+Activin A+IWP2


title: siPAPα/γ_Rep_3

description:
3_23
Poly-A RNA
processed data file: countTable.fpkm.csv


title: CD8-4155

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: zebrafish_123s_H16

value: embryo trunk


title: R1_d4_LIM [I]

value: 4 days in Lif+IWP2+PD325901

value: 3 passages in LIF+2i, then 4 days in Lif+IWP2+PD325901


title: R1_d1_LFAI [I]

value: 1 day in Lif+FGF2+Activin A+IWP2

value: 4 passages in LIF+2i, then 1 day in Lif+FGF2+Activin A+IWP2


title: zebrafish_123s_H14


title: CD8-4154

description: ftATAC-seq data of mouse thymoctyes


title: siPAPα/γ_+_siARS2_Rep_2

description:
3_21
Poly-A RNA
processed data file: countTable.fpkm.csv


title: zebrafish_123s_H13


title: siControl_Rep_3

description:
3_22
Poly-A RNA
processed data file: countTable.fpkm.csv

value: control


title: siARS2_Rep_2

description:
3_20
Poly-A RNA
processed data file: countTable.fpkm.csv


title: R1_d2_LIM [I]

value: 2 days in Lif+IWP2+PD325901

value: 4 passages in LIF+2i, then 2 days in Lif+IWP2+PD325901


title: CD8-4152

description: ftATAC-seq data of mouse thymoctyes


title: siPAPα/γ_Rep_2

description:
3_19
Poly-A RNA
processed data file: countTable.fpkm.csv


title: zebrafish_123s_H11

value: 48 hpf


title: R1_d3_LIM [I]

value: 3 days in Lif+IWP2+PD325901

value: 4 passages in LIF+2i, then 3 days in Lif+IWP2+PD325901


title: siControl_Rep_2

description:
3_18
Poly-A RNA
processed data file: countTable.fpkm.csv

value: iSLK


title: zebrafish_123s_H12


title: siPAPα/γ_+_siARS2_Rep_1

description:
3_16
Poly-A RNA
processed data file: countTable.fpkm.csv


title: CD8-4151

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: CD8-4156

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4150

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_H10


title: R1_d0_L2i [I]

value: 5 passages in LIF+2i


title: R1_d1_LIM [I]

value: 1 day in Lif+IWP2+PD325901

value: 4 passages in LIF+2i, then 1 day in Lif+IWP2+PD325901


title: CD8-4149

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: G150_M28

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using Bowtie
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadhsee showing MACS2 output, including peaks discovered and statistics per peak

source_name: K4me3 marks_male mouse liver 27 h TCPOBOP_liver4_G150_M28

extract_protocol:
ChIP was performed using antibodies against K4me1 (ab8895), K4me3 (ab8580), and K27ac (ab4729).
NEBNext Ultra DNA library prep kit for Illumina

treatment_protocol: Male and female CD1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA) at 7 weeks of age. Mice were injected with 3 mg/kg TCPOBOP or vehicle alone (1% DMSO in corn oil) between 8:00-8:45 AM on Day 1 and tissue was collected between 11:00-11:45 AM on Day 1 (3 h samples) or between 11:00-11:45 AM on Day 2 (27 h samples). For the 3 h samples, liver nuclei were isolated and then crosslinked for 9 minutes by incubation with 0.8% formaldehyde at 30°C (crosslinked nuclei).  For the 27 h samples, livers were flash frozen in liquid nitrogen. A portion was subsequently homogenized and then crosslinked by incubation with 1% formaldehyde for 10 minutes at 22°C (crosslinked frozen whole tissue). All samples were sonicated to yield genomic DNA fragments approximately 100-300 bp in length, and then used for ChIP.

value: CD-1 (Charles River)

value: 3 mg/kg TCPOBOP_27 h

value: liver

value: male

value: 7 weeks

tag: crosslinking method

value: Crosslinked frozen whole tissue

tag: mouse id number


title: zebrafish_123s_H15

value: embryo trunk


title: siARS2_Rep_1

description:
3_15
Poly-A RNA
processed data file: countTable.fpkm.csv

value: no (pathway active)

value: yes (pathway inactive)


title: CD8-4153

description: ftATAC-seq data of mouse thymoctyes


title: G150_M27

source_name: K4me3 marks_male mouse liver 27 h TCPOBOP_liver3_G150_M27


title: CD8-4148

description: ftATAC-seq data of mouse thymoctyes

source_name: mouse thymoctyes


title: zebrafish_123s_G9

source_name: zebrafish

value: 48 hpf


title: zebrafish_123s_G7


title: zebrafish_123s_G8


title: siControl_Rep_1

description:
3_13
Poly-A RNA
processed data file: countTable.fpkm.csv

value: control


title: G150_M26

source_name: K4me3 marks_male mouse liver 27 h TCPOBOP_liver2_G150_M26


title: CD8-4146

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4147

description: ftATAC-seq data of mouse thymoctyes


title: siPAPα/γ_Rep_1

description:
3_14
Poly-A RNA
processed data file: countTable.fpkm.csv

value: iSLK


title: G150_M25

source_name: K4me3 marks_male mouse liver 27 h TCPOBOP_liver1_G150_M25


title: SMMl sample 3, 138N45P fraction

first: Irene

last: Ghobrial

address: 4 Blackfan Circle, 2nd Floor, Suite 240

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: 3' barcoded RNA

data_processing:
cellranger mkfastq was used for extracting fastq files
cellranger count was used for sequence alignment and UMI counting
Genome_build: hg38
Supplementary_files_format_and_content: cellranger filtered gene barcode matrices

source_name: Bone Marrow

extract_protocol: Chromium Single Cell 3′ Library & Gel Bead Kit v3

tag: diagnosis

value: Low Risk Smoldering Myeloma

tag: marker selection

value: Bone Marrow


title: CD8-4145

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: zebrafish_123s_H1


title: zebrafish_123s_G6


title: SMMl sample 2, 138N fraction

description: 3' barcoded RNA


title: CD8-4144

description: ftATAC-seq data of mouse thymoctyes


title: G150_M23

source_name: K4me3 marks_male mouse liver 27 h vehicle_liver2_G150_M23

value: Vehicle (1% DMSO in corn oil)_27 h

tag: Sex

tag: antibody


title: zebrafish_123s_G5


title: SMMl sample 1, 138N fraction

description: 3' barcoded RNA


title: G150_M24

source_name: K4me3 marks_male mouse liver 27 h vehicle_liver3_G150_M24


title: G150_M22

source_name: K4me3 marks_male mouse liver 27 h vehicle_liver1_G150_M22


title: zebrafish_123s_G4


title: CD8-4143

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: CD8-4142

description: ftATAC-seq data of mouse thymoctyes


title: G150_M21

source_name: K4me1 marks_male mouse liver 27 h TCPOBOP_liver4_G150_M21

value: CD-1 (Charles River)


title: zebrafish_123s_G3


title: G150_M20

source_name: K4me1 marks_male mouse liver 27 h TCPOBOP_liver3_G150_M20

value: 3 mg/kg TCPOBOP_27 h


title: zebrafish_123s_G24


title: SMMh sample 7, 138N fraction

description: 3' barcoded RNA

value: High Risk Smoldering Myeloma


title: SMMh sample 8, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4140

description: ftATAC-seq data of mouse thymoctyes


title: SMMh sample 6, 138N fraction

description: 3' barcoded RNA


title: zebrafish_123s_G23


title: G150_M18

source_name: K4me1 marks_male mouse liver 27 h TCPOBOP_liver1_G150_M18

value: liver

value: male


title: CD8-4141

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4139

description: ftATAC-seq data of mouse thymoctyes


title: G150_M19

source_name: K4me1 marks_male mouse liver 27 h TCPOBOP_liver2_G150_M19

value: 7 weeks

value: Crosslinked frozen whole tissue


title: SMMh sample 4, 138N fraction

description: 3' barcoded RNA


title: zebrafish_123s_G22

value: embryo trunk


title: CD8-4138

description: ftATAC-seq data of mouse thymoctyes


title: G150_M17

source_name: K4me1 marks_male mouse liver 27 h vehicle_liver3_G150_M17


title: SMMh sample 3, 138N fraction

description: 3' barcoded RNA


title: SMMh sample 9, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4137

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_G21


title: zebrafish_123s_G20


title: G150_M16

source_name: K4me1 marks_male mouse liver 27 h vehicle_liver2_G150_M16


title: G150_M7

source_name: K27ac marks_male mouse liver 27 h TCPOBOP_liver4_G150_M7


title: SMMh sample 2, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4135

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4136

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_G2


title: NBM sample 9, 138N fraction

description: 3' barcoded RNA

value: Healthy Donor


title: CD8-4134

description: ftATAC-seq data of mouse thymoctyes


title: G150_M6

source_name: K27ac marks_male mouse liver 27 h TCPOBOP_liver3_G150_M6


title: NBM sample 8, 138N fraction

description: 3' barcoded RNA


title: zebrafish_123s_G18

value: 48 hpf


title: zebrafish_123s_G17


title: NBM sample 5, 138N fraction

description: 3' barcoded RNA


title: G150_M4

source_name: K27ac marks_male mouse liver 27 h TCPOBOP_liver1_G150_M4


title: CD8-4132

description: ftATAC-seq data of mouse thymoctyes

source_name: mouse thymoctyes


title: G150_M5

source_name: K27ac marks_male mouse liver 27 h TCPOBOP_liver2_G150_M5


title: CD8-4133

description: ftATAC-seq data of mouse thymoctyes


title: SMMh sample 10, 138N45P fraction

description: 3' barcoded RNA


title: zebrafish_123s_G16

source_name: zebrafish


title: G150_M3

source_name: K27ac marks_male mouse liver 27 h vehicle_liver3_G150_M3


title: G150_M2

source_name: K27ac marks_male mouse liver 27 h vehicle_liver2_G150_M2


title: zebrafish_123s_G14


title: NBM sample 3, 138N45P fraction

description: 3' barcoded RNA

source_name: Bone Marrow


title: zebrafish_123s_G19


title: CD8-4130

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4129

description: ftATAC-seq data of mouse thymoctyes


title: NBM sample 11, 138N fraction

description: 3' barcoded RNA


title: NBM sample 4, 138N fraction

description: 3' barcoded RNA


title: G150_M1

source_name: K27ac marks_male mouse liver 27 h vehicle_liver1_G150_M1


title: NBM sample 2, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4131

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_G13


title: CD8-4128

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_G11


title: NBM sample 10, 138N fraction

description: 3' barcoded RNA


title: zebrafish_123s_G15


title: G143_M12

source_name: K4me3 marks_male mouse liver 3 h TCPOBOP_liver3_G143_M12

value: 3 mg/kg TCPOBOP_ 3 h

value: Crosslinked nuclei


title: CD8-4127

description: ftATAC-seq data of mouse thymoctyes


title: G143_M11

source_name: K4me3 marks_male mouse liver 3 h TCPOBOP_liver2_G143_M11


title: CD8-4126

description: ftATAC-seq data of mouse thymoctyes


title: G143_M10

source_name: K4me3 marks_male mouse liver 3 h TCPOBOP_liver1_G143_M10


title: zebrafish_123s_G1


title: MM sample 7, 138N45P fraction

description: 3' barcoded RNA

value: Multiple Myeloma


title: MM sample 8, 138N45P fraction

description: 3' barcoded RNA

value: Bone Marrow


title: G143_M9

source_name: K4me3 marks_male mouse liver 3 h vehicle_liver3_G143_M9

value: Vehicle (1% DMSO in corn oil)_ 3 h


title: CD8-4124

description: ftATAC-seq data of mouse thymoctyes

value: thymocytes


title: G143_M8

source_name: K4me3 marks_male mouse liver 3 h vehicle_liver2_G143_M8


title: MM sample 6, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4123

description: ftATAC-seq data of mouse thymoctyes

value: 6-8 weeks


title: MM sample 5, 138N45P fraction

description: 3' barcoded RNA


title: zebrafish_123s_F8


title: G143_M7

source_name: K4me3 marks_male mouse liver 3 h vehicle_liver1_G143_M7

value: CD-1 (Charles River)


title: CD8-4121

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F7


title: zebrafish_123s_F6


title: zebrafish_123s_F5


title: CD8-4122

description: ftATAC-seq data of mouse thymoctyes


title: G150_M15

source_name: K4me1 marks_male mouse liver 27 h vehicle_liver1_G150_M15

value: Vehicle (1% DMSO in corn oil)_27 h


title: G121_M11

source_name: K27ac marks_male mouse liver 3 h TCPOBOP_liver2_G121_M11


title: G121_M12

source_name: K27ac marks_male mouse liver 3 h TCPOBOP_liver3_G121_M12


title: MM sample 3, 138N45P fraction

description: 3' barcoded RNA


title: zebrafish_123s_G10


title: CD8-4120

description: ftATAC-seq data of mouse thymoctyes


title: NBM sample 1, 138N45P fraction

description: 3' barcoded RNA


title: zebrafish_123s_F4


title: MM sample 1, 138N fraction

description: 3' barcoded RNA


title: CD8-4125

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4119

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F9


title: zebrafish_123s_F24


title: MM sample 4, 138N45P fraction

description: 3' barcoded RNA


title: zebrafish_123s_F3


title: MGUS sample 3, 138N45P fraction

description: 3' barcoded RNA

value: Monoclonal Gammopathy of Undetermined Significance


title: CD8-4118

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F20


title: G121_M4

source_name: K4me1 marks_male mouse liver 3 h TCPOBOP_liver1_G121_M4

value: liver


title: zebrafish_123s_F21


title: CD8-4116

description: ftATAC-seq data of mouse thymoctyes

source_name: mouse thymoctyes


title: MGUS sample 1, 138N fraction

description: 3' barcoded RNA


title: G121_M9

source_name: K27ac marks_male mouse liver 3 h vehicle_liver3_G121_M9

value: male


title: CD8-4117

description: ftATAC-seq data of mouse thymoctyes


title: MGUS sample 2, 138N45P fraction

description: 3' barcoded RNA


title: MGUS sample 4, 138N45P fraction

description: 3' barcoded RNA


title: CD8-4113

description: ftATAC-seq data of mouse thymoctyes


title: MGUS sample 6, 138N45P fraction

description: 3' barcoded RNA


title: G121_M8

source_name: K27ac marks_male mouse liver 3 h vehicle_liver2_G121_M8

value: 7 weeks


title: G121_M6

source_name: K4me1 marks_male mouse liver 3 h TCPOBOP_liver3_G121_M6


title: CD8-4114

description: ftATAC-seq data of mouse thymoctyes


title: G121_M5

source_name: K4me1 marks_male mouse liver 3 h TCPOBOP_liver2_G121_M5


title: G121_M7

source_name: K27ac marks_male mouse liver 3 h vehicle_liver1_G121_M7


title: CD8-4112

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F22

source_name: zebrafish


title: G121_M3

source_name: K4me1 marks_male mouse liver 3 h vehicle_liver3_G121_M3


title: zebrafish_123s_F18


title: G121_M2

source_name: K4me1 marks_male mouse liver 3 h vehicle_liver2_G121_M2


title: zebrafish_123s_F23


title: CD8-4115

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4111

description: ftATAC-seq data of mouse thymoctyes


title: G121_M1

source_name: K4me1 marks_male mouse liver 3 h vehicle_liver1_G121_M1


title: CD8-4109

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F16


title: zebrafish_123s_F13


title: zebrafish_123s_F14


title: zebrafish_123s_F12


title: CD8-4110

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4105

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F11


title: CD8-4107

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F15


title: CD8-4108

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4106

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F1


title: zebrafish_123s_F10


title: CD8-4103

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F19


title: M 1

city: Muenster

first: Maria

middle: V

last: Yusenko

address: Wilhelm-Klemm-Str. 2

department: Institute of Biochemistry

institute: University of Muenster

data_processing:
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled.
Trimmomatic (v. 038) was used for adapter trimming and read filtering.  (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15)
The resulted reads were aligned to the  hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9)
The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1;  Parameter: --minaqual 0,  --stranded reverse)
Testing for differential expression was performed using DESeq2 r-package (v. 1.22.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files

growth_protocol: THP-1 cells were cultured in RPMI 1640 medium containing 10% FBS and 5% L-Glut

extract_protocol:
Total RNA was harvested using Trizol reagent.
NEBNext Ultra Directional RNA II Library Prep kit  was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 500 System and NextSeq v2 sequencing reagent kit in a single read-mode with a read-length of 75 bp.

treatment_protocol: The cells were left untreated or treated with 1 µM Monensin for 16 hours. All experiments were done in triplicate.

tag: cell type

value: acute monocytic leukemia

value: with 1 µm Monensin for 16 hours


title: CD8-4102

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E9

value: embryo trunk


title: CD8-4104

description: ftATAC-seq data of mouse thymoctyes


title: CD8-4101

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E8

value: 48 hpf


title: CD8-4100

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_F17


title: M 2


title: M 3


title: THP0 2

value: no exposure


title: CD8-4098

description: ftATAC-seq data of mouse thymoctyes


title: zebrafish_123s_E6


title: CD8-4099

description: ftATAC-seq data of mouse thymoctyes


title: THP0 1