title: 26_TNF_MG132_rep2 [RNA-Seq]

value: MG132 with TNF


title: 25_TNF_BAY_rep2 [RNA-Seq]

status: Public on Apr 11 2019

type: SRA

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: Gene expression data of human endothelial cells through TNF-induced inflammatory signaling

library_source: transcriptomic

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Sequence reads (36-bp single read) were aligned to the human reference genome (GRCh37/hg19) with Tophat (version: 2.1.1) with following parameters: the mismatch to the reference genome should be supported by at least 2 reads, the lengths of insertions and deletions should be supported by at least 3bp.
The mapped sequence reads were extended to 500 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: bigwig

molecule: total RNA

organism: Homo sapiens

source_name: human umblical vein endothelial cells

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. Human monocyte cell line U937 was purchased from JCRB Cell Bank (Osaka, Japan) and grown and passaged every 2 or 3 days in RPMI1640 (Thermo Fisher Scientific) supplemented with 1% penicillin/streptomycin (Wako, Osaka, Japan) and 10% FBS. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA including miRNA was isolated from HUVECs using miRNeasy micro Kit (Qiagen, Hilden, Germany) with DNase digestion step according to the manufactures’ instructions.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were incubated with a mixture of 100 nM siRNA and Lipofectamine RNAiMax (Thermo Fisher Scientific, Waltham, MA). 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

tag: conditions

value: BAY with TNF

tag: donor

value: pooled from multiple donors

tag: passages


title: SU353_LSC_18

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

country: USA

institute: Stanford

library_source: genomic

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters.
Paired-end reads were aligned to hg19 using bwa. Duplicates were removed using PICARD tools
Reads were subsequently filtered for alignment quality  and were required to be properly paired.
Genome_build: hg19
Supplementary_files_format_and_content: reads count. The last number in the column header refers to the cell number. E.g. singles-SU353-Blast-160205-1 = SU353_Blasts_1

molecule: genomic DNA

source_name: LSC

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers  in 1x NEBnext High-Fidelity PCR Master using the following PCR conditions: 72°C for 5min; 98°C for 30 s;  Mix)  using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL.  The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries  at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: patient id

tag: patient diagnosis

value: acute myeloid leukemia

tag: cell type

value: LSC


title: SU353_LSC_17


title: 24_TNF_vehicle_rep2 [RNA-Seq]

value: vehicle with TNF


title: SU353_LSC_15


title: SU353_LSC_14


title: SU353_LSC_13


title: 21_TNF_siControl3_rep2 [RNA-Seq]

value: siControl with TNF


title: 22_TNF_siKDM7A+siUTX_rep2 [RNA-Seq]

value: siKDM7A+siUTX with TNF


title: SU353_LSC_12


title: 20_siControl3_rep2 [RNA-Seq]

value: siControl


title: 19_TNF_siUTX_rep2 [RNA-Seq]

value: siUTX with TNF


title: 18_TNF_siControl2_rep2 [RNA-Seq]


title: SU353_LSC_10


title: SU353_Blasts_9

source_name: Blasts

value: Blasts


title: SU353_LSC_11


title: SU353_Blasts_96


title: 17_siControl2_rep2 [RNA-Seq]


title: 15_TNF_siControl1_rep2 [RNA-Seq]


title: SU353_LSC_19


title: 27_TNF_0h [RNA-Seq]

value: no treatment


title: SU353_Blasts_94


title: SU353_Blasts_95


title: SU353_LSC_16


title: SU353_Blasts_93


title: 13_TNF_MG132_rep1 [RNA-Seq]


title: 23_vheicle_rep2 [RNA-Seq]

value: vehicle


title: SU353_Blasts_92


title: 12_TNF_BAY_rep1 [RNA-Seq]


title: SU353_Blasts_91


title: 10_vheicle_rep1 [RNA-Seq]


title: 11_TNF_vehicle_rep1 [RNA-Seq]


title: 9_TNF_siKDM7A+siUTX_rep1 [RNA-Seq]


title: SU353_Blasts_8


title: 8_TNF_siControl3_rep1 [RNA-Seq]


title: SU353_Blasts_90


title: SU353_Blasts_89


title: SU353_Blasts_88


title: 7_siControl3_rep1 [RNA-Seq]


title: 16_TNF_siKDM7A_rep2 [RNA-Seq]

value: siKDM7A with TNF


title: SU353_Blasts_87


title: 6_TNF_siUTX_rep1 [RNA-Seq]


title: SU353_Blasts_85


title: 14_siControl1_rep2 [RNA-Seq]


title: SU353_Blasts_86


title: 4_siControl2_rep1 [RNA-Seq]


title: 3_TNF_siKDM7A_rep1 [RNA-Seq]


title: 2_TNF_siControl1_rep1 [RNA-Seq]


title: 5_TNF_siControl2_rep1 [RNA-Seq]


title: SU353_Blasts_84


title: SU353_Blasts_81


title: SU353_Blasts_82


title: SU353_Blasts_80


title: 1_siControl1_rep1 [RNA-Seq]


title: SU353_Blasts_79


title: SU353_Blasts_7


title: SU353_Blasts_78


title: SU353_Blasts_77


title: SU353_Blasts_76


title: SU353_Blasts_83


title: SU353_Blasts_74


title: SU353_Blasts_73


title: SU353_Blasts_75


title: SU353_Blasts_72


title: SU353_Blasts_70


title: SU353_Blasts_6


title: SU353_Blasts_71


title: SU353_Blasts_69


title: SU353_Blasts_67


title: SU353_Blasts_66


title: SU353_Blasts_64


title: SU353_Blasts_65


title: SU353_Blasts_63


title: SU353_Blasts_61


title: SU353_Blasts_62


title: SU353_Blasts_60


title: SU353_Blasts_59


title: SU353_Blasts_5


title: SU353_Blasts_58


title: SU353_Blasts_53


title: SU353_Blasts_52


title: SU353_Blasts_57


title: SU353_Blasts_51


title: SU353_Blasts_54


title: SU353_Blasts_4


title: SU353_Blasts_56


title: SU353_Blasts_48


title: SU353_Blasts_55


title: SU353_Blasts_49


title: SU353_Blasts_47


title: SU353_Blasts_46


title: nintedanib.947179: Bleomycin + Nintedanib 3

city: New York

first: Lori

last: Morton

state: NY

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description: Bleomycin-treated (2.8 U/kilogram (kg); 1.75 milligram (mg)/kg) and receiving Nintedanib (60mg/kg administered by oral gavage, QD).

data_processing: The Cell Ranger Suite version 2.0.0 was used to perform sample de-multiplexing, barcode processing and single cell gene UMI (unique molecular index) counting.  Sequencing reads were aligned Refseq mm10 transcriptome.

organism: Mus musculus

source_name: Isolated Lung Cells

extract_protocol:
Singe cell isolation was completed using collagenase based tissue dissociation techniques.  Viable cells were collected and suspended in 2ml sterile PBS+0.4%BSA. Single cell suspensions were loaded on a Chromium Single Cell Instrument (10X Genomics) to generate single cell gel beads in emulsion.
Single cell RNA-Seq libraries were prepared using version 2 Chromium single cell 3’ chemistry. Sequencing was performed on Illumina NextSeq500 with a transcript length of 59 bp.

treatment_protocol: Bleomycin (2.8 U/kg), Vehicle (0.5% carboxymethyl cellulose in water), or Nintedanib (60mg/kg) plus Bleomycin administered by oral gavage, QD.

tag: strain

tag: age

value: 12-13 weeks

tag: tissue

value: Lung


title: nintedanib.947177: Bleomycin + Nintedanib 1


title: bleomycin.955738: Bleomycin 4

description: Bleomycin-treated (2.8 U/kilogram (kg); 1.75 milligram (mg)/kg) and receiving daily oral gavage with vehicle.


title: nintedanib.947178: Bleomycin + Nintedanib 2


title: bleomycin.947176: Bleomycin 3


title: SU353_Blasts_45


title: SU353_Blasts_68


title: bleomycin.947174: Bleomycin 2


title: SU353_Blasts_44


title: SU353_Blasts_43


title: bleomycin.947173: Bleomycin 1


title: SU353_Blasts_42


title: SU353_Blasts_50


title: SU353_Blasts_41


title: SU353_Blasts_40


title: SU353_Blasts_3


title: saline.955736: Saline Control 3

description: Saline-treated and receiving daily oral gavage with vehicle.  Vehicle - 0.5% carboxymethyl cellulose in water.


title: saline.947172: Saline Control 2


title: saline.947170: Saline Control 1


title: SU353_Blasts_39


title: SU353_Blasts_38


title: SU353_Blasts_37


title: TBL1_04

city: Boston

first: Mark

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

description: processed data file: 170815_MEAN_TF_around_OPTIMAL_ATAC.txt.gz

data_processing:
All samples were aligned to the mm10 genome using default parameters for the Subread (subread-1.4.6-p3, (Liao et al., 2013)) alignment software after quality trimming with Trimmomatic v0.33 (Bolger et al., 2014) with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Truseq adapters were trimmed out in ChIP- and RNA-seq experiments; Nextera adapters were specified for ATAC-seq data.
To generate UCSC genome browser tracks for ChIP- and ATAC-seq data, the aligned bam files produced by Subread were converted to BED format with the bedtools bamtobed command. The 75 base pair reads were extended in the 3’ direction to 200 basepairs (bp) (average fragment length for ChIP- and ATAC-seq experiments as measured by bioAnalyzer) with the bedtools slop command using the following parameters: -l 0 -r 125 -g [CHR_SIZES_FILE]. Published mm10 ChIP-seq blacklisted regions (Consortium, 2012) were filtered out using the following command: bedops –not-element-of 1 [BLACKLIST_BED]. The filtered BED files were converted to coverageBED format using the bedtools genomecov command with the following options: -scale [NORM_FACTOR to scale each library to 20M reads] –bg –g [CHR_SIZES_FILE] | LC_COLLATE=C sort -k1,1 -k2,2n. Finally, bedGraphToBigWig (UCSC-tools) was used to generate the bigWIG files shown throughout the manuscript.
To quantify gene expression, we applied the featureCounts package (Liao et al., 2013) after aligning RNA-seq libraries to the genome as described above, using a custom filtered annotation file: gencode.v17.annotation.gtf filtered for feature_type=”gene”, gene_type="protein_coding" and gene_status="KNOWN") to obtain gene counts for each sample. These counts tables were TMM-normalized using the edgeR software analysis package (Robinson et al., 2010). Any genes that were not expressed in at least 3 samples with TMM-normalized CPM>1 were dropped from further analysis. Differential expression (DE) analyses were conducted using the voom/limma analysis software packages (requiring FDR-corrected q<0.05).
Regions of ATAC-seq enrichment were determined using MACS2 (v 2.1.0) parameters -p 1e-5 --nolambda --keep-dup all --slocal 10000, as previously described (Buenrostro et al., 2013). Peaks from individual sample replicates were intersected to find only reproducible regions of enrichment.  Blacklist regions were removed as previously described (Consortium, 2012).
To identify sites with enriched ChIP-seq signal (peaks), we applied the IDR pipeline (Li, 2011) using the MACS2 peak calling algorithm (Zhang et al., 2008) with the following additional parameters: --nomodel --extsize 200 --keep-dup all. An IDR threshold of .01 was used for self-consistency, true replicate, and pooled-consistency analyses. The ‘optThresh’ cutoff was then used to obtain a final set of high-confidence, reproducible ChIP-seq peaks for each factor or chromatin modification at each stimulus condition tested. After calling peaks using both ATAC-seq data and H3K27ac ChIP-Seq data, we constructed a set of all putative functional regulatory elements in the embryonic cultured neuronal system by taking the union of all sites that showed significant (IDR<0.01) ATAC or H3K27Ac ChIP-seq signal in any of the unstimulated, 2 hour KCl depolarized, or 6-hour KCl depolarized conditions ± any viral treatment, resulting in a total of 31,138 sites genome-wide (referred to hereafter as annotations). We then used the HOMER software package to quantify the number of reads present across each of these annotations from each ChIP-seq experiment by first constructing tag directories (makeTagDirectory –fragLength 200), and then using the annotatePeaks.pl script with the following parameters to obtain raw counts tables: -len 200 -size given -noadj -noann -nogene. Any annotations within 1 kb of an annotated TSS were considered ‘promoter’ regulatory elements; all other annotations were termed enhancers. Fixed line plots were generated with Homer’s annotatePeaks.pl script (Heinz et al., 2010), using the following parameters: annotatePeaks.pl [PEAK_BED] mm10 -d [INPUT_TAG_DIRS] -len 200 -size 4000 –ghist -hist 25 -noann -nogene. Bioreplicates were averaged at each 25 base pair bin by peak and the average log2(x + 1) signal intensity is displayed. To generate aggregate plots, the outputs of the commands above were summed across all relevant peaks within each sample, and then these aggregated sums were averaged by bin across all replicates. The standard error of the mean is shaded around each plot’s mean signal intensity.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: 170815_MEAN_TF_around_OPTIMAL_ATAC.txt.gz: Matrix of mean transcription factor ChIP-seq count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 170913_invitro_ctx_counts.txt: UMIFM counts for inDrops dataset by cell; 170815_MEAN_ATAC_around_OPTIMAL_ATAC.txt.gz: Matrix of mean ATAC-seq count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 180413_MEAN_UPDATED_H3K27AC_around_OPTIMAL_ATAC.txt.gz: Matrix of mean H3K27Ac count data across replicates normalized by sequencing depth in 4kb window flanking each IDR .01 thresholded ATAC summit; 150805_n4oe_TMMnorm_agg_cpm.csv: TMM normalized RNA-seq expression values for Npas4-overexpression experiment; 181031_Arnt2_counts_invivo.txt: raw RNA-seq counts for Arnt2 shRNA experiments; 180216_NCoR2_counts_invivo.txt: raw RNA-seq gene counts for NCoR2 fl experiments

source_name: embryonic cortical culture

growth_protocol: Embryonic cortices from C57Bl/6 or transgenic (Npas4fl/fl) mice were dissected at ages E16.5-E17 and then dissociated with papain (Sigma Aldrich; 10108014001).  Papain digestion was terminated with the addition of ovomucoid (trypsin inhibitor; Worthington).  Cells were gently triturated through a P1000 pipette and passed through a 40 micron filter.  Neurons were plated onto cell cultures dishes pre-coated overnight with poly-D-lysine (20 μg/mL) and laminin (4 μg/mL).  Neurons were grown in Neurobasal medium (Gibco) containing B27 supplement (2%), penicillin-streptomycin (50 U/mL penicillin and 50 U/mL streptomycin) and glutaMAX (1 mM).  Neurons were grown in incubators maintained at 37C and a CO2 concentration of 5%.  Neurons were harvested in all experiments at 7DIV, and fresh media was added at 3-4DIV (25% total volume), unless otherwise indicated.  For IP-MS or ChIP, cortical neurons were plated at a density of 20-30 x 106 / dish on a 15-cm dish.  To prevent spurious activity, for IP-MS experiments, NCoR2 complex ChIPs, 7DIV neurons were silenced on 6DIV overnight by the addition of 1 mM TTX (Abcam ab120055) and 100 μM AP5 (Thermo Fisher 01-061-0 ).

extract_protocol:
For ChIP of transcription factors and histone modifications, primary neurons (E16.5) were crosslinked via addition of 1% formaldehyde for 10 min at room temperature and quenched by the addition of 0.125 M glycine for 5 min at room temperature.  To ChIP the NCoR2 complex, we found it necessary to perform dual crosslinking by incubating neurons for 30 min with 1.5 mM EGS (ethylene glycol bis(succinimidyl succinate) (Fisher, 21565)), followed by 10 min incubation in 1% formaldehyde and standard quenching with 0.125 M glycine.  Nuclei were isolated from cell pellets by incubation in lysis buffer 1 (in mM: 100 HEPES-NaOH pH 7.5, 280 NaCl, 2 EDTA, 2 EGTA, 0.5% Triton X-100, 1% NP-40, 20% Glycerol) followed by washing in buffer containing 10 mM Tris-HCl pH 8.0, 200 mM NaCl.  Chromatin was sheared using a Bioruptor (Diagenode) on high power mode for 50 cycles with 30 sec pulses in sonication buffer (in mM: 10 Tris-HCl pH 8.0, 100 NaCl, 1 EDTA, 0.5 EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine).  For H2K27ac ChIP, 10 mM sodium butyrate (Fisher NC9851678) was added to all buffers. Following sonication, chromatin was supplemented with 1% Triton and was incubated overnight with the following antibodies: H3K27ac (Abcam 4729, 0.2 μg for 2.5 million cells ), 5-8 μg Arnt2 (in house protein A purified anti-serum; see below), 8 μg Npas4 (custom made protein A purified anti-serum), NCoR2 (Millipore, 06891; 5 μg for 60-70 μg chromatin; Thermo PA1-843; 5 μg for 60-70 μg chromatin (40-50 million cells)); Tbl1 (Abcam 24528; 5 μg for 60-70 ug chromatin (40-50 million cells)); Hdac3 (Santa Cruz sc11416X; 5 μg for 60-70 μg chromatin (40-50 million cells).
Libraries were generated using the Ovation Ultralow V2 kit according to the manufacturer’s instructions and PCR amplified for 13-16 cycles depending on antibody. Library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Seventy-five bp reads were generated on the Illumina Nextseq and subsequently analyzed with our standardized ChIP-seq data analysis pipeline (below).
Tissue was collected in Trizol reagent and RNA was extracted using the RNAeasy Kit (Qiagen) according to the manufacturer’s instructions.
Total RNA (1000 ng) was used to generate libraries following rRNA depletion according to the manufacturer’s instructions (NEBNext). Seventy-five bp reads were generated on the Illumina Nextseq and subsequently analyzed with our standardized RNA-seq data analysis pipeline (below).
To assess regions of open chromatin, neurons were washed with cold PBS and lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630.
50,000 nuclei per condition were transposed using the Nextera DNA Library Prep Kit (Illumina).  Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp.

tag: chip-ed factor

tag: chip antibody

value: abcam Ab24528

tag: stimulus

tag: viral treatment

value: uninfected


title: TBL1_03


title: SU353_Blasts_35


title: TNF 60 min [ChIA-PET]

description: ChIA-PET data of human endothelial cells through TNF-induced inflammatory signaling

data_processing:
ChIA-PET libraries yielded ~35×10^6 20-bp paired-end reads each, from which 10.8×106 and 8.8×106 were successfully aligned to the genome (hg19) for the 0-, 30-, and 60-min samples, respectively. For stringency, two or more reads having the same sequences, or mapping within 2 bp of the left and right ends of another read were classified as one PET.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: bed

extract_protocol:
Chromatin interaction analysis with paired-end tag sequencing (ChIA-PET) was performed as previously described (Li et al., 2010; Papantonis et al., 2012). Briefly, cells were crosslinked using 10mM EGS in 50% glacial acetic acid (45 min) and then in 1% paraformaldehyde (20 min), quenched (5min) in 2.5 M glycine, harvested, sonicated (Digital Sonifier 250; Branson, Danbury, CT). The ChIP was performed using magnetic beads (Dynabeads M-280) with a Pd75C9 antibody directed against phospho-Ser2/-Ser5 within the heptad repeat at the C-terminus of the largest catalytic subunit of RNA polymerase II (a gift of H Kimura).
Chromatin captured on magnetic beads was trimmed to create blunt ends, phosphate groups were added to 5’ ends, ends ligated to each other via biotinylated half-linkers, and complexes eluted. Crosslinking was reversed, DNA purified and digested with MmeI (whose binding site is encoded by the linker). After immobilization on M-280 Streptavidin Dynabeads (Thermo Fisher Scientific), adaptors were ligated, and the efficiency of library production evaluated by PCR. Finally, di-tags were prepared, sequenced on a GAII analyzer (Illumina), and resulting paired-end tags (PETs) analyzed.

treatment_protocol: 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

value: HUVECs

tag: agent

value: TNF

tag: time point

value: 60 min


title: SU353_Blasts_36

value: acute myeloid leukemia


title: NPAS4_OE_B2_B2_R2

description: processed data file: 150805_n4oe_TMMnorm_agg_cpm

value: full-length Npas4 overexpression


title: TBL1_02


title: NPAS4_OE_B2_B2_R1


title: SU353_Blasts_33


title: TBL1_01


title: saline.955737: Saline Control 4


title: SU353_Blasts_34


title: TNF 30 min [ChIA-PET]

value: 30 min

value: pooled from multiple donors


title: NPAS4_OE_B1_R1


title: SU353_Blasts_32


title: control [ChIA-PET]


title: NPAS4_DELTAPAS_B2_B2_R2

value: delta-pas Npas4 overexpression


title: MPND_WT_ChIP

city: Los Angeles

first: Douglas

middle: Edmund

last: Feldman

state: CA

address: 2011 Zonal Avenue

department: Pathology

institute: USC Keck School of Medicine

data_processing:
For ChIP-seq, DIP-seq and RNA-seq, raw reads were trimmed to remove adapters and low-  quality reads using Trim Galore (v0.3.5). Bowtie (v0.12.8) was used to obtain reads mapped  uniquely to the mouse genome (mm10). ChIP and DIP peak candidates were identified with  MACS (v2.1.1) using input as the control data set. To remove nonspecific signals, IgG samples  were processed similarly and their normalized read density (RPKM) values were subtracted  from modification-specific peaks. For DIP, the empirical FDR was estimated by exchanging the  DIP and IgG control samples and identifying peaks in the control sample using the same set of  parameters used for the DIP sample. Called peaks were annotated with Gencode M1 and  Cistrome CEAS (Shin et al., 2009) . Normalized read density plots centered on annotated  elements downloaded from ENCODE were generated using NGSPLOT (Shen et al., 2014) .  Peak overlap statistics were calculated using Fisherbed. For RNA-seq, Cufflinks (v 2.2.1.0) was  used to assemble transcripts, estimate their abundances and test for differential transcript  expression. All GO analyses used DAVID (http://david.abcc.ncifcrf.gov).
Genome_build: mm10
Supplementary_files_format_and_content: bam files were mapped using TopHat, FPKM values calculated with CuffLinks

source_name: ESCs

growth_protocol: Co-derived wild-type and Srap1 KO mouse ES cells were cultured on gelatin-coated plates in high-glucose DMEM containing 15% FBS, 1x non-essential amino acids, 2 mM L-glutamine, 100 mM beta-mercaptoethanol, 1x nucleosides (Millipore), 1000U/ml leukemia inhibitory factor (StemRD) and 2i (selective GSK3β & Mek 1/2 inhibitors; Millipore), 25 mg/ml L-ascorbic acid.

extract_protocol: ChIP, MeDIP and RNA library preparation  For ChIP, strain-matched wild-type or Mettl4 KO mouse ES cells (C57BL/6N x 129/Sv  background) were fixed in 1% paraformaldehyde for 10 min at 37°C, followed by quenching with  125 mM glycine for 5 min. Cells were lysed and processed using the MAGnify ChIP system (Life  Sciences). Lysates were sonicated using an ultrasonic processor (Cole Parmer) at power  setting 3 in 30 s pulses followed by 1 min on ice, for a total of 6 min sonication. Nucleoprotein  complexes were immunoprecipitated the indicated antisera (2.5 g) equivalent amounts of  isotype-matched control IgG per sample. For MeDIP experiments, genomic DNA was isolated  from ES cells using the DNeasy Blood & Tissue DNA kit and sonicated for a total of 6 min.  Samples were processed using the hMeDIP kits (Active Motif) according to the manufacturer’s  protocol. For RNA-seq, total RNA was extracted from mouse ES cells using the Zymo RNA  Clean & Concentrator (Zymo Research), followed by mRNA enrichment and cDNA preparation  using the KAPA Stranded RNA-Seq Kit. Library preparations were performed using the Kapa  HyperPrep kit, followed by 12 cycles of PCR amplification with Kapa HiFi HotStart polymerase.  Amplified libraries were pooled, purified twice with 0.9X Ampure XP beads and analyzed on an  Illumina HiSeq2000 or NextSeq500.

tag: genotype

value: wild-type

value: ESCs

value: 3 passages

value: MPND (Invitrogen PA5-68860, Lot T02553192B)


title: SU353_Blasts_30

value: Blasts


title: MPND_KO_ChIP

value: Srap1 KO


title: SU353_Blasts_2


title: SU353_Blasts_31


title: NPAS4_DELTAPAS_B2_B2_R1


title: SU353_Blasts_29


title: SU353_Blasts_28


title: NPAS4_DELTAPAS_B1_R2


title: NPAS4_OE_B1_R2


title: NPAS4_16

value: in house 5177


title: NPAS4_DELTAPAS_B1_R1


title: SU353_Blasts_26


title: SU353_Blasts_27


title: NPAS4_15


title: NPAS4_14


title: NPAS4_12


title: SU353_Blasts_25


title: SU353_Blasts_24


title: SU353_Blasts_23


title: NPAS4_11


title: NPAS4_10

value: ctlshrna


title: SU353_Blasts_22


title: NPAS4_09


title: SU353_Blasts_21


title: NPAS4_08


title: SU353_Blasts_20


title: NPAS4_07


title: SU353_Blasts_1


title: SU353_Blasts_19


title: NPAS4_13


title: HSCATAC_P165_9

description:
sample name:
HSCATAC_P165_9

data_processing:
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters.
Paired-end reads were aligned to hg19 using bwa. Duplicates were removed using PICARD tools
Reads were subsequently filtered for alignment quality  and were required to be properly paired.
Genome_build: hg19
Supplementary_files_format_and_content: bed file with raw counts

source_name: pre-leukemic HSCs

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 7 µL of harvested libraries were amplified in 50 µL PCR for an additional 17 cycles (1.25 µM custom Nextera dual-index PCR primers  in 1x NEBnext High-Fidelity PCR Master using the following PCR conditions: 72°C for 5min; 98°C for 30 s;  Mix)  using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL.  The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries  at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

value: pre-leukemic HSCs


title: NPAS4_04

value: uninfected


title: HSCATAC_P165_96

description:
sample name:
HSCATAC_P165_96


title: NPAS4_06


title: SU353_Blasts_17


title: NPAS4_03


title: NPAS4_05


title: H9 embryonic stem cells, Ncad negative SSEA3 negative sorted population, biological rep2

type: RNA

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

hyb_protocol: In accordance with manufacturer's protocols

scan_protocol: GeneChips were scanned using  Affymetrix® Scanner 3000 7G.

data_processing: Data was normalized using Robust Multichip Averaging (RMA) algorithm using Partek Genomics Suite 6.6 software.

label: biotin

source_name: H9 embryonic stem cells

growth_protocol: MEF conditioned medium + 8ng/ml bFGF

extract_protocol: Extraction of total RNA using total RNA purification kit (Norgen Biotek, Canada) was performed according to the manufacturer's instructions.

tag: sorted cells

value: Ncad negative SSEA3 negative


title: SU353_Blasts_16


title: HSCATAC_P165_94

description:
sample name:
HSCATAC_P165_94


title: H9 embryonic stem cells, Ncad negative SSEA3 positive sorted population, biological rep2

label_protocol: In accordance with manufacturer's protocols

value: Ncad negative SSEA3 positive


title: SU353_Blasts_15

value: acute myeloid leukemia


title: SU353_Blasts_18


title: HSCATAC_P165_92

description:
sample name:
HSCATAC_P165_92


title: H9 embryonic stem cells, Ncad negative SSEA3 negative sorted population, biological rep3


title: H9 embryonic stem cells, Ncad positive sorted population, biological rep2

value: Ncad positive


title: H9 embryonic stem cells, Ncad negative SSEA3 positive sorted population, biological rep1


title: H9 embryonic stem cells, Ncad positive sorted population, biological rep1


title: H9 embryonic stem cells, Ncad positive sorted population, biological rep3


title: H9 embryonic stem cells, Ncad negative SSEA3 positive sorted population, biological rep3


title: H9 embryonic stem cells, Ncad negative SSEA3 negative sorted population, biological rep1


title: 293T_DOCK10: 293T cells transfected with pSG5-HA-DOCK10.1 vector for 24 hr

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 5 µm

data_processing: Agilent Feature Extraction software version 10.7.3.1

source_name: Reference sample: 293T cells

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: 293T cells were cultured DMEM supplemented with 10% fetal calf serum, 50 U/ml penicillin, 50 U/ml streptomycin, 2.5 µg/ml amphotericin B, and 2 mM L-glutamine

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: Transfection with pSG5 or pSG5-HA-DOCK10.1 vectors using lipofectamine followed by culture during 24 hr, and detachment using trypsin 0.05%-EDTA 0.02% in PBS

value: Human embryonic kidney 293T cells

source_name: Test sample: 293T cells transfected with pSG5-DOCK10.1 vector

value: Human embryonic kidney cell line 293T


title: NPAS4_02


title: HSCATAC_P165_95

description:
sample name:
HSCATAC_P165_95


title: HSCATAC_P165_93

description:
sample name:
HSCATAC_P165_93


title: HSCATAC_P165_90

description:
sample name:
HSCATAC_P165_90


title: SU353_Blasts_13


title: 293T_pSG5: 293T cells transfected with pSG5 empty vector for 24 hr

source_name: Test sample: 293T cells transfected with empty pSG5 vector


title: NPAS4_01


title: HSCATAC_P165_8

description:
sample name:
HSCATAC_P165_8


title: HSCATAC_P165_85

description:
sample name:
HSCATAC_P165_85


title: SU353_Blasts_14


title: HSCATAC_P165_89

description:
sample name:
HSCATAC_P165_89


title: HSCATAC_P165_91

description:
sample name:
HSCATAC_P165_91


title: SU353_Blasts_11


title: HSCATAC_P165_81

description:
sample name:
HSCATAC_P165_81


title: HSCATAC_P165_83

description:
sample name:
HSCATAC_P165_83


title: HSCATAC_P165_88

description:
sample name:
HSCATAC_P165_88


title: HSCATAC_P165_87

description:
sample name:
HSCATAC_P165_87


title: HSCATAC_P165_7

description:
sample name:
HSCATAC_P165_7


title: SU353_Blasts_10


title: HSCATAC_P165_79

description:
sample name:
HSCATAC_P165_79


title: SU070_LSC_96

value: LSC


title: SU070_LSC_9


title: HSCATAC_P165_78

description:
sample name:
HSCATAC_P165_78


title: HSCATAC_P165_75

description:
sample name:
HSCATAC_P165_75


title: HSCATAC_P165_77

description:
sample name:
HSCATAC_P165_77


title: HSCATAC_P165_74

description:
sample name:
HSCATAC_P165_74


title: HSCATAC_P165_72

description:
sample name:
HSCATAC_P165_72


title: HSCATAC_P165_73

description:
sample name:
HSCATAC_P165_73


title: SU070_LSC_94


title: SU070_LSC_95


title: HSCATAC_P165_76

description:
sample name:
HSCATAC_P165_76


title: HSCATAC_P165_71

description:
sample name:
HSCATAC_P165_71


title: HSCATAC_P165_86

description:
sample name:
HSCATAC_P165_86


title: HSCATAC_P165_70

description:
sample name:
HSCATAC_P165_70


title: HSCATAC_P165_84

description:
sample name:
HSCATAC_P165_84


title: SU070_LSC_93


title: SU353_Blasts_12


title: HSCATAC_P165_6

description:
sample name:
HSCATAC_P165_6


title: SU070_LSC_92


title: HSCATAC_P165_80

description:
sample name:
HSCATAC_P165_80


title: HSCATAC_P165_69

description:
sample name:
HSCATAC_P165_69


title: SU070_LSC_91


title: HSCATAC_P165_82

description:
sample name:
HSCATAC_P165_82


title: HSCATAC_P165_64

description:
sample name:
HSCATAC_P165_64


title: SU070_LSC_90


title: HSCATAC_P165_65

description:
sample name:
HSCATAC_P165_65


title: HSCATAC_P165_66

description:
sample name:
HSCATAC_P165_66


title: SU070_LSC_8


title: HSCATAC_P165_63

description:
sample name:
HSCATAC_P165_63


title: HSCATAC_P165_58

description:
sample name:
HSCATAC_P165_58


title: HSCATAC_P165_5

description:
sample name:
HSCATAC_P165_5


title: SU070_LSC_87


title: HSCATAC_P165_59

description:
sample name:
HSCATAC_P165_59


title: HSCATAC_P165_60

description:
sample name:
HSCATAC_P165_60


title: HSCATAC_P165_62

description:
sample name:
HSCATAC_P165_62


title: HSCATAC_P165_61

description:
sample name:
HSCATAC_P165_61


title: SU070_LSC_86


title: HSCATAC_P165_55

description:
sample name:
HSCATAC_P165_55


title: HSCATAC_P165_56

description:
sample name:
HSCATAC_P165_56


title: HSCATAC_P165_53

description:
sample name:
HSCATAC_P165_53


title: HSCATAC_P165_54

description:
sample name:
HSCATAC_P165_54


title: HSCATAC_P165_52

description:
sample name:
HSCATAC_P165_52


title: SU070_LSC_84


title: HSCATAC_P165_68

description:
sample name:
HSCATAC_P165_68


title: SU070_LSC_83


title: HSCATAC_P165_51

description:
sample name:
HSCATAC_P165_51


title: HSCATAC_P165_67

description:
sample name:
HSCATAC_P165_67


title: SU070_LSC_82


title: SU070_LSC_89


title: SU070_LSC_88


title: HSCATAC_P165_4

description:
sample name:
HSCATAC_P165_4


title: SU070_LSC_81


title: HSCATAC_P165_48

description:
sample name:
HSCATAC_P165_48


title: HSCATAC_P165_49

description:
sample name:
HSCATAC_P165_49


title: HSCATAC_P165_47

description:
sample name:
HSCATAC_P165_47


title: SU070_LSC_7


title: HSCATAC_P165_44

description:
sample name:
HSCATAC_P165_44


title: HSCATAC_P165_45

description:
sample name:
HSCATAC_P165_45


title: HSCATAC_P165_46

description:
sample name:
HSCATAC_P165_46


title: NCOR2_24

value: Fisher PA1-843


title: NCOR2_25


title: SU070_LSC_85


title: SU070_LSC_80


title: HSCATAC_P165_57

description:
sample name:
HSCATAC_P165_57


title: NCOR2_26


title: HSCATAC_P165_41

description:
sample name:
HSCATAC_P165_41


title: NCOR2_23


title: HSCATAC_P165_42

description:
sample name:
HSCATAC_P165_42


title: SU070_LSC_78


title: SU070_LSC_79


title: HSCATAC_P165_3

description:
sample name:
HSCATAC_P165_3


title: HSCATAC_P165_50

description:
sample name:
HSCATAC_P165_50


title: HSCATAC_P165_43

description:
sample name:
HSCATAC_P165_43


title: SU070_LSC_77


title: HSCATAC_P165_39

description:
sample name:
HSCATAC_P165_39


title: SU070_LSC_76


title: HSCATAC_P165_38

description:
sample name:
HSCATAC_P165_38


title: NCOR2_21


title: HSCATAC_P165_40

description:
sample name:
HSCATAC_P165_40


title: HSCATAC_P165_37

description:
sample name:
HSCATAC_P165_37


title: NCOR2_20


title: SU070_LSC_75


title: NCOR2_22


title: HSCATAC_P165_36

description:
sample name:
HSCATAC_P165_36


title: HSCATAC_P165_35

description:
sample name:
HSCATAC_P165_35


title: HSCATAC_P165_34

description:
sample name:
HSCATAC_P165_34


title: SU070_LSC_74


title: HSCATAC_P165_33

description:
sample name:
HSCATAC_P165_33


title: SU070_LSC_73


title: NCOR2_18

value: Millipore 06891


title: NCOR2_19


title: HSCATAC_P165_31

description:
sample name:
HSCATAC_P165_31


title: HSCATAC_P165_32

description:
sample name:
HSCATAC_P165_32


title: HSCATAC_P165_30

description:
sample name:
HSCATAC_P165_30


title: SU070_LSC_72


title: HSCATAC_P165_2

description:
sample name:
HSCATAC_P165_2


title: SU070_LSC_71


title: HSCATAC_P165_28

description:
sample name:
HSCATAC_P165_28


title: NCOR2_17


title: HSCATAC_P165_27

description:
sample name:
HSCATAC_P165_27


title: NCOR2_16


title: NCOR2_15


title: SU070_LSC_70


title: HSCATAC_P165_26

description:
sample name:
HSCATAC_P165_26


title: HSCATAC_P165_24

description:
sample name:
HSCATAC_P165_24


title: SU070_LSC_6


title: HSCATAC_P165_25

description:
sample name:
HSCATAC_P165_25


title: HSCATAC_P165_23

description:
sample name:
HSCATAC_P165_23


title: HSCATAC_P165_22

description:
sample name:
HSCATAC_P165_22


title: NCOR2_14


title: HSCATAC_P165_21

description:
sample name:
HSCATAC_P165_21


title: SU070_LSC_68


title: NCOR2_12


title: HSCATAC_P165_1

description:
sample name:
HSCATAC_P165_1


title: SU070_LSC_67


title: NCOR2_11


title: NCOR2_10


title: HSCATAC_P165_19

description:
sample name:
HSCATAC_P165_19


title: HSCATAC_P165_29

description:
sample name:
HSCATAC_P165_29


title: HSCATAC_P165_17

description:
sample name:
HSCATAC_P165_17


title: SU070_LSC_66


title: HSCATAC_P165_16

description:
sample name:
HSCATAC_P165_16


title: SU070_LSC_65


title: HSCATAC_P165_15

description:
sample name:
HSCATAC_P165_15


title: HSCATAC_P165_14

description:
sample name:
HSCATAC_P165_14


title: NCOR2_08


title: NCOR2_13


title: HSCATAC_P165_13

description:
sample name:
HSCATAC_P165_13


title: SU070_LSC_69


title: HSCATAC_P165_11

description:
sample name:
HSCATAC_P165_11


title: HSCATAC_P165_12

description:
sample name:
HSCATAC_P165_12


title: SU070_LSC_63


title: SU070_LSC_64


title: SU070_LSC_62


title: HSCATAC_P165_10

description:
sample name:
HSCATAC_P165_10


title: NCOR2_06


title: HSCATAC_P164_9

description:
sample name:
HSCATAC_P164_9


title: NCOR2_05


title: HSCATAC_P164_96

description:
sample name:
HSCATAC_P164_96


title: HSCATAC_P165_18

description:
sample name:
HSCATAC_P165_18


title: SU070_LSC_61


title: HSCATAC_P164_95

description:
sample name:
HSCATAC_P164_95


title: NCOR2_07


title: SU070_LSC_60


title: NCOR2_09


title: HSCATAC_P164_94

description:
sample name:
HSCATAC_P164_94


title: HSCATAC_P164_93

description:
sample name:
HSCATAC_P164_93


title: HSCATAC_P164_92

description:
sample name:
HSCATAC_P164_92


title: NCOR2_03


title: HSCATAC_P164_91

description:
sample name:
HSCATAC_P164_91


title: SU070_LSC_5


title: HSCATAC_P164_90

description:
sample name:
HSCATAC_P164_90


title: NCOR2_02


title: HSCATAC_P165_20

description:
sample name:
HSCATAC_P165_20


title: HSCATAC_P164_8

description:
sample name:
HSCATAC_P164_8


title: SU070_LSC_59


title: SU070_LSC_58


title: HSCATAC_P164_88

description:
sample name:
HSCATAC_P164_88


title: HSCATAC_P164_89

description:
sample name:
HSCATAC_P164_89


title: HSCATAC_P164_87

description:
sample name:
HSCATAC_P164_87


title: NCOR2_01


title: SU070_LSC_57


title: INPUT_23

source_name: adult hippocampus

value: input


title: HSCATAC_P164_86

description:
sample name:
HSCATAC_P164_86


title: INPUT_22


title: NCOR2_04


title: HSCATAC_P164_84

description:
sample name:
HSCATAC_P164_84


title: SU070_LSC_55


title: HSCATAC_P164_80

description:
sample name:
HSCATAC_P164_80


title: HSCATAC_P164_81

description:
sample name:
HSCATAC_P164_81


title: SU070_LSC_54


title: HSCATAC_P164_82

description:
sample name:
HSCATAC_P164_82


title: INPUT_20

source_name: embryonic cortical culture_egs


title: HSCATAC_P164_7

description:
sample name:
HSCATAC_P164_7


title: INPUT_21


title: INPUT_19


title: INPUT_18


title: SU070_LSC_53


title: HSCATAC_P164_79

description:
sample name:
HSCATAC_P164_79


title: HSCATAC_P164_83

description:
sample name:
HSCATAC_P164_83


title: HSCATAC_P164_78

description:
sample name:
HSCATAC_P164_78


title: INPUT_17


title: SU070_LSC_52


title: HSCATAC_P164_77

description:
sample name:
HSCATAC_P164_77


title: HSCATAC_P164_85

description:
sample name:
HSCATAC_P164_85


title: INPUT_16


title: SU070_LSC_56


title: SU070_LSC_50


title: HSCATAC_P164_73

description:
sample name:
HSCATAC_P164_73


title: HSCATAC_P164_75

description:
sample name:
HSCATAC_P164_75


title: HSCATAC_P164_74

description:
sample name:
HSCATAC_P164_74


title: HSCATAC_P164_76

description:
sample name:
HSCATAC_P164_76


title: SU070_LSC_51


title: HSCATAC_P164_72

description:
sample name:
HSCATAC_P164_72


title: SU070_LSC_4


title: HSCATAC_P164_71

description:
sample name:
HSCATAC_P164_71


title: INPUT_14


title: HSCATAC_P164_70

description:
sample name:
HSCATAC_P164_70


title: INPUT_15


title: SU070_LSC_49


title: INPUT_13


title: SU070_LSC_48


title: HSCATAC_P164_68

description:
sample name:
HSCATAC_P164_68


title: SU070_LSC_47


title: HSCATAC_P164_69

description:
sample name:
HSCATAC_P164_69


title: HSCATAC_P164_65

description:
sample name:
HSCATAC_P164_65


title: HSCATAC_P164_66

description:
sample name:
HSCATAC_P164_66


title: HSCATAC_P164_67

description:
sample name:
HSCATAC_P164_67


title: INPUT_11


title: HSCATAC_P164_62

description:
sample name:
HSCATAC_P164_62


title: HSCATAC_P164_60

description:
sample name:
HSCATAC_P164_60


title: HSCATAC_P164_64

description:
sample name:
HSCATAC_P164_64


title: HSCATAC_P164_59

description:
sample name:
HSCATAC_P164_59


title: INPUT_10


title: SU070_LSC_43


title: SU070_LSC_44


title: INPUT_8


title: HSCATAC_P164_61

description:
sample name:
HSCATAC_P164_61


title: HSCATAC_P164_63

description:
sample name:
HSCATAC_P164_63


title: HSCATAC_P164_5

description:
sample name:
HSCATAC_P164_5


title: INPUT_9


title: SU070_LSC_45


title: SU070_LSC_42


title: HSCATAC_P164_58

description:
sample name:
HSCATAC_P164_58


title: HSCATAC_P164_57

description:
sample name:
HSCATAC_P164_57


title: HSCATAC_P164_6

description:
sample name:
HSCATAC_P164_6


title: HSCATAC_P164_55

description:
sample name:
HSCATAC_P164_55


title: HSCATAC_P164_56

description:
sample name:
HSCATAC_P164_56


title: INPUT_6


title: INPUT_12


title: INPUT_7


title: SU070_LSC_40


title: SU070_LSC_41


title: HSCATAC_P164_54

description:
sample name:
HSCATAC_P164_54


title: HSCATAC_P164_53

description:
sample name:
HSCATAC_P164_53


title: INPUT_4


title: INPUT_5


title: INPUT_3


title: SU070_LSC_3


title: SU070_LSC_39


title: SU070_LSC_38


title: HSCATAC_P164_50

description:
sample name:
HSCATAC_P164_50


title: SU070_LSC_37


title: INPUT_1


title: INPUT_2


title: HSCATAC_P164_51

description:
sample name:
HSCATAC_P164_51


title: SU070_LSC_36


title: SU070_LSC_35


title: HSCATAC_P164_4

description:
sample name:
HSCATAC_P164_4


title: HSCATAC_P164_49

description:
sample name:
HSCATAC_P164_49


title: INDROPS_6_KCL_CTX_B2_R2

description: processed data file: 170913_invitro_ctx_counts.txt.gz

molecule: polyA RNA


title: SU070_LSC_46


title: SU070_LSC_34


title: HSCATAC_P164_52

description:
sample name:
HSCATAC_P164_52


title: INDROPS_6_KCL_CTX_B2_R1


title: INDROPS_6_KCL_CTX_B1_R2


title: HSCATAC_P164_48

description:
sample name:
HSCATAC_P164_48


title: INDROPS_6_KCL_CTX_B1_R1


title: HSCATAC_P164_47

description:
sample name:
HSCATAC_P164_47


title: HSCATAC_P164_46

description:
sample name:
HSCATAC_P164_46


title: INDROPS_1_KCL_CTX_B2_R2


title: SU070_LSC_31


title: SU070_LSC_33


title: SU070_LSC_32


title: HeLa_DOCK10_2: HeLa-C33 clone cultured for 24 hr in the presence (dox+) and absence of dox (dox–)

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions.

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 3 µm.

data_processing: Agilent Feature Extraction software version 11.0.1.1

source_name: Reference sample: HeLa-C33-dox+

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions.

growth_protocol: HeLa clones were cultured in DMEM supplemented with 10% fetal calf serum, 50 U/ml penicillin, 50 U/ml streptomycin, 2.5 µg/ml amphotericin B, and 2 mM L-glutamine. HeLa-tTA was also supplemented with 1 µg/ml puromycin and 2 ng/ml dox, and HeLa-C23 and HeLa-C33 clones with 1 µg/ml puromycin, 0.5 mg/ml G418, and 2 ng/ml dox.

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions.

treatment_protocol: HeLa clones (tTA, C23, C33) were washed free of dox and cultured for 24 h in the presence (dox+) and absence of dox (dox–). Then, cells were detached from plastic using 0.05%-EDTA 0.02% in PBS.

value: Cervical cancer epithelial HeLa cells

source_name: Test sample: HeLa-C33-dox–


title: HSCATAC_P164_45

description:
sample name:
HSCATAC_P164_45


title: HeLa_DOCK10_1: HeLa-C33 clone cultured for 24 hr in the presence (dox+) and absence of dox (dox–)


title: SU070_LSC_30


title: INDROPS_1_KCL_CTX_B2_R1


title: INDROPS_1_KCL_CTX_B1_R2


title: HeLa_CTRL_2: HeLa-C23 clone cultured for 24 hr in the presence (dox+) and absence of dox (dox–)

source_name: Reference sample: HeLa-C23-dox+

source_name: Test sample: HeLa-C23-dox–


title: HSCATAC_P164_43

description:
sample name:
HSCATAC_P164_43


title: HeLa_CTRL_1: HeLa-tTA clone cultured for 24 hr in the presence (dox+) and absence of dox (dox–)

source_name: Reference sample: HeLa-tTA-dox+

source_name: Test sample: HeLa-tTA-dox–


title: SU070_LSC_2

source_name: LSC


title: HSCATAC_P164_42

description:
sample name:
HSCATAC_P164_42


title: SU070_LSC_29


title: Diclofenac_C2_6_T.1

city: Koblenz

first: Andreas

last: Schüttler

address: Am Mainzer Tor 1

department: Department Biochemistry and Ecotoxicology

country: Germany

institute: German Federal Institute of Hydrology

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 5.77 micromol per liter

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany). Hybridization performed by OakLabs GmbH (Berlin, Germany)

scan_protocol: SureScan Microarray Scanner (Agilent Technologies). Agilent’s Feature Extraction software version 11. Scanning performed by OakLabs GmbH (Berlin, Germany)

data_processing: Cyclic loess normalization between all arrays. Software for data normalization: R v3.3.1.

organism: Danio rerio

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 5.77 micromol per liter

label_protocol: One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany). Labeling performed by OakLabs GmbH (Berlin, Germany).

extract_protocol: Trizol followed by RNeasy MiniKit cleanup (Qiagen) using the manufacturers’ protocols

tag: substance

value: Diclofenac


title: INDROPS_1_KCL_CTX_B1_R1

source_name: embryonic cortical culture


title: INDROPS_0_KCL_CTX_B2_R2


title: Diclofenac_C1_6_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 5.1 micromol per liter


title: SU070_LSC_28


title: HSCATAC_P164_41

description:
sample name:
HSCATAC_P164_41

source_name: pre-leukemic HSCs


title: Diclofenac_C3_24_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 6.52 micromol per liter


title: HSCATAC_P164_40

description:
sample name:
HSCATAC_P164_40


title: HSCATAC_P164_44

description:
sample name:
HSCATAC_P164_44


title: INDROPS_0_KCL_CTX_B2_R1


title: SU070_LSC_27


title: INDROPS_0_KCL_CTX_B1_R2


title: Diclofenac_C4_72_T.3

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 6.93 micromol per liter


title: Diclofenac_C4_48_T.2

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 6.93 micromol per liter


title: Diclofenac_C3_72_T.2

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 6.52 micromol per liter


title: Diclofenac_C5_6_T.2

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 7.36 micromol per liter


title: Diclofenac_C4_72_T.2


title: HSCATAC_P164_3

description:
sample name:
HSCATAC_P164_3


title: Diclofenac_C2_24_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 5.77 micromol per liter


title: SU070_LSC_26


title: Diclofenac_C4_24_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 6.93 micromol per liter


title: Diclofenac_C1_72_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 5.1 micromol per liter


title: SU070_LSC_25


title: HSCATAC_P164_39

description:
sample name:
HSCATAC_P164_39


title: Diclofenac_C3_12_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 6.52 micromol per liter


title: HSCATAC_P164_38

description:
sample name:
HSCATAC_P164_38


title: SU070_LSC_23


title: Diclofenac_Control_72_C.2

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 0 micromol per liter


title: HDAC3_04


title: HDAC3_02


title: HDAC3_01


title: SU070_LSC_22


title: INDROPS_0_KCL_CTX_B1_R1


title: HSCATAC_P164_36

description:
sample name:
HSCATAC_P164_36


title: H3K27AC_44

description: processed data file: 180413_MEAN_UPDATED_H3K27AC_around_OPTIMAL_ATAC.txt

value: Abcam Ab4729


title: Diclofenac_C5_48_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 7.36 micromol per liter


title: SU070_LSC_21


title: HSCATAC_P164_35

description:
sample name:
HSCATAC_P164_35


title: HDAC3_03

description: processed data file: 170815_MEAN_TF_around_OPTIMAL_ATAC.txt.gz


title: HSCATAC_P164_34

description:
sample name:
HSCATAC_P164_34


title: H3K27AC_43


title: SU070_LSC_24


title: Diclofenac_C2_12_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 5.77 micromol per liter


title: Diclofenac_Control_72_C.1

hyb_protocol: Agilent Gene Expression Hybridisation Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)

scan_protocol: Agilent DNA Microarray Scanner and Agilent Feature Extraction Software V11.5.1.1, according to manufacturer's protocol.

label_protocol: One-Color Quick Amp Labeling Kit, according to manufacturer's protocol (Agilent Technologies, Waldbronn, Germany)


title: SU070_LSC_20

source_name: LSC


title: Diclofenac_Control_24_C.2

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 0 micromol per liter


title: H3K27AC_42

source_name: embryonic cortical culture


title: H3K27AC_41


title: H3K27AC_40


title: HSCATAC_P164_33

description:
sample name:
HSCATAC_P164_33


title: HSCATAC_P164_32

description:
sample name:
HSCATAC_P164_32


title: SU070_LSC_19


title: HSCATAC_P164_31

description:
sample name:
HSCATAC_P164_31


title: SU070_LSC_18


title: H3K27AC_39


title: SU070_LSC_17


title: Diclofenac_C5_72_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 7.36 micromol per liter


title: Diclofenac_Control_72_C


title: HSCATAC_P164_30

description:
sample name:
HSCATAC_P164_30

source_name: pre-leukemic HSCs


title: H3K27AC_32


title: SU070_LSC_1


title: HSCATAC_P164_29

description:
sample name:
HSCATAC_P164_29


title: HSCATAC_P164_2

description:
sample name:
HSCATAC_P164_2


title: HSCATAC_P164_28

description:
sample name:
HSCATAC_P164_28


title: Diclofenac_C2_72_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-96hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 5.77 micromol per liter


title: Diclofenac_C1_72_T


title: SU070_LSC_15


title: H3K27AC_30


title: SU070_LSC_14


title: HSCATAC_P164_27

description:
sample name:
HSCATAC_P164_27


title: H3K27AC_31


title: SU070_LSC_13


title: SU070_LSC_12


title: Diclofenac_C5_72_T


title: Diclofenac_C5_72_R.1

description: whole zebrafish embryo, exposed to Diclofenac, 7.36 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P164_37

description:
sample name:
HSCATAC_P164_37


title: Diclofenac_C2_72_T.1


title: Diclofenac_C5_72_R


title: H3K27AC_29


title: H3K27AC_27


title: HSCATAC_P164_25

description:
sample name:
HSCATAC_P164_25


title: SU070_LSC_16


title: Diclofenac_C4_72_R.1

description: whole zebrafish embryo, exposed to Diclofenac, 6.93 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 6.93 micromol per liter


title: SU070_LSC_10


title: HSCATAC_P164_24

description:
sample name:
HSCATAC_P164_24


title: SU070_Blasts_9

source_name: Blasts

value: Blasts


title: HSCATAC_P164_23

description:
sample name:
HSCATAC_P164_23


title: H3K27AC_28


title: HSCATAC_P164_26

description:
sample name:
HSCATAC_P164_26


title: H3K27AC_26

value: ctlshrna


title: SU070_Blasts_96


title: HSCATAC_P164_22

description:
sample name:
HSCATAC_P164_22

value: pre-leukemic HSCs


title: SU070_LSC_11


title: H3K27AC_25


title: Diclofenac_C4_72_R


title: H3K27AC_24


title: H3K27AC_23


title: Diclofenac_C3_72_R

description: whole zebrafish embryo, exposed to Diclofenac, 6.52 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf

source_name: whole embryo, exposed to Diclofenac, 24hpf-96hpf, 6.52 micromol per liter


title: SU070_Blasts_93


title: HSCATAC_P164_1

description:
sample name:
HSCATAC_P164_1


title: Diclofenac_C2_72_R.1

description: whole zebrafish embryo, exposed to Diclofenac, 5.77 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P164_20

description:
sample name:
HSCATAC_P164_20


title: SU070_Blasts_94


title: Diclofenac_C1_72_R.1

description: whole zebrafish embryo, exposed to Diclofenac, 5.1 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: SU070_Blasts_95


title: HSCATAC_P164_21

description:
sample name:
HSCATAC_P164_21


title: H3K27AC_21


title: Diclofenac_C3_72_R.1


title: SU070_Blasts_92


title: H3K27AC_19


title: H3K27AC_18

source_name: n4cko_embryonic cortical culture

value: Npas4 floxed

value: cre


title: SU070_Blasts_90


title: Diclofenac_Control_48_C.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 0 micromol per liter


title: H3K27AC_22


title: HSCATAC_P164_19

description:
sample name:
HSCATAC_P164_19


title: H3K27AC_17

value: gfp


title: HSCATAC_P164_18

description:
sample name:
HSCATAC_P164_18

value: acute myeloid leukemia


title: H3K27AC_16


title: H3K27AC_20


title: HSCATAC_P164_16

description:
sample name:
HSCATAC_P164_16


title: HSCATAC_P164_15

description:
sample name:
HSCATAC_P164_15


title: SU070_Blasts_89


title: Diclofenac_C2_72_R


title: SU070_Blasts_8


title: SU070_Blasts_88


title: H3K27AC_15


title: Diclofenac_C1_72_R


title: Diclofenac_C4_48_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 6.93 micromol per liter


title: Diclofenac_C4_48_T.1


title: HSCATAC_P164_14

description:
sample name:
HSCATAC_P164_14


title: Diclofenac_Control_48_C


title: SU070_Blasts_91


title: Diclofenac_C5_48_T


title: SU070_Blasts_87


title: HSCATAC_P164_12

description:
sample name:
HSCATAC_P164_12


title: SU070_Blasts_86


title: H3K27AC_13

value: uninfected


title: HSCATAC_P164_11

description:
sample name:
HSCATAC_P164_11


title: SU070_Blasts_85


title: Diclofenac_C3_48_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 6.52 micromol per liter


title: H3K27AC_12


title: H3K27AC_14


title: HSCATAC_P164_10

description:
sample name:
HSCATAC_P164_10


title: H3K27AC_11


title: Diclofenac_C3_48_T


title: Diclofenac_C2_48_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 5.77 micromol per liter


title: H3K27AC_10


title: Diclofenac_C2_48_T


title: SU070_Blasts_84


title: SU070_Blasts_83


title: HSCATAC_P1170_9

description:
sample name:
HSCATAC_P1170_9


title: Diclofenac_C1_48_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-72hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-72hpf, 5.1 micromol per liter


title: HSCATAC_P164_13

description:
sample name:
HSCATAC_P164_13


title: Diclofenac_Control_24_C


title: SU070_Blasts_82


title: HSCATAC_P1170_96

description:
sample name:
HSCATAC_P1170_96


title: H3K27AC_08

description: processed data file: 180413_MEAN_UPDATED_H3K27AC_around_OPTIMAL_ATAC.txt


title: H3K27AC_09


title: SU070_Blasts_81


title: H3K27AC_07


title: HSCATAC_P1170_95

description:
sample name:
HSCATAC_P1170_95


title: Diclofenac_C5_24_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 7.36 micromol per liter


title: SU070_Blasts_80


title: Diclofenac_Control_24_C.1


title: HSCATAC_P1170_94

description:
sample name:
HSCATAC_P1170_94


title: H3K27AC_05


title: Diclofenac_C5_24_T


title: Diclofenac_C4_24_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 6.93 micromol per liter


title: SU070_Blasts_7


title: HSCATAC_P1170_93

description:
sample name:
HSCATAC_P1170_93


title: HSCATAC_P1170_92

description:
sample name:
HSCATAC_P1170_92


title: H3K27AC_04


title: H3K27AC_03


title: SU070_Blasts_79


title: SU070_Blasts_78


title: HSCATAC_P1170_91

description:
sample name:
HSCATAC_P1170_91


title: HSCATAC_P1170_90

description:
sample name:
HSCATAC_P1170_90


title: H3K27AC_01


title: HSCATAC_P1170_8

description:
sample name:
HSCATAC_P1170_8


title: SU070_Blasts_76


title: Diclofenac_C1_24_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 5.1 micromol per liter


title: Diclofenac_C2_24_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-48hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-48hpf, 5.77 micromol per liter


title: H3K27AC_02


title: GFP_B2_B2_R2

description: processed data file: 150805_n4oe_TMMnorm_agg_cpm

source_name: embryonic cortical culture


title: SU070_Blasts_75


title: SU070_Blasts_74


title: HSCATAC_P1170_89

description:
sample name:
HSCATAC_P1170_89


title: HSCATAC_P1170_88

description:
sample name:
HSCATAC_P1170_88


title: SU070_Blasts_77


title: GFP_B2_B2_R1


title: Diclofenac_C5_3_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 7.36 micromol per liter


title: SU070_Blasts_72


title: SU070_Blasts_73


title: SU070_Blasts_71


title: HSCATAC_P1170_85

description:
sample name:
HSCATAC_P1170_85

source_name: pre-leukemic HSCs


title: GFP_B1_R1


title: GFP_B1_R2


title: ATAC_6hr.CTRL.2

description: processed data file: 170815_MEAN_ATAC_around_OPTIMAL_ATAC.txt


title: SU070_Blasts_70


title: HSCATAC_P1170_84

description:
sample name:
HSCATAC_P1170_84


title: ATAC_6hr.CTRL.1


title: Diclofenac_C5_3_T.1


title: Diclofenac_C1_3_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 5.1 micromol per liter


title: Diclofenac_Control_3_C

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 0 micromol per liter


title: Diclofenac_C4_3_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 6.93 micromol per liter


title: Diclofenac_C2_3_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 5.77 micromol per liter


title: SU070_Blasts_6

source_name: Blasts


title: HSCATAC_P1170_83

description:
sample name:
HSCATAC_P1170_83


title: ATAC_6hr.A2shRNA.2


title: HSCATAC_P1170_87

description:
sample name:
HSCATAC_P1170_87


title: ATAC_6hr.A2shRNA.1


title: HSCATAC_P1170_86

description:
sample name:
HSCATAC_P1170_86


title: HSCATAC_P1170_82

description:
sample name:
HSCATAC_P1170_82


title: ATAC_2hr.CTRL.2


title: HSCATAC_P1170_81

description:
sample name:
HSCATAC_P1170_81


title: Diclofenac_Control_3_C.1


title: SU070_Blasts_67


title: SU070_Blasts_68


title: SU070_Blasts_66


title: ATAC_2hr.CTRL.1


title: Diclofenac_C3_3_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-27hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-27hpf, 6.52 micromol per liter


title: Diclofenac_C5_6_T.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 7.36 micromol per liter


title: HSCATAC_P1170_7

description:
sample name:
HSCATAC_P1170_7


title: Diclofenac_Control_6_C

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 0 micromol per liter


title: Diclofenac_C4_6_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 6.93 micromol per liter


title: ATAC_2hr.A2shRNA.2


title: Diclofenac_Control_6_C.1


title: Diclofenac_C3_6_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 6.52 micromol per liter


title: SU070_Blasts_65


title: HSCATAC_P1170_79

description:
sample name:
HSCATAC_P1170_79


title: SU070_Blasts_64


title: HSCATAC_P1170_78

description:
sample name:
HSCATAC_P1170_78


title: ATAC_2hr.A2shRNA.1


title: ATAC_0hr.CTRL.2


title: HSCATAC_P1170_80

description:
sample name:
HSCATAC_P1170_80


title: SU070_Blasts_63


title: HSCATAC_P1170_77

description:
sample name:
HSCATAC_P1170_77


title: Diclofenac_C2_6_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 5.77 micromol per liter


title: ATAC_0hr.CTRL.1


title: Diclofenac_Control_12_C.1

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 0 micromol per liter


title: Diclofenac_C1_6_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-30hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-30hpf, 5.1 micromol per liter


title: HSCATAC_P1170_76

description:
sample name:
HSCATAC_P1170_76


title: SU070_Blasts_62


title: ATAC_0hr.A2shRNA.2


title: HSCATAC_P1170_75

description:
sample name:
HSCATAC_P1170_75


title: SU070_Blasts_60


title: HSCATAC_P1170_74

description:
sample name:
HSCATAC_P1170_74


title: SU070_Blasts_61


title: ATAC_0hr.A2shRNA.1


title: HSCATAC_P1170_73

description:
sample name:
HSCATAC_P1170_73


title: Diclofenac_C5_12_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 7.36 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 7.36 micromol per liter


title: Arnt2_RNA_Strd.Ctrl.2

description: processed data file: 181031_Arnt2_counts_invivo.txt

source_name: adult hippocampus


title: Arnt2_RNA_Strd.Ctrl.3


title: SU070_Blasts_59


title: HSCATAC_P1170_72

description:
sample name:
HSCATAC_P1170_72


title: HSCATAC_P164_17

description:
sample name:
HSCATAC_P164_17


title: Arnt2_RNA_Strd.Ctrl.1


title: SU070_Blasts_58


title: Arnt2_RNA_Strd.A2shRNA.3


title: HSCATAC_P1170_71

description:
sample name:
HSCATAC_P1170_71


title: Arnt2_RNA_Strd.A2shRNA.2


title: Diclofenac_C5_12_T.1


title: HSCATAC_P1170_70

description:
sample name:
HSCATAC_P1170_70


title: Arnt2_RNA_Strd.A2shRNA.1


title: SU070_Blasts_57


title: SU070_Blasts_5


title: HSCATAC_P1170_6

description:
sample name:
HSCATAC_P1170_6


title: Diclofenac_C3_12_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 6.52 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 6.52 micromol per liter


title: SU070_Blasts_56


title: Diclofenac_C1_12_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 5.1 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 5.1 micromol per liter


title: Diclofenac_C4_12_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 6.93 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 6.93 micromol per liter


title: HSCATAC_P1170_69

description:
sample name:
HSCATAC_P1170_69

source_name: pre-leukemic HSCs


title: Diclofenac_Control_12_C


title: SU070_Blasts_55


title: Arnt2_RNA_KA.Ctrl.3


title: Diclofenac_C2_12_T

description: whole zebrafish embryo, exposed to Diclofenac, 24hpf-36hpf, 5.77 micromol per liter

source_name: whole embryo, exposed to Diclofenac, 24hpf-36hpf, 5.77 micromol per liter


title: Arnt2_RNA_KA.Ctrl.2


title: Diuron_Control_72_C.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 0 micromol per liter

value: Diuron


title: SU070_Blasts_54

source_name: Blasts


title: Diuron_Control_72_C


title: HSCATAC_P1170_68

description:
sample name:
HSCATAC_P1170_68


title: Arnt2_RNA_KA.Ctrl.1


title: SU070_Blasts_53


title: SU070_Blasts_52


title: HSCATAC_P1170_66

description:
sample name:
HSCATAC_P1170_66


title: HSCATAC_P1170_67

description:
sample name:
HSCATAC_P1170_67


title: Arnt2_RNA_KA.A2shRNA.2


title: Diuron_C5_72_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 29.44 micromol per liter


title: Arnt2_RNA_KA.A2shRNA.3


title: Diuron_C4_72_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 18.14 micromol per liter


title: Diuron_C5_72_T


title: HSCATAC_P1170_65

description:
sample name:
HSCATAC_P1170_65


title: Arnt2_RNA_KA.A2shRNA.1


title: SU070_Blasts_51


title: Diuron_C3_72_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 11.72 micromol per liter


title: HSCATAC_P1170_64

description:
sample name:
HSCATAC_P1170_64


title: Diuron_C4_72_T


title: HSCATAC_P1170_63

description:
sample name:
HSCATAC_P1170_63


title: SU070_Blasts_49


title: ARNT2_20

description: processed data file: 170815_MEAN_TF_around_OPTIMAL_ATAC.txt.gz

value: in-house 1048


title: SU070_Blasts_50


title: Diuron_C1_72_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 2.34 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 2.34 micromol per liter


title: SU070_Blasts_47


title: Diuron_C3_72_T


title: SU070_Blasts_4


title: ARNT2_19


title: HSCATAC_P1170_62

description:
sample name:
HSCATAC_P1170_62


title: HSCATAC_P1170_59

description:
sample name:
HSCATAC_P1170_59


title: SU070_Blasts_48


title: HSCATAC_P1170_61

description:
sample name:
HSCATAC_P1170_61


title: ARNT2_14

source_name: embryonic cortical culture


title: HSCATAC_P1170_60

description:
sample name:
HSCATAC_P1170_60


title: SU070_Blasts_46


title: ARNT2_17


title: ARNT2_18


title: Diuron_C1_72_T


title: Diuron_C2_72_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-96hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-96hpf, 5.16 micromol per liter


title: ARNT2_13


title: Diuron_C5_72_R

description: whole zebrafish embryo, exposed to Diuron, 29.44 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: Diuron_C3_72_R

description: whole zebrafish embryo, exposed to Diuron, 11.72 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P1170_57

description:
sample name:
HSCATAC_P1170_57


title: Diuron_C2_72_T


title: Diuron_C5_72_R.1


title: ARNT2_16


title: ARNT2_12


title: ARNT2_15


title: HSCATAC_P1170_5

description:
sample name:
HSCATAC_P1170_5


title: SU070_Blasts_44


title: SU070_Blasts_45


title: SU070_Blasts_41


title: Diuron_C1_72_R

description: whole zebrafish embryo, exposed to Diuron, 2.34 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P1170_58

description:
sample name:
HSCATAC_P1170_58


title: Diuron_Control_48_C.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 0 micromol per liter


title: SU070_Blasts_43


title: Diuron_C4_72_R

description: whole zebrafish embryo, exposed to Diuron, 18.14 micromol per liter, 24hpf-72hpf, subsequently transferred into clean water till 96hpf


title: HSCATAC_P1170_56

description:
sample name:
HSCATAC_P1170_56


title: SU070_Blasts_42


title: SU070_Blasts_40


title: HSCATAC_P1170_55

description:
sample name:
HSCATAC_P1170_55


title: ARNT2_10


title: HSCATAC_P1170_54

description:
sample name:
HSCATAC_P1170_54


title: SU070_Blasts_3


title: ARNT2_09


title: ARNT2_08


title: HSCATAC_P1170_4

description:
sample name:
HSCATAC_P1170_4


title: HSCATAC_P1170_53

description:
sample name:
HSCATAC_P1170_53


title: SU070_Blasts_39


title: HSCATAC_P1170_52

description:
sample name:
HSCATAC_P1170_52


title: ARNT2_04


title: Diuron_Control_48_C


title: SU070_Blasts_69


title: SU070_Blasts_38


title: ARNT2_11


title: Diuron_C5_48_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 29.44 micromol per liter


title: ARNT2_07


title: HSCATAC_P1170_51

description:
sample name:
HSCATAC_P1170_51


title: SU070_Blasts_34


title: HSCATAC_P1170_48

description:
sample name:
HSCATAC_P1170_48


title: ARNT2_05


title: ARNT2_06


title: Diuron_C4_48_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 18.14 micromol per liter


title: HSCATAC_P1170_50

description:
sample name:
HSCATAC_P1170_50


title: Diuron_C3_48_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 11.72 micromol per liter


title: Diuron_C4_48_T.1


title: Diuron_C2_48_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 5.16 micromol per liter


title: SU070_Blasts_35


title: SU070_Blasts_33


title: Diuron_C3_48_T.1


title: HSCATAC_P1170_49

description:
sample name:
HSCATAC_P1170_49


title: HSCATAC_P1170_47

description:
sample name:
HSCATAC_P1170_47


title: SU070_Blasts_36


title: ARNT2_03


title: ARNT2_02


title: ARNT2_01


title: SU070_Blasts_37


title: SU070_Blasts_31


title: Diuron_C5_48_T.1


title: SU070_Blasts_32


title: Diuron_C2_48_T


title: Donor 1 shluc

first: Vijay

last: Sankaran

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

description:
alternative 3’ splice site: A3SS.miso_bf.txt
alternative 5’ splice site: A5SS.miso_bf.txt
mutually exclusive exon: MXE.miso_bf.txt
retained intron: RI.miso_bf.txt
skipped exon: SE.miso_bf.txt

data_processing:
Paired end sequencing reads from our SF3A2 shRNA knockdown experiments and obtained from the cited SF3B1 mutant datasets were aligned using STAR version 2.5.2 in two-pass mode.
Splicing was quantified using MISO version 0.5.4 in Python 2.7 using the instructions and hg19-based annotation files provided with the package (Katz et al., 2010).
Differential splicing was identified for splicing events with a Bayes factor greater than or equal to 10 when compared to the shluc control.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files of the MISO output (see https://miso.readthedocs.io/en/fastmiso/#summary-file-output-format). In the MISO files, Sample 1 refers to the pooled samples  that received a hairpin targeting SF3A2 while Sample 2 refers to the pooled samples that received the control hairpin targeting luciferase.

source_name: Donor1 peripheral blood derived CD34+ Cells

growth_protocol: Mobilized peripheral blood-derived CD34+ cells were cultured using IMDM containing 2% human plasma, 3% human AB serum, 200 µg/ml human holo-transferrin, 3 IU/mL heparin, and 10 mg/mL insulin (base medium). During days 0 to 7, cells were supplemented with IL-3 (1 ng/mL), SCF (10 ng/ml), and EPO (3 IU/ml). (see Hu et al. 2013)

extract_protocol:
RNA was isolated using a RNAqueous Micro kit (Invitrogen) according to the manufacturer’s instructions. DNase digestion was performed before RNA was quantified using a Qubit RNA HS Assay kit (Invitrogen).
1-10 ng of RNA were used as input to a modified SMART-seq2 (Picelli et al., 2014) protocol and after reverse transcription, 8-9 cycles of PCR were used to amplify transcriptome library. Quality of whole transcriptome libraries was validated using a High Sensitivity DNA Chip run on a Bioanalyzer 2100 system (Agilent), followed by library preparation using the Nextera XT kit (Illumina) and custom index primers according to the manufacturer’s instructions. Final libraries were quantified using a Qubit dsDNA HS Assay kit (Invitrogen) and a high sensitivity DNA chip run on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: Cells from each donor were infected separately with SF3A2 sh3, sh4, and shluc

tag: donor id

value: blood

value: Stage matched CD71+/ CD235a+ cells

tag: shRNA treatment

value: shluc

tag: sequence

tag: trcn id


title: Diuron_C1_48_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-72hpf, 2.34 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-72hpf, 2.34 micromol per liter


title: HSCATAC_P1170_45

description:
sample name:
HSCATAC_P1170_45

source_name: pre-leukemic HSCs

tag: patient id

tag: patient diagnosis

tag: cell type


title: SU070_Blasts_30


title: Donor 3 shluc

source_name: Donor3 peripheral blood derived CD34+ Cells

tag: tissue


title: HSCATAC_P1170_46

description:
sample name:
HSCATAC_P1170_46


title: SU070_Blasts_2


title: HSCATAC_P1170_43

description:
sample name:
HSCATAC_P1170_43


title: HSCATAC_P1170_42

description:
sample name:
HSCATAC_P1170_42


title: SU070_Blasts_29


title: Donor 3 sh3


title: Diuron_Control_24_C

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 0 micromol per liter


title: Donor 2 sh4

source_name: Donor2 peripheral blood derived CD34+ Cells


title: HSCATAC_P1170_40

description:
sample name:
HSCATAC_P1170_40


title: Diuron_C5_24_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 29.44 micromol per liter


title: Donor 1 sh4


title: SU070_Blasts_28

source_name: Blasts


title: Donor 3 sh4


title: Donor 2 shluc


title: HSCATAC_P1170_3

description:
sample name:
HSCATAC_P1170_3


title: SU070_Blasts_26


title: SU070_Blasts_25


title: Donor 2 sh3


title: Donor 1 sh3


title: Diuron_C3_24_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 11.72 micromol per liter


title: Diuron_C4_24_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 18.14 micromol per liter


title: Diuron_Control_24_C.1


title: SU070_Blasts_24


title: Diuron_C1_24_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 2.34 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 2.34 micromol per liter


title: SU070_Blasts_27


title: HSCATAC_P1170_41

description:
sample name:
HSCATAC_P1170_41


title: Diuron_Control_3_C.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 0 micromol per liter


title: PDX_MULTI

city: San Francisco

first: Christopher

middle: S

last: McGinnis

address: 600 16th Street

department: Pharmaceutical Chemistry

institute: University of California, San Francisco

description:
MULTI-seq barcode DNA
processed data files:
PDX_MULTI_matrix.csv

data_processing:
FASTQ files were generated directly from Illumina BCL files using Illumina bcl2fastq version 2.19
Gene-barcode matrices were determined using 10X Genomics Cellranger version 2.2 with default parameters (cellranger count).
Read-depth normalization was performed (when appropriate) using 10X Genomics CellRanger version 2.2 with default parameters (cellranger aggr).
Low-quality cell barcodes were excluded as described in the paper.
MULTI-seq barcode alignment and sample classification results were performed using the deMULTIplex R package (https://github.com/chris-mcginnis-ucsf/MULTI-seq)
Genome_build: hg19 (Samples 1-3, 6-12), concatenated mm10-hg19 (Sample 13-14), concatenated mm10-hg19 pre-mRNA (Sample 4-5)
Supplementary_files_format_and_content: Expression Libraries: gene-cell matrices are provided in the format produced by CellRanger. The matrix itself is in matrix market exchange format, with the column (cell barcodes) and row (gene identities) labels given in TSV format as described in the cellranger documentation. MULTI-seq Libraries: MULTI-seq barcode-cell matrices are provided in CSV format.

organism:
Homo sapiens
Mus musculus

source_name: PDX

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C.
Library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and using a custom MULTI-seq library preparation protocol.

value: PDX

tag: multi-seq reagent

value: LMO


title: HSCATAC_P1170_38

description:
sample name:
HSCATAC_P1170_38


title: PDX_human and mouse

description:
polyA RNA
processed data files:
PDX_hs_barcodes.tsv, PDX_mm_barcodes.tsv
PDX_hs_genes.tsv, PDX_mm_genes.tsv
PDX_hs_matrix.mtx, PDX_mm_matrix.mtx


title: HSCATAC_P1170_37

description:
sample name:
HSCATAC_P1170_37


title: Diuron_Control_3_C


title: SU070_Blasts_23


title: POC_snRNAseq_Lane2

description:
nuclear polyA RNA
processed data files:
POC_nuc_barcodes.tsv
POC_nuc_genes.tsv
POC_nuc_matrix.mtx

molecule: nuclear RNA

value: mixture of HEK,HMECS, and Jurkats

value: LMO/CMO/None


title: Diuron_C5_24_T.1


title: SU070_Blasts_22

value: Blasts


title: Diuron_C2_24_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-48hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-48hpf, 5.16 micromol per liter


title: SU070_Blasts_21


title: SU070_Blasts_20


title: Diuron_C5_3_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 29.44 micromol per liter


title: HSCATAC_P1170_39

description:
sample name:
HSCATAC_P1170_39


title: Diuron_C5_3_T


title: POC_snRNAseq_Lane1


title: HSCATAC_P1170_33

description:
sample name:
HSCATAC_P1170_33


title: SU070_Blasts_1


title: HSCATAC_P1170_36

description:
sample name:
HSCATAC_P1170_36


title: Diuron_C4_3_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 18.14 micromol per liter


title: HSCATAC_P1170_34

description:
sample name:
HSCATAC_P1170_34


title: HSCATAC_P1170_44

description:
sample name:
HSCATAC_P1170_44


title: HSCATAC_P1170_35

description:
sample name:
HSCATAC_P1170_35


title: SU070_Blasts_18


title: HSCATAC_P1170_30

description:
sample name:
HSCATAC_P1170_30


title: SU070_Blasts_19


title: HSCATAC_P1170_32

description:
sample name:
HSCATAC_P1170_32


title: SU070_Blasts_17


title: HSCATAC_P1170_31

description:
sample name:
HSCATAC_P1170_31


title: SU070_Blasts_15


title: SU070_Blasts_16


title: HSCATAC_P1170_2

description:
sample name:
HSCATAC_P1170_2


title: HSCATAC_P1170_29

description:
sample name:
HSCATAC_P1170_29


title: SU070_Blasts_14


title: HSCATAC_P1170_28

description:
sample name:
HSCATAC_P1170_28


title: Blood-VitD+BPH-0min [39v4_180]

city: Quebec

first: Frederic

last: Guenard

address: 2440, Hochelage blvd

institute: Laval University

hyb_protocol: Hybridized target cRNA was stained with streptavidin phycoerythrin.

scan_protocol: Arrays were scanned on an Agilent GeneArray Scanner (Thermo Fisher Scientific Inc.) at an excitation wavelength of 488nm.

data_processing: Raw data were extracted from scanned images using Expression Console (v 1.4; Thermo Fisher Scientific Inc.). Robust Multiarray Analysis method was used to perform background correction and quantile normalization.

label: Biotin

source_name: Blood, VitD+BPH, 0 min

label_protocol: Arrays were processed at the McGill University and Genome Quebec Innovation Centre using standard Affymetrix protocols. RNA was reverse transcribed into cDNA and in-vitro transcription was performed to generate biotin-labeled cRNA.

extract_protocol: Blood samples were collected from an antecubital vein into PAXgene Blood RNA Tubes (Qiagen, Mississauga, Ontario, Canada) before and 180 min after each treatment. Total RNA was isolated and purified from blood samples using PAXgene Blood RNA Kit (Qiagen) according to the manufacturer's instructions..

tag: Sex

value: Female

value: Blood

value: VitD+BPH

value: 0 min


title: Diuron_C2_3_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 5.16 micromol per liter


title: Diuron_C3_3_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 11.72 micromol per liter


title: HSCATAC_P1170_27

description:
sample name:
HSCATAC_P1170_27

source_name: pre-leukemic HSCs

value: pre-leukemic HSCs


title: Blood-Placebo-180min [39v3_0]

source_name: Blood, Placebo, 180 min

value: Placebo

value: 180 min


title: Diuron_Control_6_C

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 0 micromol per liter

value: Diuron


title: SU070_Blasts_13

value: acute myeloid leukemia


title: Diuron_Control_6_C.1


title: Blood-VitD+BPH-180min [39v4_0]

source_name: Blood, VitD+BPH, 180 min


title: Blood-Placebo-0min [39v3_180]

source_name: Blood, Placebo, 0 min


title: Diuron_C1_3_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-27hpf, 2.34 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-27hpf, 2.34 micromol per liter


title: SU070_Blasts_12

source_name: Blasts


title: Blood-BPH-0min [39v2_180]

source_name: Blood, BPH, 0 min

value: BPH


title: HSCATAC_P1170_26

description:
sample name:
HSCATAC_P1170_26


title: Diuron_C5_6_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 29.44 micromol per liter


title: SU070_Blasts_11


title: HSCATAC_P1170_25

description:
sample name:
HSCATAC_P1170_25


title: Diuron_C5_6_T


title: Blood-VitD-Pep-C-VitDPep-180min [39v1_0]

source_name: Blood, VitD-Pep-C-VitDPep, 180 min

value: VitD-Pep-C-VitDPep


title: SU070_Blasts_10


title: Diuron_C2_6_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 5.16 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 5.16 micromol per liter


title: Blood-VitD-0min [39v1_180]

source_name: Blood, VitD, 0 min

value: VitD


title: Diuron_C3_6_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 11.72 micromol per liter


title: Diuron_C4_6_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 18.14 micromol per liter


title: HSCATAC_P1170_23

description:
sample name:
HSCATAC_P1170_23


title: TNF_rep2 [Hi-C]

description:
Hi-C data of human endothelial cells through TNF-induced inflammatory signaling
TNF_allValidPairsold.hic

data_processing:
Each paired read data obtained for the Hi-C libraries were processed with the HiC-Pro (Servant et al., 2015) pipeline using human genome (hg19) and fragment information for restriction enzyme “MboI”. Finally, 196,814,231 and 204,936,615 valid pairs of reads remained for control and TNF-α-treated sample, respectively. The Hi-C raw data was converted to a Juicebox compatible format (.hic format) using Juicer-tools.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: hic

source_name: human umblical vein endothelial cells

extract_protocol:
In-situ Hi-C was performed in two replicates for HUVECs treated with or without TNF-α for 60 min. Cells were cross-linked for 10 min at room temperature with 1% formaldehyde and quenched for 5 min at room temperature with 0.2M glycine. The cross-linked cells were centrifuged at 2,500xg for 5 min at 4°C.
To isolate nuclei, cross-linked cells were resuspended in 200 μl of lysis buffer (10 mM Tris-HCl (pH 8.0), 10mM NaCl, 0.2% NP40, Protease Inhibitor Cocktail (Sigma-Aldrich)) and incubated on ice for 15 min. The suspension was then centrifuged at 2,500xg for 5 min and the pellet washed by resuspending in 300 μl of lysis buffer and centrifuging at 2,500xg for 5 min at 4°C. The pellet was resuspended in 50 μl of 0.5% SDS and incubated for 10 min at 62°C. After heating, 170 μl of 1.47% TritonX-100 was added to the suspension and incubated for 15 min at 37°C. To digest chromatin, 25 μl of 10X NEBuffer2 and 100U MboI (New England Biolabs, Beverly, MA) was added to the suspension and incubated at 37°C overnight with rotation. Enzymes were inactivated by heating for 20 min at 62°C. Fragmented ends were biotin-labeled by adding 50 μl of mixture containing 0.3 mM biotin-14-dATP (Thermo Fisher Scientific), 0.3 mM dATP (Thermo Fisher Scientific), 0.3 mM dTTP (Thermo Fisher), 0.3 mM dGTP (Thermo Fisher Scientific), and 0.8 U/ul Klenow (Enzymatics, Beverly, MA) and incubated for 1 hr at room temperature with rotation. The biotin-labeled fragmented ends were subsequently ligated by adding 900 μl of mixture containing 120 μl of 10X T4 DNA ligase buffer (New England Biolabs), 100 μl of 10% TritionX-100, 12 μl of 10 mg/ml BSA (New England Biolabs), 5 μl of 400 U/μl of T4 DNA Ligase (New England Biolabs) and 663 μl H2O and incubated for 4 hrs at room temperature with rotation. The nuclei were pelleted for 5 min at room temperature at 2,500xg. After removing supernatant, the nuclei were resuspended in 550 μl of 10 mM Tris-HCl (pH 8.0). The nuclei were reverse-crosslinked by adding 50 μl of Proteinase K (New England Biolabs) and 57 μl of 10% SDS, and incubated for 30 min at 55°C. Subsequently, the nuclei mixed with 67 μl of 5 M NaCl were incubated at 68°C overnight. After cooling samples for 10 min at room temperature, DNA was purified by 0.8X AMPureXP beads (Beckman Coulter Inc., Brea, CA) and eluted in 100 μl of 10 mM Tris-HCl (pH 8.0). DNA shearing was performed using focused-ultrasonicators (Covaris, E220; Power 140 W, Duty factor 10%, Cycle per bust 200, Time 67 sec, temperature 7°C) and the final sample volume after shearing was brought to 200 μl using 10 mM Tris-HCl (pH 8.0). To design DNA selection for 200-600 bp size, 120 μl of AMPureXP beads was added into 200 μl of sample (beads ration: 0.6) and incubated for 5 min at room temperature with inversion. To remove DNA fragments >600 bp, the clear supernatant was collected on magnet and beads were discarded. As a second round of size selection, 80 μl of AMPureXP beads was added into the supernatant and incubated for 5 min at room temperature with inversion. The supernatant was removed on magnet and beads were washed twice with 700 μl of 70% ethanol, dried up for 5 min. DNA fragments (200-600 bp) were eluted from beads by 300 μl of 10 mM Tris-HCl (pH 8.0). For biotin pull down, 100 μl of 10mg/ml Dynabeads My One T1 Streptavidin beads (Thermo Fisher Scientific) was washed with 1X Tween Wash Buffer (5m M Tris-HCl (pH 7.5), 0.5 mM EDTA, 1 M NaCl, 0.05% Tween). The beads resuspended in 300 μl of 2X Binding Buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 2M NaCl) were transferred to sample tubes and incubated for 15 min at room temperature. The beads were subsequently washed twice with 1X Tween Wash Buffer for 2 min at 55°C with mixing and washed once with 1X NEB T4 DNA ligase buffer (Enzymatics). To repair fragmented ends and remove biotin from unligated ends, the beads were resuspended in 85 μl of 1X NEB T4 DNA ligase buffer (Enzymatics), 5 μl of 10 mM dNTP Mix (Thermo Fisher Scientific), 5 μl of 10 U/μl of NEB T4 PNK (New England Biolabs), 4 μl of 3 U/μl NEB T4 DNA Polymerase (New England Biolabs) and 1 μl of 5 U/μl Klenow (Enzymatics), and incubated for 30 min at room temperate. After supernatant was discarded on magnet, the beads were washed twice with 1X Tween Wash Buffer for 2 min at 55°C with mixing and resuspended in 100 μl of 1X NEB Buffer2. For dA-tailing, the beads were resuspended in 90 μl of 1X NEB Buffer2, 5 μl of 10 mM dATP (Thermo Fisher Scientific) and 5 μl of 5 U/μl of Klenow (3'→5' exo-) (Enzymatics), and incubated for 30 min at 37°C. The beads were subsequently washed twice with 1X Tween Wash Buffer as before and once with 1X NEB Quick Ligation Reaction Buffer (New England Biolabs). To ligate adapters, the beads were suspended in 50 μl of 1X NEB DNA Quick Ligation Reaction Buffer, 1 μl of NEXTflex® DNA Barcodes (Bioo Scientific, Austion, TX) and 2 μl of NEB DNA Quick Ligase (New England Biolabs), and incubated for 15 min at room temperature. The beads were washed twice with 1X Tween Wash Buffer as before and once with 10 mM Tris-HCl (pH 8.0), and resuspended in 20 μl of 10 mM Tris-HCl (pH 8.0). After estimating concentration and cycle number for final PCR by qPCR assay, final PCR was directly amplified off the T1 beads using KAPA Hyper Prep Kit (KAPA Biosystems Inc) and DNA was cleaned with 1X AMPure beads, and eluted in 30 μl of 10 mM Tris-HCl (pH 8.0) and sequenced paired-end.

tag: conditions

value: TNF 1h

tag: donor

value: pooled from multiple donors

tag: passages

value: HUVECs


title: Blood-VitD-0min [37v4_180]

value: Male

tag: agent

tag: time point


title: TNF_rep1 [Hi-C]


title: HSCATAC_P1170_24

description:
sample name:
HSCATAC_P1170_24


title: Blood-BPH-180min [39v2_0]

source_name: Blood, BPH, 180 min


title: control_rep2 [Hi-C]

description:
Hi-C data of human endothelial cells through TNF-induced inflammatory signaling
control_allValidPairsold.hic

value: no treatment


title: Diuron_C1_6_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-30hpf, 2.34 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-30hpf, 2.34 micromol per liter


title: HSCATAC_P1170_22

description:
sample name:
HSCATAC_P1170_22

source_name: pre-leukemic HSCs


title: Blood-VitD-180min [37v4_0]

source_name: Blood, VitD, 180 min


title: control_rep1 [Hi-C]


title: Foliar nectary secretory replicate 4 (FO S 4 Rep.1)

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description:
FO S 4 Rep.1
Cotton_protein_counts_B.xlsx

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn, normalized by upper-quartile count and reference length
Contigs aligned to cotton reference proteins
Cotton reference proteins annotated with closest Arabidopsis thaliana match
Genome_build: Cotton: UTX-JGI v1.1
Supplementary_files_format_and_content: Cotton_protein_counts_B.xls - Excel file with upper quartile and mRNA-length normalized counts

organism: Gossypium hirsutum

source_name: Foliar nectary secretory replicate 4

extract_protocol: Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: Foliar nectary tissue

tag: Stage

value: secretory


title: HSCATAC_P1170_20

description:
sample name:
HSCATAC_P1170_20


title: HSCATAC_P1170_19

description:
sample name:
HSCATAC_P1170_19


title: Diuron_Control_12_C.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 0 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 0 micromol per liter

tag: substance


title: HSCATAC_P1170_1

description:
sample name:
HSCATAC_P1170_1


title: Diuron_Control_12_C


title: Blood-VitD+BPH-180min [37v2_180]

source_name: Blood, VitD+BPH, 180 min

value: Blood

value: VitD+BPH


title: Foliar nectary secretory control replicate 3 (FO S 3C Rep.1)

description:
FO S 3C Rep.1
Cotton_protein_counts_B.xlsx

value: Near foliar nectary tissue

value: secretory control


title: Foliar nectary secretory control replicate 4 (FO S 4C Rep.1)

description:
FO S 4C Rep.1
Cotton_protein_counts_B.xlsx


title: Blood-Placebo-0min [37v3_180]

source_name: Blood, Placebo, 0 min

value: Placebo

value: 0 min


title: HSCATAC_P1170_21

description:
sample name:
HSCATAC_P1170_21

value: acute myeloid leukemia

value: pre-leukemic HSCs


title: Diuron_C5_12_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 29.44 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 29.44 micromol per liter

value: Diuron


title: HSCATAC_P1170_18

description:
sample name:
HSCATAC_P1170_18


title: Blood-VitD+BPH-0min [37v2_0]

source_name: Blood, VitD+BPH, 0 min


title: Blood-BPH-180min [37v1_180]

value: BPH

value: 180 min


title: Blood-BPH-0min [37v1_0]

source_name: Blood, BPH, 0 min


title: Blood-Placebo-0min [35v4_0]

value: Female


title: Foliar nectary secretory control replicate 2 (FO S 2C Rep.1)

description:
FO S 2C Rep.1
Cotton_protein_counts_B.xlsx


title: Blood-VitD-180min [35v3_180]

value: VitD


title: Blood-VitD+BPH-180min [35v2_180]


title: HSCATAC_P1170_16

description:
sample name:
HSCATAC_P1170_16


title: HSCATAC_P1170_17

description:
sample name:
HSCATAC_P1170_17


title: Diuron_C5_12_T.1


title: Foliar nectary secretory replicate 2 (FO S 2 Rep.1)

description:
FO S 2 Rep.1
Cotton_protein_counts_B.xlsx

source_name: Foliar nectary secretory replicate 2


title: Foliar nectary secretory replicate 3 (FO S 3 Rep.1)

description:
FO S 3 Rep.1
Cotton_protein_counts_B.xlsx

source_name: Foliar nectary secretory replicate 3


title: Blood-VitD-0min [35v3_0]

source_name: Blood, VitD, 0 min


title: Diuron_C3_12_T.1

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 11.72 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 11.72 micromol per liter


title: Diuron_C3_12_T


title: Blood-Placebo-180min [35v4_180]

source_name: Blood, Placebo, 180 min


title: Diuron_C4_12_T

description: whole zebrafish embryo, exposed to Diuron, 24hpf-36hpf, 18.14 micromol per liter

source_name: whole embryo, exposed to Diuron, 24hpf-36hpf, 18.14 micromol per liter


title: Diuron_C4_12_T.1


title: HSCATAC_P1170_14

description:
sample name:
HSCATAC_P1170_14