title: TC-797_DMSO_BRD4-NUT_replicate1 (ChIP-seq)


title: P1681

status: Public on Apr 01 2020

type: genomic

city: Bethesda

first: Ariel

middle: Fernando

last: Martinez

state: MD

address: 35 Convent Drive, Room 1B209

country: USA

institute: National Institutes of Health

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R03C01

hyb_protocol: According to the Infinium HD Assay Ultra protocol

data_processing:
BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).
The supplementary file on the series record contains the columns Genotype: AA,AB,BB,or NC (no call), Score, Theta, R, B Allele Freq, Log R Ratio, X Raw and Y Raw for each sample.  There is also a separate file with raw data only. Sample ID can be found in the 'description' field.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Blood

label_protocol: 200ng of genomic DNA were processed following the Infinium HD Assay Ultra protocol

extract_protocol: Extraction of genomic DNA from whole blood was performed using QIAGEN's QIAamp DNA Blood Maxi kit (cat No 51194)

tag: tissue

value: Blood

tag: gender

value: M

tag: adhd affection status

value: Affected


title: 2-017-2-3_S189

type: SRA

city: Lausanne

first: Gregory

last: Lefebvre

address: EPFL Scientific Parc

country: Switzerland

institute: Nestlé Institute of Health Science

library_source: transcriptomic

data_processing:
Sequence reads are trimmed from polyA and Lexogene reference sequences using bbduk software
Sequence reads are map to reference genome using RNAStar (v2.3.0e)
Matrix of counts is ctreated from HTSeq software
Genome_build: hs_GRCh38.p2
Supplementary_files_format_and_content: Text file containing counts for each genes (rows) for each sample (columns)

molecule: total RNA

source_name: adipose tisue

extract_protocol: Lexogen QuantSeq - established 3' mRNA-Seq library prep protocol

tag: cid (cid1

value: baseline, cid2 :lcd, cid3 :di):CID3

tag: individual


title: 2-017-2-2_S245

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 2-017-2-3_S93


title: TC-797_washout_H3K27ac_replicate1 (ChIP-seq)

city: Houston

first: Kyle

last: Eagen

state: TX

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequences using trimmomatic v0.36.
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using using bowtie2 v2.3.1 with option --very-sensitive.
Reads with a MAPQ ≥ 30 were retained using samtools v1.3.1.
PCR duplicates were removed with picard MarkDuplicates v2.9.2.
MACS2 (Zhang et al., 2008) was used to compute signal tracks by first running macs2 callpeak with parameters -B --SPMR --keep-dup all -g hs -f BAM and then running macs2 bdgcmp with parameter -m FE.
Histone H3K27ac ChIP-seq profiles were calibrated using spike-in normalization with D. melanogaster as the calibration genome, as previously described (Hu et al., 2015). As the NUT epitope is not expressed in Drosophila Kc167 cells, BRD4-NUT ChIP-seq profiles were not spike-in normalized.
The epic v0.2.12 implementation of the SICER algorithm (Xu et al., 2014) was used to identify broadly enriched domains from histone H3K27ac ChIP-seq data setting the window size to 2500 bp and gap size to 1 with parameters -w 2500 -g 1, respectively. Input libraries were used as controls for domain annotation.
Often, we observed closely spaced enriched regions and to span these regions and capture the entire domain, SICER/epic-identified domains within 25 kb of one another were combined using bedtools v2.27.1 with command bedtools merge.
To identify megadomains, the list of called domains was filtered by signal strength and by domain size. Signal strength was determined by subtracting the rpm normalized input reads from rpm normalized sample reads for each called domain and subsequently ranked in increasing order of counts. The ROSE algorithm (Rank Ordering of Super-Enhancers) (Whyte et al., 2013) was applied to the ranked dataset to determine the cutoff threshold for signal strength by sliding a diagonal line and finding the point along the abscissa where the diagonal line was tangent to the rank-ordered curve. The cutoff for feature size was determined in a similar manner by ranking the domain length in base pairs and applying ROSE. Domains that exceeded both the signal cutoff and the size threshold were retained using bedtools intersect with default parameters.
The above was performed for each biological replicate, and, then, to create the highest confidence domain list, domains identified in both replicates were merged using bedtools intersect with default parameters. The resulting domains were considered “megadomains”.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.bw file of ChIP-seq track in bigWig format.
Supplementary_files_format_and_content: *.bed file of megadomain locations in bed format.

source_name: TC-797 cultured cells

growth_protocol: 293TRex-Flag-BRD4-NUT-HA cells were a kind gift from Christopher A. French (Brigham and Women’s Hospital, Boston, MA). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) + 15 µg/mL blasticidin (Gibco #A1113903) + 100 µg/mL hygromycin (Corning #30240CR) at 37° C with 5% CO2. TC-797 cells were a kind gift from Jeffrey A. Toretsky (Georgetown University, Washington, DC). Cells were grown in DMEM with 4.5 g/L glucose and sodium pyruvate without L-glutamine (Corning #15013CV) + 10% Fetal Bovine Serum (Atlanta Biologicals #S10350) + 1% GlutaMAX (Gibco #35050061) + 1% Penicillin-Streptomycin (Gibco #15140122) at 37° C with 5% CO2. Kc167 cells were obtained from the Drosophila Genomics Resource Center (#1; Bloomington, IN). Cells were grown in CCM3 Media (HyClone #SH30062.02) at 25° C.

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde. Cells were lysed with detergent and chromatin solubilized by shearing (for H3K27ac IP) or shearing and enzymatic digestion (for BRD4-NUT IP). An aliquot was removed as the input control and the samples then immunoprecipitated with the respective antibody. DNA-protein cross-links were reversed and the DNA then purified.
DNA was prepared for next-generation sequencing using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO.  TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

tag: cell type

value: NUT carcinoma

tag: cell line

tag: chip antibody

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173S, lot 6 RRID:AB_10949503)

tag: spike-in

value: Drosophila melanogaster Kc167 cells


title: TC-797_washout_H3K27ac_replicate2 (ChIP-seq)


title: 2-017-2-2_S12


title: P1651

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R01C01

scan_protocol: According to the Infinium HD Assay Ultra protocol

value: Unaffected


title: TC-797_MZ1_H3K27ac_replicate2 (ChIP-seq)


title: P1211

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R06C02


title: TC-797_MZ1_H3K27ac_replicate1 (ChIP-seq)


title: 2-017-1-2_S83


title: P1429

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R05C02


title: P1771

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744140_R02C01


title: TC-797_DMSO_H3K27ac_replicate1 (ChIP-seq)


title: TC-797_DMSO_H3K27ac_replicate2 (ChIP-seq)


title: 2-016-2-3_S180


title: 2-017-1-2_S179


title: 293TRex_induced_BRD4-NUT_replicate2 (ChIP-seq)

source_name: 293TRex-Flag-BRD4-NUT-HA cultured cells

value: Human embryonic kidney

value: NUT (C52B1) Rabbit mAb (Cell Signaling Technology Signaling #3625S, lot 4 RRID:AB_2066833)


title: P1440

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R03C02


title: P1112

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R02C02


title: 2-016-1-3_S90


title: Fin_chalimus-ATTachment site_Tank_5_Fish_4_RNA#24

type: RNA

city: St. John's

first: Umasuthan

last: Navaneethaiyer

state: NL

address: 1 Marine Lab Road, Dept of Ocean Sciences, Memorial University of Newfoundland

department: Ocean Sciences

country: Canada

institute: Memorial University of NL

hyb_protocol: For each array, equal amounts (825 ng) of each Cy5-labelled experimental aRNA and Cy3-labelled reference aRNA were pooled, fragmented following the vendor’s protocol (Gene Expression Hybridization Kit, ON, Canada) and co-hybridized to a 44K salmonid oligonucleotide microarray (GEO accession: GPL11299; Agilent Technologies) according to the manufacturer’s directions. Each array was hybridized at 65 °C for ~17 h at 10 rpm rotation in an Agilent hybridization oven. Array slides were then washed with Gene Expression Wash Buffer 1 and 2 according to the manufacturer’s guidelines.

scan_protocol: Each microarray was scanned at 5 µm resolution using a SureScan D Microarray Scanner (G2600D, Agilent Technologies) using Agilent Scan Control Software (v9.1.11.7, Agilent Technologies) by applying a built-in protocol (Agilent_HD_GX_2color). Photomultiplier tube (PMT) sensitivity for Cy3 and Cy5 dye channels was set to 100%.

data_processing: The resulting TIFF images (20 bit) containing raw array data were then subjected to Agilent Feature Extraction (FE, v12.0.3.1) software to retrieve the signal intensity data of each microarray probe using a protocol provided by the developer (GE2_1200_June14). Probe signal, background signal subtraction, LOWESS normalization, outlier flagging, and log2-ratio calculation were performed by FE. Quality control (QC) parameters from QC reports of each array generated by FE were also examined. Resulting text files containing raw microarray data were then subjected to GeneSpring GX, a multi-omic analysis platform (v14.9.1, Agilent Technologies), to visualize and further process the data. The missing values were imputed using a method embedded within GeneSpring GX. Based on QC assessment and downstream analyses [such as heatmaps and principal component analyses (PCA)], samples considered as potential outliers were identified (1 fish/group) and excluded from the downstream analyses. Features absent in more than 25% of the arrays in all three groups (PRE, ADJ, and ATT) were discarded.

organism: Salmo salar

source_name: Fin tissue, chalimus-attachment (ATT) site, individual fish

label_protocol: Fin RNA samples of six animals (three from each duplicate tank) each from control (PRE) and sea lice-infected (ATT and ADJ samples from each) salmon, selected based on RNA quality, were used in the microarray experiment (i.e., 18 animals in total). The microarray study was based on a common reference design, in which the differences among sample groups in fin transcriptome were investigated by contrasting individual samples against a common reference pool prepared from the equal contribution of all 18 samples. A consortium for Genomic Research on All Salmonids Project (cGRASP)-designed 44K Atlantic salmon oligonucleotide array (GEO accession: GPL11299; Agilent Technologies) that comprises 60mer probes was used as the microarray platform. The antisense amplified RNA (aRNA) preparation and labeling were conducted using the Amino Allyl MessageAmp II aRNA amplification kit (Invitrogen). One microgram of DNase I-treated, column-purified total RNA was reverse-transcribed to the first-strand cDNA and used in second-strand cDNA synthesis. The double-stranded cDNA was then used to synthesize modified aRNA using the manufacturer’s instructions. The aRNA samples were column-purified and subjected to the quantity and quality assessment by NanoDrop spectrophotometry and agarose gel electrophoresis, respectively. A common reference was prepared by pooling 10 µg of each of the 18 experimental samples. Twenty micrograms of each experimental and common reference aRNA sample was precipitated overnight through standard molecular biology methods and then resuspended in coupling buffer. While 18 individual experimental aRNA samples were labeled with Cy5, the common reference was labeled with Cy3 (GE Healthcare, ON, Canada) through a dye-coupling reaction, as per the manufacturer’s instructions. The labeling efficiency was determined using the ‘microarray’ mode in the ND-1000 NanoDrop spectrophotometry.

growth_protocol: Eighty post-smolts (307.3 ± 27.8 g mean initial weight ± SE) were randomly distributed and maintained in two 620-L tanks (40 fish/tank and 27±1.5 kg/m3) with a flow-through water supply (at 10 ± 1 °C and >90% O2 saturation) and 24-h light photoperiod throughout the experiment. Fish were allowed to acclimate to these laboratory conditions for four weeks before lice infection. Water quality parameters, such as temperature and oxygen saturation, were monitored daily. Fish were fed nightly with a commercial diet (Dynamic S, EWOS, Cargill) to satiation using automatic feeders throughout the experimental period and starved for 24 h before any handling or sampling. Just before the se lice (Lepeophtheirus salmonis) infection, the water supply for tanks was turned off, the water level was reduced by 50%, and water was oxygenated with air diffusers to maintain ~100% oxygen saturation. Atlantic salmon were then bath-infected with sea lice by adding ~50 copepodids per fish to each tank. Water quality parameters (dissolved oxygen and temperature) were continuously monitored throughout the infection period at intervals of 10 min. Water supply was reinstated after 2 h of copepodid exposure. At least five individuals from each tank at 0 days post-infection (dpi; prior to infection, PRE), 8 dpi (when most lice were at their chalimus stage) were euthanized with a lethal dose of MS-222 (400 mg/L; Syndel Laboratories, BC, Canada) and dissected for sample collection (Figure 1A). Parasites on each salmon were counted. Tissue from pelvic fin tips at (an area of the fin with lice ‘attached’, ATT) and ‘adjacent’ (with no signs of previous lice attachment, ADJ) to chalimus attachment sites were excised as shown in Figure 1B, chalimi were removed from ATT sites using sterile forceps, and fin samples were flash-frozen in liquid nitrogen and stored at -80 °C until RNA extraction was performed.

extract_protocol: Fin tips were homogenized in 800 μl TRIzol Reagent (Invitrogen/Life Technologies, ON, Canada) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON) using a TissueLyser II (QIAGEN, Restch, GmbH, Germany), frozen on dry ice and stored at -80°C.  Frozen homogenates were slowly thawed on wet ice and the TRIzol total RNA extractions were then completed following the manufacturer’s instructions. To eliminate any residual genomic DNA contamination, 40 µg of crude RNA from each sample was treated with DNase I (6.8 Kunitz units; RNase-Free DNase Set, QIAGEN) and then column-purified by using the RNeasy Mini Kit (QIAGEN) following the vendor’s protocol. The RNA concentration and purity were assessed by ND-1000 UV spectrophotometry (NanoDrop, Wilmington, DE, USA), and the RNA integrity was examined by 1% agarose gel electrophoresis. The samples with tight 18S and 28S ribosomal RNA bands and high A260/280 and A260/230 ratios (>1.8) were used in transcriptional analyses

tag: life stage

value: Juvenile

tag: treatment

value: chalimus-attachment (ATT) site

value: Fin (pelvic)

source_name: pool of RNAs from fin tissue samples invovled in the microarray experiment

tag: sample type


title: Fin_chalimus-ATTachment site_Tank_5_Fish_5_RNA#28

value: pool of RNAs from fin tissue samples invovled in the microarray experiment


title: 293TRex_induced_BRD4-NUT_replicate1 (ChIP-seq)


title: Fin_chalimus-ATTachment site_Tank_4_Fish_5_RNA#25


title: P1129

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R01C02


title: P1327

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R04C02


title: Fin_chalimus-ATTachment site_Tank_4_Fish_6_RNA#29


title: 2-013-2-1_S164

value: baseline, cid2 :lcd, cid3 :di):CID1


title: 2-013-2-3_S179


title: 293TRex_uninduced_BRD4-NUT_replicate2 (ChIP-seq)


title: 2-017-2-1_S112


title: Fin_chalimus-ATTachment site_Tank_5_Fish_626


title: 293TRex_uninduced_BRD4-NUT_replicate1 (ChIP-seq)


title: P1590

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R06C01

value: F


title: Fin_ADJacent to chalimus-attachment site_Tank_5_Fish_5_RNA#31

source_name: Fin tissue, adjacent (ADJ) to chalimus-attachment site, individual fish


title: Fin_ADJacent to chalimus-attachment site_Tank_4_Fish_6_RNA#35

value: adjacent (ADJ) to chalimus-attachment site


title: Fin_ADJacent to chalimus-attachment site_Tank_4_Fish_5_RNA#34


title: P1094

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R05C01

value: Blood

value: M


title: 293TRex_induced_H3K27ac_replicate2 (ChIP-seq)


title: 2-013-1-3_S97

value: baseline, cid2 :lcd, cid3 :di):CID3


title: 2-012-2-2_S128

value: baseline, cid2 :lcd, cid3 :di):CID2


title: P1133

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R04C01

value: Affected


title: 293TRex_induced_H3K27ac_replicate1 (ChIP-seq)

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173S, lot 6 RRID:AB_10949503)


title: 2-012-2-1_S22


title: 2-012-1-1_S15


title: 293TRex_uninduced_H3K27ac_replicate2 (ChIP-seq)

value: Drosophila melanogaster Kc167 cells


title: P1001

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R02C01


title: 2-010-2-3_S134


title: 2-009-2-1b_S156


title: Fin_ADJacent to chalimus-attachment site_Tank_5_Fish_6_RNA#32


title: P1173

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R01C01


title: HCT116_KAP1_KO1_Rep2_MNase-seq

city: Dallas

first: Ivan

last: D'Orso

address: 5323 Harry Hines

department: Microbiology

institute: UT Southwestern Medical Center

data_processing:
Quality of reads from all experiments was determined with FASTQC v0.11.2 using default parameters.
ChIP-seq: Reads were aligned to hg38 with Bowtie2 v2.3.2 with the --very-sensitive flag. SAM files were converted to BAM and sorted by chromosome with samtools v1.6. The view command with the -q flag set to 25 was used to filter out low quality reads. The sort command was used to convert SAM to BAM and sort by chromosome. Duplicates marked and removed with picard v1.127. Drosophilla spike-in chromatin was aligned to dm6 as described above for hg38. BAM files were generated and de-duplicated as described above for hg38 aligned reads. Drosophilla normalization factors were generated by dividing the Drosophilla read counts from each sample to the sample containing the least read counts. BedGraph tracks were generated with MACS2 v2.1.0 and normalized to Drosophilla spike-in normalization factors. BedGraph then converted to BigWig using bedGraphtoBigWig.
4sU-/RNA-seq: Reads were aligned to hg38 with STAR/2.5.2b. Sorted by coordinate BAM files were created by STAR with the –outSAMtype BAM flag. RPM normalized bedgraph files were also generated using STAR with the –outWigType bedGraph and –outWigNorm RPM flags. ERCC spike-ins were similarly aligned to an ERCC fasta file. Reads for protein coding genes were counted using the Gencode v27 annotation and featureCounts. Differential expression analysis was performed using RUVseq v1.14.0 R package.
MNase-seq: Raw data files were checked for quality control; low quality reads and adapter contaminations were removed using Trimgalore v0.4.1.  High quality reads (MAPQ >20) were aligned to the human genome assembly hg38 using Bowtie2 v2.3.3 and further processed using SAMtools v1.6. Using R v3.4.1 scripts adapted from bamR package (https://github.com/rchereji/bamR) the normalized nucleosome dyad distribution was computed by rescaling the average occupancy to 1 for each chromosome. To precisely map nucleosome positions, mono-Nucleosomal DNA fragments with a size of 120–160 bp were used for the analysis. R scripts were used to calculate average dyads density around TSS of RNA polymerase II- transcribed genes and plotting of nucleosome profiles and heatmaps.
Genome_build: hg38 and dm6
Supplementary_files_format_and_content: ChIP-seq: BigWig track files containing Drosophilla normalized aligned read densities
Supplementary_files_format_and_content: 4sU-/RNA-seq: RPM normalized BigWig track files
Supplementary_files_format_and_content: 4sU-/RNA-seq: tab-delimited file containing raw transcript counts
Supplementary_files_format_and_content: MNase-seq: BigWig track files containing normalized aligned read densities

source_name: HCT116 Colorectal Carcinoma Cell Line

growth_protocol: All HCT116 cell lines were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum and 1% Pen/Strep. All cell lines were grown at 37°C with 5% CO2.

extract_protocol:
For ChIP-seq, chromatin was cross-linked with 0.5% formaldehyde for 10 min at room temperature in culture media, and the reaction was stopped by the addition of glycine (150 mM final). Cells were washed twice with PBS and re-suspended in Farnham Lysis Buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40, 1 mM PMSF, protease inhibitor (Roche)) at 10x106 [10 million cells/mL], dounced 15X, and incubated for 30 min at 4°C. Cell nuclei were collected by centrifugation at 1000xg for 5 min at 4°C, and re-suspended in Szak's RIPA buffer (50 mM Tris-HCl pH 8.0, 1% NP-40, 150 mM NaCl, 0.5% deoxycholate, 0.1% SDS, 5 mM EDTA, 0.5 mM PMSF, protease inhibitor) at 25x106 nuclei/mL. Nuclear pellets were sonicated using the Bioruptor water bath sonicator (Diagenode) using the high setting with 30 sec on 30 sec off for 45 min to generate 100-300 bp DNA fragments. Approximately 20x106 nuclei were used for each ChIP. For the ChIP step, 5-10 ug of antibody was conjugated with 100 uL of protein G dynabeads Thermo Fisher and blocked with 5% bovine serum albumin in RIPA for 1 hr at 4°C. An additional 2.5 µg of antibody specific for Drosophilla H2Av (Active Motif, 61686) was also conjugated at the same time. Drosophilla spike-in chromatin (Active Motif, 53083) was added to each sample for normalization between samples according to manufacture's instructions. Antibody-conjugated dynabeads were incubated with sheared chromatin suspension overnight at 4°C. Then the beads were sequentially washed two times with each of the following buffers: Szak's RIPA buffer (see above), low salt buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), high salt buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton, 0.1% SDS, 2 mM EDTA), LiCl wash buffer (0.25M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 20 mM Tris, pH 8.0), and 1 mM Tris-EDTA pH 8.0. Chromatin immunocomplexes were eluted by incubation for 30 min at 65°C with 1% SDS and 100 mM NaHCO3, and cross-linking was reversed by incubation in the solution adjusted to 200 mM NaCl and proteinase K (20 μg) for 1 hr at 65°C. DNA was then purified using the Zymo ChIP DNA Clean & Concentrator Kit (Zymo Research). Final ChIP DNA was quantified on a Qubit 2.0 Fluorometer (Invitrogen) and approximately 5-10 ng of DNA were submitted (used?) for library preparation.  For 4sU-seq, HCT116 Ctrl and KAP1 KO1 cells were seeded into three 10cm plates per biological replicate and grown to 70% confluency. Cells were pulsed for 10 min with DMEM + 500 µM 4sU (Sigma-Aldrich, T4509). At the 9 min mark the DMEM + 4sU media was removed and cells were washed one time with 1X PBS. The PBS was removed, and cells were lysed on-plate using the standard TRizol protocol (ThermoFisher Scientific, 15596026). RNA samples were DNase treated (NEB, M0303) and then extracted with acid:phenol chloroform (ThermoFisher Scientific, AM9720) followed by an additional chloroform extraction. RNA was then precipitated with 1/10 volume of NaCl (5M), 1 µL glycoblue, and 2.5 volumes of 100% EtOH. RNA pellets were washed with 1 mL of 75% EtOH and air dried. RNA pellets were then resuspended in RNase-free H2O. RNA (300 ug) was brought to a final concentration of 0.4 mg/mL with RNase-free H2O. A separate aqueous master mix (20mM NaOAC pH 5.2, 1 mM EDTA pH 8.0, 0.1% SDS) was added to the diluted RNA mix followed by the addition of 0.2 mg/mL Biotin-HPDP (ThermoFisher Scientific 21341) in DMF. The biotinylation reaction was incubated at room temperature for 2 hrs followed by acid:phenol chloroform extraction. Biotinylated RNA pellets were resuspended in 500 µL RPB buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 300 mM NaCl). Dyna MyOne Strepavidin T1 beads (200 uL/sample; ThermoFisher Scientific, 65601) were blocked at room temperature in beads wash buffer + 1% polyvinylpyrrolidone for 10 min. After blocking, beads were washed 1X with 1 mL beads wash (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 50 mM NaCl) buffer and then resuspended in RPB. Biotinylated, 4sU RNA was denatured at 65°C for 5 min and then placed on ice for 2 min. 200 µL of blocked beads were added to each sample and incubated for 30 min with rotation at room temperature. Beads were washed 5X with 4sU wash buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 1 M NaCl, 0.1% Tween-20). Biotinylated, 4sU RNA was eluted from beads 2 times in 75 µL of 0.1M DTT for 15 min at room temp with rotation, giving a final elution valume of 150 µL. 4sU-RNA was further purified using the Zymo RNA Clean and Concentrator Kit (Zymo Reasearch, R1013). RNA concentration was measured using the Qubit RNA HS assay (ThermoFisher Scientific, Q32852) and quality was determined using the Agilent Tapestation RNA ScreenTape (Agilent, 5067-5576).  For RNA-seq, HCT116 Ctrl and KAP1 gRNA cells were grown in 6-well dishes and total RNA extracted using the Zymo Quick-RNA Miniprep Kit (R1055) according to manufacturer instructions.  For MNase-seq, cells were crosslinked with 0.5% methanol-free formaldehyde for 10 min and reaction was quenched for 5 min with 150 mM glycine before harvesting. Cells were washed twice with PBS buffer and nuclei were gathered by lysing the cells in Franham’s lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 freshly supplemented with 1mM PMSF and EDTA free-Protease inhibitor cocktail). Nuclei were washed once with cold MNase buffer (20 mM Tris-HCl pH 7.5,15 mM NaCl, 60 mM KCl, 2 mM CaCl2) and resuspended in MNase buffer with concentration of 10x106 cells/mL before digestion. Micrococcal nuclease (New England BioLabs, M0247S) digestion was performed (240 U/106 cells) at 37C to achieve 80% mono-nucleosomes populations and reaction was stopped with 10 mM EDTA, 20 mM EGTA, 0.4% SDS solution. Samples were centrifuged for 5 min at high speed and supernatant was collected. Samples were reverse crosslinked in de-crosslinking buffer (20 mM Tris- HCl pH 6.8, 500 mM NaCl, 2mM EDTA, and 0.5 mg/mL Proteinase K) overnight at 65°C. Following phenol-chloroform extraction and ethanol precipitation, DNA samples were run on 1.5% agarose gel and fragments of ~150 bp size were excised and purified. DNA from two biological replicates were analyzed on high sensitivity DNA tape on a 2200 TapeStation and used for library preparation.
For ChIP-seq and MNase-seq, libraries were constructed using the KAPA Hyper Prep Kit (KAPA Biosystems, KK8504) according to manufacturer’s instructions. Brielfy, 5-10 ng of either ChIP or MNase digested DNA was end repaired and A-tailed. Illumina adapters (New England BioLabs, E7335L) were then ligated to DNA fragments. ChIP DNA was size selected using the double-sided selection method outlined in the KAPA Hyper Prep Kit instructions. DNA was then amplified using Illumina indexed barcoding primers (New England BioLabs, E7335L) for 8-12 cycles depending on amount of input DNA.  For 4sU-seq and RNA-seq, the KAPA Stranded RNA-seq kit with RiboErase (HMR) (KAPA Biosystems, KK8483) was used to prepare libraries according to manufacturer’s instructions. Briefly, 200 ng of 4sU RNA and 1 ug of total RNA was used to prepare 4sU-seq and RNA-seq libraries, respectively. Libraries were rRNA depleted followed by DNase treatment. RNA was fragmented and primed followed by 1st strand cDNA synthesis. 2nd strand synthesis was then performed with the incorporation of dUTP. Libraries were then A-tailed, adapter ligated, and amplified as described for ChIP-seq.  All libraries were quantified using the Qubit 2.0 fluorometer and library size verified using the Agilent Tapestation DNA D1000 ScreenTape (Agilent, 5067-5582). All libraries were submitted to the McDermott Center Sequencing Core at UTSW. 75 bp paired-end reads were generated for all libraries

value: Colorectal Carcinoma

tag: genotype/variation

value: KAP1 KO1

tag: passages

value: Under 15


title: Bad Embryo rep2 (P3 rep2)

city: Iquique

first: Angelica

last: Guerrero Castilla

address: Avda Arturo Prat #2120

country: Chile

institute: Universidad Arturo Prat

description:
9908R_P3vsC_diffexp.txt
BE2

data_processing:
Raw data was aligned using Novoalign. Aligned sequences were analyzed using Useq to identify differentially expressed genes. FDR  in Useq is represented as -10Log10(P-val/FDR) transformed values where 13=5%, 20=1%, etc., 1% of genes with an FDR = 20 will be false and not enriched.
Genome_build: Zv9
Supplementary_files_format_and_content: Differential gene expresssion data were generated using Useq

organism: Danio rerio

source_name: whole organism

growth_protocol: Zebrafish embryos were grown at 28C on a 14 h light/10 h dark light cycle. Fertilized eggs were collected following natural spawning in 1X E3 medium.

extract_protocol:
Total RNA was prepared from 50 embryos/phenotype group using RNEasy Mini kit.
Illumina TruSeq RNA Library Preparation Kit v2 with poly(A) Selection

treatment_protocol: Zebrafish embryos were treated with 100 mg/L of methanolic coal extract dissolved in DMSO at 4 hpf. Samples for each phenotype group were collected at 24 hpf.

value: whole organism

tag: age

value: 24 hpf

tag: strain

value: TU

tag: phenotype

value: small embryos, extruded yolks


title: Fin_ADJacent to chalimus-attachment site_Tank_5_Fish_4_RNA#30

value: Juvenile

tag: tissue

value: Fin (pelvic)

value: pool of RNAs from fin tissue samples invovled in the microarray experiment


title: P1203

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R06C02

value: Blood

tag: gender

value: F

value: Unaffected


title: Fin_PRE-exposure control_Tank_5_Fish_2_RNA#5

source_name: Fin tissue, PRE-exposure (sea lice) control, individual fish

value: PRE-exposure (sea lice) control


title: Fin_PRE-exposure control_Tank_4_Fish_6_RNA#23


title: 2-009-1-3_S70

value: baseline, cid2 :lcd, cid3 :di):CID3


title: Bad Embryo (P3)

description:
9908R_P3vsC_diffexp.txt
BE0


title: P1305

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R05C02

tag: adhd affection status

value: Affected


title: Fin_PRE-exposure control_Tank_4_Fish_2_RNA#2


title: P1689

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744139_R03C01

value: M


title: HCT116_Ctrl_Rep2_MNase-seq

value: Colorectal Carcinoma

value: Ctrl


title: 2-009-1-3_S166

tag: cid (cid1


title: P1059

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R04C02


title: Bad Tail rep2 (P1 rep2)

description:
9908R_P1vsC_diffexp.txt
BT2

value: deformed tail


title: 293TRex_uninduced_H3K27ac_replicate1 (ChIP-seq)

value: Human embryonic kidney

value: Acetyl-Histone H3 (Lys27) (D5E4) XP Rabbit mAb (Cell Signaling Technology #8173S, lot 6 RRID:AB_10949503)

value: Drosophila melanogaster Kc167 cells


title: Bad Tail rep1 (P1 rep1)

description:
9908R_P1vsC_diffexp.txt
BT1

value: whole organism

value: 24 hpf

value: TU


title: Fin_PRE-exposure control_Tank_5_Fish_1_RNA#4

value: Juvenile

value: Fin (pelvic)

value: pool of RNAs from fin tissue samples invovled in the microarray experiment


title: 2-007-2-2_S51

value: baseline, cid2 :lcd, cid3 :di):CID2

tag: individual


title: 2-009-1-2_S132


title: HCT116_Ctrl_Rep1_MNase-seq

tag: cell type

value: Under 15


title: P1276

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R03C02

value: Blood

value: F

value: Unaffected


title: HCT116_KAP1_KO1_Rep1_MNase-seq

tag: cell line

value: Colorectal Carcinoma

value: KAP1 KO1


title: Bad Embryo rep1 (P3 rep1)

description:
9908R_P3vsC_diffexp.txt
BE1

value: small embryos, extruded yolks


title: Bad Tail (P1)

description:
9908R_P1vsC_diffexp.txt
BT0

value: deformed tail


title: P1534

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R02C02

value: M


title: 2-005-2-2_S82


title: Bad Yolk rep1 (P2 rep1)

description:
9908R_P2vsC_diffexp.txt
BY1

value: deformed yolk


title: Fin_PRE-exposure control_Tank_4_Fish_5_RNA#20

value: PRE-exposure (sea lice) control


title: 2-004-2-3_S114

value: baseline, cid2 :lcd, cid3 :di):CID3


title: HCT116_KAP1_KO2_Rep1_RNASeq

value: KAP1 KO2


title: HCT116_KAP1_KO2_Rep2_RNASeq


title: 2-002-2-3_S24


title: P1291

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R05C01


title: Control-pooled

description:
9908R_P1vsC_diffexp.txt,9908R_P2vsC_diffexp.txt,9908R_P3vsC_diffexp.txt
2_C

value: whole organism

value: 24 hpf

value: TU

value: normal


title: 2-002-2-2_S87

value: baseline, cid2 :lcd, cid3 :di):CID2


title: HCT116_KAP1_KO1_Rep2_RNASeq

description: ERCC spike-in RNA added.

value: Under 15


title: HCT116_KAP1_KO1_Rep3_RNASeq

description: ERCC spike-in RNA added.


title: serotonin

city: New York

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

data_processing:
The fastq files were aligned to zebrafish transcript (Ensembl Version 91)by using STAR.
The BAM files were as input for Cell Ranger (10X genmoics) to generate processed data files that include gene names (row names) and cell names (column names) and counts.
Further analysis done by using Seurat package in R.
Genome_build: danRer10
Supplementary_files_format_and_content: tab-delimited file, with gene names in rows and cell names and counts in columns.

source_name: Telencephalon

growth_protocol: Fish were kept at 28 °C water system with 14/10 hours light/dark cycles

extract_protocol:
Cells from telencephalon wre dissocuated and her4.1:GFP positve ande negative cells were sorted firstly and then mixed with equal number.
The library preparation was performed by 10X Genomics as per manufactur protocol

treatment_protocol: Fish were injected serotonin by CVMI.

value: serotonin


title: HCT116_KAP1_KO2_Rep3_RNASeq


title: 2-002-2-2_S212


title: P1501

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R04C01

value: Blood

value: Affected


title: TC-797_Triptolide_input_replicate1 (HiC)

description: Input control

data_processing:
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using BWA-MEM v0.7.15-r1140.
Reads were then assigned to MboI restriction fragments, duplicates removed, reads with a MAPQ ≥ 30 were retained, and intra restriction fragment reads removed.
The genome was divided into equally spaced, non-overlapping bins and the number of reads counted in each pair of bins gave the number of contacts, generating a Hi-C contact map.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014) using Juicer Tools v1.8.9.
Biological replicates were combined after filtering and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
Loops were identified using the previously described HiCCUPs algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Megadomain-megadomain interactions were identified using a model that accounted for enrichment relative to local background based on Poisson statistics.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_TADs.bedpe file of TAD coordinates in Juicebox format.
Supplementary_files_format_and_content: *_loops.bedpe file of loop coordinates in Juicebox format.
Supplementary_files_format_and_content: *_mega-mega.bedpe file of megadomain-megadomain interactions in Juicebox format.
Supplementary_files_format_and_content: *bw

extract_protocol:
Human cells were mixed with Drosophila cells at a 2:1 ratio and then cells were cross-linked with 1% EM-grade paraformaldehyde.  Intact nuclei were crudely isolated using detergent lysis.  DNA was digested with MboI (prior to digestion an aliquot was saved as an input control), DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together in situ. DNA-protein cross-links were reversed and the DNA then purified.
DNA sheared to a size of approximately 500 bp.  DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).  The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Tetracycline hydrochloride (Sigma-Aldrich #T7660) was solubilized in water. 293TRex-Flag-BRD4-NUT-HA were induced to express BRD4-NUT with 1 µg/mL tetracycline for 8 hours. MZ1 (Cayman Chemical #21622) was solubilized in DMSO. Triptolide (TPL; Cayman Chemical #11973) was solubilized in DMSO. TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) or 500 nM triptolide (0.01% final DMSO) for 4 hours. For washout experiments, TC-797 cells were treated with 100 nM MZ1 (0.01% final DMSO) for 4 hours, washed three times with PBS, and then returned to normal culture media (as described above) for 24 hours.

value: NUT carcinoma

value: Drosophila melanogaster Kc167 cells


title: TC-797_input_replicate6 (HiC)

description: Input control


title: HCT116_Ctrl_Rep3_RNASeq

description: ERCC spike-in RNA added.

value: Colorectal Carcinoma

value: Ctrl


title: P1496

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R02C01

value: M

value: Unaffected


title: TC-797_Triptolide_input_replicate2 (HiC)

description: Input control


title: 2-001-2-3_S47

value: baseline, cid2 :lcd, cid3 :di):CID3


title: P1425

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R01C02


title: Bad Yolk (P2)

description:
9908R_P2vsC_diffexp.txt
BY0

value: deformed yolk


title: P1584

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R01C01

value: F


title: 2-001-2-2_S120


title: HCT116_Ctrl_Rep2_RNASeq

description: ERCC spike-in RNA added.


title: 1-133-2-1_S11

value: baseline, cid2 :lcd, cid3 :di):CID1


title: TC-797_input_replicate5 (HiC)

description: Input control


title: HCT116_Ctrl_Rep1_RNASeq

description: ERCC spike-in RNA added.


title: P1208

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R06C01


title: P1346

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R06C02


title: TC-797_input_replicate4 (HiC)

description: Input control


title: 1-131-1-1_S158


title: HCT116_KAP1_KO1_Rep3_4sUSeq

description: ERCC spike-in RNA added.

data_processing:
Library strategy: 4sU-Seq
Quality of reads from all experiments was determined with FASTQC v0.11.2 using default parameters.
ChIP-seq: Reads were aligned to hg38 with Bowtie2 v2.3.2 with the --very-sensitive flag. SAM files were converted to BAM and sorted by chromosome with samtools v1.6. The view command with the -q flag set to 25 was used to filter out low quality reads. The sort command was used to convert SAM to BAM and sort by chromosome. Duplicates marked and removed with picard v1.127. Drosophilla spike-in chromatin was aligned to dm6 as described above for hg38. BAM files were generated and de-duplicated as described above for hg38 aligned reads. Drosophilla normalization factors were generated by dividing the Drosophilla read counts from each sample to the sample containing the least read counts. BedGraph tracks were generated with MACS2 v2.1.0 and normalized to Drosophilla spike-in normalization factors. BedGraph then converted to BigWig using bedGraphtoBigWig.
4sU-/RNA-seq: Reads were aligned to hg38 with STAR/2.5.2b. Sorted by coordinate BAM files were created by STAR with the –outSAMtype BAM flag. RPM normalized bedgraph files were also generated using STAR with the –outWigType bedGraph and –outWigNorm RPM flags. ERCC spike-ins were similarly aligned to an ERCC fasta file. Reads for protein coding genes were counted using the Gencode v27 annotation and featureCounts. Differential expression analysis was performed using RUVseq v1.14.0 R package.
MNase-seq: Raw data files were checked for quality control; low quality reads and adapter contaminations were removed using Trimgalore v0.4.1.  High quality reads (MAPQ >20) were aligned to the human genome assembly hg38 using Bowtie2 v2.3.3 and further processed using SAMtools v1.6. Using R v3.4.1 scripts adapted from bamR package (https://github.com/rchereji/bamR) the normalized nucleosome dyad distribution was computed by rescaling the average occupancy to 1 for each chromosome. To precisely map nucleosome positions, mono-Nucleosomal DNA fragments with a size of 120–160 bp were used for the analysis. R scripts were used to calculate average dyads density around TSS of RNA polymerase II- transcribed genes and plotting of nucleosome profiles and heatmaps.
Genome_build: hg38 and dm6
Supplementary_files_format_and_content: ChIP-seq: BigWig track files containing Drosophilla normalized aligned read densities
Supplementary_files_format_and_content: 4sU-/RNA-seq: RPM normalized BigWig track files
Supplementary_files_format_and_content: 4sU-/RNA-seq: tab-delimited file containing raw transcript counts
Supplementary_files_format_and_content: MNase-seq: BigWig track files containing normalized aligned read densities

value: KAP1 KO1

tag: molecule subtype

value: nascent 4sU RNA


title: HCT116_KAP1_KO1_Rep1_RNASeq

description: ERCC spike-in RNA added.


title: P1277

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R05C02


title: P1448

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571744111_R03C01


title: HCT116_KAP1_KO1_Rep2_4sUSeq

description: ERCC spike-in RNA added.


title: HCT116_KAP1_KO1_Rep1_4sUSeq

description: ERCC spike-in RNA added.


title: 1-098-2-2_S38

value: baseline, cid2 :lcd, cid3 :di):CID2


title: 1-095-2-1b_S112


title: TC-797_washout_input_replicate2 (HiC)

description: Input control

data_processing:
Reads were aligned to concatenated hg38/Genome Reference Consortium Human Reference 38 Patch 15 (GRCh38.p15) and dm6/BDGP Release 6 + ISO1 MT assemblies of the human and Drosophila melanogaster genomes, respectively, using BWA-MEM v0.7.15-r1140.
Reads were then assigned to MboI restriction fragments, duplicates removed, reads with a MAPQ ≥ 30 were retained, and intra restriction fragment reads removed.
The genome was divided into equally spaced, non-overlapping bins and the number of reads counted in each pair of bins gave the number of contacts, generating a Hi-C contact map.
Hi-C contact maps were normalized by matrix balancing using the KR normalization algorithm (Durand et al., 2016; Knight and Ruiz, 2012; Rao et al., 2014) using Juicer Tools v1.8.9.
Biological replicates were combined after filtering and the combined contact map KR normalized.  All subsequent analysis was performed on the combined, KR normalized contact map.
TADs were identified using the previously described Arrowhead algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
Loops were identified using the previously described HiCCUPs algorithm (Durand et al., 2016; Rao et al., 2014) using Juicer Tools v1.8.9.
All of the above steps were performed using the previously described Juicer pipeline (Durand et al., 2016; Rao et al., 2014) and Juicebox visualization interface (Durand et al., 2016).
Megadomain-megadomain interactions were identified using a model that accounted for enrichment relative to local background based on Poisson statistics.
Genome_build: GRCh38.p15 concatenated with dm6/BDGP Release 6 + ISO1 MT
Supplementary_files_format_and_content: *.hic file of Hi-C contacts in compressed format.  Readable by open-source Juicebox software (http://aidenlab.org/juicebox/).
Supplementary_files_format_and_content: *_TADs.bedpe file of TAD coordinates in Juicebox format.
Supplementary_files_format_and_content: *_loops.bedpe file of loop coordinates in Juicebox format.
Supplementary_files_format_and_content: *_mega-mega.bedpe file of megadomain-megadomain interactions in Juicebox format.

tag: spike-in


title: 1-077-2-2_S70


title: TC-797_washout_input_replicate1 (HiC)

description: Input control


title: TC-797_MZ1_input_replicate2 (HiC)

description: Input control


title: P1755

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R02C02


title: HCT116_Ctrl_Rep2_4sUSeq

description: ERCC spike-in RNA added.

value: Under 15


title: HCT116_Ctrl_Rep1_4sUSeq

description: ERCC spike-in RNA added.


title: 1-072-2-1b_S49


title: P1136

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R06C01


title: TC-797_DMSO_input_replicate2 (HiC)

description: Input control


title: HCT116_KAP1_KO1_NELFE_Rep2_ChIP-seq

description: An antibody specific to Drosophilla H2Av (Active Motif, 61686) and Drosophilla chromatin  (Active Motif, 53083) was added to each sample for normalization.

tag: chip antibody

value: NELFE (Santa Cruz Biotechnology, #sc-377052, lot:L0117)


title: HCT116_KAP1_KO1_NELFE_Rep1_ChIP-seq


title: P1319

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R05C01

value: Blood


title: 1-072-2-1b_S145


title: TC-797_DMSO_input_replicate1 (HiC)

description: Input control


title: TC-797_input_replicate3 (HiC)

description: Input control


title: 1-071-2-1b_S46


title: HCT116_Ctrl_NELFE_Rep2_ChIP-seq


title: 1-071-2-1b_S142


title: 293TRex_induced_input_replicate2 (HiC)

description: Input control

value: Human embryonic kidney


title: P1829

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R04C02

value: Affected


title: P1272

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R04C01


title: HCT116_Ctrl_NELFE_Rep1_ChIP-seq


title: HCT116_Ctrl_Rep3_4sUSeq

description: ERCC spike-in RNA added.


title: P1563

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R03C01


title: 1-066-2-1_S57


title: 293TRex_induced_input_replicate1 (HiC)

description: Input control

value: Drosophila melanogaster Kc167 cells


title: P1542

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R03C02


title: 1-075-2-1_S15


title: P1140

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R02C01


title: P1741

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R01C02


title: TC-797_MZ1_input_replicate1 (HiC)

description: Input control

value: NUT carcinoma


title: 293TRex_uninduced_input_replicate2 (HiC)

description: Input control


title: 1-066-1-1b_S68


title: P1720

description:
Genomic DNA extracted from blood was genotyped using the Infinium Human Exome-12 v1.2 BeadChip kit (Illumina).
Sample name: 9571727072_R01C01


title: 1-056-2-1_S21


title: HCT116_KAP1_KO1_Input_Rep2_ChIP-seq

value: Colorectal Carcinoma

value: none (input)


title: HCT116_KAP1_KO1_Input_Rep1_ChIP-seq


title: 293TRex_uninduced_input_replicate1 (HiC)

description: Input control


title: HCT116_Ctrl_Input_Rep2_ChIP-seq

value: Ctrl


title: HCT116_Ctrl_Input_Rep1_ChIP-seq


title: 1-035-2-1b_S189


title: HCT116_KAP1_KO1_CDK9_Rep2_ChIP-seq


title: 1-030-2-2_S101


title: HCT116_KAP1_KO1_CDK9_Rep1_ChIP-seq

value: CDK9 (Santa Cruz Biotechnology, #Sc-484, lot:B2605)


title: 1-029-2-1b_S167


title: 1-015-1-1b_S163


title: HCT116_Ctrl_CDK9_Rep2_ChIP-seq


title: HCT116_Ctrl_CDK9_Rep1_ChIP-seq


title: 1-007-1-2_S87


title: SC4

city: Muenster

first: Michael

last: Heming

address: Albert-Schweitzer-Campus 1, Bldg A1

department: Department of Neurology with Institute of Translational Neurology

country: Germany

institute: University Hospital Muenster

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
3

data_processing:
Raw bcl files were de-multiplexed using the cellranger mkfastq pipeline (cellranger v3.0.2)
Subsequent reads alignments and transcript counting was done individually for each sample using the cellranger count pipeline with standard parameters
The cellranger aggr pipeline was employed, to generate a single cell-barcode matrix containing all the samples without normalization
Genome_build: mm10, Rattus_norvegicus.Rnor_6.0.dna.toplevel
Supplementary_files_format_and_content: Standard cellranger output format

organism: Mus musculus

source_name: PNS

extract_protocol:
Sciatic nerves and the brachial nerve plexus were dissected from intracardial PBS perfused the mice. Nerves were first mechanically dissociated. Cells were then isolated by combining enzymatic digestion (Trypsin, Collagenase II, Hyaluronidase and Pronase) with myelin depletion and flow cytometry-based cell sorting (Calcein-AM, Zombi NIR, DAPI). Rats sciatic nerves were isolated and enzymatically digested in Collagenase/Dispase and DNase I. Cells were centrifuged on a 30%/70% Percoll gradient and the mononuclear interphase was collected. No sorting was performed.
Single cell suspensions were loaded onto the Chromium Single Cell Controller using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (both from 10X Genomics) chemistry following the manufacturer’s instructions. Sample processing and library preparation was performed according to manufacturer instructions using AMPure XP beads (Beckman Coulter). Sequencing was either carried out on a local Illumina Nextseq 500 using the High-Out 75 cycle kit with a 26-8-0-57 read setup or commercially (Microanaly, China) on a NovaSeq 6000 using the 300 cycle kit with paired end 150 read setup. All the samples were sequenced with a sequencing depth >50,000 reads per cell
ScRNA-seq

tag: genetic background


title: 1-005-2-2_S67


title: 1-036-2-1b_S98


title: HCT116_KAP1_KO1_S2P_PolII_Rep1_ChIP-seq

value: S2P RNA Pol II (Millipore, #04-1571, lot:2724427)


title: HCT116_KAP1_KO1_S2P_PolII_Rep2_ChIP-seq


title: SC3

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
2


title: 1-003-1-1_S134


title: HCT116_Ctrl_S2P_PolII_Rep2_ChIP-seq


title: HCT116_Ctrl_S2P_PolII_Rep1_ChIP-seq


title: SC1

description:
mouse_barcodes.tsv
mouse_features.tsv
mouse_matrix.mtx.gz
1


title: Gar1513_17002R

city: Darlinghurst

first: Heloisa

middle: Helena

last: Milioli

state: NSW

address: 384, Victoria St

department: Cancer

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
The next generation sequencing data was processed on the Illumina HiSeq 2500 v4.0 System.
Sequences were trimmed using Trim Galore (version 0.4.4) and genome-guided alignment to a human reference (HG38) was performed using the STAR software (version 2.5).
Feature counts were computed in R (version 3.4.3) using the package Rsubread.
The differential gene expression analysis was conducted with edgeR and limma packages in the R environment.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Patient derived xenograft

growth_protocol: MCF7 cells (Michigan Cancer Foundation), T-47D and ZR75-1 cells (American Type Culture Collection) lines were verified through short tandem repeat profiling and tested negative for mycoplasma contamination. Parental cell lines were cultured in RPMI 1640 media (Thermo Fisher) supplemented with 10% fetal bovine serum (GE Healthcare) and 20 mM HEPES (Thermo Fisher). Endocrine resistant derivatives were developed and cultured in phenol red-free RPMI 1640 (Thermo Fisher) supplemented with 5% charcoal stripped fetal bovine serum (GE Healthcare) and 20 mM HEPES. MCF-7 derived fulvestrant resistant (FasR) and palbociclib resistant (PalbR) lines were supplemented with 10 pM 17β-estradiol (Sigma) and 100 nM fulvestrant (Assay Matrix) or 500 nM palbociclib (Selleckchem) respectively. 10,000x stock solutions of each drug were prepared in ethanol (fulvestrant, 17β-estradiol) or water (palbociclib). All cells were cultured under 5% CO2 in a humidified incubator at 37°C.

extract_protocol:
Total RNA was extracted from breast cancer cell lines and tissue samples using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. For the tumour tissue, snap frozen sections were first disrupted in lysis buffer in a TissueLyser II (QIAGEN).
The next generation sequencing data was processed on the Illumina HiSeq 2500 v4.0 System. Sequences were trimmed using Trim Galore (version 0.4.4) and genome-guided alignment to a human reference (HG38) was performed using the STAR software (version 2.5). Feature counts were computed in R (version 3.4.3) using the package Rsubread.

treatment_protocol: All in vivo experiments, procedures and endpoints were approved by the Garvan Institute of Medical Research Animal Ethics Committee (protocol 15/25). KCC_P_3837 (HREC/13/RPA/187) was derived from an untreated grade 3, ER-positive, PR-positive, HER2-negative primary invasive ductal carcinoma. PDX Gar15-13 (#14002, HREC/H2006/2633) was derived from a patient with endocrine resistant ER-positive, PR-positive, HER2-negative metastatic breast cancer. At surgery, 4 mm3 sections of tumour tissue were implanted into the 4th inguinal mammary gland of female NOD-SCID-IL2γR-/- (NSG) mice (Australian BioResources Pty Ltd). For KCC_P_3837, tumour growth was supported by implantation of a silastic pellet containing 0.72 mg 17β-estradiol. Tumour growth was assessed twice weekly by calliper measurement and mice were randomized to treatment arms when tumours reached 150-250 mm3 (using the formula: 〖width〗^2  ×length ×0.5). 100 mg/kg NVP-CGM097 (20 mg/ml in 2% DMSO) was administered by oral gavage 5 days a week. 5 mg/body fulvestrant (50 mg/ml in peanut oil – Sigma P2144) was delivered by sub-cutaneous injection once per week. Mice were treated for 60 days or until tumour volume reached 1000 mm3. Final tumour volumes were compared using 1-way ANOVA and T-tests of each pairwise combination with Tukey’s correction for multiple testing. All statistical analyses were performed using built-in functions in GraphPad Prism (version 7.04, GraphPad Software).

value: breast cancer (liver metastasis)

tag: condition

value: Combination


title: Gar1513_17000R


title: Tet2KO RP ATAC-seq 2

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

data_processing:
For RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4
For RNA-seq gene counts were derived with  htseq-count v0.8.0
RNA-seq quantification, normalization, and differnetial gene expression as performed using EdgeR release 3.9
Supplementary_files_format_and_content: RNA-Seq: tab-delimited file with raw gene counts
For ATAC-seq reads were aligned to mm10 using BWA mem.
Duplicate reads were filtered out with Picard tools.
Addiciontal ATAC-seq read filtering and then peak calling was performed with deepTools and MACS2 via SnakePipes.
Differential chromatin accessibility was determined using reads filterd for short fragment lengths, a mean of 150bp. These bam files were downsampled to contain the same number of reads. A consensus peak set was determined by intersecting all narrowPeak files. The number of reads per peak for each sample was calculated with Subread featureCounts. EdgeR was used to perform differential read density of each consensus peak.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files for ATAC_seq and a table of counts for exon transcripts for RNA-seq

source_name: Restricted Progenitor

extract_protocol:
For RNA-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-) and Rps (Lin-, cKit+, Sca1+, C-150- CD48+) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl  mice.  Total RNA was isolated from the samples using the NucleoSpin RNA XS kit
For RNA-seq, the SMARTer Ultra Low RNA kit (Clontech) was used to prepare the libraries from 3-5ng of total RNA.
For ATAC-seq, HSCs (Lin-, cKit+, Sca1+, CD150+, CD48-),MPPs ( Lin-, cKit+, Sca1+, C-150-, CD48-) and Rps (Lin-, cKit+, Sca1+, C-1-0+, CD+8-) were sorted from a pooled sample of 2 male and 2 female 8-week old mice HSCs were purified from three or four biological replicates (composed of pooled WBM from three male and three female mice) of either Vav-CRE: Dnmt3a+/+; Tet2+/+ or Vav-CRE:Dnmt3afl/fl or + or Vav-CRE:Tet2fl/fl  mice.
For ATAC-Seq, NEBNext High-Fidelity 2X PCR Master MIX (NEB M0541L) along with Nextera custom primers were used for library amplification of the ATAC DNA(5-7 cycles of PCR as determined by qPCR).  Libraries were again purified with Ampure XP beads and run on an Illumina Hiseq 3000 (PE2X150) or NovaSeq(PE2x150).

tag: genotype

tag: cre-driver

value: Vav

value: Restricted Progenitor


title: HUVEC_AEBP1siRNA2_72h_replicate2

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: HUVEC with AEBP1 siRNA2 (72h) replicate2

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: HUVECs were cultured in Endothelial Cell Basal Mesium-2 (EBM-2, Lonza) supplemented with the EGM-2 SingleQuots kit (Lonza) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: HUVECs were transfected with a control siRNA (Silencer Select Negative Control No. 1 siRNA, Thermo Fisher Scientific) or siRNAs targeting AEBP1 (Silencer Select Pre-designed siRNA; AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) using HUVEC Nucleofector Kit (Lonza) and incubated for 48h or 72h.

value: HUVEC

tag: sirna

value: AEBP1 siRNA2


title: Tet2KO RP ATAC-seq 1

tag: strain

tag: age


title: Brain_Sham_rep3

city: Nanjing

first: Bing

last: Han

address: Dingjiaqiao #87

country: China

institute: Southeast University

description: Gene expression  in sham mouse-brain tissues

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering.

source_name: brain, sham, replicate 3

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Mice were housed under a constant temperature and humidity and under a 12-hour light/12-hour dark cycle, with the lights on at 7:00 AM. Food and water were available ad libitum.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresi

treatment_protocol: Mice subjected to tMCAO were sacrificed at 12 h after reperfusion. Total RNAs were extracted from the ischemia cortex of each mouse using TRIzol reagent.

value: male

value: 8 weeks


title: Brain_tMCAO_rep3

description: Gene expression after 12hr in tMCAO mouse-ischemia brain tissues

source_name: brain, tMCAO, replicate 3


title: Brain_tMCAO_rep1

source_name: brain, tMCAO, replicate 1


title: HUVEC_AEBP1siRNA2_72h_replicate1

description: HUVEC with AEBP1 siRNA2 (72h) replicate1


title: Brain_tMCAO_rep2

source_name: brain, tMCAO, replicate 2


title: HUVEC_AEBP1siRNA2_48h_replicate2

description: HUVEC with AEBP1 siRNA2 (48h) replicate2


title: HUVEC_AEBP1siRNA1_72h_replicate2

description: HUVEC with AEBP1 siRNA1 (72h) replicate2

value: AEBP1 siRNA1


title: HCT116_KAP1_KO1_Ctrl_S5P_PolII_Rep2_ChIP-seq

description: An antibody specific to Drosophilla H2Av (Active Motif, 61686) and Drosophilla chromatin  (Active Motif, 53083) was added to each sample for normalization.

tag: genotype/variation

value: KAP1 KO1

tag: passages

value: Under 15

value: S5P RNA Pol II (ActiveMotif, #61085, lot:20017002)


title: HUVEC_AEBP1siRNA1_72h_replicate1

description: HUVEC with AEBP1 siRNA1 (72h) replicate1


title: Brain_Sham_rep2

source_name: brain, sham, replicate 2

tag: gender


title: HUVEC_siCtrl_72h_replicate2

description: HUVEC with control siRNA (72h) replicate2

value: control siRNA


title: Gar1513_17012R

tag: tissue


title: HUVEC AEBP1siRNA1 48h replicate2

description: HUVEC with AEBP1 siRNA1 (48h) replicate2

source_name: HUVEC AEBP1siRNA1 48h


title: Gar1513_16998L

value: Fulvestrant (5 mg/body)


title: Brain_Sham_rep1

source_name: brain, sham, replicate 1


title: HUVEC_AEBP1siRNA2_48h_replicate1

description: HUVEC with AEBP1 siRNA2 (48h) replicate1


title: HUVEC_AEBP1siRNA1_48h_replicate1

description: HUVEC with AEBP1 siRNA1 (48h) replicate1


title: HCT116_KAP1_KO1_S5P_PolII_Rep1_ChIP-seq

value: Colorectal Carcinoma


title: HUVEC_siCtrl_72h_replicate1

description: HUVEC with control siRNA (72h) replicate1


title: Tet2KO MPP ATAC-seq 2

source_name: Multipotent Progenitor

value: Multipotent Progenitor


title: HCT116_Ctrl_S5P_PolII_Rep2_ChIP-seq

value: Ctrl


title: MGAS27961-10TDSpy1336DSpy1337-3_ES

city: HOUSTON

first: Jesus

last: Eraso

address: 6670 Bertner

department: Pathology and Genomic Medicine

institute: Methodist Hospital

description:
MGAS27961-10TDSpy1336/R28-DSpy1337
MGAS27961-10TDSpy1336/R28-DSpy1337 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ES"

data_processing:
Multiplexed SE libraries were sequenced on an Illumina Illumina NextSeq550 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files.
RNA-seq reads from strains grown in vitro were mapped to reference strain MGAS6180 (accession number NC_007296) using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Sequencing read quality was evaluated with FASTQC software (Babraham Bioinformatics, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adapter contamination and read quality filtering was performed with Trimmomatic.
Differential expression analysis was performed using DESeq2 version 1.16.1.

organism: Streptococcus pyogenes

source_name: cell pellet

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37° C in atmosphere supplemented with 5% CO2.

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina).
Resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Epicentre).

treatment_protocol: At the desired growth stage, mid-exponential (OD 600nm 0.5) or early-stationary (OD 600nm 1.55), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation.

tag: replicate

value: Replicate 3_ES

tag: grpwth phase

value: Early-stationary (ES, OD600nm=1.5)


title: Gar1513_16997L

value: breast cancer (liver metastasis)


title: HCT116_Ctrl_S5P_PolII_Rep1_ChIP-seq

tag: cell line

tag: cell type


title: Tet2KO HSC ATAC-seq 2

source_name: Hematopoietic Stem Cell

value: Vav

value: Hematopoietic Stem Cell


title: Tet2KO MPP ATAC-seq 1


title: HUVEC_siCtrl_48h_replicate1

description: HUVEC with control siRNA (48h) replicate1

value: HUVEC


title: MGAS27961-10TDSpy1336DSpy1337-2_ES

value: Replicate 2_ES


title: Gar1513_17004R


title: Tet2KO HSC ATAC-seq 1


title: MGAS27961-10TDSpy1336DSpy1337-1_ES

value: Replicate 1_ES


title: HCT116_KAP1_KO1_RPB3_Rep1_ChIP-seq

source_name: HCT116 Colorectal Carcinoma Cell Line

value: RPB3 (Millipore, #ABE999, lot:Q2550840)


title: HUVEC_siCtrl_48h_replicate2

description: HUVEC with control siRNA (48h) replicate2


title: Gar1513_17005L

value: NVP-CGM097 (100 mg/kg)


title: Gar1513_17001R


title: HCT116_KAP1_KO1_RPB3_Rep2_ChIP-seq

value: KAP1 KO1

value: Under 15


title: MGAS27961-10TDSpy1337-3_ES

description:
MGAS27961-10TDSpy1337
MGAS27961-10TDSpy1337 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ES"


title: Dnmt3aKO RP ATAC-seq 1

value: Restricted Progenitor


title: MGAS27961-10TDSpy1337-2_ES


title: Dnmt3aKO MPP ATAC-seq 2


title: Gar1513_16999L

value: Vehicle (2% DMSO)


title: HCT116_Ctrl_RPB3_Rep1_ChIP-seq

value: Colorectal Carcinoma


title: HCT116_Ctrl_RPB3_Rep2_ChIP-seq


title: MGAS27961-10TDSpy1337-1_ES


title: Gar1513_16999R


title: MGAS27961-11T-3_ES

description:
MGAS27961-11T
MGAS27961-11T was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ES"


title: Gar1513_17006R


title: Neonatal Foreskin, Donor 23, PBS Treated

city: Worcester

last: Gellatly

state: MA

address: 368 Plantation Street

institute: University of Massachusetts Medical School

description: counts.mel.csv

data_processing:
Reads were aligned to human ribosomal RNA using Bowtie2 v2.2.3, and any mapped reads removed from downstream analysis
RSEM v1.2.28 was used to estimate gene expression in Transcripts per Million (TPM), with parameters –bowtie-chunkmbs 100
Quantification was run against the transcriptome (RefSeq v69) downloaded from UCSC Table Browser
Genome_build: hg19
Supplementary_files_format_and_content: counts.mel.csv
Supplementary_files_format_and_content: tpm.mel.csv

source_name: Neonatal Foreskin

growth_protocol: Primary melanocyte cultures were established from neonatal foreskin samples (NFS) [(Eisinger and Marko, 1982; Tsuji and Karasek, 1983)] and maintained in TIVA media (Yokoyama et al., 2008) (Hams F12 media with 7.5% FBS, 1X Pen/Strep, 100 uM dibutyryladenosine 3:5-cyclic monophosphate, 100 uM 3-isobutyl-1-methyl xanthine, 50 ng/mL 12-O-tetradecanyl phorbol-13-acetate, 1 uM Na3VO4 (Sigma)).

extract_protocol:
RLT RNA extraction (Qiagen)
Smart-seq2 protocol (Picelli et al., 2014)

treatment_protocol: NFS melanocytes were plated at 5 x 105 cells/mL and treated with 200 ng/mL IFN-γ or PBS for 48 hours before cells were collected for RNA using RLT buffer (Qiagen).

tag: treatment

value: PBS

value: Primary isolated tissue cell culture


title: Neonatal Foreskin, Donor 23, IFNg Treated

description: counts.mel.csv

value: IFNg


title: Dnmt3aKO HSC ATAC-seq 2


title: MGAS27961-11T-2_ES

value: Early-stationary (ES, OD600nm=1.5)


title: Dnmt3aKO HSC ATAC-seq 1


title: Neonatal Foreskin, Donor 22, PBS Treated

description: counts.mel.csv


title: MCF7_CGM097_Fulvestrant_p25

source_name: Cell line

value: breast cancer

value: NVP-CGM097 (1µM) and fulvestrant (1nM)


title: MCF7_CGM097_Fulvestrant_p21


title: MGAS27961-11T-1_ES


title: Dnmt3aKO RP ATAC-seq 2

value: Vav


title: Control RP ATAC-seq 2

value: Wild-type


title: MCF7_CGM097_Fulvestrant_p20


title: MCF7_Palbociclib_CGM097_p25

value: NVP-CGM097(1µM) and palbociclib (500nM)


title: Neonatal Foreskin, Donor 21, PBS Treated

description: counts.mel.csv


title: Control RP ATAC-seq 1


title: MGAS27961-9T-3_ES

description:
MGAS27961
MGAS27961 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ES"

value: Replicate 3_ES


title: Control MPP ATAC-seq 2

value: Multipotent Progenitor


title: MCF7_Palbociclib_CGM097_p21


title: MGAS27961-9T-1_ES

value: Replicate 1_ES


title: MCF7_Palbociclib_CGM097_p20


title: MGAS27961-10TDSpy1336DSpy1337-3_ME

description:
MGAS27961-10TDSpy1336/R28-DSpy1337
MGAS27961-10TDSpy1336/R28-DSpy1337 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ME"

value: Replicate 3_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: Control HSC ATAC-seq 2

value: Hematopoietic Stem Cell


title: Neonatal Foreskin, Donor 21, DMSO Treated

description: counts.mel.csv

value: DMSO


title: Neonatal Foreskin, Donor 21, IFNg Treated

description: counts.mel.csv


title: MCF7_CGM097_p25


title: Neonatal Foreskin, Donor 20, DMSO Treated

description: counts.mel.csv


title: MGAS27961-10TDSpy1336DSpy1337-2_ME

value: Replicate 2_ME


title: MCF7_CGM097_p21


title: Control HSC ATAC-seq 1


title: MGAS27961-10TDSpy1336DSpy1337-1_ME

value: Replicate 1_ME


title: Neonatal Foreskin, Donor 19, PBS Treated

description: counts.mel.csv

value: PBS

value: Primary isolated tissue cell culture


title: Neonatal Foreskin, Donor 22, IFNg Treated

description: counts.mel.csv

value: IFNg


title: MGAS27961-10TDSpy1337-3_ME

description:
MGAS27961-10TDSpy1337
MGAS27961-10TDSpy1337 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ME"


title: Neonatal Foreskin, Donor 19, IFNg Treated

description: counts.mel.csv


title: MCF7_Fulvestrant_p25

value: breast cancer

value: Fulvestrant (0.1nM)


title: scRNA-seq-E16.5

city: Beijing

first: Qingyuan

last: Sun

state: Beijing

address: Beichen West Rd., Chaoyang

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

description: PGC.txt

data_processing:
We checked the quality of raw sequencing data by FastQC software. The read2 fastq sequence was trimmed by FASTX-Toolkit. We used 10x genomics cellranger count pipeline 2.0.0 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Genome_build: mm10
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

molecule: polyA RNA

source_name: Female primordial germ cells

extract_protocol:
RNA were prepared for sequencing
Female primordial germ cells at different timepoints were harvested and resuspended at 1 × 106 cells per milliliter in 1 × PBS with 0.04% BSA. Then, cell suspensions (300-1000 living cells per microliter determined by trypan blue staining) were loaded on a Chromium Single Cell Controller (10x Genomics) to generate single-cell gel beads in emulsion (GEMs) by using Single Cell 3' Library and Gel Bead Kit V2 (10x Genomics, 120237). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs (Zheng et al., 2017). Barcoded cDNAs were pooled and cleanup by using DynaBeads® MyOne™ Silane Beads (Invitrogen, 37002D). Single-cell RNA-seq libraries were prepared using Single Cell 3' Library Gel Bead Kit V2 (10x Genomics, 120237) following the manufacture’s introduction.

value: Fetal ovaries

value: Embryonic day 16.5


title: MGAS27961-10TDSpy1337-2_ME.fastq.gz


title: Control MPP ATAC-seq 1

value: Wild-type

value: Vav


title: scRNA-seq-E12.5

description: PGC.txt

value: Embryonic day 12.5


title: MGAS27961-10TDSpy1337-1_ME


title: MCF7_Fulvestrant_p21


title: scRNA-seq-E14.5

description: PGC.txt

value: Embryonic day 14.5


title: MGAS27961-9T-2_ES

value: Replicate 2_ES

value: Early-stationary (ES, OD600nm=1.5)


title: MCF7_Fulvestrant_p20


title: MGAS27961-11T-3_ME

description:
MGAS27961-11T
MGAS27961-11T was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ME"

value: Replicate 3_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: MCF7_Palbociclib_p25

value: Palbociclib (500nM)


title: Dnmt3aKO MPP ATAC-seq 1

value: Multipotent Progenitor


title: RNAseq on EPZ-6438 treated NTG  replicate B

city: Chapel Hill

first: Jesse

last: Raab

address: 120 Mason Farm Rd

department: Genetics

institute: University of North Carolina Chapel Hill

description:
EPZ_NTG_B
processed data file:
drug_norm_counts.csv

data_processing:
Kallisto was used to quantitate transcript expression levels using GRCh38 reference with the following paramters --single -l 200 -s 50 -b 50
tximport was used to aggregate count data per gene using Kallisto output.
DESeq2 was used for differential expression analysis with an FDR of 0.5 and no explicit fold change cut off
Genome_build: GRCh38
Supplementary_files_format_and_content: csv files of count data for each sample

source_name: HepG2_EPZ-6438 treated NTG

growth_protocol: Cells were grown in DMEM + 10% FBS + P +S and maintained for less than 10 passages.

extract_protocol:
RNA was extracted using trizol and Direct-zol kit (Zymo Research) per manufacturers instructions
Libraries were constructed using Kapa stranded mRNA sequencing kit

treatment_protocol: siRNA experiments were conducted by adding 50nM siRNA in optimem using RNAimax transfection reagent per manufacturers instructions. Cells were harvested at 72 hours post transfection for processing. For drug treatment experiments. 1uM EPZ-6438 or 1uM DMSO were added 3 days prior to transfections with siRNA as previously described.

value: liver cancer cell line

value: NTG (AM4611 Life Tech.)

tag: treated with


title: RNAseq on EPZ-6438 treated NTG  replicate C

description:
EPZ_NTG_C
processed data file:
drug_norm_counts.csv


title: pLoop_80

city: Los Angeles

first: Guillaume

last: Urtecho

state: CA

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
lacZ_bc_map.txt.gz, lacZ_controls_bc_map.txt.gz

data_processing:
Counts for each unique barcode in the census files were complete in Unix as follows: Raw sequences were extracted from each fastq file and the first 20 bp (corresponding to the barcode) was extracted. This sequence was reverse complemented and the entire file was sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of total reads per sample and all samples aggregated together in R.
Barcode mapping was completed as follows: Demultiplexed reads were paired using Paired-End reAd mergeR (PEAR v0.9.1, default settings). Custom python code was used to identify reads corresponding to perfectly synthesized promoters and their respective barcodes. Briefly, this code searched the first 150 bp of each read for perfect matches to library variants. For reads with perfect matches, the last 20 bp of each read (the barcode) was extracted and a list was compiled mapping each barcode to the most frequently associated library variant. A single barcode appears many times in the sequencing data, and we took steps to ensure a barcode consistently mapped to the same variant. We required that all variants mapped to a single barcode be within an edit distance (Levenshtein distance) of 5 from one another (five single bp changes between the two sequences). We determined this number by bootstrapping a distribution of the edit distance between any two random sequences in our variant library, and setting the threshold to the first percentile (1%) of this bootstrapped distribution. Additionally, each barcode had to appear at least three times in order to be considered for downstream analysis. This step hopefully eliminates barcodes which contained sequencing errors.
Promoter variant expression was calculated in R by assigning barcodes to their mapped promoter and, for each promoter, dividing the sum of all RNA counts for all of its barcodes by the sum of all DNA counts for all of its barcodes.

organism: Escherichia coli

source_name: Escherichia coli

extract_protocol: All libraries are constructed using two-step PCR of extraced molecule (Genomic DNA, cDNA, or Plasmid DNA). Initial PCR adds custom sequencing primers and the second PCR adds flow cell adapters for Illumina systems.

tag: growth medium

value: LB

tag: extraction protocol

value: Qiagen Plasmid Plus Maxi Kit

tag: molecule

value: Plasmid DNA


title: RNAseq on EPZ-6438 treated NTG  replicate A

description:
EPZ_NTG_A
processed data file:
drug_norm_counts.csv


title: Neonatal Foreskin, Donor 22, DMSO Treated

description: counts.mel.csv

value: DMSO

value: Primary isolated tissue cell culture


title: MGAS27961-11T-2_ME

value: Replicate 2_ME


title: MCF7_Palbociclib_p21

value: breast cancer

tag: condition


title: MGAS27961-11T-1_ME

value: Replicate 1_ME


title: MCF7_Palbociclib_p20


title: RNAseq on EPZ-6438 treated siMCRS1 replicate B

description:
EPZ_MCRS1_B
processed data file:
drug_norm_counts.csv

source_name: HepG2_EPZ-6438 treated siMCRS1

tag: sirna

value: MCRS1 (s20435 Life Tech)


title: Neonatal Foreskin, Donor 19, DMSO Treated

description: counts.mel.csv


title: MGAS27961-9T-3_ME

description:
MGAS27961
MGAS27961 was streaked from a freezer stock onto a blood agar plate for O/N growth, and grown for 10-11 h O/N before sampling
The processed data file is included in the second sheet of this Excel file, under thedesignation "Normalized_counts_ME"

tag: strain


title: MCF7_CGM097_p20


title: pLacZ_86_S7

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
LacZ_mapping_barcode_statistics.txt.gz, LacZ_mapping_variant_statistics.txt.gz


title: pLoop_81


title: RNAseq on EPZ-6438 treated siMCRS1 replicate A

description:
EPZ_MCRS1_A
processed data file:
drug_norm_counts.csv


title: fLP3_LacZ_UnInduced_RNA_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 2nd biological replicate.
LacZ_variant_exp.txt.gz

value: MOPS EZ-Rich + .2% Glucose

value: Qiagen RNeasy Midi Kit

value: Total RNA


title: MGAS27961-9T-2_ME

value: Mid-exponential (ME, OD600nm=0.5)


title: fLP3_LacZ_UnInduced_RNA_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 1st biological replicate.
LacZ_variant_exp.txt.gz


title: MCF7_Vehicle_p25

value: Vehicle (0.01% DMSO)


title: RNAseq on DMSO treated NTG replicate C

description:
DMSO_NTG_C
processed data file:
drug_norm_counts.csv

source_name: HepG2_DMSO treated NTG

value: 1uM DMSO


title: MGAS27961-9T-1_ME


title: MCF7_Vehicle_p21


title: pLacZ_87_S8


title: fLP3_LacZ_UnInduced_DNA_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 1st biological replicate.
LacZ_variant_exp.txt.gz

value: Qiagen Puregene Yeast/Bact. Kit 2

value: Genomic DNA


title: MCF7_Vehicle_p20


title: RNAseq on DMSO treated siMCRS1 replicate B

description:
DMSO_MCRS1_B
processed data file:
drug_norm_counts.csv

source_name: HepG2_DMSO treated siMCRS1

value: liver cancer cell line


title: fLP3_LacZ_UnInduced_DNA_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the essQ-cspB intergenic region. This is the 2nd biological replicate.
LacZ_variant_exp.txt.gz


title: RNAseq on DMSO treated siMCRS1 replicate C

description:
DMSO_MCRS1_C
processed data file:
drug_norm_counts.csv


title: fLP3_LacZ_Induced_RNA_2

value: MOPS EZ-Rich + .2% Glucose + 1 mM IPTG


title: CB CD34+ cells with MOCK-Replicate1

city: Duarte

first: Xin

last: He

address: 1500 E Duarte Rd

institute: City of Hope

data_processing:
bcl2fastq (v2-2.18) was used for basecalling.
Sequenced reads were mapped to hg19 whole genome using tophat v2.0.8 with parameter --no-coverage-search
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM_lingli_190326_symbol.txt include gene_symbol, chromosome, start, end, width, strand, Ensembl_id, total_exon_length, and RPKM values for each Sample.

source_name: Cord blood cells

growth_protocol: CB cells were culturedin in StemSpan serum-free medium, supplemented   with human growth factors including human SCF, TPO, FLT-3 ligand, IL-3 and IL-6 .

extract_protocol:
Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture`s instructions. RNA quality was assessed by spectrophotometry(NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with mock or FLT3-ITD vectors

value: Mock transfected

value: cord blood CD34+ cells


title: CB CD34+ cells with FLT3-ITD-Replicate1

value: FLT3-ITD transfected


title: fLP3_LacZ_Induced_DNA_2


title: CB CD34+ cells with FLT3-ITD-Replicate2


title: CB CD34+ cells with MOCK-Replicate2


title: fLP3_LacZ_Induced_DNA_1


title: fLP3_LacZ_Induced_RNA_1


title: RNAseq_A2780_highISL1sorted

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig

growth_protocol: Cells  were cultured in RPMI-1640-Glutamax I (#61870-036, Life Technologies) and 10% fetal bovine serum (FBS, #FB-11, Omega Scientific) at 5% CO2 37ºC, and sub-cultured at 1:5 to 1:6 dilutions after dissociation with 0.25% trypsin. Media was changed every other day, or daily when cells reached >50-60% confluency.

extract_protocol:
GRO-seq analysis was perfromed as prevkiously reported (PMID: 21572438, Wang et al., 2011); RNA-seq and ribosome profiling was performed using the ARTseq Ribosome Profiling kit  following the manufacture’s protocol (Epicentre).
RNA quality was calculated on TapeStation (Agilent Technologies). PolyA+ RNA-seq libraries were generated using the Illumina TruSeq Stranded RNA LT kit and following manufacturer’s detailed instructions.

treatment_protocol: The treatment administrated to A2780cis cells was described in the Sigma-Aldrich website as chronic exposure of the parent A27890 line to increasing concentrations of cisplatin Sigma-Aldrich (#93112517-19). Acute treatments (IC50) were administrated for 3 days, adding fresh media with drug at day 0 and after 2 days again.

value: Cells sorted based on ISL1 protein levels


title: RNAseq on DMSO treated NTG replicate A

description:
DMSO_NTG_A
processed data file:
drug_norm_counts.csv

value: NTG (AM4611 Life Tech.)


title: Pt-msx1_st6_rep3_d24

city: Takatsuki

first: Hiroki

last: Oda

state: Osaka

address: 1-1 Murasaki-cho

institute: JT Biohistory Research Hall

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_msx_st6.txt

data_processing:
Base call and quality scoring were performed by the Real Time Analysis software application during Illumina's sequencing runs.
Sequence reads were trimmed for adaptor and primer sequences and low-quality sequences using the CLC Genomics Workbench 7.0.4 (Qiagen) with the following parameter settings for the quality trim: trim using quality scores, limit=0.05; trim ambiguous nucleotides, maximum number of ambiguities=2; filter on length, discard reads below length=50. Trimmed reads were then aligned to Ptep_1.0 genome assembly using the BLAT algorithm version 34 in the DDBJ Read Annotation Pipeline with default settings.
The output alignments were filtered based on quality, coverage, and uniqueness using a perl script filterPSL.pl available from the AUGUSTUS 3.0.1 scripts folder. The parameter settings were as follows: minimum coverage, 60%; minimum percent identity, 90%; unique threshold, 0.96. The filtered alignments were converted into sam and psl files with a custom perl script.
Using the sam files, abundance of mRNAs against AUGUSTUS gene models (Schwager et al., 2017, BMC Biol. 15, 62) was calculated with htseq-count v. 0.5.4p5 in -s reverse, -m union settings and was normalized in Reads Per Kilobase of exon per Million reads (RPKM).
Based on the abundance of mRNAs against AUGUSTUS gene models, differentially expressed genes (DEGs) were estimated using EdgeR.
The alignments in the psl format were converted into wig files using a script aln2wig available from the AUGUSTUS 3.0.1 scripts folder, and the wig files were converted into bigWig files using the program wigToBigWig available from the ucsc directory.
Genome_build: Ptep_1.0
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for gene models and the features of the gene models.
Supplementary_files_format_and_content: tab-delimited text file includes logFC and FDR values for the identified DEGs.
Supplementary_files_format_and_content: wig files ; Scores represent normalized read coverage (per 10 million reads).
Supplementary_files_format_and_content: bigWig files ; Scores represent normalized read coverage (per 10 million reads).

organism: Parasteatoda tepidariorum

growth_protocol: Embryos were incubated at 25˚C until they reached the appropriate stages.

extract_protocol:
Poly(A) mRNA was extracted using a QuickPrep Micro mRNA purification kit (GE Healthcare) and a Dynabeads mRNA DIRECT Kit (Ambion) from 50-120 embryos.
mRNA was fragmented using the NEBNext RNase III RNA Fragmentation Module (New England BioLabs). Sequencing libraries were constructed from fragmented RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set 1, New England BioLabs).

treatment_protocol: Mated adult females were injected with approximately 1-2 µl of Pt-hh, Pt-ptc, or Pt-msx1 dsRNA solution (2µg/µl) four times at 2-3 days intervals. Embryos derived from egg sacs produced by the injected females 13-24 days after the first injection of the dsRNA were used for RNA extraction. Embryos from the same females 1-3 days before the dsRNA injection were used as untreated samples.

tag: isolate

value: Osaka

value: whole embryo

value: Pt-msx1 pRNAi

tag: developmental stage

value: early stage 6


title: Control RNA-seq rep2

city: Shenzhen

first: Zhijun

state: Guangdong

address: No 1088,xueyuan Rd., Nanshan District

institute: Southern University of Science and Technology

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were trimmed using trim_galore 0.4.4_dev with default settings and then aligned to mm10 using bowtie2 with --end-to-end  -X 2000. Reads with MAPQ < 10 were removed using samtools. Singletons are removed using in house Perl script.  Duplicated reads were removed using samtools.
Filtered reads were sampled to the same reads number for comparing between samples using samtools. Differential chromatin accessible regions were identified using rgt-THOR version 0.1 with parameters --pvalue 0.05 --binsize 100 --step 50. Then significant differential peaks were further filtered according to the switch point from rank plot. Peaks were annotated to refGene annotation downloaded from UCSC Genome Browser using in house Perl script. Motifs were scanned using HOMER findMotifsGenome.pl from the top 1000 differential accessible peaks extended from the peak summit to +/- 100bp.
RNA-seq reads were mapped to mm10 with refGene annotation downloaded from UCSC Genome Browser using TopHat2 v2.1.0. Gene expression level were counted by htseq-count 0.11.0. Differential expressed genes were called by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: BigWiig files were generated by rgt-THOR, scores representing the normalized ATAC-seq reads coverage. TAB-delimited text file included the raw reads count for each gene from RNA-seq sample.

source_name: TH17(23) cells

growth_protocol: Naïve CD4+ T cells were isolated from lymph nodes or spleen of mice using a CD4+ CD62L+ T cell isolation kit II (Miltenyi Biotec) according to the manufacturer’s instruction. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε mAb (5 µg/ml) in the presence of anti-CD28 mAb (2 µg/ml) in a 48-well plate under neutral conditions (10 µg/ml anti–IL-4 mAb and 10 µg/ml anti–IFN-γ mAb), IL-6 conditions (10 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (β) conditions (2 ng/ml TGF-β1, 20 ng/ml IL-6, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb), TH17 (23) conditions (20 ng/ml IL-6, 20 ng/ml IL-1β, 20 ng/ml IL-23, 10 µg/ml anti–IL-4 mAb, and 10 µg/ml anti–IFN-γ mAb).

extract_protocol:
Naive CD4+ T cells from control and miR-21-/- mice were differentiated under pathogenic TH17 (23) differentiation condition. Total RNA was prepared from these cells using Trizol reagent (Invitrogen). RNA-seq libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina). For GFP+ TH17 cells sorted from in vivo suspensions, 50,000 cells were resuspended in 700 ul Trizol reagent, total RNA was prepared by miRNeasy Micro Kit (Qiagen), RNA-seq libraries were prepared using SMART-Seq v4 Ultra Low Input RNA Kit (clontech). Sequencing was performed on an Illumina HiSeq X Ten System in a 150 bp/150 bp Paired end mode. ATAC-seq library preparations were performed as described(Buenrostro et al., 2013). In brief, 50,000 cells were washed in cold PBS and lysed. Transposition was performed at 37 °C for 30 min. After purification of the DNA with the MinElute PCR purification kit (Qiagen), DNA was amplified for 5 cycles. Additional PCR cycles were evaluated by real time PCR. Final product was cleaned by Ampure Beads at a 1.5× ratio. Libraries were sequenced on a HiSeq X Ten System in a 150 bp/150 bp Paired end mode.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TH17(23) cells


title: Pt-msx1_st5_rep3_d24

description:
HTseq_count_per_gene_aug3.txt
HTseq_count_per_gene_aug3_RPKM.txt
DEG_msx_st5.txt

value: late stage 5


title: RNAseq_A2780_lowISL1sorted


title: Control RNA-seq rep1


title: Pt-msx1_st5_rep3_d-3

value: untreated