title: ERB-transduced-II (P5501-210)

description:
Estrogen Receptor Beta transduced cells
count_table.txt
fpkm_table.txt
P5501-210


title: Jmjd6 KO 4

status: Public on Mar 05 2021

type: SRA

city: London

first: Kamil

middle: R

last: Kranc

address: Charterhouse Square

country: United Kingdom

institute: Queen Mary University of London

library_source: transcriptomic

data_processing:
reads were aligned to the mm10 genome using hisat-2.1.0
Genome_build: mm10
Supplementary_files_format_and_content: a counts table is provided for RNA-seq data

molecule: polyA RNA

organism: Mus musculus

growth_protocol: deletion of a floxed Jmjd6 was induced in haematopoietic lineages by a cell type specific Cre

extract_protocol:
sorted Lin-Sca1+Kit+ (LSK) haematopoietic stem and progenitor cells
RNA-seq from bulk cells

tag: genotype/variation

value: Jmjd6 KO


title: Jmjd6 KO 3

source_name: Lin-Sca1+Kit+ (LSK) haematopoietic stem and progenitor cells

treatment_protocol: deletion of a floxed Jmjd6 was induced in haematopoietic lineages by a cell type specific Cre


title: ERB-transduced-I (P5501-209)

city: Solna

first: Cecilia

last: Williams

address: Tomtebodav 23

department: Protein Science

country: Sweden

institute: KTH Royal Institute of Technology

description:
Estrogen Receptor Beta transduced cells
count_table.txt
fpkm_table.txt
P5501-209

data_processing:
Mapping:  Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37.
Merging:  Bamfiles from samples run on different lanes were merged with samtools.
Sorting and Marking duplicates:  Merged bam files were sorted and duplicates removed using picard-tools/1.29.
Counts for genes:  Gene counts were generated using htseq/0.6.1 on bam files with duplicates included.
FPKMs for genes and transcripts: FPKMs for genes and transcripts were generated using  cufflinks/2.1.1 on bamfiles with duplicates included.
Genome_build: Homo Sapiens, GRch37
Supplementary_files_format_and_content: tab-delimited text files with counts and FPKM values for each sample and each gene.

molecule: total RNA

organism: Homo sapiens

source_name: Colon

growth_protocol: DMEM/10 FBS media was used to culture both cell lines

extract_protocol:
Qiagen RNAasy kit. We have done an extra on-colum DNAase treatment step.
RNA libraries for sequencing were prepared using TruSeq Stranded mRNA Sample prep kit with 96 dual indexes (Illumina, CA, USA). The protocol was modified and automated using an Agilent NGS workstation (Agilent, CA, USA) using purification steps as described in S.Lundin et al. 2011 PLoS ONE.

tag: cell line

tag: erb transduced

value: Yes

tag: transduced with empty vector

value: No

tag: treatment

value: No treatment


title: Jmjd6 KO 2


title: Empty_vector-transduced-II (P5501-208)

description:
Cells transduced with empty vector
count_table.txt
fpkm_table.txt
P5501-208


title: Small_intestine_tissue_MVMi-SD45S08

city: New York

first: Simone

last: Dallari

state: NY

address: 550 1st Ave

country: USA

institute: New York University Grossman School of Medicine

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the mm10 reference genome
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample, obtained from DESeq2

source_name: Small Intestine

growth_protocol: Piece of colonic (colon mid-section) and small intestinal (duodenum, jejunum, and ileum mid-section combined) were collected, snap frozen, and conserved at -80 until extraction

extract_protocol:
RNA for each sample was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
RNA libraries were prepared using standard CelSeq2 protocols.

treatment_protocol: Germ free mice were left uninfected or mono infected with several enteric viruses. Tissues were collected 28 days post infection

tag: tissue

value: Small Intestine

tag: infection

value: MVMi


title: Small_intestine_tissue_MVMi-SD24S08


title: Jmjd6 KO 1


title: Small_intestine_tissue_MVMi-SD24S07


title: ERB-transduced-II (P5501-206)

description:
Estrogen Receptor Beta transduced cells
count_table.txt
fpkm_table.txt
P5501-206


title: wildtype 4

value: wild type


title: ERB-transduced-I (P5501-205)

description:
Estrogen Receptor Beta transduced cells
count_table.txt
fpkm_table.txt
P5501-205


title: Small_intestine_tissue_MVMi-SD45S09


title: Parental cell line-II  (P5501-204)

description:
untransduced parental cell line
count_table.txt
fpkm_table.txt
P5501-204


title: Small_intestine_tissue_MuAstV-SD42S12

value: MuAstV


title: Parental cell line-I  (P5501-203)

description:
untransduced parental cell line
count_table.txt
fpkm_table.txt
P5501-203


title: Small_intestine_tissue_MVMi-SD45S07


title: wildtype 2


title: Small_intestine_tissue_MuAstV-SD42S10


title: Small_intestine_tissue_MuAstV-SD42S11


title: Parental cell line-I  (P5501-201)

description:
untransduced parental cell line
count_table.txt
fpkm_table.txt
P5501-201


title: Small_intestine_tissue_MuAstV-SD31S10


title: Empty_vector-transduced-I (P5501-207)

description:
Cells transduced with empty vector
count_table.txt
fpkm_table.txt
P5501-207


title: wildtype 1


title: Small_intestine_tissue_MVMi-SD24S06


title: wildtype 3


title: Small_intestine_tissue_MuAstV-SD31S09


title: PLAC_seq_Ebf1_KO_H3K4me3_rep4

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

institute: Lund University

library_source: genomic

data_processing:
Library strategy: PLAC-seq
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NextSeq 500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings. Further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using DEseq2.
ChIP-sequencing and data analysis: For ChIP-Seq samples, Libraries were single-end sequenced on a NextSeq 500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ChIP seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010) to find peaks,  perform motif-enrichment, and  other analyses in the study. Peaks were identified using with findPeaks.pl against a matched input control using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility of the duplicate experiments was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB et al., 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr).
PLAC-sequencing and data analysis: For PLAC-samples were paired end sequenced on a NextSeq500. PLAC-seq experiments were carried out in triplicates and quadruplicates, respectively. To maximize read-depth prior to analysis, fastq-files containing both read 1 and read 2 with their counterparts from the replicates were combined for a total of 517M Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al., 2015), using Bowtie2 (2.3.5) (Langmead and Salzberg, 2012; Langmead et al., 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Approximately, 230M (Wt pro-B) and 250M (Ebf1-/- pro-B) valid interaction pairs were generated.    The valid interaction files, the mm10 MboI restriction digestion map and a bed file containing the mm10 coordinates for the Myc gene’s TSS extended 2500 bp in both directions, were used as an input to the make_viewpoints.py script from the HiC-Pro pipeline. The resulting Myc centric virtual 4C bedGraph files were sorted with the bedtools sort command and uploaded to the UCSC genome browser for visualization.  Comment:  Average insert size and standard deviation N/A of the HiC data-type because they are sequenced in paired-end mode but then each read is aligned in single-end mode and later paired bioinformatically.
Genome_build: mm10
Supplementary_files_format_and_content: txt files representing IDR peaks (ChIP-seq), raw read count (RNA-seq and virtual 4C interactions (PLAC-seq)

molecule: genomic DNA

source_name: Ebf1-KO Fetal liver

growth_protocol:
Cell culture:  Fetal liver cells were purified from wild-type, Ebf1 deficient, or Pax5 deficient fetus, and expanded on OP9 stromal cells in Opti-MEM supplemented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol, 10ng/ml KIT ligand, 10ng/ml Fms-like tyrosine kinase 3 ligand, and 10ng/ml Interleukin-7. Murine pre-B cell line, 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol.
Infection:  Retronectin coated 24-well plates were pre-inkubated with 500ul viral supernatant. Cells were harvested,  resuspended 500ul media and added to 500μl of virus supernatant. Polybrene was added to supernatant at concentration of 0.5μg/ml. Spin-infection was performed at 1800xg, for 90min at 32°C.
230-238-cells were cultured in RPMI1640 with UltraGlutamine (Lonza, Basel, Swiss) supplemented with 10% heat-inactivated FCS, 20mM HEPES, 50mg/ml Gentamicin and 50mM β-ME.

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations. For ChIP-seq: Cells for transcription factor ChIP were fixed at room temperature with DSG for 30 min followed by 1% formaldehyde/PBS for 10 minutes. Reaction was then quenched by adding glycine to 0.125 M. Cells were washed  pelleted and snap-frozen and stored at -80°C until ready for ChIP or used immediately for ChIP.   Nuclei for ChIP were isolated  by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8))+ PIC and sonicated on a Bioruptor (Diagenode) max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted 5X in Dilution Buffer (1% Triton, 2mM EDTA, 150 mM NaCl, 20 mM Tris-HCl (pH 8) + PIC). Anti-bodies were hybridized to ProteinA or G Dynabeads®  (LifeTechnologies)  and added to the diluted chromatin. ChIP was performed over night at 4°C. and subsequently washed (1 time with 500 μl Low Salt Immune Complex Wash Buffer, 1 time with 200 μl High Salt Immune Complex Wash Buffer, 1 time with 200 μl LiCl Immune Complex Wash Buffer, 2 times with 200 μl TE buffer) and eluted for 4 h at 65°C ( 20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, 100 μg RNase A and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator before ChIP-seq libary preparation.PLAC-seq was carried out similar to previously reported (Ahsberg et al., 2019) with minor modifications. 15M FL derived Wt or Ebf1-/- pro-B cells that had been cross-linked with 1% formaldehyde for 5 min were thawed on ice for 5 minutes, re-suspended in ice cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40 and  Roche protease inhibitors – 11697498001 (PIC)) and incubated on ice for 15 min. Samples were spun for 5 min @ 4°C at 2,500 x g and cell pellet was washed in ice-cold lysis buffer + PIC. The pellet was resuspended in 0.5% SDS and incubated @ 62°C for 10 min. The SDS reaction was quenched by addition of water and 10% Triton X-100 followed by 15 min incubation @ 37°C. The samples were digested with 40U MboI restriction enzyme with addition of 25 µl NEBuffer2 followed by 2h incubation @ 37°C with shaking (900 RPM). After restriction enzyme digestion the samples were incubated for 20 min @ 62°C to inactivate MboI followed by a cool-down to RT. A fill in reaction was conducted using 0.3 mM Biotin-14-dATP (ThermoFisher, 19524016), 0.3 mM dCTP, 0.3 mM dTTP, 0.3 mM dGTP and 40U Klenow (NEB, M0210) @ 37°C for 1.5h with shaking (900 RPM). Next a Ligation master mix (1x T4 ligation buffer (NEB, B0202), 1% Triton-X 100, 120 ug BSA (NEB, B9000), 4000 U T4 DNA ligase (NEB, M0202)) was added and samples were incubated @ RT with rotation for 2h. The samples were centrifugated 2,500xg 5min @ 4°C, supernatant was removed and cell pellet was resuspended in 250 µl ChIP SDS-lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC followed by sonication on a Covaris ME220 for 6 min (Peak power = 75, cycles per burst = 1000, Duty Factor = 15%). Sheared chromatin was centrifuged for 10 min @ 4°C, 13000 rpm and supernatants were transferred to new tubes and diluted in 750 µl 1xHBSS + 1 ml 2x RIPA (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% sodium deoxycholate, 200 mM NaCl) + PIC. 1% input was removed from supernatant, and 10 µg H3K4-Me3 (Millipore, 07-473) antibody pre-adsorbed to 60 µl Protein-G dynabeads in PBS/0.5% BSA were added to the remaining supernatant and incubated @ 4°C overnight with rotation. Samples were washed as follows: 2 times with 1 ml Low Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton X-100, 2 mM EDTA, 50 mM Tris-HCl pH8, 150 mM NaCl), 2 times with 1 ml High Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton X-100, 2 mM EDTA, 50 mM Tris-HCl pH 8.0, 500 mM NaCl), 1 time with 1 ml LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% Igepal-CA630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), 2 times with 1 ml TE buffer (10 mM Tris–HCl, pH 8.0, 10 mM EDTA) followed by elution of chromatin from magnetic beads with two rounds of 100 µl elution buffer (1%SDS, 100 mM NaHCO3) with shaking (1500 RPM) @ RT. Supernatants were transferred to new tubes and chromatin complexes were reverse cross-linked overnight @ 65°C with the addition of 250 mM NaCl, 100 μg RNase A (ThermoFisher, EN0531) and 50 μg proteinase K (ThermoFisher, AM2546) followed by Zymo Research ChIP DNA Clean & Concentrator (BIOSITE-D5205) clean up. 25 μL of Streptavidin T1 beads (Thermo Fisher, 65601) were washed with Tween Wash Buffer (5 mM Tris-HCl pH 8, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20) then resuspended in 50 μL of 2x Biotin Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2M NaCl). Beads were added to the samples and incubated at room temperature for 15 minutes with shaking.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA). ChIP-Seq: Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures. Libraries were run on the Illumina NexSeq500.   For PLAC-seq libraries: After capture on magnetic beads, they were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 1x T4 DNA ligation buffer. Beads were collected on a magnet and resuspended on 100 µl end-repair mastermix (0.5 mM dNTPs (VWR, E636-40UMOLE), 12U T4 DNA Polymerase (NEB, M0203), 50U T4 Polynucleotide Kinase (NEB, M0201), 5U Klenow (NEB, M0210), 1x NEB T4 DNA ligase buffer) followed by incubation @ RT for 30 min with shaking (900 RPM). 300 µl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 1x NEB2 buffer. magnetic beads were collected on a magnet and resuspended on 100 µl A-tailing mastermix (0.5 mM dATP (ThermoFisher), 25U Klenow Exo- (NEB, M0212), 1x NEB2 buffer) and incubated @ 37°C for 30 min with shaking (900 RPM). 300 µl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 1x Fast-Link ligation buffer (Epicenter, LK0750H ) followed by NEXTflex DNA barcode ligation  (BIOO scientific) using the Fast-link ligation kit (Epicenter, LK0750H). 300 µl Tween Wash Buffer was added and beads were placed on a magnet and supernatant was discarded. Samples were washed twice by adding 500 μL of Tween Wash Buffer and incubated at 55°C for 2 minutes shaking followed by a 1 time wash in 100 µl 10mM Tris-HCl pH 8.0, resuspended in 45 µl and a 1:1000 dilution was made for qPCR determination of number cycles needed for final PCR amplification. After final PCR, T1 streptavidin beads were collected on a magnet, supernatant transferred to new tubes and Ampure XP beads (x0.8 sample volume) were used to clean up libraries. PLAC-seq libraries were subject to 2x 75 cycles of paired-end sequencing on a NextSeq500.

tag: strain background

value: fetal liver

tag: cell type

value: ProB

value: Cultured in Optimem +10% FBS, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol FL, KL, IL7 on OP9

tag: chip antibody

value: Rabbit anti H3K4-Me3 polyclonal (Millipore, 07-473)


title: Small_intestine_tissue_MuAstV-SD31S08


title: Parental cell line-II (P5501-202)

description:
untransduced parental cell line
count_table.txt
fpkm_table.txt
P5501-202


title: PLAC_seq_Ebf1_KO_H3K4me3_rep1


title: PLAC_seq_Ebf1_KO_H3K4me3_rep2


title: PLAC_seq_Ebf1_KO_H3K4me3_rep3


title: Small_intestine_tissue_MAdV2-SD39S04


title: PLAC_seq_WT_H3K4me3_rep3

source_name: Wt Fetal liver

value: Wt


title: PLAC_seq_WT_H3K4me3_rep2


title: Small_intestine_tissue_MAdV2-SD39S03


title: Small_intestine_tissue_MAdV2-SD39S05


title: 13501839 - ETT-CD2-2 vs ETT-C2-2

type: RNA

city: Lyon

first: Charles

middle: Patrick

last: Scutt

address: 46 allee d'Italie

department: RDP

country: France

institute: ENS de Lyon

description: Identification of target genes from three transcription factors involved in gynoecium development

hyb_protocol: ETT-C2-2 Cy5 / ETT-CD2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 620V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: flowers - Peet-based compost, hygrometry 55-75%, Temp. 15-20°C Light 12000-14000 lux

treatment_protocol: Name:CYC-2h_Gen45 - compound based treatment - compound addition,cycloheximide:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.

tag: Arabidopsis thaliana (columbia)  - dev.stage (Boyes et al. Plant Cell 2001):6.00

treatment_protocol: Name:DEX+CYC-2h_Gen45 - compound based treatment - compound addition,cycloheximide:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in both dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%) and cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.


title: 13688899 - ETT-CD2-4 vs ETT-C2-4

hyb_protocol: ETT-C2-4 Cy5 / ETT-CD2-4 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,500V,laser power 35%, Cy5:635nm,pmt voltage 500V,laser power 30%

tag: Arabidopsis thaliana (columbia)  mutant (35S::ETT-VP16GR) - dev.stage (Boyes et al. Plant Cell 2001):6.00


title: Small_intestine_tissue_MAdV2-SD26S07


title: PLAC_seq_WT_H3K4me3_rep1


title: 13501432 - ETT-CD2-3 vs ETT-C2-3

hyb_protocol: ETT-C2-3 Cy5 / ETT-CD2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%


title: 13501838 - ETT-C2-2 vs ETT-CD2-2

hyb_protocol: ETT-CD2-2 Cy5 / ETT-C2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RNA-seq_WT+pMiG_rep2.fastq.gz

description: Raw_reads_mm10_count_exons_condenseGenes_noadj_FL_WT_EKO_PKO_tranf_w_Ebf1_Pax.txt

data_processing:
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NextSeq 500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012),) with single read, standard settings. Further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using DEseq2.
ChIP-sequencing and data analysis: For ChIP-Seq samples, Libraries were single-end sequenced on a NextSeq 500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ChIP seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010) to find peaks,  perform motif-enrichment, and  other analyses in the study. Peaks were identified using with findPeaks.pl against a matched input control using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility of the duplicate experiments was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package (Li QB et al., 2011) (Karmel A. 2015. homer-idr: Second pass updated) according to (https://sites.google.com/site/anshulkundaje/projects/idr).
PLAC-sequencing and data analysis: For PLAC-samples were paired end sequenced on a NextSeq500. PLAC-seq experiments were carried out in triplicates and quadruplicates, respectively. To maximize read-depth prior to analysis, fastq-files containing both read 1 and read 2 with their counterparts from the replicates were combined for a total of 517M Trim Galore trimmed paired-end reads per sample. Reads were trimmed in pair-end mode with Trim Galore (0.6.4)(--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3) (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). Trimmed paired fastq reads were preprocessed through the HiC-Pro pipeline (v2.11.1) (Servant et al., 2015), using Bowtie2 (2.3.5) (Langmead and Salzberg, 2012; Langmead et al., 2009) for alignment against mm10 (GRCm38) reference genome, assigning mapped reads to a mm10 MboI restriction map followed by removal of PCR duplicates with Picard tools MarkDuplicates (2.21.4) (https://broadinstitute.github.io/picard/) and subsequently the generation of a list of valid interaction read pairs. Approximately, 230M (Wt pro-B) and 250M (Ebf1-/- pro-B) valid interaction pairs were generated.    The valid interaction files, the mm10 MboI restriction digestion map and a bed file containing the mm10 coordinates for the Myc gene’s TSS extended 2500 bp in both directions, were used as an input to the make_viewpoints.py script from the HiC-Pro pipeline. The resulting Myc centric virtual 4C bedGraph files were sorted with the bedtools sort command and uploaded to the UCSC genome browser for visualization.  Comment:  Average insert size and standard deviation N/A of the HiC data-type because they are sequenced in paired-end mode but then each read is aligned in single-end mode and later paired bioinformatically.
Genome_build: mm10
Supplementary_files_format_and_content: txt files representing IDR peaks (ChIP-seq), raw read count (RNA-seq and virtual 4C interactions (PLAC-seq)

value: Wt, transfected with a pMiG control vector


title: 13688900 - ETT-C2-4 vs ETT-CD2-4

hyb_protocol: ETT-CD2-4 Cy5 / ETT-C2-4 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Small_intestine_tissue_MAdV2-SD26S06


title: 13501431 - ETT-C2-3 vs ETT-CD2-3

hyb_protocol: ETT-CD2-3 Cy5 / ETT-C2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13488707 - CRC-C2-3 vs CRC-CD2-3

hyb_protocol: CRC-CD2-3 Cy5 / CRC-C2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RNA-seq_WT+pMiG_rep1.fastq.gz


title: Small_intestine_tissue_MAdV1-SD42S09


title: Small_intestine_tissue_MAdV2-SD26S05


title: RNA-seq_Pax5_KO+pMiG-Pax5_rep2

source_name: Pax5-KO Fetal liver

value: Pax5-KO, transfected with Pax5 DNA in a pMiG  vector


title: 13488706 - CRC-CD2-3 vs CRC-C2-3

hyb_protocol: CRC-C2-3 Cy5 / CRC-CD2-3 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RNA-seq_Pax5_KO+pMiG-Pax5_rep1


title: 13366273 - CRC-D2-2 vs CRC-M2-2

hyb_protocol: CRC-M2-2 Cy5 / CRC-D2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:Solvant-2h_Gen45 - compound based treatment - compound addition,water+silwet:time 2min . Mock treatment : dipping of inflorescences 2 min in solvant (Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 2 hours.

treatment_protocol: Name:DEX-2h_Gen45 - compound based treatment - compound addition,dexamethasone:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 2 hours.


title: Small_intestine_tissue_MAdV1-SD42S08


title: RNA-seq_Pax5_KO+pMiG-Ebf1_rep2

value: Pax5-KO, transfected with Ebf1 DNA in a pMiG  vector


title: MQ72_c20_2

type: genomic

city: Tampere

first: Dario

last: Greco

address: Arvo ylpön Katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 20 µg/mL of rCNT for 72 hours

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized according to manufacturer's instructions.

scan_protocol: Scanning was performed with Illumina iScan scanner.

data_processing: Preprocessing was performed with the R Bioconductor package minfi. Data was normalized using the SWAN normalization method. Unmethylated and methylated signals  were extracted from the normalized data.

label: Cy3, Cy5

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 72 hours, replicate 2

label_protocol: Labelling was performed following standard Illumina protocol.

growth_protocol: THP-1 cells (DSMZ ACC 16) were grown in culture flasks in  RPMI media ( supplemented with 10% FBS, 2 mM ultraglutamine and 1% penicillin-streptomycin, Gibco). Cells were PMA differentiated (50 nM) for 48 hours on six-well plates (1.0x10^6 cells/well). Media was replaced at 24 hours for fresh, complete RPMI including PMA. After 48h PMA was removed by fresh media without PMA.

extract_protocol: DNA was extracted from the lysates using the Maxwell RSC Cultured Cell DNA Kit and Maxwell RSC instrument following the manufacturer's instructions. (Promega Corporation)

treatment_protocol: Stock solution (1mg of rCNT /ml of RPMI) was vortexed and sonicated in a bath sonicator at RT for 3 x 15 min and diluted to final concentrations of 5, 10 and 20 µg/mL with complete RPMI. Dilutions were further vortexed and sonicated for 15 minutes prior to exposure. Cells were exposed to rCNT for 24, 48 or 72 hours. Untreated controls had the same treatment without the rCNTs. Exposures were performed as triplicates.

tag: dose

value: 20 µg/mL

tag: exposure time

value: 72 hours

tag: differentiation

value: PMA differentiated macrophage

value: rCNT

tag: position

tag: matrix


title: 13366272 - CRC-M2-2 vs CRC-D2-2

hyb_protocol: CRC-D2-2 Cy5 / CRC-M2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RNA-seq_Pax5_KO+pMiG_rep2

tag: genotype/variation

value: Pax5-KO, transfected with a pMiG control vector


title: 13371027 - CRC-M4-1 vs CRC-D4-1

hyb_protocol: CRC-D4-1 Cy5 / CRC-M4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:DEX-4h_Gen45 - compound based treatment - compound addition,dexamethasone:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 2 hours.

tag: Arabidopsis thaliana (columbia)  mutant (35S::CRC-VP16GR) - dev.stage (Boyes et al. Plant Cell 2001):6.00

treatment_protocol: Name:Solvant-4h_Gen45 - compound based treatment - compound addition,water+silwet:time 2min . Mock treatment : dipping of inflorescences 2 min in solvant (Silwet L77 0.01% and ethanol 0,1%). Plants are harvested after 4 hours.


title: Small_intestine_tissue_MAdV1-SD42S07

value: Small Intestine


title: 13366265 - CRC-D4-1 vs CRC-M4-1

hyb_protocol: CRC-M4-1 Cy5 / CRC-D4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: RNA-seq_Pax5_KO+pMiG-Ebf1_rep1


title: MQ48_ctrl_2_15

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 0 µg/mL of rCNT for 48 hours

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 48 hours, replicate 4

value: 0 µg/mL

value: 48 hours

tag: cell line

value: control


title: MQ24_c10_3

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 10 µg/mL of rCNT for 24 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 24 hours, replicate 3

value: 10 µg/mL

value: 24 hours


title: MQ24_ctrl_1_15

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 0 µg/mL of rCNT for 24 hours

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 24 hours, replicate 4


title: Small_intestine_tissue_GF-SD45S02

value: uninfected


title: Small_intestine_tissue_MAdV1-SD36S05


title: MQ24_c10_1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 24 hours, replicate 1


title: MQ72_c20_1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 72 hours, replicate 1


title: MQ48_c5_1

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 5 µg/mL of rCNT for 48 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 48 hours, replicate 1

value: 5 µg/mL


title: 13366264 - CRC-D2-1 vs CRC-M2-1

hyb_protocol: CRC-M2-1 Cy5 / CRC-D2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: aerial - Peet-based compost, hygrometry 55-75%, Temp. 15-20°C Light 12000-14000 lux


title: MQ48_c5_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 48 hours, replicate 3


title: RNA-seq_Ebf1_KO+pMiG-Pax5_rep2

value: fetal liver

value: Ebf1-KO, transfected with Pax5 DNA in a pMiG  vector

value: ProB

value: Cultured in Optimem +10% FBS, 25mM HEPES, 50μg/ml Gentamicin, 50μM β-mercaptoethanol FL, KL, IL7 on OP9


title: MQ24_ctrl_2

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 24 hours, replicate 2


title: Small_intestine_tissue_GF-SD45S01


title: RNA-seq_Ebf1_KO+pMiG-Pax5_rep1


title: MQ72_ctrl_1_15

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 0 µg/mL of rCNT for 72 hours

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 72 hours, replicate 4


title: RNA-seq_Pax5_KO+pMiG_rep1


title: MQ24_c20_3

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 20 µg/mL of rCNT for 24 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 24 hours, replicate 3

value: 20 µg/mL


title: Small_intestine_tissue_GF-SD42S03


title: MQ72_c10_1

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 10 µg/mL of rCNT for 72 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 72 hours, replicate 1

value: 72 hours


title: 13366246 - CRC-C4-1 vs CRC-CD4-1

hyb_protocol: CRC-CD4-1 Cy5 / CRC-C4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

treatment_protocol: Name:DEX+CYC-4h_Gen45 - compound based treatment - compound addition,cyclo+dex:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in both dexamethasone (once at 10(u)M diluted in Silwet L77 0.01% and ethanol 0,1%) and cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.

treatment_protocol: Name:CYC-4h_Gen45 - compound based treatment - compound addition,cycloheximide:quantity 0.01mM time 2min . Dipping of inflorescences 2 min in cycloheximide (twice at 10(u)g/ml (with 1h in between) diluted in Silwet L77 0.01% and DMSO 0.01%). Plants are harvested after 2 hours.


title: MQ72_c10_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 72 hours, replicate 2

value: PMA differentiated macrophage


title: RNA-seq_Ebf1_KO+pMiG-Ebf1_rep1

value: Ebf1-KO, transfected with Ebf1 DNA in a pMiG  vector


title: RNA-seq_Ebf1_KO+pMiG-Ebf1_rep2


title: Small_intestine_tissue_GF-SD42S01

source_name: Small Intestine


title: Small_intestine_tissue_GF-SD39S02


title: RNA-seq_Ebf1_KO+pMiG_rep2

source_name: Ebf1-KO Fetal liver

value: Ebf1-KO, transfected with a pMiG control vector


title: MQ48_c5_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 48 hours, replicate 2

value: rCNT


title: MQ48_ctrl_1

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 48 hours, replicate 1

value: 0 µg/mL


title: MQ72_ctrl_2

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 72 hours, replicate 2


title: MQ24_c10_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 24 hours, replicate 2


title: MQ48_ctrl_1_15

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 48 hours, replicate 3

value: 48 hours


title: Small_intestine_tissue_GF-SD33S02

value: Small Intestine


title: 13366263 - CRC-M2-1 vs CRC-D2-1

hyb_protocol: CRC-D2-1 Cy5 / CRC-M2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13366243 - CRC-CD4-1 vs CRC-C4-1

hyb_protocol: CRC-C4-1 Cy5 / CRC-CD4-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MQ24_c20_1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 24 hours, replicate 1


title: Small_intestine_tissue_GF-SD26S02


title: Small_intestine_tissue_GF-SD31S02


title: RNA-seq_Ebf1_KO+pMiG_rep1


title: MQ24_c5_1

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 5 µg/mL of rCNT for 24 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 24 hours, replicate 1


title: 13366274 - CRC-C2-2 vs CRC-CD2-2

hyb_protocol: CRC-CD2-2 Cy5 / CRC-C2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: MQ48_c20_2

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 20 µg/mL of rCNT for 48 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 48 hours, replicate 2


title: Small_intestine_tissue_GF-SD24S02


title: 13365878 - CRC-CD2-2 vs CRC-C2-2

hyb_protocol: CRC-C2-2 Cy5 / CRC-CD2-2 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13300949 - CRC-CD2-1 vs CRC-C2-1

hyb_protocol: CRC-C2-1 Cy5 / CRC-CD2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: Small_intestine_tissue_CW3-SD31S07


title: EMs rep2

city: Xiamen

first: Junzui

last: Li

address: Xiamen University

country: China

institute: Xiamen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM 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: Ensembl_release95
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Granulosa cells

extract_protocol:
[The collection and purification of GCs]  On the oocyte retrieval day, we collected GCs from patient follicular fluid. Only clear follicular fluid without blood or flushing solution was collected. Each follicular fluid sample in 15-ml disposable sterile tube was immediately centrifuged at 1000r/min for 10min. After removing the supernatant, the cellular precipitate was mixed 1:1 with PBS buffer, then was slowly added to the upper layer of 45% PercollTM (GE Healthcare, Sweden) separation solution, 1000 r/min, centrifugation for 20 min. then the middle ring-like layer (GCs) was collected. GCs from each participant were stored at -80°C for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
[Patients history]  The study was approved by the ethics committee of the First Affiliated Hospital of Xiamen University. Also, written informed consent was obtained from patients who met the eligibility criteria before oocyte retrievals.We enrolled a total of 6 infertile patients (3 infertile patients with ovarian endometriosis and 3 normo-ovulatory patients with tubal factor infertility) who underwent ovarian stimulation for IVF at the ART Center (the First Affiliated Hospital of Xiamen University, Xiamen), between November 2018 and December 2018.
[Ovarian stimulation protocols]  All endometriosis patients and the control group underwent improved long protocol, which was injected with long-acting GnRH agonist (Duffelin, ipson biotechnology, France) on the 2nd to 4th day of the menstrual cycle. The dose of GnRH agonist may differ depending on the patient individual differences. After 28 day~35 day, the hormone level and ultrasonic were measured, and Gn was started after reaching the down-regulation standard. The successful down-regulation standard was as follow: serum FSH < 5U/L, LH < 5U/L, serum E2 < 183.5 pmol/L, progesterone (P) < 3.18 nmol/L, ultrasonography showed endometrium thickness < 5mm, follicle diameter < 10 mm in both ovaries. In the process of controlled ovarian stimulation, the starting dose (150 ~ 300U) of Gn (rhFSH, merck serono, Germany) was determined according to the ovarian responsiveness, BMI and previous ovulation induction of the patients. When the follicle diameter ≥18mm dominated the follicle by 50%-60%, follicular maturation was triggered via an injection of 5000–10,000IU of hCG (Lizhu pharmaceutical, China), and the oocyte was retrieval after 38h.

tag: condition

value: endometriosis-related infertility

value: GC


title: MQ24_c5_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 24 hours, replicate 3

value: 24 hours

tag: treatment


title: ChIP-seq_230_238_a_EBF1_rep2

source_name: 230-238 murine PreB celline

value: 230-238 murine PreB celline

tag: cell line background

value: Abelson transformed PreB cell-line

value: PreB

value: Cultured in RPMI1640 + UltraGlutamine +10% FBS, 20mM HEPES, 50ug/ml Gentamicin and 50uM β-ME.

value: Rabbit anti-Ebf1 polyclonal IgG (Millipore, ABE1294)


title: MQ72_c10_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 72 hours, replicate 3

value: 10 µg/mL


title: Small_intestine_tissue_CW3-SD31S06

tag: tissue

tag: infection


title: ChIP-seq_230_238_Input

tag: cell type


title: ChIP-seq_230_238_a_EBF1_rep1

tag: chip antibody


title: WT.T5 scRNA

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

data_processing:
fastqs were processed using McCaroll lab core computational protocol with a custom genome (mm10 plus Trinity assemblies of transgene sequences) and gene annotation (gencode vM14 plus)
count matricies were read into R and merged into a single object for each experiment
Genome_build: custom mm10+PYMT
Supplementary_files_format_and_content: data was exported in 10X style file formats (mtx,features and barcodes)

source_name: Tumour Cells

growth_protocol: The model was treated as previously published (PLoS Biol 2015, 13:e1002330). All mice of this study are in a pure FBV/n background with more than 20 generations of backcrossing. To promote tumour progression, ELF5 expression was specifically induced in mammary epithelial cells since puberty (6 weeks-old) through doxycycline containing food . At ethical endpoint (7-13% tumour/body weight) mice were euthanized and tumours harvested and processed for single cell digestions

extract_protocol:
Cells were captured using the microfluidic devices described for Dropseq following the Online Drop-seq Laboratory Protocol version 3.1 (www.mccarrolllab.com/dropseq).
The tagmented and multiplexed cDNA libraries were sequenced in Nextseq 500 using Nextseq500 High Output v.2 kit (75 cycles, Illumina Cat# FC-404-2005) following Macosko et al. recommendations with the following modifications. Drop-seq denatured libraries were loaded at 1.3pM final concentration and were spiked in with 10% of 1.8pM PhiX Control v3 (Illumina Cat# FC-110-3001).

tag: genotype

value: MMTV-PyMT

value: untreated


title: 13275784 - CRC-C2-1 vs CRC-CD2-1

hyb_protocol: CRC-CD2-1 Cy5 / CRC-C2-1 Cy3 : 30pmol. Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: EMs rep1


title: TFI rep3

value: tubal factor infertility


title: Small_intestine_tissue_CW3-SD26S09


title: EMs rep3


title: WT.T4 scRNA


title: TFI rep2


title: Small_intestine_tissue_CW3-SD26S08


title: MQ48_c20_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 48 hours, replicate 3

value: 20 µg/mL

value: PMA differentiated macrophage


title: WT.T3 scRNA


title: Small_intestine_tissue_CR6-SD39S07


title: Small_intestine_tissue_CR6-SD39S06


title: WT.T2 scRNA


title: Pol2_mock_infected_cells_Rep2

city: Chicago

first: Mary

last: Hummel

state: IL

address: 303 E. Chicago Ave

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned to the reference genome using Bowtie2 version 2.2.6
bigWig files were created using HOMER
Genome_build: hg19
Genome_build: HCMV EF999921.1 [HCMV genome fa and gtf files for alignment of bigwig files are available at https://github.com/Mary-Hummel/HCMV-TB40-E-GFP-reference-genome.git]
Supplementary_files_format_and_content: bigWig files

source_name: Pol2_mock infected cells

growth_protocol: Kasumi-3 were grown in RPMI-1640 medium (ATCC 30-2001) supplemented with 20% fetal bovine serum (Corning) and 1,000 Units/ml Penicillin-Streptomycin (Gibco)

extract_protocol:
After fixation, cells were lysed and sonication with Covaris Focused-ultrasonicator at 10% Duty Cycle, 140 peak, 200 cycles per burst, 360 seconds. ChIP was performed by incubating the sonicated sample with Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (D5E4) XP Rabbit mAb #8173 (Cell Signaling Technologies) and the protein A/G agarose beads. Beads were washed and eluted in 200μl of elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, 1.0% SDS). The eluates were de-cross-linked and the DNA purified using the Qiagen PCR purification kit.
Libraries were prepared with the KAPA HTP Library Preparation Kit multiplexed with NEXTflex DNA Barcodes (Bio Scientific) and size selected with AMPure XB beads (Beckman Coulter) to have fragments 250-450 bp in length. Library quality control was assessed using Bioanalyzer High Sensitivity DNA Analysis kit (Agilent) and sequencing was performed with Illumina NextSeq technology (50bp single- end reads).

treatment_protocol: Kasumi-3 were infected with TB40/E wtGFP strain of HCMV at MOI 1 or mock-infected. Extracellular virus was inactivated at 24 hours post infection. HCMV-infected cells were sorted for GFP expression and live cells. Mock-infected cells were sorted for live cells. Cells were then fixed with 1% of Formaldehyde in PBS fand quenched with 0.125 M glycine.

value: live mock-infected, 24hpi

value: Rpb1 NTD (D8L4Y) Rabbit mAb #14958 (Cell Signaling Technologies)


title: WT.T1 scRNA


title: Pol2_mock_infected_cells_Rep1


title: Small_intestine_tissue_CR6-SD33S10

source_name: Small Intestine

value: Small Intestine


title: ELF5.T6 scRNA

value: doxycycline


title: input_mock_infected_cells_Rep2

source_name: input_mock infected cells


title: Small_intestine_tissue_CR6-SD33S09


title: input_mock_infected_cells_Rep1


title: TFI rep1

value: GC


title: Small_intestine_tissue_CR6-SD24S09


title: ELF5.T5 scRNA


title: Small_intestine_tissue__MDF-SD39S10

value: MDF


title: ELF5.T4 scRNA


title: ELF5.T3 scRNA


title: BS WT d3 vs BS UIS12 d3

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: polarity (+)

hyb_protocol: Microarrays were done according to the supplier’s protocol (Agilent Technologies) using the SSC wash protocol.

scan_protocol: Scanning of microarrays was performed with 5 µm resolution using a DNA microarray laser scanner (Agilent Technologies).

data_processing: Raw microarray image data were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.5.1, Agilent). The extracted MAGE-ML files were analyzed with the Rosetta Resolver Biosoftware (Rosetta Biosoftware).

organism: Plasmodium berghei

source_name: mixed blood stages

label_protocol: RNA labeling was performed with the Quick Amp Fluorescent Linear Amplification Kit (Agilent Technologies) according supplier's instructions.

growth_protocol: Parasites were P. berghei strains ANKA cl507.

extract_protocol: Total RNA was isolated by the Trizol (Invitrogen) method following the manufacturer´s protocol.

treatment_protocol: P. berghei parasites were maintained in C57BL/6 and NMRI mice. Mixed blood stages were isolated from whole blood. The samples were monitored using Giemsa stained blood smears.

value: wild type

tag: day

tag: strain

value: NMRI

value: UIS12 knock out

tag: tag


title: ELF5.T2 scRNA


title: Lung tissue - Bleomycin_rep2

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

institute: The First Affiliated Hospital of Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software.
RNAs differential expression analysis was performed by DESeq2 software between two different groups. The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute log2(fold change) ≥1 were considered differentially expressed genes/transcripts.
Genome_build: Rnor_6.0(Ensembl_release97)
Supplementary_files_format_and_content: tab-delimited text files include normalized FPKM values and raw fragment counts for each Sample

organism: Rattus norvegicus

source_name: Lung tissue

extract_protocol:
Total RNAs were isolated from lung using TRIzol (Invitrogen, Carlsbad, CA, USA), then the mRNAs were enriched by Oligo(dT) beads (Epicentre). The enriched mRNAs were fragmented into short fragments using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, adenylated, and ligated to Illumina sequencing adapters.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: On day 0, two rats were treated with bleomycin (5 mg/kg, 0.2mL) by a single intratracheal injection, and other two rats served as controls were given equal volume of normal saline. All rats were sacrificed on Day 28 and lung tissues were collected.

value: SD rat

value: lung

tag: bleomycin

value: with


title: Small_intestine_tissue__MDF-SD36S10


title: BS WT d7 vs BS UIS12 d7

description: polarity (+)


title: Lung tissue - Bleomycin_rep1


title: 4T1_IgG_Ms Control

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

data_processing:
[RNA-seq]  mRNA samples were pooled and sequenced on HiSeq2500 with Illumina TruSeq V4 chemistry. The samples have yields between 60 to 95 million reads. Pass filter reads with base call quality of Q30 or above are 94% or higher for all samples. Both reads of the samples were trimmed for adapters and low quality bases using Trimmomatic software. Total (primary) alignment with the reference genome (mm9) is above 87% with the STAR aligner. RNA mapping statistics are calculated using Picard software. The samples have less than 2% ribosomal reads. Percent coding bases are between 59-61% and there are 83-86% mRNA bases. Library complexity is measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The samples have above 77% non-duplicated reads.
[ChIP-seq]  ChIP samples were pooled and sequenced on Nextseq run using TrueSeq v2 chemistry single end sequencing. All the samples have percent of Q30 bases above 92%. All the samples have yields between 37  and 100 million pass filter reads. Samples were trimmed for adapters using trimmomatic software before the alignment. The trimmed reads were aligned with Mouse - mm10 reference using Bowtie2 alignment. Overall alignment percentage for the samples is 88%. Uniquel alignment is above 53%. There are 2 to 24% of unmapped reads. Library complexity is measured by uniquely aligned reads using picard’s markduplicate utility. All the samples have library complexity with percent non-duplicated reads ranging from 17 to 86%.
Genome_build: mouse mm10 for Chipseq, mm9_ensembl_ncbim37 for RNAseq
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample or peak in bed file.

growth_protocol: 4T1 cells are grown in DMEM containing 9% fetal bovine serum, 1% penicillin/streptomycin and1% L-glutamine.

extract_protocol:
[RNA-seq]  Total RNA was isolated from 4T1 cells using RNeasy mini kit (Qiagen) according to manufacturer's instructions
[ChIP-seq]  Chromatin was extracted from 4T1 cells using ChIP-IT Express Enzymatic Shearing kit (Active Motif) according to manufacturer's instructions.
[RNA-seq]   Library was prepared using TruSeq stranded mRNA library prep kit (Illumina).
[ChIP-seq]   Library was prepared using TruSeq ChIP library prep kit (Illumina).

tag: tumor type

value: Spontaneous mammary primary tumor

value: BALB/cJ

tag: mouse id

value: Jackson Laboratory # 000651

value: Mouse IgG Control for NPC

value: Normal Mouse IgG (Santa Cruz Biotechnology, Cat. No. # sc-2025, Lot # K1017)


title: Lung tissue - Control_rep2

value: without


title: Colon_tissue_uninfected-SD45C03

source_name: Colon

value: Colon

value: uninfected


title: BS UIS12 d3 vs BS WT d3

description: polarity (-)

tag: genotype/variation


title: BS UIS12 d7 vs Bs WT d7

description: polarity (-)


title: ELF5.T1 scRNA

value: doxycycline


title: Colon_tissue_uninfected-SD45C01


title: Small_intestine_tissue__MDF-SD39S08

value: Small Intestine


title: MQ48_ctrl_2

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 48 hours, replicate 2

tag: dose

value: 0 µg/mL

tag: exposure time

value: 48 hours

tag: differentiation

value: PMA differentiated macrophage

value: control

tag: position

tag: matrix


title: 4T1_IgG_Rb Control

tag: cell line

tag: treatment

value: Rabbit IgG Control for NUP210

value: Rabbit mAb IgG (Cell Signalling Technology, Cat. No. # 3900S, Lot # 34)


title: Colon_tissue_uninfected-SD42C03

tag: tissue

tag: infection


title: MQ72_c20_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 72 hours, replicate 3

value: 20 µg/mL

value: 72 hours

value: rCNT


title: Colon_tissue_uninfected-SD39C01


title: NUP210_sg-Ctrl

value: Spontaneous mammary primary tumor

value: BALB/cJ

value: Jackson Laboratory # 000651

value: sgRNA non-targeting control

tag: chip antibody

value: NUP210 antibody (Bethyl Laboratories, Cat. No. # A301-795A, Lot # N/A)


title: MQ24_ctrl_1

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 24 hours, replicate 1

value: 24 hours


title: MQ72_c5_1

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 5 µg/mL of rCNT for 72 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 72 hours, replicate 1

value: 5 µg/mL


title: Lung tissue - Control_rep1

value: SD rat

value: lung

value: without


title: MQ72_c5_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 72 hours, replicate 3

value: PMA differentiated macrophage


title: Input_Tbr2_neg_TSA

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling and fastq.gz conversion were performed using Illumina pipeline scripts.
Reads were mapped to mouse genome mm10.
In ChIP-Seq duplicate reads were filtered out by "rmdup" command of samtools.
In RNA-Seq reads were counted using FeaturesCount. In ChIP-Seq peaks were called using MACS2 with q-value < 0.1.
Genome_build: mm10
Supplementary_files_format_and_content: Peak files and count files.

source_name: Embryonic cortex Tbr2- cells

extract_protocol:
RNA was isolated using TRIZOL from whole tissue. Chromatin immunoprecipitation was performed either from fixed nuclei sorted by FACS or from whole tissue.
Libraries for ChIP-Seq were prepared using NEBNext Ultra DNA Library Preparation Kit for Illumina. Libraries for RNA-Seq were prepared using Illumina TruSeq RNA Sample Preparation v2 Kit.

tag: age

tag: agent

value: HDAC inhibitor (TSA)

tag: genotype


title: KYSE150_BRDT-OE_3

city: Shenzhen

first: Xin

last: Wang

address: 1068, Xueyuan Road

department: Institute of Synthetic Biology

institute: Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences

data_processing:
Alignment was done using STAR (2.6.0).
Feature counting was performed using HTSeq (0.11.2).
Differential gene analysis and counts normalization were done using DEseq2 (1.24.0).
Genome_build: hg38
Supplementary_files_format_and_content: Text files containing gene counts matrix.

source_name: Esophageal squamous cell carcinoma

growth_protocol: KYSE180 and TE6 were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin. KYSE150 cells were  RPMI-1640 medium supplemented with 5% FBS, 1% Penicillin and Streptomycin.

extract_protocol:
RNA was isolated using QIAzol lysis reagent according to the manufacturer's manual.
RNA-seq libraries were constructed using Illumina TruSeq RNA library prep kit V2 according to the manufacturer’s manual.

treatment_protocol: Cells were transfected with siRNAs or plasmids as indicated.

value: ESCC cell line KYSE150

value: BRDT Over-expression


title: H3K4me3_sg-Ctrl

tag: strain

value: H3K4me3 antibody clone MC315 (Millipore, Cat. No. # 04-745, Lot # DAM1594220)


title: PBK_KD2_T59

city: Oslo

first: Biljana

last: Stangeland

address: Sognsvannsveien 20

department: Institute of Surgical Research

country: Norway

institute: Oslo University Hospital

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: glioblastoma stem like cells

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type

value: glioblastoma stem-like cell culture T59

value: shRNA construct 2


title: NS_T59

description: replicate 1

value: non-silencing shRNA construct


title: MQ24_c5_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 24 hours, replicate 2

value: rCNT


title: Input_Tbr2_neg_Vehicle

value: vehicle


title: Colon_tissue_uninfected-SD31C01

value: Colon

value: uninfected


title: H3K27me3_KO-N13

tag: tumor type

value: Spontaneous mammary primary tumor

value: BALB/cJ

tag: mouse id

value: Jackson Laboratory # 000651

value: Nup210 knockout (CRISPR/Cas9-mediated)

value: H3K27me3 antibody (Cell Signalling Technology, Cat. No. # 9733, Lot # 8)


title: MQ48_c10_2

description: DNA methylation of PMA differentiated THP-1 macrophages after exposure to 10 µg/mL of rCNT for 48 hours

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 48 hours, replicate 2

tag: dose

value: 10 µg/mL

value: 48 hours

value: PMA differentiated macrophage


title: KYSE150_BRDT-OE_2

value: ESCC cell line KYSE150

value: BRDT Over-expression


title: MQ72_ctrl_2_15

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 72 hours, replicate 3

value: 0 µg/mL

tag: exposure time

value: 72 hours

value: control


title: Colon_tissue_uninfected-SD30C01


title: KYSE150_cont_3

value: Control


title: Input_Tbr2_pos_Vehicle

source_name: Embryonic cortex Tbr2+ cells

value: vehicle


title: Input_Tbr2_pos_TSA

value: HDAC inhibitor (TSA)


title: MQ24_ctrl_2_15

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 24 hours, replicate 3

value: 24 hours

tag: differentiation


title: H3K9ac_Tbr2_neg_TSA_4

value: H3K9ac (Millipore 07-352)


title: 4T1_IgG_R_2 Control

value: Spontaneous mammary primary tumor

value: BALB/cJ

value: Rabbit IgG Control for H3K27me3 and H3K4me3

value: Rabbit mAb IgG (Cell Signalling Technology, Cat. No. # 3900S, Lot # 34)


title: PBK_KD1_T59

description: replicate 1

value: glioblastoma stem-like cell culture T59

value: shRNA construct 1


title: Colon_tissue_T1L-SD33C07

value: Colon


title: MQ72_ctrl_1

source_name: THP-1 monocytes differentiated into macrophages, control, 0 µg/mL, 72 hours, replicate 1

value: PMA differentiated macrophage

tag: position


title: MQ72_c5_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 5 µg/mL, 72 hours, replicate 2

value: 5 µg/mL

value: rCNT

tag: matrix


title: H3K27me3_sg-Ctrl

tag: cell line

value: Jackson Laboratory # 000651

value: sgRNA non-targeting control

value: H3K27me3 antibody (Cell Signalling Technology, Cat. No. # 9733, Lot # 8)


title: Colon_tissue_uninfected-SD26C01

value: uninfected


title: Colon_tissue_T1L-SD33C08


title: Colon_tissue_T1L-SD33C06


title: KYSE150_cont_1

value: ESCC cell line KYSE150

value: Control


title: H3K9ac_Tbr2_neg_TSA_2

value: H3K9ac (Millipore 07-352)

value: HDAC inhibitor (TSA)


title: KYSE150_cont_2


title: Colon_tissue_uninfected-SD33C01


title: H3K4me3_KO-N13

value: Spontaneous mammary primary tumor

value: BALB/cJ

tag: treatment

value: Nup210 knockout (CRISPR/Cas9-mediated)

value: H3K4me3 antibody clone MC315 (Millipore, Cat. No. # 04-745, Lot # DAM1594220)


title: MQ24_c20_2

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 24 hours, replicate 2

value: 20 µg/mL

value: 24 hours


title: Normal, Tongue Mucosa [RCC_OC_48]

city: Thiruvananthapuram

first: S

last: Kannan

state: Kerala

address: Medical College Campus

department: Cancer Research

country: India

institute: Regional Cancer Centre

description: miRNA Expression

hyb_protocol: The dried Cy3 labelled sample was re-suspended in nuclease-free water, denatured and mixed with the hybridizing buffer. Incubated the mixture at 100°C for 5 minutes and immediately snap cooled in ice. The hybridizing mixture was then pipetted onto the microarray slide installed in the hybridization cassette. Then the cassette was kept for hybridization in the rotary oven at 55°C for 20 hours. After the hybridization, slides were washed sequentially with pre-warmed gene expression washing buffers 1 &2.

scan_protocol: Hybridized microarrays were scanned with a DNA microarray scanner (Agilent G2565BA) and features were extracted using the Agilent Feature Extraction (AFE) image analysis tool (version A.9.5.3) with default protocols and settings.

data_processing: Data pre-processing and differential expression analysis of the microRNA and gene expression data were done in R using available Bioconductor AgiMicroRna package.The Total Gene Signal provided by the Agilent Feature Extraction image analysis software was used for data analysis. Data were normalized between arrays using the quantile method.The image analysis software attached a flag to each feature that identifies different quantification errors of the signal and which was used to filter out microRNAs data that do not reach a minimum quality.

source_name: Tissue-Normal-Tongue

label_protocol: The miRNA Complete Labeling Kit of Agilent was used to generates fluorescently-labeled miRNA with a sample input of 100 ng of total RNA. This method involved the ligation of one Cyanine 3-pCp molecule to the 3' end of a RNA molecule with greater than 90% efficiency.

extract_protocol: Total RNA was prepared from tissue samples using miRVana miRNA isolation kit as per manufacturer’s protocol. The quality and quantity of the isolated RNA was checked using UV-Vis Spectrophotometer.

treatment_protocol: After obtaining the signed informed consent from the eligible patients, incision biopsy of tumor was taken from each patient either during the investigative biopsy procedure or surgical excision of the lesion. Normal mucosa was also collected from patients undergoing oral and maxillofacial surgery for reasons other than cancer.

tag: tissue

value: Tongue Mucosa

tag: gender

value: Male


title: H3K9ac_Tbr2_neg_TSA_3

tag: chip antibody


title: MQ48_c10_1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 48 hours, replicate 1

value: 10 µg/mL

value: 48 hours

value: PMA differentiated macrophage

value: rCNT


title: KYSE150_BRDT-OE_1

value: BRDT Over-expression


title: KYSE150_siTP63_2

value: ESCC cell line KYSE150

value: p63 Knock-down


title: Colon_tissue_T1L-SD31C05

source_name: Colon

value: Colon

tag: infection


title: H3K9ac_Tbr2_neg_TSA_1

tag: age

value: H3K9ac (Millipore 07-352)

tag: agent

value: HDAC inhibitor (TSA)


title: KYSE150_siTP63_1

tag: genotype


title: Normal, Buccal Mucosa [RCC_OC_46]

description: miRNA Expression

source_name: Tissue-Normal-Buccal

value: Buccal Mucosa

value: Female


title: Colon_tissue_uninfected-SD42C01

value: uninfected


title: MQ48_c20_1

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 20 µg/mL, 48 hours, replicate 1

value: 20 µg/mL


title: Oral Cancer, Tongue Mucosa [RCC_OC_45]

description: miRNA Expression

source_name: Tissue-Cancer-Tongue


title: MQ48_c10_3

source_name: THP-1 monocytes differentiated into macrophages, rCNT, 10 µg/mL, 48 hours, replicate 3


title: Oral Cancer, Tongue Mucosa [RCC_OC_44]

description: miRNA Expression


title: Colon_tissue_T1L-SD31C03


title: KYSE150_siCont_2

source_name: Esophageal squamous cell carcinoma

value: Control


title: H3K9ac_Tbr2_neg_Vehicle_4

source_name: Embryonic cortex Tbr2- cells

value: vehicle


title: KYSE150_siCont_1


title: H3K9ac_Tbr2_neg_Vehicle_3


title: Colon_tissue_T1L-SD31C04


title: H3K9ac_Tbr2_neg_Vehicle_2


title: Colon_tissue_RRV-SD42C06

value: RRV


title: TE6_siTP63_2

value: ESCC cell line TE6


title: Colon_tissue_RRV-SD42C05


title: TE6_siTP63_1


title: H3K9ac_Tbr2_neg_Vehicle_1


title: NPC_sg-Ctrl

value: Spontaneous mammary primary tumor

tag: strain

value: BALB/cJ

value: Jackson Laboratory # 000651

value: sgRNA non-targeting control

value: Anti-Nuclear pore complex (NPC) proteins antibody MAb414 (Abcam, Cat. No. # ab24609, Lot # 439776)


title: Colon_tissue_RRV-SD42C04


title: Colon_tissue_RRV-SD33C05


title: Oral Cancer, Tongue Mucosa [RCC_OC_43]

description: miRNA Expression

value: Tongue Mucosa

value: Male


title: Oral Cancer, Tongue Mucosa [RCC_OC_42]

description: miRNA Expression


title: H3K9ac_Tbr2_pos_TSA_4

value: H3K9ac (Millipore 07-352)


title: TE6_siBRDT_1

value: BRDT Knock-down


title: H3K9ac_Tbr2_pos_TSA_3

value: HDAC inhibitor (TSA)


title: Colon_tissue_RRV-SD33C04

value: Colon


title: TE6_siCont_2


title: H3K9ac_Tbr2_pos_TSA_2


title: Oral Cancer, Tongue Mucosa [RCC_OC_39]

description: miRNA Expression


title: Colon_tissue_RRV-SD33C03


title: Oral Cancer, Buccal Mucosa [RCC_OC_38]

description: miRNA Expression

source_name: Tissue-Cancer-Buccal

value: Buccal Mucosa


title: H3K9ac_Tbr2_pos_TSA_1


title: Colon_tissue_MVMp-SD45C06

value: MVMp


title: TE6_siCont_1

value: Control


title: H3K9ac_Tbr2_pos_Vehicle_3

value: vehicle


title: TE6_siBRDT_2


title: Colon_tissue_MVMp-SD45C05


title: Oral Cancer, Tongue Mucosa [RCC_OC_37]

description: miRNA Expression

value: Female


title: Oral Cancer, Tongue Mucosa [RCC_OC_41]

description: miRNA Expression


title: Colon_tissue_MVMp-SD45C04


title: KYSE180_siTP63_1

value: ESCC cell line KYSE180

value: p63 Knock-down


title: Oral Cancer, Tongue Mucosa [RCC_OC_36]

description: miRNA Expression


title: KYSE180_siCont(TP63-KD)_2


title: KYSE180_siTP63_2


title: Oral Cancer, Buccal Mucosa [RCC_OC_47]

description: miRNA Expression


title: Normal, Tongue Mucosa [RCC_OC_40]

description: miRNA Expression


title: H3K9ac_Tbr2_pos_Vehicle_2


title: H3K9ac_Tbr2_pos_Vehicle_1


title: Colon_tissue_MVMp-SD30C05


title: RNA_Tbr2_neg_TSA_2


title: Colon_tissue_MVMp-SD30C04


title: KYSE180_siCont(TP63-KD)_1


title: Oral Cancer, Tongue Mucosa [RCC_OC_35]

description: miRNA Expression


title: Oral Cancer, Tongue Mucosa [RCC_OC_34]

description: miRNA Expression


title: KYSE180_siBRDT_3


title: Normal, Tongue Mucosa [RCC_OC_33]

description: miRNA Expression


title: RNA_Tbr2_neg_TSA_1


title: Colon_tissue_MVMp-SD30C03


title: Oral Cancer, Tongue Mucosa [RCC_OC_32]

description: miRNA Expression


title: RNA_Tbr2_neg_Vehicle_3


title: Oral Cancer, Tongue Mucosa [RCC_OC_31]

description: miRNA Expression


title: KYSE180_siBRDT_2


title: Colon_tissue_MVMi-SD45C09

value: MVMi


title: Normal, Tongue Mucosa [RCC_OC_30]

description: miRNA Expression


title: KYSE180_siBRDT_1


title: Colon_tissue_MVMi-SD30C08


title: Colon_tissue_MVMi-SD30C07


title: RNA_Tbr2_neg_Vehicle_1


title: RNA_Tbr2_pos_TSA_2


title: KYSE180_siCont(BRDT-KD)_2


title: RNA_Tbr2_pos_TSA_1


title: Normal, Tongue Mucosa [RCC_OC_29]

description: miRNA Expression


title: KYSE180_siCont(BRDT-KD)_1


title: Normal, Tongue Mucosa [RCC_OC_27]

description: miRNA Expression


title: Oral Cancer, Tongue Mucosa [RCC_OC_28]

description: miRNA Expression


title: KYSE180_H3K27acHiChIP_2

data_processing:
Alignment, reads filtering, quality check and contact matrix building were carried out using HiC-Pro pipeline.
FitHiChIP was used to identify long-range interactions. "Peak-to-All" mode was used.
Genome_build: hg19
Supplementary_files_format_and_content: Bedpe file containing long-range interactions.

growth_protocol: KYSE180 cells were cultured in RPMI-1640 medium supplemented with 10% FBS, 1% Penicillin and Streptomycin.

extract_protocol:
HiChIP was done as previously described (Mumbach et al., 2016) with minor changes.
Libraries were prepared using the KAPA HyperPrep kit according to the manufacturer’s manual.
HiChIP

treatment_protocol: Cells were transfected with non-targeting siRNA.

value: H3K27ac (Diagenode, C15410196)

value: non-targeting siRNA


title: RNA_Tbr2_pos_Vehicle_3


title: KYSE180_H3K27acHiChIP_1


title: KYSE180_Input

data_processing:
Alignment was done using Bowtie (1.0.0) with parameters: --chunkmbs 200 -a -m 1 --best --strata.
Sam/bam files were processed using samtools (1.9). Bigwig files were generated using bamCoverage from Deeptools (3.3.2).
Peaks were called using MACS2 (2.1.1). Broad peak calling mode was used for BRDT, BRD4 and histone modifications while narrow peak calling mode was used for p63.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing signal strength (normalized to RPKM) across genome.

extract_protocol:
Cells were crosslinked using 1% formaldehyde for 20 minutes. Subsequently, fixed cells were lysed, sheared and subjected to immunoprecipitation with respective antibodies. The immunocomplexes were captured and the DNA extraction was done using phenol/chloroform/isoamyl.
ChIP-seq libraries were constructed using the KAPA HyperPrep kit according to the manufacturer’s manual.


title: Oral Cancer, Tongue Mucosa [RCC_OC_26]

description: miRNA Expression


title: Colon_tissue_MVMi-SD24C07

data_processing:
Reads were mapped by Bowtie (v2.3.1) to the mm10 reference genome
Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.18.1)
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample, obtained from DESeq2

treatment_protocol: Germ free mice were left uninfected or mono infected with several enteric viruses. Tissues were collected 28 days post infection


title: Colon_tissue_MVMi-SD24C06


title: Colon_tissue_MuAstV-SD42C12

value: MuAstV


title: Oral Cancer, Buccal Mucosa [RCC_OC_24]

description: miRNA Expression


title: Colon_tissue_MVMi-SD30C06


title: KYSE180_siCont(BRDT-KD)_3


title: Normal, Tongue Mucosa [RCC_OC_23]

description: miRNA Expression

value: Tongue Mucosa


title: Oral Cancer, Buccal Mucosa [RCC_OC_25]

description: miRNA Expression

value: Male


title: KYSE180_H3K27me3


title: RNA_Tbr2_neg_Vehicle_2


title: Colon_tissue_MuAstV-SD42C11


title: Colon_tissue_MVMi-SD45C07


title: Hg13_A3

first: Yizhe

last: Tang

state: Guangdong Province

address: 3002 Sun Gang West Road, Futian District

institute: Shenzhen Second People's Hospital Department of Geriatrics

description:
HA
gene_count.txt
gene_fpkm.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: gene_fpkm.txt: Tab-delimited text file includes FPKM values for each Sample.
Supplementary_files_format_and_content: gene_count.txt: Tab-delimited text file includes raw gene counts for every gene and every sample.

source_name: hypothalamus

growth_protocol: Five-week-old ICR female mice were fed on a control low fat diet (LFD, 10% kcal fat) or high-fat high-sucrose (HFHS, 45% kcal fat with sucrose) diet for five weeks before mating. The dams were keeping with the same diets of the pregestational one during the gestation and lactation. Ten pups per litter were adapted on the day of production.

extract_protocol:
Mice hypothalamus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent with 3 ug of total RNA for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: During the postnatal (P) 4 to 16, pups from dams feeding with LFD or HFHS were peripherally injected with PBS (vehicle) or 4-PBA daily. Thus there were offspring from LFD fed dams receiving vehicle (referred to as LP) or from HFHS fed dams receiving vehicle (referred to as HP) or 4-PBA (referred to as HA).

value: ICR

value: wild type

value: hypothalamus

value: postnatal day 21

tag: Sex

value: male

value: HFHS lactation+neonatal 4-PBA


title: Hg43_A2

description:
HA
gene_count.txt
gene_fpkm.txt


title: KYSE180_H3K4me3

value: H3K4me3 (Diagenode, C15410003)


title: RNA_Tbr2_pos_Vehicle_2

value: vehicle


title: RNA_Tbr2_pos_Vehicle_1


title: Colon_tissue_MuAstV-SD31C10

value: Colon


title: KYSE180_H3K4me1

value: ESCC cell line KYSE180

value: H3K4me1 (Diagenode, C15410194)


title: KYSE180_H4K5ac

value: H4K5ac (Diagenode, C15410025)


title: Normal, Buccal Mucosa [RCC_OC_21]

description: miRNA Expression

value: Buccal Mucosa

value: Female


title: KYSE180_H3K9ac

value: H3K9ac (Diagenode, C15410004)


title: Colon_tissue_MuAstV-SD31C08

value: MuAstV


title: Hg43_P1

description:
HP
gene_count.txt
gene_fpkm.txt

value: HFHS lactation+neonatal PBS


title: Hg43_P2

description:
HP
gene_count.txt
gene_fpkm.txt

value: ICR


title: Colon_tissue_MDF-SD39C10

value: MDF


title: KYSE180_H3K27ac

value: H3K27ac (Diagenode, C15410196)


title: KYSE180_p63

value: p63 (Santa Cruz, sc-8431)


title: Colon_tissue_MDF-SD39C09


title: Oral Cancer, Buccal Mucosa [RCC_OC_20]

description: miRNA Expression


title: Colon_tissue_MuAstV-SD42C10