title: Evf2_WT_SMC3

city: Chicago

first: Jhumku

last: Kohtz

state: Illinois

address: 303 E Chicago

institute: Northwestern University

data_processing:
ChIP-seq read alignment : Raw sequencing reads for all the individual ChIP-seq datasets were aligned using bwa (Li and Durbin 2009) (version 0.7.12) mapper with the following settings ‘aln -t 8 samse’. Two mismatches relative to the reference were allowed and only retained the unique alignments with Phred quality score greater than 30 as done in the previous study (Marinov et al. 2014).  The datasets were mapped against mm9 version of the mouse genome.
ChIP-seq data analysis : Quality assessment :- ChIP-seq quality assessment was carried out using the strategy described by ENCODE ChIP-seq data analysis guidelines (Landt et al. 2012).  Cross-correlation analysis was performed using SPP package (Kharchenko et al. 2008) using the parameter ‘-s=-100:5:600’.
ChIP-seq data analysis : Peak calling:- “Irreproducible discovery rate” (IDR) frame-work to call the peaks against their respective input ChIP libraries using MACS2 program (Feng et al. 2011) as described in the ENCODE guidelines (Landt et al. 2012).  The final conservative set of peaks for all the samples were called across technical replicates with an IDR threshold of 0.01.  MACS2 peak calling was also performed using the following settings ‘-p 1e-3 --to-large --nomodel --shiftsize’ while rest of the parameters were set to their default mode.
Differential ChIP-seq analysis : Differential ChIP-seq analysis between two conditions was performed using MACS2 program (Feng et al. 2011) by treating one of the samples as the control for the other. The peak identification by MACS2 was carried out using the same parameter settings as previously described in ChIP-seq data analysis part. The cross-correlation analysis step (Kharchenko et al. 2008) was also performed on the respective datasets to determine the ‘--shiftsize’ parameter essential for peak identification by MACS2.
4Cseq reads mapping: 4C sequencing reads for all the samples were aligned on a reduced mm9 version of mouse genome using bowtie2 alignment program (Langmead and Salzberg 2012).  The reduced genome consists of only EcoR1 (+/- 50 base-pair) cut-sites. These EcoR1 sites were selected based on the presence of a second restriction enzyme cut-site i.e. DpnII, within its +/- 500 base-pairs. The 5’ bait sequence was removed before mapping on to the reduced genome. We allowed two mismatches outside the EcoR1 sequence in the reduced genome during mapping and only retained chromosome 6 specific unique alignments with Phred quality score greater than 30.
4Cseq differential data analysis: We performed a DESeq2 (Love et al. 2014) based differential contact count analysis on these sites to obtain condition specific significantly higher (p-adjusted value ≤ 0.05 and a log2 fold change ≥ 2 for Evf2+/+ or ≤ -2 for Evf2TS/TS) and conserved (p-adjusted value > 0.05 and an absolute log2 fold change < 2) 4C interaction sites. FourCSeq program (Klein et. al., 2015) was also used to find the differential sites. We applied FourCSeq on our Evf2+/+ and Evf2TS/TS 4Cseq samples and retrieved Evf2+/+ and Evf2TS/TS specific 4C interactions (p-adjusted value ≤ 0.05 and a log2 fold change ≥ 2) and Conserved interactions (p-adjusted value > 0.05 and an absolute log2 fold change < 2).  We only considered the interaction sites that had consistent labels from the two methods for further analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig format and contains scaled ChIP-seq signals, 4C counts, Peak qvalues

source_name: embryonic brain

extract_protocol:
Crosslinked ChIP: Whole ganglionic eminences were dissected from 10 Evf2+/+ and 10 Evf2TS/TS E13.5 embryos. Tissues were pooled for each genotype, triturated by pipetting, and filtered through a cell-strainer capped 5 ml polystyrene round- bottom tube (BD Falcon) to make single-cell suspensions. For anti-DLX and anti-H3K27ac ChIP cells were fixed in 1% paraformaldehyde for 10 min. For anti-SMC1 and anti-SMC3 ChIP cells were fixed in 1% paraformaldehyde for 90 min. Cells were lysed in SDS lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 10 mM EDTA) with protease inhibitors (11836153001, Roche). The lysates were sonicated with a Bioruptor Pico (Diagenode) for 10 cycles (30 sec On, 30 sec Off). The lysates were then centrifuged to pellet cellular debris and the supernatant collected for ChIP. 25 μg of chromatin were diluted 1:10 in RIPA Buffer (10mM Tris pH 7.6, 1mM EDTA, 0.1% SDS, 0.1% Sodium Deoxycholate, 1% Triton X-100) with protease inhibitors (B14002, Biotool). The chromatin was pre-cleared by rotating at 4°C with 50 μl of Protein G–Agarose beads (11719416001, Roche) for 1 hour. After centrifugation to pellet the beads, the supernatant was further pre-cleared by rotating at 4°C with 50 μl rabbit IgG conjugated Protein G–Agarose beads for 1 hour. The pre-cleared chromatin was incubated with rabbit IgG (2.5 μg), previously validated anti-pan-DLX (2.5 μg, (Feng et al. 2006; Bond et al. 2009; Cajigas et al. 2015)), anti-H3K27ac (1 μg, Abcam Ab4729), anti-SMC1 (1 μg, Bethyl A300-055A) or anti-SMC3 (1 μg, Abcam ab9263) at 4°C for 4 hours with rotation. 50 μl of Protein G-Agarose beads blocked with 1% BSA in 1X PBS were added to each sample and incubated at 4°C overnight with rotation. Beads were pelleted by centrifugation and washed twice with Low Salt Buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 150 mM NaCl, 0.1% SDS, 1% Triton X-100), three times with High Salt Buffer (20 mM Tris-HCl pH 8.1, 2 mM EDTA, 500 mM NaCl, 0.1% SDS, 1% Triton X-100), four times with LiCl buffer (0.25M LiCl, 10 mM Tris-HCl pH 8.1, 1 mM EDTA, 1% sodium deoxycholate and 1% NP-40), twice with 0.1% Tween-20 in 1X PBS, and once with TE buffer (10 mM Tris-HCl pH 8.1 and 1 mM EDTA). Immunoprecipitated DNA was eluted from the beads by incubation with 200 μl of elution buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, 1% SDS) at 65°C for 1 hour. The beads were removed by centrifugation and DNA crosslinking was reversed at 65°C for 4 hours. The DNA was incubated with 20 mg of RNAse A at 55°C for 1 hour. 40 mg Proteinase K (3115879001, Roche) were added and incubated at 55°C for 1 hour. The Immunoprecipitated DNA was purified using the Qiaquick PCR Purification Kit (Qiagen).
Quantity of ChIP’d DNA was determined using Picogreen Reagent (Quant-iT™ PicoGreen dsDNA Assay Kit, Thermo Fisher P11496) and a fluorometer instrument.  150ng to 1ug of DNA was prepared into Illumina libraries, according to manufacturer’s instructions, using the TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4003). Resulting libraries were deep sequenced, using the Illumina HiSeq2500 system in Rapid Run mode, obtaining between 10M and 15M of 100-bp length, single-end reads per library.
Quantity of ChIP’d DNA was determined using Picogreen Reagent (Quant-iT™ PicoGreen dsDNA Assay Kit, Thermo Fisher P11496) and a fluorometer instrument.  150ng to 1ug of DNA was prepared into Illumina libraries, according to manufacturer’s instructions, using the TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4003). Resulting libraries were deep sequenced, using the Illumina HiSeq2500 system in Rapid Run mode, obtaining between 10M and 15M of 100-bp length, single-end reads per library.

value: E13.5 ganglionic eminence

value: mixed (C57/Bl6, 129Sv, FVB)

value: Abcam Cat#ab9263


title: Evf2_WT_SMC1

status: Public on Aug 23 2018

type: SRA

department: Neurology

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain

tag: chip antibody

value: Bethyl Cat#A300-055A


title: Evf2_WT_Input_90


title: Evf2_WT_Input_10


title: Evf2_WT_H3K4me3

extract_protocol:
Native ChIP: Whole ganglionic eminences were dissected from 10 Evf2+/+ and 10 Evf2TS/TS E13.5 embryos. Tissues were pooled for each genotype, triturated by pipetting, and filtered through a cell-strainer capped 5 ml polystyrene round- bottom tube (BD Falcon) to make single-cell suspensions. Cells were split into 1 x 106 cell aliquots, and pelleted through centrifugation at 1000 x g for 10 min. Cell pellets were flash frozen in liquid nitrogen, and stored at -80ºC. Nuclei were isolated using EZ Nuclei Isolation Lysis Buffer (N3408, SIGMA). Chromatin was digested in 2U/μl Micrococcal nuclease (M0247S, NEB) at 37°C for 7 min. The reaction was quenched with EDTA (10 mM final concentration). Triton X-100 and Sodium Deoxycholate were added (0.1% final concentration). Samples were incubated on ice for >15 minutes. Immunoprecipitation buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 1x Protease inhibitor cocktail, 1 mM PMSF) was added to a final volume of 200 μl and the samples were rotated at 4°C for 1 hour. The chromatin was pre-cleared by rotating at 4°C with 15 μl of Protein G–Agarose beads for 1 hour. After centrifugation to pellet the beads, the supernatant was further pre-cleared by rotating at 4°C with 15 μl rabbit IgG conjugated Protein G–Agarose beads for 1 hour. The pre-cleared chromatin was incubated with rabbit IgG (1 μg), or antibodies targeting histone modifications (1 μg) at 4°C for 1-2 hours with rotation. 15 μl of Protein G-Agarose beads blocked with 1% BSA in 1X PBS were added to each sample and incubated at 4°C overnight with rotation. The beads were pelleted by centrifugation and washed twice with 200 μl Low Salt Wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, 0.1% SDS) and twice with 200 μl High Salt Wash buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS). Immunoprecipitated DNA was eluted in 100 μl of ChIP elution buffer (100 mM NaHCO3, 1% SDS) at 65°C for 1-1.5 hour. The DNA was purified using phenol chloroform extraction and ethanol precipitated. The pellet was resuspended in 10 mM Tris-HCl pH 8.5. The DNA was incubated with 20 mg of RNAse A at 55°C for 1 hour. 40 mg Proteinase K were added and incubated at 55°C for 1 hour. The immunoprecipitated DNA was purified using the Qiaquick PCR Purification Kit.
Quantity of ChIP’d DNA was determined using Picogreen Reagent (Quant-iT™ PicoGreen dsDNA Assay Kit, Thermo Fisher P11496) and a fluorometer instrument.  150ng to 1ug of DNA was prepared into Illumina libraries, according to manufacturer’s instructions, using the TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4003). Resulting libraries were deep sequenced, using the Illumina HiSeq2500 system in Rapid Run mode, obtaining between 10M and 15M of 100-bp length, single-end reads per library.
Quantity of ChIP’d DNA was determined using Picogreen Reagent (Quant-iT™ PicoGreen dsDNA Assay Kit, Thermo Fisher P11496) and a fluorometer instrument.  150ng to 1ug of DNA was prepared into Illumina libraries, according to manufacturer’s instructions, using the TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4003). Resulting libraries were deep sequenced, using the Illumina HiSeq2500 system in Rapid Run mode, obtaining between 10M and 15M of 100-bp length, single-end reads per library.

value: Abcam Cat#ab8580


title: DMSO_3_K27Ac

city: Jerusalem

first: Yinon

last: Ben-Neriah

address: Ein Kerem

department: The Lautenberg Center for Immunology

country: Israel

institute: Hebrew University-Hadassah Medical School

description: Primary AML cells treated with DMSO

data_processing:
Following read duplication removal (picard-tools), all datasets were individually aligned to the mouse genome (GRCm38/mm10) using Bowtie2 (Langmead and Salzberg, 2012) with default parameters.  Next, peaks were called on the aligned BAMs from each IP replicate using MACS2 with the relevant input sample, a q-value threshold of 0.01, and MFOLD of 5 50.
Pileup fragment profiles per million reads were generated by MACS2 using the SPMR parameter and were used for visualization of ChIP-seq data directly on the UCSC genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Primary MLL-AF9 AML cells

growth_protocol: MLL-AF9-driven leukemic mice were sacrificed and BM was flushed with PBS from the femur and tibia. The cells were cultured ex vivo in StemPro-34 SFM media (Gibco) supplemented with 10 ng/ml of IL3, IL6, thyroid peroxidase (TPO), stem cell factor (SCF) StemPro-34 Nutrient Supplement (25μl/ml), PenSrep (Sigma, 1:100) and L-glutamine (Sigma, 1:100).

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to manufacturer’s instructions, quantified by Qubit (Invitrogen) and TapeStation (Agilent) and sequenced on an Illumina HiSeq2500 (50 SR lane V4 reagents).

treatment_protocol: Cell were treated with DMSO or A51 (1 μM) and harvested after 4 hours.

value: Primary MLL-AF9 AML cells

tag: agent

value: control

value: anti-H3K27Ac, Abcam:Cat# ab4729


title: Evf2_TSTS_SMC3

value: mixed (C57/Bl6, 129Sv, FVB), Evf2 lncRNA truncated


title: DMSO_K27_Ac_2

description: Primary AML cells treated with DMSO


title: A51_K27_Ac_2

description: Primary AML cells treated with A51


title: Evf2_WT_H3K4me1

value: Abcam Cat#ab8895


title: Evf2_TSTS_Input_90


title: Evf2_TSTS_Input


title: Evf2_TSTS_SMC1


title: Evf2_TSTS_Input_10


title: Evf2_TSTS.4C

extract_protocol:
Whole ganglionic eminences (GEs) were dissected from 10 Evf2+/+ and 10 Evf2TS/TS E13.5 embryos. Tissues were pooled for each genotype, triturated by pipetting, and filtered through a cell-strainer capped 5 ml polystyrene round- bottom tube (BD Falcon) to make single-cell suspensions.  Cells were fixed in 2% paraformaldehyde/10% Fetal Bovine Serum (FBS) at room temperature for 10 min with rotation. 125 mM glycine was used to quench the formaldehyde. The 4C method used has been described in detail (van de Werken et al. 2012) EcoRI was used for the primary restriction digestion and DpnII was used for the secondary restriction digestion.
The following steps were performed to generate the 4C library for sequencing. First, overhangs were added to the 4C template using PCR amplification with primers containing the bait sequence. Primers: Dlx5/6UCE Forward: 5’TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATGCCAAACCACTGTGAGTGTA3’, Dlx5/6UCE Reverse: 5’GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTCCCCAATGTCTGCTTCAA 3’. PCR reaction: 200 ng 4C template, 0.2 mM dNTPs, 35 pmol Primer Dlx5/6UCE-Fwd, 35 pmol Primer Dlx5/6UCE-Rev, 1.75 U Expand Long Template Enzyme Mix (Roche), 1X Buffer I. PCR cycles: 94°C - 2 min, 94°C – 10 sec, 55°C - 1min, 68°C - 3 min, 29 cycles, 68°C - 5min. The PCR product was purified using the High Pure PCR Product Purification Kit (Roche). Then, the 4C DNA containing the overhangs was used as template for a second PCR that adds index sequences and Illumina sequencing adapters to generate the 4C library for sequencing. PCR reaction (50 μl): 225 ng DNA template, 0.5 mM dNTPs, 5μl Nextera XT Index1 primer (N7XX, Illumina), 5 μl Nextera Index 2 primer (S5XX, Illumina), 3.5 U Expand Long Template Enzyme Mix (Roche), 1X Buffer I. PCR cycles: 94°C - 5 min, 94°C – 10 sec, 55°C – 30 sec, 68°C - 1 min, 8 cycles, 68°C - 7min.The PCR product was purified using the High Pure PCR Product Purification Kit (Roche).
Quantity of ChIP’d DNA was determined using Picogreen Reagent (Quant-iT™ PicoGreen dsDNA Assay Kit, Thermo Fisher P11496) and a fluorometer instrument.  150ng to 1ug of DNA was prepared into Illumina libraries, according to manufacturer’s instructions, using the TruSeq Nano DNA Library Prep Kit (Illumina, FC-121-4003). Resulting libraries were deep sequenced, using the Illumina HiSeq2500 system in Rapid Run mode, obtaining between 10M and 15M of 100-bp length, single-end reads per library.


title: Evf2_TSTS_H3K4me3


title: Evf2_TSTS_H3K27ac

value: Abcam Cat#ab4729


title: Evf2_TSTS_H3K27me3

value: Active Motif Cat#39155


title: Evf1_WT_H3K4me3


title: Evf2_WT.4C


title: SW_Input_10

value: Swiss Webster


title: Evf2_WT_Input


title: SW_Dll_10

value: anti-Dll (Feng 2006)


title: Evf1_WT_H3K4me1


title: Morphine3

city: St. Louis

first: Robi

last: Mitra

state: MO

address: 4515 McKinley Ave

institute: Washington University School of Medicine

library_source: transcriptomic

data_processing:
Drop-seq: Sequences were filtered and aligned using standard Drop-seq tools (McCarroll Lab). Briefly, raw sequence data was first filtered to remove all read pairs with a barcode base quality of less than 10. The second read (75 bp) was then trimmed at the 5′ end to remove any TSO adaptor sequence and at the 3′ end to remove poly(A) tails of length 6 or greater, then aligned to the mouse (mm10) genome using STAR v2.4.2a with default settings. Uniquely mapped reads were grouped by cell barcode. A list of UMIs (unique molecular identifiers) in each gene, within each cell, was assembled, and UMIs within ED = 1 were merged together. The total number of unique UMI sequences was counted, and this number was reported as the number of transcripts of that gene for a given cell (see summary files).
FACS-RNAseq trimming: java -jar $TRIMMOMATIC_HOME/trimmomatic-0.36.jar SE -phred33 path/to/filtered/OL_mock_1.fq path/to/trimmed/OL_mock_1.fq LEADING:3 TRAILING:3 MINLEN:36
FACS-RNAseq alignment: STAR --genomeDir path/to/mm10/genome_reference --readFilesIn path/to/trimmed/OL_mock_1.fastq  --runThreadN 16 --outFileNamePrefix OL_mock_1 --outSAMtype BAM SortedByCoordinate
FACS-RNAseq counts: htseq-count -f bam -m union -r pos -i gene_name -a 10 --stranded=no OL_mock_1Aligned.sortedByCoord.out.bam path/to/mm10.gtf  > OL_mock_1_counts.txt           The above 3 steps were repeated for all 6 samples, and outputs were combined into "FACS-RNAseq_counts.txt"
FACS-RNAseq differential expression: DESeq2 was employed (standard parameters) to assess differential expression between mock (9-11) and morphine (12-14) samples. The output is included in "FACS-RNAseq_DESeq_result.txt"
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text

molecule: polyA RNA

source_name: Mouse nucleus accumbens

extract_protocol:
Brain tissue was dissected, then the nucleus accumbens (or whole brain) was dissociated in papain solution to obtain a single-cell suspension. Samples 1-8 were then processed by Drop-seq. Samples 9-14 were immunostained and oligodendrocytes were purified by FACS, then RNA was isolated using Trizol.
For samples 1-8, standard Drop-seq (Nextera) library prep; Read 1 was 25 bp and Read 2 was 75 bp. For samples 9-14, RNA was amplified using the Seqplex RNA Amplification Kit (Sigma), then prepared for sequencing using standard Illumina protocols and sequenced 1x50.
single-cell RNAseq; total RNAseq

treatment_protocol: Intraperitoneal injection with saline (mock) or morphine sulfate

tag: Sex

value: Male

tag: age

value: P78, P82 (2 mice pooled)


title: Evf1_TSTS_Input

value: mixed (C57/Bl6, 129Sv, FVB), Evf1 lncRNA truncated


title: Evf1_WT_H3K27me3

value: E13.5 ganglionic eminence


title: Evf2_WT_H3K27ac

value: mixed (C57/Bl6, 129Sv, FVB)


title: Sample_veh6_sham

city: New York

first: Akanksha

last: Verma

state: New York

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8 software used for basecalling.
RNAseq: Sequence reads were aligned to mm10 STAR with default parameters
RNAseq: FPKM were obtained using CuffLinks
Genome_build: mm10
Supplementary_files_format_and_content: RNAseq: tab-delimited FPKM values for each Refseq gene.

source_name: Colon, Sham, Antibiotic Treated

extract_protocol:
Total RNA was extracted from samples using the RNeasy Mini kit (Life Technologies). Samples were then subject to poly(A) selection using oligo-dT beads (Life Technologies).
TotalScript RNA-Seq Kit (Epicentre)

treatment_protocol: Mice were provided with broad-spectrum antibiotics in drinking water to reduce bacterial abundance. Wound beds in the colons were collected for RNA seq analysis 6 hours following pinch biopsy and compared to mice not treated with antibiotics.

tag: tissue

value: colon

tag: condition

value: Sham, Antibiotic Treated


title: Evf2_WT_H3K27me3


title: Sample_veh6_bx

source_name: Colon, Biopsy, Antibiotic Treated

value: Biopsy, Antibiotic Treated


title: Sample_veh4_sham


title: Evf2_TSTS_H3K4me1


title: Sample_veh3_sham


title: PBMCs_C3_2

city: Bethesda

first: Daniel

middle: L

last: Kastner

state: MD

address: 9000 Rockville Pike

department: NHGRI

institute: NIH

data_processing:
RNA-seq reads were mapped against GRCh37 usingTOpHat v2.1.1. In the whole blood RNA analysis, reads mapped to hemoglobin genes were removed from further analysis.
Mapped reads were quantified using HTSeq.
All the count data were normalized using TCC and differentially expressed genes were detected using edgeR.
Genome_build: GRCh37
Supplementary_files_format_and_content: Read-count text file

molecule: total RNA

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Total RNA was isolated from whole blood collected in PAXgene Blood RNA Tubes using PAXgene Blood RNA Kit (PreAnalytiX) per manufacturer’s instructions, and PBMCs using TRIzol (Thermo Fisher Scientific)
Total RNA was used for cDNA library preparation using the TruSeq Stranded mRNA Library Preparation kit for NeoPrep (Illumina). Sequencing was performed on an Illumina HiSeq 3000 System in a 1 x 50 bp single read mode

value: PBMC

tag: disease state

value: healthy


title: Evf1_WT_Input


title: Evf1_TSTS_H3K4me3

value: Abcam Cat#ab8580


title: Sample_veh3_bx


title: Sample_veh2_bx


title: Sample_veh2_sham


title: Sample_veh5_sham


title: Evf1_TSTS_H3K27me3


title: Sample_veh5_bx


title: Evf1_TSTS_H3K4me1


title: Whole_blood_HOIP_2

source_name: whole blood RNA

value: whole blood

value: HOIP deficiency


title: Whole_blood_HOIP_1


title: Sample_abx6_sham

source_name: Colon, Sham, control

value: Sham, control


title: PBMCs_HOIP_1


title: PBMCs_HOIP_2


title: PBMCs_C3_1


title: Sample_abx5_sham


title: Sample_abx5_bx

source_name: Colon, Biopsy, control

value: Biopsy, control


title: Sample_abx4_sham


title: PBMCs_Mother_1


title: Whole_blood_Mother_2


title: Sample_veh1_bx


title: Sample_abx3_sham


title: Sample_abx3_bx


title: Whole_blood_Mother_1


title: Sample_veh1_sham


title: Sample_6hr_post_sham_5

source_name: Colon, Sham, Post 6hr

value: Sham, Post 6hr


title: Sample_abx6_bx


title: Whole_blood_C2_1


title: Whole_blood_C1_1


title: Sample_abx1_sham


city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

description: jc2838_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

growth_protocol: Doxycycline-inducible ER-beta expressing MDA-MB-231cells were maintained in phenol red-free DMEM/F12 medium supplemented with 10% fetal bovine serum (FBS), 1% antibiotic-antimycotic (AA), 5 mg/L blasticidin S and 500 mg/L zeocin.

extract_protocol:
Nuclear lysates were prepared and ER-beta bound chromatin was purified using the Flag-specific antibody.
DNA was prepared for Illumina sequencing on the HiSeq 2500 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: MDA-MB-231-ER-beta cells were plated in 15 cm dishes and allowed to grow to approximately 80% confluence in DMEM/F12 medium containing 10% charcoal stripped FBS and Doxycycline (100 ng/ml, to induce ER-beta expression).  Cells were subsequently treated in triplicate with ethanol vehicle, 1 nM estradiol or 10 nM LY500307 for 3 hours.

tag: cell line

value: Triple Negative Breast Cancer Cell Line

tag: passages

tag: treated with

value: 1 nM estradiol for 3 h


description: jc2843_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_ethanol_CRI07

value: ethanol vehicle for 3 h


description: jc2849_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07


description: jc2840_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07


description: jc2835_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07


title: Sample_6hr_post_sham_4


title: Sample_abx4_bx


description: jc2845_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07


title: Sample_veh4_bx


title: Sample_6hr_post_sham_2


title: Sample_abx2_bx


title: Sample_abx2_sham


title: colorectal adenoma_Tu9

type: RNA

city: Nanjing

first: Shizhi

last: Wang

state: Jiangsu

address: 87 Dingjiaqiao, Gulou District

department: Key Laboratory of Environmental Medicine Engineering, Ministry of Education

country: China

institute: Southeast University

hyb_protocol: After stopping the labeling procedure, the Hy3™-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.a,The total 25 μL mixture from Hy3™-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min. b, Then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA). c, Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon)

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. Discriminant miRNAs and differences between groups were analyzed using Bayes moderated t test (limma) with Benjamini Hochberg false discovery rate (FDR) at P < 0.05. A two-fold cut-off difference was applied to select the up- and down-regulated miRNAs.

source_name: primary colorectal adenoma

label_protocol: RNA labeling and array hybridization was according to Exiqon's manual.After quality control, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling by following steps:  a, 1μLRNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C. b, The Reaction was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture.The labeling reaction was incubated for 1 h at 16°C. c,Terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: gender

value: male

tag: histology

value: tubulovillous adenoma


title: colorectal adenoma_Tu15


description:
jc2841_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07
processed data file: erb_ly500307-input_ly500307_peaks.narrowPeak.gz

value: Flag (Sigma, M2)


title: colorectal adenoma_Tu3

value: female


description: jc2830_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07


description: jc2839_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_ethanol_CRI07


description:
jc2833_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07
processed data file: erb_ly500307-input_ly500307_peaks.narrowPeak.gz


title: colorectal adenoma_Tu10


title: Sample_6hr_post_Bx_5

source_name: Colon, Biopsy, Post 6hr

value: colon

value: Biopsy, Post 6hr


title: colorectal cancer_Ca33

source_name: primary colorectal cancer

value: colorectal adenocarcinoma


title: colorectal cancer_Ca34


title: Sample_6hr_post_sham_3


description:
jc2846_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07
processed data file: erb_ly500307-input_ly500307_peaks.narrowPeak.gz


title: colorectal cancer_Ca26


title: colorectal cancer_Ca25


title: normal mucosa_No34

source_name: adjacent normal mucosa

value: normal mucosa


title: colorectal adenoma_Tu16


title: colorectal adenoma_Tu8


description:
jc2844_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07
processed data file: erb_estradiol-input_estradiol_peaks.narrowPeak.gz


description:
jc2842_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07
processed data file: erb_estradiol-input_estradiol_peaks.narrowPeak.gz


title: Sample_6hr_post_sham_1


description:
jc2837_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_LY500307_CRI07
processed data file: erb_ly500307-input_ly500307_peaks.narrowPeak.gz


title: Sample_6hr_post_Bx_1


title: Sample_6d_post_sham_5

source_name: Colon, Sham, Post 6 Days

value: Sham, Post 6 Days


title: normal mucosa_No23


title: Sample_6hr_post_Bx_6


description:
jc2829_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07
processed data file: erb_estradiol-input_estradiol_peaks.narrowPeak.gz


description: jc2832_MDA-MB-231-ERb_Input_Full_24_hrs_Dox_3_hrs_ethanol_CRI07


title: Sample_6d_post_sham_3_


title: adr-1(-) Input-Rep-1

city: Santa Cruz

first: Todd

last: Lowe

state: CA

address: 1156 High Street

department: Biomolecular Engineering and Bioinformatics

institute: University of California Santa Cruz

description:
Total RNA-seq
adr1.input.1.Aligned.sortedByCoord.out

data_processing:
Basecalling performed using
Sequenced reads were trimmed of adapters then mapped to the ce11 genome using STAR v2.5.2b with parameters --outFilterMultimapNmax 1 --outFilterScoreMinOverLread .66 --outFilterMatchNminOverLread .66 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax .3
FeatureCounts v1.5.2 was used to count mapped reads to Wormbase (WS262) gene annotations using the following parameters: -T 8 -s 2 -t gene -g gene_id; genes with 0 counts across all samples were removed
Differential expression analysis between the N2 replicates and adr-2(-) replicates were carried out using DESeq2 v1.18.1 using a likelyhood ratio test to test for ratio of ratios, similarly for the adr-2(-) and adr-1(-) replicates for determining bound transcripts
Editing site calling was performed using sailor v1.0.4 and annotation of the sites was carried out using a custom python script
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited text files containing raw read counts, output of DESeq2, and the annotated sailor output

organism: Caenorhabditis elegans

source_name: Whole worm lysate

growth_protocol: 3 day old adult worms were collected from NGM plates with 1X M9, UV irradiated and frozen at -80oC

extract_protocol:
RNA was extracted from the inputs and Ipsusing standard Trizol extraction protocols
RNA samples were ribo depleted using Illumina ribo-zero gold kit (MRZ116C) and RNA libraries were prepared for sequencing using stranded RNA-seq library preparation kit (KK 8400)

treatment_protocol: Worm lysates were incubated with anti-ADR-2 for 2 hours in the cold room, washed twice with wash buffer. RIP samples were treated with proteinaseK to degrade protein and stored in Trizol.


title: WT Input-Rep-1

description:
Total RNA-seq
n2.input.1.Aligned.sortedByCoord.out


title: WT Input-Rep-2

description:
Total RNA-seq
n2.input.2.Aligned.sortedByCoord.out


title: adr-1(-) Input-Rep-2

description:
Total RNA-seq
adr1.input.2.Aligned.sortedByCoord.out


description:
jc2848_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_1nM_Estradiol_CRI07
processed data file: erb_estradiol-input_estradiol_peaks.narrowPeak.gz


title: colorectal cancer_Ca23


title: adr-1(-) RIP- rep-1

description:
ADR-2 RIP-seq
adr1.ip.1.Aligned.sortedByCoord.out

source_name: ADR-2 RIP sample


title: Sample_6hr_post_Bx_4


title: normal mucosa_No33


title: colorectal cancer_Ca5


title: adr-2(-) RIP- rep-2

description:
ADR-2 RIP-seq
adr2.ip.2.Aligned.sortedByCoord.out


title: normal mucosa_No5


description:
jc2847_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_ethanol_CRI07
processed data file: erb_ethanol-input_ethanol_peaks.narrowPeak.gz


title: Sample_6hr_post_Bx_3


title: Sample_6d_post_Bx_5_

source_name: Colon, Biopsy, Post 6 Days

value: Biopsy, Post 6 Days


title: normal mucosa_No26


title: normal mucosa_No25


title: Sample_6d_post_Bx_4


description:
jc2834_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_ethanol_CRI07
processed data file: erb_ethanol-input_ethanol_peaks.narrowPeak.gz


title: adr-2(-) Input-Rep-2

description:
Total RNA-seq
adr2.input.2.Aligned.sortedByCoord.out


description:
jc2836_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_ethanol_CRI07
processed data file: erb_ethanol-input_ethanol_peaks.narrowPeak.gz


title: adr-2(-) Input-Rep-1

description:
Total RNA-seq
adr2.input.1.Aligned.sortedByCoord.out


title: adr-1(-) RIP- rep-2

description:
ADR-2 RIP-seq
adr1.ip.2.Aligned.sortedByCoord.out


title: Sample_3d_post_sham_4

source_name: Colon, Sham, Post 3 Days

value: Sham, Post 3 Days


description:
jc2831_MDA-MB-231-ERb_ERb_Full_24_hrs_Dox_3_hrs_ethanol_CRI07
processed data file: erb_ethanol-input_ethanol_peaks.narrowPeak.gz


title: adr-2(-) RIP- rep-1

description:
ADR-2 RIP-seq
adr2.ip.1.Aligned.sortedByCoord.out


title: Sample_6d_post_sham_2


title: cMo_IN_dataset3_#4

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package. These samples were normalized together with other samples. The complete normalized data set with all other samples, both batch-corrected and not batch-corrected, is available on the series record.

label: biotin

label_protocol: 20 ng of RNA from each sample was used to synthesize biotinylated probes, using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell subset was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol. The lineage cocktail used was a combination of antibodies against CD19 (B cells), T cell receptor beta chain (alpha/beta T cells and NK T cells), NK1.1 (NK and NK T cells) and Ly6G (neutrophiles).

treatment_protocol: Mice were untreated or infected for 1.5 days i.p. with 2.5x10E4 pfu of salivary-gland extracted MCMV Smith strain.

tag: phenotype

value: Lin-CD11b+Ly6C+, viable (aquadead V-BV510 negative)

value: spleen

value: MCMV-activated (total) spleen WT CD45.2 cMo

value: WT CD45.2 CD57BL/6

tag: treatment

value: d1.5 MCMV-infected


title: RPM_UN_dataset3_#1

value: Lin-CD11b-F4/80(high)CD64+, viable (aquadead V-BV510 negative)

value: resting (total) spleen WT CD45.2 RPM

value: Uninfected


title: Sample_3d_post_sham_3


title: cMo_UN_dataset3_#2

value: resting (total) spleen WT CD45.2 cMo


title: WT RIP- rep-2

description:
ADR-2 RIP-seq
n2.ip.2.Aligned.sortedByCoord.out


title: Sample_6d_post_sham_4


title: cDC2_IN_dataset3_#3

value: Lin-CD11b+Ly6C-CD11chigh, viable (aquadead V-BV510 negative)

value: MCMV-activated (total) spleen WT CD45.2 CD11b+ DC


title: RPM_IN_dataset3_#3

value: MCMV-activated (total) spleen WT CD45.2 RPM


title: RPM_IN_dataset3_#4


title: Sample_3d_post_sham_2

value: colon


title: WT RIP- rep-1

description:
ADR-2 RIP-seq
n2.ip.1.Aligned.sortedByCoord.out


title: Sample_6d_post_Bx_3_


title: Sample_3d_post_sham_5


title: Sample_6d_post_Bx_1


title: Sample_6d_post_sham_1


title: Sample_6d_post_Bx_2


title: Sample_3d_post_sham_1


title: cMo_IN_dataset3_#3


title: Sample_3d_post_Bx_4

source_name: Colon, Biopsy, Post 3 Days

value: Biopsy, Post 3 Days


title: Sample_3d_post_Bx_3


title: DN4 -2

city: Worcester

first: Nicholas

last: Spidale

state: MA

address: 368 Plantation St.

department: Pathology

institute: University of Massachusetts Medical School

data_processing:
Sequenced read mapped to mouse NCBI Re-seq using Bowtie
Calulate Reads per kilobase of transcript per million (RPKM)
Calculate DEG
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Thymic precursor cells

extract_protocol: Libraries for RNA-sequencing were prepared using the NuGEN Ovation RNA-seq v2 library preparation kit (NuGEN Technologies Inc.). Briefly, ~10,000 cells/subset were sorted (from 10 day old B6 mice) into the NuGEN Prelude Direct Lysis Buffer and total RNA was inputted directly into the first strand synthesis step of the Ovation RNA-seq v2 system. 1ng of SPIA amplified fragmented ds-cDNA was used to prepare libraries using the NuGEN Ovation Ultralow DR Multiplex System. Size distribution and qualitative assessment of libraries was performed using the Bioanalyzer DNA Chip 1000. Libraries were quantified using the KAPA Universal Library quantification kit prior to multiplexing and sequenced on the Illumina HiSeq platform.

value: Thymus

value: post natal day 10


title: CAF5 RNA (treated with letrozole)

city: Peking

first: wang

middle: li

last: yong

state: Peking

address: No 10 xi tou tiao, you an gate

department: medical school

institute: Capital Medical University

description: CAF5 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h

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

source_name: Human primary CAF isolated from cancer tissue in ER-positive invasive ductal breast cancer patients

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

extract_protocol: Total RNA was extracted from CAF cells with a ToTALLY RNA™ Total RNA Isolation Kit (Ambion)

value: human breast cancer tissue, female, estrogen receptor positive

value: fibroblasts

tag: morphology

value: epithelial

tag: growth properties

value: monolayer


title: Sample_3d_post_Bx_5

tag: strain


title: DN2 -2


title: CAF6 RNA (control)

description: CAF6 cells co-cultured with MCF7 cells was treated with DMSO for 72 h

tag: cell type


title: DN2 -1


title: DN1 ckit+ -3


title: RPM_UN_dataset3_#2

value: spleen

value: WT CD45.2 CD57BL/6


title: cDC2_IN_dataset3_#4

value: d1.5 MCMV-infected


title: CAF4 RNA (treated with letrozole)

description: CAF4 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h


title: DN4 -1


title: CAF1 RNA ( treated with letrozole)

description: CAF1 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h


title: CAF2 RNA (control)

description: CAF2 cells co-cultured with MCF7 cells was treated with DMSO for 72 h


title: Sample_3d_post_Bx_6


title: cMo_UN_dataset3_#1

value: Lin-CD11b+Ly6C+, viable (aquadead V-BV510 negative)


title: DN2 -3


title: Sample_3d_post_Bx_2


title: CAF3 RNA (control)

description: CAF3 cells co-cultured with MCF7 cells was treated with DMSO for 72 h


title: CAF4 RNA (control)

description: CAF4 cells co-cultured with MCF7 cells was treated with DMSO for 72 h


title: Sample_1hr_post_sham_5

source_name: Colon, Sham, Post 1hr

value: Sham, Post 1hr


title: CAF2 RNA (treated with letrozole)

description: CAF2 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h


title: CAF5 RNA (control)

description: CAF5 cells co-cultured with MCF7 cells was treated with DMSO for 72 h


title: CAF1 RNA (control)

description: CAF1 cells co-cultured with MCF7 cells was treated with DMSO for 72 h


title: DN1 ckit+ -1


title: Sample_3d_post_Bx_1


title: DN1 ckit+ -2


title: ImmV2 -2


title: Sample_1hr_post_sham_4


title: DN4-3


title: Sample_1hr_post_sham_2


title: ImmV2 -1


title: Sample_1hr_post_sham_1


title: DN1e-2


title: DN1d-2


title: DN1d-1


title: DN1ab-1


title: DN1e-1


title: DN1e-3


title: CAF6 RNA (treated with letrozole)

description: CAF6 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h


title: CAF3 RNA (treated with letrozolel)

description: CAF3 cells co-cultured with MCF7 cells was treated with letrozole dissolved in DMSO for 72 h


title: Sample_1hr_post_Bx_4

source_name: Colon, Biopsy, Post 1hr

value: Biopsy, Post 1hr


title: Sample_1hr_post_Bx_6


title: DN1ab-2


title: NPC_H33_HA_rep1

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
ChIP-seq clean reads were mapped to mm9 by Bowtie2 with default parameters.
Data were filtered by samtools with "-q 10"to retain unique reads.
Enriched peaks were detected using MACS14 with input. H3.3 and HIRA peaks were called with default parameters. UBN1 and UBN2 peaks were called with "--nomodel --shiftsize=75".
Genome_build: mm9
Supplementary_files_format_and_content: bed file with four tab-delimited fields, representing chromosome name, start, end and peak score.

source_name: ES-derived neural progenitor cells

growth_protocol: Mouse ES cells were cultured in medium with 80% DMEM, 15% FBS, 1% Nonessential amino acids, 1% 2-Mercaptoethanol, 1% L-glutamine, 1% Nucleosides, 1% Pen/Strep and 1000U/ml leukemia inhibitory factor (LIF) in standard incubator with 5% CO2 at 37°C. HEK293T cells and A03_1 cells were grown in DMEM and F-12 Ham’s medium, respectively, supplemented with 10% FBS in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then sonicated in N-lauroyl-sarcosine containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with agarose conjucated with antibodies.
Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000.

treatment_protocol: mES cells were plated onto 0.1% gelatin-coated plates at a density of 0.5-1×10^4/cm2 in N2B27 medium. N2B27 medium is a 1:1 mixture of DMEM/F12 (Gibco, 11320-033) supplemented with N2 (Gibco, 17502-048) and Neurobasal medium (Gibco, 21103-049) supplemented with B27 (Gibco, 17504-044), 25 μg/ml insulin and 50 μg/ml BSA. The medium was refreshed every other day during 9 days of culture.

tag: genotype

tag: chip antibody

value: Anti-HA−Agarose(Sigma, A2095)


title: Sample_1hr_post_Bx_5


title: Calu-3 SIP/Calu-3 control

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: Calu-3 control

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA

value: bronchial epithelial cell

source_name: Calu-3 SIP


title: BEAS-2B SIP/BEAS-2B control

source_name: BEAS-2B control

source_name: BEAS-2B SIP


title: OE.2 KLF5 over-expression

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

institute: Cincinnati Childrens Hospital Medical Center

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Expression quantification was performed using RMA from within the software AltAnalyze 2.1.1.

source_name: H441 cells

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

tag: genotype/variation

value: KLF5 over-expression


title: OE.3 KLF5 over-expression


title: Sample_1hr_post_Bx_1

tag: tissue

value: colon


title: UBN2_Flag_rep2

source_name: mouse embryonic stem cell

value: Anti-Flag M2 Affinity Gel(Sigma, A2220)


title: UBN2_Flag_rep1


title: Sample_1hr_post_Bx_3

tag: condition


title: HIRA-KI-input


title: NT.3 nontargeting shRNA

value: nontargeting shRNA


title: H33BKI_input_rep2


title: UBN1_Flag_rep2


title: OE.1 KLF5 over-expression


title: UBN_FID_D8_H33_HA_rep2

value: H3f3b3XFlag-HA/3XFlag-HA  UBN1FID/FID UBN2FID/FID


title: HIRA_Flag_rep1


title: HIRA_Flag_rep2


title: Sample_1hr_post_Bx_2


title: UBN_FID_C4_H33_HA_rep1


title: NPC_H33_HA_rep2


title: NT.2 nontargeting shRNA


title: UBN2KO_siUBN1_H33_HA_rep1

value: H3f3b3XFlag-HA/3XFlag-HA  UBN2-/-


title: 37.2 KLF5 knockdown

value: KLF5 knockdown


title: NT.1 nontargeting shRNA


title: UBN2KO_H33_HA_rep2


title: H33BKI_input_rep1


title: SD_ZT4_2

city: Auckland

first: Geoffrey

middle: Owen James

last: Thomson

address: Private Bag 92019

department: School of Biological Sciences

country: New Zealand

institute: The University of Auckland

description: second experiment

data_processing:
Read trimming using the BBDuk tool in the BBTools suite (v37.54) with Phred = 20) and retaining only reads which were at least 36 bases in length. Read pairs lacking one of the pair were discarded.
Transcripts were quantified using Salmon (v0.8.2) using the Mt4.0v2 transcriptome.
Count tables were then imported into R using the tximport package (v1.4.0).
Genome_build: MedtrA17_4.0 (Mt4.0v2_GenesCDSSeq_20140818_1100.fasta)
Supplementary_files_format_and_content: CSV files containing the GeneID (gene),  either the raw counts or normalized abundances in Transcripts per Million (counts or TPM), growth condition (condition), time of sampling (time) and replicate number (replicate)

organism: Medicago truncatula

source_name: SD_ZT4, 2 trifoliate leaves

growth_protocol: Seeds were scarified and germinated overnight at 15°C in gently shaking tubes of water and dark conditions for 24 hours.  Germinated seeds were then vernalised in damp petri dishes at 4°C for a further 25 days.  The seedlings were subsequently planted in seed raising mix (Daltons Ltd., NZ) in individual cell pots and grown in growth cabinets at 22°C under 240μM/m/sec cool white fluorescent light. Soil was was kept moist with a complete liquid nutrient media.  Plants were grown in SD conditions (8 hours light/16 hour dark) for 10 days and then transferred to LD conditions (16 hours light/8 hour dark) where the timing of lights on (ZT0) was kept the same, but lights off occurred 8 h later.

extract_protocol:
In the first experiment, sampling occurred from SD and LD shifted plants when the plants were 13 days old at ZT0 and two hours later at ZT2 and in the second experiment sampling occurred at ZT4 when the plants were 15 days old.  Three biological replicates were taken each consisting of two pooled trifoliate leaves from different non-adjacent plants. Only the first trifoliate leaf to unfurl was sampled from a given plant.  Samples were immediately frozen in liquid nitrogen. Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen, Germany) following the manufacturer's instructions.
Library construction was performed by the Otago Genomics Facility using ScriptSeq Complete Kit (Plant) (Illumina Inc., USA) in the first experiment while the second experiment (ZT4 samples) used TruSeq Stranded mRNA Kits (Illumina Inc., USA).

tag: accession

value: Jester

tag: age

value: 15 days

value: SD

tag: timepoint

value: 2 trifoliate leaves


title: SD_ZT4_3

description: second experiment


title: UBN2KO_H33_HA_rep1


title: UBN1_Flag_rep1


title: UBN2KO_siUBN1_H33_HA_rep2


title: UBN_FID_D8_H33_HA_rep1


title: UBN1KO_H33_HA_rep2

value: H3f3b3XFlag-HA/3XFlag-HA  UBN1-/-


title: SPF-IEC-3

city: Seoul

first: Tae-Young

last: Roh

state: --- Select One ---

address: 52 Ewhayeodae-gil, Seodaemun-gu

department: Life Sciences

country: South Korea

institute: Ewha Womans University

description: Epithelial cells

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to mouse reference transcriptome (Ensembl 89) and genome (GRCm38, mm10) by STAR-2.5.2b [46] with parameters recommended by the ENCODE project
Transcripts per million (TPM) were calculated by RSEM with default parameters.
Differentially expressed genes were identified by edgeR-3.16.5 [49] given absolute fold change > 2 and FDR < 10-3
Genome_build: mm10
Supplementary_files_format_and_content: text file with expected_count, TPM, FPKM

source_name: SPF (specific pathogen free)

extract_protocol:
Small intestinal cells were sorted and RNA was harvested using Rneasy kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
AF (antigen free): no foreign antigens derived from microbiota and food
GF (germ free): no microbiota living in or on them
SPF (specific pathogen free): free of particular pathogens

value: small intestine

value: epithelium


title: LD_ZT4_2

description: second experiment

source_name: LD_ZT4, 2 trifoliate leaves

value: Shifted to LD


title: UBN1KO_H33_HA_rep1

value: Anti-HA−Agarose(Sigma, A2095)


title: UBN_FID_C4_H33_HA_rep2


title: SPF-IEC-4

description: Epithelial cells


title: SD_ZT4_1

description: second experiment


title: 37.3 KLF5 knockdown


title: AF-IEC-3

description: Epithelial cells

source_name: AF (antigen free)


title: 37.1 KLF5 knockdown


title: LD_ZT2_3

description: first experiment

source_name: LD_ZT2, 2 trifoliate leaves

value: 13 days


title: HIRAKO_H33_HA_rep1

value: H3f3b3XFlag-HA/3XFlag-HA  Hira-/-


title: LD_ZT4_3

description: second experiment


title: LD_ZT2_1

description: first experiment


title: CU91_12hpt-24hpt_rep1

city: Raleigh

first: Julie

last: Hicks

state: NC

address: 120 Broughton Dr

department: Animal Science

institute: NC State University

hyb_protocol: RNA samples from the same cell line and from a different time-point (either 0 or 12 or 24 hr post-treatment (hpt)) were co-hybridized.  Following overnight hybridization, slides were sequentially washed in salt sodium citrate (SSC) solutions with increasing stringency.

scan_protocol: Cy3- and cy5Cy5- TIFF images were generated from each slide using a GenePix 4000B Microarray Scanner (Molecular Devices).  Signal values of hybridized probes were extracted from the TIFF images using the adaptive circle algorithm of the ScanArray Express Software version 3.0 (PerkinElmer).

data_processing: All data analyses were performed using JMP Genomics (SAS Institute Inc.).  Log2 transformation and LOESS normalization were applied in data pre-processing steps.  Quality of the data was evaluated by MA plot and correlation and grouped scatter plot methods.

organism: Gallus gallus

source_name: CU91 cells 24hrs post sodium butyrate treatment

label_protocol: Two pools per sample were made and each pool was separately labeled with either Cy3 or Cy5 reactive dyes

growth_protocol: All cell lines were grown in RPMI-1640 media supplemented with penicillin (100U/mL)/ streptomycin (100µg/mL)/ amphotericin B (4µg/mL), 10% fetal bovine serum (FBS), 10% tryptose phosphate broth and 1% sodium pyruvate at 41 °C in a humidified incubator and 5% CO2.

extract_protocol: Cell pellets were lysed in Tri-reagent (Sigma-Aldrich), homogenized, and total RNA was extracted according to the manufacturer’s instructions, with the exception of overnight RNA precipitation at -20°C

treatment_protocol: Induction of MDV reactivation from latency was achieved by the treatment of sodium butyrate (n-butyrate) at a final concentration of 2 mM.  Cells were harvested at 0 h prior-induction, 12 h and 24 h post-induction, washed twice with PBS and subjected to RNA purification.

tag: cell line

tag: agent

value: sodium butyrate

tag: time (post sodium butyrate)

value: 24 hr

tag: replicate

source_name: CU91 cells 12hrs post sodium butyrate treatment

value: 12 hr


title: CU91_0hr-12hpt_rep1

source_name: CU91 cells 0hrs post sodium butyrate treatment

value: control

value: 0 hr


title: GF-IEC-1

description: Epithelial cells

source_name: GF (germ free)


title: GF-IEC-3

description: Epithelial cells


title: CU91_12hpt-24hpt_rep2


title: LD_ZT4_1

description: second experiment


title: LD_ZT0_2

description: first experiment

source_name: LD_ZT0, 2 trifoliate leaves


title: H33_HA_rep2


title: HIRAKO_H33_HA_rep2


title: LD_ZT0_1

description: first experiment


title: CU91_0hr-24hpt_rep1


title: CU91_0hr-12hpt_rep2


title: H33BKI_FID_C4_NPC_rep2

description: H33BKI_WT_NPC_vs_FIDC4_NPC_gene_exp_diff.txt

data_processing:
RNA-seq clean reads were mapped to mm9 by TopHat with "--library-type fr-unstranded --mate-inner-dist 50 --no-novel-juncs -G mm9_refGene.gtf".
The differential expression between samples was performed with Cuffdiff with "--min-reps-for-js-test 2 -u mm9_refGene.gtf".
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: ES-derived neural progenitor cells

extract_protocol:
RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction.
For RNA-seq, libraries were prepared according to the Illumina TruSeq protocol.

value: H3f3b3XFlag-HA/3XFlag-HA  UBN1FID/FID UBN2FID/FID


title: H33BKI_FID_D8_NPC_rep1

description: H33BKI_WT_NPC_vs_FIDD8_NPC_gene_exp_diff.txt


title: LD_ZT2_2

description: first experiment

value: Jester


title: CU91_0hr-24hpt_rep2


title: SD_ZT2_3

description: first experiment

source_name: SD_ZT2, 2 trifoliate leaves


title: H33_HA_rep1


title: H33BKI_FID_C4_NPC_rep1


title: H33BKI_FID_D8_NPC_rep2


title: CU115_0hr-24hpt_rep1

source_name: CU115 cells 0hrs post sodium butyrate treatment

source_name: CU115 cells 24hrs post sodium butyrate treatment


title: CU115_0hr-24hpt_rep2


title: T18_(HuGene-2_0-st)

city: Shanghai

first: Zhongyin

last: Yang

address: NO.197 Ruijin er road

department: Department of Surgery

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

description: take from the range of gastric cancer

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute . • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.

source_name: Gastric cancer tissue

label_protocol: Samples were enzymatically fragmented and labeled with Cy3

growth_protocol: Tissues taken from the samples were immediately frozen into liquid nitrogen and stored at -80°C until use

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: not applicable

value: Gastric cancer tissue


title: N16_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer

source_name: Normal gastric mucosa tissue

value: Normal gastric mucosa tissue


title: CU115_12hpt-24hpt_rep2

source_name: CU115 cells 12hrs post sodium butyrate treatment


title: AF-IEC-2

description: Epithelial cells


title: N18_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: CU115_12hpt-24hpt_rep1


title: H33BKI_WT_NPC_rep2


title: H33BKI_WT_NPC_rep1


title: T16_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: SD_ZT2_1

description: first experiment

value: SD

value: 2 trifoliate leaves


title: LD_ZT0_3

description: first experiment


title: SD_ZT2_2

description: first experiment


title: CU115_0hr-12hpt_rep1


title: Freshly isolated intestinal myofibroblasts, sample 4

city: Singapore

first: David

last: Virshup

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Pooled from 2 mice

data_processing:
100 bp paired-end reads were aligned to mouse reference genome (mm10/GRCm38) using STAR alignment with 0 allowed mismatches
Read counts were generated using the summarize Overlaps function in the Genomic Alignments Bioconductor package
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of raw counts per gene

source_name: Small intestine

extract_protocol:
Small intestines were isolated from mice. Crypts were isolated by chopping tissue into 1-2mm pieces, mechanically dissociating with EDTA and collecting crypt fractions. Myofibroblasts were isolated by EDTA washes and collagenase/dispase digestion with collection of the cells by 3 hour attachment to plastic tissue-treated culture dishes
RNA libraries were prepared for sequencing using standard Illumina protocols using TruSeq Stranded Specific mRNA (Illumina) kit

value: Small intestine


title: SD_ZT0_2

description: first experiment

source_name: SD_ZT0, 2 trifoliate leaves


title: THP1mac-HiC-IFNb-6h

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description:
in situ Hi-C
THP1mac-HiC-IFNb-6h
Sample138.THP1mac-HiC-IFNb-6h.hic

data_processing:
Basecalling, demultiplexing, and adapter trimming was performed using Illumina's bcl2fastq (v2.17.1.14)
Hi-C reads were trimmed at Mbo I/Dpn II recognition sites (GATC) and aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only read pairs that both map to unique genomic locations for further analysis (MAPQ > 10). Subsequent Hi-C analysis was performed using HOMER (Lin et al., 2012), and improvements made to HOMER (v4.10) for this study are available at http://homer.ucsd.edu/homer/interactions2/. Hi-C data was also processed using Juicer (v1.7.5) to generate hic files for visualization with Juicebox.
ChIP-seq reads were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012), keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). ChIP-seq peaks were called on pooled replicates using HOMER’s findPeaks program in either “histone” (histone marks, Pol II) or “factor” (CTCF, RAD21, PU.1) mode using default parameters to identify spreading or focal peaks, respectively.
RNA-seq reads were mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. Gene FPKM values were defined for primary Gencode transcripts using HOMER (v4.10) using only strand-specific exonic reads for each transcript.
Start-seq reads were trimmed to remove 3' illumina adapters and then mapped to the human genome (hg19/GRCh37) using STAR (v2.2.0c). Only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis. TSS (i.e. Start-seq peaks) were called using HOMER’s findPeaks program in "tss" mode using parameters "-style tss -F 2 -P 0.05" to identify sites of nascent transcription initiation
methylC-seq reads were mapped to the human genome (hg19/GRCh37) using Bismark/Bowtie2 (Krueger and Andrews, 2011) and reported as the number of observed methylated and unmethylated cytosines in the CpG context. HOMER (v4.10) was used process the methylation and create bedGraph genome browser tracks reporting the average %mCpG rates in 1 kb bins across the genome.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: ChIP-Seq/Start-seq: Tab-delimited BED files containing peak positions for each ChIP-seq or Start-seq experiment (one peak file per set of replicates, hg19) Columns: 1:chromosome,2:start,3:end,4:peakName,5:set to 1,6:strand.  RNA-seq: Tab-delimited table of FPKM values for all RNA-seq experiments Columns: 1:transcript ID, 2:chr, 3:start, 4:end, 5:strand, 6:mRNA length, 7:gene ID, 8: gene type, 9: gene symbol, 10-29: FPKM for each experiment. Hi-C: binary hic files generated by Juicer (visualize using Juicebox or Juicebox.js)

source_name: THP-1 monocyte AML cell line (+PMA)

growth_protocol: Monocyte derived macrophages (MDM) were prepared from buffy coats of healthy donor blood obtained from the New York Blood Center.  Peripheral blood mononuclear cells (PBMC) were isolated by centrifugation on a Ficoll density gradient (Histopaque; Sigma Aldrich), and CD14+ cells were isolated using Miltenyi liquid separation mini columns and magnetic beads labeled with anti-human CD14 antibody (Miltenyi Biotech).  For differentiation into macrophages, approximately 3 million CD14+ monocytes were cultured for 10 days in RPMI 1640 medium (CellGro, Corning) containing 10% fetal bovine serum (FBS) (HyClone; Thermo Scientific), 2 mM L-glutamine, 1 mM sodium pyruvate, and 100 U/ml penicillin–100 μg/ml streptomycin (Gibco, Invitrogen), and supplemented with 1000 U/ml human granulocyte-macrophage colony-stimulating factor (hGM-CSF) (Peprotech). THP-1 cells (“THP-1 monocytes”) were propagated in THP-1 medium (RPMI-1640 containing 10% low-endotoxin FBS (Peak Serum Inc.), 1x (100 µM) non-essential amino acids (Life Technologies), 1x MEM Sodium Pyruvate Solution (1 mM) (Life Technologies), 1x GlutaMax I (Life Technologies), 50 µM β-mercaptoethanol (Life Technologies)) at 37°C, 5% CO2, 100% humidity. Dexamethasone and, where indicated, IFNβ treatments were performed on differentiated THP-1 cells (“THP-1 macrophages”) that had been treated with 60 ng/ml phorbol myristate acetate (PMA) for 48 h followed overnight culture without PMA. For IAV infections, THP-1 cells were differentiated in the same manner, except 10 ng/ml PMA were used.

extract_protocol:
RNAseq: Cells were lysed in Trizol (Thermo) and RNA was extracted either by adding chloroform, phase separation and isolating RNA from the upper phase using RNeasy columns with on-column DNase treatment or by using DirectZol kits (Zymo) with on-column DNase treatment, following the manufacturer’s instructions. For cytoplasmic, nuclear, and large nuclear fraction RNA-seq (North-seq), RNA from 15 million live cells was isolated according to (Bhatt et al., 2012). Briefly, cells were washed with ice-cold PBS, resuspended at 75 million cells/ml final in cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 minutes. The lysate was layered onto 500 µl ice-cold sucrose buffer (10 mM Tris pH 7.5, 150 mM NaCl, 24% sucrose w/v) and centrifuged in microfuge tubes for 10 minutes at 13,000g, 4°C. The supernatant containing the cytoplasmic RNA (~ 700 µl) was transferred to a new tube, and the nuclear pellet was resuspended in 500 µl glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol, 0.85 mM DTT). RNA was extracted from the cytoplasmic and nuclear fraction with Trizol LS according to the manufacturer’s instructions, DNase-treated with RQ1 DNase (Promega), extracted once with phenol:chloroform, once with chloroform, and ethanol-precipitated. For size selection of large nuclear RNAs, two micrograms nuclear RNA were denatured with an equal amount of 2x RNA loading dye (NEB, 47.5% formamide final) for 5 minutes at 70°C and separated on a 1.5% agarose/1x TBE gel for 30 minutes. After staining the RNA with 1x SYBR Gold in 1x TBE for 15 minutes, RNA above the 45S RNA band was excised with a scalpel blade and gel-extracted (Zymoclean Gel RNA Recovery, Zymo Research).
Strand-specific total RNA-seq libraries from ribosomal RNA-depleted were prepared using the TruSeq kit (Illumina) according to the supplied protocol. ChIP-seq was essentially performed as described (Heinz et al., 2013), except that libraries were prepared using NEB Ultra II DNA library prep kit reagents. Start-seq was essentially performed as described (Scruggs et al., 2015) from total RNA with minor modifications, replacing phenol/chloroform extractions with Trizol LS (Thermo), using RppH (NEB) instead of tobacco acid pyrophosphatase, and generating sequencing libraries with a NEBNext Small RNA Library Prep kit (NEB). MethylC-seq libraries were prepared from ChIP input DNA that had been isolated as from formaldehyde-fixed samples as previously described (Heinz et al., 2013). Briefly, chromatin was sheared to an average size of 300 bp in ChIP lysis buffer, crosslinks reversed in 1% SDS/TE/300 mM NaCl ON at 65°C, treated for 30 minutes with 5 µg RNase A, digested for 2 h with 20 µg proteinase K and DNA was isolated with Speedbeads/PEG as described above. DNA libraries were made from 100 ng input DNA by adding methylated DNA sequencing adapters (Bioo) with NEB Ultra II DNA library prep kit reagents and cleaned up using Speedbeads/PEG/NaCl as above. Fifty nanograms of adapter-ligated DNA were bisulfite-treated using a Zymo EZ DNA methylation kit (Zymo Research) according to the manufacturer’s instructions, and PCR-amplified using KAPA HiFi U+ ReadyMix and Solexa 1GA/1GB primers. In situ Hi-C was performed as described (Rao et al., 2014) with modifications. Cells were pelleted by centrifugation and resuspended and cross-linked in 1% formaldehyde/PBS for 10 minutes at room temperature (RT). After quenching the reaction by adding 1/20th volume of 2.625 M glycine, cells were pelleted by centrifugation and washed twice with ice-cold 0.5% BSA/PBS. Aliquots of 2 M cells each were snap-frozen and stored at -80°C. After thawing cells on ice, nuclei were isolated by resuspending the cell pellet in 200 µl wash buffer (50 mM Tris/HCl pH 7.5, 10 mM NaCl, 1 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail (Sigma P8340)). Nuclei were spun down at 2500g for 5 minutes at room temperature. Most of the supernatant was discarded, leaving the nuclei in 10 µl liquid. Samples were resuspended in Dpn II buffer, 195 µl water and rotated at 37°C for 15 minutes. Chromatin was digested overnight (ON) with 2 µl (100 U) Dpn II (NEB) at 37°C, rotating overhead with 8 RPM. The next day, Mbo I digests (not Dpn II digests) were inactivated by incubating for 20 minutes at 62°C, and nuclei were collected centrifugation (5 minutes, 500 g, RT). Two-hundred µl of the supernatant were discarded, leaving the nuclei in 50 µl liquid, and overhangs were filled in with Biotin-14-dATP by adding 50 µl Klenow Master Mix (31.95 µl water, 5 µl NEBuffer 2, 0.35 µl 10 mM dATP (or dCTP), 0.35 µl 10 mM dTTP, 0.35 µl 10 mM dGTP, 7.5 µl 0.4 mM Biotin-14-dCTP (or Biotin-14-dATP)(Thermo), 2 µl 10% Triton X-100, 2.5 µl (12.5 U) Klenow fragment (Enzymatics) and rotating overhead at RT, 8 RPM for 40 minutes. Reactions were stopped by adding 2.5 µl 0.5 M EDTA and placed on ice. Proximity ligation was performed by transferring the entire reaction into 1.5 ml Eppendorf tubes containing 400 µl ligase mix (320 µl water, 40 µl 10x T4 DNA ligase buffer (Enzymatics), 36 µl 10% Triton X-100, 0.5 µl 10 % BSA, 1 µl (600 U) T4 DNA ligase (HC, Enzymatics) and rotating ON at 16°C, 8 RPM. Reactions were stopped with 20 µl 0.5 M EDTA, treated with 1 µl 10 mg/ml DNase-free RNAse A for 15 minutes at 42°C, 33 µl 5 M NaCl and 55 µl 10 % SDS were added and crosslinks reversed for 4 h to ON at 65°C. Proteins were digested with 10 µl 20 mg/ml DNase-free proteinase K (Thermo) for 2 h at 55°C while shaking at 800 RPM, then 90 minutes at 65°C. After extraction with 600 µl ph 8-buffered phenol/chloroform/isoamyl alcohol (Ambion) followed by 300 µl chloroform, DNA was precipitated with 1.5 µl (22.5 µg) Glycoblue (Ambion) and 1400 µl 100% ethanol ON at -20°C, pelleted for 20’ at 16000g, 4°C, washed twice with 80% ethanol, and the pellet air-dried and dissolved in 131 µl TT (0.05% Tween 20/Tris pH 8). DNA (800 ng) was sheared to 300 bp in 130 µl TT on a Covaris M220 or S220, using the manufacturer’s protocol. DNA was then directly bound to streptavidin-coated Dynabeads. Biotinylated DNA captured on Dynabeads MyOne Streptavidin T1 (Thermo) by combining the sample (50 µl or 130 µl) with 20 µl Dynabeads that had previously been washed once with 1x B&W buffer (2X B&W: 10 mM Tris-HCl pH=7.5, 1 mM EDTA, 2 M NaCl), and had been resuspended in 50 µl or 130 µl 2x B&W containing 0.2% Tween 20. The binding reaction was rotated at RT for 30 minutes, and DNA-bound beads were washed once with 1 ml 1x B&W/0.1% Triton-X 100, once with TET (0.2% Tween 20, 10 mM Tris pH 8, 1 mM EDTA). Beads were resuspended in 100 µl Blunting Mix (74.5 µl water, 0.5 µl 10% Tween 20, 10 µl 10x T4 DNA ligase buffer (Enzymatics), 4 µl 10 mM dNTP, 2 µl (6 U) T4 DNA polymerase (Enzymatics), 0.4 µl (2 U) Klenow fragment (Enzymatics), 2 µl (20 U) T4 polynucleotide kinase (Enzymatics)) and incubated for 30 minutes at 20°C. Reactions were stopped by adding 2.5 µl 0.5 M EDTA, beads collected on a magnet and washed twice with 150 µl 1x B&W/0.1% Triton-X 100, once with 180 µl TET. Beads were resuspended in 50 µl A-tail Mix (44.25 µl water, 0.5 µl 10% Tween 20, 5 µl NEBuffer 2, 0.2 µl 100 mM dATP, 0.3 µl (15 U) Exo--Klenow (Enzymatics) and incubated for 30 minutes at 37°C. Reactions were stopped by adding 1.5 µl 0.5 M EDTA, beads collected on a magnet and the SN was discarded. Beads were resuspended on ice in 48 µl ice-cold Ligation mix (25 µl 2x T4 DNA ligation buffer (Enzymatics), 0.5 µl 10% Tween 20, 22.5 µl water), 2 µl 0.6 µM Bioo Nextflex DNA sequencing adapters were added, and the reaction incubated for 20 minutes at RT. Reactions were stopped by adding 5 µl 0.5 M EDTA, and beads were washed twice with 1x B&W/0.1% Triton-X 100, once with TET and resuspended in 30 µl 0.05% Tween 20/LoTE (TE dilute 1:4 with water). Libraries were amplified by PCR for 10 or 12 cycles (98°C, 30s; 10

treatment_protocol: Influenza A/Vietnam/1203/2004 (H5N1) HAlo virus is a recombinant virus that has been engineered to remove the multibasic cleavage site in the HA protein (Steel et al., 2009).  The H5N1-dNS1  (dNS1) virus expresses a truncated NS1 protein (residues 1-73) in the H5N1 HAlo background (Steel et al., 2009).  Viruses were propagated in ten-day-old embryonated chicken eggs (Charles River Laboratories) and titers were determined by plaque assay in MDCK cells. For infections, MDMs were washed with serum-free RPMI 1640 medium, and infected at a multiplicity of two with H5N1 HAlo virus or H5N1 NS1trunc virus. After 1 hour, virus inoculum was removed, cells were washed twice with serum-free RPMI 1640 medium, and then incubated in RPMI 1640 medium containing 10% serum and antibiotics. THP-1 mRNA electroporation: IVT mRNA was generated from PCR-synthesized, T7 promoter-containing templates with an mMESSAGE mMACHINE T7 Ultra Kit (Ambion) according to the manufacturer’s instructions, using either normal NTP or incorporating methyl-cytosine and pseudo-uridine. IVT RNA preparations that were used without concomitant interferon treatment were dephosphorylated with calf intestinal phosphatase to eliminate the RIG-I response and subsequent IFNβ production that 5’-triphosphorylated RNA can trigger. For electroporations, 3 M THP-1 cells were pelleted by centrifugation, serum RNases were removed by washing cells twice at room temperature with phenol red-free OptiMEM (Life Technologies). Cells were electroporated in 200 µl phenol red-free OptiMEM in a 4 mm cuvette with a rectangular pulse of 400 V and 5 ms duration, delivering 5 µg IVT mRNA using Gene Pulser Xcell (Bio-Rad). Immediately after electroporation, the cell suspension was transferred into a well of a six-well plate filled with 2 ml pre-warmed THP-1 medium (RPMI-1640 containing 10% low-endotoxin FBS (Peak Serum Inc.), 1x (100 µM) non-essential amino acids (Life Technologies), 1x MEM Sodium Pyruvate Solution (1 mM) (Life Technologies), 1x GlutaMax I (Life Technologies), 50 µM β-mercaptoethanol) and cultured at 37°C, 5% CO2, 100% humidity for 6 h. THP-1 cells were electroporated with siRNA against WAPL and NIBPL (or control) using the same protocol as described for mRNA electroporation. Agonists were used at the following concentrations: IFNβ - 1000 U/ml , Pam3CSK4 - 1 µg/ml, Dexamethasone - 1 µM, flavopiridol - 2 µM.

value: THP-1 monocyte AML cell line (+PMA)

tag: treatment

value: IFNb treated (6h)

tag: treatment time

tag: donor or replicate

tag: electroporated mrna

tag: sirna


title: N13_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: THP1mac-HiC-IFNb-0h

description:
in situ Hi-C
THP1mac-HiC-IFNb-0h
Sample137.THP1mac-HiC-IFNb-0h.hic

tag: cell type

value: untreated


title: Freshly isolated intestinal myofibroblasts, sample 3

description: Pooled from 2 mice

tag: strain


title: CU115_0hr-12hpt_rep2


title: SD_ZT0_3

description: first experiment

value: 13 days


title: SD_ZT0_1

description: first experiment


title: THP1mac-HiC-Dex-6h

description:
in situ Hi-C
THP1mac-HiC-Dex-6h
Sample136.THP1mac-HiC-Dex-6h.hic

value: dexamethasone (6h)

tag: chip antibody


title: Freshly isolated intestinal myofibroblasts, sample 2

description: Pooled from 2 mice

tag: tissue


title: T12_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: H33BKI_WT_ESC_rep2

source_name: mouse embryonic stem cell

tag: genotype


title: N11_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: RP2_0hr-12hpt_rep1

source_name: RP2 cells 12hrs post sodium butyrate treatment

value: sodium butyrate

source_name: RP2 cells 0hrs post sodium butyrate treatment


title: RP2_12hpt-24hpt_rep2

source_name: RP2 cells 24hrs post sodium butyrate treatment

value: 24 hr


title: RP2_0hr-24hpt_rep1


title: RP2_12hpt-24hpt_rep1

value: 12 hr


title: RP2_0hr-24hpt_rep2

value: control


title: T13_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: N12_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: RP2_0hr-12hpt_rep2

value: 0 hr


title: T11_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: T9_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: T10_(HuGene-2_0-st)

description: take from the range of gastric cancer


title: THP1-HiC-Pam3csk-000m-Flavo-240m

description:
in situ Hi-C
THP1-HiC-Pam3csk-000m-Flavo-240m
Sample134.THP1-HiC-Pam3csk-000m-Flavo-240m.hic

source_name: THP-1 monocyte AML cell line

value: THP-1 monocyte AML cell line

value: Flavopiridol (4h)


title: Freshly isolated intestinal crypts, sample 4

description: From single mouse


title: Freshly isolated intestinal crypts, sample 3

description: From single mouse


title: THP1-HiC-Pam3csk-360m-Flavo-240m

description:
in situ Hi-C
THP1-HiC-Pam3csk-360m-Flavo-240m
Sample133.THP1-HiC-Pam3csk-360m-Flavo-240m.hic

value: Pam3csk4 treated (6h) + Flavopiridol (4h)


title: MSB1_12hpt-24hpt_rep2

source_name: MSB1 cells 12hrs post sodium butyrate treatment

source_name: MSB1 cells 24hrs post sodium butyrate treatment


title: Freshly isolated intestinal crypts, sample 1

description: From single mouse


title: H33BKI_WT_ESC_rep1


title: MSB1_0hr-24hpt_rep1

source_name: MSB1 cells 0hrs post sodium butyrate treatment


title: MSB1_0hr-24hpt_rep2


title: THP1-HiC-Pam3csk-000m-Flavo-000m

description:
in situ Hi-C
THP1-HiC-Pam3csk-000m-Flavo-000m
Sample131.THP1-HiC-Pam3csk-000m-Flavo-000m.hic


title: Freshly isolated intestinal myofibroblasts, sample 1

description: Pooled from 2 mice


title: N8_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer

value: Normal gastric mucosa tissue


title: 96S3

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description:
D16-10962
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

data_processing:
Sequencing run with HiSeq Control Software (HCS) version 2.2.58 and Real Time Analysis (RTA) version 1.18.64.
Fastq sequences prepared with bcl2fastq version 2.15.0.
Fastq reads were aligned to the mm9 assembly and UCSC known gene annotation using bowtie 1.0.1 and expression values were calculated using RSEM version 1.2.30.
Genome_build: mm9 (MGSCv37) with UCSC known genes annotation.
Supplementary_files_format_and_content: kknouse_IntCounts.txt: Text file of Integer counts for each UCSC known gene.
Supplementary_files_format_and_content: kknouse_l2fpkm.txt: Text file of FPKM values for each UCSC known gene transformed into log2 space by adding 1 to each FPKM value prior to calculation of Log2 value.
Supplementary_files_format_and_content: kknouse_ucscKG_annotation.txt: Text file associating UCSC known gene IDs with mouse gene symbols and gene category annotations. These data were derived from the UCSC known gene gtf file.

source_name: Mammary epithelial cells cultured in spheroids within a Matrigel substrate

growth_protocol: To culture mammary epithelial cells as monolayers, cells were trypsinized, washed with PBS, replated on collagen-coated dishes, and cultured in MEBM with supplements containing 1 µM progesterone and 1 µg/mL prolactin. To culture mammary epithelial cells as spheroids, cells were trypsinized, washed with PBS, and resuspended in MEBM with supplements at 7 x 10^5 cells per mL. Cells were then combined with four volumes of phenol red-free, growth factor-reduced Matrigel (Corning) and 100 µL gels were cast in individual wells of 24-well glass-bottom plates (Mat Tek). Gels were polymerized at 37 C for 30 minutes before adding 500 µL of MEBM with supplements, 1 µM progesterone, 1 µg/mL prolactin. Gels were cultured at 37 C with 5% CO2 for 24 to 96 hours, with medium changed after 48 hours of culture.

extract_protocol:
RNA STAT-60 (Amsbio) was added to monolayers and spheroids, homogenized with a rubber policeman or 1 mL syringe plunger, and triturated with a P1000 pipette tip. RNA was then purified by chloroform extraction according to RNA STAT-60 instructions.
Illumina TruSeq.

tag: strain/background

value: Mammary epithelial cells

tag: culture condition

value: Spheroid in Matrigel

tag: culture time


title: 96S2

description:
D16-10961
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt


title: MDM-RNAseq-IFNb-06h-r1

description:
total strand-specific RNA-seq
MDM-RNAseq-IFNb-06h-r1
fpkm.txt.gz

source_name: monocyte derived macrophages (MDM)

value: monocyte derived macrophages (MDM)

value: IFNb treated (06h)


title: THP1-HiC-Pam3csk-120m-Flavo-000m

description:
in situ Hi-C
THP1-HiC-Pam3csk-120m-Flavo-000m
Sample132.THP1-HiC-Pam3csk-120m-Flavo-000m.hic

value: Pam3csk4 treated (2h)


title: MSB1_0hr-12hpt_rep2

tag: cell line


title: MDM-RNAseq-IFNb-06h-r2

description:
total strand-specific RNA-seq
MDM-RNAseq-IFNb-06h-r2
fpkm.txt.gz


title: N4_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: T8_(HuGene-2_0-st)

description: take from the range of gastric cancer

value: Gastric cancer tissue


title: N9_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: N10_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: 96M3

description:
D16-10959
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

source_name: Mammary epithelial cells cultured in monolayers on collagen-coated dishes

value: Monolayer on Collagen


title: N7_(HuGene-2_0-st)

description: ＞5cm, from the edge of cancer


title: H3K18ac_t14_ChIPSeq

city: Boston

first: Salvador

last: Casani

address: 450 Brookline Avenue

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Quality filtering was performed using Trimmomatic v0.32
Genome mapping was done using RNA-STAR sofware using S. cerevisiae as reference genome, EnsEMBL release 91 was the version used.
Alignments were filtered for multimapped reads and subject for duplicate removal using Samtools software
Genomecov software (from bedtools) was used for coverage per nucleotide quantification
Genome_build: S. cerevisiae EnsEMBL (release 91)
Supplementary_files_format_and_content: Processed data files are per-base genome coverage. Three columns represent: chromosome, base and number of reads that fall in the given base.

organism: Saccharomyces cerevisiae

source_name: Yeast Metabolic Cycle

extract_protocol:
~50 OD cycling cells per time point were collected for ChIP 3 µg primary antibody was used per ChIP experiment. Briefly, cells were first fixed in 1% formaldehyde at 25℃ for 15 min and quenched in 125mM glycine at 25℃ for 10 min. Cells were pelleted and washed twice with buffer containing 100 mM NaCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1 mM PMSF, 1 mM benzamidine•HCl before freezing. The frozen pellet was resuspended in 0.45 ml ChIP lysis buffer (50 mM HEPES•KOH pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% deoxycholate (DOC), 0.1% SDS, 1 mM PMSF, 10 µM leupeptin, 5 µM pepstatin A, Roche protease inhibitor cocktail) and lysed by bead beating. Lysate from 50 OD cells were split into two tubes each containing 280 µl lysate and sonicated for 16 cycles (30 sec on, 1 min off, high output) using a Bioruptor (Diagenode, Denville, NJ or Tosho Denki, Japan). The supernatant of the sonicated lysate was pre-cleared. 50 µl lysate was saved as input. For ChIP with histone antibodies, 50 µl whole cell extract (WCE) was diluted 1:10 and used for each ChIP. After incubation overnight, 50 µl protein A Sepharose beads (GE Healthcare Life Sciences, Piscataway, NJ, 17-5280-01) resuspended in ChIP lysis buffer was added and incubated for 1.5 h at 4 ℃. Beads were washed twice with ChIP lysis buffer, twice with DOC buffer (10 mM Tris•Cl pH 8.0, 0.25 M LiCl, 0.5% deoxycholate, 0.5% NP-40, 1 mM EDTA) and twice with TE. 125 µl of TES buffer (TE pH8.0 with 1% SDS, 150 mM NaCl, and 5 mM dithiothreitol) was added to resuspend the beads. Supernatant was collected after incubation at 65°C for 10 min. A second round of elution was performed and the eluates were combined. Reverse crosslinking was performed by incubation for 6 h at 65°C. An equal volume of TE containing 1.25 mg/ml proteinase K and 0.4 mg/ml glycogen was added to the samples after reverse crosslinking and samples were incubated for 2 h at 37°C. Samples were extracted twice with an equal volume of phenol and once with 25:1 chloroform:isoamyl alcohol. DNA was precipitated in 0.1 volume 3.0 M sodium acetate (PH 5.3) and 2.5 volume of 100% ice-cold ethanol at -20℃ overnight. Pellets were washed once with cold 70% ethanol and resuspended in 20 µl TE.
Library construction and sequencing were performed following the Illumina protocol. Briefly, DNA was end repaired and A-tailed. Barcoded adaptors were ligated and DNA was run in 2% agarose gel. DNA fragments from 150 bp to 300 bp long were excised from gel and used for PCR. PCR products were gel-extracted again and quantified on an Agilent Bioanalyzer.

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX

value: H3K18ac (Millipore, Mi 07-354)

tag: time


title: H3K18ac_t16_ChIPSeq


title: H3K18ac_t15_ChIPSeq


title: T4_(HuGene-2_0-st)

description: take from the range of gastric cancer

source_name: Gastric cancer tissue


title: 96M1

description:
D16-10957
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt


title: H3K18ac_t13_ChIPSeq


title: MSB1_0hr-12hpt_rep1

tag: agent

value: sodium butyrate

tag: time (post sodium butyrate)


title: MDM-RNAseq-dNS1-06h-r2

description:
total strand-specific RNA-seq
MDM-RNAseq-dNS1-06h-r2
fpkm.txt.gz

tag: treatment

value: H5N1-dNS1 IAV infected (06h)


title: 96M2

description:
D16-10958
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt


title: MDM-RNAseq-dNS1-06h-r1

description:
total strand-specific RNA-seq
MDM-RNAseq-dNS1-06h-r1
fpkm.txt.gz

tag: treatment time


title: MDM-RNAseq-Mock-06h-r4

description:
total strand-specific RNA-seq
MDM-RNAseq-Mock-06h-r4
fpkm.txt.gz

value: mock infected (06h)

tag: donor or replicate


title: MDM-RNAseq-H5N1-06h-r3

description:
total strand-specific RNA-seq
MDM-RNAseq-H5N1-06h-r3
fpkm.txt.gz

value: H5N1 IAV infected (06h)

tag: electroporated mrna


title: MDM-RNAseq-H5N1-06h-r4

description:
total strand-specific RNA-seq
MDM-RNAseq-H5N1-06h-r4
fpkm.txt.gz

tag: sirna


title: H3K18ac_t12_ChIPSeq


title: 96S1

description:
D16-10960
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

tag: cell type


title: Freshly isolated intestinal crypts, sample 2

description: From single mouse

value: Small intestine

tag: strain


title: 48S1

description:
D16-10954
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt


title: Evf2TS/TS:E13.5MGE rep5

city: Chicago

first: Jhumku

last: Kohtz

address: 303 E Chicago

institute: Northwestern University

description: Gene expression from MGE in the absence of Evf2

hyb_protocol: Standard Affymetrix protocol, Affymetrix.GeneChip.Mouse430_2 were used

scan_protocol: Standard Affymetrix protocol

data_processing: The data were analyzed using GeneSpring software.  Pvalue cut-offs were set to p=0.05 for differential analysis.

label_protocol: Biotinylated cRNAs were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: E13.5 medial ganglioinc eminences were extracted from mouse embryonic brain using fine dissection tweezers, placed in ice cold L15 medium, pooled, and flash frozen in Liquid nitrogen.  Tissues were stored at -80 until RNA isolation.

extract_protocol: Total RNA was isolated using the E.Z.N.A. total RNA kit (Omega).

value: Evf2TS/TS (mutant)

tag: gender

value: Male

value: mixed background (129Sv, Bl6, Fvbn)

value: Medial ganglioinic eminences pooled from two embryonic brains (n=4)

tag: age


title: 48S3

city: Cambridge

description:
D16-10956
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

value: Mammary epithelial cells

value: Spheroid in Matrigel


title: Evf2TS/TS:E13.5MGE rep4

tag: genotype

tag: tissue


title: Evf2TS/TS:E13.5MGE rep3


title: 48M3

description:
D16-10953
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

tag: strain/background

tag: culture condition


title: H3K27me3_ChOR-seq_biotin_T0_rep2

city: Copenhagen

first: Anja

last: Groth

address: Blegdamsvej 3B

country: Denmark

institute: Novo Nordisk Foundation Center for Protein Research

data_processing:
Library strategy: ChOR-seq
Base calling software: Casava 1.8.2
Reads were aligned to  human genome assembly (GRCh37/hg19) using Bowtie v. 1.1.2 with parameters -m1 --best.
PCR duplicates were removed using rmDup v. 2-0  and unique mapped reads were extended to 500bp to account for the average library size.
Reads were summed in 250 bp non-overlapping bins and values were normalized to Reads Per Million (RPM).
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using Parental ChIP-seq of Total H3 from each experiment as a reference.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM in 250bp windows

source_name: HeLa S3 cells

growth_protocol: Human HeLa S3 cells were grown in suspension in spinners in DMEM medium (Thermo Fisher Scientific) supplemented with dialyzed FBS (Invitrogen) and penicillin and streptomycin at 37ºC and 5% CO2.

extract_protocol:
Fixed cells were lysed during 20 min in ice-cold lysis buffer (100mM NaCl, 66mM Tris HCl pH8, 5mM EDTA, 0.3% SDS, 1.6% Triton X-100) supplemented with proteases inhibitors, passed through a 21G needle and sonicated using a Bioruptor nextGen (Diagenode) to obtain chromatin frgament size of 250-500bp. Sonicated chromatin was centrifuged at 14000rpm at 4ºC for 10 min and the supernatant used for subsequent steps. Chromatin associated to each histone mark was obtained by incubating sonicated chromatin with the corresponding antibody.After ChIP, chromatin was separated from Protein A agarose beads by an incubation with Elution buffer (10 mM Tris HCL, 1 mM EDTA, 2 % SDS, 15 mM DTT, pH 8 supplemented with protease inhibitors) for 30 min at 37 ºC in rotation. Supernatant was diluted 20 times with RIPA and chromatin was then incubated with MyOne Streptavidin T1 beads. For single streptavidin pull-downs, 30 μg of input chromatin was used in the following steps. Briefly, MyOne streptavidin T1 beads were blocked by incubating with 1μg/ml free biotin (Sigma) for 10 min at room temperature. Beads were then washed three times with RIPA buffer and chromatin was pre-cleared with blocked beads for 1 h at 4 ºC. After pre-clearing, supernatant was incubated with new non-blocked T1 streptavidin beads over night at 4 ºC. Beads were then washed for 5 min rotating at room temperature, once with RIPA buffer, twice with 2 % SDS, once with RIPA 0.5 M NaCl, once with 1X LiCl buffer and twice with TE buffer. Chromatin was then purified and decrosslinked.
Libraries were costructed using the NEB Next Ultra DNA Library prep kit (New England Biolabs) following manufacturer’s instructions.Samples were indexed and 4 different samples sequenced together.

treatment_protocol: For all ChOR-seq and ChIP-seq, HeLa S3 cells were synchronized at the G1/S border by single thymidine block (2 mM, 17 h) and released into fresh media containing deoxycytidine (24 μM). Parental samples were collected 1 hour before labelling. 3h and 15 min after release, DNA was labelled during 20 min with medium containing biotin-dUTP and Nascent chromatin was collected (T0). For each time-course experiment, replicated DNA was isolated by single Streptavidin pull-down on Nascent chromatin. Harvested cells were immediately fixed in 1% formaldehyde for 15 min.  Fixation was stopped by adding Glycine (0.125M) and incubating for 5 min at RT.

tag: cell line

value: HeLa S3

value: cervical carcinoma

tag: ezh2i treatment

value: Non treated

tag: spike-in

value: NO

tag: labelling

value: biotin-dUTP

tag: cell cycle

value: Mid S (3 h and 15 min after release)

tag: antibody

value: H3K27me3 C36B11(Cell Signaling Technology, Cat No. 9733S_RRID:AB_2616029)


title: Evf2TS/TS:E13.5MGE rep1

value: Female


title: Evf2TS/TS:E13.5MGE rep2


title: 48S2

description:
D16-10955
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

tag: culture time


title: MSB1_12hpt-24hpt_rep1

tag: agent

value: sodium butyrate

tag: time (post sodium butyrate)

value: 24 hr

tag: replicate

value: 12 hr


title: H3K18ac_t10_ChIPSeq

tag: strain

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX

tag: chip antibody

value: H3K18ac (Millipore, Mi 07-354)

tag: time


title: MDM-RNAseq-Mock-06h-r3

description:
total strand-specific RNA-seq
MDM-RNAseq-Mock-06h-r3
fpkm.txt.gz

tag: cell type

value: monocyte derived macrophages (MDM)

tag: treatment

value: mock infected (06h)

tag: treatment time

tag: donor or replicate

tag: electroporated mrna

tag: sirna


title: THP1mac-HiC-Dex-0h

description:
in situ Hi-C
THP1mac-HiC-Dex-0h
Sample135.THP1mac-HiC-Dex-0h.hic

value: THP-1 monocyte AML cell line (+PMA)

value: untreated


title: H3K18ac_t11_ChIPSeq


title: T7_(HuGene-2_0-st)

description: take from the range of gastric cancer

tag: tissue

value: Gastric cancer tissue


title: H3K18ac_t9_ChIPSeq


title: Evf2+/+:E13.5MGE rep 4

description: Gene expression data from MGE expressing Evf2.

tag: genotype

value: Evf2+/+ (wildtype)

tag: gender

value: Male

value: mixed background (129Sv, Bl6, Fvbn)

value: Medial ganglioinic eminences pooled from two embryonic brains (n=4)

tag: age


title: H3K18ac_t8_ChIPSeq


title: 48M2

description:
D16-10952
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

tag: strain/background

value: Mammary epithelial cells

tag: culture condition

value: Monolayer on Collagen

tag: culture time


title: H3K27me3_ChOR-seq_biotin_T0_rep1

tag: cell line

value: HeLa S3

value: cervical carcinoma

tag: ezh2i treatment

value: Non treated

tag: spike-in

value: NO

tag: labelling

value: biotin-dUTP

tag: cell cycle

value: Mid S (3 h and 15 min after release)

tag: antibody

value: H3K27me3 C36B11(Cell Signaling Technology, Cat No. 9733S_RRID:AB_2616029)


title: H3_ChOR-seq_biotin_T0_rep1

tag: cell type

value: Total H3 (Abcam, Cat No. Ab179, RRID:AB_302613)


title: H3K18ac_t6_ChIPSeq

tag: strain

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX

tag: chip antibody

value: H3K18ac (Millipore, Mi 07-354)

tag: time


title: F1-TCPOBOP-3m

city: Mainz

first: Piyush

last: More

address: Langenbeckstrasse 1

department: Department of Pharmacology

country: Germany

institute: University Medical Center, Johannes Gutenberg University of Mainz

description: F1 mice

data_processing:
Quality of raw sequencing reads was checked using FastQC version 0.11.5 (Babraham Bioinformatics, Cambridge, UK)
RNA-Seq reads were aligned to the GRCm38 genome (GENCODE) using STAR aligner version 2.5.3a (Dobin A et al., Bioinformatics, 2013, 29(1):15-21) with the option "--quantMode GeneCounts"
Differential gene expression analysis was performed using edgeR version 3.20.1 (Robinson MD et al., Bioinformatics, 2010, 26(1):139-140)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include mapped gene counts for each sample
Supplementary_files_format_and_content: XLS files include differential gene expression analysis using edgeR

source_name: Liver

growth_protocol: All animal experiments conformed to the Guide for the Care and Use of Laboratory Animals published by the US National Institutes of Health, and they were approved by the responsible local ethics committee. C57BL/6J were obtained from Envigo (Venray, Netherlands). Maximally 5 animals per cage were kept on a 12 h light cycle at a temperature of 20–24°C and 45-65% humidity. Females were housed individually beginning with the last three days before giving birth.

extract_protocol:
Total hepatic RNA was isolated from livers of adult mice using TriFast (PeqLab, Erlangen, Germany). The hepatic RNA from newborn mice was isolated with RNeasyKit (Qiagen, Hilden, Germany).
The library was prepareed using TruSeq RNA Library Prep Kit (Illumina) at Star SEQ GmbH, Mainz, Germany

treatment_protocol: Three-day-old F0 mice were injected with TCPOBOP (3 mg/kg, i.p.) in corn oil or with corn oil alone.

value: 3 months

tag: tissue

value: Liver

tag: treatment

value: TCPOBOP


title: Streptavidin_pull-down_biotin_midS_rep2


title: H3K18ac_t7_ChIPSeq


title: Evf2+/+:E13.5MGE rep 5

department: Neurology

tag: genotype

value: Evf2+/+ (wildtype)

tag: gender

value: Male

value: mixed background (129Sv, Bl6, Fvbn)


title: H3K18ac_t4_ChIPSeq


title: Streptavidin_pull-down_biotin_midS_rep1


title: Evf2+/+:E13.5MGE rep 3

value: Female

value: Medial ganglioinic eminences pooled from two embryonic brains (n=4)

tag: age


title: 48M1

description:
D16-10951
mRNA
processed data file: kknouse_IntCounts.txt
processed data file: kknouse_l2fpkm.txt

tag: strain/background

value: Mammary epithelial cells

tag: culture condition

value: Monolayer on Collagen


title: H3_ChOR-seq_biotin_T0_rep2

tag: cell line

value: HeLa S3

value: cervical carcinoma

value: Non treated

value: NO


title: Evf2+/+:E13.5MGE rep1


title: H3K18ac_t2_ChIPSeq


title: F1-CO-6d

description: F1 mice

value: 5-6 days

value: Corn oil


title: H3K27me3_ChIP-seq_biotin_Parental_rep2

data_processing:
Base calling software: Casava 1.8.2
Reads were aligned to  human genome assembly (GRCh37/hg19) using Bowtie v. 1.1.2 with parameters -m1 --best.
PCR duplicates were removed using rmDup v. 2-0  and unique mapped reads were extended to 500bp to account for the average library size.
Reads were summed in 250 bp non-overlapping bins and values were normalized to Reads Per Million (RPM).
Peak calling was performed with MACS v. 2.0.9 under broad domain parameters using Parental ChIP-seq of Total H3 from each experiment as a reference.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bedgraph files were generated using Galaxy. Scores represent the sum of RPM in 250bp windows

tag: ezh2i treatment

value: biotin-dUTP

value: Early S (2 h and 15 min after release)

value: H3K27me3 C36B11(Cell Signaling Technology, Cat No. 9733S_RRID:AB_2616029)


title: F1-CO-3m

description: F1 mice

value: 3 months

value: Liver


title: H3K18ac_t5_ChIPSeq

value: ZKY329:CEN.PK MATa SPT7-FLAG::natMX

value: H3K18ac (Millipore, Mi 07-354)


title: H3K18ac_t3_ChIPSeq


title: F1-TCPOBOP-6d

description: F1 mice

value: TCPOBOP


title: Evf2+/+:E13.5MGE rep2

value: Evf2+/+ (wildtype)

value: Female

value: mixed background (129Sv, Bl6, Fvbn)

value: Medial ganglioinic eminences pooled from two embryonic brains (n=4)


title: H3_ChIP-seq_biotin_Parental_rep1

value: HeLa S3

value: cervical carcinoma

tag: spike-in

value: Total H3 (Abcam, Cat No. Ab179, RRID:AB_302613)


title: H3K18ac_t1_ChIPSeq


title: F0-CO-3m

description: F0 mice


title: H3K27me3_ChIP-seq_biotin_Parental_rep1

value: Non treated

value: NO

tag: labelling