title: RT_STR_24h_B3

city: Ithaca

first: Neil

middle: Scott

last: Mattson

address: 134A Plant Sci Bldg

department: School of Integrative Plant Science

institute: Cornell University

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control and preprocessing of metagenomic data were performed using FastQC software. Adapters and low quality sequences were filtered out with Ea-Utils software. Reads with phred-like quality score greater than 30 and read length greater than 50-bp were kept and aligned against the Petunia axillaris reference genome
FPKM normalization by gene length and library size (Cufflinks) was used. Table counts were also generated with HtSeq for edgeR analysis
Genome_build: Petunia axillaris
Supplementary_files_format_and_content: tab-delimited text files include  tables counts prdocuded with HtSeq

organism: Petunia x hybrida

growth_protocol: hydroponic system with Hoagland’s nutritive  solution  in a growth chamber at 22 C was used

extract_protocol:
Total RNA was isolated using Trizol Reagent (Invitrogen, USA) and purified through a Qiagen RNeasy Column (Qiagen, Germany) according to the manufacturer’s instructions.
Strand-specific libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control (CTR) no salt; 150 mM Salt (STR)

value: mitchell diploid

value: Root

tag: treatment

value: Salt stress


title: RT_STR_48h_B2

status: Public on Jun 14 2017

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cultivar

tag: tissue


title: RT_STR_48h_B3


title: RT_STR_24h_B1


title: RT_STR_24h_B2


title: Dark grown, Ground Control, WS Rep2

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
DK GC WS Rep2
3. DK GC Col-0 to DK GC WS
10. DK FLT WS to DK GC WS
15. DK GC WS to LT GC WS

data_processing:
The paired end reads were mapped to the A. thaliana var. Columbia reference genome (TAIR10) using TopHat (Trapnell et al., 2009).
Multi-step process of transcriptome assembly and differential expression analysis was done using the Cufflinks tool (Trapnell et al., 2010; Trapnell et al., 2012). Reads that map to each transcript were counted and normalized based on fragment length and total reads. Normalized counts were expressed in terms of FPKM values (fragments per kilobase of transcript per million mapped fragments). FPKM is directly proportional to abundance of the transcript. The expression data was generated at a False Discovery Rate = 0.01 (FDR=0.01). At this FDR, a total of 33,234 genes were tested.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM, fold change

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; grown on the ground, 11 day old plant harvested into KFT containing RNAlater fixative

growth_protocol: Three seed lines Wild-Type Wassilewskija (Ws), Columbia-0 (Col-0) and Col-0 PhyD (phyD) Mutants were tested for viability, sterility and ability to maintain dormancy before the launch. Tested batches of seeds were planted on phytagel plates as one genotype per plate for gene expression analysis in replicates of three. One set was planted for the flight and one for ground control. The plates were wrapped such that every surface of the plate was covered by two layers of Duvetyn Black-Out cloth (Seattle Fabrics) (Sng et al, 2014). The plates were stored 4° C until launch, and was then launched in a cold-stow bag to maintain the plates at 4° C until integration and activation on the ISS.

extract_protocol:
Seedlings stored in RNA later were recovered from -80°C freezer. Each tube containing the seedlings was allowed to thaw in the fridge overnight. After completely thawing the samples to room temperature, the seedlings were observed under the microscope. The preserved seedlings from the spaceflight and ground control harvests were dissected into distinct plant parts: leaf, hypocotyl, root tip and then the rest of the root. The root tip was defined as the last 2mm of the root for the light-grown plants and the last 1mm for the dark-grown plants. All the sections dissected were saved in RNA later and stored back to -80°C freezer.  Three independent roots were used as three biological replicates for the transcriptomic analysis. The root apex was dissected as 2mm root tip section for light grown samples and 1mm section for the dark grown samples. Dissected root tips were carefully transferred into pre-labeled micro-centrifuge tubes, flash frozen in liquid N. Total RNA was extracted from these frozen samples using Picopure RNA isolation kit (Arcturus®, Life technologies). RNA concentration was determined on a Qubit (Thermo Fisher/Life Technologies, Inc) and sample quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.). Five ng RNA from each sample was used for low input array and RNA sequencing.
RNASeq Libraries Preparation using SMART-Seq V4 ultra low input RNA kit for sequencing combined with Illumina Nextera DNA Sample Preparation Kit  Five ng of total RNA was used for cDNA library construction using CloneTech SMART-Seq V4 ultra low input RNA kit for sequencing (Clontech Laboratories, Inc, cat#: 634890) according to manufacturer's protocol. Briefly, 1st strand cDNA was primed by the SMART-Seq v4 oligonucleotide and then base-pairs with these additional nucleotides, creating an extended template. The reverse transcriptase then switches templates and continues transcribing to the end of the oligonucleotide, resulting full-length cDNA that contains an anchor sequence that serves as a universal priming site for second strand synthesis. cDNA was amplified with primer II A for 9 PCR cycles. Then Illumina sequencing libraries were generated with 120 pg of cDNA using Illumina Nextera DNA Sample Preparation Kit (Cat#: FC-131-1024) according to manufacturer’s instructions. Briefly, 120 pg of cDNA was fragmented by tagementation reaction and then adapter sequences added onto template cDNA by PCR amplification. Libraries were quantitated by Bioanalyzer and qPCR (Kapa Biosystems, catalog number: KK4824). Finallly, the libraries were pooled equal molar concentration and sequenced by Illumina 2X75 NextSeq 500.
NextSeq500 sequencing: RNA seq  In preparation for sequencing, barcoded libraries were sized on the bioanalyzer, quantitated by QUBIT and qPCR (Kapa Biosystems, catalog number: KK4824). Individual samples were pooled equimolarly at 4 nM. This “working pool” was used as input in the NextSeq500 instrument sample preparation protocol (Illumina, Part # 15048776, Rev A). Typically, a 1.3 pM library concentration resulted in optimum clustering density in our instrument (i.e., ~200,000 clusters per mm2). Samples were sequenced on three flowcells, using a 2x75 cycles (paired-end) configuration. A typical sequencing run in the NextSeq500 produced 750-800 million paired-end read with a Q30>=85%. For RNA seq, around 40 million reads provided sufficient depth for transcriptome analysis.

treatment_protocol: The dormant plates were activated on station by removing the Black-Out cloth wrapping 12 days after launch. The plates were then placed on a fabric that was mounted in the US Laboratory module on the wall adjoining the MELFI freezer and secured using Velcro. The plants were allowed to grow on orbit for 11 days; some in the ambient light of ISS and some in the dark. The dark-grown plates were first activated by exposing the seeds to light for 4 hours, and then re-wrapped in Black-Out cloth for the duration of the growth period. A corresponding set of seedlings were grown as ground control in KSC.   At 11 days, seedlings were photographed, harvested into KFT containing RNAlater solutions and returned for post-flight analysis. All plates were harvested into KFTs with their counterpart (e.g. Light 1 was harvested with Dark 1). Once the plants were placed in the KFTs, the KFT was actuated with RNAlater to preserve the sample. At 24 hours post-harvest, KFTs were then transferred to MELFI, the -32°C freezer. Following SpaceX-3 splashdown in the Pacific Ocean, the KFTs transferred to the Cold Stowage charter plane at the Long Beach Airport, placed into an insulated shipper with dry ice, and flown to Johnson Space Center (JSC). The KFTs were then transferred via FedEx ground to the Kennedy Space Center. The KFTs were removed from dry ice and transferred to a -80°C freezer on May 22, 2014. The PIs retrieved the plant samples from the KFTs on May 29, 2014 and transferred the samples back to the University of Florida.  The harvested material was used to compare the transcriptomes of each genotype. The patterns of gene expression was compared among genotypes within a treatment (spaceflight or unit gravity) and between treatments (spaceflight versus ground control) for each genotype.

value: WS

value: Roots

tag: organism part

value: root tip - the last 1mm of the root for the dark grown plants

tag: age

value: 11 days old plants

tag: protocol

value: dark grown

tag: biosource type

value: RNAlater fixed_sample


title: RT_STR_48h_B1


title: Light grown, Ground Control, Col-0 Rep1

description:
LT GC Col-0 Rep1
1. LT GC Col-0 to LT GC WS
5. LT GC Col-0 to LT GC PhyD
11. LT FLT Col-0 to LT GC Col-0
17. DK GC Col-0 to LT GC Col-0

value: root tip - the last 2mm of the root for the light grown plants

value: light grown


title: RT_STR_06h_B2


title: RT_STR_00h_B3


title: RT_STR_06h_B1


title: RT_STR_12h_B1


title: RT_STR_06h_B3


title: RT_STR_00h_B1


title: RT_CTR_48h_B2

value: Control


title: RT_CTR_48h_B3


title: RT_CTR_48h_B1


title: RT_STR_00h_B2


title: RT_CTR_24h_B3


title: RT_CTR_12h_B3


title: RT_CTR_12h_B2


title: RT_CTR_24h_B1


title: RT_CTR_24h_B2


title: RT_CTR_06h_B2


title: RT_CTR_12h_B1


title: RT_CTR_06h_B3


title: RT_STR_12h_B3


title: Mouse wild type erythroid cells Rad21 ChIP biological replicate 1

city: Oxford

first: Jelena

middle: M

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

country: United Kingdom

institute: Oxford University

library_source: genomic

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible, options: -m 9 –x 0.125)
Alignment of ChIP-seq data with bowtie 1.1.2 to mm9 (options: -m 2, -k 1, --best)
Samtools rmdup (to remove PCR duplicates)
Deeptools bamcoverage was used (options: --normalizeUsingRPKM) to normalise the reads for RPKM, and generate the bigWig file for visualisation
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of RPKM

molecule: genomic DNA

organism: Mus musculus

source_name: Ter119+ Erythroid cells

growth_protocol: C57BL/6 mice were treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days)

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (Miltenyi Biotec).
NEBnext ultra library prep kit

treatment_protocol: Ter119+ cells were isolated from mouse spleens

tag: strain

value: Phenylhydrazine treated spleen

tag: antibody

value: Anti-Rad21, Abcam ChIP Grade (ab992)


title: Mouse wild type erythroid cells Rad21 ChIP biological replicate 2


title: RT_CTR_00h_B2


title: RT_STR_12h_B2


title: LF_STR_24h_B2

value: Leaf


title: LF_STR_24h_B3


title: LF_STR_06h_B3


title: LF_STR_24h_B1


title: LF_STR_06h_B2


title: LF_STR_06h_B1


title: LF_STR_00h_B3


title: LF_STR_00h_B2


title: BV10-R-CD8-d12-Allo-RNA_CCGTCC_L006_R1_001.fastq.gz

city: Chapel Hill

first: Jonathan

middle: S

last: Serody

state: NC

address: 125 Mason Farm Rd.

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Sequenced reads were aligned to the mm9 genome using MapSplice version 2
Mapped reads were sorted and indexed using samtools version 1.2
Reads were translated into transcirptome coordinates and filtered for indels, large insterts, and zero mapping quality
Transcirptome coordinates were inputted into RSEM version 1.1.13 with pre-built RSEM mm9 references
Gene expression data was normalized to set the upper quartile count at 1000
Genome_build: mm9
Supplementary_files_format_and_content: Excel file including normalized gene expression data for each sample

source_name: Innate Lymphoid Cells

growth_protocol: Splenic T cells were isolated and sorted by CD4 or CD8 on the day of transplant or isolated 14 days after being transplanted at the time allo-BMT.

extract_protocol:
RNA was extracted from sorted splenic T cells using the RNEasy mini kit (Qiagen)
mRNA sequencing libraries were prepared according to the TruSeq protocol (Illumina)

treatment_protocol: Samples are pools of n=5 prior to flow sort

tag: cell type

value: CD8 splenic T cells

tag: time point

value: 14 days after


title: LF_STR_00h_B1

value: mitchell diploid


title: BV6-R-Donor-CD8-RNA_CTTGTA_L006_R1_001.fastq.gz

value: at the time of allogeneic transplant


title: IGF1 1h

city: Research Triangle Park

first: Sylvia

middle: C

last: Hewitt

address: 111 Alexander Dr

department: RDBL

institute: NIEHS

data_processing:
Each raw dataset was filtered to remove any reads with average base quality score <20 after trimming all reads to 36mers.
Filtered reads were mapped against the mm10 reference genome via Bowtie v0.12.8 with default parameters and '-m 1' option.
Duplicate mapped reads were removed with Picard tools v1.110 MarkDuplicates.jar.
For visualization of coverage, uniquely-mapped non-duplicate reads were extended to the estimated average fragment length (150nt) then converted to bedGraph format and normalized to 15 million reads.
Genome_build: mm10
Supplementary_files_format_and_content: Mapped read depth in bedGraph format.

source_name: uterus

extract_protocol:
Uteri were submersed in PBS + 1% formaldehyde, cut into small (~1 mm3) pieces with a razor blade and incubed at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycine (final). The tissue pieces were then treated with a TissueTearer and finally spun down and washed 2x in PBS. Chromatin was isolated from the sample by adding 5-10 ml lysis buffer containing PIPES, Igepal, PMSF and Protease Inhibitor Cocktail, followed by disruption with a Dounce homogenizer. Samples were pelleted by centrifugation and resuspended in buffer containing Na deoxycholate, SDS, and Triton X-100. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and the chromatin suspensions were transferred to new tubes and stored at -80 C. Prior to use in ChIP, protein A agarose beads (Invitrogen) were preblocked using blocking proteins and nucleic acids for 3 hr. For each ChIP reaction, an aliquot of chromatin (20-30 ug) was precleared with 30 ul preblocked protein A agarose beads for 1-2 hr. ChIP reactions were set up using precleared chromatin and antibody Eralpha (sc-542, Lot# D1310) in a buffer containing Na deoxycholate and incubated overnight at 4 C. Preblocked protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Agarose beads containing the immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. An SDS-containing buffer was added to elute the immune complexes from the beads, and the eluates were subjected to RNase treatment at 37 C for 20 min and proteinase K treatment at 37 C for 3 hr. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNAs were purified by phenolchloroform extraction and ethanol precipitation. Quality of ChIP enrichment was assayed by qPCR using primers against candidate EREs in the Igf1 and Stat5a promoters. Input DNA was queried at the same sites in parallel
ChIP DNA was amplified by following the Illumina ChIP-Seq DNA Sample Prep Kit protocol. In brief, DNA ends were polished and 5’-phosphorylated using T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. After addition of 3’-A to the ends using Klenow fragment (3’-5’ exo minus), Illumina genomic adapters were ligated and the sample was sizefractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles,Phusion polymerase), the resulting DNA libraries were quantified and tested by QPCR at the same specific genomic regions as the original ChIP DNA to assess quality of the amplification reactions. DNA libraries were sequenced on a Genome Analyzer II.

treatment_protocol: mice were ovariectomized, rested for 10-14 days, then injected with human recombinant long R3 IGF1 (0.5 mg/ml dissolved in sesame oil) or with ER antagonint ICI 182,780 (45 ug dissolved in 50 ul DMSO). Uterine tissue was collected 1 hour later, frozen in liquid notrogen, and shipped to Active Motif Inc for ERa ChIP-seq using Santa Cruz antibody sc-542

tag: agent

value: Eralpha, Santa Cruz sc-542


title: BV5-R-Donor-CD4-RNA_GGCTAC_L006_R1_001.fastq.gz

value: CD4 splenic T cells


title: LF_CTR_24h_B3


title: RT_CTR_06h_B1

value: Root


title: BV9-R-CD4-d12-Allo-RNA_ATGTCA_L006_R1_001.fastq.gz


title: LF_CTR_24h_B2


title: BAT, Input, WT / Thermoneutral / 5pm

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Deep sequencing was carried out by the Functional Genomics Core (J. Schug and K. Kaestner) of the Penn Institute for Diabetes, Obesity, and Metabolism using illumina HiSeq 2000 and sequences were obtained using the Solexa Analysis Pipeline. Sequencing reads mapped to the mouse genome (UCSC mm9) using Bowtie. BigWig files for RPM-normalized stack-height profiles were generated using bedtools and SRA tool kit.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

source_name: Brown adipose tissue

extract_protocol:
Murine BAT was collected immediately after euthanasia. It was quickly minced and cross-linked in 1% formaldehyde for 20 min, followed by quenching with 1/20 volume of 2.5 M glycine solution and two washes with ice-cold PBS. Chromatin fragmentation was performed by sonication in ChIP SDS lysis buffer (50 mM HEPES, 1% SDS, 10 mM EDTA, pH 7.5) using probe sonication. Proteins were immunoprecipitated in ChIP dilution buffer (50 mM HEPES, 155 mM NaCl, 1.1% Triton X-100, 0.11% sodium-deoxycholate, complete protease inhibitor tablet, pH 7.5). Crosslinking was reversed overnight at 65 °C in elution buffer (50 mM Tris-HCL, 10 mM EDTA, 1% SDS, pH 8.0) and DNA was isolated using phenol/chloroform/isoamyl alcohol. Precipitated DNA was analysed by quantitative PCR.
ChIP DNA was prepared for sequencing according to the amplification protocol provided by Illumina.

value: Brown adipose tissue

tag: time

tag: genotype

value: WT

tag: temperature

tag: chip antibody

value: Input


title: RT_CTR_00h_B3


title: AdQCre_HDAC3ff_5pm_29C_5

data_processing:
RNA-seq reads were aligned to the UCSC mm9 using Tophat2. For differential gene expression analysis, raw read counts were measured within RefSeq genes using featureCounts, and exact test was performed using edgeR pipeline. Genes were considered for differential expression analysis only if their expression levels are > 0.5RPKM in at least three replicates.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing edgeR differential analysis results and individual replicates expression levels

growth_protocol: Male wild-type and HDAC3 KO mice maintained on a C57BL/6 background maintained on a 12 hour dark /light cycle and were sacrificed at 5PM (ZT10) at 12 weeks of age for the collection of interscapular brown adipose tissue.

extract_protocol:
RNA was isolated, snap frozen, and thawed directly in Trizol reagent prior to bead homogenization at 4C. RNA was isolated with Qiagen's RNeasy Kit (#74104).
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation (Part# 2001-2002). The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Male mice were allowed to acclimate for 2 weeks at thermoneutrality prior to tissue harvest. Mice were acclimated to 29C in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle.

value: Adiponectin-Cre, HDAC3 floxed


title: LF_CTR_06h_B2


title: AdQCre_HDAC3ff_5pm_29C_4


title: AdQCre_HDAC3ff_5pm_29C_19


title: LF_CTR_06h_B1


title: AdQCre_HDAC3ff_5pm_29C_20


title: HDAC3ff_5pm_29C_14

value: HDAC3 floxed


title: LF_CTR_00h_B1


title: LF_CTR_00h_B3


title: HDAC3ff_5pm_29C_13


title: LF_CTR_00h_B2


title: HDAC3ff_5pm_29C_12


title: WT_RNASeq

city: Boston

first: James

last: Galagan

state: MA

address: 44 Cummington Mall

department: Biomedical Engineering

institute: Boston University

description: Processed data (RPKM) for this sample are included in the files located on GSM2453486 and GSM2453487.

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to GenBank ID U00096.2
Peak calling was done using SPAT
R scripts (Bioconductor GenomicRanges) and custom scripts were used to calculate RPKMs. Fold-change was calculated as ratio of RPKMs after TF induction to control experiment.
Genome_build: U00096.2 (GenBank)
Supplementary_files_format_and_content: text file with peak calls

organism: Escherichia coli K-12

source_name: Culture cells

growth_protocol: Cells were grown in LB media with 1mM IPTG at 37 °C with shaking for 2 hours

extract_protocol:
For chromatin immunoprecipitation, cells were fixed with formaldehyde and glycine and sheared via sonication. IP was carried out using an anti-FLAG mAb.
Total RNA extraction was done using TRIzol reagent and DNAse digested. RNA purfication was carried out using Rneasy spin columns
The appropriate protocols were performed using standard Illumina procedures

treatment_protocol: For total RNA extraction, cells were pelleted in 4 °C.

tag: transcription factor

value: none (no vector)

value: anti-FLAG mAb

tag: antibody vendor/catalog#

value: Sigma/Cat. No. F1804


title: LF_CTR_06h_B3

tag: cultivar

tag: treatment

value: Control


title: HDAC3ff_5pm_29C_11


title: GRO-seq, BAT HDAC3, Adiponectin-Cre HDAC3 floxed, 22C/5pm

description: nacent RNA

data_processing:
Library strategy: GRO-seq
GRO-seq: GRO-seq libraries were sequenced twice for better coverage, and sequencing replicates were pooled for each condition. Before alignment, sequencing reads were cleaned by trimming off low quality base, adapter and tailing poly-A sequences using cutadapt16. Trimmed reads of at least 25bp were selected and aligned to UCSC mm9 using bowtie with an option ‘--best --strata -m 1 -v 3’. Aligned reads within extremely high signal regions such as rRNA, snoRNA, snRNA and tRNA were removed before downstream analysis to minimize read-depth bias. To visualize transcriptional activity in genome browser, bigwig files were generated for (+) and (−) strands separately, where all the reads were extended to 150bp for smooth profile and (−) strand signal were presented as negative values.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

molecule: nuclear RNA

extract_protocol: Nuclear Run-On (NRO): Nuclei were mixed with an equal volume of run-on buffer (10 mM Tris pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 200 U/ml Superase-In, 1% Sarkosyl, 500 μM ATP, GTP and Br-UTP, 2 μM CTP) and incubated for 5 min at 30°C. Nuclear RNA was extracted with Trizol (Invitrogen) and treated with DNase (Ambion). RNA was hydrolyzed using fragmentation reagents (Ambion) for 13 min at 70°C and purified through a Micro Bio-Spin Column P-30 (Bio-Rad). RNA was treated with T4 polynucleotide kinase (New England Biolabs) for 1h at 37°C, then with an additional T4 polynucleotide kinase for 1h more, and inactivated for 5 min at 75°C. NRO-RNA immuno-precipitation: Anti-BrdU agarose beads (Santa Cruz) were rotated for 1h in blocking buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20, 0.1% PVP, and 0.1% BSA). Then NRO-RNA was rotated with beads for 1h, followed by washes twice in binding buffer (0.25x SSPE, 38 mM NaCl, 1 mM EDTA, 0.05% Tween-20), twice in low salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.2x SSPE, 1 mM EDTA, 0.05% Tween-20, 138 mM NaCl), and twice in TET buffer (TE pH 7.4, 0.05% Tween-20). BrdU-labeled RNA was eluted from the beads four times for 10 min with 100 μl elution buffer pre-heated to 42°C. RNA was precipitated by adding 300 mM NaCl, 1 µl of glycogen and 2.5 volumes of ethanol and incubated overnight at -20°C. RNA was resuspended in water (with 1 U/µl Superase-In and 0.05% Tween-20), denatured for 3 min at 65°C, and treated with poly(A)-polymerase (New England Biolabs) for 30 min at 37°C.

treatment_protocol: Male mice for thermoneutrality (29C) cohorts were allowed to acclimate for 2 weeks prior to tissue harvest. Mice were acclimated to 29C in environmental rodent incubator maintained on the same 12:12 hour dark/light cycle. Room temperature (22C) cohorts were maintained in standard housing room.


title: LF_CTR_24h_B1

tag: tissue

value: Leaf


title: pT7_ChIPSeq_2

value: none (empty vector)


title: GRO-seq, BAT HDAC3, HDAC3 floxed, 22C/5pm

description: nacent RNA


title: GRO-seq, BAT HDAC3, Adiponectin-Cre HDAC3 floxed, 29C/5pm

description: nacent RNA


title: BAT, Input, WT / 4C / 5pm


title: ICI 182,780, 1h


title: GRO-seq, BAT HDAC3, HDAC3 floxed, 29C/5pm

description: nacent RNA


title: WT_ChIPSeq_2


title: RT_CTR_00h_B1


title: WT_ChIPSeq_1


title: hiPSC-ENCPs 2

city: Guangzhou

first: Weiqiang

last: Li

address: Zhongshan Road 2

country: China

institute: Sun Yat-sen university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes whihe each raw show gene abundence in al samples …

organism: Homo sapiens

source_name: induced pluripotent stem cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions.
RNA sequencing libraries were constructed using the Illumina mRNA-seq Prep Kit as recommended by the manufacturer. The fragmented and randomly primed 50 bp single-end libraries were sequenced using Illumina HiSeq 2000.

value: hiPSC-ENCPs


title: hiPSC-ENs 2

value: hiPSC-ENs


title: hiPSC-ENs 1


title: ChIP-seq, BAT HDAC3, HDAC3 floxed, 29C/5pm

data_processing:
ChIP-seq: All ChIP-seq libraries were sequenced on HiSeq 2500 (single-end 50bp or 100bp) or NextSeq 500 (single-end 75). Before alignment, all the reads were adjusted to 50bp by trimming 3’-end to avoid any bias due to different read lengths. Sequencing reads were aligned to the UCSC mm9 using Bowtie. For HDAC3 ChIP-seq data, each of WT and HDAC3-KO aligned reads were downsampled to 20 million reads to adjust read-depth bias and avoid peak saturation, and any duplicate reads were removed except for one. All the bigwig files for ChIP-seq data were generated using Homer and bedGraphToBigWig command. Two biological replicates of H3K27ac ChIP-seq were pooled to make single bigwig file in each condition.
Genome_build: mm9
Supplementary_files_format_and_content: Read-per-million (RPM) normalized stack-height profile in bigWig format

extract_protocol:
ChIP-seq: Interscapular BAT was isolated and processed separately for each sacrificed mouse. The tissues were immediately minced, crosslinked in 1 % formaldehyde/PBS, and stored at -80 C. For each fat pad, material from 3-4 mice was used for sequencing. To prepare ChIP extracts, frozen tissue was thawed, immediately crosslinked, and suspended ChIP buffer (50 mM HEPES/NaOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate and Complete protease inhibitor) supplemented with 0.1% SDS. Samples were incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency. Extracts were cleared of insoluble lipid by microfuge centrifugation at full speed followed by extract transfer to a new tube. The process was repeated until minimal lipid accumulated at the top of the extract after centrifugation. GRO-seq:The nuclear run-on assay was performed as previously described (Core et al., 2008; Step et al., 2014; Wang et al., 2011). Nuclei extraction: Mouse tissues were harvested at Zeitgeber Time 10 and washed with cold swelling buffer (10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In). Nuclear extract was prepared by dounce homogenization in cold swelling buffer and filtered using the cell strainer (100 µm, BD Biosciences). Lysate was centrifuged at 400g for 10 min, then resuspended in lysis buffer (swelling buffer with 10% glycerol and 1% Igepal) and incubated on ice for 5 min. Nuclei were washed twice with lysis buffer, and resuspended in freezing buffer (50 mM Tris pH 8.3, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA).
ChIP-seq: ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.GRO-seq: Synthesis of cDNA from RNA was performed as described previously (Wang et al., 2011) using oNTI223 primer (5′-/5Phos/GA TCG TCG GAC TGT AGA ACT CT/idSp/CAA GCA GAA GAC GGC ATA CGA TTT TTT TTT TTT TTT TTT TTV N-3′) where the “5Phos” indicates 5′ phosphorylation, “idSp” indicates the abasic dSpacer furan, and “VN” indicates degenerate nucleotides. The reaction was treated with exonuclease I (Fermentas) for 15 min at 37°C, followed by 100 mM NaOH for 20 min at 98°C, and neutralized with 100 mM HCl. cDNA was denatured at 70°C for 3 min, and run on 10% TBE-urea gel, then products from 105-400 nucleotides size were excised and eluted from shredded gel pieces for 4h in TE + 0.1% Tween and precipitated by adding 1 µl of glycogen, 300 mM NaCl and 2 volumes of ethanol and incubated overnight at -20°C. cDNA was resuspended into circularization reaction and circularized with CircLigase (Epicentre) for 1 hour at 60°C, denatured for 10 min at 80°C, and relinearized by adding relinearization mix (25 mM KCl, 500 µM DTT) and APE I (15U; New England Biolabs). Linearized DNA was amplified by PCR using Phusion Hot Start II Kit, according to manufacturer’s instructions. The oligonucleotide primers oNTI200 (5′-CAA GCA GAA GAC GGC ATA-3′) and oNTI201 (5′-AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC G-3′) were used for amplification. The PCR product was run on a 10% TBE gel and products from 150-305 nucleotides size were eluted from shredded gel pieces for 4h in TE + 0.1% Tween + 150 mM NaCl and purified using ChIP DNA Clean and Concentrator Kit (Genesee Scientific). Libraries were sequenced on an Illumina HiSeq2000 with sequencing primer 5′-CGA CAG GTT CAG AGT TCT ACA GTC CGA CGA TC-3′.

value: Anti-HDAC3 [ABCAM, Cat# 7030, Lot# GR121157-6]


title: hiPSC-ENCPs 1


title: H3K4me3_diff_ChIPSeq

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

country: Germany

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: Replicates were merged for the analysis.

data_processing:
Basecalls performed using CASAVA version 1.8.0
ChIP-seq reads were aligned to the reference genome (mm9) using Bowtie (v0.12.9) with default parameters. Ambiguously mapped reads were discarded.
Replicate BAM files were merged using SAMtools (v0.1.18.0).
MACS (v1.4.2) for peak calling which gives peaks and fitted signals as output (Command used – macs14 -t treat.merged.sam -c control.merged.sam -n output -p 1e-04 –B). For MyoD we used peaks and for histone marks we used fitted signals.
Genome_build: mm9
Supplementary_files_format_and_content: MyoD peaks are provided as bed files. Histone marks and input signals are also provided as bed files.

source_name: Differentiated C2C12 cells

growth_protocol: C2C12 myoblasts were cultured at 5% CO2 and 37°C in Dulbecco's modified Eagle's medium (Gibco) supplemented with 1% penicillin/streptomycin (Gibco) and 10% fetal bovine serum (Biochrom). Mononucleate C2C12 myocyte cells were harvested before reaching 70% confluence. To induce differentiation, cells were cultured with Dulbecco's modified Eagle's medium and 2% horse serum (Biochrom) and maintained for 48h, when more than 90% of the cells had fused into myocytes.

extract_protocol:
ChIP was done with MAGnify™ Chromatin Immunoprecipitation System (life technologies, Cat#: 49-2024) following the manufacturer’s indication with some modifications. Sonication was performed using Biorupter UCD300 to obtain chromatin fragments of approximately between 100-300bp. The following antibodies were used: anti-H3K4me2 (Abcam ab7766), anti-H3K4me3 (Abcam ab8580) and anti-MyoD (Santa Cruz, sc-760).
Libraries were prepared (with modifications) using NEXTflex™ ChIP-Seq Kit (Bioo Scientific, Cat#: 5143). Sequencing was done with Illumina Hiseq 2000, producing 51bp+7 single reads.

tag: cell line

value: Differentiated C2C12 cells

value: H3K4me3 (Abcam ab8580)


title: hiPSC-NCSCs

value: hiPSC-NCSCs


title: MyoD_diff_ChIPSeq

value: MyoD (Santa Cruz, sc-760)


title: input_DNA_undiff

source_name: Undifferentiated C2C12 cells

value: Undifferentiated C2C12 cells

value: none (input)


title: MyoD_undiff_ChIPSeq


title: H3K4me2_diff_ChIPSeq

value: H3K4me2 (Abcam ab7766)


title: H1


title: hiPSCs

value: hiPSCs


title: H3K4me2_undiff_ChIPSeq


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 3, CTCF binding site HS48 capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
A5_CTCF48_DEL3839vsC57BL6.gfc

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser4.pl)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Erythroid cells

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (Miltenyi Biotec).
NG Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for generation of the 3C libraries: cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in MilliQ dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an ethanol precipitation and a wash with 70% ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next sample preparation reagent kits, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using the Illumina MiSeq (150bp paired end reads). The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage). Oligonucleotide capture technology was then used to pull down the restricion fragments containing the promoters of the genes of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

value: Phenylhydrazine treated spleen

tag: genes analysed

value: CTCF binding site HS48


title: input_DNA_diff


title: pT7_ChIPSeq_1

value: anti-FLAG mAb

value: Sigma/Cat. No. F1804


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 1, CTCF binding site HS48 capture


title: ChIP-seq, BAT HDAC3, Adiponectin-Cre HDAC3 floxed, 29C/5pm

value: Adiponectin-Cre, HDAC3 floxed


title: H3K4me3_undiff_ChIPSeq


title: Mouse wild type erythroid cells replicate 1, CTCF binding site HS48 capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
A5_CTCF48_ESvsC57BL6.gfc


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 2, CTCF binding site HS48 capture


title: Mouse embryonic stem cells replicate 3, CTCF binding site HS48 capture

source_name: E14 embryonic stem cells

value: Embryonic stem cell line


title: Mouse wild type erythroid cells replicate 2, CTCF binding site HS48 capture


title: Mouse wild type erythroid cells replicate 3, CTCF binding site HS48 capture


title: Mouse embryonic stem cells replicate 1, CTCF binding site HS48 capture


title: Mouse embryonic stem cells replicate 2, CTCF binding site HS48 capture


title: H1-NCSCs


title: Mouse wild type erythroid cells replicate 1, CTCF binding site HS-38 capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
A4_HS38_ESvsC57BL6.gfc

value: CTCF binding site HS-38


title: Mouse embryonic stem cells replicate 3, CTCF binding site HS-38 capture


title: Mouse embryonic stem cells replicate 2, CTCF binding site HS-38 capture


title: Mouse wild type erythroid cells replicate 3, CTCF binding site HS-38 capture


title: Mouse wild type erythroid cells replicate 2, CTCF binding site HS-38 capture


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 3, Rhbdf1 and Mpg promoter capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
mpg_DEL3839vsC57BL6.gfc, rhbd_DEL3839vsC57BL6.gfc

value: promoter Mpg; promoter Rhbdf1


title: Mouse embryonic stem cells replicate 1, CTCF binding site HS-38 capture


title: SK-UT-1-EV input

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

description: SK-UT-1-EV input

data_processing:
Bases were called using Illumina's CASAVA v1.8.2
Sequences were aligned to hg19 genome using Novoalign, only unique aligned reads were kept
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files containing the coverage at single base resolution were generated using in house R scripts

growth_protocol: Human Ut-LMS SK-UT-1 and SK-LMS-1 cell lines were purchased from the American Type Culture Collection (Manassas, Virginia), and were maintained in Eagle’s Minimum Essential Medium (MEM; Life Technologies, INC., Logan, UT) with 10% fetal bovine serum.

extract_protocol:
Chromatin immunoprecipitation (ChIP) were performed on SK-UT-1-FASN and SK-UT-1-EV cells using the Magna ChIP A/G kit from (Millipore, Temecula, CA) following the manufacturer’s protocol. Anti-H3K9me3 antibody was used to immunoprecipitate cross-linked and fragmented chromatin DNA. This was followed by elution of protein/DNA complexes, reversal of the cross-links, and DNA purification.
Library preparation and massively parallel DNA sequencing (ChIP-seq) was performed with eluted DNA using an Illumina Hiseq 2500 sequencer by the City of Hope Integrative Genomics Core (Duarte, CA).

treatment_protocol: FASN-expressing (-FASN) or empty vector (-EV) SK-UT-1 cell lines were produced by transduction with retrovirus prepared from pBabe-FASN-HA-Flag and pBabe-EV-HA-Flag plasmids (Dr. Massimo Loda, Dana-Farber Cancer Institute, Boston, MA).

value: uterine leiomyosarcoma

tag: passage


title: SK-UT-1-FASN input

description: SK-UT-1-FASN input


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 1, Rhbdf1 and Mpg promoter capture

tag: strain


title: SK-UT-1-FASN ChIP seq

description: SK-UT-1-FASN H3K9me3 enriched

value: H3K9me3 (Abcam, ab8898)


title: Normoxia_H9C2-derived_exosomes

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

institute: sichuan agriculture university

description: small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 20.0. The reads originated from Rattus norvegicus known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 3 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Rnor_6.0; miRbase 21.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data

organism: Rattus norvegicus

source_name: H9C2 cells

extract_protocol:
Total RNA  isolated from each sample  were prepared for sequencing using standard Illumina protocols.
small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: H9C2 cells were cultured under normoxia or hypoxia at 48h, the samples of cells and its exosomes  were collected.

value: H9C2 cells


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 2, Rhbdf1 and Mpg promoter capture


title: SK-UT-1-EV ChIP seq

description: SK-UT-1-EV H3K9me3 enriched


title: Mouse wild type erythroid cells replicate 3, Rhbdf1 and Mpg promoter capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
mpg_ESvsC57BL6.gfc, rhbd_ESvsC57BL6.gfc


title: Hypoxia_H9C2_cells

description: small RNA


title: Mouse embryonic stem cells replicate 3, Rhbdf1 and Mpg promoter capture


title: Mouse wild type erythroid cells replicate 1, Rhbdf1 and Mpg promoter capture


title: Mouse wild type erythroid cells replicate 2, Rhbdf1 and Mpg promoter capture


title: 12hInd-H4R3me2sym ChIP

city: Reno

first: Subhash

last: Verma

state: NV

address: 1664 N Virginia Street, MS 320

department: Microbiology and Immunology

institute: University of Nevada, Reno

description: H4R3sym ChIP DNA

data_processing:
The libraries were run on Illumina Next-Seq instrument and Illumina software was used for peak calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequence were imported into CLC Genomic Workbech 10.0.1 with NCBI/Sanger or Illumia pipeline 1.8 and later option.
Reads were mapped to the KSHV genome database to determine the DNA bound by H4R3sym histone H4
ChIP peaks were calculated using CLC workbench ChiP-peak tool using input as reference
Genome_build: NCBI genome build of KSHV sequence accession# NC_009333
Supplementary_files_format_and_content: ChIp peaks on the viral genomes are in wig file (CLC workbench)

organism: Human gammaherpesvirus 8

source_name: TRExBCBL1-RTA cells

growth_protocol: TRExBCBL1-Rta  cells were grown in RPMI medium with 10% FBS. Uninduced cells were grown using 10% Tet-free FBS

extract_protocol:
Latent and lytic cells were cross-linked using formaldehyde to fix the protein-DNA for ChIP assay
Chromatins were immunoprecipitated using anti-H4R3symmtreic antibody by following standard ChIP protocol

treatment_protocol: Cells were induced for lytic reactivation by Doxycycline for 24h.

value: KSHV infected Body Cavity Based Lymphoma Cells

value: RTA protein is under tet-inducible promoter

tag: antibody

value: Symmetric di-methylated histone H4 (H4R3me2s) Antibody (Abcam # ab5823)


title: Hypoxia_H9C2-derived_exosomes

description: small RNA

tag: cell type


title: 12hInd-H4 ChIP

description: Histone H4 ChIP DNA

value: Histone H4 Antibody (Active Motif #61299)


title: Mouse embryonic stem cells replicate 2, Rhbdf1 and Mpg promoter capture


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 2, Enhancer R1 capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
A1_R1_DEL3839vsC57BL6.gfc

value: alpha globin enhancer R1


title: 12hInd-Input

description: DNA extracted from the sonicated chromatin

value: none (input)


title: Und-H4R3me2sym ChIP

description: H4R3sym ChIP DNA


title: 12hInd-IgG ChIP

description: Control IgG ChIP DNA

value: Control IgG Antibody (Cell Signaling Technology #2729)


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 1, Enhancer R1 capture

value: Phenylhydrazine treated spleen


title: Und-H4 ChIP

description: Histone H4 ChIP DNA


title: Mouse wild type erythroid cells replicate 2, Enhancer R1 capture

description:
Next generation Capture-C products : 3C library prepartion followed by double oligonucleotide capture
A1_R1_ESvsC57BL6.gfc


title: Mouse wild type erythroid cells replicate 1, Enhancer R1 capture


title: Und-Input


title: Mouse wild type erythroid cells replicate 3, Enhancer R1 capture


title: Und-IgG ChIP

description: Control IgG ChIP DNA


title: lower leaf - plant 3

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood Road

department: Plant and Soil Science

country: South Africa

institute: University of Pretoria

description:
BR3B
Maize leaf with severe infection by C. zeina.
Processed data file: edgeR_BR_all.txt

data_processing:
Data were filtered to remove adapters and trimmed for quality using
Trimmomatic (v0.30; (Bolger et al., 2014); settings
TruSeq3-PE-2.fa:2:30:10 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Filtered reads were aligned to a combined Zea mays genome (v5b.60 from the Phytozome v9.1 resource, Schaeffer et al., 2013) and the draft genome of Cercospora zeina (GenBank SUB212877) using Tophat2 with following setting: -p 4 -r 0 --mate-std-dev 200.
The longest transcript gene structure in the Z. mays annotation GFF3 file (retrieved from the Phytozome v9.1 resource) was used to estimate the transcript abundance in each locus by HTSeq.
Final data output include only values for Cercospora zeina genes.
Genome_build: Cercospora zeina draft genome
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts for each gene.

organism:
Zea mays
Cercospora zeina

source_name: leaf, severe C. zeina infection

growth_protocol: Maize B73 grown in the field in Greytown, Kwazulu-Natal, South Africa with natural infection of Cercospora zeina. Planted in December 2012.

extract_protocol:
Total RNA was extracted using Qiazol, treated with DNase, and purified with RNeasy Plant Mini kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Total RNA was shown to be of good quality using an Agilent Bioanalyser (average RIN number = 7.7).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: maize cultivar

value: lower leaf

tag: c. zeina infection

value: severe

tag: plant id


title: Mouse embryonic stem cells replicate 3, Enhancer R1 capture


title: Mouse embryonic stem cells replicate 1, Enhancer R1 capture


title: lower leaf - plant 1

description:
BR1B
Maize leaf with severe infection by C. zeina.
Processed data file: edgeR_BR_all.txt


title: Mouse wild-type erythroid cells ATAC-seq biological replicate 2

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (Miltenyi Biotec).
Illumina Nextera DNA library kit, subjected to ATAC-seq (Assay for Transposase-Accessible Chromatin)


title: Mouse D38 mutant erythroid cells ATAC-seq biological replicate 2


title: YPD-media

data_processing:
Sequence read quality was evaluated with FastQC. The fastx_toolkit was used to trim the first 13 bases from the start of each sequence read.
Reads were mapped to the draft genome of cercospora zeina using Tophat2 with parameters -r 0 --mate-std-dev 200. The BAM-format output files were converted to SAM-format using samtools view
SAM-files were processed for counting reads mapping to the genome with htseq-count, using the draft genome annotation in gtf-format and with parameters -f sam -t gene -r name -s no
Raw counts from htseq-count were tabulated in Excel.
Genome_build: Cercospora zeina draft genome assembly, genbank SUB2128778
Supplementary_files_format_and_content: Tab-delimited text-files with raw counts output from htseq-count

organism: Cercospora zeina

source_name: In vitro fungal culture

extract_protocol:
Cellophane sheets with Cercospora zeina growth were removed from the respective growth media plates and flash frozen in liquid nitrogen. For the liquid growth media, the C. zeina cultures were filtered through Whatmann’s nr 1 filter paper and the mycelia flash frozen. Mycelia was ground in liquid nitrogen and 3g used for total RNA isolation using QIAzol Lysis Reagent (Qiagen) as per the manufacturer’s specifications. RNA purification and DNA digestion of 100µg of total RNA was performed using the RNeasy Mini Kit and the RNase-free DNase set for on-column DNA digestion (Qiagen) as per the manufacturer’s specifications.
Libraries were constructed according to the Illumina manufacturer's protocol by the sequencing service laboratory (BGI).

tag: culture condition

value: YPD-media


title: lower leaf - plant 2

description:
BR2B
Maize leaf with severe infection by C. zeina.
Processed data file: edgeR_BR_all.txt


title: Mouse wild-type erythroid cells ATAC-seq biological replicate 1


title: V8-media


title: PDB-pH3


title: Mouse embryonic stem cells replicate 1, Rhbdf1 and Mpg promoter capture

value: Embryonic stem cell line


title: Mouse erytrhoid cells from knockout of CTCF binding site -HS38 and -HS39 replicate 3, Enhancer R1 capture


title: PDA-pH8


title: Cornmeal-agar

value: Cornmeal-agar


title: Mouse D38 mutant erythroid cells ATAC-seq biological replicate 1


title: H5N1_smallRNA

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

institute: Regeneron Pharmaceuticals, Inc

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 miRBase database or the genomes of A/Puerto Rico/8/1934 or A/Vietnam 1203/04 using Bowtie 1.1.2
Genome_build: mm9
Tab-delimited text files include the number of small RNA reads mapping to svRNA (small-viral RNA), mRNA/cRNA (messenger RNA/complementary RNA), and vRNA (viral RNA) for each of the eight segments of Influenza A viruses A/Puerto Rico/8/1934 (H1N1) or A/Vietnam 1203/04 (H5N1).

source_name: Lungs

extract_protocol:
Lungs were homogenized in Trizol reagent and total RNA was extracted using the Trizol method.
Small RNA libraries were prepared as previously described (Pfeffer et al. 2005, Identification of microRNAs of the herpesvirus family. Nat Methods 2: 269–276)

tag: age

tag: Sex

value: Female


title: H1N1_smallRNA


title: Complete-media

value: Complete-media


title: Fresh Maize miRNAs

status: Public on Jun 13 2017

city: Chengdu

first: Yi

last: Luo

address: gongpin road #211

institute: Sichuan Agricultural University

data_processing:
The raw reads were performed using a proprietary pipeline, ACGT101-miR program (Illumina), and followed a series of additional filters: After trimming off the sequencing adapters and junk reads, the resulting reads was successively filtered by read length, sequence component. Then the retained reads were searched against the NCBI, Rfam and Repbase database to remove porcine known classes of RNAs (i.e., mRNA, rRNA, tRNA,snRNA, snoRNA and repeats). Then mapping these unique sequences to mirs(miRbase 19.0) and Genome(B73_RefGen_v2).
miRNA read  was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Zea mays (B73_RefGen_v2)
Supplementary_files_format_and_content: identified miRNAs with details (reads,normalized reads, location,length,etc)

organism: Zea mays

source_name: Maize

extract_protocol:
Zea mays' fruit  were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.Illumina Truseq Small RNA Preparation kitwas used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: Fruit


title: L39 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS

city: Barcelona

first: Josep

last: Saura

address: Casanova 143

department: Biomedicina.

country: Spain

institute: Faculty of Medicine. University of Barcelona

description: Total RNA (minus rRNAs and tRNAs)

data_processing:
Basecalls performed using CASAVA software
Raw sequence (FASTQ format) were processed through a series of sequential steps: Aggressive adapters removal;  Alignment / Mapping of RNA sequences to the mouse genome reference (mm10) using "tophat". The results were sorted and cataloged by "Samtools" in Bam files.
To identify Differentially expressed genes, the R-software packages easyRNAseq and DESeq (a method based on the negative binomial distribution, with variance and mean linked by local regression) were used. The "Coverage vectors" for all genes of each sample was obtained using "easyRNAseq" and the UCSC.mm10 Mus musculus reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the coverage vector (counts per gene) obtained from easyRNAseq analysis for each sample

source_name: Microglia culture_Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS

growth_protocol: Microglial cells were isolated from primary mixed glial cultures prepared from P1-P3 C/EBPβfl/fl and LysMCre C/EBPβfl/fl mice. Brains were dissected, meninges removed and cortices digested with 0.25% trypsin for 30 min at 37°C and brought to a single cell suspension by repeated pipetting followed by passage through a 100 μm pore mesh. Glial cells were seeded in DMEM:F12 + 10% FBS at a density of 3.5 x 105 cells/mL and cultured at 37°C in humidified 5% CO2–95% air. Medium was replaced once a week. Microglial cultures were prepared from DIV19-21 mixed glial cultures by the mild trypsinization method and used 24 h after isolation.

extract_protocol:
Microglial cells were harvested and total RNA extracted using Trizol reagent and purified using RNeasy Mini Kit and DNase I -Rnasa Free (Qiagen). Illumina TruSeq Stranded Total RNA Sample Prep Kit  (Cat# RS-122-2201) was used with 1 ug of total RNA for tRNA and rRNA depletion before the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary microglial cultures were treated with LPS (100 ng/mL), LPS + IFNγ (1 ng/mL) or vehicle for 6 h. One 75 cm2 flask was used per treatment condition.

value: Microglia culture

tag: genotype

value: LysMCre-C/EBP<beta>fl/fl

value: LPS


title: L44 Genotype: C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)

source_name: Microglia culture_Genotype: C/EBPβfl/fl. Treatment: LPS

value: C/EBP<beta>fl/fl


title: L33 Genotype: C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)


title: L43 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)


title: Mouse embryonic stem cells replicate 2, Enhancer R1 capture


title: L35 Genotype: C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)


title: L34 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)


title: C43 Genotype: LysMCre-C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)

source_name: Microglia culture_Genotype: LysMCre-C/EBPβfl/fl. Treatment: vehicle

value: vehicle


title: C44 Genotype: C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)

source_name: Microglia culture_Genotype: C/EBPβfl/fl. Treatment: vehicle


title: C39 Genotype: LysMCre-C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)


title: C35 Genotype: C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)


title: C34 Genotype: LysMCre-C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)


title: C32 Genotype: LysMCre-C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)


title: C33 Genotype: C/EBPβfl/fl. Treatment: vehicle

description: Total RNA (minus rRNAs and tRNAs)


title: PDA-AP

value: PDA-AP


title: A44 Genotype: C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)

source_name: Microglia culture_Genotype: C/EBPβfl/fl. Treatment: LPS+IFNg

value: LPS+IFNg


title: A35 Genotype: C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)


title: A43 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)

source_name: Microglia culture_Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS+IFNg


title: A39 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)


title: A33 Genotype: C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)


title: 3-SD-T50nM

city: Lyon

first: jean-baptiste

last: claude

address: 46, allée d’Italie

country: France

institute: [CNRS/ENS Lyon/UCBL/HCL] Laboratoire de Biologie Moléculaire de la Cellule UMR5239

description: 50nM of digoxin for 48h – Biological Replicate 3

data_processing:
Data generated with an Illumina HiSeq 2000 platform
Filtering & Trimming with Cutadapt (1.13) & Prinseq (lite-0.20.4)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Splicing analysis with FARLINE pipeline (publication in progress)
Gene expression analysis with HTSeq-count & package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: excel files containing splicing events differentially observed (events : acceptor, donor, mutually exclusive, multi exon skipping) and genes differentially expressed. Xls & xlsx

source_name: Human embryonic stem cells (VUB01), MSC DM1, Digoxin

growth_protocol: Human embryonic stem cells (VUB01) were manually dissociated and plated on 0.1% gelatin-coated dishes (Sigma) in Knockout DMEM medium optimized for ES cells (Invitrogen), supplemented with 20% of Fetal Bovine Serum (FBS, Eurobio), 1mM L-glutamine (Invitrogen), 1% non-essential amino-acid (Invitrogen), and 0,1% β-mercaptoethanol (Invitrogen). Medium was changed every over two days. Confluent cells were passed with trypsin/EDTA 1X (Invitrogen) in new gelatin-coated plates and plated at a density of 8.000/cm2. After three weeks of differentiation, MSC phenotype was assessed by FACS analysis for CD44, Stro1, CD73 and endoglin expression (all from ABCAM, 1/100).

extract_protocol:
Total RNA was extracted from treated and none treated cells.
Sequencing libraries were prepared according to the Illumina TruSeq Stranded mRNA Sample Prep Kit (according to manufacturer’s protocol) (Illumina, San Diego, CA). A 2 × 101 bp pairedend sequencing was performed on the HiSeq2000 instrument, using half a lane per sample, to produce on average 80 million read pairs per sample (160 million sequences) with an average insert length of 130 bp. Trimmomatic,52 Tophat2,53 Picard suite (http://www.broadinstittute.github.io/picard), RNA-SeQC,54 and in-house metrics were used to evaluate data quality.

treatment_protocol: Cells were treated with 50 nM of digoxin (from Sigma-Aldrich) for 48h.

value: MSC


title: 2-SD-T50nM

description: 50nM of digoxin for 48h – Biological Replicate 2


title: A34 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)


title: 1-SD-Ctrl

description: None treated cells - Biological Replicate 1

source_name: Human embryonic stem cells (VUB01), MSC DM1


title: 1-SD-T50nM

description: 50nM of digoxin for 48h – Biological Replicate 1


title: BJ.C.gro.rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: nascent RNA

data_processing:
Library strategy: GRO-seq
Sequenced reads were aligned to the human genome (hg19) using bowtie2, and number of reads mapping to annotated genes (Ensembl v69) were counted by Htseq and normalized using FPKM units
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts values for each sample.

source_name: BJ

growth_protocol: BJ cells were cultured in Dulbecco's modified Eagle's medium supplemented with 10% heat-inactivated fetal calf serum in 5% CO2 at 37°C.

extract_protocol:
5 x 10^6 nuclei per condition were isolated and incubated 5 min at 30°C with equal volume of reaction buffer for the nuclear-run on (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1mM DTT, 300 mM KCL, 20 units of SUPERase In, 1% sarkosyl, 500 µM ATP, GTP, and Br-UTP, 0.2 µM CTP+32P CTP). The reaction was stopped and RNA extracted with Trizol LS (Invitrogen) according to the manufacturer’s instructions. Base hydrolysis was performed using RNA fragmentation Reagents (Ambion) and the reaction was purified through p-30 RNAse-free spin column (BioRad). BrUTP labeled nascent transcripts were immunoprecipiated with anti-BrUTP agarose beads (Santa Cruz Biotech), washed once in binding buffer, once in low salt buffer (0.2X SSPE, 1 mM EDTA, 0.05% Tween-20), once in high salt buffer (0.25X SSPE, 1 mM EDTA, 0.05% Tween-20, 137.5 mM NaCl) and twice in TET buffer (TE with 0.05% Tween-20). Then, BrUTP-incorporated RNA was eluted with elution buffer (20 mM DTT, 300 mM NaCl, 5 mM Tris-Cl pH 7.5, 1 mM EDTA and 0.1% SDS) and RNA isolated with Trizol LS. End-repair of the enriched BrUTP-incorporated RNAs were achieved by the treatment with tobacco acid pyrophosphatase (TAP; Epicenter) to remove 5’-methyl guanosine caps, and followed by T4 polynucleotide kinase treatment (PNK; NEB) to remove 3’-phosphate group at low pH. Then, the BrU-incorporated RNAs were treated with T4 PNK at high pH in the presence of ATP to add 5’-phosphate group. The reaction was stopped and RNA was extracted with Trizol LS.
Sequencing libraries were generated from two biological replicates using TruSeq Small RNA kit from Illumina. Final libraries were two times cleaned-up and size-selected by Agencourt AMPure XP (Beckman Coulter)

treatment_protocol: No treatment

value: BJ


title: BJ.C.gro.rep1

description: nascent RNA


title: 2-SD-Ctrl

description: None treated cells - Biological Replicate 2


title: ADT_S751

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

institute: UT Health Science Center at Houston

description: ADT sample 751

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: ADT

growth_protocol: Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately placed in TRIzol® reagent (Invitrogen, Carlsbad, CA) and stored at -80C.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA)

value: neutrophils

tag: disease state

value: active disease

value: MTX (methotrexate)


title: 3-SD-Ctrl

description: None treated cells - Biological Replicate 3


title: ADU_S843

description: ADU sample 843

source_name: ADU

tag: treatment

value: untreated


title: HC_S969

description: HC sample 969

source_name: HC

value: healthy control


title: ADT_S801

description: ADT sample 801


title: ADT_S791

description: ADT sample 791


title: ADU_S790

description: ADU sample 790


title: L32 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS

description: Total RNA (minus rRNAs and tRNAs)

tag: tissue


title: Normoxia_H9C2_cells

description: small RNA

source_name: H9C2 cells

value: H9C2 cells


title: A32 Genotype: LysMCre-C/EBPβfl/fl. Treatment: LPS+IFNg

description: Total RNA (minus rRNAs and tRNAs)


title: NKX2-2+RWPE1_1

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

data_processing:
Fastqc was utilized to check the RNA sequencing quality
Cutadapt software was used to cut adapters for each read, and then mirdeep2 was used to do alignment and abundance calculation with miRBase reference miRNA sequences.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized count values for each Sample

source_name: human prostate epithelial cells

extract_protocol:
RNA was harvested using Trizol reagent.
After 3' and 5' adapter introduced, RNA libraries were quatified with Qubit agents.

tag: transfection


title: NKX2-2+RWPE1_3


title: b-catenin_KO

first: Liu

last: Zhenping

address: 1239 Si Ping Road

institute: Tongji University

data_processing:
Basecalls performed using Illumina CASAVA v1.8.2 at WuXi AppTec Co (sequencing service provider).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by WuXi AppTec Co (sequencing service provider).
RNA-seq reads for each sample were aligned to the human refseq using Tophat version 2.0.14 with parameters –p 8 respectively.
Fragments Per Kilobase of transcript per Million mapped reads(FPKM) were caculated by using Cufflinks v2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

growth_protocol: HepG2 cells were cultureed in DMEM media with 10% FBS.

extract_protocol:
Total RNA was extracted from each sample using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at WuXi AppTec Co.

treatment_protocol: HepG2 cells were transfected with control, LRP5/6 or β-catenin siRNA. Cells were harveated 48hour after knocking-down.

value: {beta}catenin knockdown

tag: cell line


title: ctrl

value: Normal


title: HOXC6+RWPE1_3


title: RWPE1_1


title: LRP5-6_DKO

value: LRP5/6 knockdown


title: NKX2-2+RWPE1_2


title: HC_S1009

description: HC sample 1009


title: SJSA-1

city: Hefei

first: Liang

last: Wang

state: Anhui

address: Huanhu Road 107#

department: West Branch/Anhui Cancer Hostpital

institute: Anhui Provincial Hospital

description: senescent

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: osteosarcoma cells

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: osteosarcoma cells

tag: sample type

value: human osteosarcoma cells

value: post natal day 21


title: G-292

description: resting


title: MG63.2

description: invasive


title: HOXC6+RWPE1_1


title: AR+RWPE1_3

value: AR


title: ADU_S805

description: ADU sample 805


title: AR+RWPE1_2


title: AR+RWPE1_1


title: MG63

description: non-invasive


title: HOXC6+RWPE1_2


title: siL1-1

city: LYON

first: Jean-Marc

last: Vanacker

address: 28 rue A Fleming

institute: IGFL

data_processing:
RTA software used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome Hg19 with TopHat 1.3.3
Sequences reads were counted with HTSeq-count with the union option
Differential expression was analyzed with DESeq
Genome_build: Hg19
Supplementary_files_format_and_content: this file contains count data for each sample and differential expression (siLSD1 vs siC) with fold change and padj

source_name: MDA-MB231 cells

growth_protocol: MDA-MB231 cells were grown in DMEM, supplemented with 10% FCS

extract_protocol:
RNA were extracted using RNeasy Qiagen kit
RNA libraries were prepared using standard Illumina procedures

treatment_protocol: siRNA were transfected using interferin under conditions recommended by the supplier (Ozyme)


title: siL1-2


title: siControl-1


title: siControl-2


title: siL2-1


title: siL2-2


title: RWPE1_2


title: Input_rep1

city: Mainz

first: Vijay

last: Tiwari

state: Rheinland

institute: Institute of Molecular Biology

data_processing:
ChIPseq reads were aligned using Bowtie Version v0.12.9
Peaks were called using MACS2 version v 2.0.1-.20120913
Peak Enrichment calculation was performed using QuasR package
WIG files were generated by QuasR package
genome build: mm9
processed data files format and content: WIG files generated by command qExportWig using QuasR package; Peaks files for each of the H3K27ac ChIPseq data using MACS2

source_name: Input Replicate 1

growth_protocol: A subclone of NMuMG cells (NMuMG/E9, hereafter NMuMG) was grown in DMEM supplemented with 10% FBS, 2 mM L-Glutamine and 1X Non-essential amino acids and cultured at 37°C with 7% CO2 in a humid incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For TGF-β timecourse experiments, NMuMG cells were treated with 2 ng/ml TGF-β (rhTGF-β1 240-B, R&D systems) for indicated time points with TGF-β replenishment and medium change every 2 days. For Erk inhibition cells were seeded at same densities and pretreated 30 min prior to TGF-β treatment with UO126 Erk-signaling inhibitor or its solvent DMSO at the final concentrations of 25µM and analyzed at indicated time points.

value: NMuMG

value: mammary gland

value: none (input)


title: Input_rep2

source_name: Input Replicate 2


title: Input_rep3

source_name: Input Replicate 3


title: H3K27ac_ChIPseq_Erki_24hr_rep3

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 3

value: ab4729 (abcam)


title: H3K27ac_ChIPseq_Erki_4hr_rep1

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 1


title: H3K27ac_ChIPseq_Erki_24hr_rep2

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 2


title: H3K27ac_ChIPseq_Erki_4hr_rep3

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 3


title: H3K27ac_ChIPseq_4hr_rep3

source_name: H3K27ac ChIP-seq in 4hr Replicate 3


title: H3K27ac_ChIPseq_24hr_rep3

source_name: H3K27ac ChIP-seq in 24hr Replicate 3


title: H3K27ac_ChIPseq_24hr_rep2

source_name: H3K27ac ChIP-seq in 24hr Replicate 2


title: H3K27ac_ChIPseq_Erki_24hr_rep1

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 24hr condition Replicate 1


title: H3K27ac_ChIPseq_Erki_4hr_rep2

source_name: H3K27ac ChIP-seq in Erk inhibitor treated 4hr condition Replicate 2


title: H3K27ac_ChIPseq_24hr_rep1

source_name: H3K27ac ChIP-seq in 24hr Replicate 1


title: RWPE1_3


title: H3K27ac_ChIPseq_4hr_rep2

source_name: H3K27ac ChIP-seq in 4hr Replicate 2


title: H3K27ac_ChIPseq_4hr_rep1

source_name: H3K27ac ChIP-seq in 4hr Replicate 1


title: RNAseq_Erki_4hr_rep1

description: processed data file: NormalizedReadCounts.xlsx

data_processing:
RNAseq reads were aligned using TopHat version v2.0.8
Mapped reads were used for read count per gene using HTSeq version 0.5.4p1
Read Count were normalized and differential gene expression analysis was performed using DESeq R Package
genome build: mm9
processed data files format and content: tab delimited text file representing NormalizedReadCounts for Each sample

source_name: RNAseq in Erk inhibitor treated 4hr condition Replicate 1

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.


title: H3K27ac_ChIPseq_0hr_rep2

source_name: H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 2


title: RNAseq_Erki_24hr_rep2

source_name: RNAseq in Erk inhibitor treated 24hr condition Replicate 2


title: H3K27ac_ChIPseq_0hr_rep3

source_name: H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 3


title: RNAseq_Erki_4hr_rep2

source_name: RNAseq in Erk inhibitor treated 4hr condition Replicate 2


title: H3K27ac_ChIPseq_0hr_rep1

source_name: H3K27ac ChIP-seq in Untreated condition (0hr) Replicate 1


title: RNAseq_24hr_rep1

source_name: RNAseq in 24hr condition Replicate 1


title: RNAseq_24hr_rep2

source_name: RNAseq in 24hr condition Replicate 2


title: RNAseq_0hr_rep2

source_name: RNAseq in Untreated condition (0hr) Replicate 2


title: Mif-Nacl-C

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description: polyA+ TruSeq RNA Kit (Illumina)

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters:ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the GRCm38 build of the mouse genome with STAR (version STAR_2.4.2a_modified)
Mapped reads were indexed and sorted with samtools 1.0
Gene quantification and deferential expression was performed using the GenomicAlignments (1.8.4) and DESeq2 (1.12.3) packages in Bioconductor.
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: bigwig, csv files with FPKM and fold-change data with associated peak data

source_name: IMCD3 cells (53a subclone)

growth_protocol: IMCD3 cells were grown in low glucose DMEM media supplimented with 10% FBS.

extract_protocol:
miRNeasy Mini Kit (Qiagen)
polyA+ TruSeq RNA Kit (Illumina)

value: Mifepristone

tag: nacl

value: 100mM NaCl


title: Mif-Nacl-B

description: polyA+ TruSeq RNA Kit (Illumina)


title: Mif-C

description: polyA+ TruSeq RNA Kit (Illumina)

value: Vehicle


title: Mif-Nacl-A

description: polyA+ TruSeq RNA Kit (Illumina)


title: Mif-B

description: polyA+ TruSeq RNA Kit (Illumina)


title: Mif-A

description: polyA+ TruSeq RNA Kit (Illumina)


title: Control-Nacl-B

description: polyA+ TruSeq RNA Kit (Illumina)


title: Control-Nacl-A

description: polyA+ TruSeq RNA Kit (Illumina)


title: RNAseq_Erki_24hr_rep1

source_name: RNAseq in Erk inhibitor treated 24hr condition Replicate 1


title: RNAseq_4hr_rep1

source_name: RNAseq in 4hr condition Replicate 1


title: Control-A

description: polyA+ TruSeq RNA Kit (Illumina)


title: Control-B

description: polyA+ TruSeq RNA Kit (Illumina)


title: RNAseq_0hr_rep1

source_name: RNAseq in Untreated condition (0hr) Replicate 1


title: H1933.C.rna

data_processing:
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations. Only uniquely mapped reads were used in subsequent analyses. RNA expression and Ribosome-occupancy levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

molecule: polyA RNA

growth_protocol: PC9 cell were grown in RPMI 1640 supplemented with 2mM Glutamine and 10% FBS. H19333 cells were grown in DMEM supplemented with 10%FBS

extract_protocol:
Total RNA was isolated with Trizol Reagent following the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown under normal conditions

value: control


title: MCF7.Nutlin.rna

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10%FBS

extract_protocol:
Total RNA was isolated using Trizol Reagent following the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with Nutlin-3a (8 mM) for 20 hours


title: PC9.C.ribo

description: ribosome-bound RNA

data_processing:
Library strategy: Ribo-seq
Sequenced reads were aligned to a reference set of human curated protein-coding transcripts (plus the five human rRNA transcripts) using Bowtie. This reference set of transcripts was based on Ensembl's gene annotations. Only uniquely mapped reads were used in subsequent analyses. RNA expression and Ribosome-occupancy levels were estimated by calculating reads per kilobase of mRNA per million reads (RPKM) per transcript.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

extract_protocol:
Cells were treated with cycloheximide (100 μg/ml) for 5 minutes, washed with ice-cold phosphate-buffered saline (cycloheximide, 100 μg/ml), pelleted, and lysed in buffer A (20 mM Tris-HCl, pH 7.8, 100 mM KCl, 10 mM MgCl2, 1% Triton X-100, 2 mM DTT, 100 μg/ml cycloheximide, 1X complete protease inhibitor). Lysates were centrifuged at 5,000 rpm and the supernatant was treated with 2 U/μl of RNase I (Ambion) for 45 min at room temperature. Lysates were fractionated on a linear sucrose gradient (7% to 47%) using the SW-41Ti rotor at 36,000 rpm for 2 h. Fractions enriched in monosomes were pooled and treated with proteinase K (Roche) in a 1% SDS solution. Released RNA fragments were purified using TRIsure reagent and precipitated in the presence of glycogen.
For libraries preparation, RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 30 to 33 nucleotides, the region where most of the ribosome-protected fragments are comprised, was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England BioLabs, Inc.) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England BioLabs, Inc.) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.


title: MCF7.C.ribo

description: ribosome-bound RNA


title: MCF7.C.rna


title: mpk3 - mock treated replicate3

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
The reads were mapped onto Arabidopsis thaliana TAIR10 genome
To identify regions that were significantly enriched, we used MACS2.
MACS2 parameters for peaks detection were set as follows: Number of duplicate reads at a location:1; Bandwidth:300; mfold of 5:50; q-value cutoff:0.05.
To identify the differentially expressed genes, we used UGRV platform
Genome_build: TAIR10
Supplementary_files_format_and_content: [ChIP-Seq] wig files report peaks
Supplementary_files_format_and_content: [RNA-Seq] txt file reports RPKM values

source_name: Arabidopsis thaliana 14-day-old in vitro seedlings

growth_protocol: 14-day-old in vitro seedlings were used. T-DNA insertion lines hd2b (At5g22650) from SAIL collection 41 Sail_1247_A02 and mpk3 SALK_151594 42 were obtained from the the Nottingham Arabidopsis Stock Centre (NASC).

extract_protocol:
[ChIP-seq] ChIP assays were performed on 14-day-old in vitro seedlings using anti-GFP , IgG control, or anti-H3K9ac antibodies. Briefly, after plant material fixation in 1% (v/v) formaldehyde, tissues were homogenized, nuclei isolated and lysed. Cross-linked chromatin was sonicated using a water bath Bioruptor UCD-200 (Diagenode, Liège, Belgium) (30 s on/30 s off pulses, at high intensity for 60 min). Protein/DNA complexes were immunoprecipitated with antibodies, overnight at 4°C with gentle shaking, and incubated for 1h at 4°C with 50 μL of Dynabeads Protein A (Invitrogen, Ref. 100-02D). Immunoprecipitated DNA was then recovered using the IPure kit (Diagenode, Liège, Belgium) and analyzed by quantitative real-time PCR. An aliquot of untreated sonicated chromatin was processed in parallel and used as the total input DNA control.
[ChIP-seq] 10 ng of IP or input DNA was used for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s recommendations. For all libraries, twelve cycles of PCR were  used. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent), and  the libraries were subjected to high-throughput sequencing by Illumina Sequencing technology.
[RNA-seq] Total RNA were extracted from seedlings with the RNeasy MiniPrep kit (Qiagen), according to the manufacturer's instructions.
[RNA-seq] Transcriptomic analyses were performed RNA-seq at the URGV plateform (Evry, France) with Illumina RNA-seq preparation kit. Three biological replicates were run for each condition.

treatment_protocol: For flagellin treatments (flg treated), seeds were surface-sterilized by treatment with bayrochlore and then soiled in sterile half-strenght MS liquid medium, placed for 2-4 days at 4°C to obtain homogeneous germination, and plants were grown in chambers at 20°C in long-days (16h of light) conditions. After 14 days, flg22 peptide was added in the medium to a final concentration of 1μm when necessary. For the mock condition (mock treated), the same volume of water was added to the medium instead of the flg22 peptide.

tag: ecotype

value: seedlings

value: 14-day old


title: MCF7.Nutlin.ribo

description: ribosome-bound RNA


title: PC9.C.rna


title: col0 - Input mock treated

value: Wt

tag: chip antibody


title: col0 - H3K9ac flg treated

value: 30min of flg22

value: anti-H3K9ac (Millipore 07-352)


title: mpk3 - mock treated replicate2


title: col0 - Input flg treated


title: hd2b - mock treated replicate3


title: mpk3 - mock treated replicate1


title: hd2b - mock treated replicate2


title: col0 - mock treated replicate3


title: Control-C

description: polyA+ TruSeq RNA Kit (Illumina)


title: col0 - mock treated replicate2


title: H1933.C.ribo

description: ribosome-bound RNA


title: Control-Nacl-C

description: polyA+ TruSeq RNA Kit (Illumina)


title: RNAseq_4hr_rep2

source_name: RNAseq in 4hr condition Replicate 2

tag: cell type


title: col0 - flg treated replicate3


title: col0 - flg treated replicate2


title: HD2B:GFP flg

value: hd2b pHD2B::HD2B-GFP

value: anti-GFP (abcam ab290)


title: hd2b - mock treated replicate1


title: col0 - H3K9ac mock treated


title: col0 - flg treated replicate1


title: HD2B:GFP mock


title: siH1.2

city: Oxford

first: Edward

last: Hookway

state: Oxfordshire

address: Botnar Research Centre, Windmill Road

institute: NDORMS, University of Oxford

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 and Basecalling and demultiplexing performed by their standard pipelines.
Adaptors and low quality reads were trimmed using Trim_galore version 0.3.7.
Aligned to GRCh37 using Bowtie2 v 2.2.5.
Peaks called using macs2 v 2.1.0.
Homer v4.8 used to create tag directories of all samples and produced bedgraph data normalized to 10^7 reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: NarrowPeak files are of BED6+4 format.
Supplementary_files_format_and_content: Bedgraph files show coverage normalized to 10^7.

source_name: MCF7 cell line, H1.2 knockdown, Rb ChIP

growth_protocol: Cells were grown in DMEM supplemented with 5% FCS under standard laboratory conditions.

extract_protocol:
Cells were double fixed with DMA followed by formaldehyde. Following lysis and resuspension in RIPA buffer containing 0.1% SDS, cells were sonicated using a Bioruptor Pico (Diagenode). Chromatin was pre-cleared with pre-blocked protein A and G beads overnight prior to incubation with 1ug of antibody. Beads were washed, decrosslinked, treated with proteinase K and then purified using a QIAquick PCR kit (Qiagen).
Libraries were constructed using NEBNext Ultra DNA library prep kit according to the manufacturer's instructions.

treatment_protocol: Cells were transfected with plasmid targetting either H1.2 or GFP 48 hours prior to extraction.

tag: sirna

value: Rb (4H1; Cell Signalling Technology #9309, lot 9)


title: siGFP

source_name: MCF7 cell line, control, Rb ChIP

value: siGFP


title: R0_Pbx_HoxA5_EpiSELEX_seq

city: New York City

first: Harmen

middle: J

last: Bussemaker

address: 1212 Amsterdam Avenue, MC 2441

department: Biological Sciences

institute: Columbia University

data_processing:
Library strategy: EpiSELEX-seq
Fastq files were reverse-complemented and both forward and reverse-complement read merged into one (fastx_reverse_complement -Q33 -z ; FASTX toolkit 0.0.12;Hannon lab).
Next, fixed primer sites were trimmed using the following options: fastx_trimmer -Q33 -f 12 -l 41 –z (FASTX toolkit 0.0.12;Hannon lab).
Kmer counting and relative affinity estimates were computed using the R package bioconductor.org/packages/SELEX.
To filter for kmers that are aligned with the actual Protein:DNA interface, position-specific affinity matrices were calculated for each library and probes were scanned in a sliding-window approach in either orientation to find the optimal protein footprint. Only probes where a single offset contributed at least 95% to the overall probe affinity were retained.
Oligomer-based relative affinity tables for the unmethylated and methylated libraries were generated for the set of kmers that passed the filtering criterion.
Genome_build: randomized DNA
Supplementary_files_format_and_content: txt files contain two columns describing the relative affinity of individual kmers from the unmethylated and methylated libraries. Rownames contain the specific kmer sequences.

source_name: in-vitro purification

extract_protocol: Libraries were amplified by using overhang primers targeting the GGTAGTGGAGG and GG-GAGGTGGAGTAGG parts of the library and adding the Illumina TruSEQ adapter and universal or Index primers respectively. During amplification the extracted, TF-bound DNA was split in two separate pools and Illumina primer landing sites were added from both orientations respectively (Universal-for & Index-rev or Index-for and Universal-rev). Next, Illumina-specific barcodes were added in a 5 cycles PCR to allow for multiplexing of multiple samples. In order to obtain unidirectional reads starting from the barcode end of the library, reads need to be reverse-complemented and merged with the forward reads.

tag: rounds of selection

tag: variable region length


title: R0_CEBPb_homo_EpiSELEX_seq


title: R0_Pbx_HoxA9_EpiSELEX_seq


title: R0_Pbx_HoxA1_EpiSELEX_seq


title: R1_Pbx_HoxA9_b_EpiSELEX_seq


title: R1_Pbx_HoxA9_EpiSELEX_seq


title: R1_CEBPb_homo_EpiSELEX_seq


title: R1_ATF4_homo_EpiSELEX_seq


title: R1_Pbx_HoxA1_EpiSELEX_seq


title: R1_Pbx_HoxA5_EpiSELEX_seq


title: col0 - mock treated replicate1

tag: age


title: WT_MYOEPITHELIAL_CHIPSEQ_INPUT

city: Cold Spring Harbor

first: Wesley

middle: D.

last: Frey

address: One Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Chromatin IP purified DNA

data_processing:
Reads were mapped to the indexed mm9 genome using bowtie short-read aligner tool with an allowable mismatch limit set to 2 and the --best and --strata options used to report best alignments and suppress suboptimal alignments.
MACS peak-calling program was used to identify enriched genomic regions in this data by comparing the pulldown ChIP data to the control (Input) data, using a tag size of 25 bp and a p-value cutoff of 1.00e-3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9

source_name: Primary mammary epithelial cells

growth_protocol: Eph4 Cells were grown in DMEM with 5% FBS

extract_protocol:
Chromatin fraction obtained from Eph4 cells or FACS-sorted mammary epithelial cells were incubated with antibodies that recognize mouse histone H3K27ac or mouse c-Myc protein. 1/10 of chromatin fraction was saved as Input. Chromatin-antibody were isolated with magnetic beads. DNA purified with ChIP DNA kit (Zymo) according the manufacturer's instruction
ChIP library samples were amplified and barcoded using Clontech DNA Smart Chipseq kit and Clontech Indexing set in accordance with the manufacturer’s instructions, then pooled for sequencing.

treatment_protocol: Eph4 cell line was treated for 24 hours with AU-1 (5uM) or DMSO

value: Myoepithelial mammary cells

value: Primary mammary epithelial cells

tag: strain

value: Balb/C

tag: gender

value: Female


title: WT_MYOEPITHELIAL_CHIPSEQ_H3K27ac

description: Chromatin IP purified DNA


title: EPH4_DMSO_CHIPSEQ_CMYC

description: Chromatin IP purified DNA

source_name: Eph4 Cell Line

value: Established Cell Line


title: EPH4_DMSO_CHIPSEQ_H3K27ac

description: Chromatin IP purified DNA


title: EPH4_AU1_CHIPSEQ_H3K27ac

description: Chromatin IP purified DNA


title: EPH4_DMSO_CHIPSEQ_INPUT

description: Chromatin IP purified DNA


title: EPH4_AU1_CHIPSEQ_CMYC

description: Chromatin IP purified DNA


title: EPH4_AU1_CHIPSEQ_INPUT

description: Chromatin IP purified DNA


title: Basal_BptfKO_ATACseq_Rep3b

description: Tn5 transposed purified DNA

data_processing:
ATAC-seq reads were aligned to the mm9 genome assembly using Bowtie with no mismatches allowed and multi-mappers excluded
MACS was used for peak-calling from the mapped BAM file.  Parameters used for MACS included a tag size of 25bp and a strict p-value cutoff of 1.00e-5
Peaks were annotated using HOMER with the standard mm9 reference included with the software.  Location of peaks was then grouped into intergenic, promoter and genic (containing 5’UTR, Exons, Introns, Transcription Termination Sites, 3’UTR, ncRNA, miRNA, snoRNA, and rRNA) regions.  Pie Charts were made from the resulting HOMER output.
ROSE was preformed to identify putative enhancer regions using default conditions, which included a 2.5 Kb exclusion zone surrounding the TSS and a 12.5 Kb stitching distance.
The UCSC genome browser was used to analyze enhancers for overlap, using the table browser intersect function. Any overlap was enough to consider two regions “shared” and no overlap, between the enhancers defined the regions as ONLY being in one sample.
The comparison of differential enhancers was made into a venn diagram using Galaxy’s Cistrome server. Identification of genes closest to these differentially called enhancer regions, was preformed using Genomic Regions Enrichment of Annotations Tool (GREAT)
Homer was used to create histograms of MACS-called ATAC-seq peaks and MACS-called H3K27ac peaks using standard mm9 TSS annotations in Homer’s software package. Histograms of ATAC-seq peaks distribution around distal H3K27ac peaks were made by excluding H3K27ac peaks that associated with TSS/Promoter regions, as defined by HOMER.
Spearman correlation coefficients ranging from -1 to 1, where 1 indicates the strongest relationship between samples, were used to assess the integrity of the replicates.
DREME and TOMTOM were used to identify motifs in differential enhancer regions.  Parameters used for DREME include a default E-value threshold of 0.05 and a search of both the given strand and the reverse complement strand of the queried sequence.  TOMTOM was run with a default E-value of 0.05 a well.
Genome_build: mm9

source_name: BptfKO Mammary Cells

extract_protocol:
Nuclei obtained from Eph4 cells or FACS-sorted mammary epithelial cells were incubated with reagents from Illumina Nextera kit (Illumina), following DNA purification with purified with DNA Clean-up & Concentration kit (Zymo) according the manufacturer's instruction
Nextera treated, purified DNA was amplified and barcoded using previously described protocol (Buenrostro e at, 2013), then pooled for sequencing.

treatment_protocol: Tamoxifen was given to mice (total 15mg/kg body) prioir to cell isolation; Eph4 cells were treated for 24 hours with Bptf inhibitor AU-1 (5uM) or DMSO

value: Mammary Gland

tag: compartment

value: Basal

value: Basal Mammary Epithelial Cells


title: Eph4+AU1_ATACseq

description: Tn5 transposed purified DNA


title: Basal_BptfKO_ATACseq_Rep1

description: Tn5 transposed purified DNA


title: Eph4+DMSO_ATACseq

description: Tn5 transposed purified DNA


title: Basal_BptfKO_ATACseq_Rep2b

description: Tn5 transposed purified DNA


title: Basal_BptfKO_ATACseq_Rep3a

description: Tn5 transposed purified DNA