title: gDNA_CD4_H3K4me3_Graves_rep8


title: gDNA_CD4_H3K4me3_Control_rep10

status: Public on Nov 06 2015

type: SRA

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19

department: Department of Biomedicine

country: Estonia

institute: University of Tartu

library_source: genomic

data_processing:
Read trimming and quality control. Raw reads were trimmed with Trim Galore! version 0.3.3 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using the paired-end mode and the Phred score threshold set to 30. The quality control with FastQC version 0.10.0 was performed before and after trimming.
Alignment. The trimmed paired-end reads were aligned to the human reference genome (hg19) with bowtie2 version 2.0.2 allowing clipping of read ends with the option --local.
Filtering of aligned reads. The SAMtools software suite (http://www.htslib.org/) was used to retain only properly paired alignments with mapping quality ≥ 30 and the duplicated reads were removed with MarkDuplicates from the Picard tools (http://broadinstitute.github.io/picard/).
Peak calling. Peaks were called with MACS2 (https://github.com/taoliu/MACS/). Both cell types (CD4+ and CD8+ T cells) and ChIP experiments (H3K4me3 and H3K27ac) have two input sample BAM files that were merged into single BAM files, which were used as controls in peak calling. The mappable genome size (-g 2627947484) for 50 bp reads was taken from [1]. Only the peaks with q-value <0.01 were considered to be significant. Peaks were filtered against the blacklisted regions given in wgEncodeDacMapabilityConsensusExcludable.bed.gz (available on the series record).   1. Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R et al. Fast computation and applications of genome mappability. PLoS One, 2012;7:e30377.
Differential enrichment analysis. The analysis of differentially enriched peaks was performed with the R/Bioconductor package “DiffBind” [1]. Samples were read in in batch and then split by cell type and histone modification. The statistical methods for assessing the difference of the peak signals in GD and control samples were provided by the R/Bioconductor package “edgeR” [2]. Before the statistical test, the counts in the input sample were subtracted from counts in the ChIPed samples and the resulting library sizes were used for normalization. Peaks with a fold change difference of 1.5 and with the FDR adjusted p-value < 0.01 were considered for further analysis.    1. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 2012;481:389-93.  2. Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 2010;26:139-40.
Genome_build: hg19
Supplementary_files_format_and_content: The peak lists are in ENCODE narrowPeak format that is described on the UCSC Genome Browser help pages: http://genome-euro.ucsc.edu/FAQ/FAQformat.html

molecule: genomic DNA

organism: Homo sapiens

source_name: Genomic DNA, CD4 cells, H3K4me3 ChIP, healthy control

extract_protocol:
Peripheral blood mononuclear cells were extracted using Ficoll-Paque (GE Healthcare) gradient centrifugation. CD8+ T-cells and CD4+ T cells were purified by consecutive positive separation using microbeads (CD4+ #130-045-101; CD8+ #130-045-201) and AutoMACS technology (Miltenyi Biotec) according to the manufacturer's protocol. The purified cells were fixed in 1% formaldehyde and stored as cell pellets in a -80°C freezer. ChIP assays were performed using Auto Histone ChIP-seq kit (Diagenode) with minor modifications. Briefly, IP-Buffer (2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, 1% Triton X-100) was used in exchange for kit Buffer H in IP reactions. DNA from 4-6 x 106 cells was fragmented with the Bioruptor sonicator (Diagenode) to fragments of 200-400 basepairs. Sheared chromatin from 1 million cells was immunoprecipitated with 2 μg of anti-H3K4me3 antibody (Millipore 07-473) or 2 μg of anti-H3K27Ac antibody (Abcam Ab4729) using the SX-8G IP-Star Automated System (Diagenode). ChIP-DNA was purified with MinElute PCR Purification Kit (Qiagen).
The purified ChIP and input DNAs were quantified by Qubit 2.0 Fluorometer (Life Technologies) prior to library preparation with the Ovation® Ultralow DR Multiplex System 1-96 kit (NuGeneration Limited) according to manufacturer’s instructions. The barcoded libraries were quantified by Qubit 2.0 Fluorometer and validated with Agilent 2200 TapeStation analysis (Agilent Technologies, Inc.). The ChIP-seq libraries were sequenced with HiSeq 2500 (Illumina) producing 50 bp paired-end reads. Phage PhiX sequencing library was included as 1% spike-in in the sequencing runs.

tag: tissue

value: blood

tag: diagnosis

value: Healthy control

tag: cell type

value: CD4 T cells

tag: gender

value: Female

tag: age

tag: antibody


title: gDNA_CD8_H3K4me3_Control_rep13

source_name: Genomic DNA, CD8 cells, H3K4me3 ChIP, healthy control

value: CD8 T cells


title: gDNA_CD4_H3K4me3_Control_rep9


title: gDNA_CD8_H3K4me3_Control_rep10


title: gDNA_CD4_H3K4me3_Graves_rep12

source_name: Genomic DNA, CD4 cells, H3K4me3 ChIP, Graves' patient

value: Graves' patient


title: gDNA_CD4_H3K4me3_Control_rep8


title: gDNA_CD4_H3K4me3_Control_rep11


title: Trim33_ChIP-seq

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
For ChIP-seq, sequenced reads were provided by the sequencing service provider (Active Motif) in a .fastq.gz format. Reads were mapped to the mouse mm9 genome by the service provider, using the BWA program using default settings.
For ChIP-seq, peak calling was done by the service provider (Active Motif) using MACS (Version 1.4.2) by first filtering out duplicate reads and reads with a mapping quality of less than 25, then using default parameters and the following options -s 75--bw 200 -m 10 30 –p 0.0000001
For RNA-seq, sequenced reads were provided by the sequencing service provider (Australian Genome Research Facility) in a .fastq.gz format. Reads were mapped to the mouse mm9 genome using the program Tophat (version 2.0.11) with the following parameters: -I 100000 --library-type=fr-unstranded --read-edit-dist 3 --no-coverage-search --read-mismatches 3
For RNA-seq, read counts for gene exons were extracted using the program htseq-count (version 0.6.1) with the options -s no -m intersection-strict. Normalization and differnetial gene expression was assessed using the R-package DEseq, with default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: For processed ChIP-seq data, Bigwig format files showing the fragment density for 32 nucleotide binds along the genome. For processed RNA-seq data, tab-delimited text files include raw read counts for each of the samples

organism: Mus musculus

extract_protocol:
Testis were removed and pooled from 3 mice and flash frozen on dry ice. Testis were sent to Active Motif (CA, USA) who then carried out ChIP and library construction as well as Input DNA library construction (Cat No. 25001 and 25046).
ChIP libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: FVB

value: Testis pooled

value: 84 days post partum

tag: genotype

tag: chip antibody

value: Anti-Trim33 Bethyl Laboratories A301-060A


title: gDNA_CD8_H3K4me3_Control_rep9


title: gDNA_CD4_H3K4me3_Control_rep7


title: gDNA_CD8_H3K4me3_Control_rep8


title: gDNA_CD4_H3K4me3_Graves_rep5


title: gDNA_CD8_H3K4me3_Graves_rep8

source_name: Genomic DNA, CD8 cells, H3K4me3 ChIP, Graves' patient


title: gDNA_CD8_H3K4me3_Graves_rep7


title: Esrrb_DY131_1

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

country: USA

institute: Xiphophorus Genetic Stock Center

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor seuqence were trimmed off, then low quality basecall was trimmed off, at last, low quality sequence reads were filtered out.
Short sequencing reads were aligned to homo sapiens genome hg18, gene expression value is quantified as raw read count.
Differentially gene expression was analyzed using EdgeR
Genome_build: hg18
Supplementary_files_format_and_content: csv, raw gene expression read count.

molecule: total RNA

growth_protocol: DU145 (ATCC Number: HTB-81) were obtained from the American Type Culture Collection (ATCC). DU145 cells are cultured in RPMI1640 media (Invitrogen, Grand Island, NY) with 10% Fetal Bovine Serum (FBS) (GE Healthcare Life Sciences, Logan, Utah). 70% confluent DU145 cells are transfected with either pcDNA3.1-zeo (+)-Esrrb expression vector, or control empty vector pcDNA3.1-zeo (+) (Promega, Madison, WI). Empty vector or Esrrb expression vector transfected DU145 cells are maintained in medium containing 150ug/ml Zeocine (Invitrogen, Grand Island, NY) for 3 weeks for selection. The stably transfected DU145 cells carrying Esrrb trans-gene are pooled together and are named DU145-Esrrb, while the control DU145 cells transfected with the empty vector are called DU145-pc3.1.

extract_protocol:
Total RNA was extracted using Rneasy kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For DY131 (Tocris Bioscience, Bristol, UK) treatment, cells are plated in 60mm petri dishes until confluent; DU145-pc3.1 and DU145-Esrrb are incubated with 3uM DY131 diluted in medium with charcoal-stripped FBS for indicated length of time.

tag: cell line

tag: passages

value: five to six

value: prostate cancer


title: Input_ChIP-seq

value: input


title: Esrrb_DY131_2


title: Esrrb_2


title: pcDNA3.1_DY131_2


title: Esrrb_1


title: pcDNA3.1_DY131_1


title: gDNA_CD4_H3K4me3_Control_rep6


title: pcDNA3.1_2


title: pcDNA3.1_1


title: gDNA_CD8_H3K4me3_Control_rep11


title: gDNA_CD8_H3K4me3_Control_rep6


title: gDNA_CD4_H3K4me3_Graves_rep4


title: gDNA_CD8_H3K4me3_Graves_rep5


title: gDNA_CD4_H3K4me3_Control_rep4


title: gDNA_CD4_H3K4me3_Control_rep5


title: gDNA_CD8_H3K4me3_Control_rep5


title: gDNA_CD4_H3K4me3_Graves_rep6


title: gDNA_CD8_H3K4me3_Graves_rep4


title: gDNA_CD8_H3K4me3_Control_rep4


title: gDNA_CD4_H3K4me3_Control_rep2


title: gDNA_CD4_H3K4me3_Graves_rep3


title: gDNA_CD8_H3K4me3_Graves_rep6


title: gDNA_CD8_H3K4me3_Graves_rep3


title: gDNA_CD8_H3K4me3_Control_rep2


title: gDNA_CD8_H3K4me3_Control_rep3


title: gDNA_CD8_H3K4me3_Graves_rep1


title: gDNA_CD4_H3K4me3_Control_rep1


title: gDNA_CD4_H3K4me3_Graves_rep2


title: gDNA_CD8_H3K4me3_Graves_rep9


title: PorcineEndometrium_C16_17

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description: microRNA expression in D16 cyclic endometrium

data_processing:
Illumina Sequencing Analysis Viewer v. 1.8.4 software was used for base calling and FASTQ files generation
FASTQ files were demultiplexed using Illumina Demultiplex v. 1.0.0 tool implemented in locally installed Galaxy
Multiple adaptor sequences were clipped using Galaxy tools
Quality filter for FASTQ files were implemented using phred score cut off > 20, and notion that 100% of bases should fulfill this rule.
FASTQ files were converted to FASTA, which were converted to tabular, and afterwards read counts for all the sequences were counted. Finally sequences with read counts for every library were included in one *.xlsx file
Processed sequences were annotated using criterion that sequences from the analysis should have 100% homology to the reference sequence
Filtration based on read count number was applied. Sequences with read count more or equal to 10, in at least 4 samples (in the case of group C12 in at least 3 out of 4 samples), in at least one of the group (P12, P16, P20, C12, C16, C20) were used for further analysis.
Genome_build: miRBase v.19, Ensembl Sscrofa 10.2 release 70, Rfam 11.0 ncRNAs, NCBI blast tool accessed on 3.05.2013 - EST sequences and nt collection for Sus scrofa.
Supplementary_files_format_and_content: Processed data files saved as *.txt contain read counts for sequences in single library after applying phred score filtering > 20.
Supplementary_files_format_and_content: Final processed file after applying filtering of read count was saved in *.xlsx format and containes read counts for every sample/library, sequences, annotated miRNA names,  as well not annotated miRNAs (without 100% homology to the references).

organism: Sus scrofa

source_name: Endometrium, Day 16 of estrous cycle

growth_protocol: Hampshire x Duroc crossbred gilts of similar age (7-8 months) and genetic background from one commercial herd were inseminated 12 and 24 hours after detection of the third estrus.

extract_protocol:
Total RNA containing small RNAs was extracted using a mirVana miRNA isolation kit (Life Technologies, USA) according to the manufacturer’s protocol. The protocol includes sample disruption in lysis buffer, acid phenol:chloroform extraction and an on-column RNA isolation. Quality and quantity of RNA was determined using UV spectrophotometry (NanoDrop 1000). RNA with RNA Integrity number higher than 7 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for small RNA libraries preparation.
5µg of total RNA form each sample was used for sequencing with NEXTflex Small RNA Sequencing Kit (BiooScientific, USA) according to supplier’s protocol. 3’ and 5’ adapters were ligated to the RNA using AIR ligase and T4 RNA ligase, respectively. During the 5’ ligation, NEXTflex RT primers were also incorporated to the RNA. After 3’ and 5’ primer ligation, the 140 bp RNAs were purified by Clean & Concentrator 5 Kit (Zymo Research, Irvine, CA, USA) to eliminate unligated products. PCR amplification of the ligated products was accomplished by using 1-12 primer barcodes (NEXTflex Small RNA Barcode Primers, BiooScientific) and DuroTaq 5x PCR Master Mix (BiooScientific) for multiplexing. Concentration of each library was determined with Agilent High Sensitivity DNA Kit using Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Final concentration of 30 nmol/l of each library was used to prepare 3 pools for multiplex analysis. Size fractioning of the pooled cDNA was done by 2% agarose gel electrophoresis in the presence of 0.5 ng/µl of ethidium bromide. Small RNA fraction with ligated adaptors ranging around 140-160 bp was excised from the gel with X-TRACTA II (Biozym Scientific GmbH, Hessisch Oldendorf, Germany), purified (Ultrafree-DA, Millipore, Billerica, MA, USA) and sequenced.

treatment_protocol: Samples were collected post mortem on day (D) 12, 16 and 20 of either the estrous cycle or pregnancy. Pregnancy was confirmed by the presence of at least four conceptuses. Until D16 of gestation, concepti were flushed from uterine horns with 20 ml of 0.01 M PBS. On D20, uterine horns were opened longitudinally and trophoblasts with embryos were dissected away. Endometrial samples were snap-frozen in liquid nitrogen and stored at -80°C for further use.

tag: breed

value: Hampshire x Duroc

tag: Stage

value: estrous cycle

tag: day of pregnancy

value: Day 16

tag: replicate

value: endometrium

value: biological replicate 3


title: PorcineEndometrium_C20_12

description: microRNA expression in D20 cyclic endometrium

source_name: Endometrium, Day 20 of estrous cycle

value: Day 20

value: biological replicate 2


title: PorcineEndometrium_C20_24

value: biological replicate 4


title: PorcineEndometrium_C20_6

value: biological replicate 1


title: PorcineEndometrium_C20_36

value: biological replicate 5


title: PorcineEndometrium_C16_29


title: PorcineEndometrium_C20_18


title: gDNA_CD4_H3K4me3_Control_rep12

value: blood

value: Healthy control

value: CD4 T cells

value: Female


title: gDNA_CD8_H3K4me3_Control_rep15

value: CD8 T cells


title: gDNA_CD4_H3K4me3_Control_rep3


title: PorcineEndometrium_C16_5


title: gDNA_CD4_H3K4me3_Graves_rep7

value: Graves' patient


title: gDNA_CD8_H3K4me3_Control_rep7


title: gDNA_CD8_H3K4me3_Graves_rep2


title: PorcineEndometrium_C16_11


title: PorcineEndometrium_C12_22

description: microRNA expression in D12 cyclic endometrium

source_name: Endometrium, Day 12 of estrous cycle

value: Day 12


title: PorcineEndometrium_C12_28

value: Hampshire x Duroc


title: PorcineEndometrium_C12_34

value: estrous cycle


title: PorcineEndometrium_P20_33

description: microRNA expression in D20 pregnant endometrium

source_name: Endometrium, Day 20 of pregnancy

value: pregnancy

value: biological replicate 6


title: PorcineEndometrium_P20_27

value: endometrium


title: gDNA_CD4_H3K4me3_Graves_rep1


title: gDNA_CD8_H3K27ac_input_rep2

description: Input DNA sample from CD8 cells for H3K27ac ChIPs

source_name: Genomic DNA, CD8 cells, input, Graves' patient

value: Input


title: gDNA_CD4_H3K27ac_input_rep2

description: Input DNA sample from CD4 cells for H3K27ac ChIPs

source_name: Genomic DNA, CD4 cells, input, Healthy control


title: PorcineEndometrium_C16_23

value: Day 16


title: PorcineEndometrium_P20_15

value: Day 20

value: biological replicate 3


title: PorcineEndometrium_P20_21

value: biological replicate 4


title: PorcineEndometrium_P20_9

value: biological replicate 2


title: gDNA_CD8_H3K27ac_input_rep1

source_name: Genomic DNA, CD8 cells, input, Healthy control

value: blood

value: Healthy control


title: gDNA_CD8_H3K27ac_Graves_rep14

source_name: Genomic DNA, CD8 cells, H3K27ac ChIP, Graves' patient

value: Female


title: PorcineEndometrium_P16_32

description: microRNA expression in D16 pregnant endometrium

source_name: Endometrium, Day 16 of pregnancy

value: biological replicate 5


title: gDNA_CD4_H3K27ac_Graves_rep13

source_name: Genomic DNA, CD4 cells, H3K27ac ChIP, Graves' patient

value: Graves' patient

value: CD4 T cells


title: PorcineEndometrium_P20_3

value: Hampshire x Duroc

value: biological replicate 1


title: PorcineEndometrium_P16_26

value: pregnancy


title: PorcineEndometrium_P16_20


title: gDNA_CD4_H3K27ac_Graves_rep12


title: PorcineEndometrium_C12_16

value: estrous cycle

value: Day 12


title: gDNA_CD8_H3K27ac_Control_rep15

source_name: Genomic DNA, CD8 cells, H3K27ac ChIP, healthy control

value: CD8 T cells


title: gDNA_CD4_H3K27ac_Control_rep11

source_name: Genomic DNA, CD4 cells, H3K27ac ChIP, healthy control


title: PorcineEndometrium_P16_14

value: Day 16

value: endometrium


title: PorcineEndometrium_P12_31

description: microRNA expression in D12 pregnant endometrium

source_name: Endometrium, Day 12 of pregnancy


title: PorcineEndometrium_P12_25


title: PorcineEndometrium_P12_19

value: biological replicate 3


title: gDNA_CD4_H3K27ac_Control_rep10


title: PorcineEndometrium_P12_1


title: gDNA_CD8_H3K27ac_Control_rep14


title: gDNA_CD8_H3K27ac_Graves_rep13


title: gDNA_CD4_H3K27ac_input_rep1

source_name: Genomic DNA, CD4 cells, input, Graves' patient

value: Input


title: gDNA_CD4_H3K27ac_Graves_rep11


title: gDNA_CD8_H3K27ac_Control_rep12

value: Male


title: gDNA_CD4_H3K27ac_Control_rep9

value: blood


title: gDNA_CD4_H3K27ac_Graves_rep10


title: JB1 KAP1

city: Naples

first: Marco

last: Cammisa

state: Naples

address: Via Castellino Pietro, 111

country: Italy

institute: Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)

data_processing:
Basecalls and adaptor trimming was performed using Illumina Pipeline Casava 1.8.2.
Reads were aligned to the NCBI37/mm9 genome assembly using  Bowtie ( version 0.12.7) with default parameters.
Genomic reads coverage was obtained using SAMtools (version 0.1.18) and BEDTools suite (version 2.14.3-1).
Peak-calling was performed using MACS algorithm implemented in SeqMonk software (version 0.24.1)
Genome_build: (NCBI37/mm9)
Supplementary_files_format_and_content: BedGraph file reports normalized RPM (Reads Per Million reads) scores of genomic coverage. Bed file contain genomic coordinates of called peaks.

source_name: Embryonic stem cells

growth_protocol: Hybrid embryonic stem cells JB1 and BJ1 were cultured under standard feederfree conditions on gelatinized tissue culture dishes with media containing DMEM (EuroClone ECM0101L) supplemented with 2-mercaptoethanol, non-essential amino acids, sodium pyruvate, 1 % fetal calf serum and leukemia inhiitory factor (LIF) at 37◦C under an atmosphere of 5% CO.

extract_protocol:
ChIP was performed on formaldehyde cross-linked chromatin isolated from cells grown on 10 cm dishes to ~80% confluency. Briefly, the cells were detached by adding 0.05% trypsin at 37 °C for 3 min. Formaldehyde was added to the cells resuspended in PBS at a final concentration of 1% and the cells were incubated at room temperature for 15 min with shaking. The reaction was stopped by addition of glycine to a final concentration of 0.125 M. Approximately 3x107 cells were washed twice in ice-cold PBS, centrifuged and resuspended in lysis buffer 1 (50 mM HEPES pH 8, 10 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40 and 0.25% Triton X-100) for 90 min at 4 °C. Isolated nuclei were lysed in lysis buffer 2 (10 mM Tris–HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) for 60 minat 4 °C. The chromatin was sheared in sonication buffer (10 mM Tris–HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% N-lauroylsarcosine) to an average size of 100–400 bp using the S220 Focused-ultrasonicators (Covaris). For each IP, 100 μg of sonicated chromatin were diluted in a final volume of 600 μl with sonication buffer and pre-cleared with 30 µl protein A/G agarose beads (SantaCruz) for 4 h at 4 °C on a rotating wheel. Anti-ZFP57 antibody (8 μg, Abcam ab45341), anti-KAP1 antibody (7 μg, Abcam ab10483) and anti-Histone H3K9me3 (7 μg, Abcam 8898) or rabbit IgG were added to the pre-cleared chromatin and incubated overnight at 4 °C on a rotating wheel. Chromatin was precipitated with 30 μl protein A/G agarose beads for 4 h at 4 °C with rotation. The beads were then washed five times with 500 μl RIPA buffer  (10 mM Tris–HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 1% Triton X-100and 0.1 % SDS) and once with each of the following buffers: WASH buffer (50 mM HEPES, 0.5% sodium deoxycholate, 1% Triton X-100, 1 mM EDTA, 500 mM NaCl and 0.2% NaN3), LiCl buffer  (0.25 M LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris pH 8) and TE buffer (10 mM Tris pH 8, 1 mM EDTA). The bound chromatin was eluted in 100 μl TE buffer. Crosslinks were reversed by incubation O/Nat 65°C after addition of 1 μl RNAse cocktail (Ambion) and 2h at 50°C after addition of 2.5μl SDS 20% + 2.5μl 20mg/ml proteinase K (Sigma). The DNA was extracted by using the QIAquick Gel Extraction Kit (Qiagen). Immunoprecipitated or 1% input DNAswere analysed by real-time PCR using SBYRGreen PCR Master Mix (Bio-Rad) on a C1000 Thermal Cycler (Bio-Rad).
Two nanograms of DNA from immunoprecipitated and input chromatin were used for Illumina library preparation. Libraries were generated by using the NuGen Ovation Ultralow Library System v2 Kit.

value: Embryonic stem cells

value: KAP1 (Abcam, ab10483)


title: gDNA_CD8_H3K4me3_Control_rep1

source_name: Genomic DNA, CD8 cells, H3K4me3 ChIP, healthy control

value: Healthy control

value: Female


title: gDNA_CD4_H3K27ac_Graves_rep8

value: Graves' patient

value: CD4 T cells


title: gDNA_CD8_H3K27ac_Graves_rep11


title: BJ1 KAP1


title: BJ1 ZFP57

value: ZFP57 (Abcam, ab45341)


title: gDNA_CD4_H3K27ac_Graves_rep9


title: PorcineEndometrium_P16_8

value: Hampshire x Duroc

value: pregnancy

value: biological replicate 1


title: BJ1 Input


title: Xla_J_strain_NF30_RiboZero

city: Woods Hole

first: Esther

middle: Jane

last: Pearl

state: MA

address: 7 MBL Street

department: National Xenopus Resource

institute: Marine Biological Laboratory

data_processing:
Casava version 1.8.2 was used for base calling
samples were adapter/quality trimmed using Trimmomatic
Ribosomal reads were removed and remaining high quality paired reads were aligned to reference set using Bowtie, using default parameters except setting k_min_coverage=2 to minimize noise
RSEM package was used to determine abundance estimates for all transcripts, transcripts with little read support were filtered out
Genome_build: JGI v6.1
Supplementary_files_format_and_content: tsv (showing TPM counts)

organism: Xenopus laevis

source_name: whole embryo

growth_protocol: embryos were raised in 0.1 X MMR containing gentamycin

extract_protocol:
total RNA was extracted using TRIzol and phase-lock tubes
libraries were constructed using RNA enriched for mRNA by rRNA depletion using the EpiCenter RiboZero kit and the EpiCenter ScripSeq kit V2 using 50ng input RNA, and 12 cycles amplification

treatment_protocol: embryos were snap frozen in liquid nitrogen at the desired stage, and stored at -80 until extraction

value: J

tag: developmental stage

value: whole embryo


title: Xla_J_strain_NF33_RiboZero


title: gDNA_CD4_H3K27ac_Control_rep7


title: gDNA_CD8_H3K27ac_Graves_rep10

value: CD8 T cells


title: PorcineEndometrium_P12_13

value: Day 12

value: endometrium

value: biological replicate 2


title: Xla_J_strain_NF26_RiboZero


title: JB1 ZFP57


title: Xla_J_strain_NF20_RiboZero


title: gDNA_CD4_H3K27ac_Graves_rep7

value: blood


title: gDNA_CD8_H3K27ac_Graves_rep12


title: Xla_J_strain_NF23_RiboZero


title: JB1 Input

value: Embryonic stem cells


title: 4C-seq_24hpf_Barx1Seq

city: mainz

first: lucas

last: kaaij

address: ackermannweg 4

department: RNA silencing

country: Germany

institute: IMB

data_processing:
Library strategy: 4C-seq
4C reads were aligned to sequences flanking restriction sites in the Zv9 genome assembly using a custom mapping pipeline written in Perl
Data from individual experiments were normalized for sequencing depth to the average number of mapped reads in all experiments
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: wig files were generated using custom R script

organism: Danio rerio

source_name: zebrafish embryos

extract_protocol:
phenol/chloroform
Typical 4CSeq strategy

value: embryos

value: 24 hpf


title: 4C-seq_brain_Barx1Seq

source_name: brain

value: brain


title: 4C-seq_8hpf_Barx1Seq

value: 8 hpf


title: gDNA_CD4_H3K27ac_Control_rep6

value: Healthy control

value: CD4 T cells

value: Female


title: gDNA_CD8_H3K27ac_Control_rep9


title: Xla_J_strain_NF16_RiboZero


title: gDNA_CD8_H3K27ac_Control_rep11


title: Xla_J_strain_NF18_RiboZero


title: 4C-seq_brain_NfixbSeq


title: Xla_J_strain_NF14_RiboZero


title: gDNA_CD4_H3K27ac_Control_rep5


title: Xla_J_strain_NF12_RiboZero


title: 4C-seq_8hpf_NfixbSeq


title: gDNA_CD4_H3K27ac_Control_rep4


title: 4C-seq_24hpf_Meis2aSeq


title: Xla_J_strain_NF10_RiboZero


title: 4C-seq_8hpf_Meis2aSeq


title: gDNA_CD8_H3K27ac_Control_rep8


title: gDNA_CD4_H3K27ac_Graves_rep5

value: Graves' patient


title: gDNA_CD8_H3K27ac_Control_rep10


title: Xla_J_strain_NF9_RiboZero


title: gDNA_CD8_H3K27ac_Graves_rep8


title: Xla_J_strain_NF8_II_RiboZero


title: gDNA_CD4_H3K27ac_Control_rep3


title: gDNA_CD8_H3K27ac_Control_rep7


title: 4C-seq_brain_Meis2aSeq


title: 4C-seq_24hpf_NfixbSeq


title: Xla_J_strain_NF7_RiboZero


title: gDNA_CD8_H3K27ac_Graves_rep7


title: 4C-seq_brain_Meis1Seq


title: 4C-seq_8hpf_Meis1Seq


title: Xla_J_strain_NF8_RiboZero


title: gDNA_CD4_H3K27ac_Graves_rep4


title: Xla_J_strain_NF6_5_RiboZero


title: 4C-seq_8hpf_Lmx1ba


title: Xla_J_strain_NF6_RiboZero


title: 4C-seq_24hpf_Lmx1ba


title: Xla_J_strain_NF0_RiboZero


title: 4C-seq_brain_Lmx1ba


title: Xla_J_strain_NF2_RiboZero


title: gDNA_CD4_H3K27ac_Control_rep2


title: 4C-seq_24hpf_Sox5Seq


title: gDNA_CD8_H3K27ac_Graves_rep6


title: gDNA_CD8_H3K27ac_Control_rep5


title: 4C-seq_8hpf_Sox5Seq


title: gDNA_CD8_H3K27ac_Control_rep4


title: 4C-seq_brain_Sox5Seq


title: gDNA_CD8_H3K27ac_Graves_rep5


title: 4C-seq_24hpf_Meis1Seq


title: Atac-seq_4hpf

data_processing:
data was mapped using bowtie 1.1.1
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling.
Cisgenome v.2 software package was used for peak-calling (FDR < 0.05). In the case of the Atac-Seq the called peaks were not used in the manuscript, however the provided BED file for the ATAC-seq sample was used to generate the figure.
Genome_build: zv9
Supplementary_files_format_and_content: cod files with called peaks. The BED files for the H3K4me2 ChIP and ATAC-sq samples were used to generate figures.

extract_protocol:
phenol/chloroform
Ovation Ultralow Library System V2 Workflow (NuGEN)

value: 4hpf embryos


title: Xla_J_strain_NF30_PolyA

data_processing:
Casava version 1.8.2 was used for base calling
samples were adapter/quality trimmed using Trimmomatic
Ribosomal reads were removed and remaining high quality paired reads were aligned to reference set using Bowtie, using default parameters except setting k_min_coverage=2 to minimize noise
RSEM package was used to determine abundance estimates for all transcripts, transcripts with little read support were filtered out
Genome_build: JGI v6.1

extract_protocol:
total RNA was extracted using TRIzol and phase-lock tubes
libraries were constructed using RNA enriched for mRNA by Poly(A) extraction using Dynabeads (invitrogen) and the EpiCenter ScripSeq kit V1 using 50-300ng input RNA, and 10 cycles amplification

value: J strain


title: Xla_J_strain_NF33_PolyA


title: gDNA_CD8_H3K27ac_Control_rep3


title: ChIP-Seq_H3K4me1_2.5hpf

value: 2.5hpf embryos

value: H3K4me1 ChIP grade (abcam)


title: Xla_J_strain_NF20_PolyA


title: ChIP-Seq_H3K27me3_4hpf

value: H3K27me3 (cat# 07-449 millipore)


title: gDNA_CD8_H3K27ac_Graves_rep4

value: CD8 T cells


title: gDNA_CD4_H3K27ac_Graves_rep3


title: gDNA_CD8_H3K27ac_Control_rep2


title: Xla_J_strain_NF18_PolyA


title: ChIP-Seq_H3K4me2_6hpf

value: 6hpf embryos

value: H3K4me2 ChIP grade (abcam)


title: ChIP-Seq_H3K27ac_brain

source_name: Brain

value: whole brain

value: H3K27ac ChIP grade (abcam)


title: ChIP-Seq_H3K27ac_intestine

source_name: Intestine

value: Whole intestine


title: gDNA_CD4_H3K27ac_Control_rep1

value: blood


title: gDNA_CD8_H3K27ac_Graves_rep3


title: gDNA_CD8_H3K27ac_Graves_rep1


title: Xla_J_strain_NF14_PolyA


title: gDNA_CD8_H3K27ac_Control_rep1


title: Xla_J_strain_NF26_PolyA


title: Xla_J_strain_NF10_PolyA


title: Xla_J_strain_NF9_PolyA


title: Xla_J_strain_NF8_PolyA


title: Xla_J_strain_NF8_II_PolyA


title: Xla_J_strain_NF23_PolyA


title: Xla_J_strain_NF7_PolyA


title: gDNA_CD8_H3K27ac_Control_rep13


title: gDNA_CD4_H3K27ac_Control_rep8


title: gDNA_CD8_H3K27ac_Graves_rep9


title: Xla_J_strain_NF6_5_PolyA


title: gDNA_CD4_H3K27ac_Graves_rep2


title: gDNA_CD4_H3K27ac_Graves_rep6


title: gDNA_CD8_H3K27ac_Control_rep6


title: Xla_J_strain_NF16_PolyA


title: Xla_J_strain_NF6_PolyA


title: Xla_J_strain_NF0_PolyA


title: Xla_J_strain_NF2_PolyA


title: Xla_J_strain_NF12_PolyA


title: gDNA_CD4_H3K27ac_Graves_rep1


title: gDNA_CD8_H3K27ac_Graves_rep2


title: Polytene_Hi-C_tethered_rep3

status: Public on Nov 05 2015

city: Houston

first: Kyle

last: Eagen

address: 1 Baylor Plaza

department: Department of Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Polytene chromosomes

data_processing:
Hi-C reads were aligned to genome dm3 using Bowtie 2.
Aligned reads were assigned to DpnII restriction fragments.
Reads mapping to the same restriction fragment, separated by less than the library insert size, within 4 bp of a restriction site, and duplicate reads were removed.
Exceptionally large (> 100 kb) and small (<100 bp) restriction fragments and fragments with the highest 0.5% of counts were removed.
Filtered fragments were assigned to 15 kb or 100 kb genomic bins.
Further filtering at the bin level removed bins where less than half the bin was sequenced, the lowest 1% of bins, and the highest 0.05% of interchromosomal bins.
The resulting Hi-C heatmaps were normalized using a previously described iterative approach (Imakaev, M., Fudenberg, G., McCord, R.P., Naumova, N., Goloborodko, A., Lajoie, B.R., Dekker, J., and Mirny, L.A. (2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9, 999–1003).
All of the above steps were performed using a previously described pipeline (Imakaev, M., Fudenberg, G., McCord, R.P., Naumova, N., Goloborodko, A., Lajoie, B.R., Dekker, J., and Mirny, L.A. (2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9, 999–1003).
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files of Hi-C contacts.  Each row lists the first chromosome, the start and end coordinate of the first bin, the second chromosome, the start and end coordinates of the second bin, and the normalized contact probability.

organism: Drosophila melanogaster

source_name: Male salivary glands

growth_protocol: Standard molasses medium in standard culturing vials grown at 25° C.

extract_protocol:
Cross-linked chromatin was released by detergent lysis and Dounce homogenization.  Cross-linked proteins were then biotinylated at cysteine residues and the DNA digested with DpnII.  Digested chromatin was bound to streptavidin beads, thoroughly washed to remove uncross-linked DNA, DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together.  DNA-protein cross-links were reversed, DNA purified, and biotinylated nucleotides marking unligated ends removed
DNA sheared to a mean size of approximately 200 bp.  DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).  The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Drosophila melanogaster third instar larvae salivary glands were manually dissected and fixed with 2% EM grade paraformaldehyde

tag: stock

value: yellow white

value: Third instar larvae

tag: tisse

value: Salivary gland


title: Polytene_Hi-C_in_solution

description: Polytene chromosomes


title: Hela SRAP-GFP exp2

city: WINNIPEG

first: YI

last: YAN

state: MANITOBA

address: 5029 - 675 McDermot Ave Winnipeg, Mb

department: BIOCHEMISTRY AND MEDICAL GENETICS

country: Canada

institute: UNIVERSITY OF MANITOBA

description: Hela SRAP-GFPexp2

data_processing:
XSQ files generated from SOLiD sequencer were mapped on human genome reference hg19 by LifeScope v2.5.1 (Life Technologies) with transcriptome mapping module.
adaptors, t-RNAs were filtered. Low quality portion was trimmed.
raw sequence reads were counts and rpkm was calculated for each refGene annotation by Lifescope v2.5.1.
The log of the ratio experiment (Si-pool, Si-1, Si-2, Si-3 or Si-4) rpkm /Control rpkm was calculated for each gene. Only genes with resulting values higher than 0.0969 (corresponding to a rpkm 1.25 fold higher than that of the control) or lower than -0.0969 (corresponding to a rpkm 1.25 fold lower than that of the control) in Si-pool, Si-1, Si-2, Si-3 and Si-4 were considered reproducibly up or down regulated, respectively.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include conts, RPKM values of genes for each Sample

source_name: cervical cancer Hela cells

growth_protocol: cells were routinely maintained in high-glucose (4.5 g/L) DMEM (Gibco, cat# 11965-092) supplemented with 10% FBS (Hyclone, cat# SH30396.03) and 2mM L-glutamine (Gibco, cat# 25030). Cells were grown in a 37oC humidified incubator with 5% CO2.

extract_protocol:
cDNA libraries were prepared from rRNA-depleted total RNA (200–500ng) of Hela cells transfected with the various siRNAs, using the SOLiD™ Total RNA-Seq Kit protocol according to the manufacturer’s instructions (Life Technologies).
cDNA libraries were prepared from rRNA-depleted total RNA (200–500ng) of Hela cells transfected with the various siRNAs, using the SOLiD™ Total RNA-Seq Kit protocol according to the manufacturer’s instructions (Life Technologies). ted only once.  For each gene, the raw read data were normalized and expressed as reads per kilobase per million reads (rpkm). Genes with less than 0.5 rpkm in any one sample were not considered for analysis.
The SOLiD paired read sequences were mapped onto human reference genome hg19 using LifeScope software package (Life Technologies) with 2-mismatch setting and the best score mapping when multiple mapping occurs. The sequence quality was inspected by Bamstats module. For a given gene the mapped sequence reads were counted against the current gene annotation General Transfer Format (hg19.gtf). Reads that map to overlapping exons or features of a given gene are counted only once.  For each gene, the raw read data were normalized and expressed as reads per kilobase per million reads (rpkm). Genes with less than 0.5 rpkm in any one sample were not considered for analysis.

treatment_protocol: Hela cells were plated at 2.5 x105 cells per well in 6-well plates 24 hours prior to siRNA treatment. Each well was then transfected with either 100 nM control siRNA Non-targeting Control Pool (Dharmacon, cat# D-001810-10); human SRA1 Smartpool (Dharmacon, cat# LQ-027192-00) or individual ON-TARGETplus SRA1 siRNA: Si1, Si2, Si3, Si4 (Dharmacon, cat#J-027192-09-0002, cat#J-027192-10-0002 cat#J-027192-11-0002 cat#J-027192-12-0002) for 72 hours using Dharmafect1 (Dharmacon, cat# T-2001) according to the manufacturer’s instructions.

value: Hela

value: passage number 55-65

tag: provider

value: ATCC, cat# ATCC-CCL2

tag: sirna treatment conditions

value: Hela cells were transfected with a GFP-SRAP in 10 cm dishes for 24 hours using Lipofectamin 2000 followed by sorting


title: Hela SRAP-GFP exp1

description: Hela SRAP-GFPexp1


title: Hela GFP exp2

description: Hela GFP exp2

value: Hela cells were transfected with an empty GFP vector in 10 cm dishes for 24 hours using Lipofectamin 2000 followed by sorting


title: Hela SRA RNAi 4

description: Hela SRA RNAi 4

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 siRNA4  (Dharmacon,  cat#J-027192-12-0002) for 72 h


title: 231 control RNAi exp2

description: 231 control RNAi exp 2

source_name: breast cancer MBD-MDA-231

value: passage number 21-31

value: ATCC, cat# HTB-26

value: 2.5 x105 231 cells in 6-well plates  100 nM control siRNA Non-targeting Control Pool (Dharmacon, cat# D-001810-10) for 72 h


title: Hela control RNAi

description: Hela control RNAi

value: 2.5 x105 hela cells in 6-well plates  100 nM control siRNA Non-targeting Control Pool (Dharmacon, cat# D-001810-10) for 72 h


title: Hela SRA RNAi 1

description: Hela SRA RNAi 1

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 siRNA1 (Dharmacon, cat#J-027192-09-0002 for 72 h


title: Hela GFP exp1

description: Hela GFP exp1


title: 231 SRA RNAi pool exp1

description: 231 SRA RNAi pool exp1

value: 2.5 x105 cells in 6-well plates r 100 nM RNAi for 72 h


title: Hela SRA RNAi pool

description: Hela SRA RNAi  pool

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 Smartpool (Dharmacon, cat# LQ-027192-00) for 72 h


title: Hela SRA RNAi 2

description: Hela SRA RNAi 2

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 siRNA2  (Dharmacon, cat#J-027192-10-0002 ) for 72 h


title: Hela control RNAi exp1

description: Hela control RNAi exp1


title: Hela SRA RNAi pool exp2

description: Hela SRA RNAi  pool exp2

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 Smartpool (Dharmacon, cat# LQ-027192-00)for 72 h


title: 2re_MN_rep2

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

institute: Heinrich-Heine-University

description:
processed data file: SDataset1.xlsx
single-end sequencing

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological triplicate group (drought stage) were calculated.
Differential gene expression and log2-fold change of each drought stage compared to control group (0 days drought) were determined using DESeq2 (Love et al., 2010) with multiple hypothesis correction after Benjamini-Hochberg (1995)
Supplementary_files_format_and_content: Excel sheet (SDataset1.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts and rpm for each sample, mean rpm for biological triplicates, log2-ratio (based on rpm) and Benjamini-Hochberg corrected p-values of differential expression (based on DeSeq2 for all stages (except 0 d drought) compared to 0 days drought.

molecule: polyA RNA

organism: Talinum fruticosum

source_name: Leaf

growth_protocol: Talinum triangulare plants were grown well-watered for 28 days and then subjected to drought treatment

extract_protocol:
Mature leaves of T. triangulare were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the GeneMatrix Universal RNA Purification Kit (EURx Ltd.). Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in single-end mode (Rapid Run, 150 bp read length) on an Illumina HiSeq 2000 platform.

tag: tissue

value: leaf

tag: water-limitation

value: 2 d re-watered

tag: time of collection

value: Middle of the night

tag: photosynthetic mode


title: 231 control RNAi exp1

description: 231 control RNAi exp1


title: Hela SRA RNAi 3

description: Hela SRA RNAi 3

value: Hela

value: passage number 55-65

value: 2.5 x105 hela cells in 6-well plates  100 nM human SRA1 siRNA3 (Dharmacon,cat#J-027192-11-0002) for 72 h


title: 2re_MN_rep1


title: Day12_MN_rep1

value: 12 d drought

value: CAM


title: H3_NO_RAPA

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing:
Library strategy: MNase ChIP-seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
Each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: Signal density in bigWig format.

organism: Saccharomyces cerevisiae

source_name: whole organism, HHY168, anti-histone H3 ChIP

growth_protocol: Yeast cultures were grown at 30°C in YPAD to OD600~0.4.

extract_protocol: TruSeq paired-end (Illumina).

treatment_protocol: Cells (200 ml of culture) were processed as for MNase-seq up to the step of addition of EDTA. Afterwards the lysates were frozen and thawed followed by centrifugation at 7000 rpm for 15 minutes. Anti-H3 or Anti-H2A antibody (8 µg) was added to the supernatant (2ml). Samples were further processed as described for RNA Pol II ChIP.

tag: strain/background

value: HHY168 (W303 MATalpha tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1)

tag: treatment

value: vehicle

tag: depleted factor

value: anti-histone H3 antibody - ChIP Grade (Abcam, ab12079)


title: Hela SRA RNAi pool exp1

description: Hela SRA RNAi pool exp1

tag: cell line

tag: passages

value: ATCC, cat# ATCC-CCL2


title: WTIP

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
Each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
Genome_build: R64 (sacCer3)
Supplementary_files_format_and_content: Signal density in bigWig format.

source_name: whole organism, HHY168, anti-RNA polymerase II ChIP

growth_protocol: Cells were grown in YPD to OD600=0.4.

extract_protocol:
Crosslinked cells were washed with HBS buffer, resuspended in ChIP lysis buffer (600 µl/40 ml of cell culture), flash frozen and stored at -80°C. After thawing, the cells underwent bead-beating with zirconia beads (90s) and the lysate was centrifuged for 30 minutes at 13000 rpm. The pellet was resuspended in 300 µl of ChIP lysis buffer and sonicated for 15 minutes (30s sonication/60s pause cycles). The lysate was centrifuged at 7000 rpm for 15 minutes and the antibody was added (1µg/300 µl). Samples were incubated for 1h at 4°C and then 30 µl anti-mouse antibody-coupled magnetic beads were added and samples were incubated for another 2h. After that the beads were washed and bound complexes were extracted by incubation in TE+1% SDS at 65°C for 10 minutes. DNA was precipitated from the samples using ethanol precipitation with glycogen.
TruSeq

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 5 minutes and then quenched with 125 mM Glycine for 5 min. at room temperature.

tag: chip antibody

value: anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody - ChIP Grade (Abcam, ab5131)


title: WTI

source_name: whole organism, HHY168, input

extract_protocol:
10 ul of sonicated and cleared lysate was mixed with 120 ul of buffer TE+1% SDS and incubated overnight at 65C to reverse crosslinks. DNA was precipitated as described for WTIP sample.
TruSeq


title: Day09_MN_rep3

value: 9 d drought


title: Hela control RNAi exp2

description: Hela control RNAi exp 2

value: 2.5 x105 hela cells in 6-well plates  100 nM control siRNA Non-targeting Control Pool (Dharmacon, cat# D-001810-10) for 72 h


title: Reb1veh02

source_name: whole organism, YSK229, vehicle, no factor depleted

extract_protocol:
Chromatin for MNase digestion was prepared essentially as described (Kent and Mellor, 1995). Yeast cultures were grown at 30°C in YPAD to OD600~0.4 and crosslinked with 1% formaldehyde for 5 minutes followed by 5 minutes of quenching with 125 mM glycine. After wash with 1M sorbitol, spheroplasts were derived from the cultures by 8 minute treatment with 10 mg/ml Zymolase (100T, USBiological) in spheroplasting buffer (1 mM β-mercaptoethanol, 1 M sorbitol) at room temperature. Next the spheroplasts were washed twice with 1 M sorbitol without disrupting the pellet and treated with various concentrations of MNase (Sigma), ranging from 0.2 to 4 units in digestion buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris [pH 7.4], 5 mM MgCl2, 1 mM CaCl2, 1 mM β-mercaptoethanol, 0.5 mM spermidine, 0.075% NP-40). Spheroplasts derived from an equivalent of 50 ml of culture served as one sample. The samples were incubated at 37°C for 45 minutes. The reactions were stopped by addition of EDTA (30 mM final conc.) and the crosslinks were reversed by addition of SDS (0.5% final conc.) and proteinase K (0.5 mg/ml final conc.), incubation at 37°C for 1h followed by incubation at 65°C for at least 2h. Samples underwent phenol-chloroform extraction and DNA was precipitated from the aqueous phase using ammonium acetate and ethanol. After wash with 70% ethanol, the DNA pellet was dried, resuspended in 30 μl TE with RNase (0.1 mg/ml final concentration) and the samples were incubated for 30 min at 37°C to digest RNA. 2 μl aliquots were resolved on 3% agarose gel to evaluate the digestion. The samples from anchor-away experiments treated with vehicle and rapamycin chosen for deep sequencing that were to be compared were digested to exactly the same extent, as evaluated by the intensity ratios between mono- and di-nucleosomal DNA bands.
TruSeq paired-end (Illumina).

treatment_protocol: Samples for anchor-away experiments were treated with rapamycin (1 µg/ml in 90% EtOH/10% Tween 20) or vehicle treated for 1h prior to collection.

value: YSK229 (HHY168 REB1-FRB-KanMX6)


title: H2A_NO_RAPA

source_name: whole organism, HHY168, anti-histone H2A ChIP

value: anti-histone H2A antibody - ChIP Grade (Abcam, ab13923)


title: Day12_MN_rep2

value: leaf


title: Day12_MN_rep3


title: 2re_MN_rep3

value: 2 d re-watered


title: Reb1rapa02

source_name: whole organism, YSK229, rapamycin, Reb1 depleted

value: rapamycin


title: Day09_MN_rep2

value: Middle of the night


title: Abf1rapa15

source_name: whole organism, YSK227, rapamycin, Abf1 depleted

value: YSK227 (HHY168 ABF1-FRB-KanMX6)


title: Day04_MN_rep1

value: 4 d drought


title: Reb1rapa1


title: Day00_MN_rep1

value: 0 d drought


title: Reb1veh1


title: Day04_MN_rep2


title: 2re_EN

description:
processed data file: SDataset2.xlsx
This sample was sequenced with a paired-end protocol for the purpose of creating a de novo transcript assembly. The fasta files are available on the series record.

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Paired-end reads (100 bp) were assembled using Trinity (Grabherr et al., 2011) in default mode yielding 105,520 contigs (Trinity_TalinumContigs.fasta)
Trinity contigs were collapsed to 39,781 putative open reading frames using Transdecoder (transdecoder.github.io) in default mode and manual removal of duplicate sequences (TransDecoder_TalinumContigs.fasta)
150 bp single-end reads (GSM1811409 - GSM1811423, GSM1900093-GSM1900107) were mapped against TransDecoder_TalinumContigs.fasta for quantification via "RNA-Seq Analysis" in default mode implemented in the CLC Workbench version 8.5
Means of rpm of biological triplicate group (drought stage) were calculated.
Differential gene expression and log2-fold change of each drought stage compared to control group (0 days drought) were determined using DESeq2 (Love et al., 2010) with multiple hypothesis correction after Benjamini-Hochberg (1995)
TransDecoder_TalinumContigs.fasta, Excel sheet (SDataset2.xlsx) file including Contig ID, Arabidopsis thaliana and Beta vulgaris annotation based on BlastX, raw counts and rpm for each sample, mean rpm for biological triplicates, log2-ratio (based on rpm) and Benjamini-Hochberg corrected p-values of differential expression (based on DeSeq2 for all stages (except 0 d drought) compared to 0 days drought.

treatment_protocol: for details of drought treatment see Sample Characteristics "water limitation".

value: End of the night


title: Day00_MN_rep2


title: Abf1rapa01


title: C6015

source_name: whole organism, YJB26, vehicle, no factor depleted


title: Abf1veh15

source_name: whole organism, YSK227, vehicle, no factor depleted


title: Day04_MN_rep3


title: R6002

source_name: whole organism, YJB26, rapamycin, Rap1 depleted


title: Abf1veh01


title: C6002


title: Day00_MN_rep3


title: 2re_ED

value: End of the day


title: R6015


title: Day09_MD

value: CAM

value: Middle of the day


title: Day04_MN


title: Day09_MN


title: STH1NORAPA

source_name: whole organism, YSK111, vehicle, no factor depleted

value: YSK111 (HHY168 STH1-FRB1-KanMX6)

value: vehicle


title: Day04_MD


title: RPB1_2

source_name: whole organism, HHY170, vehicle, no factor depleted

value: HHY170 (HHY168 RPB1-FRB1-KanMX6)


title: 2re_MD_rep3

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
Illumina reads were aligned to a minimal set of coding sequences of the TAIR 10 release of the Arabidopsis thaliana genome (http://www.arabidopsis.org/) using BLAT (Kent, 2002) in protein space. The minimal transcriptome was obtained as described in Gowik et al. (2011) and contains 22,079 protein coding genes.
The best BLAT hit for each read was determined by (i) lowest e-value and (ii) highest bit score.
Raw read counts were transformed to reads per million (rpm) to normalize for the number of reads available at each sampling stage
Means of rpm of biological triplicate group (drought stage) were calculated.
Differential gene expression and log2-fold change of each drought stage compared to control group (0 days drought) were determined using DESeq2 (Love et al., 2010) with multiple hypothesis correction after Benjamini-Hochberg (1995)
Excel sheet (SDataset1.xlsx) file including Arabidopsis Gene Identifier (AGI) and TAIR10_short_description, raw counts and rpm for each sample, mean rpm for biological triplicates, log2-ratio (based on rpm) and Benjamini-Hochberg corrected p-values of differential expression (based on DeSeq2 for all stages (except 0 d drought) compared to 0 days drought.

treatment_protocol: for details of drought treatment see Sample Characteristics "water limitation"..


title: Day09_MN_rep1

value: 9 d drought


title: WT_RNASeq_E12_AVC

city: Vancouver

first: Pamela

middle: A.

last: Hoodless

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratories

institute: BC Cancer Agency

description:
RNA Sequencing
processed data file: WT_versus_Sox9cKO_FPKMs_and_ Fold_Change_merged_duplicates.txt
AVC mesenchyme, endothelium and myocardium
NOTE: Sequence data were generated using two different platforms: Illumina MiSeq and NextSeq 500.

data_processing:
Aligned to mm9 genome with Tophat2.
Gene Fragments per Kilobase of exon per Million reads (FPKMs) values and differential expression between WT and Sox9 cKO AVC was determined by Cufflinks.
Normalized differential expression between WT and Sox9 cKO AVC RNA-Seq libraries was determined using edgeR in R studio.
For genes to be included for downstream analyses several criteria needed to be met: greater than or equal to 0.5 FPKM in either library, at least a 1.5 fold change (up or down) between Sox9 cKO and WT AVC, and no zero values for expression.
Supplementary_files_format_and_content: RNA-Seq text file includes FPKM values for the merged WT and Sox9 cKO AVC data from duplicate libraries. The data was filtered to exclude any values below 0.5 FPKM and any zero values. Normalized differential expression (fold change) between WT and Sox9 cKO AVC RNA-Seq libraries was determined using edgeR in R studio.
Genome_build: mm9

source_name: Atrioventicular canals (AVC) of the heart

extract_protocol:
The AVCs were manually dissected from E12.5 hearts, genotyped, and checked for level of Sox9 deletion prior to being pooled for sequencing. RNA was isolated with Trizol using the manufacturer’s protocol. Pooled AVC RNA samples were further purified by GeneJet clean up and concentration micro kit (ThermoFisher Scientific). RNA quality was assessed on the BioAnalyzer (Agilent Technologies). Duplicate RNA-Seq libraries for each genotype were generated and sequenced using Illumina Mi-Seq.
RNA-Seq libraries were prepared for sequencing using standard Illumina protocols and performed in duplicate for each genotype.

tag: strain

value: Embryonic day 12.5

tag: genotype

value: Sox9fl/fl:+/+ (WT)

tag: cell type

value: mesenchyme, endothelium and myocardium


title: Day12_MD_rep3

value: leaf

value: 12 d drought


title: 2re_MD_rep1

value: 2 d re-watered


title: RPB1_2R

source_name: whole organism, HHY170, rapamycin, Rpb1 depleted

value: rapamycin


title: STH1RAPA

source_name: whole organism, YSK111, rapamycin, Sth1 depleted


title: NORAP2U

source_name: whole organism, HHY168, vehicle, no factor depleted (WT)

value: HHY168 (W303 MATalpha tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1)


title: Day12_MD_rep2

source_name: Leaf


title: NORAP4U


title: Mock Day1

city: St Lucia

first: Kayvan

last: Etebari

state: QLD

address: Building No 8

department: School of Biological Sciences

institute: The University of Queensland

data_processing:
CLC Genomic Workbench (version 7.0.4) was used to remove adapter sequences and reads with low quality score from datasets. To avoid any impurity in sequences we also discarded the reads without 3’ adapters and less than 16 nt in length after trimming.
FASTQ/A Collapser of FASTX-toolkit was used to produce copy number based sequence lists. The tab separated files with the read sequences and their counts were used as input file for further analysis.
miRanalyzer, a powerful web-based server for next generation sequencing analysis of miRNAs was used
To detect more potential variations, we allowed three possible mismatches in the mapping criteria and all length variation and even non-templated nucleotide additions collected as isomiRs
Genome_build: AaegL2 VectorBase
Supplementary_files_format_and_content: fasta files genrated by FASTQ Collapser and CSV file generated by miRanalyzer (IsomiRs Reads Count)

organism: Aedes aegypti

source_name: Adult mosquitoes

extract_protocol:
Total RNA was extracted from non-infected control and DENV-infected mosquitoes (1, 3, and 7 d after infection) by using Tri-Reagent following the manufacturer’s protocol (Molecular Research Center). RNA concentrations were measured by using a spectrophotometer, and integrity was ensured through analysis of RNA on a 1% (wt/vol) agarose gel and bioanalyzer.
Small RNA libraries were generated from both samples by using the Illumina Truseq Small RNA Preparation kit at LC Sciences. The purified cDNA libraries were sequenced on Illumina GAIIx, and raw sequence reads (36 nt) were obtained by using Illumina’s Sequencing Control Studio software version 2.8 followed by real-time sequencing image analysis and base-calling by Illumina’s Real-Time Analysis version 1.8.70 (LC Sciences).

treatment_protocol: Ae. aegypti mosquitoes were fed with sheep blood  containing DENV-2 (New Guinea strain) at 10^7 TCID50/mL.

value: Whole body

tag: infection status

value: Non infected / Blood fed

value: Cairns

value: wild type


title: Day09_MD_rep3

value: CAM

value: Middle of the day


title: NORAP1U

value: vehicle


title: DENV infected Day 3

source_name: Adult mosquitoes- 3 days post infection

value: Blood fed/ DENV-2 (New Guinea strain)  infected at 10^7 TCID50/mL


title: DENV infected Day 1

source_name: Adult mosquitoes- 1 day post infection


title: RBP1_02

value: HHY170 (HHY168 RPB1-FRB1-KanMX6)


title: NORAP15U


title: PCBP2_KO_4

city: Philadelphia

first: Ian

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

data_processing:
Cutadapt v1.4.2 was used to trim reads with the sequence 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
TopHat2 was used to map reads to the mouse genome and transcriptome
HTseq was used to count the number of reads mapping to the mouse transcriptome (gencode vM2)
DESeq2 was used to identify differentially expressed genes (P<0.001)
Genome_build: mm10
Supplementary_files_format_and_content: PCBP2_KO_v_WT_DESeq_gencode.all.name.txt is DESeq2 output with gene IDs
Supplementary_files_format_and_content: *gencode_counts.txt are HTSeq outpust (gene counts)

source_name: Fetal Liver

growth_protocol: Not Applicable

extract_protocol:
Total RNA extracted using Trizol Reagent per the manufacturer's protocol
TruSeq Stranded mRNA-seq

treatment_protocol: Not Applicable

tag: age

value: 12.5 days post coitum

tag: genotype/variation

value: PCBP2 knockout


title: PCBP2_KO_5


title: Mock Day3


title: PCBP2_KO_3


title: Day12_MD_rep1


title: WT_4


title: Mock Day7


title: 2re_MD_rep2


title: RBP1_02R


title: Sox9cKO_RNA-Seq_AVC

tag: developmental stage

value: Embryonic day 12.5

value: Sox9fl/fl:Tie2-Cre/+ (Sox9 cKO)

value: mesenchyme, endothelium and myocardium


title: WT_3


title: Day09_MD_rep2

tag: tissue

value: leaf

value: 9 d drought


title: NORAP05U

value: HHY168 (W303 MATalpha tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1)


title: WT_2


title: Day04_MD_rep3

tag: water-limitation

value: 4 d drought


title: Day09_MD_rep1

tag: time of collection


title: Day04_MD_rep2

tag: photosynthetic mode


title: RAP2U

source_name: whole organism, HHY168, rapamycin, no factor depleted

tag: strain/background

value: rapamycin


title: NORAP02U

tag: treatment


title: RAP15U

tag: depleted factor


title: Day04_MD_rep1


title: Day00_MD_rep2

value: 0 d drought


title: Day00_MD_rep1


title: Day00_MD_rep3


title: Polytene_Hi-C_tethered_rep2

description: Polytene chromosomes

source_name: Male salivary glands

tag: stock

value: yellow white

value: Third instar larvae

tag: tisse

value: Salivary gland


title: Polytene_Hi-C_tethered_rep1

description: Polytene chromosomes


title: Amel_Queen_brain3

city: Duesseldorf

first: Christina

last: Schulte

address: Universitaetssrasse 1

department: Evolutionary Genetics

institute: Heinrich-Heine-Universitaet

data_processing:
Sequencing was performed using CASAVA version 1.8.2 on Illumina HiSeq2500 instrument
Reads that passed Illumina pipeline quality filtering criteria (those output to LaneX_X_fastq files) were mapped to a reference genome
Mapping was then performed using Tophat v.2.0.8 (Trapnell et al., 2012), with Bowtie v2.1.0 (Langmead et al., 2010), and samtools 0.1.18 (Li et al., 2009), and parameters “  A reference annotation (ref_Amel_4.5_top_level) was supplied in gtf format with the -G option.
The reference sequence for mapping was the Assembly v.4.5 from ncbi (ftp://ftp.ncbi.nih.gov/genomes/Apis_mellifera/Assembled_chromosomes/seq/)
BAM files were used to generate FPKM values using Cufflinks version 2.0.2 (Trapnell et al,. 2012)
Genome_build: Amel_4.5
Supplementary_files_format_and_content: FPKM values for the mapped and assembled reads

organism: Apis mellifera carnica

source_name: Brain

growth_protocol: Wildtype drone, worker and queen honeybee pupae were collected out of a feral colony in pupal stage 4-5. Brains were disected, frozen in liquid nitrogen and stored at 80°C until RNA isolation.

extract_protocol: Total RNA was isolated from single brains using Trizol method. 50 µl Trizol were added to a single brain and the tissue was pestled. After incubation for 5 min at room temperature 10 µl chloroform were added. The solution was mixed for 30 sec and centrifuged for 15 min on 13,000 rpm. The upper phase was transferred into a new tube and 20 µl isopropanol were added and mixed. The solution was incubated for 10 min at room temperature and then centrifuged for 10 min at 13,000 rpm and 4°C. The pellet was dired for 5 min at room temperature and then diluted in 10 µl RNAse free water.

value: Pupa (stage 4-5)

tag: Sex

value: Female

value: Brain


title: mmDC_SAHA-H3K4me3_ChIPSeq

city: Ann Arbor

first: yaping

last: sun

state: Michigan

address: 1500 E Medical Center Dr.

department: internal medicine

institute: university of michigan

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using BWA" mapping software version 0.5.8a
The enriched "peaks" were called using the Model-based Analysis of ChIP-seq algorithm (MACS)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include Peak chromosome, Peak start and end, Peak ID, score (p-value -10*log), Gene start and end, Gene strand, Entrez Gene Symbol, RefSeq Gene ID, Distance between center of peak and gene TSS.

source_name: Dendritic cells

growth_protocol: To obtain mouse DCs, Bone marrow cells isolated from tibia and fibula from C57BL/6 female mice, aged at 10 weeks were cultured with murine recombinant GM-CSF (10 ng/mL; BD PharMingen) and IL-4 (10 ng/mL; PeproTech) for 7 days and harvested and positively selected by the autoMACS Pro Separator (Miltenyi Biotec) for CD11c cells with the 95% purity

extract_protocol: Chromatin (~200 ng of DNA) was sonicated into 200-500 bp fragments, DNA ends were repaired with polynucleotide kinase and Klenow enzyme and treated with Taq polymerase for generation of a protruding 3′ “A” nucleotide for adaptor ligation. Libraries were prepared with the Illumina ChIP-seq Sample Prep Kit

treatment_protocol: Purified DCs were treated with SAHA (500nm) or diluent for 12 hours. SAHA was in Sera free media (RPMI1640) after dissolved in DMSO.

tag: strain

value: Bone marrow derived dendritic cells

tag: agent

value: SAHA (500nm)

value: female

value: 10 weeks

tag: chip antibody

value: H3K4me3 (Cat. 9751, Cell Signaling)


title: RAP05U


title: Amel_Queen_brain2


title: mmDC_SAHA-STAT3_ChIPSeq

tag: cell type

value: STAT3 (Cat. 9132, Cell Signaling)


title: mmDC_IgG_ChIPSeq

value: diluent

tag: age

value: Rabbit IgG (Cat. 2729, Cell Signaling)


title: Input_ChIPSeq_Embryonic_Heart

description:
Input chromatin (no IP)
whole heart

data_processing:
ChIP-Seq reads were aligned to the mm9 genome with Burrows-Wheeler Aligner (BWA)
Peak calling was performed using FindPeaks3.1 with fixed read extension (200bp).
A FDR was applied to threshold ChIP-Seq data. See publication for extensive details.
Post processing using control and z-scores - custom scripts. See publication for extensive details.
Supplementary_files_format_and_content: Bed files include all SOX9 peaks used for analysis.
Genome_build: mm9

source_name: Hearts

extract_protocol:
The AVCs and limb buds were isolated from E10.5/12.5 embryos in PBS. AVCs were manually dissected out from the heart.
Tissues were homogenized in 1% formaldehyde and incubated at room temperature (RT) for 10 min. Samples were incubated with 0.125 M glycine at RT for 5 min. Following pelleting and washing, samples were resuspended in 5 cell pellet volumes of ChIP cell lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40) with a protease inhibitor cocktail (PIC, Roche). Cells were re-homogenized and put on ice for 15 min. Cells were pelleted again and resuspended in 3 volumes of ChIP nuclear lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris-H Cl, pH 8.1) containing a protease inhibitor cocktail (Roche). Following a 30-60 min incubation on ice, samples were sonicated (Sonicator 3000, Misonix) in an ice water bath for 20 cycles of 30 s on, 40 s off. After a 10 min centrifugation (4˚C, 13.2krpm) to remove cellular debris, sonicated chromatin was precleared with 20 μl Protein A/G beads (ThermoFisher Scientific, 53135), 10 μl 10x PIC and ChIP dilution buffer (with a volume equal to 4x that of the chromatin volume used, 0.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 16.7 mM Tris–Cl, pH 8.1) for 1 hr, 4˚C with rotation. After 2 min 4000 rpm centrifugation, diluted chromatin removed from beads and transferred to new tubes and antibodies were added as follows: 3 μg of rabbit polyclonal anti-mouse SOX9 antibody (Millipore AB5535) or for negative controls 3 μg of normal rabbit IgG antibody (Santa Cruz, sc-2027). Samples were incubated overnight while rotating at 4˚C. Simultaneously, 20 μl of fresh Protein A/G beads (ThermoFisher Scientific) were blocked with 1 mg/ml BSA and 0.1 mg/ml herring sperm DNA in ChIP dilution buffer overnight at 4˚C. The following day, samples were incubated with blocked Protein A/G beads for four hours rotating at 4˚C. Beads were washed with several buffers as follows: low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), high salt buffer (low salt buffer with 500 mM NaCl), lithium chloride buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1) and two final washes with TE buffer. 125 μl elution buffer (1% SDS, 0.1 M NaHCO3) was added to remove the bound chromatin-antibody complexes from the beads and samples were rotated at RT for 15 min and after centrifugation the eluted solution was removed from the beads. This was repeated. To reverse the crosslinking and break the complex bonds, 10 μl 5M NaCl, 10 μl 1M Tris-HCl (pH 6.5), 5 μl 0.5M EDTA, 1 μl Proteinase K (20mg/ml), and 2.5 μl RNAseA (10mg/ml) was added to each of the samples and incubated at 65˚C overnight. Purification of DNA was performed with two rounds of phenol-chloroform extraction and ethanol precipitation. Samples were spun down and pellets were resuspended in 50 μl dH2O. A sample of unbound sonicated DNA served as input for sequencing. ChIP DNA was sent to the Genome Sciences Centre (Vancouver, BC) for library generation. DNA was purified using 8-12% PAGE to isolate 100-300bp fragments for short read (50bp) sequencing on an Illumina Genome Analyzer (GA2).

value: Embryonic day 10.5

tag: genotype

value: Wild type (WT)

value: whole heart


title: Amel_Queen_brain1

tag: developmental stage


title: mmDC_H3K4me3_ChIPSeq


title: jmj704

city: Fuyang

first: Yuxuan

last: Hou

state: Zhejiang

address: 28 Shuidaosuo Road

country: China

institute: China National Rice Research Institute

data_processing:
SOAP aligner/SOAP2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  rice RGAP 7 whole genome.
Gene expression level was calculated by Reads Per Kilobase of exon per Megabase of library size (RPKM) . 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: RGAP 7
Supplementary_files_format_and_content: files include RPKM values for each sample.

organism: Oryza sativa

source_name: rice

growth_protocol: ZH11 and jmj704 seeds were germinated, and then planted in the greenhouse for 14 days.

extract_protocol:
Total RNA of rice seedlings was isolated using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: seedling

value: 14 days

value: T-DNA insert; jmj704 mutant


title: SOX9_ChIPSeq_E12_AVC

description:
Chromatin IP against SOX9
SOX9+ valve mesenchyme

value: Embryonic day 12.5

value: SOX9 (Millipore, catalog# AB5535, lot# LV 1478872)

value: valve mesenchyme


title: SOX9_ChIPSeq_E12_Limb

description:
Chromatin IP against SOX9
SOX9+ limb mesenchyme

source_name: Limb buds

value: limb mesenchyme


title: mmDC_STAT3_ChIPSeq

value: Bone marrow derived dendritic cells


title: ZH11

value: wildtype (ZH11)


title: RAP1U

value: HHY168 (W303 MATalpha tor1-1 fpr1::NAT RPL13A-2×FKBP12::TRP1)

value: rapamycin


title: DENV infected Day 7

source_name: Adult mosquitoes- 7 days post infection

value: Whole body

tag: infection status

value: Blood fed/ DENV-2 (New Guinea strain)  infected at 10^7 TCID50/mL

value: Cairns

value: wild type


title: CD13+/ROR2+/NKX2.5-

city: Los Angeles

first: Rhys

middle: John Powling

last: Skelton

state: CA

address: 675 Charles E Young Dr S, Room 3645

department: Eli and Edythe Broad Stem Cell Research Center

institute: UCLA

data_processing:
The raw reads were generated by HiSeq 2500 sequencing control software. Illumina Casava1.8 software was used for basecalling and fastq file generation.
RNASeq data was mapped with OLego and normalized by using standard analysis pipelines such as cufflinks genome.
Clustering was performed by R software (heatmap.2, gplots) using standard hierarchical agglomerative approach with parameter pearson's correlation and complete
Gene Ontology analysis was preformed using StepMiner and GSEA analysis using software from the Stanford Broad Institute.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample.

source_name: Day 7 CD13+/ROR2+/NKX2-5- cells

extract_protocol:
All cell samples were double sorted directly into RNA Later solution (Ambion). Total RNA was extracted using RNeasy miniElute cleanup kit (Qiagen) according to manufacturer’s instructions.
The cDNA library was generated using the reagents provided in the Illumina ® TruSeq™ RNA Sample Preparation v2 Kit (Illumina). The clustering was performed on a cBot cluster generation system using an Illumina HiSeq single read cluster generation kit (Illumina) according to the manufacturer's instructions. The amplified cDNA library was sequenced on an Illumina HiSeq 2500 for estimating transcript abundance (1X50 reads and >12 million reads/sample).

treatment_protocol: hESCs were differentiated toward the cardiac lineage before being FACS sorted at their respective time points

tag: cell line

value: H3 hESC NKX2-9eGFP/alpha-MHC-mCherry

value: Unknown

tag: day

value: Day 7 of Cardiac Differentiation


title: IPSDM M2 rep6

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description: processed data files: IPSDM_MAC_M2_gene_exp.diff, IPSDM_M1_M2_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) the mapping quality score of each read is ≥ 30, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp, 3) read was uniquely mapped
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000 --library-type fr-firststrand". Annotation from RefSeq genes and the stringent set of lincRNAs from Cabili et al. 2011 was provided.
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.Tab-delimited text file include normalized FPKM values from HMDM, IPSDM and iPSC samples
HMDM_MAC_M1_gene_exp.diff contains differential expression result from HMDM and M1-HMDM. sample_1 = HMDM, sample_2 = M1-HMDM
HMDM_MAC_M2_gene_exp.diff contains differential expression result from HMDM and M2-HMDM. sample_1 = HMDM, sample_2 = M2-HMDM
HMDM_M1_M2_gene_exp.diff contains differential expression result from M1-HMDM and M2-HMDM. sample_1 = M1-HMDM, sample_2 = M2-HMDM
IPSDM_M1_M2_gene_exp.diff contains differential expression result from M1-IPSDM and M2-IPSDM. sample_1 = M1-IPSDM, sample_2 = M2-IPSDM
IPSDM_MAC_M1_gene_exp.diff contains differential expression result from IPSDM and M1-IPSDM. sample_1 = IPSDM, sample_2 = M1-IPSDM
IPSDM_MAC_M2_gene_exp.diff contains differential expression result from IPSDM and M2-IPSDM. sample_1 = IPSDM, sample_2 = M2-IPSDM
HMDM_IPSDM_gene_exp.diff contains differential expression result from HMDM and IPSDM. sample_1 = HMDM, sample_2 = IPSDM
iPS_IPSDM_gene_exp.diff contains differential expression result from iPSC and IPSDM. sample_1 = iPSC, sample_2 = IPSDM
HMDM_IPS_IPSDM.norm.expr contains normalized FPKM from all samples

source_name: Macrophage

growth_protocol: iPSC lines were maintained in hESC media consisting of Dulbecco modified Eagle medium/F12 (50:50; Life Technologies, Grand Island, NY) supplemented with 20% knockout serum replacement, 100 μM nonessential amino acids, 50 U/ml penicillin, 50 μg/ml streptomycin (Life Technologies), 10−4 M β-mercaptoethanol (Sigma-Aldrich, St. Louis, MO), and 10 ng/ml human basic fibroblast growth factor (bFGF) on irradiated mouse embryonic feeder cells (MEF, GlobalStem, Rockville, MD). PBMC were cultured in 20% FBS/RPMI with 100 ng/ml human M-CSF (Peprotech, Rocky Hill, NJ) for 7 days to induce differentiation to macrophages. iPSC were differentiated to macrophages according to established protocols and maintained in 20% FBS/RPMI with 100 ng/ml human M-CSF.

extract_protocol:
RNA samples were extracted using All Prep DNA/RNA/miRNA Universal Kit (Qiagen, Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA)
With a minimum of 300 ng input RNA, we generated first-strand cDNA using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis using RNase H and DNA polymerase, and ligation of sequencing adapters using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA). Fragments of ~350 bp were selected by gel electrophoresis. To minimize lane and batch effects in RNA-Seq experiments, barcoded libraries were mixed and pooled in equimolar (2 nmol/L) amounts and diluted to 4 pmol/L for cluster formation on a single flow cell lane, followed by 100 bp paired-end sequencing on Illumina’s HiSeq 2000.

value: M2-polarized IPSDM


title: IPSDM M2 rep5


title: CD13-/ROR2-

source_name: Day 3 CD13-/ROR2- cells

value: H3 hESC NKX2-7eGFP/alpha-MHC-mCherry

value: hESC derived endoderm progenitr

value: Day 3 of Cardiac Differentiation


title: IPSDM M1 rep6

description: processed data files: IPSDM_MAC_M1_gene_exp.diff, IPSDM_M1_M2_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

value: M1-polarized IPSDM


title: CD13+/ROR2+/NKX2.5+/aMHC+

source_name: Day 14 CD13+/ROR2+/NKX2-5+/a-MHC+ cells

value: H3 hESC NKX2-10eGFP/alpha-MHC-mCherry

value: hESC derived cardiomyocytes

value: Day 14 of Cardiac Differentiation


title: IPSDM M1 rep5


title: IPSDM MAC rep5

description: processed data files: IPSDM_MAC_M1_gene_exp.diff, IPSDM_MAC_M2_gene_exp.diff, HMDM_IPSDM_gene_exp.diff, iPS_IPSDM_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

value: iPSC derived macrophage (IPSDM)


title: HMDM M2 rep3

description: processed data files: HMDM_MAC_M2_gene_exp.diff, HMDM_M1_M2_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

value: M2-polarized HMDM


title: CD13+/ROR2+/NKX2.5+

source_name: Day 7 CD13+/ROR2+/NKX2-5+ cells

value: H3 hESC NKX2-8eGFP/alpha-MHC-mCherry

value: hESC derived cardiac progenitor


title: IPSDM MAC rep6


title: CD13+/ROR2+

source_name: Day 3 CD13+/ROR2+ cells

value: H3 hESC NKX2-6eGFP/alpha-MHC-mCherry

value: hESC derived mesoderm progenitor


title: iPS rep5

description: processed data files: iPS_IPSDM_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

source_name: Induced pluripotent stem cell

value: Induced pluripotent stem cell (iPSC)


title: iPS rep6


title: HMDM M1 rep3

description: processed data files: HMDM_MAC_M1_gene_exp.diff, HMDM_M1_M2_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

value: M1-polarized HMDM


title: KO1 Neuron

city: Bronx

first: Deyou

last: Zheng

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
RNA-seq reads were aligned to human genome (hg19) using Tophat (version 2.0.8). The number of RNA-seq fragments mapped to each gene was determined for genes in the GENCODE database (v18). Cufflink (version 2.2.1) was used to generate the gene expression value as FPKM.
Genome_build: hg19

source_name: Neuron

growth_protocol: iPSC reprogramming was carried out by nucleofection. One vial of cells was thawed out and placed in a T75 flask in DMEM/F12 supplemented with 10% FBS and fed every 2 days. Cells were grown to ~50% confluence (~4-5 days), after which they were trypsinized and subjected to nucleofection (~6 x105 cells). Reprogramming was carried out using an Amaxa 4D-Nucleofector (P2 Primary Cell Kit from Lonza cat# V4XP-2012, Program FF-135) with non-integrating plasmids containing OCT4, SOX2, KLF4, L-MYC, LIN28, and a p53 shRNA vector (Addgene Cat. # 27077, 27078, 27080), according to Okita et al., with some modifications. iPSCs were maintained on Matrigel plates in mTeSR1 medium (Stem Cell Technologies) with daily feeding in 37oC/5% CO2/85% humidity. iPSC reprogramming was carried out by nucleofection 1. One vial of cells was thawed out and placed in a T75 flask in DMEM/F12 supplemented with 10% FBS and fed every 2 days. Cells were grown to ~50% confluence (~4-5 days), after which they were trypsinized and subjected to nucleofection (~6 x105 cells). Reprogramming was carried out using an Amaxa 4D-Nucleofector (P2 Primary Cell Kit from Lonza cat# V4XP-2012, Program FF-135) with non-integrating plasmids containing OCT4, SOX2, KLF4, L-MYC, LIN28, and a p53 shRNA vector (Addgene Cat. # 27077, 27078, 27080), according to Okita et al., with some modifications 1-3. iPSCs were maintained on Matrigel plates in mTeSR1 medium (Stem Cell Technologies) with daily feeding in 37oC/5% CO2/85% humidity.

extract_protocol:
Briefly, tota cellularl RNA were extracted to produce cDNA using DT-T7 primers and the miRNeasy Kit (Qiagen) according to the manufacturer’s protoco RNA libraries were prepared for sequencing using standard Illumina protocols.
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 cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: iPSC-derived neurons


title: KO2 Neuron


title: HMDM MAC rep3

description: processed data files: HMDM_MAC_M1_gene_exp.diff, HMDM_MAC_M2_gene_exp.diff, HMDM_IPSDM_gene_exp.diff, HMDM_IPS_IPSDM.norm.expr

value: PBMC derived macrophage (HMDM)


title: control2 Neuron

value: wild-type


title: control1 Neuron


title: 231 SRA RNAi pool exp2

description: 231 SRA RNAi pool exp2

source_name: breast cancer MBD-MDA-231

tag: passages

value: passage number 21-31

tag: provider

value: ATCC, cat# HTB-26

tag: sirna treatment conditions

value: 2.5 x105 cells in 6-well plates r 100 nM RNAi for 72 h


title: KO1 NPC

source_name: Neural progenitor cells

value: iPSC-derived neural progenitor cells


title: Input, untreated, replicate 2

city: Chicago

first: Douglas

middle: David

last: Thomas

state: IL

address: 900 S Ashland Ave Room 3306

department: Medicinal Chemistry & Pharmacognosy

institute: University of Illinois at Chicago

description: Sample name: Input_C4

data_processing:
[raw data QC and genome alignment] All raw sequencing data was quality trimmed to a minimum phred score of 20 using trimmomatic 0.32. Alignment to reference genome hg19 was done with BWA 0.7.5. PCR duplicates were removed using Picard MarkDuplicates and alignments with an edit distance greater than 2 to the reference, or that were mapped multiple times to the reference, were removed.
[ChIP-seq peak calling (H3K9ac)] Peak calls for H3K9ac data were created with Macs2 against paired input samples at an FDR threshold of 0.5 to allow for sufficient false peaks for IDR analysis; high-confidence peaks from individual replicates were selected using an FDR threshold of 1e-5 from the called peaks. Highly reproducible peaks were identified using Irreproducible Discovery Rate (IDR) using the IDR R package.
[ChIP-seq peak calling (H3K9me2)] Peak calls for H3K9me2 data were created with SICER against paired input samples using redundancy threshold = 10, window size = 500, fragment size = 400, effective genome fraction = 0.8, gap size = 1500, and an FDR threshold of 1e-5
Genome_build: hg19
Supplementary_files_format_and_content: bed file fields are: chromosome, start, end, peak ID, -log10 p-value or IDR value
Supplementary_files_format_and_content: bigWig files for H3K9ac (from Macs2) are raw read counts, bigWig files for H3K9me2 are normalized by library depth and background-subtracted

growth_protocol: MDA-MB-231 human triple negative breast cancer cells were obtained from American Type Culture Collection (ATCC) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in a controlled environment (37°C and 5% CO2).

extract_protocol:
MDA-MB-231 cells in culture were crosslinked using 1% formaldehyde for 10 minutes at room temperature, following which excess reagent was quenched by the addition of 125 mM glycine for 5 minutes. Cells were washed with ice cold PBS and the pellet was resuspended in ChIP lysis buffer (1% SDS, 10 mM EDTA pH 8.0, 50 mM Tris-HCl pH 8.1, protease inhibitor cocktail and PMSF). DNA was sheared to 200-500bp using a Branson probe sonicator while keeping the sample on ice. A small aliquot of sheared chromatin was saved as “input”. Chromatin from 2 million cells was used for each ChIP reaction and diluted 10-fold using ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.1, 167 mM NaCl, protease inhibitor cocktail and PMSF). Immunoprecipitation was performed by incubating diluted chromatin with Dynabeads G (Invitrogen, pre-washed with BSA/PBS) and the following antibodies overnight at 4°C: H3K9me2 (Abcam, ab1220; 2 mg per ChIP) or H3K9ac (Millipore #07-352; 3.5 ml per ChIP). Beads were subsequently washed using the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), LiCl buffer (0.25M LiCl, 1% IGEPAL-CA630, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1) and twice with TE (1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Dissociation of chromatin-antibody complexes from the beads was facilitated by eluting twice using an appropriate buffer (1% SDS, 0.1M NaHCO3) for 15 minutes each at RT. Crosslinks in all ChIP and input samples were reversed by incubating with NaCl overnight at 65°C. Samples were treated with RNAse A for one hour at 37°C followed by addition of Proteinase K for one hour at 45°C for cleanup. In the final step, DNA was purified using the MinElute PCR Purification Kit (Qiagen).
Libraries were made using the Diagenode MicroPlex Library PreparationTM kit as per manufacturer's protocols.

treatment_protocol: For conducting experiments, cells were grown to 80% confluency and serum starved overnight prior to treatment with 500uM DETA/NO for 24 hours.

value: triple negative breast adenocarcinoma

value: none (input)


title: KO2 NPC


title: Input, treated, replicate 1

description: Sample name: Input_D1


title: hESCs

source_name: Day 0 hESCs

value: H3 hESC NKX2-5eGFP/alpha-MHC-mCherry

value: Human embryonic stem cells

value: Day 0 of Cardiac Differentiation


title: control1 NPC


title: Pol2ChIP_ICRF2_(20121019_6_12)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
Nuclei from S2 cells treated with ICRF-193 (Topo II inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted. Pol II antibody (8WG16) was used for ChIP. Replicate.
library_strategy: Modified library preparation as described in PMID 22025700

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release r5.30 (Jul 2010) of the D.melanogaster genomic sequence obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

source_name: Pol II ChIP

extract_protocol: As described in PMID 22085965

tag: treated with

value: topoisomerase inhibitor ICRF-193


title: H3K9me2, treated, replicate 2

description: Sample name: MD3


title: control2 NPC


title: H3K9me2, untreated, replicate 2

description: Sample name: MC4


title: Pol2ChIP_Camp2_(20121019_6_6)

description:
Nuclei from S2 cells treated with Camptothecin (Topo I inhibitor) were MNase-digested and the 80 mM salt soluble fraction was extracted. Pol II antibody (8WG16) was used for ChIP. Replicate.
library_strategy: Modified library preparation as described in PMID 22025700

value: topoisomerase inhibitor Camptothecin


title: Nuc_ICRF_(20121019_7_6)

description:
Nuclei from S2 cells treated with ICRF-193 (Topo II inhibitor) were MNase-digested and total DNA was extracted.
library_strategy: Modified library preparation as described in PMID 22025700

source_name: Nuc ICRF


title: WT_1

source_name: Fetal Liver

value: 12.5 days post coitum

tag: genotype/variation

value: wild type


title: Nuc_Camp_(20121019_7_5)

description:
Nuclei from S2 cells treated with Camptothecin (Topo I inhibitor) were MNase-digested and total DNA was extracted.
library_strategy: Modified library preparation as described in PMID 22025700

source_name: Nuc Camp


title: H3K9ac, treated, replicate 1

description: Sample name: AD1


title: CD13+/ROR2+/NKX2.5+/aMHC-

source_name: Day 14 CD13+/ROR2+/NKX2-5+/a-MHC- cells

value: H3 hESC NKX2-11eGFP/alpha-MHC-mCherry

value: Unknown

value: Day 14 of Cardiac Differentiation


title: H3K9ac, untreated, replicate 2

description: Sample name: AC4


title: H3K9ac, treated, replicate 2

description: Sample name: AD3


title: Input, treated, replicate 2

description: Sample name: Input_D3


title: Nuc_Ctl_(20121019_7_4)

description:
Nuclei from S2 cells were MNase-digested total DNA was extracted.
library_strategy: Modified library preparation as described in PMID 22025700

source_name: Nuc Control


title: IH03

status: Public on Nov 04 2015

city: Luebeck

first: Martin

last: Kircher

state: SH

address: Ratzeburger Allee 160

department: Humangenetics

institute: University of Luebeck

description: processed data file(s): CA01.bb, CH01.bb

data_processing:
All libraries were sequenced on HiSeq 2000 or NextSeq 500 instruments (Illumina). Barcoded paired end (PE) Illumina sequencing data was split allowing up to one substitution in the barcode sequence. Reads shorter or equal to read length were consensus called and adapter trimmed.
Remaining consensus single end reads (SR) and the individual PE reads were aligned to the human reference genome sequence (GRCh37, 1000 Genomes phase 2 technical reference downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/) using the ALN algorithm implemented in BWA v0.7.1041. PE reads were further processed with BWA SAMPE to resolve ambiguous placement of read pairs or to rescue missing alignments by a more sensitive alignment step around the location of one placed read end. Aligned SR and PE data was directly converted to sorted BAM format using the samtools API. BAM files of the sample were merged across lanes and sequencing runs.
PE provides information about the two physical ends of DNA molecules used in sequencing library preparation. We extract this information using the SAMtools application programming interface (API) from BAM files. As read starts, we use both outer alignment coordinates of PE data for which both reads aligned to the same chromosome and where reads have opposite orientations. In cases where PE data was converted to single read data by adapter trimming, we consider both end coordinates of the SR alignment as read starts. For coverage, we consider all positions between the two (inferred) molecule ends, including these end positions. We define window protection scores (WPS) of a window size k as the number of molecules spanning a window minus those starting at any bases encompassed by the window. We assign the determined WPS to the center of the window. For molecules in the 35-80 bp range (short fraction), we use a window size of 16 and, for molecules in the 120-180 bp (long fraction), we use a window size of 120.
Local maxima of nucleosome protection are called from the long fraction WPS, which we locally adjust to a running median of zero (1 kb window) and smooth using a Savitzky-Golay filter (window size 21, 2nd order polynomial). The WPS track is then segmented into above zero regions (allowing up to 5 consecutive positions below zero). If the resulting region is between 50-150 bp long, we identify the median value of that region and search for the maximum-sum contiguous window above the median. We report the start, end and center coordinates of this window. Peak-to-peak distances, etc., are calculated from the center coordinates. The score of the call is determined as the distance between maximum value in the window and the average of the two adjacent WPS minima neighboring the region. If the identified region is 150-450 bp long, we apply the same above median contiguous window approach, but only report those windows that are between 50-150bp in size. For score calculation of multiple windows derived from the 150-450bp regions, we assume the neighboring minima within the region to be zero. We discard regions shorter than 50 bp and longer than 450 bp.
Genome_build: GRCh37, 1000 Genomes phase 2 technical reference downloaded from ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/
Supplementary_files_format_and_content: Local maxima of nucleosome protection in bigBED (UCSC http://genome.ucsc.edu/FAQ/FAQformat.html#format1.5)

source_name: cell-free DNA

extract_protocol:
Bulk human peripheral blood plasma, containing contributions from an unknown number of healthy individuals, was obtained from STEMCELL Technologies (Vancouver, British Columbia, Canada) and stored in 2 ml aliquots at -80ºC until use. Individual human peripheral blood plasma from anonymous, healthy donors was obtained from Conversant Bio (Huntsville, Alabama, USA) and stored in 0.5 ml aliquots at -80ºC until use. Human peripheral blood plasma for 52 individuals with clinical diagnosis of Stage IV cancer was obtained from Conversant Bio or PlasmaLab International (Everett, Washington, USA) and stored in 0.5 ml or 1 ml aliquots at -80ºC until use. Human peripheral blood plasma for four individuals with clinical diagnosis of systemic lupus erythematosus was obtained from Conversant Bio and stored in 0.5 ml aliquots at -80ºC until use.
Barcoded double-strand preparation sequencing libraries were constructed with the ThruPLEX-FD or ThruPLEX DNA-seq 48D kits (Rubicon Genomics), comprising a proprietary series of end-repair, ligation, and amplification reactions. Between 0.5 ng and 30.0 ng of cfDNA were used as input for all clinical sample libraries. Library amplification for all samples was monitored by real-time PCR to avoid over-amplification, and was typically terminated after 4-6 cycles. Single-strand ligation libraries were prepared from dephosphorylated cell-free DNA. For dephosphorylation, 2X CircLigase II buffer (Epicentre), 5 mM MnCl2, and 1U FastAP alkaline phosphatase (Thermo Fisher) and 0.5-10 ng fragments were incubated in a 20 ul reaction volume at 37ºC for 30 minutes. Fragments were then denatured by heating to 95ºC for 3 minutes, and were immediately transferred to an ice bath. The reaction was supplemented with the biotin-conjugated adapter oligo (5 pmol), 20% PEG-6000 (w/v), and 200U CircLigase II (Epicentre) for a total volume of 40 ul, and was incubated overnight with rotation at 60ºC, heated to 95ºC for 3 minutes, and placed in an ice bath. For each sample, 20 ul MyOne C1 beads (Life Technologies) were twice washed in bead binding buffer (BBB) (10 mM Tris-HCl [pH 8], 1M NaCl, 1 mM EDTA [pH 8], 0.05% Tween-20, and 0.5% SDS), and resuspended in 250 ul BBB. Adapter-ligated fragments were bound to the beads by rotating for 60 minutes at room temperature. Beads were collected on a magnetic rack and the supernatant was discarded. Beads were washed once with 500 ul wash buffer A (WBA) (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20, 100 mM NaCl, 0.5% SDS) and once with 500 ul wash buffer B (WBB) (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20, 100 mM NaCl). Beads were combined with 1X Isothermal Amplification Buffer (NEB), 2.5 uM oligo CL9, 250 uM (each) dNTPs, and 24U Bst 2.0 DNA Polymerase (NEB) in a reaction volume of 50 ul, incubated with gentle shaking by ramping temperature from 15ºC to 37ºC at 1ºC/minute, and held at 37ºC for 10 minutes. After collection on a magnetic rack, beads were washed once with 200 ul WBA, resuspended in 200 ul of stringency wash buffer (SWB) (0.1X SSC, 0.1% SDS), and incubated at 45ºC for 3 minutes. Beads were again collected and washed once with 200 ul WBB. Beads were then combined with 1X CutSmart Buffer (NEB), 0.025% Tween-20, 100 uM (each) dNTPs, and 5U T4 DNA Polymerase (NEB) and incubated with gentle shaking for 30 minutes at room temperature. Beads were washed once with each of WBA, SWB, and WBB as described above. Beads were then mixed with 1X CutSmart Buffer (NEB), 5% PEG-6000, 0.025% Tween-20, 2 uM double-stranded adapter 2, and 10U T4 DNA Ligase (NEB), and incubated with gentle shaking for 2 hours at room temperature. Beads were washed once with each of WBA, SWB, and WBB as described above, and resuspended in 25 ul TET buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA [pH 8], 0.05% Tween-20). Second strands were eluted from beads by heating to 95ºC, collecting beads on a magnetic rack, and transferring the supernatant to a new tube. Library amplification for all samples was monitored by real-time PCR to avoid over-amplification, and required an average of 4 to 6 cycles per library.

value: blood plasma

tag: disease

value: Healthy

tag: Sex

value: F


title: Diploid

description: Diploid chromosomes

data_processing:
Hi-C reads were aligned to genome dm3 using Bowtie 2.
Duplicate reads removed using picard.
deepTools v1.5.8.1 used to quantify the log2 ratio of the sequencing-depth normalized salivary gland read coverage to embryonic read coverage in 15 kb bins (same as the Hi-C bins) across the genome.
The coverage across the salivary gland X chromosome was corrected by a factor 3/2 to account for all of the larvae being male and the mixed male:female population in the 0-6 hour embryos.
Genome_build: dm3
Supplementary_files_format_and_content: Individual sample files are in a tab-delimited text format where the first column is the chromosome, second column is bin start, third column is bin end, fourth column is coverage in that bin.  bigWig file is the log2 ratio of the salivary gland to embryo coverage as processed as described above.

source_name: 0-6 hour embryos

extract_protocol:
Total genomic DNA was isolated from unfixed Drosophila third instar larvae manually dissected salivary glands or 0-6 hour embryos using standard procedures (phenol/chloroform extraction and ethanol precipitation).
DNA sheared to a mean size of approximately 200 bp and libraries prepared using a NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs).

tag: stock

value: yellow white

value: 0-6 hours after egg laying

tag: tisse

value: embryo


title: Polytene

description: Polytene chromosomes

source_name: Male salivary glands

value: Third instar larvae

value: Salivary gland


title: IH01

description: processed data file(s): CA01.bb, CH01.bb, IH01.bb

value: M


title: IH02

description: processed data file(s): CA01.bb, CH01.bb, IH02.bb