title: Brain (Sample 10)

city: Rotterdam

first: Tjakko

last: van Ham

address: Westzeedijk 353

department: Clinical Genetics

country: Netherlands

institute: Erasmus MC

description: Sample 10

data_processing:
Image analysis and base calling were done using the Illumina pipeline. Reads were aligned to the zebrafish genome (GRCz10 ) using TopHat (version 2.0.5) (Li et al. Bioinformatics, 2009). The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads.
The aligned and filtered data was quantified with the Bioconductor package Genomic Ranges (Lawrence  et al. Plos Computational Biology, 2013).
Differential gene expression analysis was performed with Bioconductor package EdgeR (Robinson, et al., 2010).
Genome_build: GRCz10
Supplementary_files_format_and_content: [.csv] semicolon-delimited files. CPM_Values.csv, Comparison_all_groups.csv

organism: Danio rerio

source_name: brain

extract_protocol:
Zebrafish were sacrificed with ice water after 24 or 48 hours of treatment with MTZ (activated microglia) or DMSO (control microglia). Then brains were taken out of the skull and trypsinized on ice for 2 hours. Percoll gradient centrifugation was used to enrich the cell population for microglia. FACS sorting based on GFP expressing was used to isolate microglia. To extract the other brain cells, the GFP-negative population was collected. Cells were spun down and pellet was flash frozen in liquid nitrogen. Total RNA extraction was performed using the Qiagen miRNeasy kit.
cDNA libraries were created using the SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Clontech). Illumina RNAseq libraries were prepared from cDNA using the Illumina TruSeq™ RNA Sample Prep Kit v2 according to the manufacturer’s instructions (Illumina Inc.). In all libraries 50 nucleotide single-end reads (SR50) were sequenced on an Illumina HiSeq2500 sequencer according to the manufacturer’s protocol, obtaining 10-20 million reads per sample library.

value: brain

tag: cell type

value: non-microglia brain cells

value: 3 months

tag: line

value: Neuro:NTR-mCherry x mpeg1:GFP


title: UHR84

status: Public on Oct 20 2016

type: SRA

city: Rochester

first: Numrah

middle: Mohammadali

last: Fadra

state: Minnesota

address: 200 2nd Street SW

department: Health Sciences Research

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Base calling was performed by the instrument computer using Illumina Real Time Analysis (RTA) software that is integrated with HiSeq Control Software (HCS) and provides a summary of quality statistics as per Illumina's acceptance criteria for sequencing. CASAVA 1.8.2 was used for de-multiplexing and conversion of base calls to paired-end FASTQ files
RNA-Seq data was analyzed using the MAP-RSeq(http://www.ncbi.nlm.nih.gov/pubmed/24972667) pipeline v 1.2 which uses TopHat 2.0.6 to align reads to the human reference GRCh37  without alternative haplotypes. During alignment,TopHat was supplied transcript models from UCSC (March 2012 version) available from Illumina’s iGenomes Project. For the degraded KU812 samples we obtained > 13 million reads per sample and for the degraded UHR and clinical samples we obtained > 80 million reads per sample. Fusion calling was performed using TopHat-Fusion (http://www.ncbi.nlm.nih.gov/pubmed/21835007) with a minimum of 5 fusion supporting reads required
For the UHR samples read coverage was normalized to 50 million reads per sample. The utility DepthOfCoverage from the Genome Analysis Toolkit (GATK) v.1.6.7 was used to query the alignment files to obtain read depth coverage information. Read coverage as a function of the distance to the 3’ end was calculated for genes with expression > 10x at a position 300 bases from the 3’ end.  Linear models and plots were created in R (version 3.1) using ggplot2 v 2.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include fusions found in each sample with annotations on the 5' and 3' gene partners, exons, syupporting read information and genomic breakpoints for each fusion

molecule: total RNA

organism: Homo sapiens

source_name: cell line

extract_protocol:
RNA quality [RNA Integrity Number (RIN)] was assessed on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit and quantified with a Qubit® 2.0 fluorometer with the Qubit® RNA BR Assay Kit. The TruSeq® RNA Sample Preparation v2 Kit (Illumina, San Diego, CA) was used for isolation of polyadenylated mRNA with oligo-dT beads, second strand cDNA synthesis and NGS library preparation
Paired-end, 101 bp sequencing was performed on a HiSeq 2500 (Illumina) instrument in Rapid Run mode.

tag: sample type

tag: histology

value: UHR tumor*

tag: rin score


title: Microglia control (Sample 9)

description: Sample 9

source_name: microglia

tag: tissue

value: microglia

tag: treatment

value: DMSO

tag: age


title: Med8YPD_0s_(20150513_GZ_Sc_Med8_0s)

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: Med8 ChEC-seq in YPD medium, no calcium

library_source: genomic

data_processing: 1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options -a -r Random to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. 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 fragment ends mapped, and then multiplying by the total number of mapped base pairs (Supplementary file .wig).  Generation and normalization of tracks was performed with https://github.com/zentnerlab/chec-seq/blob/master/pairs_single_end_sizes.pl.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Med8 ChEC-seq

extract_protocol: See Series supplementary file Zenter_protocol.rtf

tag: strain

tag: genotype

tag: growth medium

value: YPD


title: saline control 2 [mouse]

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description:
A2
mature_counts_mm10.csv

data_processing:
Sequencing reads from small RNA-seq libraries were first trimmed adapters using cutadapt
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the mm9 or hg19 genome (UCSC assembly) using bowtie version 1.1.1 with parameters -p 8 -k 1 -m 10 -l 25 --best --chunkmbs 128
counts of reads for each gene annotated in gencode vM3 were calculated from featureCounts for mouse and v19 for human
Genome_build: mm10/hg19 for mouse and human, respectively
Supplementary_files_format_and_content: count file, csv

organism: Mus musculus

source_name: spinal cord

growth_protocol: eight-week old female C57Bl/6j mice were grown under normal coniditons

extract_protocol:
RNA was extracted by standard Trizol extraction.
TruSeq small-RNA Sample Preparation Kit

treatment_protocol: Sterotactic injections of ASO complementary to Hnrnpa2b1 were performed in eight-week old female C57Bl/b mice to deplete hnRNP A2/B1. ASOs were delivered specifically to the lateral ventricle (12.5 mg)  injection (300 mg). Mice were regularly monitored for 28 days until sacrificed.

tag: tissue type

value: spinal cord

value: saline


title: UHR59


title: Activated microglia 48h (Sample 8)

description: Sample 8

value: MTZ

tag: time


title: Med17dmed15GCSM_10m_(20160115_SG_Sc_56_pSM_4)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 10 minutes after calcium addtion

source_name: Med17 ChEC-seq

value: GC-ile-val + 0.5 _g/mL SM


title: Activated microglia 24h (Sample 7)

description: Sample 7


title: Med17dmed15GCSM_5m_(20160115_SG_Sc_56_pSM_3)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 5 minutes after calcium addtion


title: Brain (Sample 6)

description: Sample 6


title: UHR39


title: UHR49


title: GroupB_Disease D8

city: Lahore

first: Azeem

middle: Mehmood

last: Butt

address: 87-West Canal Bank Road, Thokar Niaz Baig

department: Centre of Excellence in Molecular Biology (CEMB)

country: Pakistan

institute: University of the Punjab

data_processing:
First, sequencing data were converted using the Illumina CASAVA v1.8.2 pipeline to generate FASTQ formatted text files.
The initial quality assessment of sequencing data was performed using the FastQC v0.11.2 tool
All of the samples passed the quality control analyses and were then analyzed using FASTX-Toolkit v0.0.14 for the prealignment processing of raw reads. This consisted of (i) the removal of low-quality reads based on a cut-off of Phred score (Q) > 33, (ii) the removal of adapter null and insert null reads, (iii) the removal of the adapter sequence from the 3′ end, and (iv) the removal of reads shorter than 17 nt. These steps were performed using fastx_clipper with the following parameters: fastx_clipper -Q 33 -v -l 17 -a TCGTATGCCGTCTTCTGCTTG -i <input file>-o <outputfile>,
The clean reads were mapped to the reference human genome (UCSC hg19) using the mapper.pl module from the miRDeep v2.0.0.5 package, which uses the Bowtie aligner for the mapping step. Bowtie v0.12.9 was used in the present study and mapper.pl was executed with the following parameters: mapper.pl samplereads_collapsed.fa -c -p hg19 -t reads_collapsed_vs_genome.arf
The identification and quantification of known human miRNAs expressed in CHC-infected and control liver tissues were performed using quantifier.pl and miRDeep2.pl modules from the miRDeep2 package with the default parameters. A cut-off of absolute read counts ≥ 5 in any three out of ten libraries was used for a read to be considered as a detectable mature miRNA.
The differentially expressed (DE)-miRNAs inchronic hepatitis C-infected and control liver tissues were identified using DESeq2 v1.10.0.The thresholds of a P value < 0.05 and −0.6 ≤ |log2fold change (FC)| ≥ 0.6 were considered for the selection of DE-miRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited matrix table that include raw reads counts of expressed miRNAs. Each sample column refers to single sample and each row refers to identified miRNA.

extract_protocol:
Liver tissues were taken using ultrasound guided automatic biopsy needles. Tissues were collected in RNAlater and stored at -80C until processed. Total RNA was extracted using QIAGEN miRNeasy mini kit.
The miRNA-seq libraries were prepared using the Truseq Small RNA Library Preparation Kit (Illumina, San Diego, CA, USA) from 1 µg of total RNA per sample, following the manufacturer’s instructions.

tag: subject status

value: Chronic hepatitis C positive

value: Liver

value: Treatment naive


title: GroupB_Disease D7


title: Microglia control (Sample 5)

description: Sample 5


title: KU812RIN5

source_name: Cell line (KU812)

value: Chronic Myelogenous Leukemia


title: Med17dmed15GCSM_1m_(20160115_SG_Sc_56_pSM_2)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 1 minute after calcium addition


title: KU812RIN7


title: Med17dmed15GCSM_30s_(20160115_SG_Sc_56_pSM_1)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 30 seconds after calcium addition


title: Med8YPD_30s_(20150513_GZ_Sc_Med8_30s)

description: Med8 ChEC-seq in YPD medium, 30 seconds after calcium addition


title: GroupB_Disease D6


title: KU812RIN3


title: 59711sacCer3XO_BY4741-Sua7-TAP_i5006_Sua7-TAP_rep2

city: University Park

first: Alain

middle: Roger

last: Bataille

state: PA

address: 453 North Frear

department: BMB

institute: Penn State University

description:
Biological replicate 2 of 2, IP with rabbit IgG (sigma i5006)in strain Sua7-TAP
protocol: ChIP-exo
Processed data file: 59710-11sacCer3XO_BY4741-Sua7-TAP_i5006_Sua7-TAP_shift6_1.0_normMean20_Roman.bedgraph for this sample is available on sample record GSM2249647.

data_processing:
Basecalls performed using bcl2fastq ver 2.16 for NextSeq paired reads
ChIP-exo reads were aligned to sacCer3 genome assembly using bwa mem version 0.7.9a for paired reads. Read1 tags were shift 6 bp in the 3' direction (to better reflect the crosslinking coordinates). After total tag normalization of the datasets each experiment and its control were smoothed using an average sliding window of 50 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.
Genome_build: sacCer3/R64
Supplementary_files_format_and_content: Bedgraph format. Tags (Read1 only) were shift 6 bp in the 3' direction and files were normalize by total tag number before generating bedgraph (Med subunits datasets and TFIIB datasets were normalized independantly). For combined file, after total tag normalization of the datasets (combine experiment with combined controls) each experiment and its control were smoothed using an average sliding window of 20 bp and the value in the no-tag strain subtracted to the value in the tag strain for each window.

growth_protocol: All yeast cells were grown to an OD600 of 0.6-0.8 in YPD following standard procedures and crosslinked at 1% formaldehyde.

extract_protocol:
ChIP-exo experiments were carried out essentially as described (Rhee and Pugh, 2012). Briefly, crosslinked cells were lysed, and chromatin pellets were isolated and then fragmented by sonication. Chromatin was then immunoprecipitated using Dyna PanMouse (samples 1-6) antibody-conjugated magnetic beads or Dyna conjugated with rabbit IgG (samples 7-12), followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and on beads digestion by lambda and recJ exonuclease. After elution of the single-stranded DNA, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. A second Illumina sequencing adaptor was ligated to exonuclease treated ends, and the products PCR-amplified and gel-purified.
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: kin28as strains and their controls were treated with 6μM of 1-Naphthyl PP1 (NAPP1; Tocris Bioscience) for 15 min prior to crosslinking.

tag: antibody

value: IgG from rabbit serum

tag: antibody catalogue number

value: Sigma i5006

tag: antibody lot number

value: MAT_alpha SUA7-TAP his3_delta_1 leu2_delta_0 ura3_delta_0 met15_delta_0

tag: protein tag

value: TAP


title: GroupB_Disease D5


title: Activated microglia 48h (Sample 4)

description: Sample 4

value: brain

tag: cell type

value: 3 months

tag: line

value: Neuro:NTR-mCherry x mpeg1:GFP


title: Med17dmed15GCSM_0s_(20160115_SG_Sc_56_pSM_0)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), no calcium


title: Activated microglia 24h (Sample 3)

description: Sample 3

value: microglia


title: Med17dmed15GCSM_20m_(20160115_SG_Sc_56_pSM_5)

description: Med17 ChEC-seq in med15 deletion strain in GC medium with sulfometuron methyl (SM), 20 minutes after calcium addtion


title: V3-63

source_name: Lung

tag: sample type

value: Accuracy sample

tag: histology

value: Invasive grade 3 adenocarcinoma


title: GroupB_Disease D3

tag: tissue


title: Med17dmed15GCnoSM_20m_(20160115_SG_Sc_56_mSM_5)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), 20 minutes after calcium addtion

value: GC-ile-val


title: saline control 1 [mouse]

description:
A1
mature_counts_mm10.csv

value: spinal cord

tag: treatment

value: saline


title: Brain (Sample 2)

description: Sample 2

value: non-microglia brain cells

tag: age


title: GroupB_Disease D2

value: Chronic hepatitis C positive

value: Liver


title: Med17dmed15GCnoSM_10m_(20160115_SG_Sc_56_mSM_4)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), 10 minutes after calcium addtion

tag: strain


title: Microglia control (Sample 1)

description: Sample 1

value: DMSO


title: Med17dmed15GCnoSM_5m_(20160115_SG_Sc_56_mSM_3)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), 5 minutes after calcium addtion

tag: genotype


title: GroupB_Disease D1

value: Treatment naive


title: V3-61

source_name: Liver

value: Normal tissue

tag: rin score


title: GroupA_Control C2

value: Uninfected healthy control

value: Not Applicable


title: Med17dmed15GCnoSM_1m_(20160115_SG_Sc_56_mSM_2)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), 1 minute after calcium addition

tag: growth medium


title: V3-60

source_name: Kidney


title: V3-59

source_name: Colon


title: Med17dmed15GCnoSM_30s_(20160115_SG_Sc_56_mSM_1)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), 30 seconds after calcium addition


title: GroupB_Disease D4


title: V3-45

source_name: Uterus


title: Med17dmed15GCnoSM_0s_(20160115_SG_Sc_56_mSM_0)

description: Med17 ChEC-seq in med15 deletion strain in GC medium without sulfometuron methyl (SM), no calcium


title: V3-44

source_name: Lymph node


title: Med17YPD_20m_(20150513_GZ_Sc_Med17_20m)

description: Med17 ChEC-seq in YPD medium, 20 minutes after calcium addtion

value: YPD


title: Med17YPD_10m_(20150513_GZ_Sc_Med17_10m)

description: Med17 ChEC-seq in YPD medium, 10 minutes after calcium addtion


title: V3-62

value: Adenocarcinoma


title: V1-35

value: Metastatic adenocarcinoma consistent with cholangiocarcinoma


title: RRBseq_Zeb2_Ctrl_d6_2

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Illumina Casava Pipeline 1.8.2 was used for BaseCalling
We cleaned sequencing reads with Trim Galore v0.3.7 using the parameters --phred64 --fastqc --stringency 2 --rrbs --paired
We aligned to the mouse mm10 genome with bismark v0.14.1 using the parameters --bowtie2 --phred64-quals -X 1000
We extracted methylation information from the aligned reads with bismark command bismark_methylation_extractor using parameters --paired_end --no_overlap --comprehensive
bedGraph files were created with bismark command bismark2bedgraph using paramters --remove_spaces
Further processing and analysis of the data was performed in R v3.1.3 using the methylKit v0.9.4 package and in-house custom scripts
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph file containing methylation percentage scores for all CpGs with at least 5x coverage in all samples.
Supplementary_files_format_and_content: Excel files contain the top contributing genes for the Principal Components 1 and 2 of the pairwise (VI) and temporal (VII) comparisons.

growth_protocol: ESCs were maintained feeder-cell free in 2i+LIF. N2B27 was prepared as described (Ivanova et al., 2009). For 2i+LIF medium, 0.4 μM PD0325901 and 1 μM CHIR99021 were added (Ying et al., 2008). LIF (Millipore, ESG1107) was added to a final concentration of 1,000 U/ml. On d0, 3x106 ESCs were plated in a 10-cm bacterial petri dish in EB medium [KO DMEM (Invitrogen, 10829018), 15% FBS (Life Technologies, 10270106), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 0.1mM 2-mercaptoethanol, 50 U/ml of penicilline/streptomycine]. On d2 the EB medium was refreshed. On d4 the medium was changed to N2B27 medium and retinoic acid (Sigma, R2625) was added to 500 nM. On d6 the medium was refreshed. Between d8 and d15 the EBs were cultured in N2B27, and this medium was refreshed every other day.

extract_protocol:
Total genomic DNA was isolated by proteinase K digestion and precipitation with isopropanol
RRBS was preformed by NXT-Dx (http://www.nxt-dx.com/) using the premium RRBS kit (Diagenode) according to the manufacturer’s instructions

value: Zeb2 fl/fl

tag: culture conditions

value: d6 embryoid body differentiation


title: Med17YPD_30s_(20150513_GZ_Sc_Med17_30s)

description: Med17 ChEC-seq in YPD medium, 30 seconds after calcium addition


title: V1-36

value: Accuracy sample


title: Med17YPD_1m_(20150513_GZ_Sc_Med17_1m)

description: Med17 ChEC-seq in YPD medium, 1 minute after calcium addition


title: V1-34

source_name: Cell culture

value: extraskeletal myxoid chondrosarcoma


title: Med17YPD_0s_(20150513_GZ_Sc_Med17_0s)

description: Med17 ChEC-seq in YPD medium, no calcium


title: V1-33

value: enchondroma v. fibromyxoid sarcoma


title: V3-41


title: V1-31

value: Synovial sarcoma


title: RRBseq_Zeb2_KO_d6_2


title: V1-30


title: RRBseq_Zeb2_KO_d6_1


title: FreeMNaseYPD_5m_(20150914_GZ_Sc_ChEC_ctrl_5m)

description: Free MNase ChEC-seq in YPD medium, 5 minutes after calcium addtion

source_name: Free MNase ChEC-seq


title: GroupA_Control C1

tag: subject status


title: V1-25

value: Histiocytic lymphoma


title: Med17YPD_5m_(20150513_GZ_Sc_Med17_5m)

description: Med17 ChEC-seq in YPD medium, 5 minutes after calcium addtion


title: RRBseq_Zeb2_Ctrl_d4_2

value: d4 embryoid body differentiation


title: RRBseq_Zeb2_Ctrl_d4_1


title: V1-24

value: Liposarcoma


title: V3-43


title: FreeMNaseYPD_30s_(20150914_GZ_Sc_ChEC_ctrl_30s)

description: Free MNase ChEC-seq in YPD medium, 30 seconds after calcium addition


title: V1-12

value: Ewings sarcoma


title: FreeMNaseYPD_1m_(20150914_GZ_Sc_ChEC_ctrl_1m)

description: Free MNase ChEC-seq in YPD medium, 1 minute after calcium addition


title: RRBseq_Zeb2_KO_d4_2


title: RRBseq_Zeb2_KO_d4_1


title: FreeMNaseYPD_0s_(20150914_GZ_Sc_ChEC_ctrl_0s)

description: Free MNase ChEC-seq in YPD medium, no calcium


title: ChIP_IgG Chip-seq

city: Beijing

first: xiong

last: wei

address: 5 Yiheyuan Rd, Haidian, Beijing, China

country: China

institute: peking university

description: using standard  protocol as cited in the paper (Cell. 2013 May 9;153(4):855-68)

data_processing:
FASTX-Toolkit  for assessing sequencing quality
Alignment: Bowtie 2 version 2.2.1 for chip-seq  and TopHat v2.0.11 for RNA-seq
cufflinks v2.2.0 for RNA-seq assembling and differential analysis
peaks were called using MACS1.4
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: bigwig files for RNA-seq and chip-seq

source_name: U2OS cells

growth_protocol: DMEM plus 10% for both MEF and U2OS cells

extract_protocol:
total RNA was extracted using a RNeasy MinElute Cleanup Kit
NEBNext DNA Library Prep Master Mix Set for Illumina for RNA-seq and NEXTflex ChIP-seq Kit, Bioo Scientific for chip-seq
RNA-seq: total RNA was extracted using a RNeasy MinElute Cleanup Kit (QIAGEN, Catalog no. 74204). Double-stranded cDNA was synthesized according to the mRNA Sequencing Sample Preparation Guide (part#1004898 Rev.D, Illumina, San Diego, CA) and single-end libraries were prepared using the NEBNext DNA Library Prep Master Mix Set for Illumina (New England BioLabs, Catalog no.74204 E6040L).   For RNA-seq of RNaseH treated MEF cells, the protocols were mainly adopted as previously described (Nat Methods 10: 623-629).  For qRNA-seq of MEF cells, the GeneRead rRNA Depletion Kit (Qiagen) was used to remove ribosome RNA.  Nascent RNA-seq of U2OS cells was performed as previously described (Science 322: 1845-1848), with the exception of not applying a strand specific method.
ChIP-seq procedure as previously described (Cell. 2013 May 9;153(4):855-68). For the Bmal1 and IgG ChIP-seq, the RIPA buffer was diluted 1 to 10. For HIF1A CHIP-seq, protocols are used as described (ChIP-IT high sensitive kit (Cat# 53040, Active Motif)). The library was constructed using a commercially available kit (NEXTflex ChIP-seq Kit, Bioo Scientific). Samples were indexed using NEXTflex™ DNA Barcodes (Bioo Scientific). The library was qualified using an Agilent 2100 Bioanalyzer (Agilent) and quantified using KAPA Library Quantification Kits (Kappa Biosystems). Finally, the indexed libraries were sequenced using a HiSeq 2500 (Illumina).

treatment_protocol: serum shock the MEF cell for 24h (circadian peak) and 36h (circadian trough)

value: ATCC HTB-96

value: bone

value: osteosacoma

tag: chip antibody

value: IgG santa cruz sc-2027 X


title: V1-4

source_name: Peripheral Blood

value: Acute Promyelocytic Leukemia


title: RRBseq_Zeb2_Ctrl_d0_2

value: 2i + LIF


title: FreeMNaseYPD_20m_(20150914_GZ_Sc_ChEC_ctrl_20m)

description: Free MNase ChEC-seq in YPD medium, 20 minutes after calcium addtion

value: YPD


title: V1-6

value: Endometrial Stromal Nodule


title: RRBseq_Zeb2_Ctrl_d6_1

value: Zeb2 fl/fl

value: d6 embryoid body differentiation


title: ChIP_hHIF1A Chip-seq

description: ChIP-IT high sensitive kit (Cat# 53040, Active Motif)

value: hHIF1A active motif (cat # 39665).


title: FreeMNaseYPD_10m_(20150914_GZ_Sc_ChEC_ctrl_10m)

description: Free MNase ChEC-seq in YPD medium, 10 minutes after calcium addtion


title: RRBseq_Zeb2_KO_d0_1


title: ChIP_hBMAL1 Chip-seq

value: hBMAL1 bethyl A302-616A


title: TEX+_E. coli O104:H4

status: Public on Oct 19 2016

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

description: TEX-treated sample

data_processing:
FastQ quality trimming using FastX (version 0.0.13)  and a cut-off value of 20
Fastq to fasta conversion using FastX  FastX (version 0.0.13)
5' linker and poly A-tail removal using READemption
mapping of reads to E. coli O104:H4 rRNAs and tRNAs using READemption 0.3.7 and segemehl 0.2.0
mapping of non-rRNA and tRNA reads to E. coli O104:H4 chromosome and plasmids using READemption 0.3.7 and segemehl 0.2.0
generation of coverage graphs representing the number of pAA plasmid-associated mapped reads per nucleotide using READemption 0.3.7
normalization of graphs to the total number of mapped reads per library using READemption 0.3.7
Genome_build: NC_018658.1, NC_018659.1, NC_018660.1, NC_018666.1
Supplementary_files_format_and_content: wig files representing the normalized number of pAA-associated mapped reads per nucleotide. Files contain wiggle-formatted files data for accessions  NC_018658.1, NC_018659.1, NC_018660.1, and NC_018666.1.

organism: Escherichia coli O104:H4

source_name: exponentially growing cells

growth_protocol: An overnight culture of E. coli O104:H4 strain LB226692 was diluted 1:10,000 in pre-warmed LB medium (10 g/L tryptone, 5 g/L yeast extract, 5 g/L NaCl) and cells were grown at 37oC, 180 rpm for 3.5 h to an OD600 of 0.52.

extract_protocol:
Total RNA was extracted using the Trizol reagent (Thermo Fisher Scientific) and the concentration and purity of the samples were determined using Nano Drop. RNA integrity was monitored using the R6K ScreenTape system on the Agilent 2200 TapeStation. gDNA was removed by Turbo DNase (Thermo Fisher Scientific) in the presence of 1U/L RiboLock RNase Inhibitor (Thermo Fisher Scientific) for 60 min at 37°C. Following organic extraction (1x 25:24:1 v/v phenol/chloroform/ isoamyalcohol, 1x chloroform), RNA was recovered by overnight precipitation with 3 volumes of 30:1 100 % ethanol/3 M sodium acetate (pH 5.2). Next, the sample (TEX+) was depleted of processed RNAs using 1U per 1μg of RNA Terminator 5´-Phosphate-Dependent Exonuclease (TEX, Epicentre) in the presence of 1U/μL RNase Inhibitor for 60 min at 30° C. A control reaction without TEX (TEX-) was run in parallel. Following organic extraction, RNA was recovered by overnight precipitation and resuspended in RNase-free water.
cDNA libraries for the Illumina sequencing platform were constructed by vertis Biotechnology AG, Germany, as described previously (Berezikov et al.,2006), without the RNA size-fractionation step prior to cDNA synthesis. Briefly, RNA samples were polyA-tailed using polyA polymerase. Then, the 5'-PPP termini were converted to 5'-P using tobacco acid pyrophosphatase (TAP) to allow for the ligation of the 5’ end RNA adapter. First-strand cDNA was synthesized by an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. In a PCR-based amplification step using a high fidelity DNA polymerase the cDNA concentration was increased to 20-30 ng/µl. A library-specific barcode for multiplex sequencing was part of a 3'-sequencing adapter.

treatment_protocol: 5 ml of cell suspension were added to 0.625 ml of pre-chilled stop solution (5 % phenol/95 % ethanol), vortexed and incubated for 5 min on ice. Cells were pelleted for 5 min at 5000 g, flash frozen in a dry ice-ethanol bath and stored at -80oC.

value: clinical isolate LB226692

tag: origin of isolation

value: patient with hemolytic uremic syndrome (HUS)

tag: outbreak

value: 2011 outbreak centered in Northern Germany


title: RelE_RNAseq1

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description:
media: LB
size selection: 40-60
nucleases in digestion step: none
molecule: mRNA
jh7

data_processing:
Library strategy: ribosome profiling
Reads with N bases or Phred < 10 were dropped. The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome version3 with bowtie allowing two mismatches.
Genome_build: NC_000913ver3
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli

source_name: cell cultures

growth_protocol: 400 mL cultures were grown to early log phase, filtered, and flash frozen in liquid nitrogen

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. Cell lysates were clarified, digested with nucleases, and monosomes were purified over a sucrose gradient.
Ribosome footprints and total RNA fragments were PAGE purified, ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

value: str. K-12 substr. MG1655

value: overexpressing Re1E


title: WT_RNAseq2

description:
media: MOPS
size selection: 10-40
nucleases in digestion step: none
molecule: mRNA
jh55

value: wild type


title: WT_RNAseq1

description:
media: LB
size selection: 40-60
nucleases in digestion step: none
molecule: mRNA
jh5


title: WT_RNAseq3

description:
media: MOPS
size selection: 10-40
nucleases in digestion step: none
molecule: mRNA
jh56


title: TEX-_E. coli O104:H4

description: TEX-untreated sample


title: WT_FP2

description:
media: MOPS
size selection: 10-40
nucleases in digestion step: MNase
molecule: mRNA: ribosome footprints
jh48


title: Fru_DHA_hypothalamus_rep2 [RRBS]

city: Los Angeles

first: Xia

last: Yang

address: 2000 Terasaki Life Sciences Bldg, 610 Charles E. Young Drive East

department: IBP

institute: UCLA

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to aligned to rat genome (UCSC assembly 5.0) using using the bisulfite aligner BS Seeker2, which utilizes the short read aligner Bowtie. As bisulfite treatment converted unmethylated cytosines (Cs) to thymines (Ts), we estimated the methylation level at each covered cytosine by methylation percentage which was calculated as NC/(NC + NT), where NC is the number of methylated reads and NT is the number of unmethylated reads
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files including the methylation level of cytosines in CpG, CHH and CHG context. The 8 fields in the files are (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T)., (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

organism: Rattus norvegicus

extract_protocol:
Geome DNA was extracted with Qiagen AllPrep DNA/RNA Mini Kit. Quantity and quality of DNA were checked using Nanodrop (Thermo Fisher Scientific, MA, USA), Qubit RNA assay (Life Technologies, NY, USA) and gel electrophoresis
Reduced representation bisulfite sequencing (RRBS) libraries were constructed as described previously with some modifications (Chen, P.Y. et al. Physiol Genomics 45, 565-576). Briefly, about 1,000 ng genomic DNA was digested with the MspI enzyme. Digested DNA was then purified, end-repaired, and adenylated, followed by ligation to Illumina TruSeq barcode adapters (Illumina Inc, CA, USA). Fragments of 150-300 bp in size were selected, bisulfite-treated, and sequenced using an Illumina Hiseq 2500 System (Illumina Inc, CA, USA).

treatment_protocol: Rats were fed with fructose and/or DHA for 6 weeks

value: Sprague Dawley

tag: gender

value: male

tag: fed with

value: fructose and DHA for 6 wks

value: hypothalamus


title: WT_FP1

description:
media: LB
size selection: 20-40
nucleases in digestion step: MNase
molecule: mRNA: ribosome footprints
jh1


title: Fru_DHA_hypothalamus_rep3 [RRBS]


title: Fru_DHA_hypothalamus_rep4 [RRBS]


title: Fru_DHA_hippocampus_rep3 [RRBS]

value: hippocampus


title: RRBseq_Zeb2_KO_d0_2

value: 2i + LIF


title: Fru_DHA_hippocampus_rep1 [RRBS]


title: Fru_DHA_hippocampus_rep2 [RRBS]


title: IgM Nurr77-GFP- LZ cells, 3rd biological replicate

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

description: IgM Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 3rd biological replicate

data_processing:
reads were aligned to Mouse Ensembl genes using the STAR version 2.3.0 software
Differential expression was determined by use of the Cufflinks software with default settings
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM

growth_protocol: Transgenic mice were bred to generate the combination of alleles: AID-cre/- IgH-96K/+ Nurr77-GFP; these mice were used to generate bone marrow chimeras that were then used for experiments

extract_protocol:
Antigen-specific LZ GC B cells that were Nurr77-GFP+ or Nurr77-GFP- of IgM or IgG1 isotypes were sorted by FACS directly into Trizol LS
SMARTer Ultra Low Input RNA for illumina sequencing kit (Clontech Laboratories)

treatment_protocol: Mice were immunized with R-phycoerythrin in complete's freund's adjuvant

tag: cell type

value: IgM LZ cells

tag: organ

value: spleen and lymph nodes


title: RRBseq_Zeb2_Ctrl_d0_1

value: Zeb2 fl/fl


title: IgG1 Nurr77-GFP- LZ cells, 3rd biological replicate

description: IgG1 Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 3rd biological replicate

value: IgG1 LZ cells


title: IgM Nurr77-GFP- LZ cells, 2nd biological replicate

description: IgM Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 2nd biological replicate


title: RelE_FP1

description:
media: LB
size selection: 20-40
nucleases in digestion step: MNase
molecule: mRNA: ribosome footprints
jh3


title: RelE_FP2

description:
media: MOPS
size selection: 10-40
nucleases in digestion step: MNase and RelE
molecule: mRNA: ribosome footprints
jh49


title: rat hypothalamus Fru_rep1

description: replicate 1

source_name: rat hypothalamus

value: fructose


title: rat hypothalamus Fru_rep3

description: replicate 3


title: rat hypothalamus Ctrl_rep4

description: replicate 4


title: rat hypothalamus Fru_rep4

description: replicate 4


title: rat hypothalamus Fru_rep2

description: replicate 2


title: rat hypothalamus Ctrl_rep3

description: replicate 3


title: IgM Nurr77-GFP+ LZ cells, 2nd biological replicate

description: IgM Nurr77-GFP+ LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 2nd biological replicate


title: rat hypothalamus Ctrl_rep2

description: replicate 2


title: rat hypothalamus Ctrl_rep1

description: replicate 1


title: WT_FP3

description:
media: MOPS
size selection: 10-40
nucleases in digestion step: MNase
molecule: mRNA: ribosome footprints
jh50


title: IgG1 Nurr77-GFP+ LZ cells, 2nd biological replicate

description: IgG1 Nurr77-GFP+ LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 2nd biological replicate


title: IgM Nurr77-GFP- LZ cells, 1st biological replicate

description: IgM Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 1st biological replicate


title: rat hippocampus Fru_rep3

description: replicate 3

source_name: rat hippocampus


title: Fru_DHA_hypothalamus_rep1 [RRBS]


title: rat hippocampus Fru_rep4

description: replicate 4


title: IgG1 Nurr77-GFP- LZ cells, 2nd biological replicate

description: IgG1 Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 2nd biological replicate


title: Fru_DHA_hippocampus_rep4 [RRBS]


title: rat hippocampus Fru_rep2

description: replicate 2


title: IgM Nurr77-GFP+ LZ cells, 1st biological replicate

description: IgM Nurr77-GFP+ LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 1st biological replicate


title: IgG1 Nurr77-GFP- LZ cells, 1st biological replicate

description: IgG1 Nurr77-GFP- LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 1st biological replicate


title: rat hippocampus Fru_rep1

description: replicate 1


title: rat hippocampus Ctrl_rep4

description: replicate 4

value: control


title: IgM DZ cells, 3rd biological replicate

description: IgM DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 3rd biological replicate

growth_protocol: Transgenic mice were bred to generate the combination of alleles: AID-cre/- IgH-96K/+ R26-LSL-YFP

extract_protocol:
Antigen-specific LZ or DZ GC B cells of IgM or IgG1 isotypes were sorted by FACS directly into Trizol LS
SMARTer Ultra Low Input RNA for illumina sequencing kit (Clontech Laboratories)

value: IgM DZ cells

value: AIDcre/- IgH-96K/+ R26-LSL-YFP


title: rat hippocampus Ctrl_rep3

description: replicate 3


title: rat hippocampus Ctrl_rep2

description: replicate 2


title: IgM LZ cells, 3rd biological replicate

description: IgM LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 3rd biological replicate


title: IgG1 LZ cells, 3rd biological replicate

description: IgG1 LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 3rd biological replicate


title: IgG1 DZ cells, 3rd biological replicate

description: IgG1 DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 3rd biological replicate

value: IgG1 DZ cells


title: IgM LZ cells, 2nd biological replicate

description: IgM LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 2nd biological replicate


title: IgM LZ cells, 1st biological replicate

description: IgM LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 1st biological replicate


title: IgG1 LZ cells, 2nd biological replicate

description: IgG1 LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 2nd biological replicate


title: IgM DZ cells, 2nd biological replicate

description: IgM DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 2nd biological replicate


title: IgM DZ cells, 1st biological replicate

description: IgM DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 1st biological replicate


title: IgG1 DZ cells, 1st biological replicate

description: IgG1 DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 1st biological replicate


title: IgG1 DZ cells, 2nd biological replicate

description: IgG1 DZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 2nd biological replicate


title: input DNA wild type

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

department: Genome Center

institute: UC Davis

data_processing:
Demultiplexing, adaptor and quality trimming of the raw reads was performed using the Allprep script (https://github.com/Comai-Lab/allprep).
Paired reads were merged using SeqPrep (https://github.com/jstjohn/SeqPrep) with parameters –q 30 (quality) and –L 35 (minimum merged pair length). Read pairs that did not merge were discarded.
Merged paired-end reads were mapped to the TAIR10 reference using the aln and samse algorithms of BWA and upto 10 alignments per read were saved.
Peak calling was done using MACS2 with the additional parameters ‘--nomodel --extsize 165 --keep-dup all -B’ and with the appropriate CENH3 ChIP negative control as input.
Ran MACS2 bdgcmp to generate fold-enrichment bedGraph files
Genome_build: TAIR 10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig; Scores represent fold enrichment of CENH3 ChIP over antibody specificity control IP

organism: Arabidopsis thaliana

source_name: Wild-type A. thaliana Col seedlings

growth_protocol: Seedlings were grown in liquid MS media in a baffled flask for 7-10 days with constant shaking.

extract_protocol:
Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the KAPA Hyper prep kit for Illumina (Part# KK8504). Briefly, end-repaired and adaptor ligated DNA was amplified for 5 cycles. The resulting library was size-selected using BluePippin for 200-400 bp, quantified by qPCR to determine minimum number of additinoal amplification cycles needed.

tag: ecotype

value: Columbia


title: AtCENH3_rep1

value: wild type

value: AtCENH3 (Steve Henikoff lab)


title: AtCENH3_control

source_name: A. thaliana cenh3-1/cenh3-1LoCENH3 seedlings

value: cenh3-1/cenh3-1, L. oleraceum CENH3


title: shCNKSR2_2_2

first: Andrew

last: Lane

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

data_processing:
Reads aligned using STAR (v25.1b)
FPKM expression values calculated usingn cufflinks (v2.2.1)
FPKM >1 used for expression analysis
Genome_build: mm9

source_name: 3T3 cells

growth_protocol: 3T3 cells grown in monolayer cultures on plastic

extract_protocol:
Qiagen miRNeasy
Illumina TruSeq Stranded mRNA sample preparation kit

tag: cell line


title: PolII ChIP-exo

first: Bongsoo

last: Park

address: 453 North Frear Building

data_processing:
Basecalls performed using CASAVA version 1.7 for Illumina single reads, bcl2fastq ver 2.16 for NextSeq paired reads
PIP-seq and ChIP-exo reads were aligned to theCRch37(hg19) genome assembly using bwa version 0.6.2 for single reads, and bwa mem version 0.7.9a for paired reads
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: BED format, TFIIB PIP-seq peaks are called using Genetrack and requiring simultaneous enrichment of TFIIB ChIP-exo and GRO-cap
Supplementary_files_format_and_content: BED graph format, PolII PIP-seq ('T' filtered), Input PIP-seq and ChIP-exo samples are converted into Genetrack scidx (Strand coordinated index) format, and Bedgraph files have been generated accordingly.

growth_protocol: Cells were grown in DMEM under standard conditions

extract_protocol:
For ChIP-exo, lysates were clarified from sonicated nuclei and Protein(TFIIB, PolII)-DNA complexes were isolated with IgG antibody.
PIP-Seq libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pubmed/23746353
ChIP-exo libraries were prepared for sequencing using standard Illumina protocols; Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol:
For PIP-seq, cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine
For ChIP-exo, cells were crosslinked with 1% formaldehyde for 15 min and quenched with 2.5M glycine

tag: tissue

value: Haematopoietic and lymphoid

tag: histology

value: Haematopoietic neoplasm

tag: protein-dna complex

value: PolII

tag: protocol

value: ChIP-exo


title: shCNKSR2_2_3


title: shCNKSR2_2_1


title: Input PIP-seq

value: Input

value: PIP-seq


title: IgG1 Nurr77-GFP+ LZ cells, 1st biological replicate

description: IgG1 Nurr77-GFP+ LZ cells were purified from AID-cre/-IgH-96K/+ Nurr77-GFP mice, 1st biological replicate

tag: strain

value: spleen and lymph nodes

tag: genotype


title: TFIIB ChIP-exo

value: TFIIB


title: AtCENH3_rep2


title: shCNKSR2_1_1


title: shControl_3


title: shControl_1


title: shControl_2


title: shCNKSR2_1_2


title: PolII PIP-seq Rep2


title: rat hippocampus Ctrl_rep1

description: replicate 1

value: Sprague Dawley

value: hippocampus

tag: treatment


title: PolII PIP-seq Rep1


title: IgG1 LZ cells, 1st biological replicate

description: IgG1 LZ cells were purified from AID-cre/-IgH-96K/+ R26-LSL-YFP mice, 1st biological replicate

value: IgG1 LZ cells


title: TFIIB PIP-seq Rep3

description:
PSU39743
TFIIB_PIP-seq_peaks.bed


title: TFIIB PIP-seq Rep1

description:
PSU39735
TFIIB_PIP-seq_peaks.bed


title: TFIIB PIP-seq Rep2

description:
PSU39740
TFIIB_PIP-seq_peaks.bed


title: 5LFF

city: Novosibirsk

first: Daniil

last: Maksimov

address: Lavrentjeva ave., 8/2

country: Russia

institute: MCB NSC RAS

description: The 5th generation larvae whose grandparents were born during the flight of the Foton-M4 satellite and whose parents were sent to International Space Station

data_processing:
The data obtained after sequencing were analysed using Galaxy (www.usegalaxy.org).
The intersection analisys and the comparison of direct and reverse reads, as well as the alignment relative to the reference genome were performed using the tophat2 application.
The identification of transcripts was performed using Cufflinks. The FPKM was used to determine the mRNA content of each gene
The absolute log2ratio ≥1 was used as the limit to assess the differential gene expression in different comparison groups
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: Microsoft Excel table summarising FPKM values for each gene in all samples.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: whole larva

growth_protocol: The research objects were placed in the Foton-M4 satellite in 50-ml plastic Falcon-type tubes in three BB-2 blocks of the BB-1F scientific equipment and exposed to passive oxygenation using the air medium of the satellite. Thirty tubes with air-permeable stoppers were placed into each BB-2 block. The tubes contained the firm standard (for breeding Drosophila) nutrient medium with the following composition: water – 1,000 ml, agar-agar – 7 g, sugar – 40 g, semolina – 40 g, baker’s yeast – 25 g, and propionic acid – 10 ml.

extract_protocol:
Each group contained 20 larvae. The total RNA was isolated from the larvae of all study groups using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
Equal amounts of RNA from each sample were selected and the cDNA libraries were prepared using Illumina TruSeq RNA Library Preparation Kit v2 (Illumina, USA), according to the manufacturer’s instructions.

value: Canton S

tag: developmental stage

value: 3rd stage larva


title: w-hs24-rep2

city: Moscow

first: Sergei

last: Ryazansky

address: Kurchatov sq., 2

department: Department of Molecular Genetics of Cell

institute: Institute of Molecular Genetics

data_processing:
After adapter (5'-TGGAATTCTCGGGTGCCAAGG) trimming and quality filtering, small RNA-seq reads were mapped to dm3 genome assembly with Bowtie 1.0.0 as bowtie -v 0 --all —al.
After mapping reads were annoted with BedTools (2.22.0) and using miRBase (v.19) annotaion.
Genome_build: dm3

source_name: whole organism

growth_protocol: Standard yeast medium, 25C.

extract_protocol:
Total RNA was extracted from 3-5 day old females after 1h, 6h and 24h of recovery at 25C after heat shock treatment
Total RNA was isolated using Tri-reagent (Sigma-Aldrich, USA). A total of 25µg of total RNA were separated using 15% polyacrylamide gel electrophoresis containing 8 M of urea. After incubation in ethidium bromide solution (0.5 mkg/ml), gel fragments corresponding to small RNAs fraction were excised. We used chemically synthesized RNAs (Syntol, Russia) corresponding to 21 and 27 nucleotides as size markers. Cloning of small RNA libraries were conducted using the Illumina TruSeq Small RNA Prep Kit (Illumina, USA) according to the manufacturer’s protocol. Each sample was made in two biological replicates. Sequencing of small RNAs was performed on an Illumina HiSeq 2000 (Illumina, USA).

treatment_protocol: Heat shock 38.5C, 30 min.

value: w

tag: replic

value: Replic 2

tag: time point after hs


title: w-hs6-rep1

value: Replic 1


title: w-hs6-rep2


title: w-hs1-rep2


title: 5LSS

description: The 5th generation larvae whose grandparents originated from the synchronous experiment during the flight of the Foton-M4 satellite and whose parents were left of Earth


title: 5LSF

description: The 5th generation larvae whose grandparents originated from the synchronous experiment during the flight of the Foton-M4 satellite and whose parents were sent to International Space Station


title: 5LFS

description: The 5th generation larvae whose grandparents were born during the flight of the Foton-M4 satellite and whose parents were left of Earth


title: shCNKSR2_1_3


title: 3LF+24h

description: 3rd instar Larvae from space flight collected in the liquid nitrogen 24h after satellite landing


title: w-hs1-rep1


title: 3LF+12h

description: 3rd instar Larvae from space flight collected in the liquid nitrogen 12h after satellite landing


title: 3LF

description: 3rd instar Larvae from space flight collected in the liquid nitrogen 1.5h after satellite landing


title: 3LS

description: 3rd instar Larvae Synchronous control collected in the liquid nitrogen 1.5h after satellite landing


title: 3LS+12h

description: 3rd instar Larvae Synchronous control collected in the liquid nitrogen 12h after satellite landing


title: w-hs0-rep2

value: control


title: w-hs0-rep1


title: 3LS+24h

description: 3rd instar Larvae Synchronous control collected in the liquid nitrogen 24h after satellite landing


title: w1118-hs24-rep2


title: hsp70null-hs24-rep2


title: w1118-hs6-rep1


title: w1118-hs24-rep1


title: w1118-hs1-rep2


title: hsp70null-hs1-rep1


title: hsp70null-hs0-rep2


title: w1118-hs1-rep1


title: w1118-hs0-rep2


title: w-hs24-rep1


title: w1118-hs0-rep1


title: ZmCENH3_control

value: Columbia

value: wild type

tag: chip antibody

value: ZmCENH3 (Kelly Dawe lab)


title: hsp70null-hs6-rep2


title: LoCENH3_control

source_name: A. thaliana cenh3-1/cenh3-1ZmCENH3 seedlings

value: cenh3-1/cenh3-1, Z. maysCENH3

value: LoCENH3 (this study)


title: LoCENH3_rep1

value: cenh3-1/cenh3-1, L. oleraceum CENH3


title: mESC_Hi-C 1

status: Public on Oct 18 2016

city: Rehovot

first: Pedro

last: Olivares-Chauvet

address: 234 Hertzl Street

department: Department of Computer Science and Applied Mathematics/Department of Biological Regulation

country: Israel

institute: Weizmann Institute of Science

description: processed data file: mesc_hic.adj.txt

data_processing:
Cwalks from PacBio reads were assembled using the cwalk pipeline with default parameters although the shotgun assembly step was not necessary. Components were directly transformed from fenchain files into cadj format
Hi-C reads were processed using the same Cwalk pipeline with the difference that adj files can directly represent the pair-wise information of genome contacts.
reads were mapped using bowtie2 with --reorder --local for cwalks and HiC
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: cadj.annot: tab separated text file with adjacency information, linked to cwalks, annotated by the epigenomic features of TADs who are visited by the cwalk; 38 fields  [chr1]: chromosome of side 1  [start1]: chrosomal coordinate of side 1  [chr2]: chromosome of side 2  [start2]: chromosomal coordinate of side 2  [comp]: component (cwalk) id  [amp_i]: phi29 amplification well id  [fid1]: restriction fragment id of side 1  [fid2]: restriction fragment id of side 2  [span1]: span of component 1  [span2]: span of component 2  [seq_batch]: sequencing batch  [n]: number of hops  [trans_n]: number of trans interfaces  [cmer_doms.dist.x]: distance to closest TAD for side 1  [cmer_doms.id.x]: id of domain hosting side 1  [cmer_doms.k4me3.x]: signal of k4me3 in domain side 1  [cmer_doms.size.x]: size of domain side 1  [cmer_doms.tor.x]: time of replication for domain side 1  [cmer_doms.mode.x]: classification of active or inactive for domain side 1  [cmer_doms.dist.y]: distance to closest TAD for side 2  [cmer_doms.id.y]: id of domain hosting side 2  [cmer_doms.k4me3.y]: signal of k4me3 in domain side 2  [cmer_doms.size.y]: size of domain side 2  [cmer_doms.tor.y]: time of replication for domain side 2  [cmer_doms.mode.y]: classification of active or inactive for domain side 2  [dom_n]: number of domains visited by cwalk  [tss_1]: distance to the closest tss from side 1  [k4me3_1]: distance to the closest peak of k4me3 from side 1   [k27me3_1]: distance to the closest peak of k27me3 from side 1  [actenh_1]: distance to the closest active enhancer from side 1  [ctcf_1]: distance to the closest ctcf from side 1  [border_1]: distance to the closest domain border for side 1  [tss_2]: distance to the closest tss from side 2  [k4me3_2]: distance to the closest peak of k4me3 from side 2   [k27me3_2]: distance to the closest peak of k27me3 from side 2  [actenh_2]: distance to the closest active enhancer from side 2  [ctcf_2]: distance to the closest ctcf from side 2  [border_2]: distance to the closest domain border for side 2
Supplementary_files_format_and_content: adj file: adjacency file ; 7 fields  [chrom1]: chromosome side 1  [start1]: start coordinate side 1  [end1]: end coordinate side 1  [chrom2]: chromosome side 2  [start2]: start coordinate side 2  [end2]: end coordinate side 2  [count]: number of molecules supporting this pair

source_name: v6.5 mESC

extract_protocol:
Between 25 to 50 x 10e7 cells were used to perform in-nucleus ligation 3C; biotin fill-in was omitted. Briefly, adherent cells (mES) were incubated in the presence of trypsin (Biological Industries 03-053-1) for 8-10 minutes max at 37°C and passed through a cell strainer after harvesting to ensure a single-cell suspension. Cells (including K562 from now on) were washed 1x with phosphate-buffered saline (PBS) and resuspended PBS/FBS 10% and cross-linked in formaldehyde final concentration of 2% for 5 minutes at room temperature. After quenching with 0.125 M glycine and wash with PBS, cells were incubated in permeabilization buffer (10 mM Tris–HCl pH 8, 10 mM NaCl, 0.2 % NP-40 alternative (CALBIOCHEM 492016), Protease Inhibitor Cocktail (P8340 Sigma)) for 60 minutes at 4°C while slowly mixing. Cells were split into 5 M cell aliquots and washed 2x with cold PBS. After the second wash, cell pellets were then flash frozen on liquid nitrogen. Pellets were resuspended on 175.5 µl H2O and 24.5 µl DpnII RE buffer 10x. After addition of 3 µl of 20% SDS (final concentration of 0.3%), cells were incubated for 60 minutes at 37°C while agitating (750 RPM). Triton X-100 20% was added to a final concentration of 1.8% and incubated for 60 min at 37°C. Aliquots were then digested with 15 µl HC DpnII (NEB 50,000 U/ml) ON. Cells were centrifuged for 5 minutes at 600 g and washed 1x with PBS. Incubation of pellets for 20 minutes at 65°C was performed in order to heat-inactivate any DpnII residue. In-nucleus ligation was then performed incubating cells on ligation mix (415 µl H2O, 5 µl BSA (10mg/ml NEB) and 5 µl T4 ligation enzyme NEB (2x106 U/ml)) ON at 16°C.  Cross-link was reversed by incubating aliquots with 10 mg/ml proteinase K (Roche) at 65°C ON followed by the addition of 15 µl of RNase A (Roche) for 45 minutes at 37°C. DNA was purified with AmpureXP SPRI beads 1x (Beckman Coulter; A63881) with two elution rounds of 100 µl each with the aim of size selecting for the high molecular weight portion of the sample.
Hi-C: Bioruptor Microtubes (C30010015) to reach a DNA fragment size between 400-500 bp. The sonicated DNA  was then subjected to end-repair reaction (5 µl 10x end-repair buffer + 2.5 µl end-repair mix (NEB E6050L)) at 20 °C for 30 minutes. The DNA was cleaned up with 2.2x SPRI beads and eluted in 38 µl EB. A-tailing reaction was performed with 5 µl NEB buffer 2, 4 µl Klenow fragment -3′-5′ exo (NEB M0212M) and 10 µl dATP 10 nM for 30 minutes at 37 °C, cleaned up with 2.2 x SPRI beads and eluted in 30 µl EB. DNA template was ligated with 5 µl Illumina indexed adapters 0.75 µM with 5 µl T4 quick ligase (NEB M2200) and 40 µl 10x ligase buffer for 15 minutes at 25 °C. Ligated template was then cleaned up with 1.3x SPRI beads and eluted in 41 µl.

value: Embryonic Stem Cells

tag: lineage

value: Embryonic


title: hsp70null-hs6-rep1


title: BMDM_Irrad3_24h

city: London

first: Nuria

last: Andreu

address: Keppel Street

country: United Kingdom

institute: LSHTM

description:
BG3_24
BMDM_all_RawCounts.txt

data_processing:
reads were aligned to the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.2a (Parameters: --outFilterMultimapNmax 20 --lnIntronMax 1000000 –alnSJoverhangMin 8 –alnSJDBoverhangMin 1)
Uniquely aligned reads in BAM format were annotated against the protein-coding mRNA regions using SeqMonk v.0.33.1 platform (Babraham Bioinformatics, Cambridge UK)
Raw counts per mRNA, strand-specific, merging isoforms were quantified using SeqMonk
Differential expression was analyzed in SeqMonk using the R (version 3.2.2) package DESeq2
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

growth_protocol: Bone marrow cells were flushed from the femur and tibia of 8 to 10 week old female C57BL/6 mice and differentiated into macrophages for 7 days in DMEM (Sigma) supplemented with 10% heat-inactivated fetal bovine serum (Biosera) and 20 ng/ml M-CSF (PeproTech). On day 4, cells were fed with an additional 10 ml of media. After 7 days in culture, cells were washed with DPBS and 5×106 cells were seeded into 25 cm2 tissue culture flasks.

extract_protocol:
Macrophages were lysed by adding 4 M GTC solution (4 M guanidine thiocyanate, 0.5 % sodium N–Lauroylsarcosine, 0.1M β–mercaptoethanol, 0.5 % Tween 80), and the lysate homogenized using a QIAshredder column (Qiagen). RNA was extracted by BCP phase partitioning and isopropanol precipitation, cleaned with 75% ethanol and treated with Turbo DNAse (Ambion, Life Technologies). DNA contamination was checked by PCR, and the RNA was further cleaned using an RNeasy MinElute Cleanup kit (Qiagen).
Approximately 500 ng of RNA from each sample was used to prepare individually barcoded strand-specific RNA-seq libraries. rRNA and mitochondrial RNA was removed using Ribo-Zero Gold Removal Magnetic Kit for human/mouse/rat (Epicentre, now Illumina) following the manufacturer's instructions. mRNA was purified using Agencourt RNAClean XP kit. Libraries were constructed using ScriptSeq™ Complete Kit

treatment_protocol: Log-phase cultures were collected, washed twice with PBS+0.05% Tween80 (PBS-T), and resuspended in Dulbecco's PBS (DPBS) before measuring the absorbance at 600 nm and plating CFUs. 1 ml aliquots in 2 ml tubes were irradiated at room temperature at 2.5x104 Gy using a Cs137 irradiator. Inactivation of the bacteria was verified by inoculating 100 ml in liquid and solid media and incubating for 6 weeks. Dead bacteria were diluted in DMEM+10 ng/ml M-CSF and added to BMDM cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.

value: BMDM

tag: infection

value: Dead (Irradiated) Mtb

tag: time

value: 24 hours

tag: replicate


title: BMDM_Uninf3_24h

description:
BU3_24
BMDM_all_RawCounts.txt

treatment_protocol: 6 ml of DMEM+10 ng/ml M-CSF was added to BMDM cells. After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.

tag: cell type

value: uninfected


title: hsp70null-hs24-rep1


title: hsp70null-hs1-rep2


title: w1118-hs6-rep2


title: hsp70null-hs0-rep1


title: ZmCENH3_rep2

tag: ecotype


title: input DNA cenh3-1/cenh3-1LoCENH3


title: BMDM_Irrad2_4h

description:
BG2_0
BMDM_all_RawCounts.txt

treatment_protocol: Log-phase cultures were collected, washed twice with PBS+0.05% Tween80 (PBS-T), and resuspended in Dulbecco's PBS (DPBS) before measuring the absorbance at 600 nm and plating CFUs. 1 ml aliquots in 2 ml tubes were irradiated at room temperature at 2.5x104 Gy using a Cs137 irradiator. Inactivation of the bacteria was verified by inoculating 100 ml in liquid and solid media and incubating for 6 weeks. Dead bacteria were diluted in DMEM+10 ng/ml M-CSF and added to BMDM cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Samples were immediately processed for RNA extraction

value: 4 hours


title: ZmCENH3_rep1


title: LoCENH3_rep2


title: BMDM_Live3_24h

description:
BEF3_24
BMDM_all_RawCounts.txt

treatment_protocol: Mid-log phase M. tuberculosis H37Rv were washed twice with PBS-T, once with DPBS, diluted in DMEM+10 ng/ml M-CSF and added to BMDM cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.

value: Live Mtb


title: K-562_3C-seq (PacBio)

description: Direct sequencing of raw 3C template

source_name: K-562 cells

tag: cell line

value: Lymphoblastoid leukemia

value: Hematopoietic


title: BMDM_Live3_4h

description:
BEF3_0
BMDM_all_RawCounts.txt

treatment_protocol: Mid-log phase M. tuberculosis H37Rv were washed twice with PBS-T, once with DPBS, diluted in DMEM+10 ng/ml M-CSF and added to BMDM cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Samples were immediately processed for RNA extraction


title: BMDM_Irrad3_4h

description:
BG3_0
BMDM_all_RawCounts.txt


title: BMDM_Live2_24h

description:
BEF2_24
BMDM_all_RawCounts.txt


title: BMDM_Uninf3_4h

description:
BU3_0
BMDM_all_RawCounts.txt

treatment_protocol: 6 ml of DMEM+10 ng/ml M-CSF was added to BMDM cells. After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS. Lastly, 6 ml of complete DMEM+10 ng/ml M-CSF was added to each flask. Samples were immediately processed for RNA extraction


title: BMDM_Uninf1_24h

description:
BU1_24
BMDM_all_RawCounts.txt


title: KPC_shRNA_screen_+Dox_rep2

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
For the shRNA screen, reads were mapped with Bowtie v0.12.8 (parameters: --nofw -m 1 -3 34 -v 1) to a custome reference containing the guide sequences of all 148 shRNAs present in the screen.
Reads per reference shRNA were counted and samples were normalized to the sample with the smallest number of reads.
CPM was calculated and shRNA with CPM<100 were removed.
After addition of 1 pseudo-read to every shRNA, the mean of replicates, a log2FC and a z-score were calculated.
hg19
txt file containing shRNA name, log2FC (+Dox/-Dox), z-score
Fastq files were generated using Illumina's CASAVA software.

source_name: KPC cells

extract_protocol:
Genomic DNA was chloroform/phenol extracted from KPC cells and shRNA sequences were PCR amplified.
Adapter sequences were introduced during a second PCR amplification. DNA was purified with an agarose gel extraction followed by a final Biorad Experion quantification.

value: KPC

tag: treatment1(constitutive ha-omomyc or empty vector)

value: shRNA library

tag: treatment2 (doxycycline to induce myc expression)

value: Doxycycline

tag: antibody

value: non


title: BMDM_Irrad2_24h

description:
BG2_24
BMDM_all_RawCounts.txt

tag: strain


title: BMDM_Live1_4h

description:
BEF1_0
BMDM_all_RawCounts.txt


title: BMDM_Live2_4h

description:
BEF2_0
BMDM_all_RawCounts.txt


title: BMDM_Irrad1_24h

description:
BG1_24
BMDM_all_RawCounts.txt


title: KPC_shRNA_screen_-Dox_rep4

value: Ethanol


title: BMDM_Uninf2_24h

description:
BU2_24
BMDM_all_RawCounts.txt


title: BMDM_Live1_24h

description:
BEF1_24
BMDM_all_RawCounts.txt


title: KPC_shRNA_screen_+Dox_rep3


title: BMDM_Uninf2_4h

description:
BU2_0
BMDM_all_RawCounts.txt


title: KPC_shRNA_screen_+Dox_rep4


title: KPC_shRNA_screen_-Dox_rep2


title: KPC_shRNA_screen_+Dox_rep1


title: J774_Irrad3_24h

description:
JG3_24
J774_all_RawCounts.txt

growth_protocol: J774A.1 cells obtained from the ATCC (TIB-67) were cultured in DMEM (Sigma) supplemented with 10% heat-inactivated fetal bovine serum (Biosera) and 5×106 cells were seeded into 25 cm2 tissue culture flasks for infection

treatment_protocol: Log-phase cultures were collected, washed twice with PBS+0.05% Tween80 (PBS-T), and resuspended in Dulbecco's PBS (DPBS) before measuring the absorbance at 600 nm and plating CFUs. 1 ml aliquots in 2 ml tubes were irradiated at room temperature at 2.5x104 Gy using a Cs137 irradiator. Inactivation of the bacteria was verified by inoculating 100 ml in liquid and solid media and incubating for 6 weeks. Dead bacteria were diluted in DMEM and added to J774 cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.

value: Balb/c


title: KPC_shRNA_screen_-Dox_rep1


title: BMDM_Irrad1_4h

description:
BG1_0
BMDM_all_RawCounts.txt


title: BMDM_Uninf1_4h

description:
BU1_0
BMDM_all_RawCounts.txt


title: J774_Uninf3_4h

description:
JU3_0
J774_all_RawCounts.txt

treatment_protocol: 6 ml of DMEM was added to J774 cells. After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS. Lastly, 6 ml of complete DMEM was added to each flask. Samples were immediately processed for RNA extraction


title: J774_Live2_24h

description:
JEF2_24
J774_all_RawCounts.txt

treatment_protocol: Mid-log phase M. tuberculosis H37Rv were washed twice with PBS-T, once with DPBS, diluted in DMEM and added to  J774 cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.


title: Nu_Ctl_3

city: los angeles

first: Danyang

last: Gong

address: 650 Charles Young Dr. So.

department: pharmacology

description: Study role of ORF10 on host mRNA nuclear export

data_processing:
TopHat under default parameter
Genome_build: hg38, KSHV JSC-1 clone BAC16

source_name: Nuclear RNA from 293T cells transfected with pCMVHA vector

growth_protocol: 293T cells regular culturing

extract_protocol:
Fractionate cyto and nuclear RNA, Trizol for total RNA, and then oligodT beads for polyA RNA
method based on ScriptSeq mRNA-Seq library preparation kit (Epicentre)

treatment_protocol: transfection with empty vector pCMVHA or KSHV ORF20 expression plasmid

tag: agent

value: pCMVHA vector


title: J774_Uninf3_24h

description:
JU3_24
J774_all_RawCounts.txt

treatment_protocol: 6 ml of DMEM was added to J774 cells. After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS. Lastly, 6 ml of complete DMEM was added to each flask. Macrophages were incubated for further 20 hours before processing for RNA extraction.


title: J774_Irrad3_4h

description:
JG3_0
J774_all_RawCounts.txt

treatment_protocol: Log-phase cultures were collected, washed twice with PBS+0.05% Tween80 (PBS-T), and resuspended in Dulbecco's PBS (DPBS) before measuring the absorbance at 600 nm and plating CFUs. 1 ml aliquots in 2 ml tubes were irradiated at room temperature at 2.5x104 Gy using a Cs137 irradiator. Inactivation of the bacteria was verified by inoculating 100 ml in liquid and solid media and incubating for 6 weeks. Dead bacteria were diluted in DMEM and added to J774 cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM was added to each flask. Samples were immediately processed for RNA extraction


title: J774_Live3_24h

description:
JEF3_24
J774_all_RawCounts.txt


title: Nu_10_3

source_name: Nuclear RNA from 293T cells transfected with KSHV ORF10

value: KSHV ORF10


title: Ctl_10_3

source_name: Cytoplasmic RNA from 293T cells transfected with KSHV ORF10


title: Nu_Ctl_2


title: KPC_shRNA_screen_-Dox_rep3


title: Nu_10_1


title: Cy_Ctl_3

source_name: Cytoplasmic RNA from 293T cells transfected with pCMVHA vector


title: Nu_Ctl_1


title: J774_Live2_4h

description:
JEF2_0
J774_all_RawCounts.txt

treatment_protocol: Mid-log phase M. tuberculosis H37Rv were washed twice with PBS-T, once with DPBS, diluted in DMEM and added to  J774 cells at a concentration of ∼2.5 × 106 CFU/flask (MOI of 5). After 4 h of infection at 37°C in 5% CO2, macrophages were treated with 200 mg/L amikacin for 1 h and washed twice with DPBS to eliminate any extracellular bacteria. Lastly, 6 ml of complete DMEM was added to each flask. Samples were immediately processed for RNA extraction


title: J774_Irrad2_24h

description:
JG2_24
J774_all_RawCounts.txt


title: Ctl_10_1


title: J774_Uninf2_24h

description:
JU2_24
J774_all_RawCounts.txt


title: Cy_Ctl_2


title: J774_Live3_4h

description:
JEF3_0
J774_all_RawCounts.txt


title: Cy_Ctl_1


title: Ctl_10_2


title: A12 10m10

description: Study lytic replication profile of KSHV WT and KSHV ORF10 mutant

source_name: iSLK cells with KSHV ORF10m10 mutant

growth_protocol: iSLK-puro cells latently infected with KSHV WT or mutant

extract_protocol:
Trizol for total RNA, and then oligodT beads for polyA RNA
method based on ScriptSeq mRNA-Seq library preparation kit (Epicentre)

treatment_protocol: induce with TPA+NaB for 3 days

value: iSLK


title: J774_Irrad2_4h

description:
JG2_0
J774_all_RawCounts.txt


title: Nu_10_2


title: A11 10m10


title: A10 10m10


title: A9 10m

source_name: iSLK cells with KSHV ORF10m5 mutant


title: J774_Uninf2_4h

description:
JU2_0
J774_all_RawCounts.txt


title: J774_Live1_24h

description:
JEF1_24
J774_all_RawCounts.txt


title: A7 10m5


title: A8 10m5


title: J774_Uninf1_24h

description:
JU1_24
J774_all_RawCounts.txt


title: A3 WT

source_name: iSLK cells with KSHV WT

value: KSHV-WT


title: J774_Irrad1_24h

description:
JG1_24
J774_all_RawCounts.txt

value: Dead (Irradiated) Mtb


title: A4 10S

source_name: iSLK cells with KSHV ORF10 stop mutant


title: A5 10S


title: A1 WT


title: A2 WT


title: J774_Live1_4h

description:
JEF1_0
J774_all_RawCounts.txt


title: mESC_Hi-C 2

description: processed data file: mesc_hic.adj.txt

value: Embryonic Stem Cells

value: Embryonic


title: J774_Irrad1_4h

description:
JG1_0
J774_all_RawCounts.txt

value: 4 hours


title: J774_Uninf1_4h

description:
JU1_0
J774_all_RawCounts.txt

value: uninfected


title: KPC_OmoMYC_+Dox_rep1

data_processing:
For RNA-seq, fastq files were mapped using Bowtie2 v2.2.4 (KPC cells, mm9) or TopHat v2.0.7 (U2OS cells, hg19).
Reads per gene were counted using the countOverlaps function from the R package {GenomicRanges}.
Weakly expressed genes were removed (U2OS: mean CPM over all samples <1) and differentially expressed genes were called using EdgeR.
hg19 for U2OS cells, mm9 for KPC cells
txt files containing Ensembl gene ID, gene symbol, gene description, log2FC, p-value and q-value for each comparison described in RNAseq_README.txt
Fastq files were generated using Illumina's CASAVA software.

extract_protocol:
For RNA-sequencing, total RNA was extracted using the RNeasy mini columns (Qiagen) including on-column DNase I digestion.
PolyA+-RNA was isolated from total with the NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB). The NEBNext® Ultra™ RNA Library Prep Kit for Illumina was used for library preparation following the manufacturer’s instruction. Size selection of the libraries was performed with the AMPure XP Beads (Beckman Coulter), followed by 12 PCR cycles for amplification. Library quantification and quality was assessed using the Experion Automated Electrophoresis System (Bio-Rad).

value: HA-OmoMYCwt


title: KPC_OmoMYC_-Dox_rep1


title: KPC_OmoMYC_-Dox_rep2


title: ChIP-seq H3K4Me3 D

city: Clayton

first: Wei

last: Shi

state: Victoria

address: Wellington Rd

country: Australia

institute: Monash University

data_processing:
Reads were aligned to the mouse genome by Rsubread
For the H3K4Me3 samples, read counts were summarized in a region 150bp up and down from the transcriptional start site of each gene using the Rsubread featureCounts functions and NCBI annotation.
For the H3K27Me3 samples, read counts were summarized within the gene body of each gene using the Rsubread featureCounts functions and NCBI annotation.
Peak calling was performed on the M2 Flag samples using MACS.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files were written from the R prompt for the H3K4Me3 and H3K27Me3 read counts; columns represent the Entrez Gene ID, Gene Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene. Bed files for the M2 Flag peak calls were generated by MACS2. They contain the peak summit locations for each peak; columns represent chromosome name, start position of peak, end position of peak, peak ID, and the pileup height at peak summit (the -log10(pvalue) for the peak summit).

source_name: MLL-ENL leukemia

extract_protocol:
DNA was fragmented in a Covaris Sonicator (30 minutes, 4°C) then protein-DNA complexes immunoprecipitated from clarified chromatin fractions using H3K27Me3 (2μg; Millipore: 07-449) or H3K4Me3 (2μg; Millipore: 07-473) antibodies and 30μl of Protein A-sepharose. For Hhex-Flag ChIP, 30μl of anti-Flag (M2)-agarose beads (Sigma) was added directly to clarified chromatin fractions. Following reversal of crosslinks and RNaseI and Proteinase K treatments, extracted DNA was purified using the QIAquick purification kit.
ChIP-Seq DNA libraries were constructed using TruSeq Nano DNA sample preparation according to the manufacturer’s instructions.

tag: histone

tag: genetic modification


title: ChIP-seq H3K27Me3 D


title: ChIP-seq M2 Flag D Hhex F

value: M2 Flag

value: ΔERT2 + Hhex-F


title: ChIP-seq M2 Flag fl

value: fl


title: ChIP-seq H3K4Me3 D Hhex F


title: ChIP-seq H3K4Me3 fl


title: ChIP-seq H3K27Me3 D Hhex F


title: A6 10S


title: tumor 78DKO4

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

data_processing:
Sequencing reads were mapped against the reference genome (mm9, NCBI37) using BWA (-c –l 25 –k 2 –n 10) software (Li and Durbin, 2009).
Cisgenome v2 software package (Ji et al., 2008) was used to calculate reads per 1000bp of transcript per million reads sequenced (RPKM) values for all RefSeq annotated genes.
Genome_build: mm9
Supplementary_files_format_and_content: .rna (gene,ErfSeq,EntrezID,blank,chromosome,start,end,strand,Exon_lenght,RPKM)

source_name: liver tumor (E2F7/8 DKO)

extract_protocol:
Total RNA was isolated from livers using the RNeasy kit (Qiagen) mRNA was isolated using a poly (A) purist MAG kit (Life Technologies, AM 1922) and purified with mRNA-ONLY™ Eukaryotic mRNA Isolation Kit (Epicentre)
Transcriptome libraries were then constructed using SOLiD total RNA-seq kit (Applied Biosystems Life Technologies).

tag: tissue

value: liver tumor

tag: genotype

value: E2F7/8 DKO


title: 102842-001-051

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

institute: Academic Medical Centre Amsterdam

data_processing:
Image analysis, base calling and quality checks were undertaken with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Read data was mapped to the reference sequence Homo_sapiens.GRCh37.75 using a short read aligner after trimming for adapter sequences with Trimmomatic v0.30. A default mismatch rate of 2% was used.
Genome_build: Homo_sapiens.GRCh37.75
Supplementary_files_format_and_content: File for every sample with scores representing read counts per gene

source_name: EAC celline FLO-1 parental cells

extract_protocol:
Cells were harvested at 80% confluency, 24 hr after a media change. Total RNA was extracted using the Qiagen RNeasy Kit. RNA quality was confirmed using a Fragment AnalyzerTM (Advanced Analytical Technologies).
cDNA library preparation was performed using the NEBNext Ultra directional RNA library Prep Kit (Illumina). DNA sequencing was conducted on the Illumina NextSeq 500 system.

value: FLO-1 parental


title: EF_6-8hr_FAIRE_Rep1

city: Chapel Hill

first: Daniel

middle: J

last: McKay

state: NC

address: 3344 Genome Sciences Building

department: Biology, Genetics

institute: The University of North Carolina at Chapel Hill

data_processing:
Library strategy: FAIRE-seq
Basecalls were performed with CASAVA version 1.8.2
reads were aligned to the dm3 Drosophila reference genome using Bowtie2 and the following flags: –trim5 8, –sensitive, –end-to-end
reads with a MAPQ score less than 10 were removed using samtools view –q 10
aligned reads were converted to bed format using BEDTools bamToBed, and FAIRE signal files were generated by extending each read to 110bp. The number of reads overlapping each base in the genome was counted.
FAIRE data were normalized by subtracting input signal from FAIRE at each base, and z-scores were generated using the mean and standard deviation for each chromosome arm.
FAIRE peaks were called on individual replicates or pooled data using MACS2 with Input as control, and a shift size of 125bp.
Genome_build: dm3
Supplementary_files_format_and_content: processed data files are in wig format, and contain Input-subtracted FAIRE z-scores, smoothed with a 200bp sliding window average and 10bp step size.

source_name: 6-8 hour embryos

growth_protocol: Following a pre-clearing step, embryos were collected for 2 hours and aged at 25C until the designated time.

extract_protocol:
FAIRE-enriched DNA was ethanol precipitated, heated at 65C, treated with Rnase, and column purified.
DNA was prepared for sequencing using custom internal barcodes on an Illumina Hi-Seq machine at the UNC High-Throughput Sequencing Facility

treatment_protocol: staged samples were fixed for 10 minutes at 25C, quenched with glycine, washed with Buffer A at 4C, Dounce homogenized in Buffer A, and filtered through 60uM Nitex. Nuclei were pelleted, resuspended in FAIRE lysis buffer, and subjected to bead beating with 2mm tungsten beads. Chromatin was sonicated to a size range of 500bp-2kb, and phenol-chloroform extracted.

value: OregonR

tag: developmental stage

value: 6-8 hours after egg laying

value: whole embryo


title: tumor 78DKO3


title: 102842-001-050


title: tumor 78DKO2


title: liver4

source_name: liver

value: liver

value: wt


title: Non-fluorescent cells from larval zebrafish following macrophage sorting via FACS Rep 3

city: Durham

first: Steve

last: Taylor

address: 303 Research Dr

department: Division of Infectious Diseases

institute: Duke University School of Medicine

description: Mixed larval control cells, depeleted of macrophages by FACS to remove mfap4:tdTomato fluorescent macrophages.

data_processing:
Reads were aligned to D rerio GRCz10 using STAR (default parameters)
SAM files were converted to BAM and sorted with Samtools
FPKM values were derived with Cufflinks
Statistical analysis was performed with GenomicAlignments, GenomicFeatures, and DESeq2 packages implemented in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited files with transcript abundance (FPKM) and gene expression analysis between dissected granulomas and sorted macrophages
Supplementary_files_format_and_content: iRed_over_disGran_foldchange.xlsx: Gene expression comparison (iRed - sample; disGran - reference)

source_name: Non-fluorescent cells separated from fluorescent macrophages via FACS from 4dpf larval zebrafish

extract_protocol:
Granulomas were dissected from adult animals infected with M. marinum, macrophages were sorted via FACS from M. marinum-infected adult zebrafish, and non-fluorescent cells were separated from fluorescent macrophages via FACS from 4dpf larval zebrafish
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: Larvae, 4 days post-fertilization

value: *AB Tg(mfap4:tdTomato-CAAX)^xt6

tag: tag

value: Whole fish post-FACS macrophage sorting


title: ChIP-seq M2 Flag D


title: KPC_OmoMYC_+Dox_rep2

value: KPC

value: Doxycycline

value: non


title: 102842-001-049

source_name: EAC celline FLO-1LM cells


title: Non-fluorescent cells from larval zebrafish following macrophage sorting via FACS Rep 2


title: 102842-001-048


title: liver3


title: Non-fluorescent cells from larval zebrafish following macrophage sorting via FACS Rep 1


title: U2OS_exp2_OmoMYCmutHER_+Dox_rep3

source_name: U2OS cells

value: HA-OmoMYCmutHER


title: Macrophages sorted from Mycobacterium marinum infected adult zebrafish via FACS Rep 4

description: Matched zebrafish head kidney macrophages sorted from animals infected for 2 weeks with 400 CFU/fish M. marinum. Macrophages were sorted based on mfap4:tdTomato fluorescence by FACS.

source_name: M. marinum-infected adult zebrafish macrophages sorted by FACS

value: Adult

value: Macrophages


title: tumor 78DKO1

value: liver tumor


title: ChIP-seq H3K27Me3 fl

value: fl


title: U2OS_exp2_OmoMYCmutHER_+Dox_rep2


title: liver 78DKO4

source_name: liver (E2F7/8 DKO)

value: E2F7/8 DKO


title: ycnbwsp_genomic_Input

source_name: adult female virgins

value: y;cn,bw,sp

value: adult

value: whole adult


title: liver2

value: liver


title: U2OS_exp2_OmoMYCmutHER_+Dox_rep1


title: liver 78DKO3


title: Macrophages sorted from Mycobacterium marinum infected adult zebrafish via FACS Rep 1


title: U2OS_exp2_OmoMYCmutHE_+Dox_rep3

value: HA-OmoMYCmutHE


title: Macrophages sorted from Mycobacterium marinum infected adult zebrafish via FACS Rep 2


title: Macrophages sorted from Mycobacterium marinum infected adult zebrafish via FACS Rep 3


title: U2OS_exp2_OmoMYCmutHE_+Dox_rep2


title: liver1

value: wt


title: U2OS_exp2_OmoMYCmutHE_+Dox_rep1


title: Dissected Mycobacterium marinum granuloma from adult zebrafish tissue Rep 4

description: Granulomas dissected from 2 week post infection M. marinum infected zebrafish. Fish were infected with 400 CFU/fish.

source_name: Adult zebrafish M. marinum granuloma

value: *AB Tg(mfap4:tdTomato-CAAX)^xt6

value: Dissected granuloma


title: Dissected Mycobacterium marinum granuloma from adult zebrafish tissue Rep 5


title: liver 78DKO2


title: U2OS_exp2_OmoMYCwt_+Dox_rep3

value: HA-OmoMYCwt


title: liver 78DKO1


title: U2OS_exp2_OmoMYCwt_+Dox_rep2

value: Doxycycline


title: Dissected Mycobacterium marinum granuloma from adult zebrafish tissue Rep 3


title: U2OS_exp2_OmoMYCwt_+Dox_rep1

value: non


title: U2OS_exp2_vector_+Dox_rep3

value: vector


title: worker_9am_12

city: Urbana

first: Amy

last: Cash

state: IL

address: 1206 W. Gregory Dr

department: Biology

institute: University of Illinois

data_processing:
Each pool of 8 samples was quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3.
FastQ files were generated and demultiplexed with Casava 1.8.2
Each sample's pair of fastq files were run through trimmomatic 0.30 to first remove any remaining standard Illumina PE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove individual reads shorter than 30 bp and their paired read, regardless of length (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10 TRAILING:28 LEADING:28 MINLEN:30)
Paired reads per samples were aligned to Amel 4.5 genome and OGS 3.2 gene models using Tophat2 2.0.10 with parameters --library-type fr-firststrand --mate-inner-dist 150 --mate-std-dev 40. Alignment bam files were sorted by read name using "samtools sort -n".
Fragment counts for each gene were obtained using htseq-count (htseq 0.5.4) with parameters -s reverse -m union -a 0 -t gene -i ID
Genome_build: Amel 4.5
Supplementary_files_format_and_content: tab-delimited text files of raw fragment counts per gene per sample were used directly in edgeR 3.4.2 for statistical analysis and thus are the "normalized" data.
Supplementary_files_format_and_content: Those identifiers are from Beebase.org's OGSv3.2, which is the official gene set for Apis mellifera genome assembly Amel_4.5. It is available for download from here:
http://hymenopteragenome.org/beebase/?q=download_sequences

organism: Apis mellifera

source_name: inactive worker bees collected in the morning

growth_protocol: Three colonies used in these experiments was headed by a naturally mated queen (unrelated to each other), contained 8,000-10,000 workers and several hundred drones, and were maintained according to standard methods at the University of Illinois Bee Research Facility, Urbana, Illinois, USA

extract_protocol:
Bees were flash frozen on liquid nitrogen, heads were incubated in RNAlater ICE, and mushroom bodies were dissected from the brain.  Total RNA was extracted using Picopure RNA isolation kits and poly-adenylated RNA was enriched using Oligo(dT)25 dynabeads
Libraries were constructed using the NEXTflex Directional RNA-Seq Kit from Bioo Scientific

treatment_protocol: Behavioral observations and marking were used to identify active drones and workers

tag: sex type

value: worker

tag: collection time

value: mushroom body (dissected from brain)

tag: colony

tag: pool


title: HS rep2 - 30m_MNase-seq

city: Princeton

first: Tess

last: Jeffers

state: NJ

address: 165 Carl Icahn Laboratory

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

description: sequencing of mononucleosomal DNA liberated at 30 minute timepoint

data_processing:
Paired end reads were mapped to ce10 genome release using Bowtie (v1.1.2) with stringent multimapping parameters: bowtie -q -X 2000 --fr -p 1 -S -n 2 -e 70 -l 28 --pairtries 100 --maxbts 125 -k 1 -m 1 --un /Unmapped_Reads.fastq --phred33-quals /ce10 -1 /read1.fastq -2 /read2.fastq
Reads with insert sizes between 100 and 250 bp were kept for downstream analysis.
Replicates were first processed individually, then pooled after confirming a high degree of correlation between replicates.
Nucleosome analysis was performed as described previously {Kaplan:2010we, Gossett:2012hw}.
Scaled Coverage: Nucleosome coverage was calculated by extending the filtered mapped reads to their fragment length and measuring the sum of reads covering each bp. To normalize for variation between samples, nucleosome coverage was scaled by 1/(mean coverage), yielding a mean nucleosome coverage of 1.0.
Smooth Dyads: Dyads are approximated as the center of a paired-end fragment. The number of dyads at each base pair was scaled by 1/(mean dyad density), then Gaussian smoothed with a standard deviation of 20 bp.
Nucleosome calls: Nucleosome positions were identified from dyad density maps using a previously reported greedy algorithm {Albert:2007cb, Gossett:2012hw}. Using the local maxima of the dyad density as the nucleosome center p, the size of the nucleosome (the nucleosome-protected region) was determined by measuring the average length of all reads that covered the nucleosome center. The standard deviation of the nucleosome center (the nucleosome “fuzziness”) was calculated for each called nucleosome as the standard deviation of dyads around the mean. Nucleosome occupancy was defined as the number of dyads that fell within 50 bp of the nucleosome center.
RNA-seq reads were mapped to the C. elegans WS220 Gene Annotation Model using Tophat2 (v0.7) {Trapnell:2012kp}.
HTSeq-counts: The resulting alignment files were quantified using HT-Seq (v0.4.1) and the RefSeq gene annotations for WS220 {Anders:2015gf}.
Total read counts per gene were normalized for differential expression using DESeq2 (v1.0.19) in R (v3.0.1) {Love:2014eo}.
Genome_build: UCSC C. elegans October 2010 release (ce10/WS220)
Supplementary_files_format_and_content: Scaled Coverage: wig file containing normalized signal for every basepair in the genome.
Supplementary_files_format_and_content: SmoothDyads: wig file containing normalized & smoothed dyad signal for every basepair in the genome.
Supplementary_files_format_and_content: CalledNucleosomes: bed file containing chr, start, stop, length, lengthStdev, dyad position, dyad Stdev, conditionalPosition, dyadMean, and occupancy for every nucleosome in the genome.
Supplementary_files_format_and_content: HTSeq-counts: tabular file containing total number of read counts mapping to every gene in the genome

organism: Caenorhabditis elegans

source_name: Embryo

growth_protocol: Wild type N2 worms were maintained at 20degC in liquid culture in S-medium supplemented daily with concentrated HB101 bacteria. Mixed-stage embryos were isolated from gravid adults by bleach hypochlorite treatment.

extract_protocol:
Cross-linked embryos were incubated with chitinase, washed, and dounced in dounce buffer to extract nuclei. Nuclei were pelleted and washed with MNase digestion buffer. Chromatin was digested with MNase, and at each timepoint (0, 2, 4, 8, 15, or 30 minutes after enzyme addition) a fraction of the reaction was removed, quenched with EDTA, and stored on ice. Samples were treated with Proteinase K for 2 hours at 55 degC, then incubated overnight at 65 degC to reverse crosslinks. DNA was isolated from RNA and proteins using phenol:chloroform extraction and RNase A treatment for 1 hour at 37 degC. Mononucleosome-sized fragments (100 to 200 bp) were extracted from a 2% agarose gel and purified using a Qiagen gel extraction kit.
Libraries were prepared from 100 ng of gel-extracted DNA using the Illumina TruSeq DNA library preparation kit v2 (FC-121-2001) according to manufacturer instructions. Ampure beads were used for the final purification in lieu of gel purification. Individual samples were barcoded with unique 6bp index sequences contained within the sequencing adapters.  Individual libraries were then pooled at equimolar ratios for paired-end multiplex sequencing.

treatment_protocol: Heat Shock. After hypochlorite treatment, embryos were incubated at 34 degC for 20 minutes. Embryos were then cross-linked for 30 minutes in M9 + 2% formaldehyde

value: Mixed-stage


title: U2OS_exp2_vector_+Dox_rep2

tag: cell line


title: worker_9am_11


title: HS rep2 - RNAseq

description: mRNA expression data from embryos

extract_protocol:
Embryos flash frozedn in Trizol were homogenized by thawing at 37 degC and refreezing in liquid nitrogen 3x. Total RNA was isolated using a TRIzol/chloroform extraction followed by RNeasy Mini (Qiagen) preparation with On Column DNaseI Digestion (Qiagen).
Libraries were prepared from 2 ug of total RNA using the Illumina TruSeq RNA library preparation kit v2 (RS-122-2001) according to manufacturer instructions. Individual samples were barcoded with unique 6bp index sequences contained within the sequencing adapters.  Individual libraries were then pooled at equimolar ratios for paired-end multiplex sequencing.

treatment_protocol: Heat Shock. After hypochlorite treatment, embryos were incubated at 20 degC for 20 minutes. Embryos were then resuspended in Trizol, flash frozen, and stored at -80degC.


title: worker_9am_10


title: HS rep2 - 15m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 15 minute timepoint


title: U2OS_exp2_vector_+Dox_rep1

tag: treatment1(constitutive ha-omomyc or empty vector)


title: HS rep2 - 4m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 4 minute timepoint


title: worker_9am_8


title: HS rep2 - 2m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 2 minute timepoint


title: U2OS_exp2_vector_-Dox_rep2

tag: treatment2 (doxycycline to induce myc expression)

value: Ethanol


title: U2OS_exp2_vector_-Dox_rep1

tag: antibody


title: worker_9am_9


title: U2OS_exp2_vector_-Dox_rep3


title: HS rep1 - RNA-seq

description: mRNA expression data from embryos

tag: strain


title: U2OS_exp1_OmoMYCwt_+Dox_rep3


title: worker_9am_7


title: U2OS_exp1_OmoMYCwt_+Dox_rep1


title: HS rep1 - 15m_MNase-seq


title: HS rep1 - 8m_MNase-seq

description: sequencing of mononucleosomal DNA liberated at 8 minute timepoint


title: worker_9am_5


title: worker_9am_4


title: U2OS_exp1_OmoMYCwt_+Dox_rep2


title: Dissected Mycobacterium marinum granuloma from adult zebrafish tissue Rep 1

value: Adult


title: HS rep1 - 30m_MNase-seq


title: HS rep1 - 4m_MNase-seq


title: worker_9am_6


title: HS rep2 - 8m_MNase-seq


title: Dissected Mycobacterium marinum granuloma from adult zebrafish tissue Rep 2


title: worker_9am_3


title: U2OS_exp1_vector_+Dox_rep2


title: HS rep1 - 2m_MNase-seq


title: RT rep2 - RNAseq

description: mRNA expression data from embryos

treatment_protocol: Control. After hypochlorite treatment, embryos were incubated at 20 degC for 20 minutes. Embryos were then resuspended in Trizol, flash frozen, and stored at -80degC.


title: worker_9am_2


title: worker_9am_1


title: RT rep2 - 30m_MNase-seq

treatment_protocol: Control. After hypochlorite treatment, embryos were incubated at 20 degC for 20 minutes. Embryos were then cross-linked for 30 minutes in M9 + 2% formaldehyde


title: worker_3pm_12

source_name: active worker bees collected in the afternoon as they prepared to forage


title: U2OS_exp1_vector_-Dox_rep3


title: U2OS_exp1_vector_-Dox_rep2


title: worker_3pm_11


title: RT rep2 - 8m_MNase-seq


title: U2OS_exp1_vector_-Dox_rep1


title: worker_3pm_10


title: worker_3pm_9


title: U2OS_ChIPseq_OmoMYCwt_-Dox_N262

data_processing:
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v1.1.1. and normalized to the sample with the smallest number of mapped reads.
Wiggle files were generated using MACS v1.4.2 with default parameters but a p-value cutoff of 1e-6.
hg19
Fixed step wiggle files with a resolution of 10bp.
Fastq files were generated using Illumina's CASAVA software.

growth_protocol: U2OS and KPC cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma). The U2OS tet-on-MYC cell line was generated as described previously (Walz et al., 2014). For constitutive expression, N-terminally HA-tagged OmoMYC or various mutants (generated using site-directed mutagenesis) were cloned into SFFV-driven lentiviral expression vectors. Lentiviruses were produced by co-transfection with the packaging plasmid psPAX.2, and the envelope plasmid pMD2.G into HEK293 cells using the PEI method. Cells were infected with lentiviral supernatants in the presence of 4 mg/ml polybrene (Sigma) for 24 h and selected with 2 µg/ml Puromycin (InvivoGen).

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-sepharose or Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired, A tailed and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay.

treatment_protocol: U2OS cells were treated with doxycycline (1µg/ml) for 30h (RNA-seq) or 8h (ChIP-seq) to induce MYC expression. For the shRNA screen, KPC cells were infected with doxycycline inducible lentiviral shRNA vectors and shRNA expression was induced with 1µg/ml doxycycline for 5 days.

value: c-MYC (N262, Santa Cruz)


title: RT rep2 - 2m_MNase-seq


title: U2OS_exp1_vector_+Dox_rep3


title: RT rep1 - RNA-seq

description: mRNA expression data from embryos


title: worker_3pm_7


title: worker_3pm_8


title: U2OS_ChIPseq_vector_+Dox_N262


title: U2OS_ChIPseq_vector_-Dox_N262


title: RT rep1 - 15m_MNase-seq


title: U2OS_exp1_vector_+Dox_rep1


title: worker_3pm_6


title: U2OS_ChIPseq_vector_-Dox_IgG

value: IgG (rabbit, Sigma)


title: worker_3pm_5


title: RT rep1 - 8m_MNase-seq


title: RT rep1 - 4m_MNase-seq


title: worker_3pm_4


title: RT rep2 - 15m_MNase-seq


title: worker_3pm_3


title: U2OS_ChIPseq_OmoMYCwt_+Dox_HA

value: HA (ab9110 , Abcam)


title: U2OS_ChIPseq_input


title: worker_3pm_2


title: U2OS_ChIPseq_OmoMYCwt_+Dox_N262