title: FibroblastT0Cntrl 3

city: Dallas

first: Nicole

middle: Janell

last: De Nisco

state: TX

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: UTSW Medical Center

description:
Cntrl0
F2_UN_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

data_processing:
Basecalls performed using bcl2fastq/1.8.4
Reads were trimmed using fastq-mcf (ea-utils/1.1.2-806)
Trimmed reads were mapped using TopHat 2 (2.0.12)
Raw reads were counted using featureCounts (subread/1.4.6)
Normalized counts were generated using edgeR (3.2.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files

source_name: Primary Adult Dermal Fibroblast

growth_protocol: Primary human fibroblasts were seeded onto 6-well plates at a density of 1x105 cells/mL and grown for 18-20 hours to ~80% confluency in ATCC Primary Fibroblast Basal Medium plus Low Serum Growth Kit. V. para cultures were grown over night at 30C in MLB and then normalized to an OD600 of 0.2 and subcultured to OD600 = 0.6.

extract_protocol:
At 45, 60, 75 and 90 minutes post-infection, RNAprotect Cell Reagent (Qiagen) was added. Cells were harvested by scraping, pooled and pellets were resuspended in RLT-plus buffer (Qiagen) and stored at -80C. Cells were lysed with 27G1/2 needles before homogenization with QiAshredder columns (Qiagen). Total RNA was then purified using the RNAeasy Plus Kit (Qiagen).
RNA concentration was determined with a Qubit fluorimeter prior to library prep.  4μg of total DNAse treated RNA were prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina. In brief, polyadenylated RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA was A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer.

treatment_protocol: V. para cultures were pelleted, resuspended in unsupplemented DMEM and grown at 37°C for 30 minutes to pre-induce T3SS1 expression. Primary Fibroblasts were washed with unsupplemented DMEM and then infected with pre-induced POR3 or POR4 strains at a multiplicity of infection (MOI) of 10. Plates were centrifuged at 1000xg for 5 minutes to synchronize infection and incubated at 37°C, 5% CO2

tag: infection strain

tag: infection time


title: Mouse: 2HF131; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90

status: Public on Apr 28 2017

type: SRA

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

library_source: transcriptomic

data_processing:
42nt single reads from 341 mouse islet samples (mean ~40Mio reads/sample) were mapped to mm9 reference genome using Tophat software version 1.3.3 (Trapnell, Roberts et al. 2012) with option --segment-length=20.
File format conversions and statistics for aligned reads were performed using Samtools (Version 0.1.16).
Read counts for genes were generated using htseq-count (Version 0.5.3p3) with UCSC mm9 refFlat genes in GTF format as a reference.
Percent mapped reads were calculated and 3 samples were removed with low percentage (<45%) of mapped reads. The remaining 338 samples were used for subsequent analysis.
The raw count data were first filtered for an average of 5 reads in all the samples, normalized to library size using the trimmed mean (TMM) method in edgeR (Robinson, McCarthy et al. 2010)
Genome_build: mm9
Supplementary_files_format_and_content: The raw counts file contains the counts per gene for each sample. The normalized counts file are TMM normalized and are log2 transformed

molecule: total RNA

organism: Mus musculus

source_name: pancreatic islets

extract_protocol:
At least 150 islets were selected and transferred to a 1.5mL DNA/RNA free tube. After centrifugation (1000 rpm, 10s) and disposal of the supernatant, islets were lysed in 350µL RLT Buffer (Qiagen, France). Samples were kept at -80°C before RNA extraction and RNA seq.
The Sequencing library preparation was performed using 200 ng of total RNA input with the TrueSeq RNA Sample Prep Kit v2-Set B (RS-122-2002, Illumina Inc, San Diego, CA) producing a 275bp Fragment including adapters in average size.

tag: strain

tag: mouse id

tag: diet

value: High Fat, High Sugar (HFHS)

tag: time

tag: tissue

value: pancreatic islets


title: Mouse: 2HF130; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 2HF129; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 2HF128; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 2HF127; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: FibroblastT90Cntrl 2

country: USA

description:
Cntrl4
F2_90_4_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

molecule: polyA RNA

organism: Homo sapiens

value: V. parahaemolyticus POR4

value: 90 minutes


title: FibroblastT90Cntrl 3

description:
Cntrl4
F2_90_4_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: K562-CEBPα-ER β-estradiol 2

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32a

department: Hematology and Oncology

country: Germany

institute: University of Leipzig

data_processing:
Demultiplexing all 50-bp reads from each lane using the CASAVA v1.8.2 software (Illumina)
Adaptor sequences were trimmed from raw sequences using cutadapt software
From the remaining sequences, only reads 15–27 bases long were kept for analysis
Alignment of reads to human (hsa-only) mature sequences of miRBase (5–8) v17 was done using the bowtie aligner
Mapped reads for each miRNA were counted with R/Bioconductor programming environment by application of the ShortRead library
Supplementary_files_format_and_content: abundance measurements

source_name: K562 cells

growth_protocol: Cells were grown in RPMI-1640 medium without phenolred, 10% charcoal treated FBS, 1% Pen/Strep and 1µg/ml Puromycin

extract_protocol:
Total RNA was extracted using Trizol method according to the manufacturer's instructions
500ng total RNA extracted using Trizol method was used for small RNA library preparation with the TruSeq™ Small RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions. The barcoded libraries were size restricted between 140 and 165 bp, purified and quantified using the Library Quantification Kit-Illumina/Universal (KAPA Biosystems) according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with 5µM β-estradiol to activate C/EBPα

tag: cell type

value: K562 cells stabely expressing C/EBPalpha-ER fusion protein

tag: agent

value: beta-estradiol


title: K562-CEBPα-ER ethanol 3

value: ethanol


title: FibroblastT90Cntrl 1

description:
Cntrl4
F2_90_4_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: K562-CEBPα-ER β-estradiol 3


title: Mouse: 2HF126; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: FibroblastT90Exp 3

description:
Exp4
F2_90_3_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: V. parahaemolyticus POR3


title: Mouse: 2HF125; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: FibroblastT90Exp 2

description:
Exp4
F2_90_3_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: K562-CEBPα-ER β-estradiol 1


title: Mouse: 2HF124; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Promyelocyte_I

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

country: Canada

institute: Institute for Research in Immunology and Cancer

description: Promyelocyte CD34-CD11b-CD16-

data_processing:
Basecalls performed using CASAVA 1.8
Sequenced reads were mapped to the reference genome using CASAVA 1.8
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: Lonza healthy bone marrow

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74104)
TruSeq RNA Sample Preparation (Illumina)

value: bone marrow

value: Promyelocyte CD34-CD11b-CD16-

tag: sorting markers


title: FibroblastT0Cntrl 2

description:
Cntrl0
F2_UN_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: FibroblastT75Cntrl 3

description:
Cntrl3
F2_75_4_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: 75 minutes


title: FibroblastT0Cntrl 1

description:
Cntrl0
F2_UN_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 2HF123; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: FibroblastT75Cntrl 2

description:
Cntrl3
F2_75_4_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 2HF122; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Myelocyte_I

description: Myelocyte CD34-CD11b+CD16-

value: Myelocyte CD34-CD11b+CD16-


title: K562-CEBPα-ER ethanol 2


title: Metamyelocyte_I

description: Metamyelocyte CD34-CD11b+CD16med

value: Metamyelocyte CD34-CD11b+CD16med

value: CD15+ CD33+ CD34- CD11b+ CD16med


title: K562-CEBPα-ER ethanol 1


title: Mouse: 2HF121; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: FibroblastT75Cntrl 1

description:
Cntrl3
F2_75_4_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: BandSegment_I

description: Band-segmented_granulocytes CD34-CD11b+CD16+


title: Myeloblast_I

description: CD34+CD33+ myeloid precursor

value: CD34+CD33+ myeloid precursor


title: Promyelocytes

description: Promyelocyte CD34-CD11b-CD16-


title: FibroblastT75Exp 3

description:
Exp3
F2_75_3_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: FibroblastT75Exp 2

description:
Exp3
F2_75_3_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: pre-B_2

description: Pre-B-Precursor CD34-CD10+CD19+

value: Pre-B-Precursor CD34-CD10+CD19+


title: FibroblastT75Exp 1

description:
Exp3
F2_75_3_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 2HF119; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 2HF118; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 2HF117; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: FibroblastT90Exp 1

description:
Exp4
F2_90_3_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 2HF116; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: FibroblastT60Cntrl 2

description:
Cntrl2
F2_60_4_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: 60 minutes


title: FibroblastT60Cntrl 3

description:
Cntrl2
F2_60_4_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Myelocytes

description: Myelocyte CD34-CD11b+CD16-


title: MyeloMonocytic_progenitors

description: CD34+CD33+ myeloid precursor


title: Mouse: 2HF115; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10

value: High Fat, High Sugar (HFHS)


title: Metamyelocytes

description: Metamyelocyte CD34-CD11b+CD16med


title: FibroblastT60Exp 3

description:
Exp2
F2_60_3_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: FibroblastT60Exp 2

description:
Exp2
F2_60_3_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: ERY_4

description: Mature erythroblast CD34-CD71-GlyA+

value: Mature erythroblast CD34-CD71-GlyA+

value: CD34- CD71- Gpa+


title: Mouse: 2HF113; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02

value: pancreatic islets


title: Mouse: 2HF114; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: FibroblastT60Cntrl 1

description:
Cntrl2
F2_60_4_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: V. parahaemolyticus POR4


title: Mouse: 2HF112; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: ERY_2

description: Early Eryhtroblast CD34-CD71+GlyA-

value: Early Eryhtroblast CD34-CD71+GlyA-

value: CD34- CD71+ Gpa-


title: Mouse: 2HF111; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 2HF120; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: ERY_1

description: Immature proerythroblast CD34+CD71+GlyA-

value: CD34+ CD71+ Gpa-


title: pre-B_1

description: Early Pre-B precursor CD34+CD10+CD19+

value: bone marrow

value: Early Pre-B precursor CD34+CD10+CD19+


title: Mouse: 2HF110; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: FibroblastT45Cntrl 2

description:
Cntrl1
F2_45_4_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: 45 minutes


title: FibroblastT45Cntrl 1

description:
Cntrl1
F2_45_4_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 2HF109; Strain: DBA/2J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: FibroblastT45Exp 3

description:
Exp1
F2_45_3_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

value: V. parahaemolyticus POR3


title: Pre-B-2_II

description: Pre-B-Precursor CD34-CD10+CD19+


title: Band-segmented_granulocytes


title: Pre-B-1_II

description: Early Pre-B precursor CD34+CD10+CD19+


title: Mouse: 1RC137; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90

value: Regular Chow (RC)


title: FibroblastT45Exp 2

description:
Exp1
F2_45_3_2
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: Mouse: 1RC138; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: Mouse: 1RC136; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: Myelomonocytic_precursor

description: CD34+CD33+ myeloid precursor


title: FibroblastT45Exp 1

description:
Exp1
F2_45_3_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: ERY_3

description: Erythroblast CD34-CD71+GlyA+

value: Erythroblast CD34-CD71+GlyA+

value: CD34- CD71+ Gpa+


title: Ery4_II

description: Mature erythroblast CD34-CD71-GlyA+


title: Mouse: 1RC134; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: Ery2_II

description: Early Eryhtroblast CD34-CD71+GlyA-


title: 4h_anaerobic

city: Berkeley

first: Sean

middle: D.

last: Gallaher

state: California

address: 176 Stanley Hall, room 408

department: California Institute for Quantitative Biosciences

institute: UC Berkeley

description: total RNA - rRNA

data_processing:
adaptor trimming with Scythe
alignment with RNA-Star 2.4.0j
FPKM calculation with cuffdiff v2.2.1 with --multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand
Gene models were constructed with AUGUSTUS 3.0.3 using default parameters. AUGUSTUS was trained with 6,567 genes from a de novo assembled transcriptome generated from a pool of 397 million 150+150 paired-end RNA-Seq reads, prepared from a variety of growth conditions.
Genome_build: not yet published.  The fasta file with genome sequence and gff file with gene annotations are available on the series record.
Supplementary_files_format_and_content: cuffdiff output

organism: Chromochloris zofingiensis

source_name: algae cultures

growth_protocol:
Cultures were grown at 25°C in liquid cultures (Proteose medium supplemented with Chu’s micronutrient solution) with shaking at 100–150 rpm under a diurnal light cycle (16 h light, 8 h dark)
in 100 μmol photons m^−2 s^−1 medium light in liquid cultures unless otherwise specified.

extract_protocol:
Total RNA was isolated by TRIzol extraction followed by purification by QIAgen miRNeasy mini kit.
Total RNA was depleted of rRNA by Ribo-Zero rRNA Removal Kit for Plant Leaf. Libraries were prepared with the Illumina-compatible KAPA Stranded RNA-Seq kit from Kapa Biosystems.

treatment_protocol: Various. See sample descriptions

tag: light level

value: med light (100 μmol photons m^−2 s^−1)

tag: oxidative stress

tag: media

value: Proteose medium


title: Ery1_II


title: Mouse: 1RC133; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: FibroblastT45Cntrl 3

description:
Cntrl1
F2_45_4_3
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab


title: high_light

description: total RNA - rRNA

value: high light (400 μmol photons m^−2 s^−1)


title: Mouse: 1RC131; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: BMT696_2145

city: New York

first: Jacob

middle: Lowell

last: Glass

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

library_source: genomic

data_processing:
Casava 1.7 for base calling
Adapter trimming with FAR 2.15
Alignment with Bowtie 0.12.7
Methylation calling with Bismark 0.5.4
Idh2 R140Q alignments were made to mm9, then transferred to mm10 using liftOver. Idh2 R140Q / Dnmt3a R878H alignments were made directly to mm10.
Genome_build: mm10
Supplementary_files_format_and_content: Files are in text format with the following 7 columns: chrBase, chr, base, strand, coverage, freqC, freqT. 'chrBase' is a concatenation of chromosome and base position for easy indexing. 'chr' is the chromosome, 'base' is the base position, 'coverage' ranges from 10-400. 'freqC' is the 'C' frequency representing the % of methylated bases and 'freqT' is the 'T' frequency, representing unmethylated bases.

molecule: genomic DNA

source_name: AML blast cells

growth_protocol: Primary, uncultured cells

extract_protocol: Enhanced reduced representation of bisulfite sequencing (PMC4354670): High molecular weight genomic DNA was digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads

treatment_protocol: The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice.

tag: genotype/variation

value: WT LSK


title: Mouse: 1RC130; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30


title: low_light

description: total RNA - rRNA

value: low light (40 μmol photons m^−2 s^−1)


title: med_light

description: total RNA - rRNA


title: BMT696_2143


title: Mouse: 1RC129; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30

value: pancreatic islets


title: 3h_high_RB

description: total RNA - rRNA

value: Rose Bengal Treatment 5uM 1h dark, 3h light


title: BMT696_2142


title: 4h_dark_anaerobic

description: total RNA - rRNA

value: no light


title: 1h_noS

description: total RNA - rRNA

value: Proteose medium -S


title: IDH_V16

value: Idh2 R140Q


title: Mouse: 1RC128; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30


title: Mouse: 1RC135; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D90


title: IDH_V13


title: 1h_noP

description: total RNA - rRNA

value: Proteose medium -P


title: Mouse: 1RC125; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30


title: glucose

description: total RNA - rRNA

value: Proteose medium + 20mM glucose 72h


title: 1h_noFe

description: total RNA - rRNA

value: Proteose medium -Fe


title: Mouse: 1RC124; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30


title: 2h_H2O2

description: total RNA - rRNA

value: H2O2 1mM 2h


title: 2h Rep 1 total

first: Florian

last: Uhlitz

department: Computational Oncology

data_processing:
Half-life estimates based on ActD-mediated transcriptional shut-down were derived from microarray gene expression time course data (Fig EV1 A in the accompanying publication).
Since quantile normalisation assumes constant total RNA levels across samples (Bar-Joseph et al, 2012, http://doi.org/10.1038/nrg3244), RMA was performed without quantile normalisation for ActD samples.
Samples were instead normalised to median expression of 61 long-lived mRNAs (t1/2 > 16 hours) consistently identified in two published data sets on human mRNA half-life (Friedel et al, 2009, http://doi.org/10.1093/nar/gkp542; Yang et al, 2003, http://doi.org/10.1101/gr.1272403). Both time series were than fitted to an exponential decay function to infer decay rates.
Half-life estimates based on metabolic labelling with 4SU followed by RNA sequencing were calculated using all three fractions of RNA, i.e. total RNA, labelled RNA (eluate) and unlabelled RNA (flow-through). Dynamic transcriptome analysis (DTA) was used for quantification (Miller et al, 2011, http://doi.org/10.1038/msb.2010.112).
Median, mean and standard deviation of half-lives for all expressed genes was calculated from the three different data sets (ActD ON, ActD OFF, 4SU) and are provided as supplementary data (processed data file Table_EV2.tsv).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files containing half-lives for alle expressed genes based on transcriptional shutdown (ActD) or metabolic labelling (4SU).

source_name: HEK293∆RAF1:ER cells

growth_protocol: HEK293∆RAF1:ER cells were cultured in DMEM complete w/o phenol red.

extract_protocol:
Total RNA was extraced with Trizol.
Illumina TruSeq RNA Library Prep Kit v2

treatment_protocol: For RNA labeling, 4SU at a concentration of 200µM was added as indicated. Induction of RAF was done by addition of 0.5µM 4OHT as indicated.

tag: 4su treatment

value: 1h before harvesting

tag: 4oht induction

tag: rna isolation

value: total RNA


title: Mouse: 1RC123; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30

value: Regular Chow (RC)


title: 1h_low_RB

description: total RNA - rRNA

value: med light (100 μmol photons m^−2 s^−1)

value: Rose Bengal Treatment 5uM 0.5h dark, 1h light


title: 0h Rep 2 total

tag: tissue type

value: embryonic kidney

tag: cell line


title: 0h Rep 1 total


title: Mouse: 1RC121; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10

tag: strain


title: IDH_V17


title: HL.12h_repD

description: total RNA - rRNA

data_processing:
alignment with RNA-Star 2.4.0j
FPKM calculation with cuffdiff v2.2.1 with --multi-read-correct --max-bundle-frags 1000000000 --library-type fr-firststrand
Genome_build: not published at time of GEO submission. The fasta file with genome sequence and gff with gene annotation is available on GSE92513.
Supplementary_files_format_and_content: cuffdiff output

growth_protocol:
Chromochloris zofingiensis cells were grown at 25°C in liquid cultures (Proteose medium supplemented with Chu’s micronutrient solution) with shaking at 100–150 rpm under a diurnal light cycle (16 h light, 8 h dark)
in 100 μmol photons m^−2 s^−1 medium light.
Experiments were conducted when cultures were at density ~4.5e6 cells/mL.

treatment_protocol: Transition from medium light (100 μmol photons m^−2 s^−1) to high light (400 μmol photons m^−2 s^−1).

value: high light


title: Mouse: 1RC127; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30

tag: mouse id


title: Mouse: 1RC120; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10

tag: diet


title: 0h Rep 2 flow-through

value: unlabeled RNA (flowthrough)


title: Mouse: 1RC126; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D30

tag: time

value: pancreatic islets


title: IDH_V15


title: HL.12h_repB

description: total RNA - rRNA


title: Mouse: 1RC119; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10

tag: tissue


title: Mouse: 1RC118; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10


title: 2h Rep 2 eluate

value: 2h before harvesting

value: labeled RNA (eluate)


title: 2h Rep 1 eluate


title: HL.12h_repA

description: total RNA - rRNA


title: 1h Rep 1 total


title: Mouse: 1RC116; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: HL.6h_repD

description: total RNA - rRNA


title: HL.6h_repC

description: total RNA - rRNA


title: 1h Rep 2 eluate


title: 1h Rep 1 eluate


title: 48h_dark

description: total RNA - rRNA

value: no light

value: Proteose medium


title: 0h Rep 2 eluate


title: Mouse: 1RC115; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: HL.12h_repC

description: total RNA - rRNA


title: Mouse: 1RC113; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: HL.6h_repB

description: total RNA - rRNA


title: HL.6h_repA

description: total RNA - rRNA


title: 0h Rep 1 eluate


title: HL.3h_repD

description: total RNA - rRNA


title: Mouse: 1RC112; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: HL.3h_repB

description: total RNA - rRNA


title: Mouse: 1RC111; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: Mouse: 1HF162; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90

value: High Fat, High Sugar (HFHS)


title: Mouse: 1RC117; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10


title: Mouse: 1HF161; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: HL.3h_repA

description: total RNA - rRNA


title: HL.1h_repD

description: total RNA - rRNA


title: HL.1h_repC

description: total RNA - rRNA


title: Mouse: 1HF160; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 1HF158; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 1HF159; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: FibroblastT60Exp 1

description:
Exp2
F2_60_3_1
igenomes_known_GENES_counts_normalized.counts.CPM.Fibro.tab
igenomes_known_GENES_counts_Fibro.tab

tag: infection strain

value: V. parahaemolyticus POR3

tag: infection time

value: 60 minutes


title: Mouse: 1HF157; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: HL.1h_repB

description: total RNA - rRNA


title: HL.1h_repA

description: total RNA - rRNA


title: Mouse: 1RC114; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D02


title: HL.0.5h_repC

description: total RNA - rRNA


title: Mouse: 1HF156; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 1HF155; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D90


title: Mouse: 1HF154; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: HL.0.5h_repB

description: total RNA - rRNA


title: Mouse: 1HF153; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: HL.3h_repC

description: total RNA - rRNA


title: ML.12h_repD

description: total RNA - rRNA

value: med light


title: HL.0.5h_repA

description: total RNA - rRNA


title: Mouse: 1HF152; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: ML.12h_repC

description: total RNA - rRNA


title: ML.12h_repA

description: total RNA - rRNA


title: ML.12h_repB

description: total RNA - rRNA


title: Mouse: 1HF150; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 1HF149; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 1HF148; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: ML.6h_repC

description: total RNA - rRNA


title: Mouse: 1HF147; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: Mouse: 1HF151; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D30


title: ML.6h_repB

description: total RNA - rRNA


title: Mouse: 1HF146; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: HL.0.5h_repD

description: total RNA - rRNA


title: ML.6h_repA

description: total RNA - rRNA


title: ML.3h_repC

description: total RNA - rRNA


title: ML.3h_repD

description: total RNA - rRNA


title: Mouse: 1HF145; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 1HF143; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: ML.3h_repB

description: total RNA - rRNA


title: Mouse: 1HF142; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: Mouse: 1HF141; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: ML.1h_repC

description: total RNA - rRNA


title: ML.1h_repD

description: total RNA - rRNA


title: ML.3h_repA

description: total RNA - rRNA


title: Mouse: 1HF140; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: ML.1h_repB

description: total RNA - rRNA


title: Mouse: 1HF139; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: 0h Rep 1 flow-through

value: 1h before harvesting


title: ML.1h_repA

description: total RNA - rRNA


title: ML.6h_repD

description: total RNA - rRNA


title: Mouse: 1HF137; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 1HF136; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 1HF138; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: ML0.5h_repC

description: total RNA - rRNA


title: ML0.5h_repB

description: total RNA - rRNA


title: Mouse: 1HF135; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D02


title: Mouse: 1HF144; Strain: C57Bl/6J; Diet: High Fat, High Sugar (HFHS); Time-point: D10


title: ML0.5h_repA

description: total RNA - rRNA


title: ML.0h_repC

description: total RNA - rRNA


title: ML.0h_repD

description: total RNA - rRNA


title: ML.0h_repB

description: total RNA - rRNA


title: ML.0h_repA

description: total RNA - rRNA


title: 1h_noN

description: total RNA - rRNA

value: Proteose medium -N


title: TPA_H3K4me3_1805

status: Public on Apr 27 2017

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

description: single

data_processing:
H3 ChIP-seq reads were mapped using Bowtie allowing up to 1 mismatch and counting only unique hits, obtaining the following number of mapped 100-bp paired-end reads: 248 million for undifferentiated HL-60/S4 cells, 319 million for RA-treated HL-60/S4, and 338 million reads for TPA-treated HL-60/S4. The average DNA fragments lengths were correspondingly 160 bp, 159 bp and 159 bp, reflecting a very weak chromatin digestion (in a strongly digested chromatin DNA fragments are closer to the 147bp nucleosome DNA length). Mapped reads were processed using NucTools (http://generegulation.info/index.php/nuctools) to generate genome-wide nucleosome occupancy landscapes, extract individual genomic regions and calculate NRL, as described previously. Aggregate nucleosome occupancy profiles around genomic features were calculated using HOMER and visualized using OriginPro 2016 (OriginLab Corporation). For the analysis performed in this manuscripts, we used the corresponding RefSeq definitions of promoters (extended +/-1,000 from TSS), PHANTOM definitions of enhancers, and Dfam definitions of ALU repeats.
Genome_build: hg19
Supplementary_files_format_and_content: bed - standard BED file format
Supplementary_files_format_and_content: nucleosomes*bed - Columns: (1) chromosome, (2) start, (3) end, (4) fragment length

source_name: Immortalized myeloid leukemia cell line

growth_protocol: HL-60/S4 cells were maintained in RPMI 1640 medium, plus 10% fetal calf serum and 1% Pen/Strep/Glutamine.  This cell line is available from ATCC (www.atcc.org, #CRL-3306).  For the current experiments, cells were maintained in duplicate T-75 flasks, each flask containing 30 ml.

extract_protocol:
Harvested cells were centrifuged at 300xg for 5 min, resuspended in PBS and centrifuged again.  The cell pellets were suspended in 20 ml PBS, made 1% HCHO (fresh ampule of 16% HCHO, methanol-free) and incubated 10 min at RT on a rotator.  Fixation was stopped by addition of 2.5 M glycine to a final concentration of 125 mM and incubated 5 min at RT on a rotator.  Fixed cells were centrifuged at 1000xg for 5 min and washed twice in PBS plus 50mM PMSF.  Cell pellets were suspended in 10 ml of ice-cold "swelling buffer" (10 mM KCl, 1 mM MgCl2, 0.1% NP-40, 1 mM DTT, 25 mM Hepes pH 7.8, made 0.5 mM PMSF and containing Roche COMPLETE), incubated 10 on ice, then centrifuged at 1000xg followed by plunging the cell pellets in liquid N2.
The frozen cell pellets were resuspended in MNase (Micrococcal Nuclease) buffer (25 mM KCl, 4 mM MgCl2, 1 mM CaCl2, 50 mM Tris/HCl pH 7.4) and 10 U MNase per 1x106 cells were added. After 15 min, incubation at 37°C MNase was stopped by adding 10x Covaris buffer (100 mM Tris pH 8.0, 2 M NaCl, 10 mM EDTA, 5% N-lauroylsarcosine, 1% Na-deoxycholate, supplemented with protease inhibitors). The samples were sonicated for 15 min with the following parameters with a Covaris S2 system: burst 200, cycle 20%, and intensity 8. Following centrifugation the supernatant was collected and directly used for IP.
After IgG preclearance the sheared chromatin was incubated overnight with protein G magnetic beads (Cell signaling, 9006) and 4 μg of anti-pan H3 (abcam, ab1791), H3K4me1 (abcam, ab8895), H3K9ac (active motif, 39917), H3K9me3 (abcam, ab8898), H3K27ac (abcam, ab4729), H3K36me3 (abcam, ab9050). After washes with 1x Covaris buffer (10 mM Tris–HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5% N-lauroylsarcosine, 0.1% Na–deoxycholate), high-salt-buffer (50 mM HEPES pH 7.9, 500 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na–deoxycholate, 0.1% SDS), lithium buffer (20 mM Tris–HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na–deoxycholate) and 10 mM Tris–HCl, chromatin was eluted from the magnetic beads (elution buffer: 50 mM Tris pH 8.0, 1 mM EDTA, 1% SDS, 50 mM NaHCO3) and the crosslink was reversed overnight. After RNase A and proteinase K digestion, DNA was purified and cloned in a barcoded sequencing library for the Illumina sequencing platform. In brief, after DNA repair and A-addition NEBNext adapters (NEB, E7335) were ligated and digested with the USER enzyme. Barcodes (NEB, E7335) were introduced via PCR with a maximum of 14 cycles by the NEBNext polymerase (NEB, M0541). Size selection for mononucleosomal insert fragments was done with Ampure XP beads (Agencourt, A63880). Each ChIP-seq library was sequenced on the Illumina HiSeq 2000 with 50bp single-end, whereas the H3-chip samples were sequenced with 50 bp paired-ends.

treatment_protocol: Undifferentiated HL-60/S4 cells were seeded at a concentration of 0.83x105.  RA treated cells were seeded at a concentration of 1.67x105, with RA (Sigma-Aldrich R2625) added to 1 µM.  TPA treated cells were seeded at a concentration of 4x105, with TPA (Sigma-Aldrich P1585) added to 16 nM.  After 4 days, approximately 107 were removed from each flask

tag: chip antibody

tag: treatment

value: phorbol ester


title: Mouse: 1RC122; Strain: C57Bl/6J; Diet: Regular Chow (RC); Time-point: D10

value: Regular Chow (RC)


title: RA_H3K4me3_1803

description: single

value: retinoic acid


title: 0_H3K4me3_1803

description: single

value: untreated


title: TPA_H3K9me3_1613

description: single


title: TPA_H3K9ac_1612

description: single


title: TPA_H3K4me1_1610

description: single


title: TPA_H3K36me3_1616

description: single


title: ML0.5h_repD

description: total RNA - rRNA

tag: light level


title: RA_H3K9ac_1604

description: single


title: TPA_H3K27ac_1614

description: single


title: RA_H3K9me3_1605

description: single


title: TPA_1617

description: paired-end


title: RA_H3K36me3_1608

description: single


title: RA_H3K4me1_1602

description: single


title: RA_H3K27ac_1606

description: single


title: RA_1609

description: paired-end


title: 0_H3K9ac_1596

description: single


title: 0_H3K9me3_1597

description: single


title: 0_H3K4me1_1594

description: single


title: 0_H3K36me3_1600

description: single


title: 0_H3K27ac_1598

description: single


title: 0_1601

description: paired-end


title: RH5 DNase rep3

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: DNA (DNase-sensitive regions)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq and DNase-seq peaks were called by MACS2 version 2.1.0.  DNase was run in paired-end mode
The enhancers were identified using ROSE2 pipeline in bamliquidator 1.3
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Chromatin states were learned using ChromeHMM version 1.10
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files for each sample.

source_name: RMS cell line, PAX3-FOXO1, MYCN amp

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and Pen/Strep.

extract_protocol:
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.  DNase DNA purification was performed by column (MiniElute PCR purification kit, Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit) with indicated antibodies.  DNase samples were treated with DNaseI (fresh growing cells, without fixation). DNaseI (Roche 04-716-728-001) was added to the cells (0.25 to 0.5 units) and incubated for 5 minutes at 37 ˚C.  The digestion was halted with 50 µL of stop buffer (9.5 mL H2O + 100 µL 1M TrisHCl pH 7.4 + 20µL 5M NaCl + 200µL 0.5 M EDTA, with 150 µL 10% SDS and 125 µL proteinase K added just before use).  Proteinase K activation at 55 ˚C for 1 hour was followed by DNA purification by column (MiniElute PCR purification kit, Qiagen).

tag: cell type

value: rhabdomyosarcoma

tag: antibody

tag: enrichment target

value: DNase

tag: target function

value: Open Chromatin


title: RH5 DNase rep1

description: DNA (DNase-sensitive regions)


title: RH5 DNase rep2

description: DNA (DNase-sensitive regions)


title: RH4 DNase rep1

description: DNA (ChIP-enriched)

source_name: RMS cell line, PAX3-FOXO1


title: RH4 DNase rep3

description: DNA (ChIP-enriched)


title: RH4 DNase rep2

description: DNA (ChIP-enriched)


title: 7250-empty DNase rep2

description: DNA (DNase sensitive regions)

source_name: Fibroblast cell line, empty vector added

value: fibroblast

value: DNase-sensitivity


title: 7250-PAX3-FOXO1 DNase rep1

description: DNA (DNase sensitive regions)

source_name: Fibroblast cell line, PAX3-FOXO1 vector added


title: 7250-PAX3-FOXO1 DNase rep3

description: DNA (DNase sensitive regions)


title: 7250-empty DNase rep3

description: DNA (DNase sensitive regions)


title: 7250-empty DNase rep1

description: DNA (DNase sensitive regions)


title: RH41 DMSO 6hr rep2 RNA-seq

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using TopHat.
Gene expression values were calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using Cufflinks and the UCSC reference at the gene level.
Differential gene expression was determined using Cuffdiff (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/).
Genome_build: Hg19
Supplementary_files_format_and_content: FPKM files are provided in txt format at the gene-level

extract_protocol:
RNA was extracted from RMS cell lines, RH4 and RH41 treated with DMSO or JQ1 for 6 hours, or inducible shRNA derived RH4 cells, using the RNeasy mini kit (Qiagen).
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Drug was dissolved in DMSO to a stock conentration of 10 mM, and additionally diluted in DMEM to a final concentration of 500 nM (or DMSO of equivilent final volume), exposing cells for 6 hours before extracting RNA.  For shRNA inducible experiments, cells were treated for 48 hours with doxycyclin (100 ng/mL).

tag: treatment time

value: 6 hours

value: DMSO


title: RH41 DMSO 6hr rep1 RNA-seq


title: RH41 JQ1 500nM 6hr RNA-seq

value: JQ1 500 nM


title: 7250-PAX3-FOXO1 RNA-seq


title: SCMC input

description: DNA (genomic input control)

value: SCMC

value: input DNA

value: control


title: Organoids at six month age

city: Cambridge

first: Paola

last: Arlotta

state: MA

address: 7 Divinity Avenue

department: Stem Cell & Regenerative Biology

institute: Harvard University

description: 19 single organoids from 4 different bioreactors at 6 month age

data_processing:
Raw reads from sequencer are converted to Picard-queryname-sorted BAM file
Unmapped BAMs are converted to aligned and tagged BAMs  using h19 genome assembly
Drop-seq JAVA implemented software is used to align and map reads (Drop-seq Core Computational Protocal v1.0.1)
Genome_build: hg19
Supplementary_files_format_and_content: processed data are zipped csv files that contain the digital gene expression matrix of single cells (column) vs. gene (row) of normalized transcript counts.

growth_protocol: Cerebral organoids were generated using a modified version of the protocol published by Lancaster et al., Nat Protoc (2014)

extract_protocol:
Lysis and mRNA capture occurs within nanodroplet.
Nanodroplets are broken and the captured mRNA processed for immediate reverse transcription. The resulting cDNA was amplified, fragmented and further amplified using the Nextera XT DNA library preparation kit.

value: Human pluripotent stem

tag: line


title: RMS238 input

description: DNA (genomic input control)

source_name: RMS primary tumor, PAX3-FOXO1

tag: cell line


title: SCMC H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac (Active Motif, 39133)

value: Active enhancers


title: 7250-empty RNA-seq


title: RH4 MYOD1 super enhancer 4C

description: DNA (Chromatin Conformation Capture Enriched)

data_processing:
Library strategy: 4C-seq
4C reads were checked to confirm they contained the appropriate viewpoint (from bait primer sequence). Reads were discarded if no viewpoint sequence was found, allowing up to one mismatch.
For matched reads, the barcode and viewpoint sequence were trimmed prior to mapping. Processed reads were then aligned (hg19).
Reads mapping to the viewpoint, self-ligated products and 4 kb surrounding the viewpoint were removed (Lupiáñez et al., 2015), and a coverage density map with window size of 1 kb was created. For visualization, this coverage density map was smoothed by taking an average of read count within 5 windows downstream and upstream, and visualized in IGV with normalized reads per million mapped reads.
Genome_build: Hg19
Supplementary_files_format_and_content: bedgraph of processed 4C data

source_name: Fusion Positive RMS cell line

extract_protocol:
DNA was enriched from cut and religated genomic DNA samples using inverse PCR with primers designed using standard protocols developed previously [Splinter, E., de Wit, E., van de Werken, H.J.G., Klous, P., and de Laat, W. (2012). Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation. Methods 58, 221-230.].
Standard Illumina barcodes were introduced during library preparation

treatment_protocol: Briefly, fixed cells were exposed to 4-bp cutter DpnII for the primary restriction enzyme, re-ligated in dilute conditions, followed by reversal of crosslinks and purification.  Csp6I was used to reduce template to sizes amenable to inverse PCR for viewpoint amplification.

tag: 4c viewpoint

value: MYOD1 super enhancer

tag: viewpoint primers for inverse pcr


title: Organoids at three month age

description: 12 organoids pooled into two samples by bioreactor source at 3 month age


title: RMS237 input

description: DNA (genomic input control)

source_name: RMS primary tumor, HRAS


title: RMS238 H3K27ac

description: DNA (ChIP-enriched)


title: RH41 JQ1 5000nM 6hr RNA-seq


title: RMS216 input

description: DNA (genomic input control)

source_name: RMS primary tumor, KRAS, PIK3CA


title: RMS209 H3K27ac

description: DNA (ChIP-enriched)

source_name: RMS primary tumor, PAX3-FOXO1, MYCN amp


title: 7250-PAX3-FOXO1 DNase rep2

description: DNA (DNase sensitive regions)


title: RMS206 input

description: DNA (genomic input control)

source_name: RMS primary tumor, NRAS


title: RMS216 H3K27ac

description: DNA (ChIP-enriched)


title: RMS209 input

description: DNA (genomic input control)


title: RH5 input

description: DNA (genomic input control)


title: RMS008 input

description: DNA (genomic input control)

source_name: RMS primary tumor


title: RMS008 H3K27ac

description: DNA (ChIP-enriched)


title: RH5 H3K27ac

description: DNA (ChIP-enriched)


title: RMS206 H3K27ac

description: DNA (ChIP-enriched)


title: RH4 RAD21 (cohesin)

description: DNA (ChIP-enriched)

value: Rad21, Abcam (cat992 lotGR221348-3 pAb)

value: Cohesin Complex


title: RH4 MYOD1 promoter 4C

value: rhabdomyosarcoma

value: MYOD1 promoter


title: RH4 MYOG

description: DNA (ChIP-enriched)

value: Myogenin (Santa Cruz, cat. #sc-576)

value: MYOG

value: Myogenic Transcription Factor


title: RH4 MYOD1

description: DNA (ChIP-enriched)

value: MYOD1 (Santa Cruz, sc-706)


title: RH4 p300

description: DNA (ChIP-enriched)

value: p300 (Santa Cruz, cat. #sc-585)

value: Acetylated Lysine Writer, Active enhancers


title: RH4 MYCN

description: DNA (ChIP-enriched)

value: MYCN, Santa Cruz (catsc-53993 lot mAb)

value: MYCN

value: General Amplification Transcription Factor


title: RH4 MED1 (mediator)

description: DNA (ChIP-enriched)

value: MED1 (Bethyl, cat. #A300-793A)

value: Chromatin transcriptional coactivator


title: RMS237 H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac (Active Motif, 39133)

value: Active enhancers


title: RNAseq, Ebf2KO rep2

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were aligned to mm9 using STAR pipeline (Dobin et al. 2013). Differentially expressed genes between WT and Ebf2 KO tissue were identified via an exact test using edgeR package (Robinson et al. 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file containing edgeR differential analysis results

source_name: Brown adipose tissue

growth_protocol: Mice were maintained on chow at room temperature

extract_protocol:
Brown adipose tissue was harvested from adult mice. Tissue was homogenized in TRIzol. RNA was isolated using the TRIzol method (Invitrogen) combined with Ambion PureLink RNA purification.
RNA-seq libraries were prepared using Illumina Truseq RNA Sample Preparation Kit.

tag: strain

value: Mixed

tag: genotype

value: Ebf2 KO

tag: age

value: 8 weeks


title: RH4 input rep2

description: DNA (genomic input control)

value: rhabdomyosarcoma

value: input DNA

value: control


title: RNAseq, Ebf2KO rep1


title: RH4 H3K4me3

description: DNA (ChIP-enriched)

value: H3K4me3, Active Motif (cat39159 pAb)

value: Active genes/promoters


title: RH4 H3K4me1

description: DNA (ChIP-enriched)

value: H3K4me1 (Active Motif, cat. #39297)


title: RH4 H3K4me2

description: DNA (ChIP-enriched)

value: H3K4me2, Active Motif (cat39141 lot01008001 pAb)


title: RH4 H3K27me3

description: DNA (ChIP-enriched)

value: H3K27me3, Active Motif (cat39155 pAb)

value: Polycomb Repressed and Heterochromatin


title: RNAseq, WT rep1

value: WT


title: RH4 H3K36me3

description: DNA (ChIP-enriched)

value: H3K36me3, Active Motif (cat61101 pAb)

value: Transcriptional elongation


title: RH4 input rep1

description: DNA (genomic input control)


title: RH4 CTCF rep2

description: DNA (ChIP-enriched)

value: CTCF, EMD Millipore (cat07-729 lot2628833 pAb)

value: CTCF

value: Domain Insulator


title: RH4 H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac, Active Motif (cat39133 pAb)

value: Active enhancers


title: ChIPseq, PPARg Ebf2KO

data_processing:
Reads were aligned to the mouse genome (mm9) using Bowtie. All redundant reads were discarded except for one per genomic position. BigWig files were generated in RPM-normalized scale for genome browser visualization.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files for RPM-scale stack-height profile

extract_protocol:
Interscapular BAT was isolated as described in Harms et al., Genes Dev., 2015. The tissues were minced and crosslinked in 1 % formaldehyde/PBS. To prepare ChIP extracts, crosslinked tissue was suspended in a ChIP buffer containing 20mM Tris, 0.1% SDS, 1% Triton-100, 150 mM NaCl, 1 mM EDTA, and protease inhibitors. Samples were sonicated under conditions optimized for IP efficiency. Extracts were then cleared of insoluble lipid by microfuge centrifugation at full speed followed by transfer to a new tube. IP was performed with indicated antibodies and genomic DNA purified.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. Libraries were multiplexed for sequencing.

value: Mixed

value: Ebf2 Knockout

value: 8 weeks


title: RH4 CTCF rep1

description: DNA (ChIP-enriched)

value: rhabdomyosarcoma


title: RH4 BRD4 rep2

description: DNA (ChIP-enriched)

value: BRD4, Bethyl A301-985A50

value: Acetylated Lysine Reader, Active Enhancers


title: ChIPseq, PPARg WT

value: Wildtype


title: RH4 BRD4 rep1

description: DNA (ChIP-enriched)


title: ChIPseq, Pol2 Ebf2KO

value: Pol II (Santa Cruz sc-899 or sc-9001)


title: ChIPseq, Pol2 WT


title: RD H3K27ac

description: DNA (ChIP-enriched)

source_name: RMS cell line, NRAS

value: RD

value: H3K27ac (Active Motif, 39133)


title: piwi-embKD

city: MONTPELLIER

first: SEVERINE

last: CHAMBEYRON

address: 141, rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: CNRS

description: Manual anion-exchange chromatography (HiTrapQ column) purification

data_processing:
Read mapping on D. melanogaster genome and canonical transposons: Sequenced reads were stripped of the adapter in the 3' end (TGGAATTCTCGGGTGCCAAG) and the retrieved small RNA reads (18-30nt) were mapped on D. melanogaster genome (version dm3) complemented by canonical transposable element (TE) sequences curated by Casey Bergman (available at https://github.com/cbergman). The mapping was done with bowtie2 using mismatch-tolerant parameters (-L 11 -i S,1,0.8 -N 1 --mp 4,2) and allowing up to 10 alignments for a given read (-k 10).
siRNA reads identification: Small RNA reads of 21 nucleotide long which did not map on miRNA, rRNA,snoRNA,tRNA,ncRNA
piRNA candidates identification: Small RNA reads of 23 to 30 nucleotide long which did not map on miRNA, rRNA,snoRNA,tRNA,ncRNA
piRNA candidate mapping on piRNA cluster and TE consensus sequence: To better quantify piRNA candidate origins, secondary mappings were performed on piRNA cluster and TE consensus sequences with bowtie2 using mismatch- and gap-tolerant parameters (-L 6 -i S,1,0.8 -N 1 --mp 4,2 --rdg 5,2 --rfg 5,2) and allowing up to 10 alignments for a given read (-k 10).
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: The processed data files are in .txt format and consist in a file with siRNA reads and another with piRNA reads for each of the five analyzed libraries.

organism: Drosophila melanogaster

source_name: ovaries

growth_protocol: Flies were maintained at 18°C. After appropriate cross, embryos were shifted at 28°C to induce either RNAi against white or piwi proteins. For the piwi-ctrl experiments the embryos were raised at 18°C.

extract_protocol:
Small RNAs (18-30nt) were isolated from ovaries by manual anion exchange chromatography procedure.
Extracted small RNAs were cloned by BGI (China) for white-embKD_rep2 and piwi-embKD_rep2 and by Donnelly sequencing center (Canada) for piwi-ctrl, white-embKD and Piwi-emb-KD after being selected on acrylamide gel between 18 and 30 nucleotides.

tag: embryonic temperature


title: ChIPseq, H3K27ac Ebf2KO

value: H3K27ac (Abcam ab4729)


title: RD input

description: DNA (genomic input control)

value: input DNA

value: control


title: white-embKD


title: piwi-ctrl


title: NS134 input

description: DNA (genomic input control)

source_name: human muscle tissue


title: RNAseq, WT rep2

value: WT


title: Input piwi-embKD_3

data_processing:
Read mapping on D. melanogaster genome and canonical transposons: the 50bp single-end reads were mapped on the Drosophila melanogaster genome (Release 5; dm3) with BWA. DeepTools 2.0 (bamCompare) was used to extend reads to fit average fragment length (--extendReads 200), to filter PCR duplicate (--ignoreDuplicates) and keep high quality mapped reads (and uniquely mapped) (--minMappingQuality 20) to compute the H3K9me3 enrichment with a ratio of depth normalized read (--normalizeUsingRPKM) between IP and Input. The processed data files are listed below.
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: bigWig files

growth_protocol: Flies were maintained at 18°C. After appropriate cross, embryos were shifted at 28°C to induce RNAi against white or piwi proteins.

extract_protocol:
100 dissected ovaries were crosslinked with 1.8% formaldehyde for 10 min, and the prepared chromatin was sonicated. One-third was used for immunoprecipitation by H3K9me3 antibody. After decrosslinking, DNA was extracted and used for library preparation for sequencing. The ChIP-seq experiments were performed in three biological replicates.
Library preparation and 50nt single-read sequencing were performed by Donnelly Sequencing Centre (Toronto) on an Illumina HiSeq2500.


title: H3K9me3 piwi-embKD_3

value: Abcam cat≠ ab8898


title: NS134 H3K27ac

description: DNA (ChIP-enriched)


title: ChIPseq, EBF2 rep1


title: H3K9me3 white-embKD_3


title: NS129 input

description: DNA (genomic input control)


title: Input white-embKD_3


title: piwi-embKD_rep2

description: Ribo-Zero  (Epicenter) ribosomal depletion total RNA further purified using RNA Clean & Concentrator-5 (Zymo Research)

data_processing:
Read mapping on D. melanogaster genome and canonical transposons: For each sample, paired-end raw data was analyzed using the piPipes RNA-Seq pipeline (doi:10.1093/bioinformatics/btu647) with default options. Raw data files ending in *R1_001.fastq.gz correspond to the left reads (option "-l") and those ending in *R2_001.fastq.gz correspond to right reads (option "-r"). Release 5 of D. melanogaster genome was used (option "-g dm3"). Reads are first mapped to rRNA sequences using bowtie2. Reads that do not map at this first step are mapped to the genome using STAR. The mapping results are then processed by cufflinks in order to determine a normalization factor based on reads mapping on genes. The reads are then mapped on the gene and transposon sequences using bowtie2, and the mapping results are processed with express for quantification. Quantification by express is then normalized using the cufflinks-determined gene-mapping read abundance. All these steps were performed by piPipes (commit number cd5f1cfb33e67ddf2926cea7ad57212b17695e27, october 14th 2015).
Genome_build: Drosophila melanogaster, release 5
Supplementary_files_format_and_content: The processed data consist in two tab-separated columns. The first column contains gene and transposon identifiers, and the second column contains the corresponding normalized quantification, as obtained by piPipes.

growth_protocol: Flies were maintained at 18°C. After appropriate cross, embryos were shifted at 28°C to induce either RNAi against white or piwi proteins.

extract_protocol:
Total RNAs were isolated from ovaries using TRIzol. 4µg of total RNA were subjected to Ribo-Zero ribosomal depletion (Epicenter). RNA was further purified using RNA Clean & Concentrator-5 (Zymo Research).
Library construction and 150nt paired-end read sequencing were performed by Donnelly Sequencing Centre (Toronto) on an Illumina NextSeq 500. The RNA-seq experiments were done in two biological replicates.


title: NS129 H3K27ac

description: DNA (ChIP-enriched)


title: white-embKD_rep2


title: Input white-embKD_2


title: NCI0082 input

description: DNA (genomic input control)

source_name: RMS primary tumor, PAX7-FOXO1


title: GDDH18_fruit1_9DAP

city: Beaucouzé

first: Jean-Marc

last: Celton

address: 42 rue Georges Morel

institute: INRA-IRHS

data_processing:
methylation call performed with BSMAP v 2.89
Supplementary_files_format_and_content: BSMAP standard output format

organism: Malus domestica

source_name: Malus domestica 'Golden Delicious' doubled haploid #18

growth_protocol: The GDDH13 and GDDH18 trees were grown in the orchard following common cultural practices

extract_protocol:
Following liquid nitrogen grinding, DNA was purified using the Machery-Nagel NucleoSpin plant II DNA extraction kit
Bisulfite treatment was applied to determine the cytosine methylation status using the Epitect bisulfite kit. Illumina library was then constructed following manufacturer's instructions

treatment_protocol: no treatment was applied

tag: cultivar

value: Golden Delicious

tag: tissue

value: fruits

tag: developmental stage

value: 9 days after pollination


title: GDDH18_fruit2_3DAP

value: 3 days after pollination


title: GDDH18_fruit2_9DAP


title: ChIPseq, H3K27ac WT

value: Mixed

value: 8 weeks


title: white-embKD


title: NCI0082 H3K27ac

description: DNA (ChIP-enriched)

value: rhabdomyosarcoma

value: Active enhancers


title: NCI0075 input

description: DNA (genomic input control)

source_name: RMS primary tumor, TP53


title: BMDMs_ABX464_+LPS_698

city: Montpellier

first: Laurent

last: MANCHON

address: 1919 Route de Mende

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm9 whole genome using bowtie2 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 and HISAT2 with parameters -p 8 --phred64 --sensitive -I 1 -X 1000
Genes expression level is quantified by a software package called RSEM. RSEM is a quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM values for each Sample

extract_protocol:
BMDMs cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestinal epitelium

value: BMDMs; Intestinal macrophage

tag: treated with

tag: stimulated with

value: LPS

tag: time point


title: Input piwi-embKD_1


title: H3K9me3 white-embKD_2

tag: chip antibody


title: GDDH18_fruit1_3DAP


title: GDDH13_fruit2_3DAP

source_name: Malus domestica 'Golden Delicious' doubled haploid #13


title: GDDH13_fruit1_3DAP


title: H3K9me3 piwi-embKD_1


title: Input white-embKD_1


title: NCI0075 H3K27ac

description: DNA (ChIP-enriched)

tag: cell type

tag: antibody

value: H3K27ac (Active Motif, 39133)

tag: enrichment target

tag: target function


title: BMDMs_ABX464_NS_697

value: none (unstimulated)


title: BMDMs_DMSO_+LPS_696

value: DMSO


title: BMDMs_ABX464_+LPS_694


title: CTR H3K27ac

description: DNA (ChIP-enriched)

source_name: RMS cell line, HRAS

tag: cell line

value: CTR


title: 7250-PAX3-FOXO1 P3F

description: DNA (ChIP-enriched)

source_name: Fibroblast cell line, PAX3-FOXO1 vector added

value: fibroblast

value: PAX3-FOXO1 mAb (not commercially available)

value: Fusion Transcription Factor


title: piwi-embKD


title: ChIPseq, EBF2 rep2

value: Wildtype


title: BMDMs_DMSO_NS_695


title: NBB1997-039

first: Shahar

last: Barbash

address: 1230 York Ave

institute: The Rockefeller University

description: Sample 24

data_processing:
Sequence and quality files, in Lifetech proprietary .xsq binary format, were mapped against the GRGCh37/hg19 version of the Homo sapiens genome using the Lifetech Lifescope 2.5.1 whole Transcriptome analysis pipeline. Additional details for read alignment  are provided in the readme.txt.
Tables of read counts per gene were generated from the alignments using the HTSEQ package.
Genome_build: GRGCh37/hg19
Supplementary_files_format_and_content:
Gene_list.txt: List of associated RefSeq gene names corresponding to rows in Sample*.txt files (see below).
Sample*.txt files contain RPKM values of genes for each of the SQUARE matrix fields.  Each field represents a transcript with one of the 12 different ending dinucleotides: 'AC, AG, CA, GT, CT, GA, GC, GG, AA, AT, CC, CG'. Columns correspond to matrix fields, Rows correspond to genes according to Gene_list.txt file, Gene list order is identical to all Sample*.txt files and the first row is the 12 SQUARE ending dinucleotides.
NormMatrix.txt: Scaling factor based on the mean PCR field yield after patient normalization. These values should be used normalize RPKM values per patient per field.

source_name: non-demented with AD-like pathology

extract_protocol:
RNA was extracted with the SPLIT RNA extraction kit (Lexogen GmbH, Vienna, Austria) yielding the large RNA fraction with a lower cut-off size of 150 nt. Evaluation on an Bioanalyzer RNA Nano chip (Agilent Technologies) showed medium to high RNA quality (RIN of 6.2 – 8.3).
Briefly, 4 µg Terminator-treated RNA was full-length reverse transcribed, and 1/20th of the purified cDNA was then amplified in one of 12 parallel PCR reactions. Each PCR reactions was set up with one universal 5’ primer and a 3’ primer selective for one of the 12 possible combinations of the two terminal nucleotides of the mRNA body, immediately upstream of the poly(A) tail. 200 ng of all 288 PCR products (24 RNA samples amplified separately in 12 matrix fields) were heat-fragmented and then ligated to SOLiD-compatible adapters. The libraries were PCR amplified in 17 cycles, with PCR primers indexing each sample with one out of 96 bar-codes. Three lane mixes were created, each from 96 libraries corresponding to 24 samples amplified in 4 matrix fields, dedicating equal molarities to each of the libraries. The three lane mixes SOR04 (selective 3’ primer nucleotides AC, AG, CA, GT), SOR05 (AA, AT, CC, CG) and SOR06 (CT, GA, GC, GG) were then further size-selected on a Pippin Prep automated gel elution system (Sage Biosciences, Beverly, MA, USA) in the range of 170 to 400 bp.

tag: diagnosis

value: non-demented

tag: presents ad pathology

value: yes

value: superior temporalis gyrus


title: NBB1996-125

description: Sample 23


title: 7250-empty P3F

description: DNA (ChIP-enriched)

source_name: Fibroblast cell line, empty vector added


title: NBB2009-096

description: Sample 22


title: NBB2009-075

description: Sample 21


title: BMDMs_DMSO_+LPS_692


title: BMDMs_ABX464_NS_693


title: NBB2005-073

description: Sample 20


title: 7250-PAX3-FOXO1 H3K27ac

description: DNA (ChIP-enriched)

value: H3K27ac, Active Motif (cat39133 lot pAb)


title: 7250-empty H3K27ac

description: DNA (ChIP-enriched)


title: 7250-PAX3-FOXO1 input DNA

description: DNA (genomic input control)

value: input DNA

value: control


title: BMDMs_ABX464_+LPS_678

value: Intestinal epitelium


title: CTR input

description: DNA (genomic input control)

value: rhabdomyosarcoma


title: BMDMs_ABX464_NS_677

value: BMDMs; Intestinal macrophage


title: 7250-empty input DNA

description: DNA (genomic input control)


title: BMDMs_DMSO_NS_675


title: H3K9me3 white-embKD_1

tag: genotype

value: Abcam cat≠ ab8898


title: 7250-PAX3-FOXO1 BRD4

description: DNA (ChIP-enriched)

value: BRD4, Bethyl A301-985A50

value: Acetylated Lysine Reader, Active Enhancers


title: NBB2003-084

description: Sample 18


title: BMDMs_DMSO_+LPS_676

value: DMSO

value: LPS


title: NBB2003-035

description: Sample 16

source_name: non-demented without AD-like pathology (healthy controls)

value: No


title: 7250-empty BRD4

description: DNA (ChIP-enriched)

value: fibroblast


title: NBB2009-039

description: Sample 19


title: RH4 shscramble 48hr RNA-seq

source_name: RMS cell line, PAX3-FOXO1

tag: treatment time

value: 48 hours

tag: treatment

value: doxycyclin inducible scramble control shRNA


title: BMDMs_ABX464_+LPS_674


title: NBB2005-019

description: Sample 17

value: non-demented

value: yes


title: NBB2001-086

description: Sample 15

value: superior temporalis gyrus


title: NBB2009-005

description: Sample 14


title: BMDMs_ABX464_NS_673

value: none (unstimulated)


title: RH4 DMSO 6hr RNA-seq

value: 6 hours


title: NBB2001-021

description: Sample 13

value: inferior temporalis gyrus


title: NBB2005-044

description: Sample 12


title: BMDMs_DMSO_NS_671

value: Intestinal epitelium


title: BMDMs_DMSO_NS_691

value: BMDMs; Intestinal macrophage


title: BMDMs_DMSO_+LPS_672


title: NBB2000-015

description: Sample 11


title: BMDMs_ABX464_+LPS_588


title: BMDMs_ABX464_NS_587


title: NBB2001-016

description: Sample 10


title: BMDMs_DMSO_+LPS_586


title: NBB2002-087

description: Sample 9


title: BMDMs_DMSO_NS_585


title: Mbd3abc KO rep2

city: Worcester

first: Thomas

last: Fazzio

state: Massachusetts

address: 364 Plantation Street

institute: University of Massachusetts Medical School

description:
ABCKO_sig.txt
rRNA-depleted RNA

data_processing:
Reads were mapped to the mouse mm10 genome with TopHat2 (Kim et al., 2013), using parameters --library-type fr-firststrand --segment-length 38. Mapped reads were processed in HOMER (Heinz et al., 2010) using the “analyzeRepeats” command to calculate raw counts and normalized reads per kilobase per million mapped reads (rpkm) for each gene. Differential gene expression was calculated with DESeq2 (Love et al., 2014) using the “getDiffExpression” command in HOMER. Genes with an adjusted p value < 0.05 were considered significantly changed.
Genome_build: mm10
Supplementary_files_format_and_content: UCSC bedgraph files were generated using the "makeUCSCfile" command in HOMER. Tab-delimited text files were generated from genes with adj. p < 0.05 from DESeq2 output files.

source_name: Embryonic stem cells

growth_protocol: Murine ESCs are derived from E14 and cultured on gelatin-coated plates as previously described (Chen et al., 2013). Mbd3ab, Mbd3c, Mbd3abc, and Mbd3cΔN-ab KO ESC lines were generated using the CRISPR/Cas9 system (Cong et al., 2013) to introduce mutations into Mbd3 exon 2 (Mbd3ab KO and Mbd3cΔN−ab KO), intron 2 (Mbd3c KO), or exon 5 (Mbd3abc KO).

extract_protocol:
Total RNA was isolated from 2 biological replicates each of WT, Mbd3ab KO, Mbd3c KO, Mbd3abc KO, and Mbd3cΔN−ab KO ESCs using TRIzol (Life Technologies), and purified with the Zymo RNA Clean and Concentrator kit.
2µg RNA was used for library preparation. RNA was rRNA-depleted (NEB and Clontech) and strand-specific libraries were prepared using the TruSeq Stranded mRNA LT kit (Illumina).

tag: es cell line

value: Mbd3abc -/-


title: Mbd3cΔN-ab KO rep1

description:
ABctr_sig.txt
rRNA-depleted RNA

value: Mbd3cdeltaN; ab-/-


title: NBB2005-010

description: Sample 8

source_name: demented AD patients

value: Alzheimer's disease (AD)

tag: tissue


title: Mbd3cΔN-ab KO rep2

description:
ABctr_sig.txt
rRNA-depleted RNA


title: IM-0223-KPC1_R2

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.
Fold change differences between samples were detected using the GFOLD version 1.1.4 algorithm.
Genome_build: GENCODE release 19 (GRCh37.p13)
Supplementary_files_format_and_content: tab files contain read counts and csv file contains gfold output. Columns for the tab files are as follows: 1) gene id 2) counts for unstranded RNA-seq 3) counts for the 1st read strand aligned with RNA (htseq-count option -s yes) and 4) counts for the 2nd read strand aligned with RNA (htseq-count option -s reverse).

source_name: malignant melanoma_overexpressing KPC1

extract_protocol:
Total RNA was extracted Direct-zol RNA MiniPrep kit (Zymo Research).
mRNA libraries were constructed using Illumina TruSeq RNA Sample Preparation kit v2.

tag: transfected vector


title: IM-0223-KPC1_R1


title: Mbd3c KO rep2

description:
CKO_sig.txt
rRNA-depleted RNA

value: Mbd3c -/-


title: BMDMs_ABX464_NS_583

tag: treated with


title: RH4 shPAX3FOXO1 48hr RNA-seq

value: rhabdomyosarcoma

value: doxycyclin inducible shRNA agaisnt PAX3-FOXO1


title: NBB2010-016

description: Sample 6


title: Mbd3c KO rep1

description:
CKO_sig.txt
rRNA-depleted RNA


title: NBB2001-063

description: Sample 5


title: Mbd3ab KO rep2

description:
ABKO_sig.txt
rRNA-depleted RNA

value: Mbd3ab -/-


title: BMDMs_DMSO_+LPS_582

value: DMSO

tag: stimulated with

value: LPS


title: IM-0223-V0_R1

source_name: malignant melanoma_control

value: Control


title: BMDMs_DMSO_NS_581

tag: time point


title: RH4 JQ1 500nM 6hr RNA-seq

value: JQ1 500 nM


title: IM-0223-V0_R2


title: Mbd3ab KO rep1

description:
ABKO_sig.txt
rRNA-depleted RNA


title: NBB2008-029

description: Sample 3

value: yes

value: superior temporalis gyrus


title: piwi-embKD_rep2

tag: embryonic temperature


title: NBB2001-044

description: Sample 4


title: Mbd3abc KO rep1

description:
ABCKO_sig.txt
rRNA-depleted RNA


title: B4_P3.fastq

first: Sebastian

last: Lourido

address: 455 Main St.

institute: Whitehead Institute

description: FASTQ file obtained from parasites three passages after transfection

data_processing:
Identify sequences in the FASTQ files obtained from Illumina sequencing that correspond exactly to sequences in the designed sgRNA library.
List the occurances of such perfect matches for each sgRNA in the designed library.
Genome_build: ToxoDB GT1 version 28
Supplementary_files_format_and_content: Tab-delimited text files contain the number of occurances of each sgRNA in the designed library.

organism: Toxoplasma gondii

source_name: sgRNAs isolated from T. gondii by PCR

growth_protocol: Parasites were cultured in human foreskin fibroblasts (HFFs) using DMEM containing 3% fetal bovine serum and 10 ug/mL gentamicin.

extract_protocol:
DNA was extracted from parasites using a Dneasy Blood and Tissue kit from Qiagen.
sgRNAs were appended with P5 and P7 Illumina adaptors along with indices that facilitated multiplexing. Primer sequences and other details are available in Sidik, Huet et al (2016) Cell DOI: http://doi.org/10.1016/j.cell.2016.08.019.

treatment_protocol: Parasites were transfected with a library of sgRNAs and cultured for three passages in HFFs before integrated sgRNAs were isolated by PCR.

tag: transfected with

value: a library of sgRNAs

value: 3 passages after transfection


title: NBB2009-107

description: Sample 7


title: NBB2009-040

description: Sample 2


title: E14 WT rep2

description: rRNA-depleted RNA

value: Wild type


title: white-embKD_rep2

source_name: ovaries


title: NBB2007-052

description: Sample 1

value: medial temporalis gyrus


title: BMDMs_ABX464_+LPS_584

value: Intestinal epitelium

tag: cell type

value: BMDMs; Intestinal macrophage


title: Low dose 2hr post vaccine sample 18, subject 5

status: Public on Apr 26 2017

city: York

first: Paul

last: Kaye

address: Wentworth way

institute: University of York

description:
Sample_18 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

data_processing:
Base calling and de-multiplexing was performed by CASAVA version 1.8.2
Adaptor sequences were removed using cutadapt version 1.2.1 using option -O 3
Reads were further trimmed and quality scored using sickle v 1.2 with a q value of 20 and minimum length of 10bp. Unpaired reads were seperated into an R0 file
Reads were trimmed with cutadapt and sickle and mapped to reference using tophat2 version 2.0.10, default parameters except -g 1 option
Read counts were calculated using Htseq-count
Differential gene expression was done using edgeR and using a generalised linear model (GLM)
DE genes were identified using a log2 fold change and likelihood ratios (LR) test in edgeR, significantly expressed genes had a FDR adjusted P value of < 5%
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: text file with read counts and FPKM values

source_name: Whole Blood

growth_protocol: High dose samples were taken from individuals given a dose of 7.5x10e10 vp ChAd63-KH i.m. Low dose samples were given 1x10e10 vp ChAd63-KH i.m

extract_protocol:
Qiagen PAXgene blood miRNA kit
Scriptseq v2 RNAseq library preparation kit, and sequenced on the hiseq 2500 with 2 x125bp paired end  reads with v4 chemistry

treatment_protocol: High dose samples were taken pre vaccination (V2) and 24 hours post vaccination (V3). Low dose samples were taken pre vaccination (T1), 2 hours post vaccination (T2) , 24 hours post vaccination (T3) and 14 days post vaccination (T4)

value: Whole Blood

tag: vaccine dose

value: low

value: 2hr post-vaccine


title: Low dose 2hr post vaccine sample 14, subject 4

description:
Sample_14 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 14 days post vaccine sample 16, subject 4

description:
Sample_16 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

value: 14 days post-vaccine


title: Low dose pre vaccine sample 17, subject 5

description:
Sample_17 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

value: pre-vaccine


title: Sample 7_YJ_r2 MethylC-seq

city: La Jolla

first: Julie

middle: Ann

last: Law

address: 10010 North Torrey Pines Rd

department: PLANT MOLECULAR AND CELLULAR BIOLOGY LABORATORY

institute: The Salk Institute for Biological Studies

data_processing:
Illumina Casava software used for basecalling and demultiplexing.
Read Filtering and Mapping: Illumina sequence reads were filtered to remove duplicate reads either with prinseq [71], using the remove exact duplicates option (-derep 1), or the BSseeker2[72] filterReads.py script, using default conditions.  The reads were then mapped to the YJ or LUCH transgene sequences (LUC_transgene6.fa or LUC_transgene7.fa) using bsmap-2.74 [73] with the default parameters, allowing 2 mismatches (-v 2) and allowing uniquely mapping reads and multi-mapping reads with the maximum number of equal best hits set to 2 (-w 2). In addition, the reads were also mapped to the tair10 genome using the BSseeker2 bs_seeker2-align.py script, using the bowtie1 aligner (version bowtie-1.0.0)[74] and allowing for 2 mismatches (-m 2).
Methylation levels: The percent methylation level at each cytosine was calculated using the BSseeker2 bs_seeker2-call_methylation.py script requiring a minimum coverage of 4 reads (-r 4) for mapping to the Tair10 genome or the bsmap methratio.py script, reporting loci with zero methylation ratios (-z) for the YJ and LUCH transgenes. In house scripts were used to convert the resulting .CGmap or .txt files, respectively, into wiggle files containing the percent methylation levels of cytosines covered by at least 4 reads in the CG, CHG, and CHH contexts individually.
DMR calling: DMRs were identified using parameters outlined in Stroud et al. [54] using in house scripts. Briefly, the genome was split into 100bp, non-overlapping bins and the methylation level across each bin in the CG, CHG, or CHH context was calculated independently using the percent methylation values in the wiggle files. The methylation values in each bin were then compared between two samples to call DMRs with the following requirements: (1) To account for 100bp regions of the genome with low numbers of cytosines and for regions that display lower than average coverage, only bins with at least 4 cytosines in the given context that are covered by at least 4 reads in both samples being compared were included in the DMR analysis.  (2) Only bins with an absolute change in methylation of 0.4, 0.2, and 0.1 for the CG, CHG, and CHH contexts, respectively, and with an adjusted p-value of ≤0.01 were identified as DMRs.
Genome_build: TAIR10; LUC_Transgene6.fa; LUC_Transgene7.fa
Supplementary_files_format_and_content: wiggle (.wig) file, header with Chromosome, and two columns: position, % methylation
Supplementary_files_format_and_content: bed file, which has 3 columns:Chr#, start position, end position

organism: Arabidopsis thaliana

source_name: YJ_r2 MethylC-seq

growth_protocol: Arabidopsis seeds were surface-sterilized and then planted on either half-strength Murashige and Skoog (MS) media supplemented with 8% agar and 1% sucrose or Linsmaier and Skoog (LS) media (Caissen, LSP03) supplemented with 8% agar. Seed were then stratified at 4°C for three days. Plants were grown in a growth incubator at 23°C under either continuous light or short day conditions (8 hrs light, 16 hrs dark). 10-day-old seedlings were used for all of the experiments.

extract_protocol:
For the MethylC-seq libraries corresponding to the “_r2, _r5, and_B” series (Table S4), genomic DNA was extracted using the DNeasy Plant Mini  Kit (Qiagen, Cat# 69104). One microgram of genomic DNA was sonicated into  fragments 150 to 300 bp in length using a Diagenode Bioruptor, followed by purification with the PureLink PCR Purification Kit (Invitrogen, Cat#  K3100-01). For all the remaining MethylC-seq libraries (Table S4), genomic  DNA was extracted from 10-day-old seedlings using the DNeasy Plant Mini Kit  (Qiagen, Cat# 69104). 2 ug of genomic DNA was sonicated into 200 bp fragments using a Covaris S2 Sonicator, followed by purification with Sera-Mag Magnetic SpeedBeads (ThermoScientific, Cat# 65152105050250)."
For the MethylC-seq libraries corresponding to the '_r2, _r5, and_B' series  (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-Repair Kit (Epicentre, Cat# ER0720), and the DNA fragments were purified using the Agencourt AMPure XP-PCR Purification system (Beckman Coulter, Cat# A63880). The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using the Agencourt AMPure XP-PCR Purification system. The methylated adapters in the TruSeq DNA Sample Preparation Kit (Illumina, Cat# FC-121-2001) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using AMPure XP beads, less than 400 ng DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). PfuTurbo Cx Hotstart DNA polymerase (Agilent, Cat# 600414) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 9 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. The resulting libraries were quantified, pooled and sequenced using HiSeq 2000 with the 101-cycle single-end sequencing mode (Illumina). For all the remaining MethylC-seq libraries (Table S4), the sonicated and purified genomic DNA fragments were repaired using the End-It DNA End-It DNA End-Repair Kit (Epicentre, Cat# ER81050), and the DNA fragments were purified using Sera-Mag Magnetic SpeedBeads. The purified DNAs were adenylated at the 3? end using the polymerase activity of Klenow Fragment (3?"5? exo-) (New England Biolabs, Cat# M0212), followed by purification using Sera-Mag Magnetic SpeedBeads. The methylated adapters in the NEXTflex Bisulfite-Seq Barcodes Kit (BIOO Scientific, Cat# 511911) were ligated to the DNA fragments using T4 DNA Ligase (New England Biolabs, Cat# M0202). After purification using Sera-Mag Magnetic SpeedBeads, the DNA was subjected to bisulfite conversion using the MethylCode Bisulfite Conversion Kit (Invitrogen, Cat# MECOV-50). KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit (KAPA Biosystems, Cat# KK2801) and the following PCR conditions were used for amplification: 95°C for 2 minutes; 98°C for 30 seconds; 4 cycles of 98°C for 15 seconds, 60°C for 30 seconds and 72°C for 4 minutes; and 72°C for 10 minutes. After purification using Sera-Mag Magnetic SpeedBeads, the libraries were quantified, pooled and sequenced at single-end 50 base-pair using the Illumina HiSeq 2500 v4 at the Salk NGS Core. Raw sequencing data was de-multiplexed and converted into FASTQ files using CASAVA (v1.8.2)

tag: ecotype

value: Columbia

value: ten-day-old seedlings

tag: genotype/variation


title: Sample 11_Col_B MethylC-seq

source_name: Col_B MethylC-seq

value: wild type (Columbia)


title: Low dose 24hr post vaccine sample 15, subject 4

description:
Sample_15 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

value: 24hr post-vaccine


title: Sample 8_YJ_lil-1_r2 MethylC-seq

source_name: YJ_lil-1_r2 MethylC-seq


title: Low dose pre vaccine sample 13, subject 4

description:
Sample_13 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 24hr post vaccine sample 11, subject 3

description:
Sample_11 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose pre vaccine sample 9, subject 3

description:
Sample_9 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 2hr post vaccine sample 10, subject 3

description:
Sample_10 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose pre vaccine sample 5, subject 2

description:
Sample_5 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 2hr post vaccine sample 6, subject 2

description:
Sample_6 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 24hr post vaccine sample 7, subject 2

description:
Sample_7 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 14 days post vaccine sample 4, subject 1

description:
Sample_4 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 14 days post vaccine sample 8, subject 2

description:
Sample_8 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: E14 WT rep1

description: rRNA-depleted RNA


title: B4_L.fastq

description: FASTQ file obtained from an sgRNA input library

source_name: sgRNA input library

tag: sample type

value: sgRNA input library


title: Low dose 24hr post vaccine sample 3, subject 1

description:
Sample_3 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose pre vaccine sample 1, subject 1

description:
Sample_1 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 30, trial number 32

description:
Sample_30-leish032_v3
Sample_30-leish032_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT

value: high

value: post-vaccine


title: Low dose 14 days post vaccine sample 20, subject 5

description:
Sample_20 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 24hr post vaccine sample 19, subject 5

description:
Sample_19 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 26, trial number 27

description:
Sample_26-leish027_v3
Sample_26-leish027_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 27, trial number 28

description:
Sample_27-leish028_v2
Sample_27-leish028_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 28, trial number 28

description:
Sample_28-leish028_v3
Sample_28-leish028_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 24, trial number 26

description:
Sample_24-leish026_v3
Sample_24-leish026_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 25, trial number 27

description:
Sample_25-leish027_v2
Sample_25-leish027_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 22, trial number 24

description:
Sample_22-leish_024_v3
Sample_22-leish_024_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 17, trial number 22

description:
Sample_17-leish_022_v2
Sample_17-leish_022_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 20, trial number 23

description:
Sample_20-leish_023_v3
Sample_20-leish_023_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 14 days post vaccine sample 12, subject 3

description:
Sample_12 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 23, trial number 26

description:
Sample_23-leish026_v2
Sample_23-leish026_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 18, trial number 22

description:
Sample_18-leish_022_v3
Sample_18-leish_022_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 16, trial number 21

description:
Sample_16-leish_021_v3
Sample_16-leish_021_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 19, trial number 23

description:
Sample_19-leish_023_v2
Sample_19-leish_023_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 14, trial number 19

description:
Sample_14-leish_019_v3
Sample_14-leish_019_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 15, trial number 21

description:
Sample_15-leish_021_v2
Sample_15-leish_021_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 13, trial number 19

description:
Sample_13-leish_019_v2
Sample_13-leish_019_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 10, trial number 17

description:
Sample_10-leish_017_v3
Sample_10-leish_017_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 9, trial number 17

description:
Sample_9-leish_017_v2
Sample_9-leish_017_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: Low dose 2hr post vaccine sample 2, subject 1

description:
Sample_2 File name in L_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 12, trial number 18

description:
Sample_12-leish_018_v3
Sample_12-leish_018_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 11, trial number 18

description:
Sample_11-leish_018_v2
Sample_11-leish_018_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 29, trial number 32

description:
Sample_29-leish032_v2
Sample_29-leish032_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 7, trial number 16

description:
Sample_7-leish_016_v2
Sample_7-leish_016_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 6, trial number 15

description:
Sample_6-leish_015_v3
Sample_6-leish_015_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 8, trial number 16

description:
Sample_8-leish_016_v3
Sample_8-leish_016_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 5, trial number 15

description:
Sample_5-leish_015_v2
Sample_5-leish_015_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 4, trial number 12

description:
Sample_4-leish_012_v3
Sample_4-leish_012_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose post vaccine sample 2, trial number 11

description:
Sample_2-leish_011_v3
Sample_2-leish_011_v3 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 3, trial number 12

description:
Sample_3-leish_012_v2
Sample_3-leish_012_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: High dose pre vaccine sample 1, trial number 11

description:
Sample_1-Leish_011_v2
Sample_1-Leish_011_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: IL2RA high_rep2

middle: Ellery

last: Corn

address: 2151 Berkeley Way

department: Innovative Genomics Institute

institute: University of California, Berkeley

data_processing:
Basecalls were performed with Bcl2Fastq version 2.17
Reads failing CASAVA quality filters were excluded.
Reads were then trimmed of the gRNA common sequence using the cutadapt script and the command “cutadapt -a GTTTAAGAGCTAAGCTG”. Ref: Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).
Reads were then aligned against a database of gRNA sequences containing the gRNA name and the gRNA sequence appended with a 5' G.
Alignment was performed using bowtie2-2.2.6 with options -U --norc --no-hd and requiring full length alignment.
gRNA counts were generated by counting the number of times the guide id occurred in the aligned sam file
sgRNAs with fewer than 50 reads in either of the background samples were removed from all downstream analysis
Read counts for each sgRNA in each sample were then normalized to the total number of sgRNA read counts in that sample. A pseudo-count of 1 was added to all normalized guide counts.
sgRNA enrichment was calculated as follows: mean(log2(gene_gate_rep1/gene_background_rep1),log2(gene_gate_rep2/gene_background_rep2)), e.g. mean(log2(CD69_top_rep1/CD69_background_rep1),log2(CD69_top_rep2/CD69_background_rep2))
All non-targeting control sgRNAs and any sgRNAs that map perfectly to multiple sequences within the sgRNA library window were excluded from visualization.
Genome_build: hg19
Supplementary_files_format_and_content: Individual sgRNA enrichment was visualized in .bedgraph format, plotting the log2-fold enrichment (as indicated above) for each sgRNA. The genomic coordinate used for an individual sgRNA is the 3' end of the PAM for that sgRNA.
Supplementary_files_format_and_content: Windowed sgRNA enrichmend was also visualized in .bedgraph format. The average log2-fold enrichment, and the average genomic coordinate, were calculated for a 5-sgRNA sliding window.

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI 1640 media supplemented with 10% fetal calf serum, 1 mM Sodium Pyruvate (Gibco), 100 U/mL penicillin (Gibco) and 100 μg/mL streptomycin (Gibco). Cell line identity was authenticated by short tandem repeat (STR) analysis and verified mycoplasma free using the MycoAlert Mycoplasma Detection Kit (Lonza). Jurkat cells were passaged every 2-3 days and maintained at 0.1-2.0x10^6 cells/mL of media. Jurkat cells were transduced with a lentiviral dCas9-VP64-2A-GFP expression vector (Addgene 61422). Single GFP+ cells were sorted by FACS into the wells of a 96-well plate, and a clone with bright uniform GFP expression were selected for use in these experiments.

extract_protocol:
Genomic DNA was isolated from sorted cells using NucleoSpin Blood kits (Macherey-Nagel), or by Proteinase K digestion and isopropanol precipitation for samples with fewer than 106 cells.
PCR was used to amplify sgRNA cassettes with Illumina sequencing adapters and indexes as described in Kampmann, et al (Nature Protocol, 9, 1825-1847 (2014). Genomic DNA samples containing less than 10 μg of gDNA were loaded directly into PCR. For genomic DNA samples containing more than 10 μg of DNA, samples were first digested for 18 hours with SbfI-HF (NEB) to liberate a ~500 bp fragment containing the gRNA cassette. The amplified sgRNA cassette was isolated by gel electrophoresis as described in Kampmann, et al., and the isolated DNA was then used for PCR. Briefly, DNA was amplified using Phusion polymerase (NEB) for 23-28 cycles. The custom 5’ PCR primer used for each sample is listed in the sample information section. The custom 3’ PCR primer was caagcagaagacggcatacgacgactcggtgccactttttc, The thermocycling protocol was 98 °C, 30”, followed by 23-28 cycles of 98 °C, 15”, 56 °C, 15”, 72 °C, 15”. Indexed samples were pooled and sequenced on an Illumina HiSeq-2500 with the custom sequencing primer 5’-gtgtgttttgagactataagtatcccttggagaaccaccttgttg-3’. Sequencing libraries were pooled proportional to the number of sorted cells in each sample. The target sequencing depth was 2,000 reads/gRNA in the library for unsorted “background” samples, and 10 reads/cell in sorted samples.
PCR amplicon sequencing.

treatment_protocol: Jurkat cells stably expressing dCas9-VP64 were transduced with the lentiviral sgRNA library. Transduction was performed at a low multiplicity of infection to ensure that only one gRNA was present per cell. Cells were selected in media containing 1.5 μg/mL puromycin for days 2-5 post-infection to remove uninfected cells. After selection, cells were grown in fresh media without puromycin. The number of initially infected cells was at least 500x the number of sgRNAs in the library, and at least this many cells were maintained throughout the course of the experiment. 7-10 days post-infection cells were sorted based on IL2RA/CD25 or CD69 expression. Briefly, cells were resuspended in sterile sort buffer (PBS + 2% FBS) containing either CD25-PE or CD69-PE antibody at a 1:25 dilution. Cells were stained for 30 minutes on ice, washed twice with sort buffer, and passed through a 70 μm mesh. Cells were sorted into 4 bins based on IL2RA/CD25 or CD69 expression using a BD Influx cell sorter. The total number of cells collected was at least 500x the number of sgRNAs in the library. Additional unsorted cells totaling 500x the number of sgRNAs in the library were collected at this time. Duplicate infections and sorts were performed for each library. Collected cells were centrifuged at 500 xg for 5 minutes, and cell pellets were stored at -80 °C until genomic DNA was isolated.

value: Jurkat E6-1

tag: sgrna library

value: IL2RA sgRNA library

value: Sorted IL2RA-high

tag: custom 5' pcr primer

tag: illumina truseq index number

tag: illumina truseq index sequence

value: TAGCTT


title: High dose pre vaccine sample 21, trial number 24

description:
Sample_21-leish_024_v2
Sample_21-leish_024_v2 File name in H_DE_genes_count.txt
Illumina universal adaptor used AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT


title: IL2RA low_rep2

tag: treatment

value: Sorted IL2RA-low

value: GCCAAT