title: P0_14

description: Pregnancy, Day 0


title: BCR/ABL+IM+DFC+BCI 2

status: Public on Mar 20 2017

type: SRA

city: Cincinnati

first: Mohammad

last: Azam

state: OH

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

country: USA

institute: Cincinnati Childrens Hospital and Medical Center

library_source: transcriptomic

data_processing:
RNA-Seq analysis is based on the TopHat/Cufflinks pipeline.  First, sequences were aligned to the reference genome with TopHat, which efficiently aligns reads spanning known or novel splice junctions.  Each sample is then independently processed with Cufflinks2 in order to generate an initial transcriptome.  We then used the Cuffmerge tool to merge the private transcriptomes into a single reference, and at the same time annotate known genes and extend partial transcripts.  This common transcriptome was then  used in a second pass with Cufflinks, which  quantified each transcript and gene (known or novel) in each sample.  The reference annotation used is based on the UCSC knownGenes table and includes the long non-coding RNAs.
Genome_build: mm10
Supplementary_files_format_and_content: abundance

molecule: total RNA

organism: Mus musculus

source_name: Kit+ Bone marrow cells

growth_protocol: Kit+ cells from the bonemarrow of WT and ROSACreERT2c-Fosfl/fl /Dusp1-/- mice were isolated using the CD117 MicroBead Kit (Miltenyi biotec) according to their instructions. These cells were incubated overnight in IMDM media supplemented with 10% FBS and cytokine cocktail of FLT3, IL-6, IL-3, and mSCF.

extract_protocol:
Total RNA was isolated using miRNA easy Mini Kit according to the manufacturers protocol. (Qiagen)
TruSeq Stranded mRNA library preparation method.  The protocol was followed as per the manufacturer.

treatment_protocol: After 12 hours of stimulation cells were transduced with BCR/ABL-IRES-YFP virus using retronectin (Takara). One to two million positive cells (isolated by FACS) from each group was treated for four hours with imatinib alone, DFC+BCI, and imatinib+DFC+BCI (3 mM of Imatinib, 0.2 mM of DFC and 0.5 mM of BCI alone or in combinations in duplicates).

tag: cell type

value: Kit+ Bone marrow cells

tag: strain


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 37

city: Groningen

first: Floris

last: Foijer

address: Antonius Deusinglaan 1

department: European Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

library_source: genomic

data_processing:
Basecalling was done with bcl2fastq v1.8.2
Reads were mapped with bowtie2 v2.1.0
PCR duplicates were marked with BAMUtil v.1.0.3
Sortind and indexing of BAM files was done with Samtools v0.1.18
BAM files were analysed using BAIT v1.0 (Hills et al., 2013 - Genome Medicine 5(9):82)
Chromosome copy numbers were determined per cell library using the BAIT read outs, manually curated based on read counts per megabase, and plotted in Excel
Genome_build: mm10
Supplementary_files_format_and_content: Excel files contain the individual cell IDs and chromosome copy number counts as determined through manual curating of BAIT read outs

molecule: genomic DNA

source_name: thymus

growth_protocol: Mad 2f/f; p53 f/f mice were crossed with Lck-Cre+ mice to generate Mad2 f/f; p53 f/f; Lck-Cre+ mice.

extract_protocol:
Tumours were harvested from mice displaying T-ALL (enlarged thymus and peripheral lymph nodes) and were then homogenized using scalpels and cell strainers. Upon sorting, cells were incubated in a PI/Hoechst staining butter with NP-40 to dissociate the cytoplasm. Single cell nuclei were then sorted into a 96-well plate and stored at -80°C in freezing medium until library preperation.
Genomic DNA was digested using Mnase to 150 bp fragments. Subsequent end-repair, A-tailing and adapter ligation were peformed, followed by a nested indexed PCR.
Whole genome seq

treatment_protocol: Experimental mice were monitored for 3-4 months and sacrificed upon signs of dyspnea

tag: genotype/variation

value: Mad2 wt; p53 wt; Lck-Cre-

tag: tissue

value: thymus

value: T-cell


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 33


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 34


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 35


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 31


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 28


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 26


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 29


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 25


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 32


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 24


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 27


title: BCR/ABL+IM 2


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 23


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 22


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 19


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 17


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 13


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 18


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 16


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 20


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 10


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 21


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 30


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 8


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 12


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 14


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 5


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 6


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 4


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 11


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 7


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 3


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 1


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 45

source_name: T-ALL

value: Mad2 f/f; p53 f/f; Lck-Cre+

value: T-cell acute lymphoblastic lymphomas (T-ALL)


title: Mad2 wt; p53 wt; Lck-Cre- Thymus 10 Cell control


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 2


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 0 Cell control


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 46


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 44


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 15


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 43


title: Mad2 wt; p53 wt; Lck-Cre- Thymus Cell 9


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 41


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 39


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 32


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 35


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 37


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 30


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 33


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 38


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 28


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 24


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 27


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 25


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 23


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 26


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 40


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 20


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 29


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 16


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 19


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 42


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 18


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 17


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 15


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 34


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 21


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 36


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 14


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 13


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 31


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 11


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 10


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 8


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 9


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 7


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 2


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 4


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 3


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 5


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 6


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 10 Cell control

description: Mad2_p53_Lck-Cre_T-ALL_2_10-cell_control


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 22


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 1


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 0 Cell control


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 46


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 45


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 42


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 44


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 40


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #2 Cell 12


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 39


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 37


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 36


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 38


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 35


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 34


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 33


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 32


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 30


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 28


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 26


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 22


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 23


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 24


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 31


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 43


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 29


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 41


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 19


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 16


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 21


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 25


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 15


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 14


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 17


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 20


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 13


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 12


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 9


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 18


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 11


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 10


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 7


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 6


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 27


title: AML 12 ChIP H3K9me2 exp. 1

city: Cambridge

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0.
Domains were called using the RSEG software version 0.4.8 RC with the provided deadzone file “deadzones-k41-hg19.bed” and the following parameters: -s 10000 -i 20 -duplicates.  The chrX and chrY mapped sequences of the male samples were duplicated prior to calling RSEG.
To comply with Penn State's IRB, sequence reads had individual SNPs eliminated based on hg19.
Genome_build: hg19
Supplementary_files_format_and_content: bed files contain domains output by RSEG

organism: Homo sapiens

source_name: AML blast cells from blood

growth_protocol: Normal polymorphonuclear granulocytes (predominantly neutrophils) were isolated from discarded fresh white blood cells (buffy coats) from unidentified healthy donors using standard OptiPrep density centrifugation, resuspended in PBS buffer and fixed with 1% formaldehyde. Cryopreserved CD34+ bone marrow hematopoietic progenitors were obtained from Allcells, Emeryville, Ca. Cryopreserved AML cellswere  isolated from bone-marrow samples by Ficoll-Pacque density gradient centrifugation. The cryopreserved samples  were thawed, resuspended in PBS, and fixed with 1% formaldehyde immediately after thawing. The human samples were collected and analyzed under Penn State Hershey IRB protocols  2000-186,  HY03-136EP-A, and STUDY00002518.   Cultured cells K562 (ATCC CCL-243) were  grown in suspension as recommended by ATCC, washed  with PBS and fixed with 1% formaldehyde.

extract_protocol:
cells were fixed with 1% formaldehyde for 10 min. After fixation, nuclei were isolated, the nuclear DNA was digested by micrococcal nuclease to 150-200 bp DNA fragments,  the DNA fragments with attached proteins were resuspended in SDS-containing lysis buffer, and immunoprecipitated by antibodies against various histone modifications.
For Illumina Hi-Seq 2500 sequencing we used New England BioLabs NEBNext ChIP-Seq library preparation reagent set for Illumina and and constructed library as described in the E6240 instruction manual.  For  SOLiD  sequencing we used Applied Biosystems SOLiD 4 System and constructed library as described in the SOLiD 4 System Library Preparation Guide.

treatment_protocol: Some K562 samples (K562-UNC0638) were grown for 5 days with 0.5 micromole UNC0638, a specific  inhibitor of histone methyltransferase G9a, before isolation.

tag: sample id

value: AML 12

tag: gender

value: female

tag: chip antibody

value: H3K9me2 (ab1220 Abcam)


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 3


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 4


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 2


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 10 Cell control

description: Mad2_p53_Lck-Cre_T-ALL_1_10-cell_control


title: CTL rep 3

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

data_processing:
Reads were trimmed to 40 bases and mapped to the hg18 genome with bowtie (0.12.7) with setting --best --m 1 --v 2.
Counts per gene were calculated by counting reads mapping to constitutive exons using Htseq
counts for each gene were then analyzed with the R package DESeq (1.0.6) to identify differentially expressed genes with a single comparison of HD versus non-disease. A 10% false discovery rate cutoff and log2 difference of 0.5 between wild-type and HD conditions was used for significance. Outliers were further excluded by restricting the residual variance quotients to less than 10.
Counts were also used to calculate ‘reads per kilobase of exon per million mapped reads’ (RPKM) values for each gene. Data are shown in RPKMs.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files with RPKM abundance measurements

source_name: iPSC-derived neural cells

extract_protocol:
RNA was isolated from cell pellets with a Qiagen RNeasy Kit with QIAshredder homogenization. RNA-Seq libraries were made with 1µg of RNA using the Illumina Tru-Seq v2 protocol. Libraries were sequenced on one lane of the Hi-Seq 2000 at 50 bases.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iPSC-derived neural cells

tag: genotype

value: control


title: HD rep 3

value: Huntington's disease


title: HD rep 4


title: CTL rep 2


title: CTL rep 1


title: HD rep 2


title: HD rep 1


title: H3K4me3_Ctrl

data_processing:
Sequences were aligned to the hg19 genome from UCSC using Bowtie with an m parameter of 1.
Reads were corrected for over-dispersion using FIXSEQ with default parameters
To call peaks, MACS was run on each cell line sample individually, with an mfold parameter of 10, 30, and p value threshold of 1e-5.
As MACS results for individual lines were very similar, sequences for all HD cell lines were combined as were all non-disease cell line for each histone mark. MACS was run on these samples against a uniform background, with the same parameters
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are bigWig files containing the results of MACS called with the --wig option, performed on the concatenated samples for each genotype

extract_protocol:
Cells were cross-linked with 1% (vol/vol) formaldehyde for 10 min, and the cross-linking was quenched by 0.125 M final concentration glycine. The cross-linked tissue was then homogenized, and rinsed with PBS, and frozen in liquid nitrogen. Later, Crosslinked tissues were fragmented to the size range of 100–500 bp using a Bioruptor (Bioruptor Next Gen; Diagenode). Antibodies for each mark were incubated with beads for 6 h before incubating with sonicated chromatin overnight.
Resulting immunoprecipitated DNA was prepared for high-throughput sequencing using a library preparation kit from Beckman Coulter (catalog #A88267). Libraries were sequenced on an Illumina platform following the manufacturer’s standard protocol.

value: H3K4me3 (Millipore cat #17-614)


title: H3K36me3_Ctrl

value: H3K36me3 (Abcam cat #ab9050)


title: H3K36me3_HD


title: H3K4me3_HD


title: H3K27ac_Ctrl

value: H3K27ac (Abcam cat #ab4729)


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 8


title: PBI104: phr1phl1_HighP_SynCom_expE-rep2

city: Piracicaba

first: Paulo

last: Teixeira

state: SP

address: Av. Pádua Dias, 11

department: Biology

country: Brazil

institute: University of São Paulo (ESALQ/USP)

data_processing:
Illumina Casava version 1.8 was used for basecalling
Quality assessment of the sequencing reads was performed using the FASTX-Toolkit version 0.0.13.2
cutadapt version 1.3 was used to identify and discard reads containing Illumina adapter sequences
Quality-filtered reads were mapped to the Arabidopsis thaliana TAIR10 genome using Tophat version 2.1.1 with parameters set to allow only one mismatch (-N 1)
The Python package HTSeq version 0.6.1p1 was used to count reads that mapped to each one of the 27,206 nuclear protein-coding genes
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text file including read counts per gene for each sample

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Arabidopsis seedlings were grown on Johnson medium and solidified with 1 % bacto-agar. Media were supplemented with Pi (KH2PO4) at distinct concentrations; 625 µM Pi was used for complete medium (+Pi) and 50 µM Pi was used in the Low Pi medium (-Pi). Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night).

extract_protocol:
Total RNA was extracted from Arabidopsis seedlings according to Logemann, J. et al. Anal. Biochem. 163, 16–20 (1987). PMID: 2441623.
poly(A) RNA was isolated from 1000 ng total RNA and used to prepare non-stranded Illumina RNA-seq libraries. Following library preparation, quality control and quantification were performed using a 2100 Bioanalyzer instrument (Agilent) and the Quant-iT PicoGreen dsDNA Reagent (Invitrogen), respectively.

treatment_protocol: Arabidopsis plants were germinated on Johnson medium (0.5 % sucrose) containing 1 mM Pi for 7 days in the vertical position and then transferred to 625 µM Pi (high) and 50 µM Pi (low) media (without sucrose) in the presence or not of a bacterial synthetic community at 105 c.f.u / mL. Plants were grown for another 12 days before harvesting

value: whole seedling

value: phr1 phl1

tag: phosphate availability

value: High (+Pi)

tag: bacteria presence

value: SynCom


title: PBI101: phr1_HighP_SynCom_expE-rep1


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 5


title: PBI102: phr1_HighP_SynCom_expE-rep2


title: PBI098: phr1phl1_LowP_SynCom_expE-rep2

value: Low (-Pi)


title: PBI103: phr1phl1_HighP_SynCom_expE-rep1


title: PBI099: Col-0_HighP_SynCom_expE-rep1


title: PBI096: phr1_LowP_SynCom_expE-rep2


title: PBI095: phr1_LowP_SynCom_expE-rep1


title: Mad2 f/f; p53 f/f; Lck-Cre+ T-ALL #1 Cell 1

value: T-cell


title: PBI097: phr1phl1_LowP_SynCom_expE-rep1


title: PBI092: phr1phl1_HighP_noBact_expE-rep2

value: noBact


title: PBI093: Col-0_LowP_SynCom_expE-rep1


title: PBI091: phr1phl1_HighP_noBact_expE-rep1


title: PBI094: Col-0_LowP_SynCom_expE-rep2


title: H3K27ac_HD


title: PBI090: phr1_HighP_noBact_expE-rep2


title: PBI085: phr1phl1_LowP_noBact_expE-rep1


title: PBI088: Col-0_HighP_noBact_expE-rep2


title: PBI087: Col-0_HighP_noBact_expE-rep1


title: PBI084: phr1_LowP_noBact_expE-rep2


title: PBI086: phr1phl1_LowP_noBact_expE-rep2


title: PBI080: phr1phl1_LowP_SynCom_expD-rep2


title: PBI089: phr1_HighP_noBact_expE-rep1


title: PBI083: phr1_LowP_noBact_expE-rep1


title: PBI081: Col-0_LowP_noBact_expE-rep1


title: PBI100: Col-0_HighP_SynCom_expE-rep2


title: PBI079: phr1_LowP_SynCom_expD-rep2


title: PBI082: Col-0_LowP_noBact_expE-rep2


title: PBI078: Col-0_LowP_SynCom_expD-rep2


title: PBI076: phr1_LowP_SynCom_expD-rep1


title: PBI074: phr1phl1_HighP_SynCom_expD-rep2


title: PBI077: phr1phl1_LowP_SynCom_expD-rep1


title: PBI071: phr1phl1_HighP_SynCom_expD-rep1


title: PBI073: phr1_HighP_SynCom_expD-rep2


title: PBI072: Col-0_HighP_SynCom_expD-rep2


title: PBI069: Col-0_HighP_SynCom_expD-rep1


title: PBI066: Col-0_LowP_noBact_expD-rep2


title: PBI070: phr1_HighP_SynCom_expD-rep1


title: PBI075: Col-0_LowP_SynCom_expD-rep1


title: PBI068: phr1phl1_LowP_noBact_expD-rep2


title: PBI063: Col-0_LowP_noBact_expD-rep1


title: PBI065: phr1phl1_LowP_noBact_expD-rep1


title: PBI067: phr1_LowP_noBact_expD-rep2


title: PBI064: phr1_LowP_noBact_expD-rep1


title: PBI062: phr1phl1_HighP_noBact_expD-rep2


title: PBI061: phr1_HighP_noBact_expD-rep2


title: PBI055: phr1_LowP_SynCom_expC-rep2


title: PBI054: Col-0_LowP_SynCom_expC-rep2


title: PBI057: Col-0_HighP_noBact_expD-rep1


title: PBI050: phr1phl1_HighP_SynCom_expC-rep2


title: PBI052: phr1_LowP_SynCom_expC-rep1


title: PBI060: Col-0_HighP_noBact_expD-rep2


title: PBI056: phr1phl1_LowP_SynCom_expC-rep2


title: PBI053: phr1phl1_LowP_SynCom_expC-rep1


title: PBI051: Col-0_LowP_SynCom_expC-rep1


title: PBI046: phr1_HighP_SynCom_expC-rep1


title: PBI047: phr1phl1_HighP_SynCom_expC-rep1


title: PBI045: Col-0_HighP_SynCom_expC-rep1


title: PBI048: Col-0_HighP_SynCom_expC-rep2


title: PBI042: Col-0_LowP_noBact_expC-rep2


title: PBI040: phr1_LowP_noBact_expC-rep1


title: PBI039: Col-0_LowP_noBact_expC-rep1


title: PBI038: phr1phl1_HighP_noBact_expC-rep2


title: PBI044: phr1phl1_LowP_noBact_expC-rep2


title: PBI037: phr1_HighP_noBact_expC-rep2


title: PBI041: phr1phl1_LowP_noBact_expC-rep1


title: PBI035: phr1phl1_HighP_noBact_expC-rep1


title: PBI036: Col-0_HighP_noBact_expC-rep2


title: PBI034: phr1_HighP_noBact_expC-rep1


title: PBI033: Col-0_HighP_noBact_expC-rep1


title: PBI058: phr1_HighP_noBact_expD-rep1


title: PBI059: phr1phl1_HighP_noBact_expD-rep1


title: PBI032: phr1_HighP_SynCom_expB-rep2


title: PBI049: phr1_HighP_SynCom_expC-rep2


title: PBI031: Col-0_HighP_SynCom_expB-rep2


title: PBI027: Col-0_HighP_noBact_expB-rep2


title: PBI030: phr1_HighP_SynCom_expB-rep1


title: PBI023: Col-0_LowP_noBact_expB-rep2


title: PBI029: Col-0_HighP_SynCom_expB-rep1


title: PBI028: phr1_HighP_noBact_expB-rep2


title: PBI022: phr1_LowP_noBact_expB-rep1


title: PBI024: phr1_LowP_noBact_expB-rep2


title: PBI021: Col-0_LowP_noBact_expB-rep1


title: PBI026: phr1_HighP_noBact_expB-rep1


title: PBI019: Col-0_LowP_SynCom_expB-rep2


title: PBI020: phr1_LowP_SynCom_expB-rep2


title: PBI043: phr1_LowP_noBact_expC-rep2


title: PBI017: Col-0_LowP_SynCom_expB-rep1


title: PBI015: Col-0_LowP_SynCom_expA-rep2


title: PBI018: phr1_LowP_SynCom_expB-rep1


title: PBI014: phr1_LowP_SynCom_expA-rep1


title: PBI008: phr1_LowP_noBact_expA-rep2


title: PBI012: phr1_HighP_SynCom_expA-rep2


title: PBI011: Col-0_HighP_SynCom_expA-rep2


title: PBI009: Col-0_HighP_SynCom_expA-rep1


title: PBI005: Col-0_LowP_noBact_expA-rep1


title: PBI006: phr1_LowP_noBact_expA-rep1


title: PBI004: phr1_HighP_noBact_expA-rep2


title: PBI003: Col-0_HighP_noBact_expA-rep2


title: PBI025: Col-0_HighP_noBact_expB-rep1


title: PBI013: Col-0_LowP_SynCom_expA-rep1


title: PBI258: phr1phl1_preTreat(+Phi)_HighP_SynCom_expA-rep2

growth_protocol: Arabidopsis seedlings were grown on Johnson medium and solidified with 1 % bacto-agar. In these pre-treatments, media were supplemented with high Pi (1 mM KH2PO4; +Pi) or phosphite (1 mM KH2PO3; + Phi).  The phosphate concentration in the medium not supplemented with Pi (-Pi) was 5 µM (traces of Pi in the agar). Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night).

treatment_protocol: Seven-day-old seedlings grown in the presence of 1mM Pi (+Pi), 5 µM Pi (-Pi) or 1mM phosphite (+Phi) were transferred to 50 µM Pi (low Pi) or 625 µM Pi (high Pi) media (without sucrose) alone or with the Synthetic Community at 10E5 c.f.u / mL for another 12 days before harvesting.

tag: pre-treatment

value: +Phi


title: PBI253: Col-0_preTreat(+Phi)_HighP_SynCom_expA-rep1


title: PBI254: phf1_preTreat(+Phi)_HighP_SynCom_expA-rep1


title: PBI255: phr1phl1_preTreat(+Phi)_HighP_SynCom_expA-rep1


title: PBI249: phr1phl1_preTreat(+P)_HighP_SynCom_expA-rep1

value: +P


title: PBI016: phr1_LowP_SynCom_expA-rep2


title: PBI250: Col-0_preTreat(+P)_HighP_SynCom_expA-rep2


title: PBI248: phf1_preTreat(+P)_HighP_SynCom_expA-rep1


title: PBI252: phr1phl1_preTreat(+P)_HighP_SynCom_expA-rep2


title: PBI256: Col-0_preTreat(+Phi)_HighP_SynCom_expA-rep2


title: PBI010: phr1_HighP_SynCom_expA-rep1


title: PBI247: Col-0_preTreat(+P)_HighP_SynCom_expA-rep1


title: PBI246: phr1phl1_preTreat(-P)_HighP_SynCom_expA-rep2

value: -P


title: PBI251: phf1_preTreat(+P)_HighP_SynCom_expA-rep2


title: PBI244: Col-0_preTreat(-P)_HighP_SynCom_expA-rep2


title: PBI242: phf1_preTreat(-P)_HighP_SynCom_expA-rep1


title: PBI241: Col-0_preTreat(-P)_HighP_SynCom_expA-rep1


title: PBI007: Col-0_LowP_noBact_expA-rep2


title: PBI243: phr1phl1_preTreat(-P)_HighP_SynCom_expA-rep1


title: PBI245: phf1_preTreat(-P)_HighP_SynCom_expA-rep2


title: PBI239: phf1_preTreat(+Phi)_HighP_noBact_expA-rep2


title: PBI237: phr1phl1_preTreat(+Phi)_HighP_noBact_expA-rep1


title: PBI238: Col-0_preTreat(+Phi)_HighP_noBact_expA-rep2


title: PBI240: phr1phl1_preTreat(+Phi)_HighP_noBact_expA-rep2


title: PBI236: phf1_preTreat(+Phi)_HighP_noBact_expA-rep1


title: PBI001: Col-0_HighP_noBact_expA-rep1


title: PBI002: phr1_HighP_noBact_expA-rep1


title: PBI235: Col-0_preTreat(+Phi)_HighP_noBact_expA-rep1


title: PBI257: phf1_preTreat(+Phi)_HighP_SynCom_expA-rep2


title: PBI234: phr1phl1_preTreat(+P)_HighP_noBact_expA-rep2


title: PBI231: phr1phl1_preTreat(+P)_HighP_noBact_expA-rep1


title: PBI230: phf1_preTreat(+P)_HighP_noBact_expA-rep1


title: PBI233: phf1_preTreat(+P)_HighP_noBact_expA-rep2


title: PBI232: Col-0_preTreat(+P)_HighP_noBact_expA-rep2


title: PBI228: phr1phl1_preTreat(-P)_HighP_noBact_expA-rep2


title: PBI226: Col-0_preTreat(-P)_HighP_noBact_expA-rep2


title: PBI224: phf1_preTreat(-P)_HighP_noBact_expA-rep1


title: PBI227: phf1_preTreat(-P)_HighP_noBact_expA-rep2


title: PBI218: phf1_preTreat(+Phi)_LowP_SynCom_expA-rep1


title: PBI221: phf1_preTreat(+Phi)_LowP_SynCom_expA-rep2


title: PBI225: phr1phl1_preTreat(-P)_HighP_noBact_expA-rep1


title: PBI219: phr1phl1_preTreat(+Phi)_LowP_SynCom_expA-rep1


title: PBI223: Col-0_preTreat(-P)_HighP_noBact_expA-rep1


title: PBI216: phr1phl1_preTreat(+P)_LowP_SynCom_expA-rep2


title: PBI212: phf1_preTreat(+P)_LowP_SynCom_expA-rep1


title: PBI215: phf1_preTreat(+P)_LowP_SynCom_expA-rep2


title: PBI211: Col-0_preTreat(+P)_LowP_SynCom_expA-rep1


title: PBI213: phr1phl1_preTreat(+P)_LowP_SynCom_expA-rep1


title: PBI214: Col-0_preTreat(+P)_LowP_SynCom_expA-rep2


title: PBI208: Col-0_preTreat(-P)_LowP_SynCom_expA-rep2


title: PBI206: phf1_preTreat(-P)_LowP_SynCom_expA-rep1


title: PBI205: Col-0_preTreat(-P)_LowP_SynCom_expA-rep1


title: PBI209: phf1_preTreat(-P)_LowP_SynCom_expA-rep2


title: PBI229: Col-0_preTreat(+P)_HighP_noBact_expA-rep1


title: PBI207: phr1phl1_preTreat(-P)_LowP_SynCom_expA-rep1


title: PBI203: phf1_preTreat(+Phi)_LowP_noBact_expA-rep2


title: PBI202: Col-0_preTreat(+Phi)_LowP_noBact_expA-rep2


title: PBI204: phr1phl1_preTreat(+Phi)_LowP_noBact_expA-rep2


title: PBI200: phf1_preTreat(+Phi)_LowP_noBact_expA-rep1


title: PBI222: phr1phl1_preTreat(+Phi)_LowP_SynCom_expA-rep2


title: PBI201: phr1phl1_preTreat(+Phi)_LowP_noBact_expA-rep1


title: PBI220: Col-0_preTreat(+Phi)_LowP_SynCom_expA-rep2


title: PBI197: phf1_preTreat(+P)_LowP_noBact_expA-rep2


title: PBI217: Col-0_preTreat(+Phi)_LowP_SynCom_expA-rep1


title: PBI199: Col-0_preTreat(+Phi)_LowP_noBact_expA-rep1


title: PBI196: Col-0_preTreat(+P)_LowP_noBact_expA-rep2


title: PBI192: phr1phl1_preTreat(-P)_LowP_noBact_expA-rep2


title: PBI193: Col-0_preTreat(+P)_LowP_noBact_expA-rep1


title: PBI198: phr1phl1_preTreat(+P)_LowP_noBact_expA-rep2


title: PBI194: phf1_preTreat(+P)_LowP_noBact_expA-rep1


title: PBI195: phr1phl1_preTreat(+P)_LowP_noBact_expA-rep1


title: PBI190: Col-0_preTreat(-P)_LowP_noBact_expA-rep2


title: PBI191: phf1_preTreat(-P)_LowP_noBact_expA-rep2


title: PBI188: phf1_preTreat(-P)_LowP_noBact_expA-rep1


title: PBI186: phr1phl1_preTreat(+Phi)_HighP_SynCom_expB-rep2


title: PBI187: Col-0_preTreat(-P)_LowP_noBact_expA-rep1


title: PBI185: phf1_preTreat(+Phi)_HighP_SynCom_expB-rep2


title: PBI189: phr1phl1_preTreat(-P)_LowP_noBact_expA-rep1


title: PBI184: Col-0_preTreat(+Phi)_HighP_SynCom_expB-rep2


title: PBI210: phr1phl1_preTreat(-P)_LowP_SynCom_expA-rep2


title: PBI183: phr1phl1_preTreat(+Phi)_HighP_SynCom_expB-rep1


title: PBI182: phf1_preTreat(+Phi)_HighP_SynCom_expB-rep1


title: PBI181: Col-0_preTreat(+Phi)_HighP_SynCom_expB-rep1


title: PBI180: phr1phl1_preTreat(+P)_HighP_SynCom_expB-rep2


title: PBI179: phf1_preTreat(+P)_HighP_SynCom_expB-rep2


title: PBI176: phf1_preTreat(+P)_HighP_SynCom_expB-rep1


title: PBI177: phr1phl1_preTreat(+P)_HighP_SynCom_expB-rep1


title: PBI178: Col-0_preTreat(+P)_HighP_SynCom_expB-rep2


title: PBI174: phr1phl1_preTreat(-P)_HighP_SynCom_expB-rep2


title: PBI175: Col-0_preTreat(+P)_HighP_SynCom_expB-rep1


title: PBI173: phf1_preTreat(-P)_HighP_SynCom_expB-rep2


title: PBI172: Col-0_preTreat(-P)_HighP_SynCom_expB-rep2


title: PBI171: phr1phl1_preTreat(-P)_HighP_SynCom_expB-rep1


title: PBI168: phr1phl1_preTreat(+Phi)_HighP_noBact_expB-rep2


title: PBI167: phf1_preTreat(+Phi)_HighP_noBact_expB-rep2


title: PBI170: phf1_preTreat(-P)_HighP_SynCom_expB-rep1


title: PBI169: Col-0_preTreat(-P)_HighP_SynCom_expB-rep1


title: PBI164: phf1_preTreat(+Phi)_HighP_noBact_expB-rep1


title: PBI166: Col-0_preTreat(+Phi)_HighP_noBact_expB-rep2


title: PBI165: phr1phl1_preTreat(+Phi)_HighP_noBact_expB-rep1


title: PBI163: Col-0_preTreat(+Phi)_HighP_noBact_expB-rep1


title: PBI161: phf1_preTreat(+P)_HighP_noBact_expB-rep2


title: PBI162: phr1phl1_preTreat(+P)_HighP_noBact_expB-rep2


title: PBI160: Col-0_preTreat(+P)_HighP_noBact_expB-rep2


title: PBI158: phf1_preTreat(+P)_HighP_noBact_expB-rep1


title: PBI157: Col-0_preTreat(+P)_HighP_noBact_expB-rep1


title: PBI156: phr1phl1_preTreat(-P)_HighP_noBact_expB-rep2


title: PBI155: phf1_preTreat(-P)_HighP_noBact_expB-rep2


title: PBI153: phr1phl1_preTreat(-P)_HighP_noBact_expB-rep1


title: PBI152: phf1_preTreat(-P)_HighP_noBact_expB-rep1


title: PBI151: Col-0_preTreat(-P)_HighP_noBact_expB-rep1


title: PBI150: phr1phl1_preTreat(+Phi)_LowP_SynCom_expB-rep2


title: PBI148: Col-0_preTreat(+Phi)_LowP_SynCom_expB-rep2


title: PBI149: phf1_preTreat(+Phi)_LowP_SynCom_expB-rep2


title: PBI145: Col-0_preTreat(+Phi)_LowP_SynCom_expB-rep1


title: PBI146: phf1_preTreat(+Phi)_LowP_SynCom_expB-rep1


title: PBI143: phf1_preTreat(+P)_LowP_SynCom_expB-rep2


title: PBI144: phr1phl1_preTreat(+P)_LowP_SynCom_expB-rep2


title: PBI142: Col-0_preTreat(+P)_LowP_SynCom_expB-rep2


title: PBI141: phr1phl1_preTreat(+P)_LowP_SynCom_expB-rep1


title: PBI140: phf1_preTreat(+P)_LowP_SynCom_expB-rep1


title: PBI139: Col-0_preTreat(+P)_LowP_SynCom_expB-rep1


title: PBI138: phr1phl1_preTreat(-P)_LowP_SynCom_expB-rep2


title: PBI136: Col-0_preTreat(-P)_LowP_SynCom_expB-rep2


title: PBI137: phf1_preTreat(-P)_LowP_SynCom_expB-rep2


title: PBI132: phr1phl1_preTreat(+Phi)_LowP_noBact_expB-rep2


title: PBI133: Col-0_preTreat(-P)_LowP_SynCom_expB-rep1


title: PBI134: phf1_preTreat(-P)_LowP_SynCom_expB-rep1


title: PBI128: phf1_preTreat(+Phi)_LowP_noBact_expB-rep1


title: PBI131: phf1_preTreat(+Phi)_LowP_noBact_expB-rep2


title: PBI129: phr1phl1_preTreat(+Phi)_LowP_noBact_expB-rep1


title: PBI127: Col-0_preTreat(+Phi)_LowP_noBact_expB-rep1


title: PBI154: Col-0_preTreat(-P)_HighP_noBact_expB-rep2


title: PBI124: Col-0_preTreat(+P)_LowP_noBact_expB-rep2


title: PBI125: phf1_preTreat(+P)_LowP_noBact_expB-rep2


title: PBI126: phr1phl1_preTreat(+P)_LowP_noBact_expB-rep2


title: PBI123: phr1phl1_preTreat(+P)_LowP_noBact_expB-rep1


title: PBI147: phr1phl1_preTreat(+Phi)_LowP_SynCom_expB-rep1


title: PBI122: phf1_preTreat(+P)_LowP_noBact_expB-rep1


title: PBI120: phr1phl1_preTreat(-P)_LowP_noBact_expB-rep2


title: PBI118: Col-0_preTreat(-P)_LowP_noBact_expB-rep2


title: PBI116: phf1_preTreat(-P)_LowP_noBact_expB-rep1


title: PBI119: phf1_preTreat(-P)_LowP_noBact_expB-rep2


title: PBI115: Col-0_preTreat(-P)_LowP_noBact_expB-rep1


title: JFC210: phr1phl1_LowP_flg22_expB-rep3

growth_protocol: Arabidopsis seedlings were grown on Johnson medium and solidified with 1 % bacto-agar. Media were supplemented with Pi (KH2PO4) at distinct concentrations; 1 mM Pi was used for complete medium (+Pi) and approximately 5 µM Pi (traces of Pi in the agar) was the Pi concentration in the medium not supplemented with Pi (-Pi). Plants were grown in a growth chamber in a 15-h dark/9-h light regime (21°C day /18°C night).

treatment_protocol: Arabidopsis plants were germinated on Johnson medium (1 % sucrose) containing 1 mM Pi for 7 days in the vertical position and then transferred to 1 mM Pi and 5 µM Pi media containing 1 % sucrose either alone or supplemented with 10 µM MeJA or 1 µM flg22 for 12 days.

tag: treatment


title: PBI135: phr1phl1_preTreat(-P)_LowP_SynCom_expB-rep1


title: PBI159: phr1phl1_preTreat(+P)_HighP_noBact_expB-rep1


title: PBI130: Col-0_preTreat(+Phi)_LowP_noBact_expB-rep2


title: JFC198: Col-0_LowP_flg22_expB-rep3


title: JFC196: Col-0_LowP_flg22_expB-rep1


title: JFC192: phr1phl1_LowP_MeJA_expB-rep3

value: MeJA


title: JFC197: Col-0_LowP_flg22_expB-rep2


title: JFC190: phr1phl1_LowP_MeJA_expB-rep1


title: JFC191: phr1phl1_LowP_MeJA_expB-rep2


title: JFC180: Col-0_LowP_MeJA_expB-rep3


title: JFC172: phr1phl1_LowP_noTreatment_expB-rep1


title: JFC162: Col-0_LowP_noTreatment_expB-rep3


title: JFC160: Col-0_LowP_noTreatment_expB-rep1


title: JFC178: Col-0_LowP_MeJA_expB-rep1


title: JFC159: phr1phl1_HighP_flg22_expB-rep3


title: JFC161: Col-0_LowP_noTreatment_expB-rep2


title: JFC208: phr1phl1_LowP_flg22_expB-rep1


title: JFC173: phr1phl1_LowP_noTreatment_expB-rep2


title: JFC174: phr1phl1_LowP_noTreatment_expB-rep3


title: PBI121: Col-0_preTreat(+P)_LowP_noBact_expB-rep1


title: JFC179: Col-0_LowP_MeJA_expB-rep2


title: PBI117: phr1phl1_preTreat(-P)_LowP_noBact_expB-rep1


title: JFC158: phr1phl1_HighP_flg22_expB-rep2


title: H3K27ac ChIP-seq_4121_DGC

city: cleveland

first: xiuxing

last: wang

address: 9500 euclid ave

institute: cleveland clinic

description: antibody: H3K27ac, Active Motif, cat #39133

data_processing:
Fastq files were trimmed of  adaptors using Trimgalore, aligned using Bowtie2 (HG19) with default parameters, and duplicate reads removed using Picard tools.
Chip-seq peaks called using MACS2.1 using input control reads provided with a cutoff of p < 1e-9
Genome_build: Hg19
Supplementary_files_format_and_content: Peak files are provided as .BED files

source_name: human glioblastoma sample

extract_protocol:
1 million cells were crosslinked in 1% formaldehyde for 10 minutes, lysed, sonicated to ~500bp, and immunoprecipated using H3K27ac antibody. ChIP DNA was purified using the Qiagen PCR purification kit.
Libraries were prepared according to manufacturers instructions using the Rubicon Thruplex DNA-seq kit

value: glioblastoma, serum-differentiated glioma cell


title: JFC147: Col-0_HighP_flg22_expB-rep3


title: H3K27ac ChIP-seq_4121_BTIC

value: glioblastoma, brain tumor initiating cells


title: JFC209: phr1phl1_LowP_flg22_expB-rep2


title: 4121 - input control

description:
antibody: none
Control input DNA for ChIP

data_processing:
Fastq files were trimmed of  adaptors using Trimgalore, aligned using Bowtie2 (HG19) with default parameters, and duplicate reads removed using Picard tools.
ChIP-seq peaks were called using MACS2.1 with input control, p < 1e-9.
Genome_build: Hg19
Supplementary_files_format_and_content: Peak files are provided as .BED files

value: glioblastoma


title: JFC146: Col-0_HighP_flg22_expB-rep2


title: JFC145: Col-0_HighP_flg22_expB-rep1


title: JFC141: phr1phl1_HighP_MeJA_expB-rep3


title: AML 11 ChIP H3K4me2

value: AML 11

value: male

value: H3K4me2 (07-030 Upstate)


title: AML 11 ChIP H3K9me3  exp. 3

value: H3K9me3 (ab8898 Abcam)


title: AML 11 ChIP H3K27me3

value: H3K27me3 (Abcam, ab6002)


title: AML 10 ChIP H3K27ac

value: AML 10

value: H3K27ac (Abcam ab4729)


title: JFC139: phr1phl1_HighP_MeJA_expB-rep1

value: whole seedling

value: phr1 phl1

value: High (+Pi)


title: AML 10 ChIP H3K9me3 exp. 2


title: JFC129: Col-0_HighP_MeJA_expB-rep3


title: JFC128: Col-0_HighP_MeJA_expB-rep2


title: JFC127: Col-0_HighP_MeJA_expB-rep1


title: AML 8 ChIP H3K27ac

value: AML 8

value: female


title: JFC123: phr1phl1_HighP_noTreatment_expB-rep3


title: AML 8 ChIP H3K9me3


title: JFC122: phr1phl1_HighP_noTreatment_expB-rep2


title: AML 8 ChIP H3K4me2


title: JFC157: phr1phl1_HighP_flg22_expB-rep1


title: AML 8 ChIP H3K27me3


title: JFC110: Col-0_HighP_noTreatment_expB-rep2


title: CD34+ ChIP input exp. 3

source_name: CD34+ from blood


title: AML 11 ChIP H3K27ac


title: JFC111: Col-0_HighP_noTreatment_expB-rep3


title: CD34+ ChIP H3K9me3


title: JFC105: phr1phl1_LowP_flg22_expA-rep3

value: Low (-Pi)


title: AML 10 ChIP H3K27me3


title: CD34+ ChIP H3K27ac


title: JFC103: phr1phl1_LowP_flg22_expA-rep1


title: JFC093: Col-0_LowP_flg22_expA-rep3


title: K562-UNC0638 ChIP H3K9me2  exp. 2

source_name: K562  strain

value: H3K9me2 (ab1220 Abcam)


title: CD34+ ChIP H3K4me2


title: JFC109: Col-0_HighP_noTreatment_expB-rep1


title: JFC140: phr1phl1_HighP_MeJA_expB-rep2

value: MeJA


title: JFC121: phr1phl1_HighP_noTreatment_expB-rep1


title: JFC104: phr1phl1_LowP_flg22_expA-rep2


title: AML 16 ChIP H3K9me2 exp. 2

value: AML 16


title: CD34+ ChIP H3K9me2 exp. 3


title: JFC085: phr1phl1_LowP_MeJA_expA-rep1


title: AML 12 ChIP H3K9me2 exp. 2

value: AML 12


title: AML 16 ChIP input


title: JFC087: phr1phl1_LowP_MeJA_expA-rep3


title: JFC091: Col-0_LowP_flg22_expA-rep1


title: AML 15 ChIP input

value: AML 15


title: JFC086: phr1phl1_LowP_MeJA_expA-rep2


title: JFC075: Col-0_LowP_MeJA_expA-rep3


title: JFC074: Col-0_LowP_MeJA_expA-rep2


title: AML 9 ChIP H3K9me2 exp. 2

value: AML 9


title: JFC068: phr1phl1_LowP_noTreatment_expA-rep2


title: JFC069: phr1phl1_LowP_noTreatment_expA-rep3


title: JFC073: Col-0_LowP_MeJA_expA-rep1


title: AML 9 ChIP input


title: AML 14 ChIP ChIP input

value: AML 14

value: male


title: Granulocyte 1 ChIP H3K9me2 exp.2

source_name: Granulocyte from blood

value: Granulocyte 1


title: K562 ChIP H3K9me2 exp. 3


title: JFC057: Col-0_LowP_noTreatment_expA-rep3


title: JFC092: Col-0_LowP_flg22_expA-rep2


title: JFC067: phr1phl1_LowP_noTreatment_expA-rep1


title: AML 12 ChIP input


title: AML 10 ChIP input

value: AML 10


title: AML 7 ChIP H3K9me2 exp. 2

value: AML 7


title: JFC056: Col-0_LowP_noTreatment_expA-rep2

value: whole seedling


title: AML 15 ChIP H3K9me2 exp. 2


title: JFC055: Col-0_LowP_noTreatment_expA-rep1


title: AML 7 ChIP input


title: JFC051: phr1phl1_HighP_flg22_expA-rep3

value: phr1 phl1


title: AML 14 ChIP H3K9me2 exp. 2


title: 43 AML 13 ChIP input

value: AML 13


title: JFC039: Col-0_HighP_flg22_expA-rep3

value: High (+Pi)


title: AML 13 ChIP H3K9me2 exp. 2

value: female


title: JFC050: phr1phl1_HighP_flg22_expA-rep2


title: JFC049: phr1phl1_HighP_flg22_expA-rep1


title: Granulocyte 3 ChIP H3K9me2 exp. 2

value: Granulocyte 3


title: JFC038: Col-0_HighP_flg22_expA-rep2


title: JFC037: Col-0_HighP_flg22_expA-rep1


title: K562 ChIP H3K9me3

source_name: K562 strain

value: H3K9me3 (ab8898 Abcam)


title: AML 11 ChIP input

value: AML 11


title: JFC031: phr1phl1_HighP_MeJA_expA-rep1

value: MeJA


title: Control#3

city: New York

first: Lisa

middle: E

last: Pomeranz

state: NY

address: 1230 York Avenue, Box 305

department: Molecular Genetics

institute: Rockefeller University

data_processing:
RNA yield (ng/μl) and quality (RIN value) were quantified using an Agilent 2100 Bioanalyzer.
Libraries sequenced on an Illumina HiSeq 2000 using 100 base single reads
Reads in FASTQ format were filtered and trimmed using Bowtie (v 0.12.9)
Reads > 35 bases were aligned to the mouse mm10 genomic assembly using TopHat (v2.0.7)
Transcript abundance was quantified and differential expression and q-values were calculated using TopHat and Cufflinks (2.1.1)
Genome_build: mouse mm10 genomic assembly

source_name: Control

extract_protocol:
RNA purified from brain homogenates using Agilent Absolutely RNA nanoprep kit
RNA prepared with oligo dT priming using the SMARTer Ultra Low Input RNA Kit (Clontech)

tag: injected with

value: none (wild type control)

value: CNS section including hypothalamus and midbrain


title: JFC033: phr1phl1_HighP_MeJA_expA-rep3


title: AML 11 ChIP H3K9me2 exp. 2

value: H3K9me2 (ab1220 Abcam)


title: AML 10 ChIP H3K9me2 exp. 2


title: AML 11 ChIP H3K9me3


title: K562 ChIP H3 C-tail

value: H3 C-tail (ab1791 Abcam)


title: Input #1

source_name: Input

value: DAT-cre X Syn-NBL10

value: PRV-Introvert-GFP


title: Control #2


title: JFC020: Col-0_HighP_MeJA_expA-rep2


title: JFC032: phr1phl1_HighP_MeJA_expA-rep2


title: Control #1


title: Input #3


title: Immunoprecipitation #2

source_name: Immunoprecipitation

tag: ip antibody

value: anti-GFP monoclonal antibody


title: JFC021: Col-0_HighP_MeJA_expA-rep3


title: K562-UNC0638 ChIP input


title: Input #2


title: AML 8 ChIP input

value: AML 8


title: Granulocyte 1 ChIP H3K4me2

value: Granulocyte 1

value: male

value: H3K4me2 (07-030 Upstate)


title: JFC019: Col-0_HighP_MeJA_expA-rep1

value: whole seedling

value: High (+Pi)


title: JFC013: phr1phl1_HighP_noTreatment_expA-rep1

value: phr1 phl1


title: Immunoprecipitation #3


title: K562 ChIP input

value: female


title: 15 AML 13 ChIP input

value: AML 13


title: JFC015: phr1phl1_HighP_noTreatment_expA-rep3


title: WT3_pair_2

city: Elk Grove

first: joseph

middle: M

last: dhahbi

state: ca

address: 9700 West Taron Drive

department: Medical Education

institute: California Northstate University College of Medicine

data_processing:
Paired-end sequencing reads aligned to mm10 mouse genome with Tophat using default parameters.
Cufflinks package used to assemble transcripts and measure relative abundance in FPKM.
Assembled transcripts were compared with RefSeq from UCSC genome browser.
Differential expression was examined using the Cuffcompare and Cuffdiff in the Cufflinks package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample. This is the differential expression file generated by cuffdiff.

molecule: polyA RNA

source_name: WT

growth_protocol: 16 to 20-week-old WT or α7HMZ mice (both in a mixed 129/Sv-C57/Bl6 background) were fed vivarium chow.

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen).
Sequencing libraries were constructed using the iIllumina TruSeq RNA Sample Prep Kit v2.

value: liver

tag: age

value: 16 to 20 weeks old

tag: diet

value: Vivarium chow

value: WT

tag: background strain

value: mixed 129/Sv-C57/Bl6 background


title: Rrp44-HTP_Rrp41-channel_2

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

country: United Kingdom

institute: University of Edinburgh - WTCCB

description: barcode: NNNCACTAGC

data_processing:
Library strategy: CRAC-seq
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00 and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gtf format

organism: Saccharomyces cerevisiae

growth_protocol: S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: cleavage site

value: HISx6-TEV proteas cleavage site-protA

tag: tagged protein


title: AML 8 ChIP H3K9me2 exp. 2

value: H3K9me2 (ab1220 Abcam)


title: WT3_pair_1


title: Rrp44-HTP_Rrp41-channel_1

description: barcode: NNNCACTAGC

tag: strain


title: Granulocyte 1 ChIP input


title: JFC002: Col-0_HighP_noTreatment_expA-rep2

tag: tissue


title: JFC003: Col-0_HighP_noTreatment_expA-rep3


title: CD34+ ChIP input exp. 2

tag: sample id


title: WT2_pair_2


title: Rrp44-HTP_Rrp41p

description: barcode: NNNTCTCTAGC


title: Immunoprecipitation #1

value: DAT-cre X Syn-NBL10

value: PRV-Introvert-GFP

value: CNS section including hypothalamus and midbrain

value: anti-GFP monoclonal antibody


title: JFC001: Col-0_HighP_noTreatment_expA-rep1


title: WT1_pair_2


title: WT2_pair_1


title: WT1_pair_1


title: CD34+ ChIP H3K9me2 exp. 1

tag: gender


title: CD34+ ChIP H3K9me2 exp. 2

tag: chip antibody


title: K562-UNC0638 ChIP H3K9me2


title: JFC014: phr1phl1_HighP_noTreatment_expA-rep2

tag: genotype


title: RNA_vjbR1

city: Buenos Aires

first: Sieira

last: Rodrigo

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
Low-quality reads were removed using Trimmomatic v0.32
Reads were aligned witth Burrows Wheeler Alignment software (BWA)
Bigwig files were generated with custom bash scripts and BEDtools
ChIP-seq peaks were called using MACS2
RNA-seq differential expression analysis was performed using DESeq
Supplementary_files_format_and_content: narrowPeak files generated by MACS2 provide genomic coordinates, signal value (ChIP-seq) enrrichment, p-, and q-values for each detected ChIP-seq peak.
Supplementary_files_format_and_content: tsv file generated by DESeq provides gene ID, base mean reads, fold-change, log2 fold-change, p-value and adjusted p-value for the expression of each gene, baseMeanA represents wild type samples and baseMeanB represents mutant samples

organism: Brucella abortus

source_name: bacteria

growth_protocol: Bacteria were growth in bacteriological rich medium (TSB) until optical density of 1.0

extract_protocol:
VjbR-DNA complexes were isolated with the anti-VjbR antibody and protein G magentic beads
total RNA was isolated using MasterPure RNA Purification Kit (Epicentre) and then treated with TURBO DNAse (Ambion – Life Technologies)
Samples were submitted to Illumina TruSeq library preparation

treatment_protocol: Bacteria were shifted to minimal medium MM1 pH 5.5 in the presence of Urocanic acid for 3 h

value: DvjbR


title: HZ3_pair_2


title: Csl4-HTP_Rrp44-exo_1

description: barcode: NNNTCTCTAGC


title: K562 ChIP H3K9me2 exp. 1


title: Rrp41-HTP_Rrp44-exo_1

description: barcode: NNNCACTAGC


title: RNA_WT2


title: CD34+ ChIP input exp. 1


title: CD34+ ChIP H3K27me3

value: male

value: H3K27me3 (Abcam, ab6002)


title: Rrp6-HTP_Rrp44-exo_1

description: barcode: NNNATTAGC


title: RNA_WT1


title: Input_vjbR

description: Input


title: Rrp44-exo-S1-HTP_2

description: barcode: NNNCACTAGC


title: HZ3_pair_1


title: HZ2_pair_1


title: Input_WT2

description: Input


title: Input_WT1

description: Input


title: IP_vjbR

description: Immunoprecipitated chromatin

value: Anty-VjbR


title: Rrp41-HTP_Rrp44-exo_2

description: barcode: NNNAGAGC


title: IP_WT2

description: Immunoprecipitated chromatin


title: Mtr4-HTP_Rrp44-exo_1

description: barcode: NNNTAAGC


title: Input_WT3

description: Input


title: Granulocyte 1 ChIP H3 C-tail

value: Granulocyte 1

value: H3 C-tail (ab1791 Abcam)


title: RNA_vjbR2


title: CD117+ ILC, donor 1

status: Public on Mar 19 2017

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
AAI1_ILCP
Freshly isolated by FACS.
mRNA
Single read (read2 used to read sample barcodes and UMI only).
Processed data file: 20161009_Pasteur_exons_homer.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7, followed by UMI of size 8.
Alignment: hisat 0.1.5 with default parameters.
Filter PCR amplification bias using alignment break site and UMI barcode (size 8).
Create tag directory using makeTagDirectory from HOMER tools (http://homer.salk.edu/homer/ngs/).
HOMER, quantifying RNA expression in genes: analyzeRepeats.pl rna hg19 -d <List of tag dir> -count 3utr -condenseGenes -strand + -norm 1e7
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: 20161009_Pasteur_exons_homer.txt: Tab-delimited text file includes mRNA molecule count values for each Sample.

source_name: Healthy adult, CD117+ ILC, donor 1

extract_protocol:
Dynabeads mRNA Direct Purification Kit (Ambion).
Modified Mars-Seq (Jaitin et al., Science 2014).

treatment_protocol: Whole blood was donated by healthy individuals. Mononuclear cells were isolated by Ficoll centrifugation gradient. Lineage (CD3 CD4 CD19 CD14 CD123) cells were deleted by MACS column. Cells were stained for surface antibody and the interested population were isolated by FACS.

value: Adult

tag: disease state

value: Healthy

value: Peripheral blood

tag: selection markers

value: Viable CD45+ Lin- CD7+ CD127+ CD117+

value: Unstimulated

tag: donor


title: H3K4Me2_ILCP_rep4

city: Rotterdam

first: Ralph

last: Stadhouders

address: Dr. Molewaterplein 50

department: Pulmonary Medicine

institute: Erasmus Medical Center

data_processing:
Reads were aligned using bowtie 2 using default parameters.
Sorted and indexed bam files were parsed to HOMER to creat tag directories without duplicates and bedgraphs for browser visualization.
HOMER was used to identify enriched regions ('peak calling') using findPeaks with -region -size 1000 -minDist 2500 options
Genome_build: hg19
Supplementary_files_format_and_content: HOMER peak calling files

source_name: peripheral blood

extract_protocol:
Human peripheral blood mononuclear cells (PBMC) from peripheral blood were isolated by Ficoll-Paque density gradient centrifugation. Cells were isolated by FACS (ILCP: viable CD45+ Lin- (CD3- CD4- CD5- TCRαβ- TCRγδ- CD14- CD19-) CD7+ CD127+ CRTh2- CD117+ cells, HSC: CD45+ CD34+)
Nextera DNA library construction (as described in Schmidl et al. Nature Methods 2015).

value: peripheral blood

tag: cell type

value: Innate lymphoid cell precursors (ILCPs)

tag: antibody

value: anti-H3K4Me2, Abcam ab32356


title: H3K4Me2_ILCP_rep3


title: H3K4Me2_ILCP_rep1


title: HZ1_pair_2

value: liver

value: 16 to 20 weeks old

value: Vivarium chow

value: mixed 129/Sv-C57/Bl6 background


title: Rrp44-exo-S1-HTP_1

description: barcode: NNNGTGAGC

value: HISx6-TEV proteas cleavage site-protA


title: Granulocyte 1 ChIP H3K9me2 exp.1

value: male

value: H3K9me2 (ab1220 Abcam)


title: HZ1_pair_1


title: Csl4-HTP_Rrp44-exo_2

description: barcode: NNNTGGAGC


title: Con replication 3

status: Public on Mar 18 2017

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website (ftp://ftp.ensembl.org/pub/release-74/fasta/drosophila_melanogaster).Index of the reference genome was built using Bowtie v2.0.6 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
Quantification of gene expression level: HTSeq v0.5.4p3 was used to count the reads numbers mapped to each gene. And then  RPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene.
Differential expression analysis: Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq  R package (1.10.1). DESeq provide statistical routines for determining differential  expression in digital gene expression data using a model based on the negative binomial  distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05  found by DESeq were assigned as differentially expressed.
Genome_build: BDGP5 version, Ensembl Release 87 (ftp://ftp.ensembl.org/pub/release-74/fasta/drosophila_melanogaster)
Supplementary_files_format_and_content: Table files include RPKM values for each Sample.

organism: Drosophila melanogaster

source_name: late 3rd instar larval fat body

extract_protocol:
Late 3rd instar larval fat bodies were dissected. RNA was immediately extracted 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: fat body

tag: Stage

value: late 3rd instar larva


title: Con replication 1


title: F1_NonAddict_RNA

city: Shanghai

first: Qiumin

last: Le

address: 130 Dong'an Road

country: China

institute: Fudan University

data_processing:
Illumina Casava1.8 software used for basecalling.
For RRBS, the raw sequencing reads were quality checked and trimmed by Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for low quality (Phred score < 30) nucleotides, adapters and artificially introduced bases in the end-repair step. Reads too short (< 20bp) were filtered. For RNA-seq, Fastq quality trimmer was used for data cleaning.
Alignment to rat genome (RGSC Rnor_5.0/rn5) and methylation calling of the filtered reads were performed with Bismark. Parameters used were default except that 3 maximum mismatches in the "seed" were allowed and “paired-end” was specified. Bowtie short read aligner was used. RNA-seq data was aligned to rn5 and calculated for differential expression with the Tuxedo suite using default settings.
The bisulfite conversion rate was estimated by calculating the C to T conversion at non-CpG sites.
Differential methylation was calculated with BiSeq. Differential transcription was performed with Cuffdiff.
Genome_build: rn5
Supplementary_files_format_and_content: Bed files contains: the chromosome name, cytosine coordinate, cytosine coordinate (again), methylation  value in percent, number of methylated reads (#M) and the number of unmethylated  reads (#U). The file does not contain a header line. Coordinates are 1-based. Strand  information does not need to be provided, but is inferred from the coordinates: Coordinates  on the negative strand specify the cytosine base position (G on the positive strand). .txt is the normalized FPKM value of RNA-seq data.  Coordinates referring to cytosines not in CpG content are automatically discarded.

organism: Rattus norvegicus

source_name: Nuclear accumbens

extract_protocol:
Testes and cauda epidymides from mature male SDs were dissected, washed with PBS and placed in 35mm petri dishes containing HBSS supplemented with 20 mM HEPES pH 7.2, 1.2 mM MgSO4•7H2O, 1.3 mM CaCl2•2H2O, 6.6 mM sodium pyruvate, 0.05% lactate, 2 mM GlutaMAXT Supplement (Gibco®) and 0.5% BSA. Released sperm-containing supernatant was moved to 5 ml collection tubes and let stand for 10 min at 37℃ for swimming up. Supernatant was further filtered through 40 μm nylon mesh and laid on top of a three-layer gradient of 80%, 60% and 30% Percol, centrifuged for 10 min at 1,000 g at room temperature. Sperms were collected from 60% layer of the gradient, washed with the incubation buffer and cryopreserved. DNA was extracted from purified sperm by lysis with ,phenol-chloroform extraction followed by isopropanol precipitation and then preserved in TE buffer. RNA was prepared with standard Trizol protocol.
For RRBS library preparation, 1 ug genomic DNA was digested by MspI to generate short fragments that contain CpG dinucleotides at the ends. Then digested DNA was end-repaired, A-tailed and ligated to methylated Illumina adapters following the user manual of TruseqTM DNA Sample Prep Kit (Illumina, USA) Then, the CpG-rich DNA fragments (160-340 bp) are size selected, subjected to bisulfite conversion by MethylCode™ Bisulfite Conversion Kit (Life Technologies, USA) , and PCR amplified by ZymoTaqTM PreMix (Zymo, USA). Barcodes are indicated in the file names of each raw .fastq file. For RNA-seq,1 ug total RNA was extracted from nuclear accumbens and subjected to Truseq library preparation.

value: SD

tag: generation

tag: phenotype

value: Non-Addict

tag: cocaine exposure

value: N


title: H3K4Me2_HSC_rep1

value: hematopoietic stem cell (HSCs)


title: Rrp6-HTP_Rrp44-exo_2

description: barcode: NNNCTAGC

tag: cleavage site


title: IP_WT1

description: Immunoprecipitated chromatin

value: Anty-VjbR


title: CD34+ HSC, donor 1

description:
AAI2_CD34
Freshly isolated by FACS.
mRNA
Single read (read2 used to read sample barcodes and UMI only).
Processed data file: 20161009_Pasteur_exons_homer.txt

source_name: Healthy adult, CD34+ HSC, donor 1

tag: age

value: Adult

value: Healthy

value: Peripheral blood

value: Viable CD45Low CD34+

tag: treatment

value: Unstimulated


title: H3K4Me2_HSC_rep2

tag: tissue

value: peripheral blood

value: anti-H3K4Me2, Abcam ab32356


title: CD34+ HSC, donor 2

description:
AAI7_CD34
Freshly isolated by FACS.
mRNA
Single read (read2 used to read sample barcodes and UMI only).
Processed data file: 20161009_Pasteur_exons_homer.txt

source_name: Healthy adult, CD34+ HSC, donor 2


title: CD117+ ILC, donor 2

description:
AAI6_ILCP
Freshly isolated by FACS.
mRNA
Single read (read2 used to read sample barcodes and UMI only).
Processed data file: 20161009_Pasteur_exons_homer.txt

source_name: Healthy adult, CD117+ ILC, donor 2

value: Viable CD45+ Lin- CD7+ CD127+ CD117+


title: Hetero_24hr_rep1

city: Houston

first: Alin

last: Tomoiaga

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: Mus musculus and Homo sapiens fused

data_processing:
RNA-Seq reads were aligned to the mm9 whole genome using tophat v2.0.12 with parameters --mate-std-dev 200 -p 8 -r 203. We use the full set of knownGene downloaded from the UCSC Genome browser (http://genome.ucsc.edu/cgi-bin/hgTables ) as reference genes. RNA-Seq read counts for each gene in each sample was calculated using Cuffdiff function in Cufflinks version 2.2.1. The Cuffdiff also calculates fragment per kilobase per million reads (FPKM) for each gene.
Fragments Per Kilobase of transcript per Million mapped reads were calculated using cuffdiff v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: [.fpkm_tracking] tab-delimited text files include FPKM values for each Sample

organism:
Homo sapiens
Mus musculus

source_name: Hetero, 24hr

growth_protocol: Cell preparation: One day before cell fusion, 4X105 endothelial cells were seeded on one well of a 6-well dish. The endothelial cells were confluent on the day of cell fusion. On the same day, 1 h prior to cell fusion, the endothelial cell medium was replaced with fresh EGM-2 MV medium supplemented with 1 μM Cell Tracker Red, then cells were incubated at 37oC in darkness for 30 mins. Human iPSCs or murine ESCs labeled by transduction with retroviruses encoding GFP were rinsed with PBS followed by accutase treatment at 37oC for 5 mins to dissociate the pluripotent stem cells into single cell suspension.

extract_protocol: Heterokaryons (GFP+ and CellTracker Red+) were harvested by FACS at 6, 12 and 24 hours post-fusion and prepared for analysis by RNA-seq. Total RNA from heterokaryons were isolated. Human and mouse mRNA transcripts were isolated from the total RNA samples using polyA-based enrichment using oligo-dT magnetic beads. The majority of contaminating ribosomal RNA was eliminated by this approach. The resulting mRNA was fragmented, reverse transcribed to cDNA, ligated to adapters, and subject to brief PCR amplification in preparation of the Illumina library. The integrity and quality of RNA and complementary DNA were monitored using an Agilent Bioanalyzer 2100.

treatment_protocol: Heterokaryon formation and isolation: The cells were collected in conical tubes after neutralization by MEF media containing 10% FBS. The cells were then counted with hemocytometer and 2X105 pluripotent stem cells were taken. The cells were then centrifuged at 200xg for 5 mins at 4oC, the supernatant was removed, and the cell pellet was resuspended in 25 μL ice-cold cell fusion buffer with 2.5 μL ice-cold HVJ-envelope fusagen. The reaction mixture was placed on ice for 5 mins with regular agitation in 2.5 mins apart. After 5 mins, the cells were centrifuged again and the supernatant was discarded and 2 mL cell fusion buffer was added. The pluripotent cells were then plated onto the endothelial cells. The 6-well dish was then centrifuged at 200g for 5 mins at 4oC.  After centrifugation the dish was placed into a 37oC incubator to induce cell fusion. Twenty minutes later, the medium was removed and EGM-2 MV medium was added. For the Co-culture Control, the described procedure was the same except HVJ-enveloped fusagen was not added. The heterokaryons (double-positive cells) can be efficiently sorted by FACS. Heterokaryons (GFP+ and CellTracker Red+) were harvested by FACS at 6, 12, 24, 48, and 72 hours post-fusion.

tag: sample type

value: mouse ESC and human endothelial cell, fused

tag: time

tag: replicate


title: HZ2_pair_2

value: liver

value: 16 to 20 weeks old

tag: diet

value: Vivarium chow

tag: genotype

tag: background strain

value: mixed 129/Sv-C57/Bl6 background


title: Con replication 2

tag: strain

value: fat body

value: late 3rd instar larva


title: CoCulture_6h

description: Mus musculus and Homo sapiens coculture

source_name: CoCulture, 6h

value: mouse ESC and human endothelial cell, cocultured


title: H3K4Me2_ILCP_rep2

tag: cell type

value: Innate lymphoid cell precursors (ILCPs)


title: CoCulture_24h

description: Mus musculus and Homo sapiens coculture

source_name: CoCulture, 24h


title: AKH-overexpression replication 3


title: AKH-overexpression replication 2


title: AKH-overexpression replication 1


title: IP_WT3

description: Immunoprecipitated chromatin

tag: chip antibody

value: Anty-VjbR


title: Hetero_12hr_rep2

description: Mus musculus and Homo sapiens fused

source_name: Hetero, 12hr


title: Mtr4-HTP_Rrp44-exo_2

description: barcode: NNNGCGCAGC

value: HISx6-TEV proteas cleavage site-protA

tag: tagged protein


title: N rep2

city: Bar Harbor

first: Xulong

last: Wang

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were checked with FASTX-Toolkit, trimmed with Trimmomatic, and aligned to the GRCm38.73 assembly transcriptome with Bowtie
Transcript expression levels were estimated in transcripts per million (TPM) using RSEM
Genome_build: GRCm38.73
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: Spleen

extract_protocol:
Total RNA from FACS-purified VFP-ICOS-, VFP-ICOS+, and VFP+ICOS+ CD4+ cell pools were extracted with Qiagen RNeasy Mini Kits (Qiagen, Hilden, Germany) in 2 replicates.
Poly-A-enriched mRNA was reverse transcribed and amplified using the Nugen Ovation Kit (NuGEN, San Carlos, CA, USA).

value: post natal day 28

tag: genotype/variation

value: IL21-VFP reporter

value: Spleen

value: FACS-purified VFP-ICOS- CD4+ cell pool


title: F1_Addict_RNA

value: SD

tag: generation

tag: phenotype

value: Addict

value: N


title: mESC_day4_rep2

description: Mus musculus

source_name: mESC, day4

value: mouse ESC


title: mESC_day4_rep1

description: Mus musculus


title: mESC_day0_rep2

description: Mus musculus

source_name: mESC, day0


title: Hetero_24hr_rep2

description: Mus musculus and Homo sapiens fused

value: mouse ESC and human endothelial cell, fused


title: N rep1


title: Hetero_6hr_rep2

description: Mus musculus and Homo sapiens fused

source_name: Hetero, 6hr


title: Hetero_12hr_rep1

description: Mus musculus and Homo sapiens fused


title: Hetero_6hr_rep3

description: Mus musculus and Homo sapiens fused


title: mESC_day0_rep1

description: Mus musculus


title: Hetero_6hr_rep1

description: Mus musculus and Homo sapiens fused


title: ACT IL21 rep2

value: FACS-purified VFP+ICOS+ CD4+ cell pool


title: hMeDIP-seq_LNCaP_rep1

status: Public on Mar 17 2017

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute

data_processing:
Sequenced reads from hMeDIP immunoprecipitated and input control human brain samples were mapped to the human reference genome (hg19) with bowtie v.1.1.0
, allowing up to three mismatches. Reads mapping to multiple locations and/or deemed as PCR duplicates were filtered out
MACS2 (v2.1.0) was called in broad peak mode to give summits of broad peaks for Adult Brain hMeDIP.
Bigwig files were generated using a scaling factor of 1,000,000 reads/library size, average fragment length of 300
and duplicates removed.
Genome_build: hg19
Supplementary_files_format_and_content: bed and bigwig

source_name: LNCaP cell line DNA

growth_protocol: Adult Brain Frontal Lobe genomic DNA from a single donor was purchased from Banksia Scientific Company (Bulimba, Australia, cat no D1234035). LNCaP cells were cultured as described previously [Song JZ et al, Oncogene 2002, 21:1048-1061].

extract_protocol:
Genomic DNA from LNCaP cells was exctracted using QIAamp DNA Mini kit (Qiagen, USA)
TruSeq LT DNA Sample Preparation kit
Illumina Adaptor ligation prior to the IP

treatment_protocol: no treatment

value: LNCaP clone FGC (ATCC CRL-1740). Androgen-sensitive human prostate adenocarcinoma cells derived from metastatic site:left supraclavicular lymph node

tag: passage number

tag: ip antibody

value: 5hmC polyclonal antibody (Active Motif cat no 55010)


title: Hetero_24hr_rep3

description: Mus musculus and Homo sapiens fused


title: mESC_day8_rep2

description: Mus musculus

source_name: mESC, day8


title: ACT IL21 rep1

tag: age


title: hMeDIP-seq_Adult_Brain_rep2

source_name: Adult Brain DNA from a single donor

value: Adult Brain Frontal Lobe


title: mESC_day8_rep1

description: Mus musculus


title: Oregon-R strain + 11 generations, Fab2L Red* rep 2

city: Taipei

first: Jia-Ming

last: Chang

address: NO.64, Sec. 2, ZhiNan Rd., Wenshan District

department: Department of Computer Science

country: Taiwan

institute: National Chengchi University

data_processing:
For samples 1-18
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie2 with standard parameters.
Uniquely aligned read pairs were extracted using custom scripts and reads mapping to unplaced or unlocalized scaffolds were discarded.
BAM files containing uniquely aligned reads were pooled within each line using Picard, and sorted and indexed using SAMtools.
Structural variations (SVs) detection was carried out using the DSVD pipeline as previously described. Seed-based alignment was performed using Bowtie2 with parameters -3 95 –N 1 –L 30 –k 11.
Sixteen different SV types, including small insertions and deletions, inversions and complex chromosomal rearrangements, were considered (see Sievers et al. 2014 for details).
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: FILE FORMAT: text file (TXT)
Supplementary_files_format_and_content: FILE CONTENT:
Supplementary_files_format_and_content: For the single_bp files: column1: breakpoint number; column2: chromosome name; column3: genomic position; columns4-5: the number of discordant reads (weight) that support the breakpoint
Supplementary_files_format_and_content: For the double_bp files: column1: breakpoint number, first breakpoint; column2: chromosome name for the first breakpoint;
Supplementary_files_format_and_content: column3: genomic position of the first breakpoint; column4: breakpoint number, second breakpoint; column5: chromosome name for the second breakpoint; column6: genomic position of the second breakpoint; columns7-8: the number of discordant reads (weight) that support the connection between first and second breakpoint; column9: the type of structural variation
Supplementary_files_format_and_content: For the triple_bp files: column1: breakpoint number, first breakpoint; column2: chromosome name for the first breakpoint;
Supplementary_files_format_and_content: column3: genomic position of the first breakpoint; columns4-5: the number of discordant reads (weight) that support the first breakpoint; column6: breakpoint number, second breakpoint; column7: chromosome name for the second breakpoint; column8: genomic position of the second breakpoint; columns9-10: the number of discordant reads (weight) that support the second breakpoint; column11: breakpoint number, third breakpoint; column12: chromosome name for the third breakpoint; column13: genomic position of the third breakpoint; columns14-15: the number of discordant reads (weight) that support the third breakpoint; column16: the type of structural variation
For samples 19-26 and 35-42
Fastq files were aligned against the dm6 Drosophila reference genome using STAR v2.5 with the following parameters: --outFilterType BySJout --outFilterMultimapN  max 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999  --alignIntronMin 21 --alignIntronMax 1000000 --alig  nMatesGapMax 1000000 --outFilterIntronMotifs RemoveNoncanonical
BAM files were processed using summarizeOverlaps function from the GenomicAlignments R package (http://bioconductor.org/) to produce counts per gene matrix.
DeSeq2 (http://bioconductor.org/)  was used to calculate the expression levels in Fragments Per Kilobase of exon per Million Fragments Mapped (FPKM) per gene.
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: FILE FORMAT: text file (TXT)
Supplementary_files_format_and_content: FILE CONTENT:
Supplementary_files_format_and_content: column1:FlyBase ID, column2: FPKM
For samples 27-34 and 43-50
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie1
The number of unique read mapping to known microRNAs (based on miRBase) were extracted using custom scripts.
Genome_build: Drosophila melanogaster dm6
Supplementary_files_format_and_content: FILE FORMAT: text file (TXT)
Supplementary_files_format_and_content: FILE CONTENT:
Supplementary_files_format_and_content: column1:miRBase ID, column2: Unique reads count
For samples 51-59
Fastq files were aligned against the dm6 Drosophila reference genome using Bowtie2 with standard parameters.
Uniquely aligned read pairs were extracted using custom scripts and reads mapping to unplaced or unlocalized scaffolds were discarded.
BAM files containing uniquely aligned reads were pooled within each line using Picard, and sorted and indexed using SAMtools.
Structural variations (SVs) detection was carried out using the DSVD pipeline as previously described. Seed-based alignment was performed using Bowtie2 with parameters -3 95 –N 1 –L 30 –k 11.
Sixteen different SV types, including small insertions and deletions, inversions and complex chromosomal rearrangements, were considered (see Sievers et al. 2014 for details).
Genome_build: Drosophila melanogaster dm6

source_name: adult female

extract_protocol: For each line, gDNA was extracted and purified from 150 adult female flies using the Gentra Puregene Cell Kit (Qigen) following the manufacturer’s instructions; Libraries were prepared by FASTERIS following the standard protocol with a gel size selection at 230 bp

tag: developmental stage

value: adult female

value: 4 days old adult fly

value: w[1118] with Fab2L transgenic insertion

value: Oregon-R strain + 11 generations


title: Oregon-R strain + 11 generations, Fab2L Red* rep 3


title: Oregon-R strain + 11 generations, Fab2L rep 3


title: Hetero_12hr_rep3

description: Mus musculus and Homo sapiens fused

tag: sample type


title: ACT rep2

value: post natal day 28

tag: tissue

value: FACS-purified VFP-ICOS+ CD4+ cell pool


title: Oregon-R strain + 11 generations, Fab2L White* rep 2


title: Oregon-R strain + 11 generations, Fab2L White* rep 1


title: LNCaP_OxBis_rep1

description:
LNCaP clone FGC(ATCC® CRL-1740™). Androgen-sensitive human prostate adenocarcinoma cells derived from metastatic site: left supraclavicular lymph node
bigTable_LNCaP.tsv.gz

data_processing:
Bisulphite reads were aligned to the human genome using version 1.2 of an internally developed pipeline, publicly available for download from http://github.com/astatham/Bisulphite_tools.
Adaptor sequences and poor quality bases were removed using Trimgalore (version 0.2.8, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) in paired-end mode with default parameters.
Bismark v0.8.326 was then used to align reads to hg19 using the parameters “-p 4 –bowtie2 –X 1000 –unmapped –ambiguous –gzip –bam”
PCR duplicates were removed using Picard v1.91 (http://broadinstitute.github.io/picard)
Count tables of the number of methylated and unmethylated bases sequenced at each CpG site in the genome were constructed using bismark_methylation_extractor with the parameters “-p –no_overlap –ignore_r2 4 –comprehensive –merge_non_CpG –bedgraph –counts –report –gzip –buffer_size 20G”
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited

growth_protocol: Adult Brain Frontal Lobe genomic DNA from a single donor was purchased from Banksia Scientific Company (Bulimba, Australia, cat no D1234035). LNCaP cells were cultured as desribed previously [Song JZ et al, Oncogene 2002, 21:1048-1061].

extract_protocol:
Genomic DNA from LNCaP cells was exctracted using QIAamp DNA Mini kit (Qiagen, USA)
CEGX TrueMethyl® WG

tag: tissue type

value: LNCaP clone

tag: passage


title: LNCaP_OxBis_rep2


title: LNCaP_Bis_rep1


title: Oregon-R strain + 11 generations, Fab2L White* rep 3

tag: genotype


title: Adult_Brain_Bis


title: LNCaP_Bis_rep2


title: hMeDIP-seq_LNCaP_rep2


title: Adult_Brain_OxBis


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L rep 1

description: small RNAs (18-30 nt)

source_name: unfertilized eggs

extract_protocol: For each line, 4.5 ug of total RNA was extracted and purified from adult male heads. The biological samples were  homogenized in Trizol and Chloroform. Total RNA was finally extracted with the RNA Clean & Concentrator kit (Zymo Research) following the manufacturer’s instruction. Libraries were prepared by FASTERIS, following the standard protocol after removal of 2S RNA and polyacrilamide gel size selection (18-30 nt). Libraries were sequenced single end 1x50bp on a HiSeq2500 machine.

value: unfertilized eggs

value: Oregon-R strain


title: Oregon-R strain, small RNAs (18-30 nt) , w[1118] rep 2

description: small RNAs (18-30 nt)


title: Oregon-R strain, small RNAs (18-30 nt) , w[1118] rep 1

description: small RNAs (18-30 nt)


title: ACT rep1

value: IL21-VFP reporter

value: Spleen


title: hMeDIP-seq_input


title: Oregon-R strain, long RNAs (>200nt) , Fab2L rep 2

description: long RNAs (>200nt)

extract_protocol: For each line, 4.5 ug of total RNA was extracted and purified from adult male heads. The biological samples were  homogenized in Trizol and Chloroform. Total RNA was finally extracted with the RNA Clean & Concentrator kit (Zymo Research) following the manufacturer’s instruction. Libraries were prepared by FASTERIS, following the standard protocol without the polyA purification step and after removal of rRNA (RiboZero step). Libraries were sequenced single end 1x125bp on a HiSeq2500 machine.


title: Oregon-R strain, long RNAs (>200nt) , Fab2L Red* rep 1

description: long RNAs (>200nt)


title: Oregon-R strain, long RNAs (>200nt) , Fab2L rep 1

description: long RNAs (>200nt)


title: Oregon-R strain, long RNAs (>200nt) , Fab2L White* rep 1

description: long RNAs (>200nt)


title: Oregon-R strain + 11 generations, Fab2L Red* rep 1


title: Oregon-R strain + 11 generations, Fab2L rep 2


title: Oregon-R strain + 11 generations, Fab2L rep 1


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L Red* rep 1

description: small RNAs (18-30 nt)


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L Red* rep 2

description: small RNAs (18-30 nt)


title: Oregon-R strain, long RNAs (>200nt) , w[1118] rep 2

description: long RNAs (>200nt)


title: smg-2(qd101) rep2

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
The BCL (base calls) binary is converted to FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Sequenced reads were trimmed for adaptor sequence, then mapped to C. elegans genome (WS220/ce10) with transcriptome (Ensembl 65) using Tophat-2.0.14 (bowtie2-2.2.5) with default parameters.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using Cufflinks with default parameters.
Genome_build: ce10
Supplementary_files_format_and_content: Tab-delimited text files with BigWig format that read counts are normalized to 107.

organism: Caenorhabditis elegans

source_name: Caenorhabditis elegans smg-2 mutant

growth_protocol: All strains were grown on OP50-seeded NGM plates.

extract_protocol:
Total RNA from synchronized day 1 adult worms was extracted by using RNA Isoplus (Takara, Shiga, Japan).
We used TruSeq RNA library preparation kit (illumina, San Diego, USA). RNA is first purified using polyA selection, then chemically fragmented and converted into single-stranded cDNA using random hexamer priming. Next, the second strand is generated to create double-stranded cDNA that is ready for the TruSeq library construction. The short ds-cDNA fragments were then connected with sequencing adapters, and suitable fragments were separated by agarose gel electrophoresis. Finally, truseq RNA libraries were built by PCR amplification and quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using the Agilent Technologies 2100 Bioanalyzer. (Agilent technologies,Palo Alto CA, USA).

value: Whole body

value: Day 1 adult


title: Oregon-R strain, long RNAs (>200nt) , w[1118] rep 1

description: long RNAs (>200nt)


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L rep 2

description: small RNAs (18-30 nt)


title: smg-2(qd101); daf-2(e1370) rep1

source_name: Caenorhabditis elegans smg-2; daf-2 mutant


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L White* rep 2

description: small RNAs (18-30 nt)


title: smg-2(qd101); daf-2(e1370) rep2


title: smg-2(qd101) rep1


title: Oregon-R strain, long RNAs (>200nt) , Fab2L White* rep 2

description: long RNAs (>200nt)


title: Oregon-R strain, small RNAs (18-30 nt) , Fab2L White* rep 1

description: small RNAs (18-30 nt)


title: Oregon-R strain, long RNAs (>200nt) , Fab2L Red* rep 2

description: long RNAs (>200nt)


title: daf-2(e1370) rep2

source_name: Caenorhabditis elegans daf-2 mutant


title: daf-2(e1370) rep1


title: Wild-type rep2

source_name: Caenorhabditis elegans wild-type

value: Bristol N2


title: Wild-type rep1


title: TP-059(N) Deletion Neurons

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
dscDNA were prepared using the NuGEN Ovation V2 kit and sequenced using an Ion Torrent PGM 314
These were aligned to the human genome (hg19) using TopHat version 2.0.10, Bowtie 1 version 1.0.0 and Samtools version 0.1.19
Reads were mapped to known genes using HTseq.  Gene expression was analyzed using DESeq2 version 1.2.10
Genome_build: hg19
Supplementary_files_format_and_content: comma seperated text files include RPKM values for each Sample

source_name: Human Dental Pulp Stem Cells

extract_protocol:
Control teeth were obtained through the Department of Pediatric Dentistry at the University of Tennessee Health Science Center (UTHSC). Teeth from AS deletion and idic15 subjects were shipped from various locations by the parents of children with these conditions. The UTHSC Institutional Review Board (IRB) approved this study and informed consent was obtained in accordance with IRB policy. Immediately following extraction, the teeth were placed in transportation media (DMEM/F12 with HEPES and 100 U/ml penicillin, 100μg/ml streptomycin). DPSC were isolated and culture as previously described in (Kiraly et al (2009) Neurochemistry International 55: 323-332) with slight modifications. Briefly, the pulp was minced and digested in a solution of 3 mg/ml Collagenase type I and 4 mg/ml Dispase II for 1 h at 37°C. Cells were seeded in poly-D-Lysine 12-well dishes and maintained under standard conditions (37°C, 5% CO2) in DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS) and 100 U/ml penicillin, 100μg/ml streptomycin. Sub-confluent cultures were passaged regularly with 0.1μM HyQTase (HyClone).
Total RNA was extracted from ~3 week cultured Neurons and DPSCs using the miRNeasy Mini kit from Qiagen.
Total RNA was subjected to analysis on a Agilent Bioanalyzer 6000 pico chip and determined to have a RIN of >8.0. 5ng of total RNA then used to prepare dscDNA using the NuGEN Ovation V2 kit. 500ng of this dscDNA then used to prepare libraries for sequencing using the AB Library Builder™ Fragment library Kit for 5500 Genetic Analysis Systems on a Library Builder system. Libraries were amplified 7 cycles before 5500 Wildfire primers added by 5 cycles of fusion primer amplification as described in the 5500 Wildfire manual (Applied Biosystems). Before sequencing, small aliquots of this material pooled and sequenced on an Ion Torrent PGM 314 chip after additional amplification with PGM fusion primers. Barcode quantification data from the PGM was used to pool the samples with Wildfire primers equally. Following this final pooling the library pools were examined and quantified on an Agilent high sensitivity DNA chip, immobilized on flow cells for the 5500 Wildfire instrument, and sequenced (50bp reads) on this instrument.

treatment_protocol: 20,000 cells/cm2 were seeded in poly-D-lysine coated 12 well plates in DMEM/F12 (1:1), 2.5% FCS, 100 U/ml penicillin and 100 μg streptomycin, and culture for 24 hours. Epigenetic reprogramming was performed by exposing the DPSCs to 10 μM 5-azacytidine in DMEM/F12 containing 2.5% FCS and 10 ng/ml bFGF for 48 hours. Neural differentiation was induced by exposing the cells to 250μM IBMX, 50μM forskolin, 200 nM TPA, 1mM dbcAMP, 10ng/ml bFGF, 10 ng/ml NGF, 30 ng/ml NT-3, and 1% insulin-transferrin-sodium selenite premix (ITS) in DMEM/F12 for 3 days. At the end of the neural induction treatment, the cells were washed with 1X PBS. Neuronal maturation was performed by maintaining the cells in Neurobasal A media supplemented with 1mM dbcAMP, 1% N2, 1% B27, and 30 ng/ml NT-3 and 1X Glutamax for 3 days.

value: Neurons

value: Deletion 15q (Angelman syndrome)

tag: 15q copy number


title: TP-078 Deletion DPSC

value: DPSC


title: TP-078(N) Deletion Neurons


title: TP-058(N) Duplication Neurons

value: Duplication 15q (Isodicentric)


title: TP-044(N) Duplication Neurons


title: TP-055(N) Deletion Neurons


title: TP-059 Deletion DPSC


title: hMeDIP-seq_Adult_Brain_rep1

value: Adult Brain Frontal Lobe

value: 5hmC polyclonal antibody (Active Motif cat no 55010)


title: TP-044 Duplication DPSC


title: TP-055 Deletion DPSC


title: TP-041(N) Duplication Neurons

value: Duplication 15q (Interstitial)


title: TP-058 Duplication DPSC


title: TP-037(N) Control Neurons

value: Neurotypical Control


title: TP-076(N) Control Neurons


title: TP-076 Control DPSC


title: TP-023(N) Control Neurons


title: TP-037 Control DPSC


title: F1_NonAddict_3

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw sequencing reads were quality checked and trimmed by Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) for low quality (Phred score < 30) nucleotides, adapters and artificially introduced bases in the end-repair step. Reads too short (< 20bp) were filtered.
Alignment to rat genome (RGSC Rnor_5.0/rn5) and methylation calling of the filtered reads were performed with Bismark. Parameters used were default except that 3 maximum mismatches in the "seed" were allowed and “paired-end” was specified. Bowtie short read aligner was used.
The bisulfite conversion rate was estimated by calculating the C to T conversion at non-CpG sites.
Differential methylation was calculated with BiSeq.
Genome_build: rn5
Supplementary_files_format_and_content: Bed files contains: the chromosome name, cytosine coordinate, cytosine coordinate (again), methylation  value in percent, number of methylated reads (#M) and the number of unmethylated  reads (#U). The file does not contain a header line. Coordinates are 1-based. Strand  information does not need to be provided, but is inferred from the coordinates: Coordinates  on the negative strand specify the cytosine base position (G on the positive strand).  Coordinates referring to cytosines not in CpG content are automatically discarded.

source_name: sperm

extract_protocol:
Testes and cauda epidymides from mature male SDs were dissected, washed with PBS and placed in 35mm petri dishes containing HBSS supplemented with 20 mM HEPES pH 7.2, 1.2 mM MgSO4•7H2O, 1.3 mM CaCl2•2H2O, 6.6 mM sodium pyruvate, 0.05% lactate, 2 mM GlutaMAXT Supplement (Gibco®) and 0.5% BSA. Released sperm-containing supernatant was moved to 5 ml collection tubes and let stand for 10 min at 37℃ for swimming up. Supernatant was further filtered through 40 μm nylon mesh and laid on top of a three-layer gradient of 80%, 60% and 30% Percol, centrifuged for 10 min at 1,000 g at room temperature. Sperms were collected from 60% layer of the gradient, washed with the incubation buffer and cryopreserved. DNA was extracted from purified sperm by lysis with ,phenol-chloroform extraction followed by isopropanol precipitation and then preserved in TE buffer.
For library preparation, 1 mg genomic DNA was digested by MspI to generate short fragments that contain CpG dinucleotides at the ends. Then digested DNA was end-repaired, A-tailed and ligated to methylated Illumina adapters following the user manual of TruseqTM DNA Sample Prep Kit (Illumina, USA) Then, the CpG-rich DNA fragments (160-340 bp) are size selected, subjected to bisulfite conversion by MethylCode™ Bisulfite Conversion Kit (Life Technologies, USA) , and PCR amplified by ZymoTaqTM PreMix (Zymo, USA). Barcodes are indicated in the file names of each raw .fastq.gz file.

tag: strain

value: SD

value: Non-Addict

tag: cocaine exposure

value: N


title: F1_NonAddict_2


title: F1_NonAddict_1


title: F1_Addict_3

value: Addict


title: F1_Addict_2


title: RNA130128RH_32

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

description: Very Heavy Drinker: average daily ethanol intake exceeding 3 g/kg AND have >= 10% of open access days with an ethanol intake exceeding 4 g/kg

data_processing:
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
Alignment: Reads were aligned to MacaM assembly (Zimin et al., 2014) using STAR v.2.3.0e (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax=3,outFilterScoreMinOverLread=0.33,outFilterMismatchNoverLmax=0.03, outFilterMultimapNmax=1.
After removing one sample outlier from the set, upper-Quartile normalization was performed using the edgeR Bioconductor package. Genes with at least 100 average reads per sample and exons with more than 10 average reads were retained for further analysis.
Genome_build: MacaM
Supplementary_files_format_and_content: RNASeq017_exon_reads_UQNormalized_for_GEO.csv: first column has the exon ID (a combination of chromosome number, start, and end location of exon, and gene symbol). subsequent 30 columns provide the normalized reads for each sample for each exon
Supplementary_files_format_and_content: RNASeq017_gene_reads_UQNormalized_for_GEO.csv: first column has the Gene Symbol, and subsequent 30 columns provide the normalized reads for each sample for each gene

organism: Macaca mulatta

source_name: Dissected Tissue (Brain) - Cortical Area 32 (A32)

extract_protocol:
Monkeys were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session. Preparation of brain tissue was described previously (Davenport et al., 2014) and the tissues were collected as part of the MATRR. Necropsy occurred at the time when they would normally begin their drinking session; monkeys were anesthetized with ketamine (10 mg/kg) and maintained on isoflurane. The brains were perfused with ice-cold oxygenated artificial cerebral spinal fluid, removed (< 5 min post-mortem) and sectioned according to each monkey’s individual MRI (Daunais et al., 2010). The prefrontal cortex was isolated, and Area 32 was dissected and frozen in liquid nitrogen.
Library formation (TruSeq Stranded RNA-Seq with RiboZero Gold rRNA depletion) and sequencing on a HiSeq 2000 were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 4 per lane, yielding approximately 50 million total reads per sample.

treatment_protocol: Male rhesus monkeys that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 31, 4-11 years-old, 6-8 kg) were used. They were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. They were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session.The monkeys were from four cohorts, referred to as cohorts 4, 5, 7a and 7b in the Monkey Alcohol Tissue Research Resource (www.MATRR.com). These cohorts where selected because they all had approximately 90 days of induction followed by approximately two 6-month periods of alcohol open access. All monkeys were individually housed (quadrant cages, 0.8 m x 0.8 m x 0.9 m) in a room with controlled light cycle (11 hours lights on, 13 hours lights off), temperature (20-22oC) and humidity (65%). The monkeys had visual, auditory and olfactory contact with other monkeys. They were weighed weekly.

tag: matrr (monkey alcohol tissue research resource) id

tag: cohort

value: COHORT 5

tag: avg age at beginning of 1.5 g/kg etoh induction

tag: avg age after second 6 months of open access

tag: Sex

value: Male

tag: drinking category

value: VHD


title: F1_Addict_1

tag: generation

tag: phenotype


title: F0_NonAddict_3

value: Y


title: RNA130128RH_30

description: Low Drinker: not BD, not HD, and not VHD

value: COHORT 4

value: LD


title: RNA130128RH_31

value: COHORT 7b


title: TP-041 Duplication DPSC

tag: cell type

value: DPSC


title: RNA130128RH_29

description: Heavy Drinker: ethanol consumption of >= 3 g/kg for >= 20% of days

value: HD


title: F0_NonAddict_2


title: RNA130128RH_25

description: Binge Drinker:  ethanol consumption of >= 2 g/kg for >= 55% of days AND a recorded BEC >= 80 mg/dl at least once per year

value: BD


title: RNA130128RH_27


title: F0_Addict_3


title: F1_NonAddict_4


title: F0_Addict_2


title: F0_NonAddict_1


title: RNA130128RH_28

value: COHORT 7a


title: F0_Saline_3

value: Saline-exposed


title: F0_Addict_1


title: RNA130128RH_23


title: TP-023 Control DPSC

value: Neurotypical Control


title: RNA130128RH_20


title: F0_Saline_2

value: SD


title: F0_Saline_1


title: RNA130128RH_24


title: H3K27acChIP_input

city: Marburg

first: Magdalena

last: Huber

address: Hans-Meerwein-Str. 2

country: Germany

institute: Institute of Medical Microbiology

data_processing:
Mapping was performed against GRCm38 reference genome using bowtie2 (version 2.2.9)
Peak calling was performed with MACS2 using sharp peak calling algorithm. Downstream analyses were performed with ChIPPeakAnno package.
Genome_build: GRCm38
Supplementary_files_format_and_content: BW files were generated

source_name: Th9 cells

growth_protocol: For the generation of Th9 cells, mice were sacrificed by cervical dislocation. Spleen and lymph nodes were removed and T cells were isolated by magnetic negative selection. Th9 cell cultures were cultured in RPMI supplemented with 10% FCS in the presence of IL-2, IL-4 and TGF-b.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed using KAPA Library Preparation Kit Ion Torrent (KAPPA Biosystems). Ion Torrent S5 (Thermo Fisher) was used for single-end Sequencing.

treatment_protocol: Th9 cells were cultures in the absence or presence of recombinant rat IFN-g (5 ng/ml).

value: Foxp3-IRES-DTR/GFP knock-in (Foxp3GFP)

tag: chip antibody


title: RNA130128RH_22


title: TFChIP_B6_input


title: IRF4_Th9IFNg

source_name: Th9 cells + IFN-g

value: abcam,  ab101168


title: RNA130128RH_19


title: IRF4_Th9


title: RNA130128RH_16


title: RNA130128RH_17


title: Ctrl (HT)

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Read alignments to the mm10 genome were made using tophat -4 -r 0.
Raw counts were calculated using featureCounts (v1.4.6-p4). This counts were used as inputs to DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts were calculated using featureCounts (v1.4.6-p4)

source_name: Ctrl (HT)

growth_protocol: Animals were bred and housed in the Association for Assessment and Accreditation of Laboratory Animal Care-accredited animal facility of Cincinnati Children’s Hospital Medical Center.

extract_protocol:
Total RNA was isolated from optic nerves using Trizol reagent (Invitrogen) followed by chloroform extraction and purification by RNeasy kit (Qiagen)
Total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies).

treatment_protocol: Adult animals (> 2 month old) were treated with tamoxifen to induce genetic recombination.

tag: tissue

value: Optic Nerve


title: NF1 f/f (FL)

source_name: NF1 f/f (FL)


title: RNA130128RH_15


title: IRF1_santacruz_Th9_IFNg

value: santa cruz, sc-640x


title: NF1 f/f (FH)

source_name: NF1 f/f (FH)


title: IRF1_abcam_Th9_IFNg

value: abcam, ab186384


title: H3K27Ac_Th9_IFNg

value: GeneTex,  GEX60815


title: RNA130128RH_13

value: Male


title: RNA130128RH_12

value: COHORT 5

value: VHD


title: NF1 f/f (EZ)

source_name: NF1 f/f (EZ)


title: Ctrl (IB)

source_name: Ctrl (IB)


title: Ctrl (IF)

source_name: Ctrl (IF)


title: H3K27Ac_Th9


title: RNA130128RH_11

value: COHORT 4


title: Mature sample 2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

data_processing:
Contigs assembled with Trinity v.2.2
Reads aligned to contigs using NCBI blastn
Supplementary_files_format_and_content: SuppFile1.xls; normalized counts in Excel spreadsheet

organism: Thlaspi arvense

source_name: Nectary tissue

extract_protocol:
Two types of RNA samples were prepared from pennycress nectaries: mature nectaries (equivalent to Stage 14–15 flowers from Arabidopsis thaliana), and immature nectaries (equivalent to Stage 11–12 flowers from Arabidopsis thaliana). Mature nectaries secrete nectar, whereas immature nectaries are pre-secretory. All nectary tissues were separately dissected by hand from the flowers of primary inflorescences of ca. 40 day-old plants. Due to the small size of nectaries, dissections took place over several days from 4–8 hours after dawn (h.a.d.). Isolated nectaries were pooled in RNAlater™ solution (Ambion, Austin, TX) on ice, and stored at 4°C prior to RNA extraction. Up to four nectaries were collected per flower, with approximately 100 nectaries being processed as a single RNA sample. Each biological replicate was represented by nectaries pooled from different sets of plants. RNA was extracted from nectaries by mechanical disruption, with a microcentrifuge pestle, and using the RNAqueous®-Micro micro scale RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX).
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

tag: developmental stage

value: mature


title: RNA130128RH_10


title: Mature sample 3


title: Mature sample 1


title: RNA130128RH_9

value: HD