title: iNKT 1

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Natural killer T cell

data_processing:
All sequence reads were extracted in FASTQ format using BCL2FASTQ  Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequence reads were mapped to hg19 reference genes, downloaded on December 10, 2012 using Tophat v2.0.8b and quantified using RPKMforGenes.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: lymphocyte

extract_protocol:
mRNA extraction was performed using RNeasy micro kit (QIAGEN) according to standard instructions.
Sample1-13: cDNA synthesis was performed following to Ovation RNA-seq2 (NuGEN), after which the Illumina library was prepared using Encore NGS Multiplex System I (NuGEN). The libraries were sequenced using a HiSeq 2500 in 101 cycle Single-Read mode.
Sample14-17: cDNA was synthesized using SMARTer Ultra Low Input RNA for Illumina Sequencing-HV kit (Clontech), after which the Illumina library was prepared using a Low Input Library Prep kit (Clontech). The libraries were sequenced using a HiSeq 2500 in 101 cycle Single-Read mode.

tag: cdna synthesis

value: iNKT


title: NK 3

status: Public on Oct 04 2016

type: SRA

description: Natural killer cell

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: Ovation RNA-Seq System V2 NuGEN)

tag: cell type

value: NK


title: CD8 T 1

description: CD8+ T cell

value: CD8 T


title: CD8a- re-iNKT 2

description: CD8a- re-differentiated natural killer T cell

value: SMARTer Ultra Low Input RNA for Illumina Sequencing-HV kit (Clontech)

value: CD8a- re-iNKT


title: Donor D29, live sorted cells, library 6

city: Utrecht

first: Mauro

last: Muraro

state: Utrecht

address: Uppsalalaan, 8

country: Netherlands

institute: Single Cell Discoveries

data_processing:
Paired end reads obtained by automated CEL-seq2 were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the human genome release hg19 downloaded from the UCSC genome browser. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode followed by a 4bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases.
Genome_build: hg19
Supplementary_files_format_and_content: cellsystems_dataset_4donors.csv: Tab separated data file for all sequencing libraries combined, listing all genes (rows) and the number of sequenced unique transcripts for all samples. Column name indicates the originating donor (D*) and the cell number of the experiment, separated by an underscore. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: human pancreas

extract_protocol:
Cells were sorted into 5µl Vapor-Lock (Qiagen) containing a droplet with primers and dNTPs. Cells were lysed at 65 degrees Celsius for 5 minutes. mRNA was then reverse transcribed by adding RT mix.
RNA was processed by an automated version of the previously described Cel-Seq2 technique. Libraries were sequenced on a Illumina NextSeq500 using 75bp paired end sequencing.

tag: tissue

value: pancreas


title: DIF_STAT3_B

city: Stuttgart

first: Cristiana

last: Lungu

state: BW

address: Allmandring 31

department: Institute of Cell Biology and Immunology

country: Germany

institute: University of Stuttgart

description: processed data file: Merged_DIF_STAT3.bigwig

library_source: genomic

data_processing:
The FASTQ files were mapped to the human reference genome (assembly hg19) using BOWTIE2 with very-sensitive presets in end-to-end mode on Galaxy Platform (version 2.2.6). The resulting BAM files of ChIPs were deduplicated with RmDup Samtools (Galaxy version 2.0). The corresponding BAM files of the replicates were merged within condition. The merged BAM files were normalized to fragments (reads) per kilobase per million (RPKM) using the bamCoverage tool on Deeptools Galaxy (version 1.1.4) with minimum mapping quality (MAPQ) set to 10 and with removal of duplicates (--ignoreDuplicates).
Genome_build: hg19
Supplementary_files_format_and_content: bigwig represent the normalized RPKM values of ChIP-seq signal

molecule: genomic DNA

growth_protocol:
Human fetal osteoblasts (hFOB) were maintained as previously described (Harris et al., 1995). In short, cells were maintained at 34⁰C in 5% CO2-atmosphere incubator in phenol red-free high-glucose Dulbecco’s modified Eagle’s media (DMEM/F12, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich).
L3.6 cells were maintained in Minimum Essential Media (MEM, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich) as previously described (Herreros-Villanueva et al., 2013).

extract_protocol:
The ChIP was performed with 20 min crosslinking in 1 % formaldehyde in PBS. Following chromatin shearing , 1-2µg antibody was used for immunoprecipitation overnight. The immunocomplexes were incubated 2 additional hours with protein A sepharose beads and subjected to washes. After reversing the cross-linking, the DNA was isolated by standart phenol-chloroform-isoamyl extraction procedure.
ChIP-Seq libraries were prepared with MicroPlex Library Preparation Kit following the manufacturer's instructions.

treatment_protocol: For induction of osteoblastic differentiation, the confluent cells were treated with differentiation cocktail as described previously (Karpiuk et al., 2012) and shifted to 39⁰C incubator.The undifferentiated cells were incubated with DMSO for 24 hr and then harvested. For differentiated state, cells were preatreated with JQ1 (250nM) or equal volume of DMSO one hour before the induction of differentiation. The media was refreshed every 48 hr with subsequent addition of inhibitor. The cells were differentiated for 5 days.

tag: immortalization type

value: SV40 large T antigen immortalized

value: human Fetal Osteoblasts (hFOB)

tag: protocol

value: differentiated for 5 days into osteoblastic lineage

tag: chip antibody

value: Santa Cruz, sc-482, C-20


title: DIF_TEAD1_B

description: processed data file: Merged_DIF_TEAD1.bigwig

value: BD Biosciences,  610922, 31/TEF-1


title: CD8 T 2

description: CD8+ T cell


title: CD8a+ re-iNKT 1

description: CD8a+ re-differentiated natural killer T cell

value: CD8a+ re-iNKT


title: DIF_TEAD1_A


title: Donor D28, live sorted cells, library 5


title: DIF_JUND_A

description: processed data file: Merged_DIF_JUND.bigwig

value: Santa Cruz, sc-74,329


title: expanded DN iNKT 2

description: CD4- natural killer T cell

value: expanded DN iNKT


title: iNKT 2

description: Natural killer T cell


title: UND_RNAPII_C

description: processed data file: Merged_UND_RNAPII.bigwig

value: undifferentiated

value: Santa Cruz, sc-899, N-20


title: CD4 T 1

description: CD4+ T cell

value: CD4 T


title: DIF_FOSL2_B

description: processed data file: Merged_DIF_FOSL2.bigwig

value: Santa Cruz, sc-604, Q-20


title: DIF_CEBPb_A

description: processed data file: Merged_DIF_CEBPb.bigwig

value: Santa Cruz, sc-150, C-19


title: expanded re-iNKT 2

description: re-differentiated natural killer T cell

value: Ovation RNA-Seq System V2 NuGEN)

value: expanded re-iNKT


title: CD4 T 2

description: CD4+ T cell


title: DIF_RNAPII_C

description: processed data file: Merged_DIF_RNAPII.bigwig


title: expanded re-iNKT 1

description: re-differentiated natural killer T cell


title: DIF_FOSL2_A


title: DIF_CEBPb_B


title: NK 2

description: Natural killer cell

value: NK


title: NK 1

description: Natural killer cell


title: expanded CD4+ iNKT 1

description: CD4+ natural killer T cell

value: expanded CD4+ iNKT


title: DIF_RNAPII_B

value: SV40 large T antigen immortalized


title: expanded DN iNKT 1

description: CD4- natural killer T cell


title: UND_RNAPII_B

value: human Fetal Osteoblasts (hFOB)


title: expanded CD4+ iNKT 2

description: CD4+ natural killer T cell


title: ChIP-seq WCE H1 hESC differentiated at 48 hours

city: Boston

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

country: USA

institute: Mass General Hospital, Harvard Medical School

data_processing:
ChIP-seq data were mapped into human reference genome (hg19) by bowtie2 and then the mapped reads were processed by using MACS2 to call peaks.
genome build: hg19
Mapped ChiP-seq reads were processed with MACS2.  Bigwig files contain the signal tracks of SMAD3 ChIP of hESC differentiated at 0 hr after subtracting the background (WCE) (generated by MACS2).

source_name: H1 human Embryonic stem cells (hESC)

growth_protocol: H1 (WA01) cells (WiCell) were cultured in mTeSR1 (Stem Cell Technologies) in feeder-free conditions and differentiated toward endoderm as previously described (Sigova et al., 2013) except hESCs were passaged with 0.5 mM EDTA in DPBS (Life Technologies)

extract_protocol:
For ChIP, cells were crosslinked with 1% formaldehyde for 10 minutes prior to sonication to solubulize the chromatin.  The sheared chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using antibody against SMAD3. Purified immunoprecipitated DNA samples were prepared for sequencing using the Truseq ChIP kit from Illunima.
ChIP-seq libraries were prepared according to instructions accompanying the TruSeq ChIP Kit and barcoded for sequencing.

treatment_protocol: hESCs were differentiated in RPMI with B27 supplement in the presence of 50 ng/ml Activin A (R&D Systems)

tag: cell line

value: H1 hESC

tag: state

value: RPMI+ B27 media for 24hrs and 50 ng/ml Activin for 48 hrs


title: ChIP-seq SMAD3 H1 hESC differentiated at day 0

value: RPMI+ B27 media for 24hrs

tag: antibody

value: SMAD3, Abcam, AB28379


title: DIF_RNAPII_A

value: differentiated for 5 days into osteoblastic lineage


title: UND_BRD4_C

description: processed data file: Merged_UND_BRD4.bigwig

value: N-terminal BRD4 antibody, Wu et al., 2006


title: ChIP-seq WCE H1 hESC differentiated at day 1

value: RPMI+ B27 media for 24hrs and 50 ng/ml Activin for 1 hr


title: ChIP-seq SMAD3 H1 hESC differentiated at day 1


title: UND_BRD4_B

value: undifferentiated


title: UND_RNAPII_A

value: Santa Cruz, sc-899, N-20


title: ChIP-seq SMAD3 H1 hESC differentiated at 48hours


title: DIF_BRD4_C

description: processed data file: Merged_DIF_BRD4.bigwig


title: ChIP-seq WCE H1 hESC differentiated at day 0


title: UND_BRD4_A


title: DIF_BRD4_B


title: UND_H2Bub1_B

description: processed data file: Merged_UND_H2Bub1.bigwig

tag: treatment

value: DMSO

value: Cell Signalling, 5546, D11


title: iPSC_2

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Base-calling performed by Illumina pipeline
Alignment to hg19 UCSC transcript map using TopHat
Comparisons between groups performed using Cuffdiff
Data analysis and visualization using Cummerbund in R
Genome_build: hg19
Supplementary_files_format_and_content: Processed data obtained using the fpkmMatrix function in Cummerbund, results are FPKM per replicate

source_name: Induced pluripotent stem cells derived from CD4+ T-cells

growth_protocol: iPSC culture and mDA differentiation protocols are described in the methods section of the article

extract_protocol:
Total cellular RNA was prepared using a Qiagen Rneasy kit
Libraries were built using the PureLink Kit

treatment_protocol: No treatment

tag: genotype/variation

value: WT


title: iPSC_1


title: DIF_H2Bub1_C

description: processed data file: Merged_DIF_H2Bub1.bigwig


title: ChIP-seq WCE H1 hESC

value: cultured in mTESR1


title: DIF_JQ1_H2Bub1_C

description: processed data file: Merged_DIF_JQ1_H2Bub1.bigwig


title: iPSC_3


title: iPSC_0


title: ChIP-seq SMAD3 H1 hESC


title: DIF_H2Bub1_B


title: DIF_JQ1_H2Bub1_B


title: DIF_BRD4_A


title: UND_H2Bub1_C


title: N398_1

source_name: Midbrain dopaminergic neuron cultures derived from iPSC

tag: subline

value: SB


title: N398_2

value: SG


title: N398_0

value: SA


title: D398_1


title: Col-0 4 hour ethylene RNAseq, rep2

city: Austin

first: Hong

last: Qiao

state: TEXAS

address: 2506 speedway, NMS5.324

department: Department of Molecular Biosciences

institute: The University of Texas at Austin

description: ethylene treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome usingTopHat version 2.0.8 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.1.1
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample, generated by Cuffdiff version 2.1.1

organism: Arabidopsis thaliana

source_name: whole COL-0 seedling after ethylene treatment

growth_protocol: Arabidopsis seeds were  dark-grown at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million  (ppm) ethylene) for 4 hours

tag: developmental stage

value: whole seedling

tag: genotype


title: UND_H3K27me3_C

description: processed data file: Merged_UND_H3K27me3.bigwig

value: SV40 large T antigen immortalized

value: human Fetal Osteoblasts (hFOB)

value: Diagenode, C15410195


title: D398_2


title: UND_H2Bub1_A


title: UND_H3K27me3_A


title: Col-0 4 hour ethylene RNAseq, rep1

description: ethylene treated for 4 hours


title: DIF_JQ1_H3K27me3_C

description: processed data file: Merged_DIF_JQ1_H3K27me3.bigwig


title: DIF_JQ1_H3K27me3_B


title: ENAP1ox 4 hour air RNAseq, rep1

description: air treated for 4 hours

source_name: whole COL-0, ENAP1ox seedling after air treatment

value: ENAP1ox in COL background


title: DIF_JQ1_H3K27me3_A

value: differentiated for 5 days into osteoblastic lineage


title: DIF_H3K27me3_C

description: processed data file: Merged_DIF_H3K27me3.bigwig


title: DIF_JQ1_H2Bub1_A


title: DIF_H2Bub1_A


title: DIF_H3K27me3_B


title: DIF_H3K27me3_A


title: UND_H3K27ac_A

description: processed data file: Merged_UND_H3K27ac.bigwig

value: Diagenode, C15410196


title: ein2_ethylene_IgG control

description: ethylene treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using bowtie2 (version  2.1.0) with default parameters
Duplicate reads were removed using SAMtools
For each histone modification in each condition,mapped reads were pooled across ChIP-seq replicates as described (Gjoneska, Pfenning et al.Nature, 2015)
Peaks significantly enriched in ChIP-seq tags were identified by Model-based Analysis for ChIP-Seq (MACS2, version 2.1.0.20150603; parameters: --nomodel, -p 0.01, -B)
Genome_build: tair10
Supplementary_files_format_and_content: the txt and bedgraph files are generated using MACS2 (version 2.1.0.20150603; parameters: --nomodel, -p 0.01, -B) software.

source_name: whole ein2-5 seedling after ethylene treatment

extract_protocol:
Histone proteins were extracted from seedlings and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to NEB instructions of the ChIP-seq Library Kit (NEB #E6240S/L)

value: Magnetic Protein G Beads (Promega, G747A)


title: DIF_JQ1_H3K27ac_C

description: processed data file: Merged_DIF_JQ1_H3K27ac.bigwig


title: ein2_H3K14Ac_ethylene_ChIPseq_rep2

description:
ethylene treated for 4 hours
bedgraph file: 17add23_16_treat_pileup.bedgraph
bedgraph file: 17add23_16_control_lambda.bedgraph
peak file: 17add23_16_peaks.xls

value: antiH3K14Ac (Millipore; 07-353)


title: ein2_H3K23Ac_ethylene_ChIPseq_rep1

description:
ethylene treated for 4 hours
bedgraph file: 18add24_16_treat_pileup.bedgraph
bedgraph file: 18add24_16_control_lambda.bedgraph
peak file: 18add24_16_peaks.xls

value: anti-H3K23Ac (Millipore; 07-355)


title: D398_0


title: UND_H3K27me3_B

value: undifferentiated

value: DMSO


title: DIF_JQ1_H3K27ac_B


title: ein2_H3K14Ac_ethylene_ChIPseq_rep1


title: ein2_air_IgG control

description: air treated for 4 hours

source_name: whole ein2-5 seedling after air treatment


title: DIF_H3K27ac_B

description: processed data file: Merged_DIF_H3K27ac.bigwig


title: DIF_JQ1_H3K27ac_A


title: ein2_H3K23Ac_air_ChIPseq_rep1

description:
air treated for 4 hours
bedgraph file: 15add21_19_treat_pileup.bedgraph
bedgraph file: 15add21_19_control_lambda.bedgraph
peak file: 15add21_19_peaks.xls


title: ein2_H3K23Ac_air_ChIPseq_rep2


title: DIF_H3K27ac_A


title: ein2_H3K14Ac_air_ChIPseq_rep2

description:
air treated for 4 hours
bedgraph file: 14add20_19_treat_pileup.bedgraph
bedgraph file: 14add20_19_control_lambda.bedgraph
peak file: 14add20_19_peaks.xls


title: ENAP1ox 4 hour air RNAseq, rep2

description: air treated for 4 hours


title: UND_INPUT_C

description: processed data file: Merged_UND_INPUT.bigwig


title: UND_INPUT_B


title: COL_ethylene_IgG control

description: ethylene treated for 4 hours


title: COL_H3K23Ac_ethylene_ChIPseq_rep2

description:
ethylene treated for 4 hours
bedgraph file: 6add12_4_treat_pileup.bedgraph
bedgraph file: 6add12_4_control_lambda.bedgraph
peak file: 6add12_4_peaks.xls


title: ein2_H3K14Ac_air_ChIPseq_rep1


title: UND_H3K27ac_B


title: ein2_H3K23Ac_ethylene_ChIPseq_rep2


title: UND_INPUT_A


title: DIF_JQ1_INPUT_A

description: processed data file: Merged_DIF_JQ1_INPUT.bigwig


title: DIF_JQ1_INPUT_B


title: DIF_INPUT_C

description: processed data file: Merged_DIF_INPUT.bigwig


title: COL_H3K23Ac_ethylene_ChIPseq_rep1


title: COL_H3K9Ac_ethylene_ChIPseq_rep2

description:
ethylene treated for 4 hours
bedgraph file: 26add28_4_treat_pileup.bedgraph
bedgraph file: 26add28_4_control_lambda.bedgraph
peak file: 26add28_4_peaks.xls

value: AntiH3K9aC (Millipore; 07-352)


title: COL_H3K9Ac_ethylene_ChIPseq_rep1


title: DIF_INPUT_B


title: COL_H3K23Ac_air_ChIPseq_rep1

description:
air treated for 4 hours
bedgraph file: 3add9_7_treat_pileup.bedgraph
bedgraph file: 3add9_7_control_lambda.bedgraph
peak file: 3add9_7_peaks.xls

source_name: whole COL-0 seedling after air treatment


title: DIF_INPUT_A


title: COL_air_IgG control

description: air treated for 4 hours


title: COL_H3K23Ac_air_ChIPseq_rep2


title: mRNA_DIF_siBRD4_#4_C

data_processing:
The FASTQ  files were mapped to the human genome (assembly hg19) using TopHat Gapped-read mapper for RNA-seq data with very-sensitive BOWTIE2 settings on Galaxy Platform (Version 0.9). The read counting was performed via HTSeq (version 0.6.0) with following parameters: -f bam -r pos -s reverse -a 10 -t exon -m union. The count files were subsequently subjected for differential analysis using the DESeq2 Package on R (Bioconductor version 3.2.2). The Wald Test was utilized for a comparisons. The resulting tables for log2fold gene expression changes are provided for following comparisons: 1. DESeq2_Results_DIF(DMSO+siCNTR)_vs_UND(DMSO+siCNTR).csv – for differentiation induced changes, where DMSO and siCNTR treated conditions were treated as replicates of one state, undifferentiated (UND) and differentiated (DIF), respectively; 2. DESeq2_Results_DIF_siBRD4_(#3+#4)_vs_DIF_siCNTR.csv – for BRD4 knockdown mediated effects versus siCNTR in differentiated state, where the replicates of two BRD4 siRNAs used were treated as replicates of one condition; 3. DESeq2_Results_DIF_JQ1_vs_DIF_DMSO.csv – for comparison of JQ1 induced effects in differentiated state versus DMSO.  The variance stabilization transformed read counts (All_conditions_variancestabilized_counts.csv) for all the conditions were obtained through DESeq2 analysis using Likelihood Ratio Test reduced by “treatment”.
Genome_build: hg19
Supplementary_files_format_and_content: The provided mRNA-Seq analysis files in .csv format represent the differential gene expression analysis results obtained by DESeq2. The variance stabilization transformed read counts for all conditions and replicates is included in an additional .csv file

growth_protocol: Human fetal osteoblasts (hFOB) were maintained as previously described (Harris et al., 1995). In short, cells were maintained at 34⁰C in 5% CO2-atmosphere incubator in phenol red-free high-glucose Dulbecco’s modified Eagle’s media (DMEM/F12, Invitrogen) supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin (Sigma-Aldrich).

extract_protocol:
The total cell RNA was isolated with standard TRIzol extraction protocol.
For mRNA-Seq, 1 µg of total cell RNA was subjected to mRNA enrichment by NEXTflex Poly(A) Beads Protocol which was then used for library preparation with NEXTflex Rapid Directional mRNA-Seq from Bioo Scientific.

treatment_protocol: For induction of osteoblastic differentiation, the confluent cells were treated with differentiation cocktail as described previously (Karpiuk et al., 2012) and shifted to 39⁰C incubator. siRNA transfections were performed using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer’s instructions. The cells were first transfected, and 24 hours later (the undifferentiated controls were harvested at this point)  the cells were pretreated with JQ1 (250nM) or equal volume of DMSO one hour before the induction of differentiation.The cells were differentiated for 5 days. After 72 hours cells were re-transfected following forward-transfection protocol.

value: siBRD4 #4


title: mRNA_DIF_siBRD4_#4_B


title: COL_H3K14Ac_air_ChIPseq

description:
air treated for 4 hours
bedgraph file: 2_7_treat_pileup.bedgraph
bedgraph file: 2_7_control_lambda.bedgraph
peak file: 2_7_peaks.xls


title: mRNA_DIF_siBRD4_#4_A


title: mRNA_DIF_siBRD4_#3_B

value: siBRD4 #3


title: mRNA_DIF_siBRD4_#3_C


title: COL_H3K9Ac_air_ChIPseq_rep1

description:
air treated for 4 hours
bedgraph file: 25add27_7_treat_pileup.bedgraph
bedgraph file: 25add27_7_control_lambda.bedgraph
peak file: 25add27_7_peaks.xls


title: COL_H3K9Ac_air_ChIPseq_rep2


title: mRNA_DIF_JQ1_C


title: mRNA_DIF_siBRD4_#3_A


title: COL_H3K14Ac_ethylene_ChIPseq

description:
ethylene treated for 4 hours
bedgraph file: 5_4_treat_pileup.bedgraph
bedgraph file: 5_4_control_lambda.bedgraph
peak file: 5_4_peaks.xls


title: mRNA_DIF_JQ1_A


title: mRNA_DIF_JQ1_B


title: mRNA_UND_siCNTR_C

value: siCNTR


title: mRNA_UND_DMSO_B


title: mRNA_UND_DMSO_A


title: mRNA_UND_DMSO_C


title: mRNA_DIF_siCNTR_B


title: mRNA_DIF_siCNTR_C


title: mRNA_DIF_siCNTR_A


title: mRNA_DIF_DMSO_C


title: mRNA_DIF_DMSO_B


title: RNA-seq H1 hESC DIGIT KO1 day4 rep2

data_processing:
Raw RNA-seq data were mapped into human reference genome (hg19) with bowtie2 (v2.1.0). Furthermore, HTSeq (v0.6.1) was used to quantify expression of coding genes and long noncoding RNA genes in WT and DIGIT KO hESC lines.
genome build: hg19
processed data files format and content: Mapped RNA-seq reads were processed with HTSeq. Text files contain the number of reads mappped into the coding and noncoding genes.

molecule: polyA RNA

extract_protocol:
Total RNA was isolated by RNeasy column (Qiagen).  1000 ug of RNA with a RIN score of greater than 9.0 was used for library construction.
RNA-seq libraries were prepared according to instructions for the TruSeq Stranded mRNA Kit and barcoded for sequencing.

value: DIGIT KO hESC KO1

value: DIGIT KO hESC differentiated towards endoderm for 4 days

tag: index

value: GTGGCC


title: mRNA_DIF_DMSO_A

value: SV40 large T antigen immortalized

value: human Fetal Osteoblasts (hFOB)


title: RNA-seq H1 hESC WT day4 rep2

value: H1 hESC Wild Type (WT)

value: H1 hESC differentiated towards endoderm for 4 days

value: ATTCCT


title: RNA-seq H1 hESC DIGIT KO1 day4 rep1

value: GTTTCG


title: RNA-seq H1 hESC DIGIT KO2 day4 rep1

value: DIGIT KO hESC KO2

value: ACTGAT


title: RNA-seq H1 hESC DIGIT KO2 day4 rep2

value: GAGTGG


title: RNA-seq H1 hESC DIGIT KO2 day0 rep1

value: cultured in mTESR1

value: TAGCTT


title: RNA-seq H1 hESC WT day4 rep1

value: GGCTAC


title: RNA-seq H1 hESC DIGIT KO2 day0 rep2

value: CGTACG


title: RNA-seq H1 hESC DIGIT KO1 day0 rep1

value: ACTTGA


title: RNA-seq H1 hESC DIGIT KO1 day0 rep2

value: DIGIT KO hESC KO1

value: GATCAG


title: RNA-seq H1 hESC WT day0 rep2

value: TTAGGC


title: RNA-seq H1 hESC WT day0 rep1

value: ATCACG


title: 10_A_Total human milk cells

city: Crawley

first: Mohammed

last: Alsaweed

state: WA

address: 35 stirling hwy

department: Biochemistry

country: Australia

institute: UWA

description:
A_group_known_miRNA.txt
10_A

data_processing:
Illumina Casava1.7 software used for basecalling.
Cleaning reads: including getting rid of low quality reads, rid of reads with 5' primer contaminants, rid of reads without 3' primer, rid of reads without the insert tag, rid of reads with poly A, rid of reads shorter than 18nt.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
length distribution of all clean reads
Analysis of base composition and quality
map to human genome
reads aligned to miRBase database
Novel miRNA prediction
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files includ include reads for each identified SE50 molecules in each Sample
Supplementary_files_format_and_content: B_group_known_miRNA.txt
Supplementary_files_format_and_content: A_group_known_miRNA.txt

source_name: Total human milk cells

extract_protocol:
Isolate of total humam ilk cell by centrifugation of whole milk, then cells were whashed three times using PBS, total RNA/miRNA was extracted using miRNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: collection time

value: Collected during month 2 of lacation (week 4-8)

tag: body fluid

value: Breastmilk

tag: fraction

value: Total cell content


title: 10_B_Total human milk cells

description:
B_group_known_miRNA.txt
10_B


title: 9_A_Total human milk cells

description:
A_group_known_miRNA.txt
9_A


title: mRNA_UND_siCNTR_A

value: SV40 large T antigen immortalized

tag: cell type

value: human Fetal Osteoblasts (hFOB)

value: undifferentiated

value: siCNTR


title: 8_A_Total human milk cells

description:
A_group_known_miRNA.txt
8_A


title: mRNA_UND_siCNTR_B


title: 9_B_Total human milk cells

description:
B_group_known_miRNA.txt
9_B


title: 8_B_Total human milk cells

description:
B_group_known_miRNA.txt
8_B


title: 7_A_Total human milk cells

description:
A_group_known_miRNA.txt
7_A


title: 6_B_Total human milk cells

description:
B_group_known_miRNA.txt
6_B


title: 5_A_Total human milk cells

description:
A_group_known_miRNA.txt
5_A


title: 7_B_Total human milk cells

description:
B_group_known_miRNA.txt
7_B


title: 5_B_Total human milk cells

description:
B_group_known_miRNA.txt
5_B


title: 4_A_Total human milk cells

description:
A_group_known_miRNA.txt
4_A


title: 4_B_Total human milk cells

description:
B_group_known_miRNA.txt
4_B


title: 2_A_Total human milk cells

description:
A_group_known_miRNA.txt
2_A


title: 3_A_Total human milk cells

description:
A_group_known_miRNA.txt
3_A


title: 6_A_Total human milk cells

description:
A_group_known_miRNA.txt
6_A


title: 1_A_Total human milk cells

description:
A_group_known_miRNA.txt
1_A


title: 2_B_Total human milk cells

description:
B_group_known_miRNA.txt
2_B


title: GAS1 shRNA3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

description: Sample 6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced readsmapped to hg19 whole genome using TopHat v2.0.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each group (C1=control; C2=GAS1-shRNA)

source_name: BGC823_GAS1 shRNA

growth_protocol: The human gastric cancer cells BGC823 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
total RNA of BGC23 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The shRNA adenovirus against human lncRNA GAS1 were introduced into the BGC823 gastric cells, while nonspecific shRNA virus was used as negative controls.

value: human gastric cancer cells

tag: passage

tag: transfected with


title: GAS1 shRNA1

description: Sample 4

value: shRNA adenovirus against human lncRNA GAS


title: Control shRNA1

description: Sample 1

source_name: BGC823_Control shRNA

value: nonspecific shRNA virus


title: Control shRNA2

description: Sample 2


title: H3K9ac NC_ChIPSeq

data_processing:
Basecalls performed using HOMER v4.7.2
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie 1.0.1
Data were filtered with a FDR value cutoff 0.05
peaks were called using HOMER v.4.7.2.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files were generated and compressed by IGV

source_name: BGC823 cells

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

treatment_protocol: The shRNA adenovirus against human lncRNA PRLGC were introduced into the BGC823 gastric cells, while nonspecific shRNA virus was used as negative controls.

tag: passages

value: H3(acetyl K9) (Abcam, ab10812)


title: GAS1 shRNA2

description: Sample 5


title: NC_Input_ChIPSeq

tag: chip antibody

value: IgG


title: H3K4me3 KO_ChIPSeq

tag: cell line

value: shRNA adenovirus against human lncRNA PRLG

value: H3K4me3 (Abcam,ab8580)


title: H3K9ac KO_ChIPSeq


title: H3K4me3 NC_ChIPSeq


title: KAT2A KO_ChIPSeq


title: 3_B_Total human milk cells

description:
B_group_known_miRNA.txt
3_B


title: KAT2A NC_ChIPSeq


title: 1_B_Total human milk cells

description:
B_group_known_miRNA.txt
1_B


title: BC30

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
Base calling and quality scoring: Real-Time Analysis v1.18.61
FASTQ file generation and de-multiplexing: CASAVA pipeline version 1.8.2
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.16.1) using the in-built mm10 annotation.
Count data from two batches were combined and batch effects removed using removeBatchEffect from limma
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) in the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million.
Gene-wise generalised linear models (McCarthy et al NAR 2012) were fitted to summarise the values from replicates samples using functionality from the edgeR package (version 3.22.0, Smyth, 2005).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID and the number of reads mapping to that gene from each sample.

organism: Mus musculus

extract_protocol:
Bone marrow cells were flushed and single cell suspension were stained with appropriate antibodies. Cells were FACS-sorted directly into 384 well-plate containing lysis buffer.
3' biased mRNA libraries were prepared according to the CEL-Seq protocol (Hashimshony et al., 2012) with the following deviations: 1) all column clean-ups were exchanged for AmpPure XP magnetic bead  (Beckman Coulter) clean-ups; 2) aRNA underwent TurboDNase I (NEB) tretment proir to fragmentation; 3) fragmentation was done using the Covaris system 4) Phosphatase and PNK treatment were omitted

value: CILP

tag: initial sequence

value: GCTTGCGC

value: TCF

tag: batch


title: WDR5 KO_ChIPSeq


title: WDR5 NC_ChIPSeq


title: BC29

value: CLP

value: CTAACCGC


title: BC28

description:
Negative Control containing only ERCC
counts_batch1.txt

source_name: CTRL

value: CTRL

value: ATGTGGAG

value: Control


title: CPEB4_IP_shCPEB4_replicate 1

city: Madrid

first: Eva

last: Pérez-Guijarro

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology

country: Spain

institute: Spanish National Cancer Research Centre

description: RIP-seq

data_processing:
Read files were quality-checked with FastQC.
40-nt single-end reads were aligned to the human genome (GRCh37/hg19) with TopHat-2.0.4 (using Bowtie 0.12.7 and processed with Samtools 0.1.16), allowing 2 mismatches and selecting the best hit.
Transcripts quantification and differential expression calculated with Cufflinks 1.3.0
Ensembl Homo_sapiens.GRCh37.72 transcript annotations used
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tables were generated with Cufflinks 1.3.0 and contain transcripts abundance measured in FPKM values

source_name: SK-Mel-103 melanoma cell line

growth_protocol: Cells were cultured in Dulbecco’s modified Eagle’s medium (Life Technologies) supplemented with 10% fetal bovine serum (Nova-Tech Inc.)

extract_protocol:
RNA was extracted after immunoprecipitation using TRI Reagent (Sigma) including DNase I treatment step.
An estimated mass of 20 ng of RNA per sample was used. Ribosomal RNAs were removed with the Ribo-Zero Gold Kit (Epicentre Cat. No. RZHM11106/RZG1224) and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C). Adapter-ligated library was completed by 10 cycles of PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

treatment_protocol: Cell lysates from parental and shCPEB4 expressing SK-Mel-103 cells were immunoprecipitated using CPEB4 antibody (ab830009, abcam) coupled to Dynabeads Protein A (Invitrogen). Lentivirus-driven gene silencing of CPEB4 was performed using the validated shRNA targeting the sequence GCTGTTGGAAAGACTTGATAA, purchased from Sigma.

tag: time point

value: post infection day 6

tag: treatment

value: shRNA CPEB4 (pLKO backbone, sigma, GCTGTTGGAAAGACTTGATAA)


title: CPEB4_IP_shCPEB4_replicate 2

description: RIP-seq


title: CPEB4_IP_NI_replicate 2

description: RIP-seq

value: parental cells (non-infected)


title: CPEB4_IP_NI_replicate 1

description: RIP-seq


title: BC24

source_name: WT

value: ILCP

value: ATGTGTCA

value: WT


title: BC23

value: GACACTCA


title: BC27

value: GACACGAG


title: BC26

value: CGTGTGAG


title: BC25

value: TCACAGAG


title: Control shRNA3

description: Sample 3

value: human gastric cancer cells

value: nonspecific shRNA virus


title: BC22

value: CGTGTTCA


title: BC14

value: CILP

value: GTCGTGAA

value: TCF


title: BC13

value: CLP

value: CATCAGAA


title: BC9

value: CATCATCC


title: BC11

value: ACGACTCC


title: BC10

value: CTRL

value: GTCGTTCC

value: Control


title: BC8

value: TGATGATC


title: BC21

value: TCACATCA

value: WT


title: BC20

value: ATGTGCGC


title: BC17

value: TCACACGC


title: BC16

value: TGATGGAA


title: BC3

value: ACGACCGC


title: BC15

value: ACGACGAA


title: BC19

value: CILP

value: GACACCGC


title: BC5

value: CATCAATC


title: BC4

value: TGATGCGC


title: BC1

value: CATCACGC


title: BC7

value: CLP

value: ACGACATC


title: L8_selected_blocked_striatum_MID69337_S36_GCCAAT

status: Public on Oct 03 2016

city: Bar Harbor

first: Michael

middle: C.

last: Saul

state: ME

address: 600 Main St

institute: The Jackson Laboratory

data_processing:
Reads were demultiplexed and fastq files were generated using CASAVA v. 1.8.2.
The fastq files were aligned to the GRCm38 (mm10) genome with Ensembl annotation v. 75 using Tophat2 v. 2.0.10 in paired-end mode with Bowtie2 v. 2.1.0 and Samtools v. 0.1.19.
Aligned reads were sorted using Samtools v. 0.1.19.
Gene tag counts were calculated using htseq-count from HTSeq v. 0.6.1.
Exon bin counts were calculated using a flattend GTF file from Ensembl v. 75 with the dexseq_count.py script from the DEXSeq R package v. 1.9.7.
Genome_build: GRCm38 (Ensembl v. 75 annotation)
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files with output of htseq-count on gene IDs (gene_id.counts) or dexseq-count (DEXSeq.counts).

organism: Mus musculus domesticus

source_name: striatum, selected

growth_protocol: The 31 adult male mice from generation 66 used for this experiment were weaned in groups of 2-4 when they were 21 days old, and individually marked, following the usual procedure. When they were 35 days old (+/- 5 days), they were placed individually with access to wheels. Wheel running was monitored continuously for 6 days following the routine phenotyping procedure. Rooms were kept on a shifted light-dark cycle with lights on at 00:00 and off at 12:00. On day 7 at approximately 00:00 hrs, mice were blocked from entering the running wheel by placing a barrier to cover the tunnel connecting the wheel to the cage.

extract_protocol:
Tissue was homogenized with an RNase-free disposable pellet pestle (Fisher) and RNA was extracted using the commercially available RNeasy® Lipid Tissue Mini Kit (Qiagen). Purification of the isolated RNA included treatment with DNase I (Qiagen), accordingly to the manufacturer's instructions. For assessing total RNA yield, aliquot samples were measured with a Qubit® 2.0 (Life Technologies). Quality and integrity of isolated RNA samples were determined by 28S/18S rRNA analysis with an Agilent 2100 Bioanalyzer (Santa Clara, CA).
RNA-Seq libraries were prepared with Illumina's TruSeq Stranded RNA Sample Prep kit. The libraries were pooled and each pool was quantitated by qPCR before sequencing. Libraries were sequenced in 4 lanes for 101 cycles from each end of the fragments on an Illumina HiSeq 2000 using a TruSeq SBS sequencing kit, version 3.

treatment_protocol: Starting at 13:00 and ending at 17:00 (1-4 hours after lights shut off) when mice are normally most active on running wheels, mice were removed from their cages and immediately decapitated. All surfaces and instruments were sprayed with RNase away. The brains were immediately placed on an aluminum platform on wet ice with ventral surface exposed. Using the olfactory tubercles and optic chiasm as landmarks, a razor blade was used to cut a coronal section approximately 1.7 mm thick containing the striatum. The section was then flipped horizontally and the entire striatum (dorsal and ventral) was carefully dissected from the cortex, medial septum, and olfactory tubercles. The striatum was then immediately placed in a centrifuge tube on dry ice and subsequently stored at -80° C.

tag: line

tag: tissue

value: striatum

tag: Sex

value: male

tag: age

value: adult

tag: selection

value: selected

value: blocked

value: GCCAAT


title: L8_selected_blocked_striatum_MID69857_S20_AGTCAA

value: AGTCAA


title: L8_selected_blocked_striatum_MID69557_S32_ATGTCA

value: ATGTCA


title: L8_selected_blocked_striatum_MID69549_S18_GAGTGG

value: GAGTGG


title: L7_selected_blocked_striatum_MID69072_S26_AGTTCC

value: AGTTCC


title: L7_selected_blocked_striatum_MID69081_S52_CTTGTA

value: CTTGTA


title: BC6

value: CILP

value: GTCGTATC

tag: genotype

value: WT


title: BC18

value: ILCP

value: CGTGTCGC


title: BC2

value: CLP

value: GTCGTCGC


title: L7_selected_blocked_striatum_MID69098_S6_CGTACG

value: striatum

value: male

value: CGTACG


title: L6_selected_blocked_striatum_MID69488_S58_GTTTCG

value: adult

value: selected

value: blocked

value: GTTTCG


title: BC12

value: TGATGTCC


title: L7_selected_blocked_striatum_MID69046_S54_ACAGTG

value: ACAGTG


title: L6_selected_blocked_striatum_MID69230_S17_GGCTAC

value: GGCTAC


title: L6_selected_blocked_striatum_MID69181_S7_AGTCAA

value: AGTCAA


title: L3_selected_blocked_striatum_MID69620_S37_TAGCTT

value: TAGCTT


title: L6_selected_blocked_striatum_MID69278_S44_TGACCA

value: TGACCA


title: L3_selected_blocked_striatum_MID69810_S59_ACTTGA

value: ACTTGA


title: L3_selected_blocked_striatum_MID69638_S13_ATTCCT

value: ATTCCT


title: L5_control_blocked_striatum_MID69833_S4_TAGCTT

source_name: striatum, control

value: control


title: L5_control_blocked_striatum_MID69132_S45_CTTGTA

value: CTTGTA


title: L4_control_blocked_striatum_MID69783_S53_GGCTAC

value: striatum


title: Gln-Pro

city: Wuxi

first: Peng

last: Zhang

address: 1800 Lihu road

institute: Jiangnan University

description: nucleosome DNA

data_processing:
MNase-seq reads were aligned to the S288C genome assembly using CLC Genomics Workbench
Data were normalized and analyzed using a nucwave software.
Genome_build: Genome of Saccharomyces cerevisiae S288C
Supplementary_files_format_and_content: wig format, nucleosome score

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae_supplemented with Gln then shifted to Pro

growth_protocol: Yeast was grown on yeast nitrogen base (YNB) medium without ammonia, without amino acids and with 3% (w/v) glucose, supplemented with 1 g/L glutamine (M.Gln) or 1 g/L proline (M.Pro) as the sole nitrogen source. The shift from M.Gln to M.Pro (M.Gln-Pro) was achieved by recovering then filtering the cells grown on M.Gln and cultivating them in fresh M.Pro for 2 h

extract_protocol:
Yeast were treated with 2% formaldehyde for 30 minutes (identical results are obtained with 15 minute incubations), stopped with 125 mM glycine,  then collected by centrifugation, washed, and treated with zymolyase (Seigaku) at 0.25 mg/ml. Then the Lysates were digested with micrococcal nuclease, treated with proteinase K and reverse formaldehyde crosslinks. Finally the nucleosome DNA were phenol:chloroform extracted, ethanol precipitated, and treated with DNase-free RNase. Samples were examined by gel electrophoresis, and reactions with ~90% mononucleosomal DNA were used for squencing.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq® Nano DNA LT Sample Preparation Kit (Part# FC-121-4001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: strain


title: L4_control_blocked_striatum_MID69398_S38_ATCACG

value: male

value: ATCACG


title: Pro

description: nucleosome DNA

source_name: S. cerevisiae_supplemented with Pro


title: PBAT_MERVL+Zscan4+_to_Neg_72h_C

city: Cambridge

first: Simon

middle: Richard

last: Andrews

state: Cambs

address: Babraham Research Campus

department: Science Services

country: United Kingdom

institute: The Babraham Institute

data_processing:
BS-Seq (PBAT): Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1, parameters: --paired). Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to use overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.14.4 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults.  Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
Genome_build: GRCm38
Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

source_name: PBAT MERVL+Zscan4+ to Neg 72h C

growth_protocol: Steady state MERVL+Zscan4c+ ESCs were sorted using the fluorescent reporters. The cells were then returned to culture and the newly emerging negative cells sorted after 72 hours or 7 days for bisulfite analysis.

extract_protocol:
Whole genome bisulfite sequencing libraries were generated using the PBAT method as per Peat et al. 2014 Cell Reports using 10 cycles of PCR
BS-Seq (PBAT)

treatment_protocol: Either 72 hours or 7 days culture time before first and second sorts

value: E14 embryonic stem cell

value: C57BL/6 wild-type


title: L4_control_blocked_striatum_MID69372_S41_GATCAG

value: adult

value: blocked

value: GATCAG


title: L2_control_blocked_striatum_MID69710_S9_GATCAG


title: PBAT_MERVL+Zscan4+_to_Neg_7d_C

source_name: PBAT MERVL+Zscan4+ to Neg 7d C


title: L1_control_blocked_striatum_MID69747_S39_ACTTGA


title: L2_control_blocked_striatum_MID69839_S47_CCGTCC

value: CCGTCC


title: PBAT_MERVL+Zscan4+_to_Neg_72h_A

source_name: PBAT MERVL+Zscan4+ to Neg 72h A


title: L2_control_blocked_striatum_MID69155_S35_CAGATC

value: CAGATC


title: PBAT_MERVL+Zscan4+_to_Neg_7d_A

source_name: PBAT MERVL+Zscan4+ to Neg 7d A


title: L2_control_blocked_striatum_MID69775_S50_ACTGAT

value: ACTGAT


title: L1_control_blocked_striatum_MID69792_S22_GAGTGG

value: GAGTGG


title: L1_control_blocked_striatum_MID69419_S21_ATGTCA

value: ATGTCA


title: PBAT_MERVL+Zscan4+_to_Neg_72h_B

source_name: PBAT MERVL+Zscan4+ to Neg 72h B


title: L3_selected_blocked_striatum_MID69586_S33_GTCCGC

value: selected

value: GTCCGC


title: PBAT_MERVL+Zscan4+_to_Neg_7d_B

source_name: PBAT MERVL+Zscan4+ to Neg 7d B


title: L5_control_blocked_striatum_MID69405_S55_GTGGCC

value: control

value: GTGGCC


title: L5_control_blocked_striatum_MID69010_S5_CGATGT

value: striatum

value: CGATGT


title: L4_control_blocked_striatum_MID69683_S64_GTGAAA

value: male

value: GTGAAA


title: Tfh Activated 4

status: Public on Oct 02 2016

first: Arlene

last: Sharpe

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Samples were run on an illumina HiSeq sequencer using 50bp single end reads
Samples were analyzed with CLC Genomics Workbench 8.0.1 software utilizing standard RNA-seq pipeline alignment (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8)
Samples were normalized as reads per million
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated file containing exonic reads per million

source_name: In Vitro Assay

growth_protocol: in Vitro assay was performed by culturing Tfh and B cells with NP-OVA (Activated condition) or Tfh, B and Tfr cells with NP-OVA (Suppressed condition) for 4 days, cells were resorted

extract_protocol:
Cells were sorted, centrifuged and RNA extracted
RNA-libraries were constructed by enriching for mRNA using OligoDT beads, samples were fragmented, barcoded and then amplified
3' targeted RNA-seq

tag: cell type

value: Tfh Activated


title: Tfh Suppressed 4

value: Tfh Suppressed


title: Tfh Suppressed 3


title: B Suppressed 4

value: B Suppressed


title: Tfh Activated 3


title: B Activated 4

value: B Activated


title: B Activated 2


title: B Activated 3


title: Gln

description: nucleosome DNA

source_name: S. cerevisiae_supplemented with Gln


title: B Suppressed 3


title: Tfh Suppressed 1


title: B Suppressed 2


title: Suppressed B 2

data_processing:
Library strategy: ATAC-seq
Samples were sequenced on an Illumina NextSeq sequencer, with 50bp paired end reads
Peak calling was performed using CLC Genomics workbench peak calling software utilizing all catenated data
Samples were analyzed with CLC Genomics Workbench 8.0.1 software utilizing standard alignment settings (mismatch cost=2, insertion cost=3, deletion cost=3, length fraction=0.8, similarity fraction=0.8)
Samples were normalized as reads per kilobase per million (RPKM)
Genome_build: mm10
Supplementary_files_format_and_content: Tab deliminated files containing peak number, RPKM, chromosome number, chromosome start, chromosome end

extract_protocol:
Cells were sorted, centrifuged and DNA extracted
Lysed nuclei were incubated with Tn5 tranposase, amplified, and Illumina Nextera barcodes added

value: B cell

tag: condition

value: Suppressed


title: Tfh Activated 2


title: Suppressed B 1


title: Activated B 1

value: Activated


title: B Activated 1


title: Supp_21_4

growth_protocol: in Vitro assay was performed by culturing Tfh and B cells with NP-OVA (Activated condition), Tfh, B and Tfr cells with NP-OVA (Suppressed condition) or Tfh, B, Tfr and IL21 and NP-OVA (IL21 rescue condition) for 4 days, cells were resorted

value: IL21 Rescue


title: B Suppressed 1


title: Supp B 4


title: Activated B 2


title: GC B cells

source_name: Ex Vivo NP-OVA imm. mice

value: GC B cells


title: Naive B cells

value: Naive B cells


title: Act B 4


title: Supp_21_3


title: Supp B 3


title: Act B 3


title: Supp B 2


title: Supp_21_2


title: Supp_21_1


title: Supp B 1


title: Tfh Suppressed 2


title: Act B 1


title: Act B 2


title: AGE+LPS, rep1

status: Public on Oct 01 2016

city: San Marcos

first: Yuan

last: Lu

state: TX

address: university drive

institute: Xiphophorus Genetic Stock Center

description:
PolyA RNA
AGE_RNA-Seq-04_TGACCA_L003_R1_001
Processed data file: overall_count_table.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor sequence was trimmed off, then low-quality basecall was trimmed off, at last, low-quality sequence reads were filtered out.
Short sequencing reads were aligned to Mus musculus genome Mus_musculus.GRCm38, gene expression value is quantified as raw read using featureCount.
Differential gene expression was analyzed using EdgeR.
Genome_build: GRCm38
Supplementary_files_format_and_content: overall_count_table.txt: Tab-delimited text file includes raw gene expression counts.

source_name: BV-2 microglia cells, AGE+LPS

growth_protocol: Mouse microglia BV-2 cells were gifted from co-author Dr. Grace Sun. The cells, as previously described, were grown in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Grand Island, NY, USA) supplemented with 5% (v/v) heat-inactivated fetal bovine serum (FBS) (Atlanta Biologicals, Inc., Lawrenceville, GA, USA), 25U/mL penicillin, and 25mg/mL streptomycin (Gibco, Grand Island, NY, USA) in a saturated humidity atmosphere containing 95% (v/v) air and 5% (v/v) CO2 at 37 ̊C.

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

treatment_protocol: Cells were cultured in DMEM without serum for 4 hours at 70-80% confluence and exposed to 100ng/mL LPS (rough strains from Escherichia coli F583 Rd mutant, Sigma-Aldrich, St. Louis, MO, USA) with or without aqueous AGE (0.5%, v/v) (Wakunaga of America, Mission Viejo, CA, USA) and FruArg (3mM), which were added 1 hour prior to LPS exposure, respectively.

value: Microglia cell line

value: Five to six

value: Aged garlic extract (AGE) + lipopolysaccharide (LPS)


title: Control, rep2

description:
PolyA RNA
UNT_020614_RNAseq-12_CTTGTA_L006_R1_001
Processed data file: overall_count_table.txt

source_name: BV-2 microglia cells, Control

value: Control


title: AGE+LPS, rep2

description:
PolyA RNA
AGE_020614_RNAseq-10_TAGCTT_L006_R1_001
Processed data file: overall_count_table.txt


title: FruArg+LPS, rep1

description:
PolyA RNA
FruArg_RNA-Seq_03_TTAGGC_L003_R1_001
Processed data file: overall_count_table.txt

source_name: BV-2 microglia cells, FruArg+LPS

value: FruArg + lipopolysaccharide (LPS)


title: Control, rep1

description:
PolyA RNA
UNT_RNA-Seq-06_GCCAAT_L003_R1_001
Processed data file: overall_count_table.txt


title: FruArg+LPS, rep2

description:
PolyA RNA
FruArg_020614_RNAseq-09_GATCAG_L006_R1_001
Processed data file: overall_count_table.txt


title: Tfh Activated 1


title: LPS, rep2

description:
PolyA RNA
LPS_020614_RNAseq-11_GGCTAC_L006_R1_001
Processed data file: overall_count_table.txt

source_name: BV-2 microglia cells, LPS

value: Lipopolysaccharide (LPS)


title: LPS, rep1

description:
PolyA RNA
LPS_RNA-Seq-05_ACAGTG_L003_R1_001
Processed data file: overall_count_table.txt


title: T22_Obese_whole blood

city: Tempe

first: Samantha

middle: Elaine

last: Day

state: AZ

address: University Dr. and Mill Ave.

institute: Arizona State University

data_processing:
Data was collected using HiSeq data collection version 1.5.15.1 software, and the bases were called using Illumina’s RTA version 1.13.48.
Briefly, FASTQ were trimmed to remove adaptor sequences, and any reads with less than 15bp were discarded. Trimmed Fastqs were then aligned against the reference genome Hg19 using BSMAP
Samtools was used to get mpileup and custom PERL scripts were used to determine CpG methylation and bisulfite conversion ratios
To determine differences in methylation between groups, the aligned data was imported into the free open source R package, methylSig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig data files were generated using custom scripts and score represent the methylation level at that loci.

source_name: Female_Obese_Whole blood

extract_protocol:
DNA was isolated using the PAXgene Blood DNA Kit, as per the manufacturer’s instructions (Qiagen, Valencia, CA).
Briefly, DNA was digested with Msp1 (New England Biolabs) and purified using QIAquick Nucleotide Removal Kit (Qiagen).  End-repair A tailing was performed (New England Biolabs) and TruSeq methylated indexed adaptors (Illumina) were ligated with T4 DNA ligase (New England Biolabs). Size selection was performed with Agencourt AMPure XP beads (Beckman Coulter). Bisulfite conversion was performed using EZ-DNA Methylation Kit (Zymo Research) as recommended by the manufacturer with the exception that incubation was performed using 55 cycles of 95 ̊C for 30 seconds and 50°C for 15 minutes.  Following bisulfite treatment, the DNA was purified as directed and amplified using Pfu Turbo C Hotstart DNA Polymerase (Agilent Technologies). The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3. The flow cell was then loaded into the Illumina cBot for generation of cluster densities. After cluster generation, the flow cells were sequenced as 51 x 2 paired end reads using Illumina HiSeq 2000 with TruSeq SBS sequencing kit version 3.

treatment_protocol: Blood was collected into PAXgene Blood DNA and RNA tubes (BD Diagnostics, Franklin Lakes, NJ) and stored at -80°C until processed.

value: Female

tag: age (yrs)

tag: obese status

value: Obese

value: whole blood


title: T37_Obese_whole blood


title: T35_Obese_whole blood


title: T21_Obese_whole blood

source_name: Male_Obese_Whole blood

value: Male


title: T17_Obese_whole blood


title: 2_4NC

city: Pittsburgh

first: David Peter

middle: G.

last: Peters

state: PA

address: 204 Craft Avenue

department: Department of Obstetrics, Gynecology and Reproductive Sciences

institute: University of Pittsburgh/Magee-Womens Research Institute

data_processing:
Illumina Casava 1.8 software used for basecalling.
Reads were trimmed to include bases 9-57 only
Sequenced reads were mapped to mm9 using Tophat with bowtie 1 option.
Calculated number of reads mapping to each gene. 1 was added to all raw counts then result was log2 transformed.
DESeq used for differential expression analysis. Reported as the log2 fold change.
Genome_build: mm9
Supplementary_files_format_and_content: table_of_counts.csv reports the raw counts of reads assigned to each gene. 1 was added to all raw counts and then they were log2 transformed. RNA-seq.results.txt is tab-delimited text file with the DESeq differential expression analysis output.

source_name: liver

extract_protocol:
RNA was extracted using Tri Reagent and subsequently treated with DNase 1.
TruSeq RNA Sample Prep Kit per the manufacturer’s protocol. Briefly, mRNA was purified from total RNA using oligo dT magnetic beads, fragmented and then reverse transcribed via random hexamers and SuperScript II Reverse Transcriptase.  Second strand cDNA was synthesized using a proprietary master mix.  The double stranded cDNA was then blunt ended, the 3’ ends were adenylated and indexed Illumina adaptors were ligated.  DNA fragments were enriched by PCR using the following conditions: initial denaturation of 98° C for 30 seconds, 15 cycles of 98° C for 10 sec, 60° C for 30 sec and 72° C for 30 sec, followed by a final extension of 72° C for 5 min.  RNA-seq libraries were visualized by Bioanalyzer and quantified by qPCR.  Libraries were pooled by quantity and sequenced via 50 bp single reads on a HiSeq2000.

tag: diet

value: high fat/high sucrose

value: liver


title: 2_4RC


title: T15_Obese_whole blood


title: 2_4LC


title: 1_4RC


title: 1_4BC


title: 1_4NC


title: 1_4LC


title: 2_1RC

value: low fat/low sucrose


title: T10_Obese_whole blood


title: 2_1NC


title: T20_Lean_whole blood

source_name: Female_Lean_Whole blood

value: Lean


title: T24_Lean_whole blood


title: T08_Lean_whole blood


title: 2_1LC


title: T05_Lean_whole blood

source_name: Male_Lean_Whole blood


title: T09_Lean_whole blood


title: T07_Obese_whole blood


title: T16_Lean_whole blood


title: 1_1RC


title: T06_Lean_whole blood


title: T28_Obese_whole blood


title: 1_1NC


title: T04_Lean_whole blood


title: T19_Obese_whole blood


title: T01_Lean_whole blood


title: U937-C07-Res

first: David

middle: B

last: Sykes

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: Massachusetts General Hospital

data_processing:
RNA-Seq reads from mouse and human libraries were aligned in a splice-aware fashion to annotated transcripts based on mm10 and hg19 references, respectively, using Tophat v.2.0.11 with default settings.
Differential expression analysis was performed using Cuffdiff version 2.2.1 with default parameters.
Genome_build: mm10,hg19
Supplementary_files_format_and_content: a tab-delimited text file includes expression and fold change values for each sample

source_name: U937 cells

growth_protocol: RPMI1640 + 10% FBS + Pen/Strep + Glutamine + Stem Cell Factor + Beta-estradiol (0.5 micromolar) for the Lys-GFP-ER-HoxA9 cells. RPMI1640 + 10% FBS + Pen/Strep + Glutamine for the U937 cells.

extract_protocol:
Qiagen RNEasy PLUS kit with additional on-column DNAse step
RNA-Seq using TruSeq. 250 ng high quality total RNA was used in the Illumina TruSeq RNA-Seq v2 kit (Cat # RS-122-2001). 5 ul of ERCC spike-ins were added at a 1:1000 dilution. The library construction process involves the purification of poly-A containing mRNA molecules using oligo-dT attached to magnetic beads, followed by the reduction in complexity of the mRNA by fragmentation using divalent cations. The fragmented mRNA is then converted to double stranded cDNA in a 2 step process: first strand synthesis is carried out using reverse transcriptase and random priming, then second strand synthesis with DNA polymerase 1 and RNase H. The cDNA fragments are then end repaired, A-tailed and ligated with Illumina specific indexed adaptors. These products are then purified and enriched by low cycle PCR. This process can be carried out manually, in the case of low sample number, or automated on a Perkin Elmer Janus. Libraries are QC’d by quantitation with qubit, size analysis on an Agilent Bioanalyzer or Tapestation 2200 and qPCR quantitation against a standard curve.

treatment_protocol: DMSO or Compound 3 or Compound 7 was added to the media at 5 micromolar (starting concentration) up to 50 micromolar (end concentration).

tag: cell line


title: U937-C03-Res


title: 1_1LC


title: T18_Lean_whole blood


title: 1_1BC


title: U937-DMSO


title: G2_4NC

data_processing:
Illumina Casava 1.8 software used for basecalling.
Quality and adaptor trimming were done using Trim Galore.
Alignment with Bismark to mm9. Duplicates were removed.
MethylKit used from differential methylation calling and calculations.
Genome_build: mm9
Supplementary_files_format_and_content: mouse_methylseq_results_name_update.txt is a tab-delimited text file containing avg_meth and differential per site methylation.

extract_protocol:
Liver tissue was homogenized via Tissue Lyser II and DNA was extracted via DNeasy Blood and Tissue Kit per manufacturer’s instructions
DNA libraries were prepared as per the SureSelectXT Methyl-Seq Target Enrichment System Protocol (Agilent) with a 9 cycle PCR post bisulfite conversion and a 6 cycle indexing PCR. SureSelect Mouse All Exon V1 52 Mbp was used for capture.


title: G2_4RC


title: P29

city: TOULOUSE

first: Etienne

last: DE CLARA

address: 2 avenue Hubert Curien

country: France

institute: INSERM

data_processing:
Alignment and mapping were performed using Tophat
mapped reads were assembled by Cufflinks 2.0.2
The Cuffcompare program was used to merge the RefSeq, ENCODE and UCSC database
For novel lncRNAs prediction, transcripts having long exonic length (>200 nt) according to the lncRNA’s definition were extracted
The coding potential of the extracted transcripts which do not align to protein databases was assess with CPC
The known ncRNAs and predicted novel ncRNAs were combined as the reference, and reads were aligned to this reference by SOAP2
Genome_build: HG19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Acute Myeloid Leukemia

extract_protocol:
Total RNAs from fresh or thawed samples were extracted with TRIzol reagent according to manufacturer's protocol. Non-coding RNAs were enriched by removing rRNA form the total RNA with Ribo-Zero™ rRNA Removal Kits (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Acute Myeloid Leukemia

value: Hematopoietic

value: NPM1 WT FLT3 WT


title: P35


title: G2_4LC


title: P38


title: P33


title: P36


title: P32


title: P37


title: P30


title: P40


title: P31


title: P27


title: G2_1RC


title: P24


title: G2_1NC


title: P26


title: P25


title: P28


title: P22


title: G2_1LC


title: P23


title: P21 FLT3ITD

value: NPM1 WT FLT3 ITD


title: P20 FLT3ITD


title: P39


title: P34


title: P19 FLT3ITD


title: G1_1RC


title: G1_4RC


title: G1_4BC


title: G1_1NC


title: P17 FLT3ITD


title: P15 FLT3ITD


title: P16 FLT3ITD


title: G1_1BC


title: P13 NPM1+

value: NPM1+ FLT3 WT


title: P10 NPM1+


title: P11 NPM1+


title: Lys-GFP-ER-HoxA9-C07-Res

source_name: Lys-GFP-ER-HoxA9 cells


title: P8 NPM1+


title: P14 NPM1+


title: Lys-GFP-ER-HoxA9-DMSO


title: Lys-GFP-ER-HoxA9-C03-Res


title: P9 NPM1+


title: R07 - 120 hour treatment

data_processing:
Base calls performed with Illumina RTA (version unknown)
Illumina base calls converted to BAM with Picard IlluminaBasecallsToSam version 1.764
RNA-Seq reads were aligned to the mm10 genome assembly, including the sequence of eGFP, and counted with STAR version 2.4.2a with default settings
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file includes raw read counts for each sample

growth_protocol: RPMI1640 + 10% FBS + Pen/Strep + Glutamine + Stem Cell Factor + Beta-estradiol (0.5 micromolar)

extract_protocol:
Qiagen RNEasy PLUS kit with additional on-column DNAse step
Total RNA is quantified using the Quant-iT™ RiboGreen® RNA Assay Kit and normalized to 5ng/ul. An aliquot of 200ng for each sample is transferred into library preparation which is an automated variant of the Illumina TruSeq™ Stranded mRNA Sample Preparation Kit.  This method preserves strand orientation of the RNA transcript. It uses oligo dT beads to select mRNA from the total RNA sample.  It is followed by heat fragmentation and cDNA synthesis from the RNA template.  The resultant 500bp cDNA then goes through library preparation (end repair, base ‘A’ addition, adapter ligation, and enrichment) using Broad designed indexed adapters substituted in for multiplexing. After enrichment the libraries were quantified with qPCR using the KAPA Library Quantification Kit for Illumina Sequencing Platforms and then pooled equimolarly.  The entire process is in 96-well format and all pipetting is done by either Agilent Bravo or Hamilton Starlet.
Pooled libraries are normalized to 2nM and denatured using 0.1 N NaOH prior to sequencing. Flowcell cluster amplification and sequencing were performed according to the manufacturer’s protocols using either the HiSeq 2000 or HiSeq 2500. Each run is a 101bp paired-end with an eight-base index barcode read. Data is analyzed using the Broad Picard Pipeline which includes de-multiplexing and data aggregation.

treatment_protocol: Culture out of beta-estradiol for the indicated times


title: P7 NPM1+


title: P4 NPM1+ FLT3ITD

value: NPM1+ FLT3 ITD


title: R07 - 72 hour treatment


title: P3 NPM1+ FLT3ITD


title: P2 NPM1+ FLT3ITD


title: R07 - 36 hour treatment


title: R07 - 12 hour treatment


title: 120 hour - Replicate 2


title: P18 FLT3ITD


title: G1_1LC


title: P12 NPM1+


title: 120 hour - Replicate 1


title: 96 hour - Replicate 2


title: P6 NPM1+ FLT3ITD


title: HS5

city: Pullman

middle: K

last: Skinner

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by the FastQC program. The reads for each sample for both CNV and DMR analyses were mapped to the GRCh38 human genome using Bowtie2 with default parameter options. The mapped read files were then converted to sorted BAM files using SAMtools. To identify DMR, the reference genome was broken into 100 bp windows. The MEDIPS R package was used to calculate differential coverage between control and exposure sample groups. The edgeR p-value was used to determine the relative difference between the two groups for each genomic window. Windows with an edgeR p-value less than 10-4 were considered DMRs. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR. CpG density and other information was then calculated for the DMR based on the reference genome. The DMRs that included at least two windows with an edgeR p-value <10-4 were then selected for further analysis and annotated.
The cn.MOPS R package was used to identify potential CNV. The cn.MOPS analysis detects CNVs by modeling read depth across all samples. The window size used by the cn.MOPS analysis was chosen dynamically for each chromosome based on the read coverage. For chromosomes 1 to 22 the window size ranged from 10 kb to 20 kb. For the MT, X, and Y chromosomes the window sizes were 1 kb, 31 kb, and 42 kb, respectively. We considered only CNV that occurred exclusively in either all control or all treatment samples.
DMR clusters were identified with R script (www.skinner.wsu.edu under genomic data) using a 2 Mb sliding window with 50 kb intervals. DMR were annotated using the biomaRt R package to access the Ensembl database. The genes that overlapped with DMR were then input into the KEGG pathway search to identify associated pathways. The DMR associated genes were manually then sorted into functional groups by consulting information provided by the DAVID, Panther, and Uniprot databases incorporated into an internal curated database (www.skinner.wsu.edu under genomic data).
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: The processed data file called methResults.cvs contains read counts and edgeR.

source_name: chemotherapy exposed cancer survivors_Sperm

growth_protocol: The patients were 19-30 year-old male survivors of osteosarcoma recruited between 2/6/2010 and 11/15/2012 from the Seattle Children’s Hospital in Seattle WA and four collaborating institutions (Children’s Hospital of Pennsylvania, Philadelphia, PA; Miller Children’s, Long Beach, CA; Children’s Hospital, University of Minnesota, Minneapolis, MN; and Children’s Hospital, Vanderbilt University, Nashville, TN). These men had been treated for their disease with cisplatin-based chemotherapy regimens, including ifosfamide in some cases, when they were 14-20 years of age. Each patient was recruited by in-clinic or mail recruitment protocols. Male survivors were eligible if they met the following criteria: alive, with no evidence of disease; diagnosed with bone or soft tissue sarcoma; off all cancer treatment, including radiation treatment, for at least 2 years; at least 15 years of age at study entry; less than 21 at diagnosis; had received cisplatin as part of cancer treatment; must not have received any other alkylating agent (Cyclophosphamide, Melphalan, Busulfan, BCNU, CCNU, Chlorambucil, Nitrogen Mustard, Procarabazine, or Thiotepa); must have received all or part of their cancer treatment at one of the collaborating sites; free of any pre-condition to cancer treatment that could result in infertility; have had no CNS, abdominal, pelvic, or gonadal radiation therapy or total body irradiation (TBI); proficiency in English as designated in patient’s medical record; provided informed consent or assent, and authorization to access medical records under HIPAA. Note that relapsed patients and patients with a subsequent malignancy (SMN) that are treated with surgery alone for the relapse or SMN were eligible for this study as long as they meet the above criteria. Controls were recruited from among adult men with no history of cancer who had previously participated as controls in the Fred Hutchinson Cancer Research Center, Seattle WA, ATLAS study. These men were re-contacted regarding participation in the current study. Each patient and control was asked to provide a semen sample via home seminal fluid collection, which we used to allow for ease of subject participation since the sample can be obtained without the individual traveling to a laboratory. Sperm concentration and morphology measures were performed on semen that had undergone liquefication during shipping, consistent with the WHO protocol for semen analysis. For sperm concentration (per ml), each participant’s semen was diluted and assessed by CASA (Computer Assisted Sperm Analysis). Three separate counts were performed and the results averaged. A known volume of semen was washed for making smears for morphology assessments, based on 200 sperm. Although sperm motility was not assessed (because it requires a fresh sample), count and morphology data nonetheless provide a great deal of information regarding spermatogenesis and abnormalities and both are associated with an increased risk of infertility. All protocols were approved by the Seattle Children’s Hospital institutional IRB committee (#12839 and 13158).

extract_protocol:
Frozen human sperm samples were stored at -20 C and thawed for analysis. Genomic DNA from sperm was prepared as follows: One hundred μl of sperm suspension was used then 820 μl DNA extraction buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) and 80 μl 0.1 M Dithiothreitol (DTT) added and the sample incubated at 65 C for 15 minutes. 80 μl Proteinase K (20 mg/ml) was added and the sample incubated on a rotator at 55 C for 2 hours. After incubation, 300 μl of protein precipitation solution (Promega, A795A, Madison, WI) was added, the sample mixed and incubated on ice for 15 minutes, then spun at 4 C at 13,000 rpm for 20 minutes. The supernatant was transferred to a fresh tube, then precipitated over night with the same volume 100% isopropanol and 2 μl glycoblue at -20 C. The sample was then centrifuged and the pellet washed with 75% ethanol, then air-dried and resuspended in 100 μl H2O. DNA concentration was measured using the Nanodrop (Thermo Fisher, Waltham, MA). Methylated DNA Immunoprecipitation (MeDIP) with genomic DNA that was isolated, as described before, was performed as follows: Human sperm DNA pools were generated using 2 μg of genomic DNA from each individual for 3 pools each of control and chemotherapy exposed subjects. Each pool contained 3 individuals for a total of n=9 per exposure group. The resulting 6 μg of genomic DNA per pool was diluted to 150 μl with 1x Tris-EDTA (TE, 10 mM Tris, 1 mM EDTA) and sonicated with a probe sonicator using 5 x 20 pulses at 20% amplitude. Fragment size (200-800 bp) was verified on a 1.5% agarose gel. Sonicated DNA was diluted to 400 μl with 1xTE and heated to 95 ˚C for 10 minutes, then incubated in ice water for 10 minutes. Then 100 μl of 5 x immunoprecipitation (IP) buffer (50 mM Sodium Phosphate pH 7, 700 mM NaCl, 0.25% Triton X-100) and 5 μg of 5-mC monoclonal antibody (Diagenode, Denville, NJ, C15200006-500) were added and the sample incubated on a rotator at 4 ˚C over night. The next day Protein A/G Agarose Beads from Santa Cruz were prewashed with 1xPBS/0.1% BSA and resuspended in 1 x IP buffer. Eighty μl of the bead slurry were added to each sample and incubated at 4 ˚C for 2 hours on a rotator. The bead-DNA-antibody complex was washed 3 times with 1 x IP buffer by centrifuging at 6,000 rpm for 2 minutes and resuspending in 1 x IP buffer. After the last wash the bead-complex was resuspended in 250 μl of digestion buffer (50 mM Tris pH 8, 10 mM EDTA pH 8, 0.5% SDS) with 3.5 μl Proteinase K (20mg/ml) per sample and incubated on a rotator at 55 ˚C for 2 hours. After incubation DNA was extracted with the same volume of Phenol-Chloroform-Isoamyalcohol and then with the same volume chloroform. To the supernatant from chloroform extraction 2 μl glycoblue, 20 μl 5M Sodium Chloride and 500 μl 100% cold ethanol were added. DNA was precipitated at  -20 ˚C over night, then spun for 20 minutes at 13,000 rpm at 4 ˚C, washed with 75% ethanol and air-dried. Dry pellet was resuspended in 20 μl H2O and concentration measured in Qubit using the Qubit ssDNA Assay Kit (Life Technologies, Carlsbad, CA).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) at the University of Reno, NV Genomics Core Laboratory using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed. Each pool received a separate index primer. NGS was performed at that same laboratory using the Illumina HiSeq 2500 with a PE50 application, with a read size of approximately 50bp and approximately 100 million reads per pool. Two libraries each were run in one lane comparing one control with one chemotherapy exposed pool in each lane.

tag: subject status

value: survivors of osteosarcoma

tag: gender

value: male

tag: developmental stage

value: Adult; 19-30 year-old

value: Sperm


title: HS6

treatment_protocol: Male survivors were eligible if they met the following criteria: alive, with no evidence of disease; diagnosed with bone or soft tissue sarcoma; off all cancer treatment, including radiation treatment, for at least 2 years; at least 15 years of age at study entry; less than 21 at diagnosis; had received cisplatin as part of cancer treatment; must not have received any other alkylating agent (Cyclophosphamide, Melphalan, Busulfan, BCNU, CCNU, Chlorambucil, Nitrogen Mustard, Procarabazine, or Thiotepa); must have received all or part of their cancer treatment at one of the collaborating sites; free of any pre-condition to cancer treatment that could result in infertility; have had no CNS, abdominal, pelvic, or gonadal radiation therapy or total body irradiation (TBI); proficiency in English as designated in patient’s medical record; provided informed consent or assent, and authorization to access medical records under HIPAA. Note that relapsed patients and patients with a subsequent malignancy (SMN) that are treated with surgery alone for the relapse or SMN were eligible for this study as long as they meet the above criteria. Controls were recruited from among adult men with no history of cancer who had previously participated as controls in the Fred Hutchinson Cancer Research Center, Seattle WA, ATLAS study.


title: HS1

source_name: no previous chemotherapy control_Sperm

value: control (no previous chemotherapy)


title: 48 hour - Replicate 2


title: HS4


title: HS2


title: P5 NPM1+ FLT3ITD


title: THP1-si5S-OT

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling.
poly(A) reads were aligned to genome with Tophat2 allowing 1 mismatch
Reads were counted using htseq-count and Ensembl-based gff ﬁle and normalized for RPM (reads per million).
Genome_build: hg19,mm9
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

source_name: THP1 cell

growth_protocol: THP-1 cells were maintained with RPMI-1640, and 293T, Hela, N2a and 3T3 cells were cultured under standard conditions with DMEM plus 10% FBS at 37℃ with 5% CO2.

extract_protocol:
none provided by submitter
none provided by submitter

treatment_protocol: Transfection of siRNA was conducted with Lipofectamine 2000 or Oligofectamine (Invitrogen) according to the standard protocol.

value: epithelial

tag: passages

tag: treatment

value: KD 5S-OT


title: HS3

tag: tissue


title: 96 hour - Replicate 1


title: shPTBP1

source_name: 293T cell

value: KD PTBP1


title: 72 hour - Replicate 1


title: G1_4NC

value: high fat/high sucrose

value: liver


title: 36 hour - Replicate 2


title: 36 hour - Replicate 1


title: 24 hour - Replicate 1


title: shCOO2

value: Negative Control


title: Induced-THP1-si5S-OT


title: P1 NPM1+ FLT3ITD

value: Acute Myeloid Leukemia


title: 12 hour - Replicate 2


title: Induced-THP1-NC


title: Hela-si2-U2AF

source_name: Hela cell

value: KD U2AF


title: 72 hour - Replicate 2


title: 12 hour - Replicate 1


title: 8 hour - Replicate 2


title: Hela-si1-U2AF


title: 48 hour - Replicate 1


title: Hela-si2-5S-OT


title: 8 hour - Replicate 1


title: THP1-NC


title: 4 hour - Replicate 1


title: 4 hour - Replicate 2


title: Hela-NC


title: Hela-si1-5S-OT


title: 0 hour - Replicate 2


title: 24 hour - Replicate 2


title: 293T-si2-U2AF


title: 293T-si1-U2AF


title: P1_PCK

city: Hangzhou

first: chenjia

last: shen

address: Xuelin

institute: Hangzhou Normal University

description: phytoalexin deficient 4 under –Fe treatments

data_processing:
Prior to assembly, the low quality reads, such as reads containing sequences adaptors, reads containing sequencing primer and nucleotide with a quality score lower than 20, were eliminated. Then, a total of 69.1 G bp of cleaned, paired-end reads were obtained.
The samples from each type were harvested in three different batches. The expression abundance of each assembled transcript was determined though reads per kilobase per million mapped reads (RPKM) values. All of the reads were mapped onto the non-redundant set of transcripts to calculate the abundance of assembled transcripts. The expressions of each gene between sample pairs (+Fe/WT vs. +Fe/pad4, -Fe/WT vs. –Fe/pad4, +Fe/WT vs. –Fe/WT and +Fe/pad4 vs. –Fe/pad4) were measured using the numbers of reads having a specific match. Among the four samples, a minimum of a two-fold difference in log 2 expression was considered as an expression significant difference.
Genome_build: TAIR10
Supplementary_files_format_and_content: expression data of genes and differential analysis reuslts, and function of interest of differential genes and .xlsx

organism: Arabidopsis

source_name: seedlings

growth_protocol: A. thaliana Col-0 (Columbia ecotype), phytoalexin deficient 4 (pad4), enhanced disease susceptibility 1 (eds1) and isochorismate synthase 1 (ics1) were used in the present study. The information on these mutants is listed in Table S1. Seeds were surface-sterilized and germinated on plates containing 0.75% agar solidified Murashige and Skoog (MS) nutrient medium, adjusted to pH 5.8 with 1 M NaOH. The seedlings were grown in an environmentally controlled growth chamber at 24 °C, a light intensity of 140 μmol photons m−2s−1 and a 16/8 h day/night rhythm.

extract_protocol:
The leaves and roots of 7-d-old seedlings were used for RNA isolation. The methods of RNA extraction, reverse transcription, and qRT-PCR, were performed as follows. Total RNA was extracted from different tissues using RNeasy plant mini kits (Qiagen) according to the manufacturer’s protocol. RNA quality was assessed by A260-A280 ratios (~2.0) using an ND-1000 UV Nanodrop spectrophotometer (Thermo Scientific, Shanghai, China) and by RNA integrity (>7.0) determined with a Bioanalyzer (Agilent, Santa Clara, CA, United States). In the total RNA, DNA contamination was removed by DNase I.
The purified mRNAs were fragmented using divalent cations under elevated temperatures, and then converted to dsDNA by two rounds of cDNA synthesis using reverse transcriptase and DNA polymerase I. After an end repair step, most dsDNA fragments were ligated with adaptor oligos (Pruitt et al. 2007).

treatment_protocol: The seedlings were then subjected to two treatments, +Fe (the complete nutrient solid medium as a control) and –Fe (the complete nutrient solid medium, but without Fe), for 7 d.

value: phytoalexin deficient 4

tag: harvest stage

value: seedlings

value: shoot


title: 0 hour - Replicate 1

city: Boston


title: P2_PCK


title: 293T-si2-5S-OT


title: 293T-si1-5S-OT


title: WT2_WCK

description: wild type under –Fe treatments

value: wild type


title: WT3_WCK

description: wild type under –Fe treatments


title: MLL/AF9-GFP-Vehicle

data_processing:
Base calls performed with Illumina RTA (version unknown)
Illumina base calls converted to BAM with Picard Tools version 2.2.4
Sequenced reads were trimmed for adaptor sequences with Picard Tools version 1.99
RNA-Seq reads were aligned to the mm10 genome assembly and counted with STAR version 2.4.2a with default settings
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file includes raw read counts for each sample

source_name: Bone marrow leukemia blasts

growth_protocol: GFP-positive leukemia cells were purified by FACS (fluorescence activated cell sorting) from the bone marrow of leukemic mice.

treatment_protocol: The mice were treated with vehicle or brequinar prior to euthanasia and bone marrow harvest for FACS.


title: WT1_WCK

description: wild type under –Fe treatments


title: MLL/AF9-GFP-Brequinar


title: 293T-NC


title: D10 5µM GSK126

city: Rochester

first: Andre

middle: J

last: van Wijnen

state: MN

address: 200 First Street SW

department: Orthopedic Surgery & Biochemistry and Molecular Biology

institute: Mayo Clinic

description: GeneCount.tsv

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
The ChIP-Seq samples were analyzed using the HiChIP pipeline (http://bioinformaticstools.mayo.edu/research/hichipseq-pipeline/). Briefly, the reads were aligned to the mm10 genome using bwa v0.5.9 and read pairs were if at least on read in the pair mapped uniquely. Peaks were identified using SICER v1.1.
The RNA-Seq samples were analyzed using MAP-Rseq (http://bioinformaticstools.mayo.edu/research/maprseq/). Briefly, the reads were mapped using TopHat v2.0.6 and gene counts were generated using HTSeq 0.5.3p9.
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] The peak files contain peak calls output from SICER for the ChIP-Seq samples, with the following columns: Chromosome, PeakStart, PeakEnd, InputReadCount, ControlReadCount, p-value, FoldChange, FDR
Supplementary_files_format_and_content: [.tsv] The gene abundance measurement file contains raw and RPKM gene counts for each RNA-Seq sample

extract_protocol:
RNA (RNA-Seq) was isolated using the miRNeasy mini kit (Catalog # 217004, Qiagen). DNA (ChIP-Seq) was isolated from ChIP assays with the use of Phenol: Chloroform: Isoamyl Alcohol (25:24:1 v/v) solution (Invitrogen, Catalog 15593-031). The DNA was then precipitated overnight using 0.3M sodium acetate  in the presence of 20µg of glycogen in 70% ethanol. The DNA was then spun down, washed with 70% ethanol, and dissolved in 50µl of water.
RNA-Seq libraries were prepared using the Illumina TruSeq v2 mRNA protocol. ChIP-Seq libraries were prepared using the NEBNext ChIP-Seq Library prep kit for Illumina sequencing.

value: MC3T3 cells

tag: time

value: day 10


title: P3_PFE

description: phytoalexin deficient 4 under +Fe treatments

tag: genotype


title: D10 Vehicle

description: GeneCount.tsv

value: Vehicle


title: D6 5µM GSK126

description: GeneCount.tsv

value: day 6


title: Sample_60574_mportazole

city: Las Vegas

first: Aurelio

last: Lorico

state: NV

address: 10530 Discovery Drive

department: Cancer Research Center

institute: Roseman University of Health Sciences

data_processing:
TopHat was used to align reads to the genome
The FPKM values are from cuffdiff within cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: summarized fpkm values for two compared samples

growth_protocol: Mesenchymal stromal cells were grown for 24 hr in medium with exosome-depleted serum

extract_protocol:
Trizol was used for RNA purification followed by DNaseI treatment and concentration normalization to 10ng/ul in 50ul = 50ng total RNA.
magnetic poly-A beads were used to purify mRNAs from 50ng total RNA.
Illumina-based HiSeq2500, 52 nucleotide long reads, Single-Ended

value: Primary mesenchymal stem cells from volunteers

tag: treated with

value: mportazole


title: Sample_60575_Importazole

tag: cell type

value: Importazole


title: P2_PFE


title: P3_PCK


title: Sample_60573_Leptomycin B

source_name: MSCs_Leptomycin B

value: Leptomycin B


title: D6 Vehicle

description: GeneCount.tsv


title: WT3_WFE

description: wild type under +Fe treatments


title: D3 5µM GSK126

description: GeneCount.tsv

value: day 3


title: Sample_60572_Leptomycin B


title: D3 Vehicle

description: GeneCount.tsv


title: P1_PFE


title: 5µM GSK126 H3K27me3 DNA

tag: chip antibody


title: WT2_WFE

description: wild type under +Fe treatments


title: 5µM GSK126 Input DNA


title: WT1_WFE

description: wild type under +Fe treatments


title: Vehicle H3K27me3 DNA


title: Sample_60569_Extracellular vesicles + Leptomycin B

source_name: MSCs_Extracellular vesicles + Leptomycin B

value: Extracellular vesicles + Leptomycin B


title: Sample_60571_Extracellular vesicles + Importazole

source_name: MSCs_Extracellular vesicles + Importazole

value: Extracellular vesicles + Importazole


title: Vehicle Input DNA


title: Sample_60565_Extracellular vesicles

source_name: MSCs_Extracellular vesicles

value: Extracellular vesicles


title: Rev KO ZT20 rep2

city: Fribourg

first: Sara

middle: S

last: Fonseca Costa

address: Chemin du Musée 5

country: Switzerland

institute: University of Fribourg

data_processing:
Sequenced reads were mapped to mm10 whole genome using Tophat with default parameters.
Using just accepted hits .bam files to performed the counts using the HTSeq-count.
HTSeq-count --> Command: samtools view sample.bam | htseq-count -a 10 -s no -i gene_name -Mus_Musculus.gtf > sample_counts.txt
DESeq2 Version 1.6.3 was used to performed the statistical analysis
Using the follow command to performed the matrix: sampleCondition=factor(c(rep("Condiction_1",3), rep("Condiction_2",3)), levels=c("Condiction_2","Condiction_1"))
Genome_build: mm10
Supplementary_files_format_and_content: Counts referent to each gene.

source_name: Rev KO ZT20 liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using NucleoSpin RNA (Machery-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

tag: genotype/variation

value: Rev KO

tag: age

value: 12 weeks

tag: time point

value: liver


title: Sample_60566_Extracellular vesicles from CD9sh cells

source_name: MSCs_Extracellular vesicles from CD9sh cells

value: Extracellular vesicles from CD9sh cells


title: Rev KO ZT20 rep1


title: Sample_60568_Extracellular vesicles + Leptomycin B


title: Sample_60567_Extracellular vesicles from CD9sh cells


title: Sample_60564_Extracellular vesicles


title: WT ZT20 rep3

source_name: WT ZT20 liver

value: wild type


title: Rev KO ZT8 rep3

source_name: Rev KO ZT8 liver


title: WT ZT20 rep2


title: Sample_60570_Extracellular vesicles + Importazole


title: scramble-sponge-31

city: Munich

first: Mareen

last: Engel

address: Kraepelinstr. 2-10

department: Stress Neurobiology and Neurogenetics

institute: Max-Planck-Institute of Psychiatry

data_processing:
FASTQC, Cutadapt (15-40nt insert, TruSeq Small RNA Adapter trimmed), alignment to miRbase v21 and counting sRNAbench v10/14, differential expression DESeq2 (minimum 5 reads in all samples)
Genome_build: miRbase v21

source_name: basolateral amygdala

extract_protocol:
total RNA isolation
Illumina TruSeq Small RNA Library of 400ng total RNA, DNA-PAGE library size selection to 145-155nt

tag: strain

tag: Sex

value: male

tag: manipulation

value: scramble sponge virus


title: WT ZT8 rep2

source_name: WT ZT8 liver


title: WT ZT8 rep3


title: WT ZT20 rep1


title: Rev KO ZT8 rep2


title: Sample_60562_Untreated (solvent only)

source_name: MSCs_none (solvent only)

value: none (solvent only)


title: scramble-sponge-30


title: ChiP HA-Fbxl10 cell W

city: Freiburg

first: Dominica

last: Willmann

address: Breisacherstr. 66

institute: Uniklinik-Freiburg

data_processing:
ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the mm10 reference genome using bowtie 2
peak finding algorithm MACS
Genome_build: mm10
Supplementary_files_format_and_content: The processed data are wiggle and bed files. The wig files include the read data mapped to mm10 genome. The bed files contain the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input.

source_name: MEF

growth_protocol: MEFs were cultured in DMEM containing 10 % fetal bovine serum,1 % L-glutamine, 1 % penicillin / streptomycin and 1 % non essential amino acids.

extract_protocol:
ChIP was performed with SimpleChIP Enzymatic Chromatin IP Kit according to the manufacturer's protocol and 7 μg of chromatin was immunoprecipitated with 5 μg of HA antibody.
We isolated MEFs from our gain of function model and three independent ChIp-Seq samples were generated from non-induced and induced MEFs. Chromatin was immunoprecipitated with an HA antibody and ChIP-Seq libraries were sequenced using a HiSeq 2000 (Illumina).

treatment_protocol: To induce HA-Fbxl10 expression 1 µg/ml doxycycline was added to growth medium for 48 hours.

value: mouse embryonic fibroblast (MEF)

value: overexpressing HA-tagged Fbxl10

tag: induced with

value: 1 µg/ml doxycycline for 48hrs

value: HA antibody (ab9110; Abcam)


title: scramble-sponge-28


title: Input W


title: Input W/O


title: ChiP HA-Fbxl10 cell W/O


title: miR-sponge-46

value: miR-15a sponge virus


title: miR-sponge-44


title: ATAC-Seq.Zscan4+_3

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq2000 platform using the default RTA analysis software.
BS-Seq (PBAT): Raw sequence reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.4.1, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Cutadapt version 1.8.1, parameters: --paired). Trimmed reads were first aligned to the mouse genome in paired-end mode to be able to use overlapping parts of the reads only once while writing out unmapped singleton reads; in a second step remaining singleton reads were aligned in single-end mode. Alignments were carried out with Bismark v0.14.4 (Krueger and Andrews, 2011) with the following set of parameters: a) paired-end mode: --pbat; b) single-end mode for Read 1: --pbat; c) single-end mode for Read 2: defaults.  Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output ignoring the first 6bp of each read to reduce the methylation bias typically observed in PBAT libraries using the Bismark methylation extractor (v0.14.4) with the following parameters: a) paired-end mode: --ignore 6 --ignore_r2 6; b) single-end mode: --ignore 6.
RNA-Seq: Raw FastQ data were trimmed with Trim Galore (v0.4.1, default parameters) and mapped to the mouse GRCm38 genome assembly using TopHat v2.0.12, guided by gene models from Ensembl v70. Data were quantitated at mRNA level using the RNA-seq quantitation pipeline in SeqMonk software (www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
ATAC-Seq: Raw FastQ data were trimmed with Trim Galore to remove Nextera adapters and poor basecall qualities (v0.4.1, default parameters) and mapped to the mouse GRCm38 genome assembly using Bowtie 2 (v2.2.5). Data were quantitated using SeqMonk (www.bioinformatics.babraham.ac.uk/projects/seqmonk/)
Genome_build: GRCm38
Supplementary_files_format_and_content: genome-wide CpG methylation report: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>
Supplementary_files_format_and_content: gene expression report: Quantitated RNA-Seq data files are tab delimited and contain the following 7 columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) Description (Ensembl); (7-16) log2 RPM value
Supplementary_files_format_and_content: ATAC-Seq count report: Quantitated ATAC-Seq files are tab delimited Seqmonk probe annotation reports for 500bp tiling windows across the genome and contain the following columns: (1) probe name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (8) Description (Ensembl); (12-21) raw counts

source_name: E14 embryonic stem cell

growth_protocol:
Cell culture and reporter line construction: E14 mouse embryonic stem cells were grown under standard serum/LIF conditions (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 mg/ml streptomycin, 0.1 mM nonessential amino acids, 50 mM b-mercaptoethanol, and 103 U/ml LIF ESGRO). The Zscan4::emerald plasmid (90636) was kindly provided by Minoru Ko (Zalzman et al., 2010), the MERVL::tdTomato Reporter (Macfarlan et al., 2012) was a gift from Samuel Pfaff (Addgene plasmid # 40281). Single and double reporter lines were generated by transfecting plasmids with Fugene6 (Promega), selecting stable integrants with the relevant drug and subcloned to generate stable clonal lines. Flow cytometry analysis was performed using BD LSRFortessa and sorts performed on BD Aria III or BD Influx High-Speed Cell Sorter. Post-acquisition analysis was performed using FlowJo software.
The MuERVL+_Zscan4+ line is a double reporter ESC line constructed containing stable transgene integrations of MERVL and Zscan4 promoter driven tdTomato and eGFP fluorescent reporters respectively. The Zscan4+ line was a rare subpopulation that expressed Zscan4 (and its reporter) but not MERVL. Neg would be the E14 cell line untransfected negative control.

extract_protocol:
ATAC-seq was performed according to the original protocol (Buenrostro et al., 2015) with the following modifications. 10,000 cells were treated with 0.5μl Tn5 transposase in a total volume of 20μl for 30 minutes at 37 degrees. A total of 15 PCR cycles were performed and two rounds of Ampure Bead clean-up
RNA was isolated using Qiagen RNA-DNA allprep columns or TriReagent (Sigma) and treated with DNAseI (Ambion DNA-free DNA Cat #1311027) using manufacturers instructions

tag: cell line


title: miR-sponge-45


title: Sample_60563_Untreated (solvent only)

value: Primary mesenchymal stem cells from volunteers

tag: passages


title: ATAC-Seq.Zscan4+_2


title: WT ZT8 rep1

tag: tissue


title: miR-sponge-43


title: Rev KO ZT20 rep3


title: ATAC-Seq.Zscan4+_1


title: scramble-sponge-26


title: ATAC-Seq.neg_3

value: E14 cell line untransfected negative control


title: Rev KO ZT8 rep1


title: miR-sponge-42


title: ATAC-Seq.neg_2


title: ATAC-Seq.neg_1


title: scramble-sponge-25


title: ATAC-Seq.MuERVL+_Zscan4+_1