title: D6_siH3.3

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Libraries were mapped to mm9 genome using STAR aligner.
Gene expression quantification was performed using SeqMonk.
Genome_build: mm9
Supplementary_files_format_and_content: Table containing the FPKM values of all genes during several stages of cellular reprogramming

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were cultured in Dulbecco’s modified Eagle medium high glucose medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Hyclone), 2mM L-glutamine (Gibco) and 1X PenStrep (Gibco). Reprogramming was performed   in  FF medium (DMEM/F12 (Gibco) supplemented with 15% Knockout Serum Replacement (Gibco), 2mM L glutamine (Gibco), 1X PenStrep (Gibco) 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 50 ug/ml ascorbic acid (Sigma), 10 ng/ml basic fibroblast growth factor (bFGF, Gibco), 3 uM CHIR99021 (Stemgent) and 0.5× N-2 Supplement (Gibco)) without any feeder layer or passage procedure; iPSCs and mESCs D3 cells were cultured in FF medium;

extract_protocol:
Cells were harvested using trypsin, and RNA was harvested using Trizol reagent and RNA Isolation Kit: RNeasy Mini Kit (QIAGEN).
Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Cat#RS-122-2101) was used with 3 ug of  mRNA for the construction of sequencing libraries.

treatment_protocol: pMXs-Sox2, Klf4, Oct4 and c-Myc were used to infect MEFs with 4 μg/ml polybrene for 24 h to induce reprogramming process. After 24 hrs of infection, FF medium was changed every day. Cells were transfected with 30 nM siRNA using DharmaFECT 1 (Dharmacon) two days prior to reprogramming.

tag: reprogramming time-point

value: Day 6 post OSKM induction

tag: sirna treatment


title: D6_siNT

status: Public on Feb 28 2018

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

value: Non-Targeting


title: Adult_64Y_C3_041

city: Cleveland

first: Peng

last: Jiang

state: OH

address: 2121 Euclid Ave

country: USA

institute: Cleveland State University

description:
single cell RNA-seq
processed data file:
Adult_QC_Pass_Samples_TPM.txt.gz

data_processing:
FASTQ files were generated by CASAVA (v1.8.2).
Reads were mapped to the human transcriptome using Bowtie 0.12.8 (Langmead et al. 2009).
The gene expected read counts and TPMs were estimated by RSEM.
Genome_build: hg19
Supplementary_files_format_and_content: text file with gene expression values (TPM)

molecule: total RNA

organism: Homo sapiens

source_name: Human Retina

growth_protocol: hESC WA09 (WiCell) cells were harvested for transfection 2 days post-passaging and resuspended in OptiMEM (Life Technologies) at 5 x 10^6 cells/mL. 500 μl of cells was added to a cuvette containing 30 μg of linearized CRX reporter construct and 10 μg mRNA encoding a pair of zinc finger proteins (5 μg each) specific to CRX (Sigma) in 300 μl PBS.

extract_protocol:
All procedures of cell loading, capture, and library preparations were performed following the Fluidigm user manual and as previously described (Chu et al., 2016).
Full-length, single-cell cDNA libraries were harvested from the C1 chip and diluted to 0.1–0.3 ng/μl, fragmented, and amplified using the Nextera XT DNA Sample Preparation and Index Kits (Illumina). Libraries were multiplexed at 24-48 libraries per lane and single-end reads were sequenced (Illumina HiSeq 2500 system).

treatment_protocol: CRX+/tdTomato OVs and adult retinas were dissociated using papain.

tag: cell source

value: Adult

tag: tissue

value: retina


title: D0_siNT

value: Day 0


title: Adult_64Y_C3_040


title: D3_siH3.3

value: Day 3 post OSKM induction


title: Adult_64Y_C3_039


title: telencephalon

city: Goyaongsi

first: Charny

last: Park

state: Gyeonggi-do

address: 323 Ilsan-ro,

country: South Korea

institute: National Cancer Center

description: MET

data_processing:
Alignment using Tophat to GRCm38 referring genemodel ENSEMBL release 78
Gene expression quantification and differential expression test using Cufflinks and Cuffdiff
Genome_build: GRCm38
Supplementary_files_format_and_content: gene and transcription expression matrix of text format

source_name: mouse fetus at E12.5

growth_protocol: Wild type mouse was used in a typical laboratory mouse facility

extract_protocol:
Total RNA was extracted from whole body and telencephalon of mouse fetus at E12.5 using RNeasy mini kit (QIAGEN).
TruSeq RNA Library Preparation kit v2 purchased from Illumina was used
RNA-seq data was obtained using Illumina HiSeq 2000

treatment_protocol: No special treatment was applied

value: telencephalon

tag: strain

value: ICR

tag: developmental stage

value: fetus at E12.5


title: D4_Input

library_source: genomic

data_processing:
Libraries were mapped to mm9 genome using STAR aligner with the option -alignIntronMax set to 1.
A tag Directory for each mapped file was created using makeTagDirectory script of HOMER.
Binding sites were identified using findPeaks script HOMER with the option -style set to histone.
Genome_build: mm9
Supplementary_files_format_and_content: The files contain the coordinates of the loci enriched by H3.3, H3K4me3 or H3K36me3 in the corresponding library in a tabular format.

molecule: genomic DNA

growth_protocol: MEFs were cultured in Dulbecco’s modified Eagle medium high glucose medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Hyclone), 2mM L-glutamine (Gibco) and 1X PenStrep (Gibco). Reprogramming was performed   in  FF medium (DMEM/F12 (Gibco) supplemented with 15% Knockout Serum Replacement (Gibco), 2mM L glutamine (Gibco), 1X PenStrep (Gibco) 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 50 ug/ml ascorbic acid (Sigma), 10 ng/ml basic fibroblast growth factor (bFGF, Gibco), 3 uM CHIR99021 (Stemgent) and 0.5× N-2 Supplement (Gibco)) without any feeder layer or passage procedure; iPSCs and mESCs D3 cells were cultured in Feeder-Free medium;

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 TruSeq ChIP Library Preparation Kit  (IP-202-1012).

treatment_protocol: pMXs-Sox2, Klf4, Oct4 and c-Myc were used to infect MEFs with 4 μg/ml polybrene for 24 h to induce reprogramming process. After 24 hrs of infection, Feeder-Free medium was changed every day.

tag: cell fate transition type

value: Transdifferentiation

tag: time-point

value: Day 4 post SLBR induction

tag: antibody

tag: sorting


title: Adult_64Y_C3_038


title: D0_siH3.3


title: cKit+_Input

value: Fully Transdifferentiated

value: cKit+


title: D070_R1_003

description:
single cell RNA-seq
processed data file:
D070_QC_Pass_Samples_TPM.txt.gz

value: hPSC-derived retina


title: whole body

description: ME

value: whole body


title: MEF_Input

value: Day 0 post SLBR induction


title: cKit-_H3.3

value: cKit-


title: D4_H3.3


title: Adult_64Y_C3_037


title: MEF_H3.3


title: cKit+_H3.3


title: Adult_64Y_C3_036


title: D12S-_Input

value: Cellular Reprogramming

value: Day 12 post OSKM induction


title: D16S-_Input

value: Day 16 post OSKM induction


title: Adult_64Y_C3_034

value: Adult

value: retina


title: D3_siNT

value: Day 3 post OSKM induction

value: Non-Targeting


title: D6T+_Input

value: Day 6 post OSKM induction


title: D9T+_Input

value: Day 9 post OSKM induction


title: Adult_64Y_C3_033


title: D12S+_Input


title: iPSCs_Input

value: Fully reprogrammed


title: Adult_64Y_C3_031


title: cKit-_Input

value: Transdifferentiation


title: D6T-_Input


title: Adult_64Y_C3_030


title: D16S+_H3K36me3


title: iPSCs_H3K36me3


title: D3_Input


title: D12S+_H3K36me3


title: Adult_64Y_C3_027


title: D9T-_H3K36me3


title: Adult_64Y_C3_035


title: D3_H3K36me3


title: Adult_64Y_C3_026


title: Adult_64Y_C3_029


title: Adult_64Y_C3_025


title: D6T-_H3K36me3


title: ESD3_Input

source_name: ESD3 mouse embryonic stem cells


title: D0_H3K36me3

value: Day 0


title: D9T-_H3K4me3


title: iPSCs_H3K4me3


title: D16S+_H3K4me3


title: Adult_64Y_C3_024


title: Adult_64Y_C3_023


title: D9T-_Input


title: D12S+_H3K4me3


title: D6T-_H3K4me3


title: D3_H3K4me3


title: D0_Input


title: D16S+_Input


title: Adult_64Y_C3_032


title: Adult_64Y_C3_028


title: D16S-_H3.3


title: D0_H3K4me3


title: Adult_64Y_C3_022


title: Adult_64Y_C3_021


title: D6T+_H3.3


title: D9T+_H3.3


title: ESD3_H3.3


title: iPSCs_H3.3


title: Adult_64Y_C3_019


title: D12S+_H3.3


title: D16S+_H3.3


title: D9T-_H3.3


title: D6T-_H3.3


title: D3_H3.3


title: D0_H3.3


title: D16S-_mRNA

data_processing:
Libraries were mapped to mm9 genome using STAR aligner.
Differential gene expression and gene expression quantification was performed using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: Table containing the FPKM values of all genes during several stages of cellular reprogramming

treatment_protocol: pMXs-Sox2, Klf4, Oct4 and c-Myc were used to infect MEFs with 4 μg/ml polybrene for 24 h to induce reprogramming process. After 24 hrs of infection, FF medium was changed every day.


title: Adult_64Y_C3_015


title: D12S-_mRNA


title: D9T+_mRNA


title: Adult_64Y_C3_016


title: Adult_64Y_C3_014


title: D6T+_mRNA


title: Adult_64Y_C3_012


title: Adult_64Y_C3_013


title: D12S-_H3.3


title: Adult_64Y_C3_020


title: D16S+_mRNA


title: D9T-_mRNA


title: ESD3_mRNA

value: N/A (WT)


title: iPSCs_mRNA


title: Adult_64Y_C3_018


title: D6T-_mRNA


title: Adult_64Y_C3_010


title: Adult_64Y_C3_009


title: D3_mRNA


title: D0_mRNA

value: Day 0 (WT)


title: D6_siH3.3_ATAC

data_processing:
Library strategy: ATAC-Seq
Libraries were mapped to mm9 genome using STAR aligner with the option -alignIntronMax set to 1.
Duplicates were removed from the mapped files using PICARD tools.
Accessibility regions were determined using MACS2 with the following parameters –nolambda –nomodel –keep-dup all –call-summits
Genome_build: mm9
Supplementary_files_format_and_content: Tabular files including the coordinates of the accessible regions.

growth_protocol: MEFs were cultured in Dulbecco’s modified Eagle medium high glucose medium (DMEM; Gibco), supplemented with 10% fetal bovine serum (FBS; Hyclone), 2mM L-glutamine (Gibco) and 1X PenStrep (Gibco). Reprogramming was performed   in  FF medium (DMEM/F12 (Gibco) supplemented with 15% Knockout Serum Replacement (Gibco), 2mM L glutamine (Gibco), 1X PenStrep (Gibco) 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), and 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore), 50 ug/ml ascorbic acid (Sigma), 10 ng/ml basic fibroblast growth factor (bFGF, Gibco), 3 uM CHIR99021 (Stemgent) and 0.5× N-2 Supplement (Gibco)) without any feeder layer or passage procedure; iPSCs and mESCs D3 cells were cultured in Feeder-Free medium

extract_protocol:
Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Nuclei were spun at 500g for 10 min using a refrigerated centrifuge immediately after lysis.
Libraries were prepared according to published protocol (Jason D Buenrostro et.al, 2013). Briefly, 50k cells were lysed, and transposed in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water).The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 (Supplementary Table 1), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min.The libraries were purified using a Qiagen PCR cleanup kit

value: Day 6 (siH3.3)


title: D6_siNT_ATAC

value: Day 6 (siNT)


title: Adult_64Y_C3_017


title: iPSCs_ATAC


title: D12S+_ATAC


title: D9T-_ATAC


title: D6T-_ATAC


title: Adult_64Y_C3_006


title: Adult_64Y_C3_008


title: Adult_64Y_C3_007


title: D0_ATAC


title: D16S+_ATAC


title: D12S+_mRNA


title: Adult_64Y_C3_005


title: Adult_64Y_C3_004


title: Adult_64Y_C3_011


title: SMG_M rep3

city: Rochester

first: Catherine

middle: E.

last: Ovitt

state: NY

address: 601 Elmwood Ave, Box 611

department: Center for Oral Biology

institute: University of Rochester Medical Center

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using STAR with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks. Between-gland differentially expressed genes were called using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Male submandibular gland

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

tag: Sex

value: Male

value: submandibular gland

tag: age

value: 12 weeks


title: Adult_64Y_C3_003


title: PG_M rep2

source_name: Male parotid gland

value: parotid gland


title: PG_M rep3


title: PG_F rep3

source_name: Female parotid gland

value: Female


title: PG_M rep1


title: Adult_64Y_C3_002

value: Adult

value: retina


title: SMG_M rep2


title: PG_F rep1


title: Adult_64Y_C3_001


title: SMG_F rep3

source_name: Female submandibular gland


title: D3_ATAC

value: Day 3 post OSKM induction


title: SMG_M rep1


title: SMG_F rep1


title: PG_F rep2


title: SMG_F rep2


title: SLG_M rep2

source_name: Male sublingual gland

value: sublingual gland


title: SLG_F rep3

source_name: Female sublingual gland


title: SLG_M rep1


title: SLG_F rep2


title: Adult_64Y_C2_039


title: SLG_M rep3


title: Adult_64Y_C2_036


title: Adult_64Y_C2_037


title: Adult_64Y_C2_035


title: Adult_64Y_C2_034


title: SLG_F rep1


title: Adult_64Y_C2_033


title: Adult_64Y_C2_029


title: Adult_64Y_C2_031


title: Adult_64Y_C2_027


title: Adult_64Y_C2_026


title: Adult_64Y_C2_024


title: Adult_64Y_C2_032


title: Adult_64Y_C2_030


title: Adult_64Y_C2_028


title: Adult_64Y_C2_038


title: Adult_64Y_C2_025


title: Adult_64Y_C2_017


title: Adult_64Y_C2_020


title: Adult_64Y_C2_023


title: Adult_64Y_C2_016


title: Adult_64Y_C2_018


title: Adult_64Y_C2_015


title: Adult_64Y_C2_014


title: Adult_64Y_C2_021


title: pDC_NOD Rag1-/-_PBS_3

city: Bethesda

first: Kristin

middle: V

last: Tarbell

state: MD

address: 10 Center Dr, Bldg 10 5-5832

department: Diabetes, Endocrinology, and Obesity Branch

institute: NIH/NIDDK

data_processing:
remove adapter sequences: Paired-end RNA sequencing reads were trimmed to remove Illumina’s adapter sequences.
remove poor quality reads and/or reads mapping to mouse rRNA and tRNA sequences using ArrayStudio package. Trim reads with base quality score (Sanger Quality Score) < 10. Filter out reads if trim length is < 25 bp. Filter out reads if maximal base quality score is < 15. Filter out reads if average quality score is < 10. Filter out reads if poly AGCT rate is >=80%. Filter out the pair of reads if either read fails the filtering criteria.
align reads to mouse reference genome (Build38) using OSA version 4 (Hu et al., 2012).
Obtain transcript counts data using RSEM package (Li and Dewey, 2011) and NCBI mouse RefSeq gene model (released July 2015).
criteria-based filtering: transcripts with zero counts in more than two third of the smaples were discarded from downstream analysis to reduce noise in the expression data.
quantile normalization and CPM conversion with limma voom
ComBat to remove batch effects from sort date (only for nonRag KO samples). Used with defaults, no co-variates, and for each subset separately. Performed after conversion to CPM within the vool function, but before calculation of precision weights within Voom function.
Differential gene expression: Calculation of precision weights using limma voom. Limma eBayes and topTable functions, utilizing the precision weights calculated from Voom normalization.
Genome_build: Build38
Supplementary_files_format_and_content: supplementary file is an excel file that includes CPM values for each Sample (before and after post processing steps) and Differential Expression results on separate tabs

source_name: pDC

extract_protocol:
Total RNA was extracted using Arcturus PicoPure RNA isolation kit per the manufacturer’s protocol
Low-input RNA sequencing libraries were generated from about 300 pg of total RNA using SMART-seq v4 Ultra Low Input RNA kit (Clontech, CA). All samples were subjected to 14 PCR amplification cycles to minimize PCR biases (Bhargava et al., 2014). Amplified cDNA libraries were later fragmented through sonication to obtain 200 – 500 bp fragments. Standard Illumina sequencing libraries were prepared using Rubicon ThruPLEX DNA-seq kit (Rubicon Genomics, MI) according to manufacturer’s protocol. Sample barcoded libraries were sequenced on Illumina’s NextSeq 500 instrumentation using NextSeq 300 Cycle Kit, High Output, V1 reagents (Illumina, CA) and data analysis workflow, bcl2fastq -v2.17.1.14, to obtain 150 bp paired-end reads.

treatment_protocol: sacrificed mice and collected tissues 5 hours after IP injection

value: spleen

tag: in-vivo treatment

value: PBS

value: NOD Rag1-/-

tag: sort date

value: RNAseq run 1

tag: number of cells

tag: volume (ul)

tag: post extraction volume (ul)

tag: post extraction concentration from bioanalyzer (pg/ul)

tag: post extraction total quantity (pg)

tag: post extraction rin

tag: input to cdna contruction (pg)


title: pDC_NOD Rag1-/-_PBS_1

tag: tissue

tag: strain


title: Adult_64Y_C2_013

tag: cell source


title: pDC_NOD Rag1-/-_PBS_2


title: Adult_64Y_C2_012


title: pDC_NOD_PBS_1

value: NOD

value: RNAseq run 2


title: pDC_NOD_PBS_2


title: pDC_B6g7_PBS_3


title: Adult_64Y_C2_011


title: Adult_64Y_C2_010


title: Adult_64Y_C2_022


title: Adult_64Y_C2_009


title: Adult_64Y_C2_019


title: pDC_B6g7_PBS_2


title: pDC_B6g7_PBS_1


title: Adult_64Y_C2_008


title: pDC_B6 Rag1-/-_PBS_3


title: Adult_64Y_C2_007


title: Adult_64Y_C2_006


title: pDC_NOD_PBS_3


title: Adult_64Y_C2_004


title: Adult_64Y_C2_003


title: monocyte_NOD_PBS_3

source_name: monocyte


title: pDC_B6 Rag1-/-_PBS_1


title: monocyte_NOD_PBS_1


title: Adult_64Y_C2_002


title: monocyte_NOD_PBS_2


title: monocyte_B6g7_PBS_3


title: monocyte_B6g7_PBS_1


title: monocyte_B6g7_PBS_2


title: Adult_64Y_C2_001


title: Adult_64Y_C1_055


title: Adult_64Y_C1_056


title: moDC_NOD Rag1-/-_PBS_3

source_name: moDC


title: Adult_64Y_C1_054


title: Adult_64Y_C1_052


title: moDC_NOD_PBS_5


title: Adult_64Y_C1_051


title: moDC_NOD_PBS_4


title: moDC_NOD Rag1-/-_PBS_2


title: pDC_B6 Rag1-/-_PBS_2


title: Adult_64Y_C1_050


title: moDC_NOD Rag1-/-_PBS_1


title: Adult_64Y_C1_053


title: moDC_NOD_PBS_2


title: Adult_64Y_C2_005


title: Adult_64Y_C1_049


title: moDC_NOD_PBS_3


title: moDC_NOD_PBS_1


title: Adult_64Y_C1_048


title: moDC_B6g7_PBS_5


title: moDC_B6g7_PBS_6


title: Adult_64Y_C1_047


title: Adult_64Y_C1_046


title: Adult_64Y_C1_044


title: Adult_64Y_C1_045


title: moDC_B6g7_PBS_3


title: Adult_64Y_C1_043


title: Adult_64Y_C1_041


title: moDC_B6g7_PBS_1


title: Adult_64Y_C1_040


title: moDC_B6g7_PBS_2


title: moDC_B6 Rag1-/-_PBS_1


title: cDC2_NOD Rag1-/-_PBS_3


title: cDC2_NOD Rag1-/-_PBS_2


title: Adult_64Y_C1_038


title: Adult_64Y_C1_039


title: Adult_64Y_C1_037


title: moDC_B6 Rag1-/-_PBS_2


title: cDC2_NOD Rag1-/-_PBS_1


title: Adult_64Y_C1_036


title: cDC2_NOD_PBS_6


title: Adult_64Y_C1_035


title: cDC2_NOD_PBS_5


title: Adult_64Y_C1_034


title: cDC2_NOD_PBS_4


title: Adult_64Y_C1_033


title: moDC_B6g7_PBS_4


title: Adult_64Y_C1_032


title: cDC2_NOD_PBS_3


title: Adult_64Y_C1_042


title: cDC2_NOD_PBS_2


title: cDC2_NOD_PBS_1


title: Adult_64Y_C1_031


title: Adult_64Y_C1_029


title: cDC2_B6g7_PBS_5


title: Adult_64Y_C1_030


title: Adult_64Y_C1_028


title: cDC2_B6g7_PBS_4


title: Adult_64Y_C1_027


title: cDC2_B6g7_PBS_3


title: cDC2_B6g7_PBS_2


title: Adult_64Y_C1_026


title: Adult_64Y_C1_025


title: Adult_64Y_C1_024


title: OsJAZ1-OE-D1

city: Wuhan

first: Jie

last: Fu

state: Hubei

address: 1 lion hill street

country: China

institute: Huazhong Agricultural University

description: OsJAZ1 overexpression line1 (OE-1) replicate 1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house Perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Tophat2 tools soft were used to map with reference genome.
Gene function was annotated based on the following databases: Nr (NCBI non-redundant protein sequences); Nt (NCBI non-redundant nucleotide sequences); Pfam (Protein family); KOG/COG (Clusters of Orthologous Groups of proteins); Swiss-Prot (A manually annotated and reviewed protein sequence database); KO (KEGG Ortholog database); GO (Gene Ontology).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
Quantification of gene expression levels: Gene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Genome_build: Rice Genome Annotation Project (RGAP) 7.0
Supplementary_files_format_and_content: *_Processed_Data.xls: The processed data is presented in Microsoft Excel file format, and includes "GeneID", "Length", "FPKM", "Locus", "Strand", "Count".

organism: Oryza sativa Japonica Group

source_name: Rice plants at four-leaf stage

growth_protocol: Plants were grown in a barrel during the summer of 2016 in Wuhan, Hubei Province, China.

extract_protocol:
RNA for the RNA-Seq analysis was extracted using TRIzol® reagent (AmbionTM, Lot No. 15596018) according to the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Seedlings at the 4-leaf stage were subjected to drought stress treatment until the water content of the soil maintained at 10%-15%.

tag: variety/background

value: Zhonghua 11 (ZH11)

tag: genotype/variation

value: OsJAZ1 overexpression line1 (OE-1)

value: Shoot

tag: developmental stage

value: Four-leaf stage

tag: condition

value: Drought


title: OsJAZ1-OE-D2

description: OsJAZ1 overexpression line1 (OE-1) replicate 2


title: Adult_64Y_C1_023


title: OsJAZ1-OE-N3

description: OsJAZ1 overexpression line1 (OE-1) replicate 3

value: Normal


title: cDC2_B6g7_PBS_1


title: cDC2_B6 Rag1-/-_PBS_3


title: cDC2_B6 Rag1-/-_PBS_2


title: OsJAZ1-OE-N2


title: Adult_64Y_C1_022


title: Adult_64Y_C1_021


title: OsJAZ1-OE-N1


title: Adult_64Y_C1_020


title: cDC2_B6 Rag1-/-_PBS_1


title: cDC2_B6g7_PBS_6


title: cDC1_NOD Rag1-/-_PBS_3


title: ZH11-D2

description: Wild-type ZH11 replicate 2

value: Wild-type


title: cDC1_NOD Rag1-/-_PBS_2


title: Adult_64Y_C1_019

value: Adult


title: ZH11-D1

description: Wild-type ZH11 replicate 1


title: Adult_64Y_C1_017

value: retina


title: ZH11-N2

description: Wild-type ZH11 replicate 2


title: cDC1_NOD_PBS_5


title: ZH11-N1

description: Wild-type ZH11 replicate 1


title: Adult_64Y_C1_016


title: cDC1_NOD_PBS_4


title: cDC1_NOD_PBS_3


title: cDC1_NOD_PBS_2


title: cDC1_NOD_PBS_1


title: cDC1_B6g7_PBS_6


title: cDC1_B6g7_PBS_5


title: cDC1_B6g7_PBS_4


title: Adult_64Y_C1_009


title: Adult_64Y_C1_014


title: Adult_64Y_C1_010


title: Adult_64Y_C1_012


title: Adult_64Y_C1_015


title: Adult_64Y_C1_013


title: cDC1_B6g7_PBS_3


title: Adult_64Y_C1_008


title: cDC1_NOD_PBS_6


title: Adult_64Y_C1_018


title: cDC1_NOD Rag1-/-_PBS_1


title: Adult_64Y_C1_007


title: Adult_64Y_C1_011


title: cDC1_B6g7_PBS_1


title: ZH11-N3

description: Wild-type ZH11 replicate 3


title: cDC1_B6g7_PBS_2


title: cDC1_B6 Rag1-/-_PBS_3


title: Adult_64Y_C1_005


title: cDC1_B6 Rag1-/-_PBS_2


title: Adult_64Y_C1_003


title: cDC1_B6 Rag1-/-_PBS_1


title: Adult_64Y_C1_006


title: AGXX_120

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description: AGXX 120 min

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Staphylococcus aureus 04-02981|VERSION Date:   2010/11/05 | GenBank assembly accession: GCA_000025145.2
Supplementary_files_format_and_content: Tab delimited text file

organism: Staphylococcus aureus

source_name: Cell culture

growth_protocol: Bacterial cells were grown in Tryptic Soy Broth at 37°C, 150 rpm shaking

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: The bacterial culture was exposed to Ag or AGXX, the culture without addition of any metal sheet served as the control

tag: accession


title: ChIP-seq H3K4me3_rep2

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description: replicate 2

data_processing:
Illumina pipeline Casava 1.82
For ChIP-seq: Reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads); For RNA-seq: reads were aligned to the mm9 genome assembly using HISAT 2 v.2.0.1 with default parameters (--rna-strandness R was added when it applied)
For ChIP-seqs: Peaks were called using MACS v1.4 or SICER v1.1 for H3K27me3
For RNA-seq; only reads uniquely mapped (NH:i:1 flag) were selected for further processing
For RNA-seq, read summarization for genes were performed using featureCounts v1.5.1. For ERE, bedtools 2.25 multicov was used. For MeDIP counts on genes, htseq-count 0.6 was used. For all other MeDIP counts, bedtools multicov was used.
Genome_build: mm9
Supplementary_files_format_and_content: Count table: read counts [RNA-seq or ChIP-seq] for each feature of interest – either ensembl gene name or genome coordinates [last column is read counts]. Bed: peaks as called by MACS or SICER peak caller

source_name: ChIP-seq H3K4me3

growth_protocol: Naive murine embryonic stem cells were cultured in N2B27 medium with 1x MEM non-essential amino acids, 0.1 mM 2-mercaptoethanol, 1x penicillin/streptomycin, 25µg/mL Bovine serum albumin, leukaemia inhibitory factor (LIF), and 2i containing 1µM MEK inhibitor  PD 0325901 (Axon 1408) and 3µM GSK3 inhibitor CHIR 99021 (Axon 1386). Cells were grown on 0.1% gelatin-coated plates and split every two days. Cells were transduced, selected with 4μg/mL puromycin and collected after 5 days.

extract_protocol:
Cells were harvested, washed with Episerf (LifeTechnologies, #10732), fixed in 10mL per 1x107 cells (10 min in 1% formaldehyde), quenched with TrisHCl in 50mL (at 250 mM final), washed with PBS, and pelleted. Each pellet containing 1x107 cells was lysed, resuspended in 1 mL of sonication buffer on ice (10 mM Tris at pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% NaDOC, 0.25% NLS, and protease inhibitors), transferred to TC 12x12 tubes (Covaris), and sonicated (Covaris settings: 20 min, 5% duty cycle, 140W, 200 cycles). Sonication was assessed by reverse cross-linking (65°C, RNAse A at 1μg/μL, overnight), followed by DNA extraction. Fragment size (between 200-400bp) was checked on a Bioanalyzer (Agilent 2100). Immunoprecipitations were performed with chromatin from 1x107 cells with Dynabeads (ThermoFisher) in IP buffer (16.25 mM Tris at pH 8.1, 137.5 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1.25% Triton X-100, and protease inhibitors) overnight. Chromatin was reversed cross-linked (65°C, Proteinase K at 400ng/μL, overnight) and DNA was further extracted for analysis.
Paired-end libraries were prepared and sequenced in 75bp reads runs according to Illumina instructions.

tag: cell line

tag: cell type

value: Embryonic stem cells

value: wild type

tag: antibody

value: H3K4me3 (Cell Signalling Technology, #9751)


title: Adult_64Y_C1_002


title: Adult_64Y_C1_004


title: ChIP-seq H3K4me3_rep1

description: replicate 1


title: Adult_64Y_C1_001


title: Ag_120

description: Ag 120 min


title: ChIP-seq H3K27me3_rep2

description: replicate 2

source_name: ChIP-seq H3K27me3


title: control_120

description: Control 120 min


title: AGXX_80

description: AGXX 80 min


title: BD2_IP

city: Toronto

first: Alejandro

last: Saettone

state: Ontario

address: 686 Bay Street

department: Genetics & Genome Biology

country: Canada

institute: The Hospital for Sick Children

description:
BD1_BD2_IntergenicRegions_Peaks.xlsx
BD1_BD2_ORF_peaks.xlsx
MACS2_BD2_NA_peaks.xlsx

data_processing:
ChIP-seq reads were assessed for quality using fastqc
ChIP-Seq reads were aligned using BWA and SAMtools
Heursitic method: Peak calling from the genetic and intergenic regions were respectively counted and extracted
MACS2 was use for broad peaks calling
Peaks normalization and Fold enrichment calculations were performed
Genome_build: T_thermophila_June2014_assembly.fasta (http://ciliate.org/index.php/home/downloads)
Supplementary_files_format_and_content: xlsx files containing peaks and fold enrichmet were generated using heuristic method and MACS2. For the heuristic methods the peaks are represented by the normalized reads from genic and intergenic regions and the fold enrichment are represented as IP/INPUT

organism: Tetrahymena thermophila

source_name: Cells grown in SPP liquid media

growth_protocol: 30C; 100rpm; SPP liquid media

extract_protocol:
Lysates were clarified from sonicated nuclei and Ibd1-histone-DNA complexes were isolated with ANTI-FLAG® M2 Affinity Gel (Sigma)
Illumina's  TruSeq ChIP Sample Preparation Kit (cat# IP-202-1012)

value: B2086 IBD1-FZZ

value: Vegetative Growth

tag: extraction

value: Immunoprecipitation


title: ChIP-seq H3K27me3_rep1

description: replicate 1


title: Ag_12

description: Ag 12 min


title: AGXX_24

description: AGXX 24 min


title: control_6

description: Control 6 min


title: control_12

description: Control 12 min


title: control_80

description: Control 80 min


title: Ag_6

description: Ag 6 min


title: AGXX_12

description: AGXX 12 min


title: control_24

description: Control 24 min


title: BD2_INPUT

value: Whole cell extraction


title: control_0_a

description: Control


title: Ag_24

description: Ag 24 min


title: Ag_80

description: Ag 80 min


title: AGXX_6

description: AGXX 6 min


title: BD1_INPUT

description:
BD1_BD2_IntergenicRegions_Peaks.xlsx
BD1_BD2_ORF_peaks.xlsx
MACS2_BD1_NA_peaks.xlsx


title: ZF_mir29_3

status: Public on Feb 27 2018

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

country: Germany

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Raw reads were assessed for quality, adapter content and duplication rates with FastQC version 0.11.2.
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl zebrafish genome version GRCz10 using STAR 2.5.2b with the parameters “--outFilterMismatchNoverLmax 0.1 --alignMatesGapMax 1000 --alignIntronMax 200000”.
The number of reads aligning to genes was counted with featureCounts 1.5.0 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Raw counts were normalized using DESeq2 and rounded to the next integer.
Genome_build: GRCz10
Supplementary_files_format_and_content: matrix.txt contains DESeq2 normalized count values for all genes overlapped by at least one read.

organism: Danio rerio

source_name: Heart tissue

extract_protocol:
For next generation sequencing (NGS) RNA was isolated using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA and libraries integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer). 500 ng total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech). Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry with 2x75bp paired end setup.

tag: construct

value: mir29 sponge

value: heart


title: ZF_mir29_2


title: ZF_mir29_1


title: ZF_WT_2


title: ZF_WT_1


title: 418

city: Cambridge

first: James

last: Hockley

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

data_processing:
Illumina RTAv2 was used for base calling.
Samples were demultiplexed and converted to FASTQ with bcl2fastq2 (v. 2.15.0.4), aligned to GRCm38.p3 (Ensembl version 80, retrieved 2015-05-27) using STAR (v. 2.4.1)
Genomic features were determined using featureCounts (v. 1.4.4)
Low-quality cells were filtered by threshold for the number of unique genes detected (>5000 genes/cell), proportion of reads aligning to mitochondrial RNA (< mean +/- 2*SD (~8.5%)) and normalized gene coverage (median 5' to 3' bias > 0.27).
Counts were standardized for gene length by converting to Transcript Per Million and normalized using size factors as described by Lun et al. 2016 Genome Biology (PMID:27122128)
Genome_build: GRCm38.p3 (Ensembl version 80; retrieved 2015-05-27)
Supplementary_files_format_and_content: counts.txt contain TPM values for 325 cells (excl. samples not passing quality control)

source_name: Colonic sensory neuron

extract_protocol:
Colon-projecting sensory neurons were labelled by Fast Blue injection into the wall of the colon via laparatomy. Three to ten days after surgery, thoracolumbar (TL; T10-L1) and lumbosacral (LS; L5-S2) dorsal root ganglia (DRG) were dissected and dissociated into two separate primary cultures. Individual Fast Blue-positive colonic sensory neurons free from debris were manually isolated by pulled patch pipette. 13 negative bath samples were also collected.
RNA sequencing libraries were prepared using standard Illumina protocols

value: Colonic sensory neuron

tag: spinal segment

value: Lumbosacral

tag: negative control

value: No

tag: plate


title: control_0_b

description: Control


title: 416


title: 415


title: 417


title: 413


title: 414


title: BD1_IP


title: 399


title: 407


title: 411


title: 401


title: 403


title: 412


title: 408


title: 398


title: 405


title: 404


title: 402


title: 410


title: 409


title: 396


title: 397


title: 395


title: ZF_WT_3


title: 406


title: 394

value: Thoracolumbar


title: 385


title: 388


title: 390


title: 386


title: 387


title: 400


title: 384


title: 375


title: 378


title: 380


title: 382


title: 379


title: 377


title: 381


title: 383


title: 370

value: Yes


title: 372


title: 369


title: 374


title: 393


title: 376


title: 392


title: 367


title: 389


title: 368


title: 391


title: 364


title: 363


title: 360


title: 362


title: 366


title: 358


title: 357


title: 359


title: 356


title: 353


title: 354


title: 349


title: 347


title: 351


title: 344


title: 346


title: 348


title: 345


title: 371


title: 373


title: 365


title: 342


title: 343


title: 341


title: 361


title: 338


title: 337


title: 339


title: 340


title: 335


title: 333


title: 355


title: 334


title: 352


title: 350


title: 331


title: 330


title: 336


title: 326


title: 320


title: 322


title: 323


title: 325


title: 327


title: 324


title: 329


title: 328


title: 319


title: 321


title: 318


title: 317


title: 316


title: 313


title: 314


title: 315


title: 332


title: 306


title: 307


title: 303


title: 309


title: 304


title: 311


title: 302


title: 305


title: 308


title: 299


title: 298


title: 297


title: 301


title: 291


title: 294


title: 292


title: 290


title: 296


title: 312


title: 293


title: 289


title: 288


title: 287


title: 283


title: 285


title: 310


title: 286


title: 284


title: 280


title: 282


title: 279


title: 278


title: 276


title: 275


title: 274


title: 281


title: 277


title: 295


title: 300


title: 273


title: 272


title: 270


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title: 196


title: 197


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title: 89


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title: 72


title: 87


title: 64


title: 65


title: 70


title: 69


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title: 60


title: 83


title: 67


title: 68


title: 63


title: 150


title: 61


title: 59


title: 56


title: 62


title: 54


title: 52


title: 51


title: 50


title: 71


title: 49


title: 48


title: 55


title: 46


title: 44


title: 53


title: 42


title: 58


title: 40


title: 39


title: 35


title: 37


title: 41


title: 57


title: 36


title: 34


title: 38


title: 30


title: 33


title: 47


title: 26


title: 25


title: 24


title: 22


title: 23


title: 28


title: 45


title: 21


title: 20


title: 19


title: 43


title: 17


title: 32


title: 16


title: 13


title: 15


title: 31


title: 6


title: 5


title: 1


title: 2


title: 3


title: 4


title: 29


title: 14


title: 27


title: SB3

city: Thuwal

first: Prof. Heribert

last: HIRT

address: 4700 KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Reads were trimmed to using trimmomatic to have minimum length 36 bps and phred score quality 30 using a sliding window of 4:15. leading and trailing bases were removed with base quality below 3
Trimmed reads were aligned against TAIR10 using TOPHAT.
The differentially expressed genes were identified using cuffdiff2.2.0. We used a cut-off of 1 Fold change and q-val <= 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Sterilized seeds were stratified for 3 days and then plated on ½ MS agar plates (Murashige and Skoog basal salts, Sigma), grown vertically for 5 days at 22 C and 16h light, then transferred to fresh ½ MS agar plates with (samples S, SB) or without (samples M, B) 100 mM NaCl (6 seedlings per plate) and cultivated for additional 12 days.

extract_protocol:
Total RNA was extracted from 17-day-old seedlings flash frozen in liquid nitrogen, using "RNA extraction plant kit" following manufacturer's instructions,  was used with 1 ug of total RNA for the construction of sequencing libraries.
Total RNA from plant and dual (plant + bacteria) samples was treated with Ribo-Zero Magnetic Gold Kit to remove ribosomal rRNA (rRNA). For rRNA depletion of plant samples (M and S), rRNA Removal solution from Ribo-Zero Magentic kit (Plant Leaf) was used. For rRNa depletion of dual samples (B and BS), rRNA Removal solution from Ribo-Zero Magnetic kit (Plant Leaf) and rRNA Removal Solution from Ribo-Zero Gold kit (Epidemiology) were mixed in a ratio 1:1. An amount of 1 ug of total RNA was used for the contruction of RNA-Seq libraries. Pair-end sequencing of the 12 RNA-Seq libraries was performed by using Illumina Genome Analyzer IIx (GAIIx) with a read length of 101 bp, which yielded and average of 60-70 million reads each.

treatment_protocol: Initial plates for sterilized seeds germination containing bacterial strain SA187 (2·10E+5 cfu·mL-1) were used to prepare samples B and SB. Control plates for samples M and S were non-inoculated.

tag: ecotype

tag: age

value: 17 days

tag: genotype

value: wildtype


title: M3


title: B3


title: B2


title: SB2


title: S3


title: 18

tag: strain


title: S2


title: M1


title: M2


title: B1


title: S1


title: LNCaP BETi Resistant Pool 1

city: Philadelphia

first: Irfan

middle: A

last: Asangani

state: Pennylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control.
Read quality was checked for each sample using FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each sample

source_name: LNCaP BETi Resistant Pool 1

growth_protocol: Cells were grown in RPMI containing 10% FBS

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 22RV1 and LNcaP prostate cancer cells were cultured in RPMI1640 (Gibco) supplemented with 10% (v/v) FBS (Gibco). BETi (JQ1) resistant lines were developed by culturing in above mentioned media with IC50 concentration of the drug (100nM and 200nM for LNcaP and 22RV1 respectively) for over a period of 14-16 weeks.

tag: tissue

value: prostate

value: LNCaP

tag: treatment

value: BETi resistant cells


title: LNCaP

value: control cells


title: 22RV1 BETi Resistant Pool 1

source_name: 22RV1 BETi Resistant Pool 1


title: 22RV1 BETi Resistant Pool 2

source_name: 22RV1 BETi Resistant Pool 2


title: Vector2

first: Yutaka

last: Amemiya

state: ON

address: 2075 Bayview Ave.

institute: Sunnybrook Research Institute

description:
VC2
Vector2_S70

data_processing:
bcl2fastq v2.17 was used for both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
FASTQ files were mapped to mm10 genome by HISAT2 protocol (Kim et al., 2015) (Pertea et al., 2016)
Expression data were normalized by the transcripts per million reads (TPM) method (Wagner et al., 2012)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: vector control

growth_protocol: Tau-GFP P1 spiral ganglia were dissected and sorted. GFP positive fraction was collected as endogenous primary auditory neurons.

extract_protocol:
RNA was extracted using the Single Cell RNA Purification Kit (NORGEN, #51800). RNA library preparation was performed using a two-pronged approach: (1) Two ng of input RNA was converted to double stranded cDNA using Clontech SMARTer Ultra Low Input RNA Kit v3: (2) one ng of double stranded cDNA was used as input material for the illumina’s Nextera XT library preparation kit
RNA libraries were prepared for sequencing following Clonthech and Illumina's recommended protocol.

treatment_protocol: GFP negative fraction containing Schwann cells and mesenchymal cells was cultured and transfected with Ascl1 and NeuroD1 vectors for inducing neurons, or Empty vectors as control.

tag: strain background

tag: genotype/variation

value: Empty transfected


title: 22RV1


title: LNCaP BETi Resistant Pool 2

source_name: LNCaP BETi Resistant Pool 2


title: Vector3

description:
VC3
Vector3_S71


title: Vector1

description:
VC1
Vector1_S69

value: Empty vector transfected


title: DoubleiN2

description:
iN2
DoubleiN2_S67

source_name: induced neuron

value: induced neuron

value: Ascl1 and NeuroD1 transfected


title: DoubleiN1

description:
iN1
DoubleiN1_S66


title: Endogenous1

description:
PAN1
Endogenous1_S60

source_name: endogenous primary auditory neuron

value: P1 primary auditory neuron


title: Endogenous3

description:
PAN3
Endogenous3_S62


title: Endogenous2

description:
PAN2
Endogenous2_S61


title: activatedCD4Tcells_individual26

city: Stockholm

first: Karine

last: Chemin

address: 4th floor

department: Medicine

country: Sweden

institute: CMM, KI

description: Activated helper T cells from peripheral blood

data_processing:
The reads were aligned using STAR 2.4.0g1
Expression values (FPKM) were determined using rpkmforgenes.py version 13 March 2015 (available at https://github.com/danielramskold/S3_species-specific_sequencing), with settings -minqual 255 -rmnameoverlap -midread -fulltranscript and ReqSeq gene annotation from 21 December 2014.
Individual names is according to supplementary Table 1 (Chemin K. PMID: 29388193)
Genome_build: hg38
Supplementary_files_format_and_content: Excel file

source_name: Naïve helper T cells from peripheral blood

growth_protocol: Influx sorter (BD), sorting of peripheral blood mononuclear cells for CD4+ CD45RA+ CCR7+ cells

extract_protocol:
RNA extraction Mini-kit, Qiagen
Illumina TruSeq mRNA protocol

tag: individual

tag: in vitro t cell activation

value: anti-CD3/CD28 beads (1bead/cell, Dynabeads) for 16 hours

value: AA

value: 66 years

tag: Sex

value: Female

tag: hla-drb1 genotype

tag: cytomegalovirus status


title: 9845_GOF0

first: Radhika

middle: Paresh

last: Atit

state: Ohio

address: 2074 Adelbert Road, Millis 316

department: Biology

institute: Case Western Reserve University

data_processing:
The resulting 100bp reads were aligned to the mouse genome release mm10 genome using TopHat
Differential gene expression was determined with CuffDiff using the default settings plus genomic bias correction.
CuffDiff (Differential expression on the basis of FPKM)
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs and significant genes
[mRNA] mRNA mm10 genes.read_group_tracking FPKM
[mRNA] gene_exp-diff-significdown
[mRNA] isoform_exp-diff-significdown
[mRNA] gene_exp-diff-significup
[mRNA] isoform_exp-diff-significup
[lncRNA] LncRNA mm10 genes.read_group_tracking FPKM
[lncRNA] cufsig-cuf2x_gene_exp-diff-significdown
[lncRNA] cufsig-cuf2x_isoform_exp-diff-significdown
[lncRNA] cufsig-cuf2x_gene_exp-diff-significup
[lncRNA] cufsig-cuf2x_isoform_exp-diff-significup

source_name: AdCre mutant

growth_protocol: DMEM + penn/strep + antimyotic/antibiotici +10% Fetal Bovine Serum

extract_protocol:
Total RNA was harvested using Trizol reagent and stored at -80c for under one month. RNA was isolated using Qiagen Rneasy Kit. Illumina TruSeq RNA Sample Prep Kit was used with 200-400ng of total RNA for the construction of sequencing libraries.
Libraries were prepared by the CWRU Genomics Sequencing Core, using True-Seq Stranded Kit (Illumina).
Illumina HiSeq 2500 v2 Rapid Run

treatment_protocol: 366-500 MOI adCre for 6 hours in Serum free DMEM

value: AdCre; Ctnnb1{delta}ex3/+

tag: age (at harvest)

value: CD1, C57Bl6

tag: cell type

value: dermal fibroblast


title: 9843_GOF1


title: SB1

value: 17 days

value: wildtype


title: activatedCD4Tcells_individual25

value: GG

value: 67 years


title: activatedCD4Tcells_individual23

value: 65 years


title: activatedCD4Tcells_individual24

value: 61 years


title: 9845_Control2

source_name: AdGFP control

value: AdGFP; +/+


title: activatedCD4Tcells_individual16

value: 42 years

value: Male


title: 9852_Control0


title: ATAC-seq from 50k dox- 24h induced SA-tTA-MyoD embryonic stem cells

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

description: ATAC-seq from murine ES cells

data_processing:
All samples were ran on a Illumina Hi-Seq 2500 and basecalls were performed using CASAVA
Sequence reads for each sample were mapped to the mm10 genome assemblies as relevant with Bowtie (v2.2.6)
Duplicate reads were removed, and the remaining unique reads were normalized to 10 million reads
Differential peak calling of ATAC-seq data was performed by HOMER (v4.7) using an FDR cutoff of 0.001, a cumulative Poisson p-value of <0.0001, and required a 4-fold enrichment of normalized sequenced reads in the treatment sample over the control sample
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: SA-tTA-MyoD Embryonic Stem Cells

growth_protocol: Cells were raised in DMEM-based ES culture media. Formulation is detailed in text.

extract_protocol:
ATAC-seq was performed using 50k ES cell,s as described in Buenrostro et al 2015
Serial PCR was performed using Nextera-based multiplexing primers
ATAC-seq was performed using 50k ES cells, as described in Buenrostro et al 2015

treatment_protocol: Cells were cultured in doxycycline-containing media, induced by serial PBS washes and culture in media lacking doxycycline to induce expression of transgene, as described in text.

value: MC1 mouse ES cells derived from 129S6/SvEvTac


title: ATAC-seq from 50k dox+ ctrl uninduced SA-tTA-MyoD Embryonic Stem Cells

description: ATAC-seq from murine ES cells


title: ATAC-seq from 50k dox- 24h induced SA-tTA-Ascl2 embryonic stem cells

description: ATAC-seq from murine ES cells

source_name: SA-tTA-Ascl2 Embryonic Stem Cells


title: DoubleiN3

description:
iN3
DoubleiN3_S68

value: induced neuron

value: Ascl1 and NeuroD1 transfected


title: activatedCD4Tcells_individual14

value: anti-CD3/CD28 beads (1bead/cell, Dynabeads) for 16 hours

value: AA

value: 41 years


title: 9852_GOF2

value: AdCre; Ctnnb1{delta}ex3/+

value: CD1, C57Bl6


title: ATAC-seq from 50k dox+ ctrl uninduced SA-tTA-Ascl2 Embryonic Stem Cells

description: ATAC-seq from murine ES cells


title: activatedCD4Tcells_individual9

value: 37 years

value: Female


title: activatedCD4Tcells_individual4

value: 27 years


title: activatedCD4Tcells_individual10

value: 35 years


title: ATAC-seq from 50k dox+ ctrl uninduced SA-tTA-Ascl1 Embryonic Stem Cells

description: ATAC-seq from murine ES cells

source_name: SA-tTA-Ascl1 Embryonic Stem Cells


title: activatedCD4Tcells_individual15

value: GG

value: 44 years


title: ATAC-seq from 50k dox- 24h induced SA-tTA-Ascl1 embryonic stem cells

description: ATAC-seq from murine ES cells


title: RNA-seq replicate 3 from dox- 24h induced SA-tTA-MyoD ESCs

description: RNA purified from 24h induced  ESCs

data_processing:
Mouse samples were run on a Illumina Hi-Seq 2500 and basecalls were performed using CASAVA
Mouse sequence reads were aligned to the mm10 genome assembly using TopHat v2.1.0 (Trapnell et al. 2009). All Default settings were used except: -G option and --no-novel-juncs.
RPKM values were estimated using EdgeR (v. 3.6.8)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text spreadsheet

extract_protocol:
RNA purification was performed from 10cm plates of ~80% confluent murine ES cells from the cell lines described above. Zymo R1054 RNA purification kit was used to purify DNAse treated RNA. Sample collection was performed by briefly washing plates in phosphate buffered saline prior to the addition of RNA lysis buffer. Sterile cell lifters were used to disrupt cells, and lysates transferred to microfuge tubes for cold storage prior to purification according to manufacturer-supplied protocol.
Purified samples were evaluated by Agilent Bioanalyzer and prepared for RNA sequencing libraries using Illumina reagents.
Library preparation was performed according to Illumina guidelines for sequencing on HiSeq 2500 line.


title: RNA-seq replicate 2 from dox- 24h induced SA-tTA-MyoD ESCs

description: RNA purified from 24h induced  ESCs


title: activatedCD4Tcells_individual3

value: 25 years


title: 9844_Control1

value: AdGFP; +/+

value: dermal fibroblast


title: RNA-seq replicate 1 from dox- 24h induced SA-tTA-MyoD ESCs

description: RNA purified from 24h induced  ESCs

value: MC1 mouse ES cells derived from 129S6/SvEvTac


title: activatedCD4Tcells_individual5

value: 23 years


title: activatedCD4Tcells_individual2

value: 21 years

value: Male


title: RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-MyoD ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-MyoD ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 3 from dox- 24h induced SA-tTA-Ascl2 ESCs

description: RNA purified from 24h induced  ESCs


title: activatedCD4Tcells_individual1

value: anti-CD3/CD28 beads (1bead/cell, Dynabeads) for 16 hours


title: activatedCD4Tcells_individual6

value: AA

value: 28 years


title: RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-MyoD ESCs

description: RNA purified from uninduced ESCs


title: naiveCD4Tcells_individual26

description: Naïve helper T cells from peripheral blood

value: No

value: 66 years


title: activatedCD4Tcells_individual17

value: Female


title: naiveCD4Tcells_individual25

value: 67 years


title: RNA-seq replicate 1 from dox- 24h induced SA-tTA-Ascl2 ESCs

description: RNA purified from 24h induced  ESCs


title: RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 2 from dox- 24h induced SA-tTA-Ascl1 ESCs

description: RNA purified from 24h induced  ESCs


title: RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 2 from dox- 24h induced SA-tTA-Ascl2 ESCs

description: RNA purified from 24h induced  ESCs


title: naiveCD4Tcells_individual17


title: naiveCD4Tcells_individual14

value: 41 years


title: RNA-seq replicate 1 from dox- 24h induced SA-tTA-Ascl1 ESCs

description: RNA purified from 24h induced  ESCs


title: RNA-seq replicate 3 from dox- 24h induced SA-tTA-Ascl1 ESCs

description: RNA purified from 24h induced  ESCs


title: naiveCD4Tcells_individual15

value: GG


title: naiveCD4Tcells_individual16

value: 42 years


title: naiveCD4Tcells_individual23

value: 65 years


title: RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs

description: RNA purified from uninduced ESCs


title: RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs

description: RNA purified from uninduced ESCs


title: naiveCD4Tcells_individual3

value: 25 years


title: RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs

description: RNA purified from uninduced ESCs


title: naiveCD4Tcells_individual9

value: 37 years


title: naiveCD4Tcells_individual10

value: 35 years


title: naiveCD4Tcells_individual5

value: 23 years


title: H3K27ac ChIP-matched input from dox- 24h ind SA-tTA-MyoD ESCs

data_processing:
All samples were ran on a Illumina Hi-Seq 2500 and basecalls were performed using CASAVA
Sequence reads for each sample were mapped to the mm10 genome assemblies as relevant with Bowtie (v2.2.6)
Duplicate reads were removed, and the remaining unique reads were normalized to 10 million reads
Peak calling was performed by HOMER (v4.7) using an FDR cutoff of 0.001, a cumulative Poisson p-value of <0.0001, and required a 4-fold enrichment of normalized sequenced reads in the treatment sample over the control/input sample
Genome_build: mm10

extract_protocol:
ChIP-seq was performed on samples of 10M formaldehyde-fixed murine ES cells. Frozen samples were thawed and lysed to purify nuclei. Nuclei were then incubated in nuclear lysis/ChIP buffer and sonicated using a Diagenode standard sonicator for a total of 35 minutes. Samples were centrifuged to remove cellular debris, and antibodies added. Antibody-binding incubation was performed, rotating overnight at 4C. Sequential washes to remove nonspecific genomic template were performed using Life Technologies Protein G Dynabeads, and immunopurified samples were further purified. Samples were eluted from Dynabeads using a 70C benchtop shaker, and crosslink reversal performed overnight at 65C using heated shaker, prior to proteinase K and RNAse treatment.  Detailed description, including buffer components and formulae, is described in the text.
Library preparation was performed according to manufacturer-supplied literature (NEB E6240L).
Libraries were prepared using NEB ChIP purification reagents (E6240L) and Illumina indexing primers were used to facilitate demultiplexing.

value: MC1 mouse ES cells derived from 129S6/SvEvTac

tag: antibody

value: input control


title: naiveCD4Tcells_individual4

value: 27 years

value: Male


title: naiveCD4Tcells_individual6

value: AA

value: 28 years


title: H3K27ac ChIP from dox- 24h ind SA-tTA-MyoD ESCs

value: Abcam Ab4729 rabbit polyclonal anti-H3K27ac


title: H3K27ac ChIP-matched input from dox+ ctrl SA-tTA-MyoD ESCs


title: naiveCD4Tcells_individual1

value: No


title: H3K27ac ChIP from dox+ ctrl SA-tTA-MyoD ESCs


title: H3K27ac ChIP-matched input from dox- 24h ind SA-tTA-Ascl2 ESCs


title: naiveCD4Tcells_individual24

value: 61 years

value: Female


title: naiveCD4Tcells_individual2

value: 21 years


title: H3K27ac ChIP-matched input from dox+ ctrl SA-tTA-Ascl2 ESCs


title: H3K27ac ChIP from dox+ ctrl SA-tTA-Ascl2 ESCs


title: H3K27ac ChIP from dox- 24h ind SA-tTA-Ascl1 ESCs


title: ASCL2-FLAG ChIP-matched input from dox- 24h ind SA-tTA-Ascl2 ESCs


title: H3K27ac ChIP from dox+ ctrl SA-tTA-Ascl1 ESCs


title: MYOD-FLAG ChIP-matched input from dox- 24h ind SA-tTA-MyoD ESCs


title: H3K27ac ChIP-matched input from dox+ ctrl SA-tTA-Ascl1 ESCs


title: MYOD-FLAG ChIP from dox+ ctrl SA-tTA-MyoD ESCs

value: Sigma FLAG F1804 applied to uninduced control


title: MYOD-FLAG ChIP from dox- 24h ind SA-tTA-MyoD ESCs

value: Sigma F1804 mouse monoclonal M2 anti-FLAG


title: ASCL2-FLAG ChIP from dox- 24h ind SA-tTA-Ascl2 ESCs


title: H3K27ac ChIP-matched input from dox- 24h ind SA-tTA-Ascl1 ESCs


title: TAK1093_pol3L612M_pol2-4_rnh201delta

city: Research Triangle Park

first: Marta

middle: Anna

last: Garbacz

state: NC

address: 111 T.W. alexander Dr.

department: GISBL

institute: NIEHS/NIH

data_processing:
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.12, discarding pairs with one or both reads shorter than 15 nt
Combine technical replicates
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 1.2 -k1 -v2)
Align remaining pairs to W303 reference genome, trim single nt from 3' end of reads to allow mapping of 100% overlapping pairs (bowtie 1.2 -m1 -v2 -X10000 -3 1)
Align end 1 of unmapped pairs to W303 reference genome (bowtie 1.2 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, shift 1 base upstream and combine
Genome_build: W303 background RNR1 assembly (see supplementary files)
Supplementary_files_format_and_content: bigWig, count of HydEn-seq 5' ends per position

organism: Saccharomyces cerevisiae

source_name: TAK1093 pol3L612M pol2-4 rnh201delta

growth_protocol: Yeast strains were grown to mid log phase (OD600=0.5-1) at 23°C in YPDA medium supplemented with 0.25 mg/ml adenine

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
Ribonucleotides were mapped in the genomic DNA using Hydrolytic End Sequencing technique (HydEn-seq) described by Clausen et al., 2015. Briefly, DNA was isolated from exponentially growing yeast (OD600: 0.5 – 1/ ml) with using a kit for genomic DNA isolation from yeast (Epicenter). Libraries for Next Generation Sequencing were prepared with using 1 µg of DNA, which was treated with 20 U of restriction enzyme SbfI-HF (New England Biolabs) at 37o C for 1h. Next DNA was treated under 300 mM KOH at 55o C for 2 hours and precipitated with ethanol. Library were constructed as described in Clausen et al., 2015. Briefly, DNA was denatured for 3 min at 85o C, phosphorylated with 10 U of T4 PNK (#M0236, New England Biolabs) and purified with 1.8 volume of magnetic beads (Magbio). After denaturation for 3 min at 85o C, DNA fragments were ligated with adapter ARC140 over night at 25o C using 10 U of T4 RNA ligase (#M0204, New England Biolabs). This was followed by DNA purification with magnetic beads and the second strand synthesize using 4 U of T7 DNA polymerase (#M0274, New England Biolabs) and ARC76/77 duplex. After DNA purification with magnetic beads, unique indexes were added to DNA fragments using KAPA HiFi HotStart Ready Mix (#KK2602, KAPA Biosystems). The library concentrations and sizes were determined using Bioanalyzer. Libraries were pooled and subject for paired end sequencing with Illumina HiSeq 2500.
HydEn-seq

value: pol3L612M pol2-4 rnh201delta


title: TAK1092_pol3L612M_pol2-16_rnh201delta

source_name: TAK1092 pol3L612M pol2-16 rnh201delta

value: pol3L612M pol2-16 rnh201delta


title: ASCL1 ChIP-matched input from dox- 24h ind SA-tTA-Ascl1 ESCs


title: TAK1089_pol3L612M_pol2-4

source_name: TAK1089 pol3L612M pol2-4

value: pol3L612M pol2-4


title: TAK1083_pol2-16_rnh201delta

source_name: TAK1083 pol2-16 rnh201delta

value: pol2-16 rnh201delta


title: ASCL2-FLAG ChIP from dox+ ctrl SA-tTA-Ascl2 ESCs

value: MC1 mouse ES cells derived from 129S6/SvEvTac


title: TAK1086_pol1L868M_rnh201delta

source_name: TAK1086 pol1L868M rnh201delta

value: pol1L868M rnh201delta


title: TAK1087_pol3L612M_rnh201delta

source_name: TAK1087 pol3L612M rnh201delta

value: pol3L612M rnh201delta


title: TAK1079_rnh201delta

source_name: TAK1079 rnh201delta


title: TAK1082_pol3L612M_pol2-16

value: pol3L612M pol2-16


title: TAK1080_pol2M644G

source_name: TAK1080 pol2M644G


title: TAK1074_WT

source_name: TAK1074 WT

value: WT


title: ASCL1 ChIP from dox- 24h ind SA-tTA-Ascl1 ESCs

value: BD Pharmingen 556604 Rat anti-MASH1 (ASCL1)


title: TAK1077_pol1L868M

source_name: TAK1077 pol1L868M


title: TAK1075_pol2-16


title: TAK1078_pol3L612M

source_name: TAK1078 pol3L612M


title: H3K27ac ChIP from dox- 24h ind SA-tTA-Ascl2 ESCs

value: Abcam Ab4729 rabbit polyclonal anti-H3K27ac


title: TAK1085_pol2M644G_rnh201delta

source_name: TAK1085 pol2M644G rnh201delta

value: pol2M644G rnh201delta


title: TAK1070_pol2M644G

source_name: TAK1070 pol2M644G


title: TAK961_pol3L612M_pol2-4

source_name: TAK961 pol3L612M pol2-4


title: TAK964_pol3L612M_pol2-16_rnh201delta

source_name: TAK964 pol3L612M pol2-16 rnh201delta


title: TAK959_pol3L612M_rnh201delta

source_name: TAK959 pol3L612M rnh201delta


title: TAK965_pol3L612M_pol2-4_rnh201delta

source_name: TAK965 pol3L612M pol2-4 rnh201delta


title: TAK953_rnh201delta

source_name: TAK953 rnh201delta


title: TAK955_pol3L612M_pol2-16

source_name: TAK955 pol3L612M pol2-16


title: TAK952_pol3L612M

source_name: TAK952 pol3L612M


title: TAK949_pol2-16


title: TAK948_WT

source_name: TAK948 WT


title: TAK951_pol1L868M

source_name: TAK951 pol1L868M


title: XM001-PP_PDX1_Lane3_CTTGTA

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: XM001-PP_PDX1_CTTGTA_GEM_events_Filtered_Merged.bed

data_processing:
Fastq files were preprocessed with Trimmomatic (0.35) with parameters CROP:50 ILLUMINACLIP:path/to/adapter.fa:2:30:10:1 LEADING:0 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:36.
Preprocessed Fastq files were aligned to hg19 genome using bowtie2 (2.2.6) with very-sensitive option.
SAM files were converted to BAM and duplicate reads were removed using samtools (1.3).
Binding sites for PDX1 were then called using GEM (2.7) and filtered, after visual inspection, using a Q-value cut-off of 10^-4 and overlapping regions were merged using bedtools (2.26.0).
Regions of H3K27ac enrichment were called using BCP-HM with default parameters.
Regions and binding sites within 20 kb of a TSS or within a gene body were annotated with the respective gene using bedtools (2.26.0).
Genome_build: hg19
Supplementary_files_format_and_content: BED file containing peak locations

source_name: iPS derived pancreatic precursor cells

growth_protocol: XM001 iPSCs were cultured on 1:100 diluted Matrigel (BD Biosciences) in mTeSR™1 medium (Stem Cell Technologies). At ~70–80% confluency, cultures were rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) followed by incubation with 1× TrypLE Select Enzyme (Life Technology) for 3–5 min at 37 °C. Single cells were rinsed with mTeSR™1 medium, and spun at 1,000 rpm for 3 min. The resulting cell pellet was resuspended in mTeSR™1 medium supplemented with 10 μM Y-27632 (Sigma-Aldrich) and the single cell suspension was seeded at ~1.0 × 105 cells/cm² on Matrigel-coated surfaces. Cultures were fed every day with mTeSR™1 medium and differentiation was initiated 48 h following seeding, resulting in ~90% starting confluency.

extract_protocol:
XM001 PP cells (2 × 10^6 cells) were cross-linked in 1% formaldehyde in culture medium for 10 min at room temperature. The cross-linking reaction was stopped by the addition of glycine to a final concentration of 125 mM. For chromatin fragmentation, cells were resuspended in lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 0.5% SDS) and sonicated in a Covaris S220 sonicator with a duty cycle of 2%, a peak incident power of 105 W and 200 cycles per burst for 20 min. The fragmented chromatin was diluted 1:5 in IP-Buffer (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-Desoxycholate, 140 mM NaCl, H2O, Protease Inhibitors) and directly used for immunoprecipitation. For PDX1 ChIP, 60% of the chromatin (equivalent of 1.2 × 10^6 cells) was processed in two parallel ChIPs using magnetic beads, preloaded with 3 µl goat anti PDX1 antibody (kindly provided by C. Wright), for each ChIP. For H3K27ac ChIP, 40% of the chromatin (equivalent 0.4 × 10^6 cells) was processed in three parallel IPs using magnetic beads, preloaded with 3 µg anti H3K27ac antibody (Diagenode, pAb-174-050). For all ChIPs, antibody incubation was performed at 4 °C for 5 h. Beads were then washed 5 times using (1.) IP-Buffer, (2.) Washing-Buffer 1 (500 mM NaCl, 50 mM Tris-HCl (pH 8.0), 0.1% SDS, 1% NP-40), (3.) Washing-Buffer 2 (250 mM LiCl, 50 mM Tris-HCl (pH 8.0), 0.5% Na-Deoxycholate, 1% NP-40) and (4. & 5.) Washing-Buffer 3 (10 mM Tris-HCl (pH 8.0), 10 mM EDTA). Subsequently, protein-DNA complexes were eluted from the beads in Elution-Buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% SDS) at 65 °C for 20 min. Cross-links were reversed at 65 °C overnight and DNA was purified by ethanol precipitation.
Libraries were constructed using the MicroPlex kit (Diagenode, C05010010). Library construction, purification and size selection using AMPureXP (Beckman Coulter) were performed according to the MicroPlex kit instruction manual (version 4 / 03.09.14)

treatment_protocol: XM001 iPSCs plated on 1:100 diluted Matrigel were first rinsed with 1× DPBS without Mg2+ and Ca2+ (Invitrogen) and then cultured in RPMI 1640 medium (Invitrogen) further supplemented with 1.2 g/L sodium bicarbonate (Sigma), 0.2% ESC-qualified FBS (Life Technologies), 100 ng/mL Activin-A (R&D Systems), and 20 ng/mL of Wnt3A (R&D Systems) for day 1 only. For the next 2 days, cells were cultured in RPMI with 0.5% FBS, 1.2g/L sodium bicarbonate and 100 ng/mL Activin-A ; Cells were rinsed with 1× DPBS (without Mg2+ and Ca2+) once and then exposed to DMEM-F12 (Life Technologies) medium further supplemented with 2 g/L sodium bicarbonate, 2% FBS and 50 ng/mL of FGF7 (R&D Systems) for 3 days; Cultures were maintained for 4 days in DMEM-HG medium (Life Technologies) supplemented with 0.25 µM SANT-1 (Sigma-Aldrich), 2 µM retinoic acid (RA; Sigma-Aldrich), 100 ng/mL of Noggin (R&D Systems), and 1% B27 (Invitrogen).

value: iPS derived pancreatic precursor cells

tag: chip target

tag: lane

value: Goat anti PDX1 (Christopher V. E., Wright)


title: TAK1072_pol2M644G_rnh201delta

source_name: TAK1072 pol2M644G rnh201delta


title: XM001-PP_Input_Lane2_GGCTAC

value: none (Input)


title: XM001-PP_H3K27ac_Lane3_TAGCTT

description: XM001-PP_H3K27ac_TAGCTT_BCP-HM_Peaks.bed

value: Rabbit anti H3K27ac, Diagenode, C15410176


title: XM001-PP_Input_Lane1_GGCTAC


title: XM001-PP_H3K27ac_Lane2_TAGCTT

value: Rabbit anti H3K27ac, Diagenode, C15410175


title: XM001-PP_PDX1_Lane1_CTTGTA


title: XM001-PP_PDX1_Lane2_CTTGTA


title: Volasertib_20nM_4h_rep2

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Base calling was performed using Illumina RTA 1.18.64, afterwards multiplexed samples were converted to FASTQ files using CASAVA 1.8.2 allowing for 1 mismatch in the index sequence.
Reads were mapped to hg19 (hs37d5) with gsnap version 2012-12-20. The ENSEMBL 70 gene annotation was used for further expression estimations. Raw counts were computed using HTSeq version 0.5.3p9, FPKM expression values were estimated using Cufflinks version 2.0.2. Differential gene expression was computed using DESeq filtering out genes with less than 10 reads across the tested samples.
Genome_build: hg19
Supplementary_files_format_and_content: All processed data files contain tab-separated values. Differential gene expression files list all genes and attach associated statistics from DESeq.

source_name: MV-4-11-B cells

growth_protocol: The cell lines were cultured with the media suggested by ATCC at 37 degree Celsius incubators with 5% CO2.

extract_protocol:
Cells were lysed in TRI lysis reagent (Sigma-Aldrich, T9424, St. Louis, US-MO), with tissue grinders.
RNA-seq sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit v2 with PolyA selection.

treatment_protocol: The corresponding compounds (dissolved in DMSO) were added directly into cell culture media, and cells were kept at normal growth conditions for the treatment duration.

tag: method

value: RNA-seq

value: Volasertib, 20nM, 4h

tag: replicate

tag: internal id


title: Volasertib_20nM_4h_rep3


title: Volasertib_20nM_4h_rep1


title: Volasertib_20nM_24h_rep3

value: Volasertib, 20nM, 24h


title: DMSO_4h_rep3

value: DMSO, 4h


title: Volasertib_20nM_24h_rep2


title: Volasertib_20nM_24h_rep1


title: TAK958_pol1L868M_rnh201delta

source_name: TAK958 pol1L868M rnh201delta

tag: strain


title: DMSO_4h_rep2

tag: treatment


title: DMSO_4h_rep1


title: BI00894999_35nM_4h_Volasertib_20nM_4h_rep3

description: BI00894999_35nM_Volasertib_20nM_vs_DMSO_4h_dge.tsv.gz

value: BI00894999, 35nM, 4h and Volasertib, 20nM, 4h


title: DMSO_24h_rep3

value: DMSO, 24h


title: DMSO_24h_rep1


title: DMSO_24h_rep2


title: BI00894999_35nM_4h_Volasertib_20nM_4h_rep1


title: T cells with DEM Rep2 (ATAC-Seq)

city: Freiburg

first: Claudio

last: Mussolino

address: Breisacherstr. 115

institute: Institute for Transfusion Medicine and Gene Therapy

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina CASAVA.
Reads were aligned to hg19 using Bowtie with the parameter –m 1
Data was analyzed using HOMER (http://homer.salk.edu/homer)
Tag directories were generated using parameter – tbp 1, which removed most of the reads arising from mitochondrial DNA.
Genome_build: hg19
Supplementary_files_format_and_content: The data are provided in .xlsx. This file can be opened in excel and in the first four columns contains the normalized reads for the 4 samples analyzed (2 control and 2 DEM). Columns 5 and 6 contain the normalized reads derived by combinining the two replicates. The additional columns contain information relative to the genomic locations and nearest genes.

source_name: T cells with DEM

growth_protocol: Human CD4+ T cells were obtained from the peripheral  blood mononuclear cells (PBMCs) of healthy donors by Ficoll density gradient centrifugation followed by  human CD4+ T Cell Isolation Kit (Miltenyi Biotec) separation according to the manufacturer’s instructions.  The cells were activated for 3 days using magnetic beads conjugated with antibodies against CD2, CD3  and CD28 (Miltenyi Biotec) at a 2:1 cell to bead ratio and kept at a density of 1.3 x 10^6 cells/cm2 and  2.5x10^6 cells/ml in X-VIVO 15 Chemically Defined Serum-free Hematopoietic Cell Medium (Lonza). To  maintain the cells in culture long-term the activation was repeated every seven days and beads were  removed after 3 days of activation. After beads removal, growth medium was supplemented with 20 U/ml  interleukin 2 (Miltenyi Biotec).

extract_protocol:
50000 cells pelleted by centrifugation, nuclei were prepared prior to transposition
12 cycles of PCR using indexing primers from Illumina Nextera kit

treatment_protocol: Delivery in primary human  lymphocytes was achieved via nucleofection, 3 days post activation using the 4D Nucleofector X device  and the P3 Primary Cell 4D Nucleofector X kit (Lonza) following the manufacturer’s instructions

value: Cultured T cells

tag: agent

value: DEM


title: BI00894999_35nM_4h_Volasertib_20nM_4h_rep2


title: BI00894999_35nM_4h_rep2


title: BI00894999_35nM_4h_rep3


title: T cells with DEM Rep1 (ATAC-Seq)


title: BI00894999_35nM_4h_rep1


title: BI00894999_35nM_24h_Volasertib_20nM_24h_rep3

description: BI00894999_35nM_Volasertib_20nM_vs_DMSO_24h_dge.tsv.gz

value: BI00894999, 35nM, 24h and Volasertib, 20nM, 24h


title: Control T cells Rep 1 (ATAC-Seq)

source_name: Control T cells

value: control


title: PG_Séance RNAi 44 hrL3 S1

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

institute: University of Alberta

description: PG gal4>Séance RNAi

data_processing:
Total RNA sequencing was performed by McGill University and Génome Québec Innovation Centre (Montréal, Canada) on Illumina's next generation sequencing platform. In brief, raw sequences were obtained and de-multiplexed using Illumina pipeline CASAVA 1.8. FastQC was used to check read quality (all of the reads had a minimal quality score of 10 at every position). TopHat2 was employed for read alignment. We normalized raw data and did all analysis in ArrayStar11, Access (Microsoft) and DAVID (Huang et al., 2009).
Genome_build: dm6
Supplementary_files_format_and_content: Excel file contains normalized data of both control and Sean RNAi animals.

organism: Drosophila melanogaster

source_name: Ring gland

growth_protocol: Animals were raised on standard cornmeal food and kept at 25 degrees until staging.

extract_protocol:
RNA extraction was carried out using NucleoSpin RNA kit, quantified by RiboGreen RNA quantification assay.
The Encore Complete RNA-Seq library systems (NuGEN Technologies) were used to produce the cDNA libraries for next generation sequencing following the manufacturer’s instruction.

treatment_protocol: Ring glands were dissected and immdiately put into TRIzol reagent for later RNA isolation.

tag: developmental stage

tag: genotype/variation

value: PG-specific knockdown of Seance

tag: tissue

value: Ring gland


title: PG_Séance RNAi 44 hrL3 S2

description: PG gal4>Séance RNAi


title: Control 44hrL3 S2

description: control PG gal4>w1118


title: Control 44hrL3 S1

description: control PG gal4>w1118


title: BI00894999_35nM_24h_Volasertib_20nM_24h_rep1


title: BI00894999_35nM_24h_rep3


title: H1

city: Aurora

first: David

middle: P

last: Astling

state: CO

address: 12801 East 17th Ave.

department: Department of Biochemistry and Molecular Genetics

institute: University of Colorado Denver

description: Human embryonic stem cells

data_processing:
Illumina CASAVA 1.8 was used for basecalling
Sequenced reads were filtered and trimmed to remove low quality bases (Phred score < 15) from the 3' ends using a custom perl script
Filtered reads were aligned to the human genome (hg19) using GSNAP (version 2012-07-20)
Fragments per killobase per million (FPKM) measures were calculated using using Cufflinks (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Human embryonic stem cells

extract_protocol:
Illumina TruSeq RNA Sample Prep Kit  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: Fibroblasts were reprogrammed into iPSC using mRNA/miRNA transfections

tag: age

value: fetal

tag: gender

value: male

value: embryo

tag: cell line

value: Human embryonic stem cells

tag: health state

value: normal

tag: sample type

value: cell culture


title: I50S-2

description: Induced pluripotent stem cell line, derived from F50S

treatment_protocol:
F50S was reprogrammed into iPSC using mRNA/miRNA transfections
Fibroblasts were reprogrammed into iPSC using mRNA/miRNA transfections

value: 50 years old

value: female

value: skin

value: Human Dermal Fibroblast Normal

tag: cell type

value: Induced Pluripotent Stem Cells


title: TAK956_pol2-16_rnh201delta

source_name: TAK956 pol2-16 rnh201delta

value: pol2-16 rnh201delta


title: BI00894999_35nM_24h_rep2

value: RNA-seq


title: I50S-1

source_name: Induced pluripotent stem cell line, derived from F50S


title: Control T cells Rep 2 (ATAC-Seq)

value: Cultured T cells


title: F50S

description: Senescent  human fibroblast line, derived by continuos culture of F50

value: fibroblasts


title: BI00894999_35nM_24h_rep1


title: BI00894999_1nM_4h_Volasertib_20nM_4h_rep3

description: BI00894999_1nM_Volasertib_20nM_vs_DMSO_4h_dge.tsv.gz

value: BI00894999, 1nM, 4h and Volasertib, 20nM, 4h


title: XM001-PP_H3K27ac_Lane1_TAGCTT

value: iPS derived pancreatic precursor cells

tag: chip target

tag: antibody

value: Rabbit anti H3K27ac, Diagenode, C15410174


title: I50-3

description: Induced pluripotent stem cell line, derived from F50

treatment_protocol:
F50 was reprogrammed into iPSC using mRNA/miRNA transfections
Fibroblasts were reprogrammed into iPSC using mRNA/miRNA transfections


title: BI00894999_1nM_4h_Volasertib_20nM_4h_rep2

tag: method


title: I50-2

source_name: Induced pluripotent stem cell line, derived from F50

tag: replicate


title: BI00894999_1nM_4h_Volasertib_20nM_4h_rep1

tag: internal id


title: BI00894999_35nM_24h_Volasertib_20nM_24h_rep2

value: BI00894999, 35nM, 24h and Volasertib, 20nM, 24h


title: siago2_1 (2)

city: Bethesda

first: Ryan

last: Dale

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

description: nht promoter anchor

data_processing:
We used the 4c-ker algorithm to analyze 4C-seq data following the authors' recommendations documented in https://github.com/rr1859/R.4Cker. The reduced genome was created around HindIII sites with the fragment size of 13 bp on either side. The primer sequence was ACCGTTTTTGACAACAGCAGCTGTA and was flanked by a HindIII site starting at genomic position chr2L:15318918 in the dm6 assembly. Results from the "near-bait" analysis mode (defined by 4c-ker to be 5Mb on either side of the bait) are presented here, and used k=5, and pval=0.05.
Genome_build: dm6
Supplementary_files_format_and_content: bedGraphs of normalized read counts within adaptive windows, as output by 4c-ker

source_name: Kc167 cell line

extract_protocol:
Crosslinking was performed by adding formaldehyde directly to the media at final concentration of 1% and incubating for 10 min at RT. Reactions were quenched by adding glycine to a final concentration of 0.125 M and incubating for 5 min at RT. Reactions were incubated on ice 5 min followed by centrifugation at 1200 xg  at 4°C for 5 min. Cells were then washed with 5 mL of cold PBS and centrifuged at 1200 xg at 4°C for 5 min. Lysis was  performed by incubating cells in 1 mL of Lysis buffer (10 mM NaCl, 0.2% NP-40, 10 mM Tris pH8, 1 Mini Complete tablet (Roche) per 10 mL lysis buffer) at 37°C for 20 min. Samples were then centrifuged at 4200 xg at 4°C for 5 min, and the lysis step was repeated once. 800 μL of Lysis buffer was added, and samples were incubated at 37°C for 20 min. Samples were then centrifuged at 4200 xg at 4°C for 5 min, and resuspended in 1 mL Lysis buffer and incubated another 20 min at 37°C. Pellets from cell samples were then washed with 0.8 mL of digestion buffer [(0.2% NP-40, 1X NEBuffer 3 (NEB)] and centrifuged at 4200 xg at 4°C for 5 min. Nuclei were resuspended in 1.6 mL of digestion buffer with SDS added to a final concentration of 0.1% and incubated at 65°C for 30 min. Triton X-100 was added to a final concentration of 1% and samples incubated at 37°C for 15 min. A 40 μL aliquot of the sample was taken and used as the undigested control. The remaining sample was digested with 1600 U of HindIII (NEB) at 37°C overnight. Samples were incubated 20 min at 65°C to inactivate HindIII. A 40 μL aliquot of the sample was taken here and used as the digested control. The remaining sample was then diluted to 4 mL with ligation buffer [final concentrations were 1% Triton X-100, 1X T4 DNA Ligase Reaction Buffer (NEB)] and incubated at 37°C for 30 min. After the addition of 4800 U of T4 DNA Ligase (NEB), each sample was incubated at 16°C overnight. Proteinase K was added to all samples including the controls. Samples were then incubated at 65°C overnight to reverse crosslinking. After de-crosslinking, samples were combined with 1 vol of phenol/chloroform/isoamyl alcohol (25:24:1), vortexed 15 s, and centrifuged for 4 min at 10,000 xg. The top layer was transferred to a new tube, and the procedure was repeated using 1 vol chloroform. The top layer was collected and subsequently diluted with 1 vol of water. The sample was combined with 0.1 vol of 3M NaOAc pH 5.2 and 2.5 vol of 100% ethanol, supplemented with 2 μL of Glycoblue (Ambion). After incubating 1 h at -80°C, samples were centrifuged 20 min at 4°C at 10,000 xg. Pellets were washed with 75% ethanol and centrifuged 5 min at 4°C at 10,000 xg. Pellets were air dried at RT prior to resuspension in 350 μL water.  After resuspending the final pellet with 350 μl of dH2O, 300 μL of the 3C library was digested with 5 μL of DpnII (50 U, NEB) overnight at 37°C. After the enzyme was inactivated, digested chromatin was re-ligated using 20 μL of ligase (100 U, NEB) in a total volume of 8 mL ligation reaction. Finally purification of the library was carried out by adding 1 vol of phenol/chloroform/isoamyl alcohol (25:24:1), vortexed 15 s, and centrifuged for 4 min at 10,000 xg. The top layer was transferred to a new tube, and the procedure was repeated using 1 vol chloroform. The top layer was collected and precipitated with 0.1 vol of 3M NaOAc, pH 5.2 and 2.5 vol of 100% ethanol supplemented with 7 μL of Glycoblue.
Inverse PCR was carried out using primers containing a 6 nucleotide barcode and one universal forward primer to produce Illumina-4C-seq libraries. PCR amplification was carried out using Phusion High Fidelity DNA Polymerase (NEB) with 60-70 ng of DNA and 1 μL of forward primer (10mM) and 1 μL of reverse primer (10mM). Amplification program: 95°C for 3 min, 30 cycles of 98°C for 20 s, 50°C for 1 min and 72°C for 2 min; final elongation step was 72°C for 5 min. After pooling together 3 PCR reactions, samples were purified using Agencourt AMPure XP beads (Beckman Coulter).
4C-seq

tag: develomental stage

value: dorsal closure stage

value: Female Embryonic cell line


title: dslamin_1

description: nht promoter anchor

tag: treatment

value: dsLaminB


title: siago2_2 (2)

description: nht promoter anchor


title: mock_2 (2)

description: nht promoter anchor

value: Mock


title: F50

description: Primary human adult fibroblasts

source_name: Primary human adult fibroblasts

value: 50 years old

value: normal

value: cell culture

tag: lot number


title: H9

description: Human embryonic stem cells

value: fetal

value: female

value: embryo

value: Human embryonic stem cells


title: BI00894999_1nM_4h_rep3

value: RNA-seq


title: dslamin_2

description: nht promoter anchor


title: IN2-5

description: Induced pluripotent stem cell line, derived from FN2

treatment_protocol:
FN2 was reprogrammed into iPSC using mRNA/miRNA transfections
Fibroblasts were reprogrammed into iPSC using mRNA/miRNA transfections

value: Neonatal

value: male

value: foreskin

value: Primary Dermal Fibroblast Normal

value: Induced Pluripotent Stem Cells


title: IN2-4

source_name: Induced pluripotent stem cell line, derived from FN2


title: BI00894999_1nM_4h_rep2


title: mock_1 (2)

description: nht promoter anchor

value: dorsal closure stage


title: BI00894999_1nM_4h_rep1


title: IN2-2


title: BI00894999_1nM_24h_Volasertib_20nM_24h_rep3

description: BI00894999_1nM_Volasertib_20nM_vs_DMSO_24h_dge.tsv.gz

value: BI00894999, 1nM, 24h and Volasertib, 20nM, 24h


title: siago2_1

data_processing:
Raw reads were trimmed with cutadapt v 1.10 to remove any adapters and poly-A tails while performing light quality trimming using parameters "--quality-cutoff=20 --minimum-length=25 --overlap=10 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -a AGATCGGAAGAGC".
Trimmed reads were mapped to the primary chromosomes (2L, 2R, 3L, 3R, 4, X, Y, and mitochondrion_genome) of the FlyBase release 6.11 dm6 assembly with HISAT2 2.0.4 using default parameters.
Reads were counted in annotated genes in FlyBase release 6.11 using featureCounts v1.5.0-p3. Since neuRNA-seq enriches for nascent RNA and the libraries are stranded, we counted reads in full gene bodies using featureCounts parameters "-s 1 -t gene -g gene_id -f".
Counts tables were aggregated across samples into experiment-specific counts matrices.
Genome_build: dm6
Supplementary_files_format_and_content: Counts tables in TSV format, aggregated from featureCounts output, with headers corresponding to the fastq file names. Each counts file containst the set of samples from a single experiment that should be considered together.

extract_protocol:
neuRNA labeling and capture were performed with Click-iT Nascent RNA Capture Kit (Thermo Fisher Scientific) according to manufacturer’s protocol with the following minor modifications. Cells were incubated with EU at  0.2 mM for 1 h and RNA was extracted with TRizol (Thermo Fisher Scientific). The Click-iT reaction was performed with 0.25 mM biotin azide, and biotinylated RNA was captured with 12 μL T1 beads.
Nascent RNA was used to generate RNA-seq libraries with Ovation RNA-seq Systems 1-16 for Model Organisms (Nugen). All samples were sequenced with HiSeq2500 (Illumina) at the NIDDK Genomics Core Facility by 50 bp single-end sequencing.
neuRNA-seq

value: Female Embryonic cell line


title: siago2_2


title: siago2_3


title: BI00894999_1nM_24h_Volasertib_20nM_24h_rep2


title: si5utr_ago2_pwahf_v966m_3

value: si5utr ago2 pwahf v966m


title: IN2-1


title: BI00894999_1nM_24h_Volasertib_20nM_24h_rep1


title: FN2

description: Primary human neonatal fibroblasts

source_name: Primary human neonatal fibroblasts

value: fibroblasts


title: si5utr_ago2_pwahf_ago2_2

value: si5utr ago2 pwahf ago2


title: FN1

description: Primary human neonatal fibroblasts

value: normal

value: cell culture


title: si5utr_ago2_pwahf_v966m_2


title: si5utr_ago2_pwahf_ago2_1


title: BI00894999_1nM_24h_rep2


title: si5utr_ago2_3

value: si5utr ago2


title: BI00894999_1nM_24h_rep1


title: si5utr_ago2_2


title: mock_8

value: mock


title: mock_7


title: mock_3


title: NIH3T3-H3.3GFP-Infect0h-ATAC-rep2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description: countMatrix_SubNuc20-150_GENCODEvM9_ATAC-NIH3T3_exonUp2k.edit.txt.gz

data_processing:
The raw sequence reads were aligned to mouse genome (GRCm38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained for ChIP-seq/ATAC-seq analysis.
The matrices of read counts on gencode genes (release M9) were generated using featureCounts (version 1.5.0-p3). For ATAC-seq, the option of featureCounts: -B -C -P -d 20 -D 150, were used to extract subnucleosomal fraction.
The coverage tracks of ATAC-seq (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.txt files include tab-delimited read count matrices
Supplementary_files_format_and_content: bigWig

source_name: Histone H3.3 overexpressing NIH3T3 cells

extract_protocol:
50,000 sorted cells were centrifuged at 800 × g for 5 min, followed by a wash using 500 µl of cold PBS and centrifugation at 800 × g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 min using a refrigerated centrifuge. Next, the pellet was resuspended in the transposase reaction mix (10 µl of 2× TAPS+DMF buffer, 1.5 µl transposase (in house) and 8.5 µl nuclease-free water). The transposition reaction was carried out for 30 min at 37°C and immediately placed on ice. Directly afterwards, the sample was purified using a Qiagen MinElute kit.
Following purification, the library fragments were amplified using custom Nextera PCR primers 1 and 2 for a total of 15 cycles. Following PCR amplification, the libraries were purified using a Qiagen MinElute kit.

treatment_protocol: NIH3T3 cells were infected with retrovirus expressing MyoD.


title: NIH3T3-H3.3GFP-Infect48h-ATAC-rep2


title: NIH3T3-H3.3GFP-UnInfect-ATAC-rep2


title: V16D

city: Portland

first: Joshi

last: Alumkal

state: OR

address: 3303 SW Bond Ave. CH14R

institute: Knight Cancer Institute

data_processing:
Library strategy: Exome-Seq
Aligned to the human reference (hg19) with bwa v0.7.3a
Duplicates were sorted and removed with samtools 0.1.19 and picard-tools 1.51
Local realignment and quality score recalibration was done with GATK version 2.1-13
Copy number segmentation analysis was performed using package DNACopy (v1.44.0) in R (v3.2.3)
Genome_build: hg19
Supplementary_files_format_and_content: .seg (txt file)

source_name: Prostate Cancer Cell Line

growth_protocol: MR49F, V16D cells were plated in triplicate in 6-well plates, 300,000 cells/well in RPMI+10% FBS

extract_protocol:
Agilent SureSelect XT2
Human All Exon 50Mb

treatment_protocol: Cells were treated with  0.1% DMSO after 96hrs (50% confluent), and harvested 24hrs post-treatment

value: Vehicle


title: NIH3T3-H3mm7GFP-Infect48h-ATAC-rep2

source_name: Histone H3mm7 overexpressing NIH3T3 cells


title: mock_2


title: MR49F


title: mock_12


title: mock_10


title: NIH3T3-H3mm7GFP-UnInfect-ATAC-rep2


title: mock_11


title: BI00894999_1nM_24h_rep3

value: RNA-seq


title: mock_1


title: dslaminb_3

value: dslaminb


title: dslaminb_2


title: dslaminb_1


title: NIH3T3-H3.3GFP-Infect0h-ATAC-rep1


title: NIH3T3-Control-Infect0h-ATAC-rep2

source_name: NIH3T3 cell line


title: NIH3T3-H3.3GFP-Infect48h-ATAC-rep1


title: NIH3T3-Control-Infect48h-ATAC-rep2


title: dsdicer2_3


title: dsdicer2_2


title: NIH3T3-H3.3GFP-UnInfect-ATAC-rep1


title: NIH3T3-H3mm7GFP-Infect48h-ATAC-rep1


title: dsdicer2_1


title: NIH3T3-H3mm7GFP-UnInfect-ATAC-rep1


title: NIH3T3-H3mm7GFP-Infect0h-ATAC-rep1


title: wt_4

description: True-seq (Illumina)

data_processing:
Raw reads were trimmed with cutadapt v 1.10 to remove any adapters and poly-A tails while performing light quality trimming using parameters "--quality-cutoff=20 --minimum-length=25 --overlap=10 -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT -a AGATCGGAAGAGC".
Trimmed reads were mapped to the primary chromosomes (2L, 2R, 3L, 3R, 4, X, Y, and mitochondrion_genome) of the FlyBase release 6.11 dm6 assembly with HISAT2 2.0.4 using default parameters.
Reads were counted in annotated genes in FlyBase release 6.11 using featureCounts v1.5.0-p3 with parameters "-t exon -g gene_id".
Genome_build: dm6
Supplementary_files_format_and_content: Counts tables in TSV format

source_name: 3rd instar larvae

extract_protocol:
Whole female larvae were collected and total RNA extracted with TRizol (Invitrogen). Polyadenylated RNA and ribosomal (rRNA)-depleted RNA was purified from total RNA using the MicroPoly(A)Purist Kit (Ambion) and the RiboMinus Eukaryote Kit for RNA-seq (Invitrogen), respectively.
Sequencing libraries were prepared from Poly(A)+ and rRNA depleted RNA samples according to the manufacturer’s protocol (Illumina). All samples were sequenced with HiSeq2500 (Illumina) at the NIDDK Genomics Core Facility by 50 bp single-end sequencing.

tag: strain

value: w

value: Female

value: Whole larvae


title: wt_3

description: True-seq (Illumina)


title: NIH3T3-Control-Infect48h-ATAC-rep1


title: NIH3T3-H3mm7GFP-Infect0h-ATAC-rep2


title: v966m_4

description: True-seq (Illumina)


title: NIH3T3-Control-UnInfect-ATAC-rep1


title: NIH3T3-H3.3GFP-Infect48h-H3K27me3

description: countMatrix_GENCODEvM9_3T3ChIPseq.edit.txt.gz

extract_protocol:
Cultured cells were cross-linked in 0.5% formaldehyde and suspended in ChIP buffer (5 mM PIPES, 200 mM KCl, 1 mM CaCl2, 1.5 mM MgCl2, 5% sucrose, 0.5% NP-40, and protease inhibitor cocktail; Nacalai Tesque Inc.).
ChIP libraries  were prepared using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).


title: NIH3T3-Control-Infect0h-ATAC-rep1


title: NIH3T3-H3.3GFP-UnInfect-H3K27me3


title: v966m-v966m_3

description: True-seq (Illumina)


title: NIH3T3-H3mm7GFP-Infect48h-H3K27me3


title: NIH3T3-Control-UnInfect-ATAC-rep2


title: 51b_4

description: True-seq (Illumina)


title: 51b-51b_4

description: True-seq (Illumina)


title: NIH3T3-Control-Infect48h-H3K27me3


title: NIH3T3-Control-UnInfect-H3K27me3


title: 51b-51b_3

description: True-seq (Illumina)


title: 51b_3

description: True-seq (Illumina)


title: NIH3T3-H3.3GFP-Infect48h-H3K4me3


title: NIH3T3-H3.3GFP-UnInfect-H3K4me3


title: NIH3T3-H3mm7GFP-UnInfect-H3K4me3


title: NIH3T3-Control-Infect48h-H3K4me3


title: NIH3T3-H3mm7GFP-UnInfect-H3K27me3


title: NIH3T3-Control-UnInfect-H3K4me3


title: NIH3T3-H3mm7GFP-Infect48h-H3K4me3


title: v966m_3

description: True-seq (Illumina)


title: NIH3T3-H3.3GFP-Infect48h-GFP


title: v966m-v966m_4

description: True-seq (Illumina)


title: NIH3T3-H3.3GFP-UnInfect-GFP