title: 51.Scid.adh.2c2_PU.1-ert2_2h_4-OHT_ATAC-seq-rep2

city: Pasadena

first: Ellen

last: Rothenberg

address: 1200 E. California Blvd

department: Division of Biology and Biological Engineering

institute: California Institute of Technology

description:
processed data file:
Read counts derived around combined Scid.adh.2c2 PU1ert2 0h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 2h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 8h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 24h 4-OHT aPU1 HOMER IDR peaks OR Scid.adh.2c2 Mock_aSatb1 HOMER IDR peaks/Scid.adh.2c2 PU.1_aSatb1 HOMER IDR peaks OR Scid.adh.2c2 Mock_aRunx1 HOMER IDR peaks/Scid.adh.2c2 PU.1_aRunx1 HOMER IDR peaks OR Scid.adh.2c2 PU1WTHA aHA HOMER IDR peaks.

data_processing:
ChIP-Sequencing and data analysis: ChIP sequences were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory {Heinz, 2010 #67} for further downstream analysis. In addition, read alignments from the Scid.adh.2c2-PU.1ert2 experiment were filtered against PCR duplicates using Samtools as well as genomic repeats and Broad blacklisted regions using Bedtools (full script provided upon request) prior to tag directory generation. Transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score >= 15, were considered for further analysis.  Regions enriched for histone modifications were identified with findPeaks.pl with the option –style histone against a matched input control. Only regions consistently called in two independent experiments were used for downstream analyses.  Motif enrichment analysis was performed with the findMotifsGenome.pl command in the HOMER package using a 200bp window or a window size defined by the width of each identified peak. Overlapping peaks between samples were derived using mergePeaks.pl (default parameters). Annotation of peaks to nearest genes and genomic regions (e.g. promoters, CG-rich regions, repeat regions) were performed with annotatePeaks.pl (default settings). Tag density plots and heat maps were created with annotatePeaks.pl ( –hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment.
RNA-Sequencing and data analysis:  RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) {Li, 2011 #81} according to the settings in the ENCODE long-rna-seq-pipeline with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistically significance among differently expressed genes the data was raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) or the gene count tables were imported into R and analyzed for differential expression using the DESeq2 package (v1.4.5; https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html)  For data visualization rpkm normalized reads were derived analyzeRepeats.pl command with the options –count exons –¬condenseGenes –rpkm followed by log transformation, and separately performed replicate set normalizations to prevent nondevelopmental differences in gene expression. Processed data for all the, in the study, included RNA-seq samples were derived from HOMER tagdirectories as either raw counts (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -noadj) or rpkm normalized values (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -rpkm). Data is derived as one value per gene and the accession number associated with the highest expressing isoform is displayed (-condenseGenes option).
ATAC-Sequencing and data analysis: ATAC-sequences were mapped to mm9 as described in the Data processing-ChIP section. Additionally, Tag directories with reads mapped to the mitochondrial chromosome filtered were created using the HOMER platform (makeTagDirectory).  ATAC-seq peaks were identified using findPeaks.pl in HOMER (scipt available upon request). Only regions consistently called in two independent experiments were used for downstream analyses. Abundance of ATAC-tags on ATAC or transcription factor ChIP-seq peaks was analyzed in HOMER using the annotatePeaks.pl command.   For differential peak analysis, raw tag counts were derived from the tagdirectories using annotatePeaks.pl with the ”-noadj” setting  was carried out with the EdgeR  and limma (v3.20.9; http://bioconductor.org/packages/release/bioc/html/limma.html)  Bioconductor packages via  HOMER getDifferentialExpression.pl. Differential peaks with adjusted p-value <= 0.05 and log2 fold change >= |1| were considered significantly different.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include HOMER peak file  All genomic coordinates are relative to mm9 mouse assembly.

extract_protocol:
ChIP-Seq:  Primary cell experiments:  Briefly, lin- FLPs were expanded for 7 days on OP9-DL1, CD25+ enriched and retrovirally infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were co-cultured on OP9-DL1 for ~40h and then sorted as LiveGFP+CD25+ or LiveGFP+CD44+CD25- on BD FACSAriaTM.    Scid.adh.2c2:    HA-tagged-ChIP: Scid.adh.2c2 cells were infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were expanded for ~40h and then sorted as LiveGFP+on BD FACSAriaTM.  4-OHT experiment: Scid.adh.2c2 cells were transduced with Lzr-PU.1ert2 (Scid.adh.2c2-PU.1ert2) or Lzr-ert2 (Scid.adh.2c2-ert2) control, cells were expanded for 48h and infected (GFP+) cells followed by sorting of GFP+ cells on BD FACSAriaTM and further expanded in vitro prior to 2, 8 or 24h activation with 0.1 μM 4-OHT (4-hydroxytamoxifen).  Satb1, Runx1, Fog1 and GATA3 ChIP: Scid.adh.2c2 cells were infected with retroviral supernatant of pMxs-Myc-Flag-PU.1-IRES-hNGFR and cultured for 48h.    Approximately 3-5 million primary sorted CD25+ -or 10 million Scid.adh.2c2 cells for ChIP were fixed at RT in 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min followed by additional 10 min after addition of formaldehyde (FA) up to 1% (Satb1, Runx1, Fog1 and Ets1) or 10 min of 1% FA only (PU.1, HA,-tag, GATA3, H3-modifications). The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in ice-cold 1xHBSS (Gibco). Cell pellets were snap frozen on dry ice and stored in -80°C. For DSG+FA crosslinked cells, nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in 0.5% Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC. FA crosslinked cells only were resuspended 1% Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8). Lysates were sonicated on a Bioruptor (Diagenode) for 18 cycles, max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to a new tube and chromatin was diluted 3X in 1xHBSS+PIC followed by 2xRIPA (2% Triton, 2mM EDTA, 200 mM NaCl, 20 mM Tris-HCl (pH 7.5), 1% sodium deoxycholate, 0.1%SDS + PIC). Approximately 10 μg per 107 cells of antibody (Rabbit anti-PU.1 polyclonal IgG (sc-352x, Santa Cruz Biotechnology), Rabbit HA-probe polyclonal IgG (sc-805x, Santa Cruz Biotechnology), Rabbit anti-Ets1 polyclonal IgG (sc-350x, Santa Cruz Biotechnology), Mouse anti-Gata3 monoclonal IgG (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems), Rabbit anti-Satb1 monoclonal IgG (ab109122, Abcam), Rabbit anti-Runx1 polyclonal IgG (ab23980, Abcam), Goat anti-Fog1 polyclonal IgG (sc-9361, Santa Cruz Biotechnolog), Rabbit polyclonal anti-H3K27Ac (ab4729, Abcam), Rabbit polyclonal anti-H3K4me2 (07-030, Millipore) or Rabbit polyclonal anti-H3K27me3 (07-449, Millipore) were hybridized to Dynabeads M-280 Sheep anti- Rabbit or Dynabeads M-280 Sheep anti- Mouse or Dynabeads Protein A/G (Invitrogen), respectively in 1ml 1xRIPA+PIC for 4h, washed twice with 1xRIPA, resuspended in 100 μl 1xRIPA+PIC and added to the diluted chromatin. For polyclonal and monoclonal antibodies, 20 and 50 μl of Dynabeads were used per μg antibody, respectively. ChIP was performed over night at 4°C, and subsequently washed (1 time with 1 ml Low Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton-X, 2 mM EDTA, 50 mM Tris-Hcl pH8, 150 mM NaCl), 1 time with 1 ml High Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton-X, 2 mM EDTA, 50 mM Tris-Hcl pH8, 500 mM NaCl), 1 time with 1 ml LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% Igepal-CA630, 1% natrium deoxycholate, 1 mM EDTA, 10 mM Tris-Hcl pH8), 2 times with 1 ml TE buffer (10 mM Tris–HCl, pH 8.0, 10 mM EDTA)) and eluted for 6 h to O/N at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.
RNA-seq: CD25+ cell experiments:  Briefly, lin- FLPs were expanded for 7 days on OP9-DL1, CD25+ enriched and retrovirally infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were co-cultured on OP9-DL1 for ~40h and then sorted as LiveGFP+CD25+ or LiveGFP+CD44+CD25- on BD FACSAriaTM.    Scid.adh.2c2: Scid.adh.2c2 cells were transduced with Lzr-PU.1ert2 (Scid.adh.2c2-PU.1ert2) or Lzr-ert2 (Scid.adh.2c2-ert2) control, cells were expanded for 48h and infected (GFP+) cells followed by sorting of GFP+ cells on BD FACSAriaTM and further expanded in vitro prior to 2, 8 or 24h activation with 0.1 μM 4-OHT (4-hydroxytamoxifen).    Total RNA was isolated from 200.000-500.000 primary or Scid.adh.2c2 cells using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.
ATAC-seq: Eighty thousand Scid.adh.2c2 or Scid.adh.2c2 transduced Lzr-PU.1-ert2 or Lzr-er2 control vector followed by 0.1 uM 4-hydroxytamoxifen stimulation, 18.4 thousand primary sorted thymic ETP or 50,000 thymic DN3 cells were washed in ice cold HBSS-HEPES prior to the assay. For the primary cells, the final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio) using SPRIselect-beads (Beckman-Coultier). Libraries were single-end sequenced on a HiSeq2500 (Illumina) (primary cells) or a NextSeq500 (Scid.adh.2c2) and produced approximately 30-50 million reads per sample.

treatment_protocol:
Lin- FLP or Lin- BM isolation/ culture protocol/Facs staining:
Cell isolation: Fetal livers (FL) were disected from E13.5 (day of plug, E0.5) C57BL/6 animals. Suspensions of FL cells were then prepared, stained for lineage markers using biotin-conjugated lineage antibodies (CD11c, Gr1, TER-119, NK1.1, CD19, F4/80), incubated with streptavidin-coated magnetic beads (Miltenyi Biotec), and passed through a magnetic column (Miltenyi Biotec). Lineage-depleted (Lin−) cells were eluted and stored in liquid nitrogen in freezing media (50% FBS, 40% αMEM, 10% DMSO) for future use. Cell culture:  Frozen lineage depleted FL cells from E13.5 were thawed and used to initiate OP9-DL1 cultures in OP9 medium (α-MEM, 20% FBS, 50 μM β-ME, Pen-Step-Glutamine) supplemented with IL-7 and Flt3L (5 ng/ml each).  Cells were incubated at 7% CO2 and 37°C.  Scid.adh.2C2 cells were cultured in RPMI1640 with 10% fetal bovine serum (Sigma-Aldrich), sodium pyruvate, non-essential amino acids, Pen-Strep-Glutamine and 50 μM β-mercaptoethanol. Cells were incubated at 5% CO2 and 37°C.
FACS staining. For sorting of transduced CD25 enriched FLP derived cells, surface antibodies against c-Kit, CD25, CD44, CD45, Mac1/CD11b were used for staining of Lin- FLP derived CD25+ cells (7AAD-CD45+GFP+CD25+) (EVGFP, PU1WTHA, PU1ENGHA and PU1ETSHA) or CD44+CD25 cells (7AAD-CD45+GFP+CD44+CD25-) (PU1WTHA). Transduced Scid.adh.2c2 cells for Lzr-PU.1 ChIP and RNA-sequencing were sorted as LiveGFP+.  For sorting for primary cell ATAC experiment, thymocytes were pre-depleted with biotin-conjuagated a-CD8a, a-TCRrd, a-TCRb, a-Ter119 followed by MACS magnetic column purifcation as described above.  Depleted thymocytes were stained with CD45, CD44, c-Kit, CD25, and a biotin-conjugated lineage cocktail (CD8a,CD11b,CD11c,CD19,Ly-6G(Gr-1),NK1.1,TER119,TCRrd,TCRb) and were sorted for ETP progenitors (Lin−CD45+c-KithiCD44hiCD25−) or DN3 progenitors (Lin−CD45+c-KitlowCD44lowCD25+).

tag: strain/cell line background

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

tag: cell line/type

value: Scid.adh.2c2 cells

tag: treatment

value: Transduced with Lzr-PU.1ert2, treated 2h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 50.Scid.adh.2c2_PU.1-ert2_8h_4-OHT_ATAC-seq-rep2

status: Public on Jun 21 2018

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

value: Transduced with Lzr-PU.1ert2, treated 8h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 40.Scid.adh.2c2_PU.1-ert2_24h_4-OHT_ATAC-seq-rep1

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 41.Scid.adh.2c2_PU.1-ert2_8h_4-OHT_ATAC-seq-rep1


title: 49.Scid.adh.2c2_PU.1-ert2_24h_4-OHT_ATAC-seq-rep2


title: 44.Scid.adh.2c2-ert2_24h_4-OHT_ATAC-seq-rep1

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 52.Scid.adh.2c2_PU.1-ert2_0h_4-OHT_ATAC-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: C57BL6.0hr.KDM2B.iWTr

city: New York

first: Danny

last: Reinberg

state: NY

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Bowtie2 v2.2.6 was used to align reads to reference genome with default parameters.
Aligned reads were normalized based on the mapped reads in spike-in Drosophila control.
BedGraph files were generated from the aligned reads using 'genomecov' function in bedtools v2.17.0
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated from BedGraph files using 'bedGraphToBigWig' function in USCS.

growth_protocol: E14Tga2 and C57BL/6 ESCs were grown in standard medium supplemented with LIF, 1 μM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 μM GSK3 inhibitor (CHIR99021, Stemgent).

extract_protocol:
Cells were fixed with 1% Formaldehyde. Nuclei was isolated and  chromatin was fragmented. Chromatin immunoprecipitation (ChIP) was performed and the libraries was prepared using the eluted DNA from ChIP.
Eluted DNA from ChIP was repaired to generate blunt 5' P ends using 'EndIT DNA End Repair kit' (Epicentre), 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB).  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Next libraries were size selected using 'Ampure beads' (Beckman Coulter) .  After around 13 cycles of amplification, libraries were cleaned, quantified and pooled.

tag: genotype

value: inducible WT EED rescue  0hr

tag: chip antibody

value: Gift from Robert J. Klose


title: 43.Scid.adh.2c2_PU.1-ert2_0h_4-OHT_ATAC-seq-rep1


title: 54.Scid.adh.2c2-ert2_0h_4-OHT_ATAC-seq-rep2

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: C57BL6.12hr.KDM2B.iWTr

value: inducible WT EED rescue  12hr


title: 45.Scid.adh.2c2-ert2_0h_4-OHT_ATAC-seq-rep1


title: 48.Scid.adh.2c2-ATAC-seq-rep2

description:
processed data file:
Scid.adh.2c2_ATAC_peaks

value: Unperturbed


title: 39.Scid.adh.2c2-ATAC-seq-rep1


title: AcBac_Rep2_Cap2_48h_2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description:
replicate 2
genome: Bacmid_dCC_Rep2_Cap3

library_source: transcriptomic

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions.
RNA-Seq results were trimmed to remove A-stretches originating from the library preparation using by cutadapt and filtered for reads mapping to Sf21 genome
Alignment was performed using bowtie to the custom genomes.
Homer-software (http://homer.ucsd.edu/homer/) was used to prepare bedGraphs and quantify the reads for all annotations in reads per kb per million reads (RPKM).
Genome_build: custom fasta for genomes in supplementary files

molecule: total RNA

organism: Spodoptera frugiperda

source_name: Sf9 cells transfected with AcMNPV bacmid carrying recombinant AAV2 insert (Rep2 Cap2)

growth_protocol: 1 million of Sf9 cells were plated on a 6 well plate with 2 mL of Sf900-III medium (Gibco #12658-027 1000 mL) and incubated at 27°C.

extract_protocol:
RNA was purified using RNeasy Mini Kit and enriched for Poly(A)-RNA with MicroPoly(A) Purist Kit.
The RNA was base-hydrolyzed, dephosphorylated with PNK and purified using RNA Clean & Concentrator kit (Zymo). Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers containing Illumina adapter sequences. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified using ChIP DNA Clean & Concentrator kit. The recovered cDNA was RNaseH treated and circularized (CircLigase) and amplified for 10 cycles. The final product was ran on 10% TBE gel, gel purified (180-350 bp) and cleaned-up using ChIP DNA clean & Concentrator Kit.

treatment_protocol: Two microgram of bacmid DNA were transfected into cells using Cellfectin II (Invitrogen) reagent according to the manufacturer instructions.

value: 48h incubation

tag: cell line

value: Sf9 insect cells


title: AcBac_Rep2_Cap2_48h_1

description:
replicate 1
genome: Bacmid_dCC_Rep2_Cap2


title: AcBac_AAV2wt_94h_1

description:
replicate 1
genome: Bacmid_dCC_AAV2wt

source_name: Sf9 cells transfected with AcMNPV bacmid carrying WT AAV2 insert

value: 94h incubation


title: AcBac_AAV2wt_48h_1

description:
replicate 1
genome: Bacmid_dCC_AAV2wt


title: AcBac_AAV2wt_48h_2

description:
replicate 2
genome: Bacmid_dCC_AAV2wt


title: 42.Scid.adh.2c2_PU.1-ert2_2h_4-OHT_ATAC-seq-rep1


title: NHF1 UV 0hr 20J part A

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

data_processing:
Library strategy: CPD-seq
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences and the final base in the sequencing read were trimmed, using a custom perl script. The resulting fastq files were uploaded as the raw sequencing data for each experiment.
Fastq files were aligned to the human genome (hg19 or hg19+pUC19) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine (dipy; i.e., TT, TC, CT, CC) or cytosine-containing (Cdipy; i.e., TC, CT, CC) damage coordinate were retained in BED files using custom perl script
BED files were converted to WIG file using COUNT function of IGVTools
Genome_build: hg19
Supplementary_files_format_and_content: WIG files containing counts of CPD damage reads filtered for only dipyrimidine mapping sequences (dipy files) or cytosine-containing dipyrimidine (i.e., TC, CT, CC) mapping sequences (Cdipy files).

organism: Homo sapiens

source_name: NHF1 cells

growth_protocol: Telomerase-immortalized normal human fibroblast (NHF1) cells were grown in 10 cm plates to confluence in Dulbecco's  modified Eagle's medium (DMEM) containing 10% fetal bovine serum (FBS) at 37 C and 5% CO2.

extract_protocol:
NHF1 genomic DNA was isolated with Puregene Cell and Tissue kits (158388, Qiagen) or GenElute Mammalian Genomic DNA Miniprep kits (G1N70, Sigma), following the manufacturer’s manual.
CPD-seq procedure is adopted from the recently published emRiboSeq method (Nature Protocols 2015 10, 1433-1444) and our own CPD-seq publication in yeast (Mao et al, PNAS 2016,113, 9057-9062). Briefly, DNA fragments were ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by  terminal transferase and dideoxy-ATP.  CPD lesions were cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE1, to generage new 3'-OHs. DNA was then ligated to one of six different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT; A4:ATCGCGAT; A5: TACTGGA; and A6: GAACTGAT) were used to generate libraries for different time points. DNA was purified with Streptavidin beads and amplified for ~5 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: For UV treatment of cells, growth medium was first removed and NHF1 cells were rinsed with sterile phosphate-buffered saline (1*PBS) to remove any residual medium. Cells were then wetted with 2 ml of PBS and irradiated with UV light (254 nm). PBS was removed and the irradiated cells were immediately trypsinized and harvested for DNA isolation. For UV treatment of naked DNA, genomic DNA was first isolated from untreated NHF1 cells. The purified DNA was spotted on a clean microscope cover glass, 10 ul in each spot, and the glass with DNA spots was irradiated with UV light. The irradiated DNA was collected and used for CPD-seq library preparation.

value: UV irradiated 20 J/m2

tag: repair time

value: 0 hr


title: 53.Scid.adh.2c2-ert2_24h_4-OHT_ATAC-seq-rep2

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice


title: NHF1 UV 0hr 20J part B


title: NHF1 UV 0hr Replicate 3 part A

value: UV irradiated 100 J/m2


title: NHF1 UV 0hr Replicate 3 part B


title: AcBac_Rep2_Cap2_94h_2

description:
replicate 2
genome: Bacmid_dCC_Rep2_Cap5


title: No UV Replicate 2

description: This No UV sample was a control for NHF1 UV 0hr Replicate 2


title: NHF1 UV 0hr Replicate 2


title: Naked DNA UV Replicate 1

source_name: NHF1 genomic DNA (control)

value: UV irradiated 80 J/m2


title: Naked DNA UV Replicate 2


title: No UV

description: NoUV sample was a control for NHF1 UV 0hr Replicate 3 part A


title: TALE MO zebrafish 12hpf biological replicate1

status: Public on Jun 22 2018

city: Worcester

first: Franck

last: Ladam

state: Massachusetts

address: 364 plantation street , LRB 870D

institute: University of Massachusetts Medical School

description: Prep1 and Pbx2/4 morpholino injected (TALE MO) 12hpf zebrafish embryos, biological replicate 1

data_processing:
reads quality check with FastQC
alignment and read counts with RSEM_v1.2.28
Normalized abundance measurements and identification of differentially expressed genes with DESeq2
Genome_build: GRCz10/DanRer10 sept2014
Supplementary_files_format_and_content: .tsv containing read count tpm values from RSEM for each biological replicate and experimental condtion

molecule: polyA RNA

organism: Danio rerio

source_name: total 12hpf zebrafish embryo

growth_protocol: zebrafish egg water maintained at 28°C

extract_protocol:
Total RNA extraction using the RNeasy kit (Qiagen) with on column DNAse treatment.
3ug of total RNA was used to construct RNA-seq libraries with the Illumina Truseq stranded mRNA library kit after PolyA+ RNA enrichment

treatment_protocol: Injection of

tag: tissue

value: total 12hpf zebrafish embryo

tag: strain

value: Ekwill

tag: developmental stage

value: 12 hours post-fertilization (segmentation)


title: L119-RNA sequencing rep-1

city: Beijing

first: Jinkui

last: Cheng

address: No.2 Yuanmingyuan West Road

country: China

institute: China Agricultural University

description: processed data file: genes and TEs up and down regulated in sams3.xlsx

data_processing:
For Bisulfite-seq, clean data were generated by trimming adaptor bases and removing low quality reads. For data analysis, paired-end clean reads were mapped to the reference genome sequence of Arabidopsis genome (TAIR10) with Bismark
For RNA-seq, the trimmed reads were mapped to the reference genome sequence of Arabidopsis genome (TAIR10) using bowtie2. (http://computing.bio.cam.ac.uk/local/doc/bowtie2.html) with default settings.Differential gene expression analyses were performed using edgeR (http://bioinf.wehi.edu.au/edgeR/). We selected genes with fold change >2 and P-value <0.0001 comparing to wild type as differential expression genes and TEs.
Genome_build: tair10
Supplementary_files_format_and_content: bedgraph for Bisulfite samples; Excel file with differentially-regulated genes for RNA-seq samples.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were grown on MS medium plates supplemented with 20 g/L sucrose and 0.8% agar at 22°C under long-day (23 h) illumination

extract_protocol:
The genomic DNA was extracted from 15-day seedlings using DNeasy Plant Mini Kit (QIAGEN 69104).; The total RNAs were extracted from 15-day seedlings using RNeasy Plant Mini Kit (QIAGEN 74904).
2 µg DNA was used for bisulfite treatment and library construction, and MethylC-seq was carried out using HiSeq 2000 (Illumina); A 2 µg quantity RNA was used for library construction.

value: seedling

tag: growth period

value: 15 days

tag: ecotype

value: transgenic wild type


title: sams3-RNA sequencing rep-1

value: sams3 mutant


title: sams3-Bisulfite sequencing


title: AcBac_Rep2_Cap2_94h_1

description:
replicate 1
genome: Bacmid_dCC_Rep2_Cap4


title: L119-RNA sequencing rep-2


title: L119-Bisulfite sequencing


title: sams3-RNA sequencing rep-2


title: AcBac_AAV2wt_94h_2

description:
replicate 2
genome: Bacmid_dCC_AAV2wt


title: siMettl3-1-IP

city: Nanjing

first: Xiang

last: Zhong

state: Jiangsu

address: No. 6, Tongwei Road, Xuanwu District

department: College of Animal Science and Technology

institute: Nanjing Agricultural University

data_processing:
Library strategy: m6A-seq
Basecalls performed using CASAVA version 1.8.2
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2.0.13 with --segment-mismatches 2 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 –r 70 --library-type fr-unstranded
peaks were called using MACS version 1.4.2 with the following setting: Pvalue cutoff:e-05
Genome_build: hg19
Supplementary_files_format_and_content: txt file. Peaks

growth_protocol: The human HepG2 cell line  were grown in DMEM media supplemented with 10% FBS, 1% 100× Pen Strep, and GlutaMAXTM Supplement. Cells were incubated with 5% CO2 and 95% air at 37℃.

extract_protocol:
Total RNA was extracted using TRIzol reagent followed by purification using PolyATtract® mRNA Isolation.Immunoprecipitated RNA fragments and comparable amounts of input were subjected to first-strand cDNA synthesis
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hepatocellular Carcinoma cell Hep G2

tag: passage

tag: ip antibody

value: anti-m6A (Synaptic systems, catalog#:202003, RRID:AB_2279214)


title: siMettl3-2-input

value: input


title: siMettl3-2-IP


title: siMettl3-1-input


title: siControl2-IP

source_name: siControl-IP

value: control


title: siControl2-input

source_name: siControl-input


title: no dox, xyloside, rep2

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
The first 6 nucleotides and the last nucleotides with a quality score below 20 for each read were trimmed using in-house scripts. If, after trimming, the read was shorter than 45-bp, the whole read was discarded
Trimmed reads were mapped to the human reference genome (hg19) with a known transcriptome index (UCSC Known Gene annotation) using Tophat v2.0.13 (Trapnell, Pachter, and Salzberg 2009). Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results
Tophat alignments were then processed by Cufflinks v2.2.1 (Trapnell et al. 2010) to obtain differential gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Cuffdiff output format.

source_name: Flp-In T-REx 293 Cell Line

growth_protocol: HEK293 cells were passaged at 37°C and 5% CO2 with DMEM supplemented with 10% FBS and 1% pen-strep.

extract_protocol:
Cells were pelleted and total RNA was extracted using the QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions.
Twelve strand-specific sequencing libraries, two replicates per conditions, were produced from the total RNA. Total mRNA was purified from approximately 500ng of total RNA with Ribo-Zero and sheared by incubation at 94°C. Following first-strand synthesis with random primers, second strand synthesis was performed with dUTP for generating strand-specific sequencing libraries. Libraries underwent 76 bp single-end sequencing on an Illumina HiSeq 2500, according to Illumina protocols, generating between 22M and 31M reads per library.

treatment_protocol: Cells were plated and the following day treated with doxycycline for 24 hours. Subsequently, cells were treated with the stressor molecule for 12 hours.

tag: doxycycline

value: 0 ng/ml

tag: treatment type

value: xyloside

value: 4 mM


title: dox induced, HyT36, rep2

value: 100 ng/ml

value: 10 µM


title: dox induced, DMSO, rep2

value: DMSO


title: dox induced, HyT36, rep1


title: no dox, xyloside, rep1


title: dox induced, DMSO, rep1


title: no dox, nigericin, rep1

value: nigericin

value: 1 µM


title: NHF1 UV 0hr Replicate 1

value: UV irradiated 100 J/m2

value: 0 hr


title: no dox, nigericin, rep2


title: no dox, DMSO, rep1


title: 446_N_ITC

first: Panos

last: Roussos

address: 1470 Madison Ave

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads from each sample were aligned on gender specific hg19 reference genome (pseudoautosomal region was masked on the chromosome Y for males) using the STAR aligner (v2.5.0) with the following parameters: --alignIntronMax 1, --outFilterMismatchNmax 100, --alignEndsType EndToEnd, --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads. We excluded reads that: (1) mapped to more than one locus; (2) were duplicated; and (3) mapped to the mitochondrial genome. For each sample, this produced a coordinate-sorted BAM file of mapped paired-end reads.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated from BAM files using the genomeCoverageBed and bedGraphToBigWig functions

source_name: inferior temporal cortex

extract_protocol:
50mg of frozen powdered brain tissue was homogenized in cold lysis buffer (0.32M Sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM, EDTA, 10mM Tris-HCl, pH8, 1 mM DTT, 0.1% Triton X-100) and filtered through a 40µm cell strainer. The flow-through was underlaid with sucrose solution (1.8 M Sucrose, 3 mM Mg(Ace)2, 1 mM DTT, 10 mM Tris-HCl, pH8) and subjected to ultracentrifugation at 24,000 rpm for 1 hour at 4°C. Pellets were thoroughly resuspended in 500µl DPBS and incubated in BSA (final concentration 0.1%) and anti-NeuN antibody (1:1000, Alexa488 conjugated, Millipore) under rotation for 1 hour, at 4 °C. Prior to FANS sorting, DAPI (Thermoscientific) was added to a final concentration of 1µg/ml. DAPI positive neuronal (NeuN+) and non-neuronal (NeuN-) nuclei were sorted into tubes pre-coated with 5%BSA using a FACSAria flow cytometer (BD Biosciences) equipped with a 70μm nozzle.
Briefly, 50,000 sorted nuclei were centrifuged at 500 ×g
for 10 min, 4°C. Pellets were re-suspended in transposase reaction mix (25 μL 2x TD Buffer (Illumina Cat #FC-121-1030) 2.5 μL Tn5 Transposase (Illumina Cat #FC-121-1030) and 22.5 μL Nuclease Free H2O) on ice. Samples were incubated at 37°C for 30 min and then purified using the MinElute Reaction Cleanup kit (Qiagen Cat #28204), eluting in 10µl of buffer EB. Following purification, library fragments were amplified using the Nextera index kit (Illumina Cat #FC-121-1011), using the following cycling conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute for a total of 5 cycles. In order to prevent saturation due to over-amplification, a 5µl aliquot was then removed and subjected to qPCR for 20 cycles to calculate the optimal number of cycles needed for the remaining 45 μL reaction. The additional number of cycles was determined as follows: (1) Plot linear Rn vs. Cycle
(2) Calculate the # of cycle that is corresponded to 1⁄4 of maximum fluorescent intensity. In general, we found adding 4-6 cycles to this estimate yielded optimal ATACseq libraries, as determined by analysis on Bioanalyzer High Sensitivity DNA Chips (Agilent technologies Cat#5067-4626). Libraries were amplified for a total of 12–18 cycles. Following PCR, ATACseq libraries were resolved on 2% agarose gels supplemented with SYBR green. Fragments ranging in size from 100bp-1Kbp were excised and purified (Qiagen Minelute Gel Extraction Kit – Qiagen Cat#28604). Libraries were quantified by Qubit HS DNA kit (Life technologies) and by quantitiative PCR (KAPA Biosystems Cat#KK4873) prior to sequencing. Libraries were sequenced on Hi-Seq2500 (Illumina) obtaining 2x50 paired-end reads.

tag: cell type

value: Neuronal

tag: gender

value: Female

tag: age of death

tag: postmortem interval (hours)

tag: heart weight (grams)

tag: alcohol toxicology

value: negative

tag: Cause of death

value: sudden cardiac death


title: 446_N_INS

source_name: insula


title: 446_N_PVC

source_name: primary visual cortex


title: 446_N_HIPP

source_name: hippocampus


title: 446_N_PMC

source_name: primary motor cortex


title: 446_N_PUT

source_name: putamen


title: 446_N_VLPFC

source_name: ventrolateral prefrontal cortex


title: siControl1-input

tag: cell line

value: Hepatocellular Carcinoma cell Hep G2

tag: genotype


title: 446_N_AMY

source_name: basal amygdala


title: 446_G_STC

source_name: posterior superior temporal cortex

value: Non-Neuronal


title: 446_N_OFC

source_name: medial orbitofrontal cortex


title: 446_N_MDT

source_name: mediodorsal thalamus


title: 446_N_ACC

source_name: anterior cingulate cortex


title: C57BL6.12hr.H3K27Me2.iWTr

value: inducible WT EED rescue  12hr

tag: chip antibody

value: H3K27Me2, Cell Signaling, #9728


title: no dox, DMSO, rep2

value: 0 ng/ml

tag: treatment


title: no dox, HyT36, rep2


title: 446_G_VLPFC


title: 446_G_OFC


title: 446_G_PMC


title: siControl1-IP

value: control

value: anti-m6A (Synaptic systems, catalog#:202003, RRID:AB_2279214)


title: C57BL6.0hr.H3K27Me2.iWTr

value: inducible WT EED rescue  0hr


title: no dox, HyT36, rep1

value: 10 µM


title: 446_G_PVC


title: 446_G_MDT


title: C57BL6.36hr.H3K27Me2.iWTr

value: inducible WT EED rescue  36hr


title: 446_G_PUT


title: 446_N_DLPFC

source_name: dorsolateral prefrontal cortex


title: C57BL6.36hr.H3K27Me3.iMTr

value: inducible MT EED rescue  36hr

value: H3K27Me3, Cell Signaling, #9733


title: 446_N_STC


title: 446_G_INS


title: 446_G_HIPP


title: E14Tga2.WT.EED

value: EED WT

value: in house


title: 446_G_DLPFC

value: Female


title: E14Tga2.KO.H3K27Me2

value: EED KO


title: E14Tga2.Y365A.EED

value: EED Y365A


title: 446_G_ITC

value: negative

value: sudden cardiac death


title: E14Tga2.Y365A.H3K27Me2


title: E14Tga2.WT.H3K27Me2


title: 440_N_STC

value: Neuronal

value: Male


title: RNAseq.E14Tga2.Y358A.rep1

data_processing:
mapped to mm9 with BOWTIE -m40 -v2
reads were assigned to the ENSEMBL annotation using DEGseq
Normalized differential expression (taking into account biological replicates) was calculated using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: Raw read count and RPKM matching the ENSEMBL annotation

growth_protocol: mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated  in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) for 2 days to initiate formation of embryoid bodies (EB_d2).

extract_protocol:
Total RNA was isolated with TRIzol (Life Technologies) and reverse transcribed using Superscript III and random hexamers (Life Technologies) to synthesize the 1st strand. Second strand was synthesized with dUTP to generate strand asymmetry using DNA Pol I (NEB, M0209L) and the E. coli ligase (Enzymatics, L6090L).
Libraries were repaired to generate blunt 5' P ends using 'EndIT DNA End Repair kit' (Epicentre), 3' A overhang was generated using 'Klenow Fragment (3´→ 5´ exo-)' (NEB).  Illumina barcodes were ligated using 'Rapid T4 DNA Ligase' (Enzymatics). Next libraries were size selected using agarose gel extraction method.  After around 13 cycles of amplification, libraries were cleaned, quantified and pooled.

value: EED Y358A


title: RNAseq.E14Tga2.KO.rep2


title: 440_N_VLPFC


title: 446_G_ACC

value: Non-Neuronal


title: RNAseq.E14Tga2.KO.rep1


title: RNAseq.E14Tga2.F97A.rep1

value: EED F97A


title: 440_N_PVC


title: RNAseq.E14Tga2.F97A.rep2


title: RNAseq.E14Tga2.Y358A.rep2


title: 440_N_DLPFC


title: 440_N_OFC


title: E14Tga2.KO.EED


title: RNAseq.E14Tga2.Y365A.rep1


title: RNAseq.E14Tga2.Y365A.rep2


title: 440_N_INS


title: RNAseq.E14Tga2.WT.rep1

value: WT


title: 440_N_ACC


title: 446_G_AMY


title: 440_G_VLPFC


title: RNAseq.EB_d2.Y365A.rep1


title: 440_N_ITC


title: RNAseq.EB_d2.KO.rep1


title: RNAseq.EB_d2.WT.rep1


title: 440_G_STC


title: 440_G_PVC


title: 440_G_PUT


title: E14Tga2.WT.Input.rep2

data_processing:
Bowtie2 v2.2.6 was used to align reads to reference genome with default parameters.
Aligned reads were normalized based on the mapped reads in spike-in Drosophila control.
BedGraph files were generated from the aligned reads using 'genomecov' function in bedtools v2.17.0
BigWig files were generated from BedGraph files using 'bedGraphToBigWig' function in USCS.
Genome_build: mm10


title: 440_G_PMC


title: 440_N_PMC


title: 440_G_OFC


title: 440_G_MDT


title: E14Tga2.KO.H3K27Me3.rep2


title: E14Tga2.Y358A.H3K27Me3.rep2


title: 440_G_DLPFC


title: 440_G_ACC


title: 440_G_INS


title: 440_G_ITC


title: E14Tga2.WT.H3K27Me3.rep2


title: E14Tga2.Y358A.H3K27Me3.rep1


title: 437_N_STC


title: RNAseq.E14Tga2.WT.rep2


title: E14Tga2.Y365A.H3K27Me3.rep1


title: E14Tga2.F97A.H3K27Me3.rep2


title: E14Tga2.KO.H3K27Me3.rep1


title: E14Tga2.Y365A.H3K27Me3.rep2


title: 437_N_PVC


title: 437_N_PMC


title: E14Tga2.WT.H3K27Me3.rep1


title: 437_N_PUT


title: E14Tga2.F97A.H3K27Me3.rep1


title: 437_N_OFC


title: C57BL6.0hr.HA_EED.iWTr

value: inducible WT EED rescue  0hr


title: C57BL6.0hr.Input.iWTr


title: 437_N_ITC


title: C57BL6.12hr.H3K27Me3.iWTr

value: inducible WT EED rescue  12hr


title: E14Tga2.WT.Input.rep1


title: C57BL6.0hr.H3K27Me3.iWTr


title: E14Tga2.WT.JARID2


title: 437_N_DLPFC


title: 437_N_HIPP


title: E14Tga2.pEvx2Del.input

value: EVX2 promoter deletion


title: 437_N_ACC


title: E14Tga2.pEvx2Del.H3K27Me3

value: H3K27Me3, Cell Signaling, #9733


title: 437_G_VLPFC


title: 437_G_PVC


title: 437_G_STC


title: E14Tga2.Evx2Del.H3K27Me3

value: Evx2 deletion


title: E14Tga2.ctrlDel.input

value: ctrl deletion


title: 437_G_PMC


title: 437_G_OFC


title: E14Tga2.Evx2Del.input


title: 437_G_PUT


title: E14Tga2.ctrlDel.H3K27Me3


title: 4C.Specc1.Hind3.WT.rep2

data_processing:
Reads were mapped to a reduced genome of unique 25 bp sequences adjacent to the primary restrcition enzyme sequence used in each experiment. Alignment was done with bowtie with -N 0.
Self ligated and undigested fragments were removed after mapping
Normalization was performed using the cisAnalysis function of 4C-ker using a k=10 or a k=5
Genome_build: mm10

extract_protocol:
10 million cells were trypsinized and crosslinked in 2% formaldehyde for 10 min at room  temperature. First digestion was performed using HinDIII  restriction enzyme. After ligation and crosslink reversal, second digestion was performed using DpnII restriction enzyme. DNA was purified for 4C library preparation.
Following DNA purification, 1mg of total DNA was amplified for 30 cycles using 4C primer sets. Fragments of 100-700bp were selected using agarose gel extraction. Libraries were quantified and pooled.
4C-seq


title: 437_N_INS


title: C57BL6.36hr.H3K27Me3.iWTr

value: inducible WT EED rescue  36hr


title: 437_G_INS


title: 437_G_ITC


title: 4C.Pou5f1.Hind3.WT.rep2


title: 4C.Specc1.Hind3.WT.rep1


title: 437_G_HIPP


title: 4C.Pou5f1.Hind3.WT.rep1


title: 437_G_DLPFC


title: 4C.Hoxc.Hind3.WT.rep2


title: 4C.Irak4.Hind3.WT.rep1


title: 4C.Lhx2.Hind3.WT.rep2


title: 437_G_ACC


title: 372_N_PUT


title: 372_N_PVC


title: 4C.Lhx2.Hind3.WT.rep1


title: 4C.Irak4.Hind3.WT.rep2


title: 372_N_STC


title: 4C.HoxB.Hind3.WT.rep2


title: 372_N_VLPFC


title: 4C.HoxB.Hind3.WT.rep1


title: 4C.HoxA.Hind3.WT.rep1


title: 372_N_OFC


title: 4C.Evx2.Hind3.KO.rep2

value: EED KO


title: 4C.Hoxc.Hind3.WT.rep1


title: 372_N_NAC

source_name: nucleus accumbens


title: 372_N_INS


title: 372_N_DLPFC


title: 4C.Evx2.Hind3.KO.rep1


title: 4C.Evx2.Hind3.Y365A.rep1

value: EED Y365A


title: 372_N_HIPP

value: negative


title: 4C.HoxA.Hind3.WT.rep2


title: 372_N_ITC

value: sudden cardiac death


title: 372_N_MDT

value: Neuronal


title: 372_N_ACC

value: Male


title: 4C.Desert.Hind3.WT.rep2


title: 4C.Evx2.Hind3.WT.rep1


title: 4C.Desert.Hind3.WT.rep1


title: 4C.Evx2.Hind3.WT.rep2


title: 372_G_PUT


title: 372_G_STC


title: 372_G_PMC


title: 372_G_VLPFC


title: 4C.Cyp26b1.Hind3.WT.rep2


title: 372_G_OFC


title: 4C.Cyp26b1.Hind3.WT.rep1


title: 15875.Thymic_DN3-ATAC-seq-rep2

description:
processed data file:
Thy_DN3.ATAC_peaks

tag: strain/cell line background

tag: cell line/type

value: Thymic DN3 cells

value: Fresh sorted


title: 4C.Evx2.Hind3.Y365A.rep2


title: 372_G_MDT

value: Non-Neuronal


title: 372_G_ITC


title: 372_G_NAC


title: 15871.Thymic_ETP-ATAC-seq-rep2

description:
processed data file:
Thy_ETP.ATAC_peaks

value: Thymic ETP cells


title: 15864.Thymic_ETP-ATAC-seq-rep1

description:
processed data file:
Thy_ETP.ATAC_peaks


title: 372_G_DLPFC


title: 372_G_AMY


title: 18068.Cas9_BM_CD25+_sgRunx1_RNA-seq-rep2

description:
processed data file:
JU_HH_et_al_RNA-seq_rpkm_table/JU_HH_et_al_RNA-seq_raw_counts_table

value: Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J (Cas9) x C57BL/6-Tg(Bcl2)25Wehi/J (Bcl2Tg)

value: Lin- BM derived CD25+ cells

tag: sorted fraction

value: Sorted as LiveLin-CD45+CD25+CFP+

value: Transduced with sgRunx1-CFP


title: 18067.Cas9_BM_CD25+_sgSatb1_RNA-seq-rep2

value: Transduced with sgSatb1-CFP


title: 17741.Cas9_BM_CD25+_sgRunx1_RNA-seq-rep1


title: 351_N_VLPFC


title: 372_G_HIPP


title: 17740.Cas9_BM_CD25+_sgSatb1_RNA-seq-rep1


title: 18066.Cas9_BM_CD25+_sgPU.1_RNA-seq-rep2

value: Transduced with sgPU.1-CFP


title: 372_G_ACC


title: 17739.Cas9_BM_CD25+_sgPU.1_RNA-seq-rep1


title: 351_N_STC


title: 15874.Thymic_DN3-ATAC-seq-rep1

description:
processed data file:
Thy_DN3.ATAC_peaks


title: 17738.Cas9_BM_CD25+_sgCont_RNA-seq-rep1

value: Transduced with sgCIntrol-CFP


title: 351_N_PUT


title: 351_N_OFC


title: 351_N_PMC


title: 351_N_ITC


title: 351_N_MDT


title: 18076.Scid.adh.2c2_sgRunx1-PU.1-RNA-seq-rep2

value: Scid.adh.2c2 cells

value: Transduced with Cas9-GFP, sgRunx1-CFP, PU.1-hNGFR


title: 17642.Scid.adh.2c2_sgRunx1-PU.1-RNA-seq-rep1


title: 17641.Scid.adh.2c2_sgSatb1-PU.1-RNA-seq-rep1

value: Transduced with Cas9-GFP, sgSatb1-CFP, PU.1-hNGFR


title: 18075.Scid.adh.2c2_sgSatb1-PU.1-RNA-seq-rep2


title: 351_N_DLPFC

value: negative

value: sudden cardiac death


title: 351_N_ACC

value: Neuronal

value: Male


title: 351_N_PVC


title: 17628.Scid.adh.2c2_sgRunx1-Mock-RNA-seq-rep1

value: Transduced with Cas9-GFP, sgRunx1-CFP, Mock-hNGFR


title: 18065.Cas9_BM_CD25+_sgCont_RNA-seq-rep2


title: 351_G_PVC

value: Non-Neuronal


title: 18072.Scid.adh.2c2_sgRunx1-Mock-RNA-seq-rep2


title: 351_G_VLPFC


title: 351_G_STC


title: 372_G_INS


title: 17627.Scid.adh.2c2_sgSatb1-Mock-RNA-seq-rep1

value: Transduced with Cas9-GFP, sgSatb1-CFP, Mock-hNGFR


title: 351_G_PMC


title: 17640.Scid.adh.2c2_sgCont-PU.1-RNA-seq-rep1

value: Transduced with Cas9-GFP, sgControl-CFP, PU.1-hNGFR


title: 351_G_PUT


title: 17626.Scid.adh.2c2_sgCont-Mock-RNA-seq-rep1

value: Transduced with Cas9-GFP, sgControl-CFP, Mock-hNGFR


title: 18070.Scid.adh.2c2_sgCont-Mock-RNA-seq-rep2


title: 351_G_MDT


title: 351_G_OFC


title: 351_G_INS


title: 351_N_INS


title: 351_G_ITC


title: 17081.Scid.adh.2c2_PU.1-RNA-seq-rep1

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Transduced with pMxs-PU.1-hNGFR


title: 17084.Scid.adh.2c2_Mock-RNA-seq-rep2

value: Transduced with pMxs-Mock-hNGFR


title: 17085.Scid.adh.2c2_PU.1-RNA-seq-rep2


title: 18074.Scid.adh.2c2_sgCont-PU.1-RNA-seq-rep2


title: 351_G_DLPFC


title: 351_G_ACC


title: 16773.Scid.adh.2c2_PU.1ert2_24h-RNA-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 18071.Scid.adh.2c2_sgSatb1-Mock-RNA-seq-rep2


title: 437_N_VLPFC


title: 22q13-1_PAX6-GFP_negative

city: Cambridge

first: Reinhard

last: Roessler

address: 455 Main street

institute: Whitehead Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-seq reads were aligned to the HG18 genome assembly using the tophat alignment pipeline
SeqMonk software was used for data processing and data analysis
Genome_build: HG18
Supplementary_files_format_and_content: log2 RPM (reads per million) was exported from SeqMonk

growth_protocol: neuroectoderm was induced from pluripotent stem cells by differentiation as described in Chambers, Nat Biotech (2009) and Shi, Nat. Prot. (2012). NPCs were collected after 21-28 days of differentioation.

extract_protocol:
cells were collected 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: subject status

value: Phelan-Mcdermid patient

value: iPSC-derived neural progenitors

tag: genotype/variation

value: PAX6 +/GFP

tag: tissue

value: neural

tag: passage

tag: cell population/fraction

value: GFP-negative


title: 22q13-1_PAX6-GFP_unsorted

tag: cell type

value: unsorted


title: 22q13-1_PAX6-GFP_positive

value: GFP-positive


title: WIBR3_PAX6-GFP_negative

value: control

value: ESC-derived neural progenitors


title: 16882.Scid.adh.2c2_PU.1ert2_2h-RNA-seq-rep2

value: Scid.adh.2c2 cells

value: Transduced with Lzr-PU.1ert2, treated 2h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16770.Scid.adh.2c2_PU.1ert2_24h-RNA-seq-rep1


title: 16879.Scid.adh.2c2_PU.1ert2_2h-RNA-seq-rep1


title: WIBR3_PAX6-GFP_positive


title: 16774.Scid.adh.2c2_PU.1ert2_0h-RNA-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16771.Scid.adh.2c2_PU.1ert2_0h-RNA-seq-rep1


title: WIBR3_PAX6-GFP_unsorted


title: 16775.Scid.adh.2c2_ert2_0h-RNA-seq-rep2

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16880.Scid.adh.2c2_ert2_24h-RNA-seq-rep1

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16772.Scid.adh.2c2_ert2_0h-RNA-seq-rep1


title: 16881.Scid.adh.2c2_PU.1ert2_8h-RNA-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 8h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16878.Scid.adh.2c2_PU.1ert2_8h-RNA-seq-rep1


title: 17263.FLP_CD25+_PU1WTHA44_RNA-seq-rep4

value: Lin- FLP derived CD25+ cells

value: Sorted as LiveGFP+CD44+CD25-

value: Transduced with Lzr-PU1WTHA, cultured on OP9DL1


title: 15912.FLP_CD25+_PU1WTHA44_RNA-seq-rep2


title: 17174.FLP_CD25+_PU1WTHA44_RNA-seq-rep3


title: 15775.FLP_CD25+_PU1WTHA44_RNA-seq-rep1


title: 17262.FLP_CD25+_PU1ETSHA_RNA-seq-rep4

value: Sorted as LiveGFP+CD25+

value: Transduced with Lzr-PU1ETSHA, cultured on OP9DL1


title: 17173.FLP_CD25+_PU1ETSHA_RNA-seq-rep3


title: 15911.FLP_CD25+_PU1ETSHA_RNA-seq-rep2


title: 15774.FLP_CD25+_PU1ETSHA_RNA-seq-rep1


title: 15773.FLP_CD25+_PU1ENGHA_RNA-seq-rep1

value: Transduced with Lzr-PU1ENGHA, cultured on OP9DL1


title: 15910.FLP_CD25+_PU1ENGHA_RNA-seq-rep2


title: 17172.FLP_CD25+_PU1ENGHA_RNA-seq-rep3


title: 16883.Scid.adh.2c2_ert2_24h-RNA-seq-rep2


title: 17171.FLP_CD25+_PU1WTHA25_RNA-seq-rep3


title: 17080.Scid.adh.2c2_Mock-RNA-seq-rep1

value: Transduced with pMxs-Mock-hNGFR


title: 15909.FLP_CD25+_PU1WTHA25_RNA-seq-rep2


title: 17260.FLP_CD25+_PU1WTHA25_RNA-seq-rep4


title: 15772.FLP_CD25+_PU1WTHA25_RNA-seq-rep1


title: 17259.FLP_CD25+_EVGFP_RNA-seq-rep4

value: Transduced with Lzr-EVGFP, cultured on OP9DL1


title: 17170.FLP_CD25+_EVGFP_RNA-seq-rep3


title: 17576.Scid.adh.2c2_PU.1_1%input-ChIP-seq-rep1

value: Transduced with pMxs-PU.1-hNGFR


title: 16963.Scid.adh.2c2_Mock_1%input-ChIP-seq-rep2


title: 17577.Scid.adh.2c2_PU.1_1%input-ChIP-seq-rep2


title: 17261.FLP_CD25+_PU1ENGHA_RNA-seq-rep4


title: 15908.FLP_CD25+_EVGFP_RNA-seq-rep2


title: 15771.FLP_CD25+_EVGFP_RNA-seq-rep1


title: 16960.Scid.adh.2c2_Mock_1%input-ChIP-seq-rep1


title: 17575.Scid.adh.2c2_PU.1_aFog1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU.1_aFog1 HOMER IDR peaks

value: Goat anti-Fog1 polyclonal IgG (sc-9361, Santa Cruz Biotechnolog)


title: Ogye_eye_RRBS

city: Seoul

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

country: South Korea

institute: Hanyang University

data_processing:
Libraries were sequenced on the Illumina HiSeq platform.
Trimmed sequences were mapped to the Ogye draft genome using Bismark (Krueger and Andrews, 2011) (v0.7.0).
CpG methylation calls were extracted using Bismark.
Genome_build: Ogye draft genome
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

organism: Gallus gallus

source_name: Eye

extract_protocol:
DNA was isolated using a DNeasy kit.
Preparation of reduced representation bisulfite sequencing (RRBS) libraries were followed by the Illumina’s RRBS protocol.

value: Eye

tag: age

value: 8 months

tag: Sex

value: female


title: Ogye_skin_RRBS

source_name: Skin

value: Skin


title: Ogye_pancreas_RRBS

source_name: Pancreas

value: Pancreas


title: Ogye_uterus_RRBS

source_name: Uterus

value: Uterus


title: Ogye_lung_RRBS

source_name: Lungs

value: Lungs


title: Ogye_shank_RRBS

source_name: Shank

value: Shank


title: Ogye_heart_RRBS

source_name: Heart

value: Heart


title: Ogye_kidney_RRBS

source_name: Kidney

value: Kidney


title: Ogye_gallbladder_RRBS

source_name: Gall bladder

value: Gall bladder


title: Ogye_cerebellum_RRBS

source_name: Cerebellum

value: Cerebellum


title: 17557.Scid.adh.2c2_Mock_aFog1-ChIP-seq-rep1

description:
processed data file:
Scid.adh.2c2 Mock_aFog1 HOMER IDR peaks

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Scid.adh.2c2 cells


title: 17573.Scid.adh.2c2_PU.1_aGATA3-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU.1_aGATA3 HOMER IDR peaks

value: Mouse anti-GATA3 monoclonal IgG (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems),


title: Ogye_matureegg_RRBS

source_name: Mature egg

value: Mature egg


title: Ogye_immatureegg_RRBS

source_name: Immature egg

value: Immature egg


title: Ogye_gizzard_RRBS

source_name: Gizzard

value: Gizzard


title: Ogye_fascia_RRBS

source_name: Fascia

value: Fascia

value: 8 months


title: 17555.Scid.adh.2c2_Mock_aGATA3-ChIP-seq-rep1

description:
processed data file:
Scid.adh.2c2 Mock_aGATA3 HOMER IDR peaks

value: Transduced with pMxs-Mock-hNGFR


title: Ogye_cerebrum_RRBS

source_name: Cerebrum

value: Cerebrum

value: female


title: Ogye_comb_RRBS

source_name: Comb

value: Comb


title: Ogye_breast_RRBS

source_name: Breast

value: Breast


title: 17558.Scid.adh.2c2_PU,1_aFog1-ChIP-seq-rep1

value: Transduced with pMxs-PU.1-hNGFR

value: Goat anti-Fog1 polyclonal IgG (sc-9361, Santa Cruz Biotechnolog)


title: 16897.Scid.adh.2c2_PU,1_aRunx1-ChIP-seq-rep1

description:
processed data file:
Scid.adh.2c2 PU.1_aRunx1 HOMER IDR peaks

value: Rabbit anti-Runx1 polyclonal IgG (ab23980, Abcam)


title: 17552.Scid.adh.2c2_PU.1_aRunx1-ChIP-seq-rep2


title: 17551.Scid.adh.2c2_Mock_aRunx1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 Mock_aRunx1 HOMER IDR peaks


title: Ogye_shank_single_end_RNAseq

data_processing:
Illumina Casava1.8 software used for basecalling
For protein-coding gene annotation, two mapping tools were used. GMAP (ver 2014-12-22) was performed in junction mapping by transcript assembly result from Trinity (ver 2.0.3), and Tophat (ver 2.0.13) alignment in unigenes and assembling transcripts with cufflinks (ver 2.2.1) were adopted to obtain the gene structures and new genes.
For lncRNA annotation, sequenced reads were mapped to Ogye genome using STAR ver 2.4.2 and assembled transcript using Cufflinks.
Fragemets Per Kilobase of exon per Megabase of library size (FPKM) were calculated using RSEM program.
The FPKM values across tissues were normalized using the quantile normalization method.
Genome_build: ogye_gene.fasta
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNAs were extracted from twenty respective tissues using Trizol reagent.
A library was independently prepared with 300ng of total RNA for each sample by Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA).

value: Shank


title: 17574.Scid.adh.2c2_Mock_aFog1-ChIP-seq-rep2

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice


title: Ogye_eye_single_end_RNAseq

source_name: Eye

value: Eye


title: 16894.Scid.adh.2c2_Mock_aRunx1-ChIP-seq-rep1

value: Scid.adh.2c2 cells


title: 17554.Scid.adh.2c2_PU.1_aSatb1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU.1_aSatb1 HOMER IDR peaks

value: Rabbit anti-Satb1 monoclonal IgG (ab109122, Abcam)


title: Ogye_uterus_single_end_RNAseq

value: Uterus


title: Ogye_pancreas_single_end_RNAseq

value: Pancreas


title: Ogye_lung_single_end_RNAseq

source_name: Lung

value: Lungs


title: Ogye_heart_single_end_RNAseq

value: Heart

value: 8 months


title: Ogye_skin_single_end_RNAseq

source_name: Skin

value: Skin


title: Ogye_spleen_RRBS

source_name: Spleen

value: Spleen

value: female


title: 17556.Scid.adh.2c2_PU,1_aGATA3-ChIP-seq-rep1

value: Mouse anti-GATA3 monoclonal IgG (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems),


title: 17572.Scid.adh.2c2_Mock_aGATA3-ChIP-seq-rep2

value: Transduced with pMxs-Mock-hNGFR


title: 17553.Scid.adh.2c2_Mock_aSatb1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 Mock_aSatb1 HOMER IDR peaks


title: Ogye_kidney_single_end_RNAseq

value: Kidney


title: 16900.Scid.adh.2c2_PU,1_aSatb1-ChIP-seq-rep1

value: Transduced with pMxs-PU.1-hNGFR


title: Ogye_bonemarrow_RRBS

source_name: Bone marrow

value: Bone marrow


title: Ogye_cerebellum_single_end_RNAseq

value: Cerebellum


title: 16898.Scid.adh.2c2_Mock_aSatb1-ChIP-seq-rep1

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice


title: Ogye_liver_RRBS

source_name: Liver

value: Liver


title: 17222.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_24h_4-OHT_1%input-ChIP-seq-rep1

value: Scid.adh.2c2 cells

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16997.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_24h_4-OHT_1%input-ChIP-seq-rep2


title: Ogye_comb_single_end_RNAseq

value: Comb


title: 17223.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_0h_4-OHT_1%input-ChIP-seq-rep1

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: 16998.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_0h_4-OHT_1%input-ChIP-seq-rep2


title: Ogye_spleen_single_end_RNAseq


title: Ogye_fascia_single_end_RNAseq

value: Fascia


title: 16999.Scid.adh.2c2_ert2_aH3K27Ac_24h_4-OHT_1%input-ChIP-seq-rep2

description:
processed data file:
Read counts derived around combined Scid.adh.2c2 PU1ert2 0h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 2h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 8h 4-OHT aPU1 HOMER IDR peaks/Scid.adh.2c2 PU1ert2 24h 4-OHT aPU1 HOMER IDR peaks

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).

value: Rabbit polyclonal anti-H3K27Ac (ab4729, Abcam)


title: Ogye_gizzard_single_end_RNAseq

value: Gizzard

value: 8 months


title: Ogye_cerebrum_single_end_RNAseq

value: Cerebrum

value: female


title: 17224.Scid.adh.2c2_ert2_aH3K27Ac_24h_4-OHT_1%input-ChIP-seq-rep1


title: Ogye_immatureegg_single_end_RNAseq

value: Immature egg


title: 17000.Scid.adh.2c2_ert2_aH3K27Ac_0h_4-OHT_1%input-ChIP-seq-rep2

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: Ogye_liver_single_end_RNAseq


title: Ogye_gallbladder_single_end_RNAseq

value: Gall bladder


title: 16805.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_24h_4-OHT-ChIP-seq-rep1


title: Ogye_shank_paired_end_RNAseq

source_name: Shank

value: Shank


title: 17225.Scid.adh.2c2_ert2_aH3K27Ac_0h_4-OHT_1%input-ChIP-seq-rep1

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice


title: 16970.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_8h_4-OHT-ChIP-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 8h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: Ogye_breast_single_end_RNAseq

value: Breast


title: 16969.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_24h_4-OHT-ChIP-seq-rep2

value: Scid.adh.2c2 cells

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: Ogye_eye_paired_end_RNAseq

value: Eye


title: 16806.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_8h_4-OHT-ChIP-seq-rep1


title: 16971.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_2h_4-OHT-ChIP-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 2h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: MT_CRISPR_Control_rep6

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a DEP mutant bio-tagged Notch Intracellular Domain (NICD). Replicate 2
RiboMinus - depleted total RNA

data_processing:
Quality control of FATSQ files was done using fastqc.  Removal of low-quality reads and trimming was done using trimmomatic  Read mapping was done using STAR  The aligned readswere analyzed with featureCounts in order to obtain expression measures and differential gene expression measures.  DESeq2 was used for calling of differentially expressed genes
Genome_build: mm9
Supplementary_files_format_and_content: featureCounts output containing information about read counts per gene

source_name: mouse mature T-cells

extract_protocol: RNeasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and RNase-free DNase (Qiagen #79254)  Library-prep kit: Illumina TruSeq® Stranded Total RNA LT - Ribo-Zero Gold (RS-122-2301/2)

value: hybridoma called E2-10HA

tag: integrated plasmid

tag: selection

value: puromycin


title: Ogye_matureegg_single_end_RNAseq

value: Mature egg


title: Ogye_lung_paired_end_RNAseq

value: Lung

value: 8 months


title: 16807.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_2h_4-OHT-ChIP-seq-rep1

value: Rabbit polyclonal anti-H3K27Ac (ab4729, Abcam)


title: MT_CRISPR_Control_rep5

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a DEP mutant bio-tagged Notch Intracellular Domain (NICD). Replicate 1
RiboMinus - depleted total RNA

tag: cell line


title: MT_CRISPR_Control_rep4

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a wildtype bio-tagged Notch Intracellular Domain (NICD). Replicate 2
RiboMinus - depleted total RNA


title: Ogye_uterus_paired_end_RNAseq

source_name: Uterus

value: Uterus

value: female


title: Ogye_bonemarrow_single_end_RNAseq

value: Bone marrow


title: Ogye_kidney_paired_end_RNAseq

source_name: Kidney

value: Kidney


title: Ogye_heart_paired_end_RNAseq

source_name: Heart

value: Heart


title: 16994.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_0h_4-OHT-ChIP-seq-rep2

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen).


title: MT_CRISPR_Control_rep3

description:
RNA-seq in mouse mature T-cells infected with plamids encoding for the bacterial biotin ligase BirA and for a wildtype bio-tagged Notch Intracellular Domain (NICD). Replicate 1
RiboMinus - depleted total RNA


title: MT_sgH2afv/H2afz_#12_rep5

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 encoding for sgRNAs targeting H2afv and H2afz genes. Replicate 1
RiboMinus - depleted total RNA


title: 16808.Scid.adh.2c2_PU.1-ert2_aH3K27Ac_0h_4-OHT-ChIP-seq-rep1

value: Scid.adh.2c2 cells


title: MT_sgH2afv/H2afz_#12_rep6

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 encoding for sgRNAs targeting H2afv and H2afz genes. Replicate 2
RiboMinus - depleted total RNA


title: Ogye_gallbladder_paired_end_RNAseq

source_name: Gall bladder

value: Gall bladder


title: 16996.Scid.adh.2c2_ert2_aH3K27Ac_0h_4-OHT-ChIP-seq-rep2

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16809.Scid.adh.2c2_ert2_aH3K27Ac_24h_4-OHT-ChIP-seq-rep1

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: Ogye_cerebellum_paired_end_RNAseq

source_name: Cerebellum

value: Cerebellum


title: MT_sgH2afv/H2afz_#12_rep4

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 empty vector. Replicate 2
RiboMinus - depleted total RNA

value: hybridoma called E2-10HA

value: puromycin


title: MT_sgH2afv/H2afz_#12_rep3

description:
RNA-seq in mouse mature T-cells infected with lentiCRISPRv2 empty vector. Replicate 1
RiboMinus - depleted total RNA


title: Ogye_skin_paired_end_RNAseq

value: Skin


title: 16810.Scid.adh.2c2_ert2_aH3K27Ac_0h_4-OHT-ChIP-seq-rep1


title: Ogye_matureegg_paired_end_RNAseq

source_name: Mature egg

value: Mature egg

value: 8 months


title: 16700.Scid.adh.2c2_PU.1-aH3K4me2_24h_4-OHT_1%input-ChIP-seq

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16701.Scid.adh.2c2_PU.1-aH3K4me2_0h_4-OHT_1%input-ChIP-seq

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: Ogye_comb_paired_end_RNAseq

value: Comb

value: female


title: Ogye_spleen_paired_end_RNAseq

value: Spleen


title: Ogye_pancreas_paired_end_RNAseq

source_name: Pancreas

value: Pancreas


title: Ogye_immatureegg_paired_end_RNAseq

source_name: Immature egg

value: Immature egg


title: Ogye_gizzard_paired_end_RNAseq

source_name: Gizzard

value: Gizzard


title: 16695.Scid.adh.2c2_PU.1-ert2_aH3K4me2_8h_4-OHT-ChIP-seq

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Scid.adh.2c2 cells

value: Transduced with Lzr-PU.1ert2, treated 8h 0.1 uM 4-OHT (4-hydroxytamoxifen)

value: Rabbit polyclonal anti-H3K4me2 (07-030, Millipore)


title: 16995.Scid.adh.2c2_ert2_aH3K27Ac_24h_4-OHT-ChIP-seq-rep2

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen).

value: Rabbit polyclonal anti-H3K27Ac (ab4729, Abcam)


title: Ogye_cerebrum_paired_end_RNAseq

source_name: Cerebrum

value: Cerebrum


title: Ogye_fascia_paired_end_RNAseq

source_name: Fascia

value: Fascia


title: Ogye_breast_paired_end_RNAseq

source_name: Breast

value: Breast

value: 8 months


title: 16536.Scid.adh.2c2_PU.1-ert2_0h_4-OHT_aPU1_1%_input-ChIP-seq-rep1

value: Transduced with Lzr-PU.1ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16697.Scid.adh.2c2_PU.1-ert2_aH3K4me2_0h_4-OHT-ChIP-seq


title: 16698.Scid.adh.2c2_ert2_aH3K4me2_24h_4-OHT-ChIP-seq

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16699.Scid.adh.2c2_ert2_aH3K4me2_0h_4-OHT-ChIP-seq

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: Ogye_bonemarrow_paired_end_RNAseq

value: Bone marrow

value: female


title: 16535.Scid.adh.2c2_PU.1-ert2_24h_4-OHT_aPU1_1%_input-ChIP-seq-rep2

value: Transduced with Lzr-PU.1ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16537.Scid.adh.2c2_ert2_24h_4-OHT_aPU1_1%_input-ChIP-seq-rep2


title: 16694.Scid.adh.2c2_PU.1-ert2_aH3K4me2_24h_4-OHT-ChIP-seq


title: 16526.Scid.adh.2c2_PU.1-ert2_24h_4-OHT_aPU1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ert2 24h 4-OHT aPU1 HOMER IDR peaks

value: Rabbit anti-PU.1 polyclonal IgG (sc-352x, Santa Cruz Biotechnology)


title: 16538.Scid.adh.2c2_ert2_0h_4-OHT_aPU1_1%_input-ChIP-seq-rep1

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice


title: Virus_APC positive_3

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases .
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1.
Genome_build: The reference genome and annnotation is download from ftp://ftp.ensembl.org/pub/release-73/fasta/gallus_gallus/dna/
Supplementary_files_format_and_content: text file with gene level FPKM values.

source_name: LMH infected with ILTV and apoptotic

growth_protocol: LMH cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LMH cells were infected with ILTV at MOI 0.1 or cultured in conditioned medium

value: embryonic liver

value: LMH


title: 16527.Scid.adh.2c2_PU.1-ert2_8h_4-OHT_aPU1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ert2 8h 4-OHT aPU1 HOMER IDR peaks

data_processing:
ChIP-Sequencing and data analysis: ChIP sequences were mapped to the mouse genome build NCBI37/mm9 using Bowtie (v1.1.1; http://bowtie-bio.sourceforge.net/index.shtml) with “-v 3 -k 11 -m 10 -t --best –strata” settings and HOMER tagdirectories were created with makeTagDirectory {Heinz, 2010 #67} for further downstream analysis. In addition, read alignments from the Scid.adh.2c2-PU.1ert2 experiment were filtered against PCR duplicates using Samtools as well as genomic repeats and Broad blacklisted regions using Bedtools (full script provided upon request) prior to tag directory generation. Transcription factor peaks were identified with findPeaks.pl against a matched control sample using the settings “-P .1 -LP .1 -poisson .1 -style factor”. Transcription factor peak reproducibility was determined by a HOMER adaptation of the IDR (Irreproducibility Discovery Rate) package according to ENCODE guidelines (https://sites.google.com/site/anshulkundaje/projects/idr). Only reproducible high quality peaks, with a normalized peak score >= 15, were considered for further analysis.  Regions enriched for histone modifications were identified with findPeaks.pl with the option –style histone against a matched input control. Only regions consistently called in two independent experiments were used for downstream analyses.  Motif enrichment analysis was performed with the findMotifsGenome.pl command in the HOMER package using a 200bp window or a window size defined by the width of each identified peak. Overlapping peaks between samples were derived using mergePeaks.pl (default parameters). Annotation of peaks to nearest genes and genomic regions (e.g. promoters, CG-rich regions, repeat regions) were performed with annotatePeaks.pl (default settings). Tag density plots and heat maps were created with annotatePeaks.pl ( –hist or –hist & -ghist respectively), normalizing data to 10 million mapped reads per experiment.
RNA-Sequencing and data analysis:  RNA-sequenced reads were trimmed with Trimmomatic (v.033; http://www.usadellab.org/cms/?page=trimmomatic) for removal of adapter –and low quality sequences (settings: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36). Resulting reads were then mapped onto the mouse genome build NCBI37/mm9 with STAR (v2.4.0) and post-processed with RSEM (v1.2.25; http://deweylab.github.io/RSEM/) {Li, 2011 #81} according to the settings in the ENCODE long-rna-seq-pipeline with the minor modifications that settings “--output-genome-bam --sampling-for-bam” was added to rsem-calculate-expression. STAR and RSEM reference libraries were created from genome build NCBI37/mm9 together with the Ensembl gene model file Mus_musculus.NCBIM37.66.gtf. The resulting bam-files were used to create HOMER tag directories (makeTagDirectory with –keepAll setting). For analysis of statistically significance among differently expressed genes the data was raw gene counts were derived from each tag directory with analyzeRepeats.pl with the –noadj -condenseGenes options followed by the getDiffExpression.pl command using EdgeR (v3.6.8; http://bioconductor.org/packages/release/bioc/html/edgeR.html) or the gene count tables were imported into R and analyzed for differential expression using the DESeq2 package (v1.4.5; https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html)  For data visualization rpkm normalized reads were derived analyzeRepeats.pl command with the options –count exons –¬condenseGenes –rpkm followed by log transformation, and separately performed replicate set normalizations to prevent nondevelopmental differences in gene expression. Processed data for all the, in the study, included RNA-seq samples were derived from HOMER tagdirectories as either raw counts (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -noadj) or rpkm normalized values (analyzeRepeats.pl rna mm9 -count exons -condenseGenes -rpkm). Data is derived as one value per gene and the accession number associated with the highest expressing isoform is displayed (-condenseGenes option).
ATAC-Sequencing and data analysis: ATAC-sequences were mapped to mm9 as described in the Data processing-ChIP section. Additionally, Tag directories with reads mapped to the mitochondrial chromosome filtered were created using the HOMER platform (makeTagDirectory).  ATAC-seq peaks were identified using findPeaks.pl in HOMER (scipt available upon request). Only regions consistently called in two independent experiments were used for downstream analyses. Abundance of ATAC-tags on ATAC or transcription factor ChIP-seq peaks was analyzed in HOMER using the annotatePeaks.pl command.   For differential peak analysis, raw tag counts were derived from the tagdirectories using annotatePeaks.pl with the ”-noadj” setting  was carried out with the EdgeR  and limma (v3.20.9; http://bioconductor.org/packages/release/bioc/html/limma.html)  Bioconductor packages via  HOMER getDifferentialExpression.pl. Differential peaks with adjusted p-value <= 0.05 and log2 fold change >= |1| were considered significantly different.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include HOMER peak file  All genomic coordinates are relative to mm9 mouse assembly.

value: Scid.adh.2c2 cells

value: Transduced with Lzr-PU.1ert2, treated 8h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: 16520.Scid.adh.2c2_PU.1-ert2_24h_4-OHT_aPU1-ChIP-seq-rep1


title: Virus_EGFP positive_3

source_name: LMH infected with ILTV


title: Virus_APC positive_1


title: Virus_APC positive_2


title: 16528.Scid.adh.2c2_PU.1-ert2_2h_4-OHT_aPU1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ert2 2h 4-OHT aPU1 HOMER IDR peaks

value: Transduced with Lzr-PU.1ert2, treated 2h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: Virus_EGFP positive_1


title: Virus_EGFP positive_2


title: 16522.Scid.adh.2c2_PU.1-ert2_2h_4-OHT_aPU1-ChIP-seq-rep1


title: 16696.Scid.adh.2c2_PU.1-ert2_aH3K4me2_2h_4-OHT-ChIP-seq

value: Rabbit polyclonal anti-H3K4me2 (07-030, Millipore)


title: Control_3

source_name: LMH


title: 16529.Scid.adh.2c2_PU.1-ert2_0h_4-OHT_aPU-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ert2 0h 4-OHT aPU1 HOMER IDR peaks


title: Ogye_liver_paired_end_RNAseq

source_name: Liver

value: Liver


title: CM_APC positive_1

source_name: LMH apoptotic cells cultured in conditioned medium


title: CM_APC positive_3


title: 16523.Scid.adh.2c2_PU.1-ert2_0h_4-OHT_aPU-ChIP-seq-rep1


title: CM_APC positive_2


title: 16521.Scid.adh.2c2_PU.1-ert2_8h_4-OHT_aPU1-ChIP-seq-rep1


title: Control_1


title: Control_2


title: 16533.Scid.adh.2c2_ert2_24h_4-OHT_aPU1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 EVert2 24h 4-OHT aPU1 HOMER IDR peaks


title: Resistant strains S6 4 h treatment rep3

city: Singapore

first: Thuyen

last: Truong

address: 11 Lower Kent Ridge Road

department: Faculty of Dentistry

country: Singapore

institute: National University of Singapore

data_processing:
Illumina CASAVA v1.8 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SC5314 whole genome
FPKM, short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairssequenced, is calculated following Trapnell et al., 2010
Genome_build: ASM18296v3
Supplementary_files_format_and_content: .txt file includes FPKM values for each Sample

organism: Candida albicans

source_name: Planktonic cultures

growth_protocol: 30 °C

extract_protocol:
Qiagen RNA extraction kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatment control, 2 µg/ml SM21 (1 h), or 2 µg/ml SM21 (4 h)

value: 2 µg/ml SM21, 4 h

tag: ploidy

value: Haploid

tag: genotype

value: Mutated

tag: phenotype

value: SM21 resistant


title: Resistant strains S6 4 h treatment rep2

tag: treatment


title: 16534.Scid.adh.2c2_ert2_0h_4-OHT_aPU1-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 EVert2 0h 4-OHT aPU1 HOMER IDR peaks

extract_protocol:
ChIP-Seq:  Primary cell experiments:  Briefly, lin- FLPs were expanded for 7 days on OP9-DL1, CD25+ enriched and retrovirally infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were co-cultured on OP9-DL1 for ~40h and then sorted as LiveGFP+CD25+ or LiveGFP+CD44+CD25- on BD FACSAriaTM.    Scid.adh.2c2:    HA-tagged-ChIP: Scid.adh.2c2 cells were infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were expanded for ~40h and then sorted as LiveGFP+on BD FACSAriaTM.  4-OHT experiment: Scid.adh.2c2 cells were transduced with Lzr-PU.1ert2 (Scid.adh.2c2-PU.1ert2) or Lzr-ert2 (Scid.adh.2c2-ert2) control, cells were expanded for 48h and infected (GFP+) cells followed by sorting of GFP+ cells on BD FACSAriaTM and further expanded in vitro prior to 2, 8 or 24h activation with 0.1 μM 4-OHT (4-hydroxytamoxifen).  Satb1, Runx1, Fog1 and GATA3 ChIP: Scid.adh.2c2 cells were infected with retroviral supernatant of pMxs-Myc-Flag-PU.1-IRES-hNGFR and cultured for 48h.    Approximately 3-5 million primary sorted CD25+ -or 10 million Scid.adh.2c2 cells for ChIP were fixed at RT in 1 mg/ml DSG (Thermo Scientific) in PBS for 30 min followed by additional 10 min after addition of formaldehyde (FA) up to 1% (Satb1, Runx1, Fog1 and Ets1) or 10 min of 1% FA only (PU.1, HA,-tag, GATA3, H3-modifications). The reaction was quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in ice-cold 1xHBSS (Gibco). Cell pellets were snap frozen on dry ice and stored in -80°C. For DSG+FA crosslinked cells, nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in 0.5% Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC. FA crosslinked cells only were resuspended 1% Lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8). Lysates were sonicated on a Bioruptor (Diagenode) for 18 cycles, max power for 30s followed by 30 s rest. Sonication was followed by pelleting of debris and the supernatant was transferred to a new tube and chromatin was diluted 3X in 1xHBSS+PIC followed by 2xRIPA (2% Triton, 2mM EDTA, 200 mM NaCl, 20 mM Tris-HCl (pH 7.5), 1% sodium deoxycholate, 0.1%SDS + PIC). Approximately 10 μg per 107 cells of antibody (Rabbit anti-PU.1 polyclonal IgG (sc-352x, Santa Cruz Biotechnology), Rabbit HA-probe polyclonal IgG (sc-805x, Santa Cruz Biotechnology), Rabbit anti-Ets1 polyclonal IgG (sc-350x, Santa Cruz Biotechnology), Mouse anti-Gata3 monoclonal IgG (a mixture of sc-268, Santa Cruz Biotechnology and MAB26051, R&D Systems), Rabbit anti-Satb1 monoclonal IgG (ab109122, Abcam), Rabbit anti-Runx1 polyclonal IgG (ab23980, Abcam), Goat anti-Fog1 polyclonal IgG (sc-9361, Santa Cruz Biotechnolog), Rabbit polyclonal anti-H3K27Ac (ab4729, Abcam), Rabbit polyclonal anti-H3K4me2 (07-030, Millipore) or Rabbit polyclonal anti-H3K27me3 (07-449, Millipore) were hybridized to Dynabeads M-280 Sheep anti- Rabbit or Dynabeads M-280 Sheep anti- Mouse or Dynabeads Protein A/G (Invitrogen), respectively in 1ml 1xRIPA+PIC for 4h, washed twice with 1xRIPA, resuspended in 100 μl 1xRIPA+PIC and added to the diluted chromatin. For polyclonal and monoclonal antibodies, 20 and 50 μl of Dynabeads were used per μg antibody, respectively. ChIP was performed over night at 4°C, and subsequently washed (1 time with 1 ml Low Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton-X, 2 mM EDTA, 50 mM Tris-Hcl pH8, 150 mM NaCl), 1 time with 1 ml High Salt Immune Complex Wash Buffer (0.1% SDS, 1 % Triton-X, 2 mM EDTA, 50 mM Tris-Hcl pH8, 500 mM NaCl), 1 time with 1 ml LiCl Immune Complex Wash Buffer (0.25 M LiCl, 1% Igepal-CA630, 1% natrium deoxycholate, 1 mM EDTA, 10 mM Tris-Hcl pH8), 2 times with 1 ml TE buffer (10 mM Tris–HCl, pH 8.0, 10 mM EDTA)) and eluted for 6 h to O/N at 65°C in ChIP elution buffer (20 mM Tris-HCl, pH 7.5, 5 mM EDTA 50 mM NaCl, 1% SDS, and 50 μg proteinase K) treated and finally cleaned up using Zymo ChIP DNA Clean & Concentrator. ChIP-seq libraries were constructed using NEBNext ChIP-Seq Library Preparation Kit (NEB #E6240) following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.
RNA-seq: CD25+ cell experiments:  Briefly, lin- FLPs were expanded for 7 days on OP9-DL1, CD25+ enriched and retrovirally infected with empty vector control or HA-tagged versions of Lzr-PU.1WT, -PU.1ENG, -PU.1ETS. Cells were co-cultured on OP9-DL1 for ~40h and then sorted as LiveGFP+CD25+ or LiveGFP+CD44+CD25- on BD FACSAriaTM.    Scid.adh.2c2: Scid.adh.2c2 cells were transduced with Lzr-PU.1ert2 (Scid.adh.2c2-PU.1ert2) or Lzr-ert2 (Scid.adh.2c2-ert2) control, cells were expanded for 48h and infected (GFP+) cells followed by sorting of GFP+ cells on BD FACSAriaTM and further expanded in vitro prior to 2, 8 or 24h activation with 0.1 μM 4-OHT (4-hydroxytamoxifen).    Total RNA was isolated from 200.000-500.000 primary or Scid.adh.2c2 cells using RNAeasy MicroKit (Qiagen) according to manufacturer’s recommendations. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB #E7530) from ~1 μg of total RNA following manufacturer’s instructions. Libraries were sequenced on Illumina HiSeq2500 in single read mode with the read length of 50 nt following manufacturer's instructions. Base calls were performed with RTA 1.13.48.0 followed by conversion to FASTQ with bcl2fastq 1.8.4 and produced approximately 30 million reads per sample.
ATAC-seq: Eighty thousand Scid.adh.2c2 or Scid.adh.2c2 transduced Lzr-PU.1-ert2 or Lzr-er2 control vector followed by 0.1 uM 4-hydroxytamoxifen stimulation, 18.4 thousand primary sorted thymic ETP or 50,000 thymic DN3 cells were washed in ice cold HBSS-HEPES prior to the assay. For the primary cells, the final amplified libraries were purified and size-selected (x1.2 bead-to-DNA ratio) using SPRIselect-beads (Beckman-Coultier). Libraries were single-end sequenced on a HiSeq2500 (Illumina) (primary cells) or a NextSeq500 (Scid.adh.2c2) and produced approximately 30-50 million reads per sample.

tag: strain/cell line background

tag: cell line/type

value: Transduced with Lzr-ert2, treated 0h 0.1 uM 4-OHT (4-hydroxytamoxifen)

tag: chip antibody


title: 16524.Scid.adh.2c2_ert2_24h_4-OHT_aPU1-ChIP-seq-rep1

value: Transduced with Lzr-ert2, treated 24h 0.1 uM 4-OHT (4-hydroxytamoxifen)


title: Resistant strains S6 1 h treatment rep3

value: 2 µg/ml SM21, 1 h


title: Resistant strains S6 4 h treatment rep1


title: Resistant strains S6 1 h treatment rep2


title: Resistant strains S6 1 h treatment rep1


title: Resistant strains S6 control rep3

value: No treatment


title: 6525.Scid.adh.2c2_ert2_0h_4-OHT_aPU1-ChIP-seq-rep1

value: Rabbit anti-PU.1 polyclonal IgG (sc-352x, Santa Cruz Biotechnology)


title: 16539.Scid.adh.2c2_aH3K4me2-ChIP-seq

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: Unperturbed


title: 16608.Scid.adh.2c2_aH3K27me3-ChIP-seq

value: Rabbit polyclonal anti-H3K27me3 (07-449, Millipore)


title: 16541.Scid.adh.2c2_aH3_1%_input-ChIP-seq

value: Scid.adh.2c2 cells


title: Resistant strains S6 control rep1


title: 16162.Scid.adh.2c2_1%_input_DSG+FA-ChIP-seq-rep1


title: Resistant strains S5 4 h treatment rep3


title: 16607.Scid.adh.2c2_aH3K4me2-ChIP-seq


title: 16263.Scid.adh.2c2_aEts1_DSG+FA-ChIP-seq-rep3

description:
processed data file:
Scid.adh.2c2 Ets1 HOMER IDR peaks

value: Rabbit anti-Ets1 polyclonal IgG (sc-350x, Santa Cruz Biotechnology)


title: Resistant strains S5 4 h treatment rep2


title: 16262.Scid.adh.2c2_aEts1_DSG+FA-ChIP-seq-rep2


title: 16264.Scid.adh.2c2_1%_input_DSG+FA-ChIP-seq-rep2


title: Resistant strains S5 1 h treatment rep3


title: Resistant strains S5 4 h treatment rep1


title: 16160.Scid.adh.2c2_aEts1_DSG+FA-ChIP-seq-rep1


title: Resistant strains S5 1 h treatment rep2


title: 15320.Scid.adh.2c2_EVGFP_1%_input-ChIP-seq-rep2

value: Transduced with Lzr-EVGFP


title: 15319.Scid.adh.2c2_PU1ETSHA_aHA-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ETSHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1ETSHA

value: Rabbit HA-probe polyclonal IgG (sc-805x, Santa Cruz Biotechnology)


title: 15237.Scid.adh.2c2_EVGFP_1%_input-ChIP-seq-rep1


title: 15236.Scid.adh.2c2_PU1ETSHA_aHA-ChIP-seq-rep1


title: 16540.Scid.adh.2c2_aH3K27me3-ChIP-seq


title: 15318.Scid.adh.2c2_PU1ENGHA_aHA-ChIP-seq-rep2

description:
processed data file:
Scid.adh.2c2 PU1ENGHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1ENGHA


title: Resistant strains S5 1 h treatment rep1

value: Haploid


title: Resistant strains S5 control rep1

value: Mutated


title: Resistant strains S5 control rep3

value: SM21 resistant


title: Resistant strains S5 control rep2


title: Resistant strains S3 4 h treatment rep3

value: 2 µg/ml SM21, 4 h


title: Resistant strains S6 control rep2


title: Resistant strains S3 4 h treatment rep2


title: 15235.Scid.adh.2c2_PU1ENGHA_aHA-ChIP-seq-rep1


title: 15234.Scid.adh.2c2_PU1WTHA_aHA-ChIP-seq-rep1

description:
processed data file:
Scid.adh.2c2 PU1WTHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1WTHA


title: 15317.Scid.adh.2c2_PU1WTHA_aHA-ChIP-seq-rep2


title: Resistant strains S3 4 h treatment rep1


title: 15230.Scid.adh.2c2_PU1WTHA_aPU1-ChIP-seq-rep1

description:
processed data file:
Scid.adh.2c2 PU1WTHA aPU1 HOMER IDR peaks


title: 15314.Scid.adh.2c2_PU1WTHA_aPU1-ChIP-seq-rep2


title: Resistant strains S3 1 h treatment rep3

value: 2 µg/ml SM21, 1 h


title: Resistant strains S3 1 h treatment rep1


title: Resistant strains S3 1 h treatment rep2


title: Resistant strains S3 control rep3

value: No treatment


title: 15316.Scid.adh.2c2_EVGFP_aHA-ChIP-seq-rep2


title: 15233.Scid.adh.2c2_EVGFP_aHA-ChIP-seq-rep1


title: 17646.FLP_CD25+_EVGFP_1%_input-ChIP-seq-rep2

value: Lin- FLP derived CD25+ cells

value: Transduced with Lzr-EVGFP, cultured on OP9DL1


title: Resistant strains S3 control rep2


title: GZY803 4 h treatment rep3

value: Wild type

value: SM21 susceptible


title: 17637.FLP_CD25+_PU1ETSHA_aHA-ChIP-seq-rep2

description:
processed data file:
FLPCD25 PU1ETSHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1ETSHA, cultured on OP9DL1


title: 17636.FLP_CD25+_PU1ENGHA_aHA-ChIP-seq-rep2

description:
processed data file:
FLPCD25 PU1ENGHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1ENGHA, cultured on OP9DL1


title: 17221.FLP_CD25+_EVGFP_1%_input-ChIP-seq-rep1


title: GZY803 4 h treatment rep2


title: Resistant strains S3 control rep1


title: GZY803 4 h treatment rep1


title: GZY803 1 h treatment rep3


title: GZY803 1 h treatment rep2


title: 17634.FLP_CD25+_PU1WTHA_aHA-ChIP-seq-rep2

description:
processed data file:
FLPCD25 PU1WTHA aHA HOMER IDR peaks

value: Transduced with Lzr-PU1WTHA, cultured on OP9DL1


title: 17219.FLP_CD25+_PU1ENGHA_aHA-ChIP-seq-rep1


title: 17217.FLP_CD25+_PU1WTHA_aHA-ChIP-seq-rep1


title: GZY803 1 h treatment rep1


title: GZY803 control rep3


title: 17635.FLP_CD25+_PU1WTHA_aPU1-ChIP-seq-rep2

description:
processed data file:
FLPCD25 PU1WTHA aPU1 HOMER IDR peaks

value: Rabbit anti-PU.1 polyclonal IgG (sc-352x, Santa Cruz Biotechnology)


title: GZY803 control rep1


title: 17633.FLP_CD25+_EVGFP_aPU.1-ChIP-seq-rep2

description:
processed data file:
FLPCD25 EVGFP aPU1 HOMER IDR peaks


title: 17632.FLP_CD25+_EVGFP_aHA-ChIP-seq-rep2

value: Rabbit HA-probe polyclonal IgG (sc-805x, Santa Cruz Biotechnology)


title: 17215.FLP_CD25+_EVGFP_aHA-ChIP-seq-rep1


title: P1

city: Zhenjiang

first: Xiangfeng

last: Zheng

address: 301, Xuefu Road

department: Food school

institute: Jiangsu university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: FPKM

organism: Meyerozyma caribbica

source_name: Yeast cell

growth_protocol: Rhodotorula mucilaginosa  was inoculated in NYDB medium, an was incubated at 28℃， 180 rpm. For 24 h.

extract_protocol:
Retinas 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

treatment_protocol: The sample  of Y is the control which no treatment with patulin, sample P was treated with 20mg/mL patulin

value: Pichia caribbica cell cultured  in NYDB medium which contained 20 mg/mL patulin

tag: incubation time

tag: incubation conditions


title: GZY803 control rep2

value: Haploid


title: P2


title: Y2

value: Pichia caribbica cell cultured  in NYDB medium


title: P3


title: Y3


title: A549_paclitaxel

status: Public on Jun 20 2018

city: Dalian

first: Yang

last: Wang

address: No.9 West section, South Lv Road

institute: Dalian Medical University

data_processing:
Base-calling performed with CASAVA 1.8.2 software
Alignment performed with Tophat software, aligning to Human Genome Consortium Reference Human Genome hg38
Relative abundances calculated using Cufflinks software
The change of splicing isoforms were analyzed using MISO package with the annotation of all known alternative splicing events
Genome_build: hg38

growth_protocol: A549 cells were cultured in F12K medium containing 10% FBS.

extract_protocol:
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

treatment_protocol: A549 cells were treated with DMSO or 7.22nm paclitaxel for 72 hours.

value: non-small cell lung cancer

value: paclitaxel


title: Y1


title: 17220.FLP_CD25+_PU1ETSHA_aHA-ChIP-seq-rep1


title: 17216.FLP_CD25+_EVGFP_aPU.1-ChIP-seq-rep1


title: 51_35d miRNA-Seq

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

data_processing:
mRNA and miRNA: Basecalls and sample de-multiplexing performed by CASAVA with default parameters
miRNA: Adapter trimming was performed by sRNABench.
miRNA: Trimmed sequence reads were mapped with sRNABench by "genome mode" using Bowtie onto hg19 including known micro RNAs from miRBase
miRNA: Read counts and normalized reads counts (RPM) were generated by sRNABench
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM and read count values for each mRNA sample, and RPM for each miRNA sample.

source_name: Retinal epithelial cells

growth_protocol: Human primary Retinal Pigmented Epithelium (hpRPE) cells were purchased from Sciencell (6540). Cells were seeded in transwells (Costar, 3450 and 3460) previously coated with Laminin 521 (BioLamina, LN521-03). During the first week EpiCM 2% FBS (Sciencell, 0010F) media was employed to allow for attachment and proliferation (Sciencell, 4101). Four days after cell seeding, samples were decreased in FBS to a concentration of 1%. At day 7, cells were transferred to a media stimulating the differentiation of the cells that was a modification of the formulation previously reported to be effective for the culture of or primary RPE cells (Maminishkis et al., 2006; Sonoda et al., 2009). This medium is made with MEM Alpha media (Sigma, M-4526) supplemented with N1 supplement at 1% concentration (Sigma, N-6530), Glutamine-Penicillin-Streptomycin 1X (Sigma, G-1146), Non-essential Amino Acid (NEAA, M-7145), Taurine 0.25 mg/mL (Sigma, T-0625), Hydrocortisone 20 µg/L (Sigma, H-03966) and Triiodo-thyronin 13 ng/L (Sigma, T-5516). To enhance the differentiation of the RPE cells we cultured the apical side of the transwells with the supplemented media and added Bovine Serum Albumin (BSA) to a concentration of 0.1% (Sigma, A-9647). The basloateral side was cultured with the supplemented media with 1% FBS instead of BSA. Cells were cultured in a humidified incubator at 37°C with 5% CO2 atmosphere.

extract_protocol:
miRNA-Seq: 1 microgram total RNA of every sample was processed following the Illumina TruSeq small RNAseq library prep protocol (cat. RS-200- 0012 – 0024). A single stranded 3’-RNA adapter and a single stranded 5’-RNA adapter were ligated to the total RNA of all samples. After reverse transcription, PCR-amplification of the resulting cDNA was performed using a unique primer pair for each sample. Each library was quantified before gel-purification based on Kapa® quantification (Kapa Biosystems®, cat KK4835) using 3 independent 10 -6 dilutions. The concentrations ranged 1.3-2.9 microgram cDNA with an average of 2.1 microgram. The fragment size distribution of each library was quality-controlled using the Agilent Tapestation® 2200. The 20 libraries were pooled and electrophoresed on a 10% acrylamide gel for purification of fragments spanning 140-160 base pairs. This fragment size covers the adaptor-ligated mature miRNAs, where the adaptors account for 120 bp. The content of this extract was quality-controlled using the Agilent Tapestation® 2200. The average library size was 150 bp. The concentration was determined with the Kapa® library quantification kit (Kapa Biosystems®, cat KK4835) using 3 independent 10 -6 dilutions of the gel-purified library pool. The concentration was normalized to 2nM, spiked in with 10% PhiX library and loaded onto two flow cell lanes of a rapid HiSeq2500 run at a concentration of 13 pM. Each template molecule was clonally amplified using a Cbot2® system (Illumina). Sequencing by synthesis was performed on the Illumina HiSeq2500®, using a strategy of 50bp single-end. The total read depth ranged 4.5-13.3 million reads per sample, with an average of 8.4 million reads after subtracting off-target sequences.
After cell lysis and total RNA extraction in phenol/chloroform, the aqueous phase was processeded using the RNeasy® Mini Kit (QIAGEN) with DNAse digestion as per the manufacturer’s instructions

tag: tissue

value: Retinal epithelial cells

value: differentiation day 35


title: 38_28d miRNA-Seq

value: differentiation day 28


title: 49_35d miRNA-Seq


title: 40_28d miRNA-Seq


title: 25_21d miRNA-Seq

value: differentiation day 21


title: 28_21d miRNA-Seq


title: 17218.FLP_CD25+_PU1WTHA_aPU1-ChIP-seq-rep1

first: Ellen

last: Rothenberg

institute: California Institute of Technology

value: Lin- FLP derived CD25+ cells


title: 52_35d miRNA-Seq


title: 18_14d miRNA-Seq

value: differentiation day 14


title: A549_control


title: 37_28d miRNA-Seq


title: 17_14d miRNA-Seq


title: 14_14d miRNA-Seq


title: 27_21d miRNA-Seq


title: 13_14d miRNA-Seq


title: 4_7d miRNA-Seq

value: differentiation day 7


title: 50_35d miRNA-Seq


title: 39_28d miRNA-Seq