title: E11F_MNase_INP

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

data_processing:
Covaris sheared single-end ChIP-seq reads were aligned to the reference genome (dmel release 6) using Bowtie2 (version 2.2.9) and were filtered using samtools with parameter -q 2. MNase-based paired-end ChIP-seq reads were concordantly aligned using Bowtie2 with distinguishing sub- (parameters: -I 10 -X 130) or mono-nucleosomal (-I 130 -X 220) fragments and were filtered using samtools with parameter -q 12.
Reads were processed and normalized (to total number of reads and to input) by Homer Software package (Heinz et al. 2010). Peak calling was performed on pooled replicates by Homer findPeaks tool with parameters -style histone -size 1000 -F 2 for H4K16ac, H3K36me3 covaris ChIP; -size 2000 -F 2 for MSL2 and  -size 1000 -F 2.5 for MOF and H4K16ac MNase mono-nucleosomal fragments or with -style factor -size 200 -F 6 for MSL2 sub-nucleosomal fragments.
Genome_build: dm6
Supplementary_files_format_and_content: BED format: called peaks on pooled replicates. BEDGRAPH: ChIP-seq profiles normalized to total number of reads and to corresponding input in each replicate

organism: Drosophila melanogaster

source_name: Embryo 11-12h

extract_protocol:
1 g embryos were washed in 50 mL PBSTx-0.01% (PBS/0.01% Triton X-100 ) and resuspended in 10 mL fixation solution (50 mM Hepes pH 8.0, 100 mM NaCl, 1 mM EDTA, and 0.5 mM EGTA)/3.7% formaldehyde (Merck, Cat. No. 1040031000). After addition of 30 mL n-heptane, embryos were rigorously shaken for 1 min and incubated on a rotating wheel at room temperature for 13.5 min. Following a spin at 2000 g for 1 min, cross-linking was halted by addition of 50 mL PBSTx-0.01%/125 mM Glycine. After two washes with PBSTx-0.01% for 10 min each, embryos were flash-frozed and stored at -80°C until further use.  To process, frozen embryos were resuspended in 10 mL Homogenization Buffer (15 mM Hepes pH 7.6, 10 mM KCl, 2 mM MgCl2, 0.1 mM EDTA, 0.5 mM EGTA, 350 mM sucrose, 1 mM DTT, 0.2 mM PMSF, Roche cOmplete Protease inhibitor without EDTA) and dounced 20 times with a loose pestle and 20 times with a tight pestle before being spun down at 170 g for 10 min at 4°C. The pellet consisting of nuclei was then resuspended in 4 mL RIPA Buffer (25 mM Hepes-NaOH pH 7.6, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 1 mM PMSF, Roche cOmplete Protease inhibitor without EDTA). Fragmentation of chromatin was done either by treatment with the MNase enzyme (Sigma, Cat. No. N5386) or sonication shearing using the Covaris S220 instrument. To obtain similar digestion degree, stage 5-8 embryo were digested using 0.9 units MNase/g embryo and stage 13-15 embryo were digested using 2.9 units MNase/g embryo at 37°C for 30 min, shaking. Reaction was stopped by the addition of EDTA to a final concentration of 10 mM. Additional mechanical shearing was done by passing lysate through a 27G needle 15 times. Alternatively, sonication was performed at 100 W Peak Power, 20% Duty Factor, 200 Cycles/Burst for 20 min. Thereafter, soluble chromatin was retrieved by centrifugation at 15000 g for 15 min at 4°C. Chromatin fragment size distribution was evaluated on a Bioanalyzer (Agilent). 1-2 µg soluble chromatin was used as input for each ChIP. In short, pre-cleared soluble chromatin was incubated with antibody in RIPA buffer overnight and retrieved by incubation with 50% slurry mix of protein A+G (1:1) sepharose beads. Reversal of cross-linking was done by an overnight incubation, shaking at 65°C, followed by an incubation with 1 µg RNase for 30 min at 37°C and with 0.1% SDS/1 µg Proteinase K for 1.5 hrs at 55°C. DNA was then purified by phenol-chloroform extraction using MaXtract tube (Qiagen, Cat. No. 129046).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New Englands Biolab, E7654).

tag: chromatin

value: MNase

tag: ChIP

value: Input


title: E11E_MNase_INP

status: Public on Jun 28 2019

type: SRA

city: Munich

country: Germany

library_source: genomic

molecule: genomic DNA


title: E11D_MNase_INP


title: RNA-seq, RPE, CRISPRa, PTN, rep2 [4862_3_plb162_ACTTGAA]

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

library_source: transcriptomic

data_processing:
Reads were aligned to hg19  using TopHat version 2.1, with Ensembl genome build 75.
Genome_build: GRCh37.75

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were cultured according to 4DNucleome SOP, https://www.4dnucleome.org/cell-lines.html

extract_protocol: total RNA was extracted using TRIsure and selected for polyadenylated fraction

treatment_protocol: sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.

tag: cell line

tag: genotype/variation

value: stably expressing SunTag-CRISPRa

tag: transfected protein

value: PTN


title: RNA-seq, RPE, CRISPRa, MLK4, rep2 [4862_8_plb182_GTTTCGG]


title: RNA-seq, RPE, CRISPRa, GRID2, rep2 [4862_6_plb171_GGCTACA]


title: RNA-seq, RPE, CRISPRa, PCNX2, rep1 [4861_7_plb181_AGTCAAC]


title: RNA-seq, RPE, CRISPRa, MLK4, rep1 [4861_8_plb182_AGTTCCG]


title: RNA-seq, RPE, CRISPRa, PTN, rep1 [4861_3_plb162_ACAGTGA]


title: RNA-seq, RPE, CRISPRa, PCNX2, rep2 [4862_7_plb181_GTGGCCT]


title: E03D_MNase_INP

source_name: Embryo 3-4h


title: E11D_MNase_H4K16ac

value: H4K16ac (EMD Millipore, Cat. No. 07-329)


title: E03F_MNase_H4K16ac


title: E11E_MNase_MOF

value: MOF (Becker lab stock)


title: E03F_MNase_MOF


title: E03E_MNase_MOF


title: E11E_MNase_H4K16ac


title: E03D_MNase_MOF


title: E03D_MNase_H4K16ac


title: E03E_MNase_H4K16ac


title: E11F_MNase_MOF


title: RNA-seq, RPE, CRISPRa, GRID2, rep1 [4861_6_plb171_CTTGTAA]


title: E11F_MNase_H4K16ac


title: E03F_MNase_INP


title: E03E_MNase_INP


title: RNA-seq, RPE, CRISPRa, CCSER1, rep2 [4862_5_plb170_TAGCTTA]


title: E8G_rnaseq

data_processing:
Paired-end RNA-seq reads were aligned to the reference genome (dmel release 6) using STAR (version 2.5.3a) with the parameter --outFilterMultimapNmax 1.
Genic reads were counted using STAR --quantMode GeneCounts and the Flybase GTF annotation (dmel-all-r6.17).
Genome_build: dm6
Supplementary_files_format_and_content: TAB: genic read counts.

molecule: total RNA

source_name: Embryo

extract_protocol:
RNA-seq on individual embryos was described previously in Scacchetti et al. 2018. Briefly, embryos were hand-picked from collection plates and soaked in a drop of Voltalef 10 S halocarbon oil (Lehman and Voss Co.). Stages were determined by morphological features under stereomicroscope. Embryos were smashed with a needle into 200 µl lysis buffer (Agencourt RNAdvance Tissue kit, Beckman Coulter, Cat. No. A32645) and 10 μl 1:100 ERCC Spike-in RNA mix was added (Ambion, Cat. No. 4456740). RNA was extracted from the lysate following the manufacturers protocol with volume adjustment.
Ribosomal RNA was depleted using rRNA depletion kit (human/mouse/rat) (New Englands Biolab, Cat. No. E6310). Directional (except 8 embryos non-directional) libraries were prepared using NEBnext Ultra RNA Library Prep kit for Illumina (New Englands Biolab, Cat. No. E7530S) following the recommended protocol. In total 54 embryos from 8 stages were sequenced on an Illumina HiSeq1500 instrument in paired-end mode

tag: Stage

value: Stage 15

tag: tissue

value: embryo


title: E8H_rnaseq


title: E8I_rnaseq


title: E11D_MNase_MOF


title: E8F_rnaseq


title: RNA-seq, RPE, CRISPRa, CCSER1, rep1 [4861_5_plb170_CAGATCA]


title: RNA-seq, RPE, CRISPRa, ADAM22, rep2 [4862_10_plb187_GAGTGGA]


title: E8D_rnaseq


title: RNA-seq, RPE, CRISPRa, ABCB1, rep2 [4862_9_plb186_CGTACGT]


title: E8B_rnaseq


title: RNA-seq, RPE, CRISPRa, ADAM22, rep1 [4861_10_plb187_CCGTCCC]


title: RNA-seq, RPE, CRISPRa, ABCB1, rep1 [4861_9_plb186_ATGTCAG]


title: RNA-seq, RPE, CRISPRa, ctrl, rep2 [4862_1_CM1502_ATCACGA]

value: ctrl


title: E8A_rnaseq


title: RNA-seq, RPE, CRISPRa, ctrl, rep1 [4861_1_CM1502_CGATGTA]


title: E7G_rnaseq

value: Stage 13


title: DamID, Dam-LMNB1, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2

description: 4791_38_RPE_Plb184_Plb185_Plb186_Plb187_DL_CCTCCT_S38

data_processing:
Data analysis of DamID samples: First, the constant DamID adapter was trimmed from the 65 bp single-end reads (with cutadapt 1.11 and custom scripts). The remaining gDNA starting with GATC was mapped to hg19 with bowtie2 2.2.6. Uniquely mapped reads (filtered for bowtie’s XS-tag) were counted to GATC fragments.
Genome_build: hg19 for homo sapiens samples, mm10 for mus musculus samples

extract_protocol:
sgRNAs were cloned into Lentiguide-Puro vector (Addgene#52963) using restriction enzyme BsmBI and Lentivirus was prepared. CRISPRa RPE cells were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell lines. DamID-seq was performed as described in (Brueckner et al. 2016) with slight modifications. Instead of plasmid transfections, Dam-LMNB1 or Dam were added by Lentiviral transduction. Three days after infection, cells were collected for gDNA isolation. gDNA was pre-treated with SAP (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 1 h followed by heat inactivation at 65°C for 20 min to remove signal from apoptotic fragments. gDNA was digested with DpnI (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 8 h followed by heat inactivation at 80 °C for 20 min. Fragments were ligated to 12.5 pmol DamID adapters using T4 ligase (2.5 U, New England Biolabs) in T4 ligase buffer in a total volume of 20 µl incubated at 16 °C for 16 h. The reaction was heat inactivated for 10 min at 65 °C. Products were then digested with DpnII to remove partially methylated fragments. DpnII buffer and DpnII (10 U, New England Biolabs) were added in a total volume of 50 µl and incubated at 37 °C for 1 h. 8 µl of DpnII-digested products was amplified by PCR with MyTaq Red Mix (Bioline) and 2.5 µM primers Adr-PCR-Rand1 in a total volume of 40 µl. PCR settings were 8 min at 72 °C (1×) followed by 20 s at 94 °C, 30 s at 58 °C, 20 s at 72 °C (24× for Dam, 28x for DamLMNB1 samples) and 2 min at 72 °C (1×). Remaining steps were performed as previously described.
DamID-seq was performed as described in (Brueckner et al. 2016) with slight modifications. Instead of plasmid transfections, Dam-LMNB1 or Dam were added by Lentiviral transduction. Three days after infection, cells were collected for gDNA isolation. gDNA was pre-treated with SAP (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 1 h followed by heat inactivation at 65°C for 20 min to remove signal from apoptotic fragments. gDNA was digested with DpnI (10 U, New England Biolabs) in CutSmart buffer in a total volume of 10 µl at 37 °C for 8 h followed by heat inactivation at 80 °C for 20 min. Fragments were ligated to 12.5 pmol DamID adapters using T4 ligase (2.5 U, New England Biolabs) in T4 ligase buffer in a total volume of 20 µl incubated at 16 °C for 16 h. The reaction was heat inactivated for 10 min at 65 °C. Products were then digested with DpnII to remove partially methylated fragments. DpnII buffer and DpnII (10 U, New England Biolabs) were added in a total volume of 50 µl and incubated at 37 °C for 1 h. 8 µl of DpnII-digested products was amplified by PCR with MyTaq Red Mix (Bioline) and 2.5 µM primers Adr-PCR-Rand1 in a total volume of 40 µl. PCR settings were 8 min at 72 °C (1×) followed by 20 s at 94 °C, 30 s at 58 °C, 20 s at 72 °C (24× for Dam, 28x for DamLMNB1 samples) and 2 min at 72 °C (1×). Remaining steps were performed as previously described.

treatment_protocol: RPE-1 cells: sgRNAs were cloned into Lentiguide-Puro vector (Addgene #52963) using restriction enzyme BsmBI, and Lentivirus was prepared. RPE-1 cells stably expressing SunTag-CRISPRa were infected with LentiGuide virus and selected with 10 µg/µl Puromycin for one week to obtain stable polyclonal cell pools.

tag: genotype/cell type

value: RPE-1 cell line stably expressing SunTag-CRISPRa


title: DamID, Dam-LMNB1, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1

description: 4711_36_Plb184_Plb185_Plb186_Plb187_DL_CCGAAG_S88


title: E7I_rnaseq


title: Ventricle, 0 Gy Proton irradiation biol rep 1

city: Portland

first: Soren

last: Impey

state: OR

address: 3181 SW Sam Jackson Park Rd, LBRB Rm 709

department: Dept of Pediatric

country: USA

institute: OHSU

data_processing:
Library strategy: 5hmC DIP-Seq
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
Reads were trimmed to 44 bases (first 4 bases were discared, next 44 were kept, and remaining bases were also discarded).
Trimmed reads were aligned to mm9 with Bowtie version 1.0.0 (Up to 3 mismatches were allowed, but unique best matches were required.)
Peaks were called in all samples and merged to create a common set of regions to analyze. Aligned sequnce tags in these regions were counted for each sample to create a count matrix for enriched regions.
Genome_build: mm9
Supplementary_files_format_and_content: There are two supplementary files per sample.  The *.bw files are UCSC bigWig format and represent the aligned tag density for each sample in a set of merged peaks from the whole experiment (all four samples).  The *_MergedPeakCounts.bed files are 5 field bed format with the name set to a sequencial number and the score set to the un-normalized tag counts for each merged peak region (suitable for count based tools such as DESeq2).

organism: Mus musculus

source_name: 5hmC DIP-Seq of 0 Gy (sham) irradiated ventricle tissue

extract_protocol:
Qiagen All-prep DNA/RNA kit
Libraries were made using Illumina TrueSeq DNA Sample Prep Kits.

treatment_protocol: Mice were exposed to 0 Gy (sham) or 1 Gy of Proton radiation.

tag: strain

tag: treatment

value: 0 Gy Proton irradiation

value: Ventricle


title: Ventricle, 0 Gy Proton irradiation biol rep 2


title: Ventricle, 1 Gy Proton irradiation biol rep 2

source_name: 5hmC DIP-Seq of 1 Gy irradiated ventricle tissue

value: 1 Gy Proton irrdadiation


title: E7D_rnaseq


title: Ventricle, 1 Gy Proton irradiation biol rep 1


title: E8C_rnaseq


title: E7C_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1+GRID2, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, ZNF804B, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, ZNF804B


title: DamID, Dam-LMNB1, RPE, CRISPRa, ZNF804B, rep1


title: E7H_rnaseq


title: PNPase mitochondria 1

city: Solna

first: Florian

middle: Andreas

last: Schober

address: Solnavägen 9

department: Department of Medical Biochemistry and Biophysics (MBB)

country: Sweden

institute: Karolinska Institutet

data_processing:
Transcripts per million (TPM) values were determined by quasi-mapping of paired-end reads with salmon v0.11.3 (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Meth. 2017;14: 417–419. doi:10.1038/nmeth.4197) against a cDNA library of BDGP6 (release 94).
Genome_build: BDGP6 (release 94)
Supplementary_files_format_and_content: TPM

source_name: mitochondria

growth_protocol: All genomically engineered fly lines were maintained and experiments performed at 25°C and 60% humidity on a 12h:12h light:dark cycle and fed on a standard yeast–sugar–agar (10-5-1) medium.

extract_protocol:
DsRNA-seq was performed as described previously (Dhir A, Dhir S, Borowski LS, Jimenez L, Teitell M, Rötig A, et al. Mitochondrial double-stranded RNA triggers antiviral signalling in humans. Nature. 2018;560: 238–242. doi:10.1038/s41586-018-0363-0) with slight modifications. 5μg of RNA from purified mitochondrial and cytoplasmic fractions were used for IP with anti-dsRNA J2 ab. The RNA was diluted in 1.5ml NET-2 buffer (reconstituted to 10mM MgCl2 and 0.1% NP-40) and incubated with 5μg of J2 ab bound to 50μl Protein-G beads for 2 hrs in cold room. Washings were done twice with HSWB and NET-2 buffer respectively. The bound RNA was extracted using Trizol.
100 ng of J2-IPed dsRNA were used to make the libraries according to the 565 manual of NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs). Libraries were quantified using Agilent 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced on Illumina NextSeq 550 with 42bp paired-end reads.

tag: age

value: larvae, 4dae

tag: genotype

value: ;;dmpnpase-/dmpnpase-

tag: cell type

value: mitochondria

tag: genetic background

value: wDah


title: PNPase cytoplasm 2

source_name: cytoplasm

value: cytoplasm


title: T_CCR6+_VitD_1614

type: RNA

city: Rotterdam

first: Jeroen

last: van de Peppel

address: 's Gravendijkwal 230

institute: ErasmusMC

description:
CD4+CD45RO+CCR6+CD25low/int  facs sorted cells treated with VitD from donor 2
SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted, vst transformation and a quantile normalization was applied (computed using bioconductor package lumi). Probes that were detected at least once in the experiments (illumina detection p-value <0.01), were considered to be expressed and further analyzed for differential expression using Limma.

label: biotin

source_name: CCR6+ T-Cells_VitD donor 2

label_protocol: cDNA and Biotinylated cRNA were prepared with the Illumina Totalprep RNA Amplification kit (Ambion)

growth_protocol: PBMC were isolated using a Ficoll-gradient and stored in liquid nitrogen until use. Frozen PBMC were thawed and stained with monoclonal antibodies against CD45RO (clone UCHL1), CD4 (clone RPA-T4), CCR6 (clone 11A9) (all BD Biosciences, San Diego, CA, USA), CD3 (clone UCHT1) and CD25 (clone BC96) (all Biolegend, San Diego, CA, USA) as appropriate in 0.5% BSA + 2mM EDTA in PBS. Dead cells (typically <5% of all cells) were excluded from analysis by 4'6-Diamidino-2-Phenylindole Dilactate (DAPI). For sorting CCR6+ Th memory cells, PBMC were pre-purified via automated magnetic-activated cell sorting (autoMACS; Miltenyi Biotec, Leiden, The Netherlands) using CD4 microbeads (Miltenyi Biotec) following manufacturer’s instructions. Target cells were sorted on the FACSARIA III flow cytometer (BD Biosciences)

extract_protocol: Total RNA was isolated from cells using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) following manufacturer’s instructions

treatment_protocol: Memory CCR6+ Th cells, excluding Tregs, (CD4+CD45RO+CCR6+CD25low/int) were cultured at a density of 2.5 × 10^4 cells/ml in Iscove’s Modiﬁed Dulbecco’s Medium (IMDM) supplemented with 10% fetal calf serum (FCS; Gibco, Waltham, MA, USA), 100 U/ml penicillin/streptomycin, 2mM L-glutamine (all Lonza, Verviers, Belgium), and 50µM b-mercaptoethanol (Sigma-Aldrich, St. Louis, MO, USA). Cells were stimulated with soluble 0.3µg/ml anti-CD3 and 0.4µg/ml anti-CD28 (Sanquin, Amsterdam, The Netherlands) and cultured with 100nM 1,25(OH)2D3 dissolved in 100% ethanol (Leo Pharmaceutical Products, Ballerup, Denmark) or with an equal volume of 100% ethanol (vehicle treatment). Final ethanol concentration in medium was 0.1%.

tag: disease state

value: RA

tag: individual

value: donor 2

value: CCR6+ T-cell

value: VitD


title: PNPase cytoplasm 1


title: T_CCR6+_VitD_1811

description:
CD4+CD45RO+CCR6+CD25low/int  facs sorted cells treated with VitD from donor 3
SAMPLE 6

source_name: CCR6+ T-Cells_VitD donor 3

value: donor 3


title: T_CCR6+_1811

description:
CD4+CD45RO+CCR6+CD25low/int  facs sorted cells treated with vehicle from donor 3
SAMPLE 5

source_name: CCR6+ T-Cells_EtOH donor 3

value: vehicle


title: T_CCR6+_VitD_1588

description:
CD4+CD45RO+CCR6+CD25low/int  facs sorted cells treated with VitD from donor 1
SAMPLE 2

source_name: CCR6+ T-Cells_VitD donor 1

value: donor 1


title: E7F_rnaseq

value: Stage 13

value: embryo


title: DamID, Dam-LMNB1, RPE, CRISPRa, TRAM1L1, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, TRAM1L1

value: RPE-1 cell line stably expressing SunTag-CRISPRa


title: T_CCR6+_1614

description:
CD4+CD45RO+CCR6+CD25low/int  facs sorted cells treated with vehicle from donor 2
SAMPLE 3

source_name: CCR6+ T-Cells_EtOH donor 2


title: Control mitochondria 2


title: DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1+GRID2, rep2


title: DamID, Dam-LMNB1, RPE, CRISPRa, TRAM1L1, rep1


title: T_CCR6+_1588

description:
CD4+CD45RO+CCR6+CD25low/int facs sorted cells treated with vehicle from donor 1
SAMPLE 1

source_name: CCR6+ T-Cells_EtOH donor 1


title: E6H_rnaseq

value: Stage 12


title: PNPase mitochondria 2


title: Control cytoplasm 2


title: Control mitochondria 1


title: E6C_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, SOX6, rep1

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, SOX6


title: DamID, Dam-LMNB1, RPE, CRISPRa, SOX6, rep2


title: E6G_rnaseq


title: E7B_rnaseq


title: E7A_rnaseq


title: E6B_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, PTN, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, PTN


title: Control cytoplasm 1


title: E5I_rnaseq

value: Stage 10


title: Repli-seq, late, RPE, CRISPRa, CCSER1+GRID2, rep2

data_processing:
Data analysis of RepliSeq samples: Repi-seq reads from early and late replicating fraction were processed in the same way as DamID reads in this study, i.e., they were mapped to GATC fragments.
Genome_build: hg19

extract_protocol: RepliSeq was performed as described in Marchal et al. 2018, PMID 29599440; Genome-wide analysis of replication timing by next-generation sequencing with E/L Repli-seq. Nat Protoc 13, 819-839 (2018).

value: SunCas CRISPRa RPE


title: DamID, Dam-LMNB1, RPE, CRISPRa, PCNX2, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, PCNX2


title: E6D_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, PCNX2, rep1


title: Repli-seq, late, RPE, CRISPRa, GRID2, rep2


title: Repli-seq, late, RPE, CRISPRa, PTN, rep1

value: PTN


title: E5F_rnaseq


title: Repli-seq, late, RPE, CRISPRa, GRID2, rep1


title: E5H_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, NLGN1, rep1

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, NLGN1


title: E5G_rnaseq

source_name: Embryo


title: Repli-seq, late, RPE, CRISPRa, PTN, rep2


title: siPaf1_Spt6_ChIPSeq

city: New York

first: Liming

last: H ou

institute: NYU Langone Health

data_processing:
[RNA-seq]  For RNA-seq analysis, paired-end reads were aligned using STAR aligner. Reads that were not properly paired, non-uniquely aligned, or potential PCR duplicates were removed, and the remaining reads were used for subsequent analysis. DESeq2 (1.10.1) was used to identify differentially expressed mRNA. Only genes that had both a DESeq2 adjusted p value < 0.05 and a log2 (FPKM) of at least 1 (fold change = 2) in either direction were considered as differentially expressed genes.
[ChIP-seq and MNase-seq analysis]   Reads were aligned using Bowtie2. Only reads that were properly paired and uniquely aligned were used for subsequent processing. Potential PCR duplicates were removed using Picard Suite. Reads for ChIP-seq and Proseq data were normalized per kilobase per million for data visualization in IGV.
[ATACseq]  For ATAC-seq analysis, raw reads were aligned to the mm9 reference genome using Bowtie2. PCR duplicates were removed with Picard. Mitochondrial reads were removed prior to downstream analysis, and the remaining reads were corrected to account for the 9 bp insert introduced by the Tn5 transposase by offsetting the 5' ends by either +4 (for plus strand) or -5 (for minus strand).
[Pro-seq ]   Reads were aligned using Bowtie2. Only reads that were properly paired and uniquely aligned were used for subsequent processing. Potential PCR duplicates were removed using Picard Suite. Reads for ChIP-seq and Proseq data were normalized per kilobase per million for data visualization in IGV.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: mouse C2C12 myoblast cells

growth_protocol: [growth protocol]  C2C12 myoblasts (ATCC, Cat# CRL-1772) were grown in DMEM (Corning, Cat #15-013-CV) supplemented with 100 IU penicillin, 100 μg/ml streptomycin, 2 mM L-Glutamine (Thermo Fisher, Cat#25030081), and 10 % fetal bovine serum (Thermo Fisher, Cat# MT35011CV). All cells were cultured at 37°C under 5% (vol/vol) CO2. Paf1 inducible KO clones were maintained in 1 mg/ml doxycycline (Dox).

extract_protocol:
[ATAC-seq extract and library construction protocol]   ATAC-seq was performed as described previously (1). Briefly, 500,000 cells were harvested and washed with 500 μl cold PBS and resuspended in 500 μl cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40), and nuclei were pelleted with low speed centrifugation (500g, 4°C, 10 min). Nuclei from 50,000 cells were resuspended in 25 μl TD Buffer (10 mM Tris-HCl pH 7.5, 10 mM MgCl2, 10% dimethlyformamide), and 2.5 μl Tn5 Transposase (Illumina, Cat #FC-121-130) and incubated at 37°C for 30 min. Fragmented DNA was purified using a MinElute kit (Qiagen, Cat#28206), and libraries were generated by PCR using NEB Next High-Fidelity 2x PCR Master Mix (NEB, Cat#M0541). An appropriate number of PCR cycles was determined by qPCR as described (2). Tagmentation was confirmed via Tapestation. Libraries were sequenced on HiSeq 2500 with paired-end reads (51bp).
[ssRNA-seq extract and library construction protocol]  TRIzol (Thermo Fisher, Cat# 15596018) was used to isolate total RNA according to the manufacturer’s instructions. For RNA-seq, genomic DNA was removed from total RNA using the TURBO DNA-free™ Kit (Thermo Fisher, Cat#AM1907), the quality of RNA was assessed using Agilent High Sensitivity RNA ScreenTape (Agilent, Cat#5067-5579), 2 μg of total RNA (with RIN® > 8) was depleted of ribosomal RNA using a Ribo-Zero Gold rRNA Removal Kit (H/M/R) (Illumina, Cat# MRZG126) according to manufacturer's instructions, and RNA was purified using RNA Clean & Concentrator-5 kit (Zymo Research, Cat#R1015). Purified mRNA was fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB, Cat#E6150S1) at 94°C for 5 min followed by purification and elution into 17.5 μl H2O. Dephosphorylation of the 3’phosphate group was performed with shrimp alkaline phosphatase (SAP) (Worthington, Cat#M0371S), followed by inactivation of phosphatase. Phosphorylation of RNA was performed with T4 Kinase (NEB, Cat# M0201S). Strand-specific cDNA libraries were prepared using NEBNext® Multiplex Small RNA Library Prep kit for Illumina (NEB, Cat#E7300S) according to manufacturer’s instructions. Libraries were quantified using Qubit dsDNA HS assay kit (Thermo Fisher, Cat#Q32854), and the quality and average size of the libraries were assessed using Agilent D1000 ScreenTape (Agilent, Cat#5067-5582) on the Agilent 2200 Tapestation. Paired-end sequencing was performed using NextSeq 500/550 High Output v2 kit (75 cycles) (Illumina, Cat# FC-404-2005) on NextSeq 550 System.
[ChIP-seq extract and library construction protocol]  ChIP and ChIP-seq libraries were prepared as described (Asp, P., Blum, R., Vethantham, V., Parisi, F., Micsinai, M., Cheng, J., . . . Dynlacht, B. D. (2011). Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 108(22), E149-158. doi:10.1073/pnas.1102223108) and sequenced (51 bp, single-end reads) using an Illumina HiSeq2500 machine or (37bp, paired end) using an Illumina NextSeq 500 machine
[MNase-seq extract and library construction protocol]  MNase-seq libraries were prepared as described (Asp, P., Blum, R., Vethantham, V., Parisi, F., Micsinai, M., Cheng, J., . . . Dynlacht, B. D. (2011). Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A, 108(22), E149-158. doi:10.1073/pnas.1102223108) and sequenced (51 bp, single-end reads) using an Illumina HiSeq2500 machine or (37bp, paired end) using an Illumina NextSeq 500 machine
[extract nuclei for Pro-seq ]  Nuclei were isolated from C2C12 cell as described (Core et al., 2008) with some modifications. Briefly, 3-4 15 cm2 plates of C2C12 cells (20 x106 cells) were washed twice with ice cold PBS and collected into 50 ml centrifuge tubes using a plastic cell scraper in cold room. Cells were resuspended in 5 ml of ice cold swelling buffer (20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1:10000 dilution of 20 U/μL SUPERase• In™ RNase Inhibitor) and allowed to swell on ice for 5 min. Cells were pelleted at 4 °C for 10 min (2000 rpm), cells were resuspended in 5 ml of lysis buffer tNuclei were isolated from C2C12 cell as described (5) with some modifications. Briefly, 3-4 15 cm2 plates of C2C12 cells (~ 20 x106 cells) were washed twice with ice cold PBS and collected using a cell scraper. Cells were resuspended in 5 ml of ice cold swelling buffer (20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 1:10000 dilution of 20 U/μL SUPERase In™ RNase Inhibitor) and allowed to swell on ice for 5 min. Cells were pelleted at 4 °C for 10 min (2000 rpm) and resuspended in 5 ml of lysis buffer twice (swelling buffer + 0.5 % NP40, + 10 % glycerol + 1:10000 dilution of 20 U/μL SUPERase  In™ RNase Inhibitor) and gently pipetted up and down 20 times using a p1000 tip with the end cut off to reduce shearing, the nuclei were pelleted and resuspended in 1ml Freezing buffer (50 mM Tris-HCl pH 8.3, 40 % glycerol, 5 mM MgCl2, 0.1 mM EDTA), and transferred to a 1.5 ml centrifuge tube. Nuclei were spun down and resuspended in Freezing Buffer (5x106 nuclei per 100 μl). wice (swelling buffer + 0.5 % NP40, + 10 % glycerol + 1:10000 dilution of 20 U/μL SUPERase• In™ RNase Inhibitor) and gently pipetted up and down 20 times using a p1000 tip with the end cut off to reduce shearing, the nuclei were pelleted and resuspended in 1ml Freezing buffer (50 mM Tris-HCl pH 8.3, 40 % glycerol, 5 mM MgCl2, 0.1 mM EDTA), and transferred to a 1.5 ml centrifuge tube. Nuclei were spun down and resuspended in Freezing Buffer (5x106 nuclei per 100 μl).
[Pro-seq library construction protocol]  Proseq was based on a published Proseq protocol (6) with some modifications. Nuclear run-on reactions were performed by adding 100 μl of nuclei (5x106) to 100 μl of preheated (37°C) 2x nuclear run-on (NRO) master mix (10 mM Tris-HCl, pH 8.0, 5 mM MgCl2, 300 mM KCl , 1 mM DTT, 250 mM ATP, 250 mM GTP, 50 mM biotin-11-CTP, 50 mM biotin-11-UTP, and 1% Sarkosyl), pipetting the mixture 15 times, and incubating reactions at 37°C for 5 min. Reactions were stopped with Trizol LS, and RNA was extracted once with chloroform and precipitated with ethanol (vol/vol), and the pellet was washed in 75% ethanol once and re-dissolved in DEPC-H2O. Next, RNA fragmentation was performed using base hydrolysis, biotin RNA enrichment was performed using pre-washed streptavidin beads once at room temperature for 30 min, and the beads were washed twice in ice-cold high-salt wash buffer (50 mM Tris-HCl pH 7.4, 2 M NaCl and 0.5 % (vol/vol) Triton X-100 in DEPC H2O), twice in binding buffer (10 mM Tris-HCl pH 7.4, 300 mM NaCl and 0.1 % Triton X-100), and once in low-salt wash buffer (5 mM Tris-HCl pH 7.4 and 0.1 % Triton X-100). RNA was extracted from beads using Trizol, ethanol precipitated, and dissolved in H2O. The 5' cap of RNA was removed from unhydrolyzed short nascent RNA using 5U RNA 5' pyrophosphohydrolase (RppH), and the 5' OH generated by base hydrolysis was then converted to 5' phosphate by treatment with 25U T4 polynucleotide kinase (PNK). RNA was extracted with Trizol and dissolved in H2O, and libraries were prepared using NEB Next Multiple Small RNA library Prep set for Illumina (NEB, Cat#E7300S), following manufacturer's indications. Libraries were sequenced on the Illumina NextSeq 550.

treatment_protocol:
[DRB treatment protocol ]   For Proseq experiments, DRB (Sigma, Cat# D1916) in DMSO was added to the media at a final concentration of 100 mM for indicated times (5 min, 15 min, and 30 min), and the cells were quickly washed twice with cold PBS and collected.
[siRNA KD treatment protocol ]   All siRNAs were synthesized by Dharmacon or Qiagen. Six hours before transfection, 1x105 C2C12 cells were seeded in 6-well plates and siRNAs were transfected into cells using Lipofectamine RNAiMAX (Invitrogen), at a final concentration of 50 nM. Cells were harvested 48 h post transfection.

value: wild type

value: C2C12 cells

tag: treatment condition

value: siPaf1 for 2d (final concentration of 50 nM)

tag: chip antibody

value: Rabbit polyclonal anti-Spt6 (Novus,NB100-2582)


title: Repli-seq, late, RPE, CRISPRa, CCSER1, rep2


title: E5E_rnaseq


title: siPaf1_input DNA_ChIPSeq (Spt6)

description: siPaf1_input DNA_ChIPSeq (Spt6)


title: DamID, Dam-LMNB1, RPE, CRISPRa, KIAA1804, rep2


title: DamID, Dam-LMNB1, RPE, CRISPRa, NLGN1, rep2


title: DamID, Dam-LMNB1, RPE, CRISPRa, KIAA1804, rep1


title: Repli-seq, late, RPE, CRISPRa, CCSER1, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, SLC35F3, rep1

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, SLC35F3


title: E5J_rnaseq


title: E5D_rnaseq


title: Repli-seq, late, RPE, CRISPRa, CCSER1+GRID2, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, PTN, rep1


title: Repli-seq, late, RPE, CRISPRa, ADAM22, rep2


title: siNS_Spt6_ChIPSeq

value: siNS for 2d (final concentration of 50 nM)


title: DamID, Dam-LMNB1, RPE, CRISPRa, GRID2, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, GRID2


title: E5C_rnaseq


title: E5B_rnaseq


title: siNS_input DNA_ChIPSeq (Spt6)

description: siNS_input DNA_ChIPSeq (Spt6)


title: DamID, Dam-LMNB1, RPE, CRISPRa, GRID2, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1


title: Repli-seq, late, RPE, CRISPRa, ABCB1, rep2


title: Repli-seq, late, RPE, CRISPRa, ADAM22, rep1


title: E4G_rnaseq

value: Stage 8


title: siPaf1_input DNA_H2Bub_ChIPSeq

description: siPaf1_input DNA_ChIPSeq (H2B&H2Bub)


title: siPaf1_H2Bub_ChIPSeq

value: anti-Ubiquityl Histone H2B clone 56 (Millipore, 051312 )


title: E4D_rnaseq


title: DamID, Dam-LMNB1, RPE, CRISPRa, CCSER1, rep1


title: Repli-seq, early, RPE, CRISPRa, PTN, rep2


title: DamID, Dam-LMNB1, RPE, CRISPRa, ADAM22, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, ADAM22


title: siNS_input DNA_H2Bub_ChIPSeq

description: siNS_input DNA_ChIPSeq (H2B&H2Bub)


title: Repli-seq, early, RPE, CRISPRa, PTN, rep1


title: siNS_H2Bub_ChIPSeq


title: Repli-seq, late, RPE, CRISPRa, ABCB1, rep1


title: E4B_rnaseq


title: siPaf1_ATAC-seq_rep2


title: Repli-seq, early, RPE, CRISPRa, CCSER1+GRID2, rep2


title: DamID, Dam-LMNB1, RPE, CRISPRa, ABCB1, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, ABCB1


title: E3H_rnaseq

value: Stage 6


title: siNS_ATAC-seq_rep2


title: Repli-seq, early, RPE, CRISPRa, CCSER1+GRID2, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, ABCB1, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, ADAM22, rep1


title: E3G_rnaseq


title: Repli-seq, early, RPE, CRISPRa, GRID2, rep2


title: siPaf1_ATAC-seq_rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, control, rep2

source_name: DamID, Dam-LMNB1, RPE, CRISPRa, control


title: E4H_rnaseq


title: Repli-seq, early, RPE, CRISPRa, GRID2, rep1


title: siNS_ATAC-seq_rep1


title: E3D_rnaseq


title: siPaf1_MNase-seq


title: E3C_rnaseq


title: Repli-seq, early, RPE, CRISPRa, CCSER1, rep2


title: DamID, Dam, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep2

description: 4791_18_RPE_Plb184_Plb185_Plb186_Plb187_D_ACAGCA_S23


title: Repli-seq, early, RPE, CRISPRa, CCSER1, rep1


title: DamID, Dam, RPE, CRISPRa, ABCB4+ABCB1+ADAM22+RUNDC3B, rep1

description: 4711_18_Plb184_Plb185_Plb186_Plb187_D_ACAGCA_S74


title: E4C_rnaseq


title: Repli-seq, early, RPE, CRISPRa, ADAM22, rep2


title: E2I_rnaseq

value: Stage 5


title: LN-scOVAscCpG-AVG

city: Vancouver

first: Jan

middle: Peter

last: Dutz

state: BC

address: 950 West 28th Avenue

department: Dermatology & Skin Science

country: Canada

institute: University of British Columbia

description:
Average (mathematical) of Treatment 2 replicates 1-3
scOVAscCpG_AVG

data_processing:
Raw data analyzed on the QIAGEN website under the GeneGlobe Data Analysis Center (http://www.qiagen.com/us/shop/genes-and-pathways/data-analysis-center-overview-page/). Raw Ct values of target genes (CtTarget) for samples from individual mice were entered into the online program. Average CtTarget  of the three biological replicates was first computed for each target gene (AvgCtTarget). Then using beta-actin (Actb) as the housekeeping gene for data normalization, 2^-ΔCt was calculated, where -ΔCt = -(AvgCtTarget − AvgCtActb). Fold change data of different treatment groups (Test1/Test2) was calculated as 2^-ΔCtTest1 / 2^-ΔCtTest2]
non-normalized file reports CtTarget:  Raw Ct values for target genes of individual biological replicates
non-normalized file also reports AvgCtTarget:  Average Ct values of biological triplicates for each target gene
Matrix normalized file reports 2^-ΔCt: normalized signal against the housekeeping gene beta-actin (Actb) using average Ct of biological triplicates (AvgCt), where -ΔCt = -(AvgCtTarget − AvgCtActb)
Fold change file report fold change of Test1/Test2: normalized average gene expression 2^-ΔCt of samples in Test1 (2^-ΔCtTest1) divided the normalized average gene expression 2^-ΔCt of samples in Test 2 (2^-ΔCtTest2)

label: SYBR Green

source_name: skin draining lymph nodes, 24 hrs post immunization with s.c. OVA and s.c. CpG ODN1826

label_protocol: RNA was reversed transcribed into cDNA using the RT2 First Strand Kit with genomic DNA elimination (QIAGEN). Then real time PCR performed using the RT2 Profiler PCR Array Mouse Cytokines & Chemokines (QIAGEN cat# PAMM-150Z) with RT2 SYBR Green ROX qPCR Mastermix (QIAGEN) on the ABI ViiA7 system.

growth_protocol: Adult mice (6 - 12 weeks old) housed in animal facility with ad libitum food and water

extract_protocol: RNA was extracted with the RNeasy Fibrious Tissue Mini Kit with DNase I treatment (QIAGEN). RNA quality was checked by the A260/A280 ratio using NanoDrop 2000c Spectrophotometer (Thermo Fisher Scientific)

treatment_protocol: Mice administered s.c.OVA alone, s.c.OVA with s.c.CpG ODN1826, s.c.OVA with epicutaneous (e.c.) CpG ODN1826, or left unimmunized. Skin draining lymph nodes (axillary, brachial, inguinal lymph nodes) were harvested 24 hours later, and homogenized with the Retsch MM301 tissuelyser (QIAGEN)

tag: Sex

value: female

tag: developmental stage

value: adult

value: skin draining lymph nodes


title: Repli-seq, early, RPE, CRISPRa, ADAM22, rep1

tag: cell line

tag: genotype/variation


title: E3B_rnaseq

tag: Stage

value: embryo


title: DamID, Dam, RPE, CRISPRa, CCSER1+GRID2, rep1

source_name: DamID, Dam, RPE, CRISPRa, CCSER1+GRID2

value: RPE-1 cell line stably expressing SunTag-CRISPRa


title: E2J_rnaseq

tag: tissue


title: Repli-seq, early, RPE, CRISPRa, ABCB1, rep2

tag: transfected protein


title: LN-scOVAecCpG-AVG

description:
Average (mathematical) of Treatment 3 replicates 1-3
scOVAecCpG_AVG

source_name: skin draining lymph nodes, 24 hrs post immunization with s.c. OVA and e.c. CpG ODN1826

tag: strain


title: LN-scOVA-AVG

description:
Average (mathematical) of Treatment 1 replicates 1-3
scOVA_AVG

source_name: skin draining lymph nodes, 24 hrs post immunization with s.c. OVA

tag: treatment

value: 24 hrs post immunization with s.c. OVA


title: LN-naive-AVG

description:
Average (mathematical) of control replicates 1-3
Naïve_AVG

source_name: skin draining lymph nodes, naïve

value: naïve


title: E2H_rnaseq


title: E2G_rnaseq


title: Repli-seq, early, RPE, CRISPRa, ABCB1, rep1

value: SunCas CRISPRa RPE


title: DamID, Dam, RPE, CRISPRa, ZNF804B, rep2

source_name: DamID, Dam, RPE, CRISPRa, ZNF804B

tag: genotype/cell type


title: DamID, Dam, RPE, CRISPRa, ZNF804B, rep1


title: DamID, Dam-LMNB1, RPE, CRISPRa, control, rep1


title: E2F_rnaseq


title: LN-scOVAecCpG-Rep3

description:
Treatment 3, replicate 3
scOVAecCpG_3

value: 24 hrs post immunization with s.c. OVA and e.c. CpG ODN1826


title: siNS_MNase-seq

value: wild type

value: C2C12 cells


title: LN-scOVAscCpG-Rep3

description:
Treatment 2, replicate 3
scOVAscCpG_3

value: 24 hrs post immunization with s.c. OVA and s.c. CpG ODN1826


title: E2E_rnaseq


title: HNF4alpha12-GFP, replicate 3 [A12N3]

city: Sherbrooke

first: Francois

last: Boudreau

state: Quebec

address: 3201 rue Jean-Mignault

department: Anatomie et biologie cellulaire

institute: Université de Sherbrooke

description:
processed data file:
HNF4A12.tsv

data_processing:
FASTQ files were filtered using Trimmomatic 0.36 (PE ILLUMINACLIP:adapters.fa:2:30:10 LEADING:25 TRAILING:25 MINLEN:45), and the quality was assessed with FastQC 0.11.5. The adapter fasta file contains the two NEBNext dual sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Complete read pairs were aligned and quantified on a human transcriptome using Kallisto 0.44.0 (index built with –kmer-size=31). The transcriptome was generated with gffread, using the GRCh38.p12 genome and the latest RefSeq annotation (NCBI Homo sapiens Annotation Release 109).
Differential expression was calculated using DESeq2 1.22.2. All isoforms were individually compared to the empty control.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Results from each isoform are presented in a different file. The first three columns are expressions (in TPM) from the Kallisto output. The fourth column is the gene symbol. The other columns are the standard output from DESeq2. The empty control (A0) does not have results from DESeq2

source_name: Cell line

growth_protocol: Cell were grown in DMEM 10% FBS containing penecillin and streptomycin. Depending on the cell line, blasticidin, zeocin and hygromycin was added or not to culture media in order to maintain the constructs. Cells were cultivated at 37oC in an atmosphere containing 5% carbon dioxide (CO2) and kept at sub-confluency.

extract_protocol:
Total RNA were extracted from cells using QIAGEN RNeasy mini kit.
The mRNA enrichment was performed using the NEBNext Poly(A) Magnetic Isolation Module (New England BioLabs). cDNA synthesis was achieved with the NEBNext RNA First Strand Synthesis and NEBNext Ultra Directional RNA Second Strand Synthesis Modules (New England BioLabs). The remaining steps of library preparation were done using and the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs).

treatment_protocol: To induced the expression of HNF4alpha's isoforms, cells were incubated for 48 hours in DMEM 10% FBS +Pen/Strep containing 2.5 ug/ml of doxycyclin. The selection antibiotics hygromicin B, blasticidin S and zeocin normally used to maintain the cell lines were removed from media upon induction of HNF4alpha's isoforms expression. Empty control cells were treated the same way as the ones containing the HNF4alpha's constructs.

value: Colorectal cancer cell

tag: hnf4alpha isoforms

value: Isoform 12

tag: growth media

value: DMEM 10%, Penecillin (100U/ml), Streptomycin (100 ug/ml), Blasticidin S (5 ug/ml), Hygromycin B (100 ug/ml).


title: HNF4alpha12-GFP, replicate 2 [A12N2]

description:
processed data file:
HNF4A12.tsv

tag: cell type


title: DamID, Dam, RPE, CRISPRa, TRAM1L1, rep1

source_name: DamID, Dam, RPE, CRISPRa, TRAM1L1


title: DamID, Dam, RPE, CRISPRa, CCSER1+GRID2, rep2


title: HNF4alpha12-GFP, replicate 1 [A12N1]

description:
processed data file:
HNF4A12.tsv


title: E2D_rnaseq


title: E2C_rnaseq


title: LN-scOVA-Rep3

description:
Treatment 1, replicate 3
scOVA_3


title: LN-naive-Rep3

description:
Control, replicate 3
Naïve_3


title: HNF4alpha11-GFP, replicate 3 [A11N3]

description:
processed data file:
HNF4A11.tsv

value: Isoform 11


title: DamID, Dam, RPE, CRISPRa, SOX6, rep2

source_name: DamID, Dam, RPE, CRISPRa, SOX6


title: DamID, Dam, RPE, CRISPRa, SOX6, rep1


title: E2B_rnaseq

source_name: Embryo

value: Stage 5


title: LN-scOVAecCpG-Rep2

description:
Treatment 3, replicate 2
scOVAecCpG_2

value: female


title: LN-scOVAscCpG-Rep2

description:
Treatment 2, replicate 2
scOVAscCpG_2

value: adult


title: DamID, Dam, RPE, CRISPRa, SLC35F3, rep1

source_name: DamID, Dam, RPE, CRISPRa, SLC35F3


title: HNF4alpha11-GFP, replicate 1 [A11N1]

description:
processed data file:
HNF4A11.tsv


title: LN-scOVA-Rep2

description:
Treatment 1, replicate 2
scOVA_2

value: skin draining lymph nodes


title: HNF4alpha11-GFP, replicate 2 [A11N2]

description:
processed data file:
HNF4A11.tsv


title: E1G_rnaseq

value: Stage 4

value: embryo


title: LN-naive-Rep2

description:
Control, replicate 2
Naïve_2


title: E1H_rnaseq


title: DamID, Dam, RPE, CRISPRa, TRAM1L1, rep2

value: RPE-1 cell line stably expressing SunTag-CRISPRa


title: DamID, Dam, RPE, CRISPRa, PTN, rep1

source_name: DamID, Dam, RPE, CRISPRa, PTN


title: E1C_rnaseq


title: HNF4alpha10-GFP, replicate 2 [A10N2]

description:
processed data file:
HNF4A10.tsv

value: Isoform 10


title: DamID, Dam, RPE, CRISPRa, PCNX2, rep2

source_name: DamID, Dam, RPE, CRISPRa, PCNX2


title: LN-scOVAecCpG-Rep1

description:
Treatment 3, replicate 1
scOVAecCpG_1


title: HNF4alpha10-GFP, replicate 1 [A10N1]

description:
processed data file:
HNF4A10.tsv


title: LN-scOVAscCpG-Rep1

description:
Treatment 2, replicate 1
scOVAscCpG_1


title: HNF4alpha10-GFP, replicate 3 [A10N3]

description:
processed data file:
HNF4A10.tsv


title: E1B_rnaseq


title: HNF4alpha9-GFP, replicate 3 [A9N3]

description:
processed data file:
HNF4A9.tsv

value: Isoform 9


title: DamID, Dam, RPE, CRISPRa, NLGN1, rep2

source_name: DamID, Dam, RPE, CRISPRa, NLGN1


title: LN-scOVA-Rep1

description:
Treatment 1, replicate 1
scOVA_1

value: 24 hrs post immunization with s.c. OVA


title: LN-naive-Rep1

description:
Control, replicate 1
Naïve_1

value: naïve


title: DamID, Dam, RPE, CRISPRa, NLGN1, rep1


title: DamID, Dam, RPE, CRISPRa, GRID2, rep2

source_name: DamID, Dam, RPE, CRISPRa, GRID2


title: HNF4alpha8-GFP, replicate 3 [A8N3]

description:
processed data file:
HNF4A8.tsv

value: Isoform 8


title: E03C_MNase_INP

data_processing:
Covaris sheared single-end ChIP-seq reads were aligned to the reference genome (dmel release 6) using Bowtie2 (version 2.2.9) and were filtered using samtools with parameter -q 2. MNase-based paired-end ChIP-seq reads were concordantly aligned using Bowtie2 with distinguishing sub- (parameters: -I 10 -X 130) or mono-nucleosomal (-I 130 -X 220) fragments and were filtered using samtools with parameter -q 12.
Reads were processed and normalized (to total number of reads and to input) by Homer Software package (Heinz et al. 2010). Peak calling was performed on pooled replicates by Homer findPeaks tool with parameters -style histone -size 1000 -F 2 for H4K16ac, H3K36me3; -size 2000 -F 2 for MSL2 mono-nucleosomal fragments or with -style factor -size 200 -F 6 for MSL2 sub-nucleosomal fragments.
Genome_build: dm6
Supplementary_files_format_and_content: BED format: called peaks on pooled replicates. BEDGRAPH: ChIP-seq profiles normalized to total number of reads and to corresponding input in each replicate

source_name: Embryo 3-4h

tag: chromatin

value: MNase


title: E11B_MNase_INP

source_name: Embryo 11-12h


title: E11C_MNase_INP


title: DamID, Dam, RPE, CRISPRa, PTN, rep2


title: HNF4alpha9-GFP, replicate 1 [A9N1]

description:
processed data file:
HNF4A9.tsv

value: Colorectal cancer cell


title: DamID, Dam, RPE, CRISPRa, KIAA1804, rep2

source_name: DamID, Dam, RPE, CRISPRa, KIAA1804


title: HNF4alpha8-GFP, replicate 2 [A8N2]

description:
processed data file:
HNF4A8.tsv


title: E11A_MNase_INP


title: DamID, Dam, RPE, CRISPRa, KIAA1804, rep1


title: DamID, Dam, RPE, CRISPRa, GRID2, rep1


title: HNF4alpha9-GFP, replicate 2 [A9N2]

description:
processed data file:
HNF4A9.tsv


title: EVOL_Hypoxia.r2

city: Riverside

first: Jason

last: Stajich

state: CA

address: 900 University Ave

department: Microbiology and Plant Pathology

institute: University of California-Riverside

description:
Liquid Culture Mycelium
S29
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.

data_processing:
Data were aligned to genome with GSNAP (v 2018-02-12) with splice-aware, single-ended mode
Alignments were processed with Picard (v2.14.1) to clean, sort, and assign read groups (tools CleanSam, AddOrReplaceReadGroups) (http://broadinstitute.github.io/picard/).
Sequence read counts overlapping genes were computed with featureCount tool in the Subread package (v1.6.2)
The read count table was processed in R using the DESeq2 (3.8) to identify differentially regulated genes and generate heat maps
Pipeline BASH scripts for the alignment, read count pipeline, and R analysis is available in github repository (https://github.com/stajichlab/Afum_RNASeq_hrmA; doi: 10.5281/zenodo.3257984)
Genome_build: Afumigatus_Af293 FungiDB-35
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. FPKM_Collapsed.csv = abundance measurements replicates collapsed

organism: Aspergillus fumigatus

growth_protocol: RNA-sequencing and qRT-PCR, 50 mL cultures of 106 spores/mL were grown in normoxia (21% O2) at 37 C at 200 rpm for 18 hours before being shifted to low oxygen (0.2% O2). When necessary, 25 mL of the culture was collected at 18 hours for the normoxia samples.

extract_protocol:
Mycelia from liquid shaking cultures was flash frozen (~50mg) and bead beat for 1 minute with 2.3 mm beads in 200 ul of Trisure (Bioline Reagents). Homogenate was brought to a total volume of 1 mL Trisure and then eluted using RNeasy columns (Qiagen) following manufacturer’s instructions.  5ug of RNA was DNAse treated with Ambion Turbo DNAse (Life Technologies) according to the manufacturer’s instruction
RNA-sequencing and RNA library preparation was carried out by SeqMatic LLC (Fremont, CA). DNAse treated RNA (400-600 ng/L) were sent for QC using RNA Screen Tape Analysis (Agilent) and RNA library preparation using an Illumina TruSeq Standard mRNA library 19 preparation kit with Poly A mRNA enrichment.

tag: genotype

value: strain evolved from the reference AF293

tag: oxygen

value: HYPOXIA

value: mycelia


title: E03B_MNase_INP

tag: chip antibody


title: EVOL_Hypoxia.r3

description:
Liquid Culture Mycelium
S30
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.


title: HNF4alpha8-GFP, replicate 1 [A8N1]

description:
processed data file:
HNF4A8.tsv

value: DMEM 10%, Penecillin (100U/ml), Streptomycin (100 ug/ml), Blasticidin S (5 ug/ml), Hygromycin B (100 ug/ml).


title: EVOL_Normoxia.r3

description:
Liquid Culture Mycelium
S27
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.

value: NORM


title: HNF4alpha7-GFP, replicate 3 [A7N3]

description:
processed data file:
HNF4A7.tsv

value: Isoform 7


title: EVOL_Normoxia.r2

description:
Liquid Culture Mycelium
S26
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.


title: E03A_MNase_INP


title: HNF4alpha7-GFP, replicate 2 [A7N2]

description:
processed data file:
HNF4A7.tsv


title: E11C_MNase_MSL2

description:
MSL2_E11_mono.bed
MSL2_E11_sub.bed

value: MSL2 (generated in Peter B Becker's lab )


title: DamID, Dam, RPE, CRISPRa, PCNX2, rep1


title: E11B_Mnase_MSL2

description:
MSL2_E11_mono.bed
MSL2_E11_sub.bed


title: EVOL_Normoxia.r1

description:
Liquid Culture Mycelium
S25
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.


title: DamID, Dam, RPE, CRISPRa, CCSER1, rep1

source_name: DamID, Dam, RPE, CRISPRa, CCSER1


title: DamID, Dam, RPE, CRISPRa, ADAM22, rep2

source_name: DamID, Dam, RPE, CRISPRa, ADAM22


title: HNF4alpha7-GFP, replicate 1 [A7N1]

description:
processed data file:
HNF4A7.tsv


title: DamID, Dam, RPE, CRISPRa, ADAM22, rep1


title: hrmA_REV_Hypoxia.r2

description:
Liquid Culture Mycelium
S23
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.

value: hrmAR-EV

value: hrmA (Afu5g14900) deletion complemented with EVOL20 allele (D304G) of hrmA at the native locus


title: DamID, Dam, RPE, CRISPRa, ABCB1, rep2

source_name: DamID, Dam, RPE, CRISPRa, ABCB1

value: RPE-1 cell line stably expressing SunTag-CRISPRa


title: HNF4alpha6-GFP, replicate 1 [A6N1]

description:
processed data file:
HNF4A6.tsv

value: Isoform 6


title: E11A_MNase_MSL2

description:
MSL2_E11_mono.bed
MSL2_E11_sub.bed

value: embryo


title: HNF4alpha6-GFP, replicate 3 [A6N3]

description:
processed data file:
HNF4A6.tsv


title: hrmA_REV_Normoxia.r3

description:
Liquid Culture Mycelium
S21
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.


title: E03A_MNase_MSL2

description:
MSL2_E03_mono.bed
MSL2_E03_sub.bed


title: DamID, Dam, RPE, CRISPRa, CCSER1, rep2


title: hrmA_REV_Hypoxia.r3

description:
Liquid Culture Mycelium
S24
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.


title: EVOL_Hypoxia.r1

description:
Liquid Culture Mycelium
S28
EVOL20 is an experimentally evolved strain from the reference AF293, generated following 20 passages (80 days total) of growth at 0.2% Oxygen.


title: HNF4alpha6-GFP, replicate 2 [A6N2]

description:
processed data file:
HNF4A6.tsv


title: hrmA_REV_Normoxia.r2

description:
Liquid Culture Mycelium
S20
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.


title: HNF4alpha5-GFP, replicate 2 [A5N1]

description:
processed data file:
HNF4A5_1.tsv

value: Isoform 5


title: E11B_Covaris_INP

value: Covaris


title: E03C_MNase_MSL2

description:
MSL2_E03_mono.bed
MSL2_E03_sub.bed


title: DamID, Dam, RPE, CRISPRa, control, rep1

source_name: DamID, Dam, RPE, CRISPRa, control


title: hrmA_REV_Hypoxia.r1

description:
Liquid Culture Mycelium
S22
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.


title: hrmA_REV_Normoxia.r1

description:
Liquid Culture Mycelium
S19
hrmA R-EV is the complemented hrmA (Afu5g14900) deletion in AF293 with the EVOL20 allele (D304G) of hrmA at the native locus.


title: E11A_Covaris_INP


title: E03B_MNase_MSL2

description:
MSL2_E03_mono.bed
MSL2_E03_sub.bed


title: HNF4alpha4-GFP, replicate 3 [A4N1]

description:
processed data file:
HNF4A4_1.tsv

value: Isoform 4


title: E03B_Covaris_INP


title: hrmA_OE_Hypoxia.r3

description:
Liquid Culture Mycelium
S18

value: hrmA OE

value: hrmaA overexpression


title: HNF4alpha5-GFP, replicate 1 [A5N1]

description:
processed data file:
HNF4A5_1.tsv

value: Colorectal cancer cell


title: DamID, Dam, RPE, CRISPRa, ABCB1, rep1


title: hrmA_OE_Hypoxia.r2

description:
Liquid Culture Mycelium
S17

value: HYPOXIA


title: DamID, Dam, RPE, CRISPRa, control, rep2


title: HNF4alpha4-GFP, replicate 2 [A4N1]

description:
processed data file:
HNF4A4_1.tsv


title: HNF4alpha4-GFP, replicate 1 [A4N1]

description:
processed data file:
HNF4A4_1.tsv


title: hrmA_OE_Normoxia.r3

description:
Liquid Culture Mycelium
S15

value: mycelia


title: E11A_Covaris_H3K36me3

value: H3K36me3 (abcam, Cat. No. ab9050)


title: E11B_Covaris_H3K36me3


title: hrmA_OE_Hypoxia.r1

description:
Liquid Culture Mycelium
S16


title: HNF4alpha3-GFP, replicate 3 [A3N3]

description:
processed data file:
HNF4A3.tsv

value: Isoform 3

value: DMEM 10%, Penecillin (100U/ml), Streptomycin (100 ug/ml), Blasticidin S (5 ug/ml), Hygromycin B (100 ug/ml).


title: E03A_Covaris_H3K36me3


title: HNF4alpha3-GFP, replicate 2 [A3N2]

description:
processed data file:
HNF4A3.tsv


title: hrmA_OE_Normoxia.r2

description:
Liquid Culture Mycelium
S14

value: NORM


title: hrmA_OE_Normoxia.r1

description:
Liquid Culture Mycelium
S13


title: HNF4alpha3-GFP, replicate 1 [A3N1]

description:
processed data file:
HNF4A3.tsv


title: MCF_7_E1_1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Agilent's human GXP_8X60k Array. (AMADID: 072363). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the percentile shift normalization method .

source_name: MCF7-48hr-100ug/ml- Ethanol fraction

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The HCT116 and MCF7 cell lines were grown in RPMI-1640 with L-glutamine and Sodium pyruvate at 37 degree celsius.

extract_protocol: The good quality RNA was isolated from HCT-116 and MCF-7 cell lines using the QIANGEN RNA isolation kit

treatment_protocol: Each of the cell lines were treated with 100 micrograms per microlitres of the fractions and incubated for 48 hours at 37 degree celsius.


title: MCF_7_E1


title: MCF_7_C1

source_name: MCF7-48hr-100ug/ml- Chloroform fraction


title: MCF_7_B1_1

source_name: MCF7-48hr-100ug/ml- Butanol fraction


title: Delta_hrmA_AF293_Hypoxia.r3

description:
Liquid Culture Mycelium
S12

source_name: Delta hrmA_hypoxia

value: Delta hrmA

value: hrmA deletion


title: HNF4alpha2-GFP, replicate 3 [A2N3]

description:
processed data file:
HNF4A2.tsv

source_name: Cell line

value: Isoform 2


title: MCF_7_C1_1


title: E03A_Covaris_INP


title: E11B_Covaris_H4K16ac

value: H4K16ac (EMD Millipore, Cat. No. 07-329)


title: MCF_7_B1


title: E11A_Covaris_H4K16ac

value: embryo


title: Delta_hrmA_AF293_Hypoxia.r2

description:
Liquid Culture Mycelium
S11


title: E03B_Covaris_H4K16ac


title: Delta_hrmA_AF293_Hypoxia.r1

description:
Liquid Culture Mycelium
S10


title: E03A_Covaris_H4K16ac


title: Delta_hrmA_AF293_Normoxia.r3

description:
Liquid Culture Mycelium
S9

source_name: Delta hrmA_normoxia


title: MCF_7_Control_II


title: E03B_Covaris_H3K36me3


title: HNF4alpha2-GFP, replicate 2 [A2N2]

description:
processed data file:
HNF4A2.tsv


title: HNF4alpha1-GFP, replicate 2 [A1N2]

description:
processed data file:
HNFA1.tsv

value: Isoform 1


title: RNA-Seq of pseudomonas aeruginosa:Control4

city: hefei

first: Yeye

last: zhao

state: anhui

address: qianjiang

country: China

institute: Anhui University of Chinese Medicine

description:
bacterial culture12
fpkm_Control4

data_processing:
This project uses SOAPnuke, a filtering software independently developed by huada, to make statistics and trimmomatic to filter
Clean reads after filtration are compared to the reference genome
RSEM was used to calculate the expression levels of genes and transcripts

organism: Pseudomonas aeruginosa

source_name: P. aeruginosa_control

growth_protocol: Pseudomonas aeruginosa was cultured under different conditions for 24 hours.

extract_protocol:
Raw reads are subjected to quality control, filtered clean reads are compared to a reference genome, and then RSEM is used to calculate the expression levels of genes and transcripts.
TotalRNA is treated by mRNA enrichment method or rRNA removal method, and the required RNA is obtained after purification. The obtained RNA is fragmented, reverse transcribed by random N6 primer, and then cDNA double strand is synthesized to form double stranded DNA.  The synthesized double-stranded DNA is flattened at the end and phosphorylated at the 5' end, the 3' end forms a sticky end protruding from an "A", then a bubbly joint protruding from a "T" at the 3' end is connected, the connected product is subjected to PCR amplification by a specific primer, the PCR product is thermally denatured into a single strand, and the single-stranded DNA is cyclized by a bridge primer to obtain a single-stranded circular DNA library, which is sequenced on a computer.

treatment_protocol: SH, SNH

value: no drug treatment; control

tag: treatment time


title: MCF_7_Control_I


title: HCT_116_E1

source_name: HCT_116-48hr-100ug/ml- Ethanol fraction


title: Delta_hrmA_AF293_Normoxia.r2

description:
Liquid Culture Mycelium
S8


title: E1D_rnaseq

source_name: Embryo

value: Stage 4


title: RNA-Seq of pseudomonas aeruginosa:Control3

description:
bacterial culture11
fpkm_Control3


title: HNF4alpha5-GFP, replicate 3 [A5N1]

description:
processed data file:
HNF4A5_1.tsv

value: Isoform 5


title: Delta_hrmA_AF293_Normoxia.r1

description:
Liquid Culture Mycelium
S7


title: AF293_Hypoxia.r3

description:
Liquid Culture Mycelium
S6

value: wildtype


title: RNA-Seq of pseudomonas aeruginosa:Control2

description:
bacterial culture10
fpkm_Control2


title: AF293_Hypoxia.r2

description:
Liquid Culture Mycelium
S5


title: Empty Control, replicate 3 [A0N3]

description:
Parental HCT116 Flp-In cells used for HNF4alpha's isoforms expression.
processed data file:
A0.tsv

value: Colorectal cancer cell

value: DMEM 10%, Penecillin (100U/ml), Streptomycin (100 ug/ml), Blasticidin S (5 ug/ml), Zeocin (100 ug/ml).


title: RNA-Seq of pseudomonas aeruginosa:Control1

description:
bacterial culture9
fpkm_Control1


title: HNF4alpha1-GFP, replicate 1 [A1N1]

description:
processed data file:
HNFA1.tsv


title: HNF4alpha1-GFP, replicate 3 [A1N3]

description:
processed data file:
HNFA1.tsv


title: RNA-Seq of pseudomonas aeruginosa:SNH4

description:
bacterial culture8
fpkm_SNH4

source_name: P. aeruginosa_SNH

value: SNH


title: HNF4alpha2-GFP, replicate 1 [A2N1]

description:
processed data file:
HNF4A2.tsv


title: Empty Control, replicate 1 [A0N1]


title: AF293_Hypoxia.r1

description:
Liquid Culture Mycelium
S4

value: HYPOXIA

value: mycelia


title: HCT_116_C1_1


title: RNA-Seq of pseudomonas aeruginosa:SNH3

description:
bacterial culture7
fpkm_SNH3


title: HCT_116_B1

source_name: HCT_116-48hr-100ug/ml- Butanol fraction


title: N7D

city: ShenYang

first: Li

last: Hailong

state: Liaoning

address: NO. 3-11, Wenhua Road, Heping District

institute: Northeastern University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using bowtie v0.12.2.
Genome_build: Mus_musculus.GRCm38
Genome_build: GCF_000364345.1_Macaca_fascicularis_5.0
Genome_build: Cryptococcus neoformans var. grubii H99
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include NCBI Gene IDs and reads values (raw counts) for each Sample.

organism:
Mus musculus
Cryptococcus neoformans H99

source_name: Brain RNA-seq sample, extracted from infected mouse, replicate 3

extract_protocol:
For the transcriptome analysis, mice and monkey were sacrificed at 7-day post infection. Lung and brain tissue were isolated and resuspended in RNAlater. Monkey lung tissues were removed from the chest, and cut into 0.5 cm X 0.5 cm X 0.5 cm cubes. Tissues were then processed for RNA-seq analysis. PBS treated mice and monkeys were used as RNA-seq analysis reference samples. Total RNA was isolated with Trizol. RNA library construction and sequencing were generated by using the TruSeq RNA Sample Preparation Kit based on the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: gender

value: female

tag: age

value: 6-8 weeks

value: Brain

value: infected with C. neoformans


title: HCT_116_B1_1

tag: cell line


title: LR-CL3

organism: Macaca fascicularis

source_name: Lung RNA-seq sample, extracted from uninfected Macaca fascicularis, replicate 3

value: 4-8 years

tag: tissue

value: Lung

value: uninfected


title: HCT_116_C1


title: HCT_116_E1_1


title: AF293_Normoxia.r2

description:
Liquid Culture Mycelium
S2

value: NORM


title: RNA-Seq of pseudomonas aeruginosa:SNH2

description:
bacterial culture6
fpkm_SNH2


title: AF293_Normoxia.r3

description:
Liquid Culture Mycelium
S3


title: LR-CL2

source_name: Lung RNA-seq sample, extracted from uninfected Macaca fascicularis, replicate 2


title: N7B

source_name: Brain RNA-seq sample, extracted from infected mouse, replicate 2


title: N7A

source_name: Brain RNA-seq sample, extracted from infected mouse, replicate 1


title: RNA-Seq of pseudomonas aeruginosa:SH4

description:
bacterial culture4
fpkm_SH4

source_name: P. aeruginosa_SH

value: sodium houttuyfonate (SH)


title: LR-CL1

source_name: Lung RNA-seq sample, extracted from uninfected Macaca fascicularis, replicate 1


title: F7F

source_name: Lung RNA-seq sample, extracted from infected mouse, replicate 3


title: HCT_116_Control


title: AF293_Normoxia.r1

description:
Liquid Culture Mycelium
S1


title: RNA-Seq of pseudomonas aeruginosa:SH3

description:
bacterial culture3
fpkm_SH3


title: HCT_116_Control_1


title: 99s-3

organism: Cryptococcus neoformans H99

source_name: H99 strain RNA-seq sample, replicate 3

tag: growth phase

value: logarithmic phase, OD600=1.0


title: RNA-Seq of pseudomonas aeruginosa:SNH1

description:
bacterial culture5
fpkm_SNH1


title: 99s-2

source_name: H99 strain RNA-seq sample, replicate 2


title: LR-99L2

organism:
Macaca fascicularis
Cryptococcus neoformans H99

source_name: Lung RNA-seq sample, extracted from infected Macaca fascicularis, replicate 2


title: LR-99L3

source_name: Lung RNA-seq sample, extracted from infected Macaca fascicularis, replicate 3


title: F7E

source_name: Lung RNA-seq sample, extracted from infected mouse, replicate 2


title: RNA-Seq of pseudomonas aeruginosa:SH1

description:
bacterial culture1
fpkm_SH1


title: F7D

source_name: Lung RNA-seq sample, extracted from infected mouse, replicate 1


title: 99s-1

source_name: H99 strain RNA-seq sample, replicate 1


title: Empty Control, replicate 2 [A0N2]

source_name: Cell line


title: LR-99L1

source_name: Lung RNA-seq sample, extracted from infected Macaca fascicularis, replicate 1


title: PBMCs, 24HM2

status: Public on Jun 27 2019

city: Seoul

first: Suji

last: Kim

state: Gwanak-gu

address: 1, Gwanak-ro

department: Veterinary Medicine

country: South Korea

institute: Seoul National University

data_processing:
QuantSeq 3' mRNA Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
Bowtie2 indices were either generated from genome assembly sequence or the representative transcript sequences for aligning to the genome and transcriptome.
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed based on quantile normalization method using EdgeR within R (R development Core Team, 2016) using Bioconductor (Gentleman et al., 2004).
Genome_build: canFam3
Supplementary_files_format_and_content: abundance measurement

organism: Canis lupus familiaris

source_name: canine peripheral blood mononuclear cells

extract_protocol:
total RNA was extracted from the cells using the RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s instruction.
the construction of library was performed using QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer's instructions. In brief, each 500ng total RNA were prepared and an oligo dT primer containing an Illumina compatible sequence at its 5 end was hybridized to the RNA and reverse transcri ption was performed. After degradation of the RNA template, second strand synthesis was initiated by a random primer containing an Illumina compatible linker sequence at its 5 end. T he double stranded library was purified by using magnetic beads to remove all reaction components. The library was amplified to add the complete adapter sequences required for cluster generation. The finished library is purified from PCR components. High throughput sequencing was performed as single end 75 sequencing using Next Seq 500 (Illumina, Inc., USA).
QuantSeq

value: whole blood

value: PBMC

value: 10 months old

tag: infection

value: M. avium hominissuis strain 104

tag: time


title: PBMCs, 24HM1


title: PBMCs, 24HC2

value: control


title: PBMCs, 12HC2


title: PBMCs, 12HM2


title: PBMCs, 6HM2


title: PBMCs, 12HC1


title: PBMCs, 6HM1


title: PBMCs, 6HC2


title: PBMCs, 0HM2


title: PBMCs, 0HM1


title: PBMCs, 0HC2


title: PBMCs, 0HC1


title: YY1_RBM25-KD ChIP-seq Input  rep1

city: Wuhan

first: Rui

last: Xiao

state: Hubei

address: Medical Research Institute, Wuhan University

department: Medical Research Institute

institute: Wuhan University

description: input DNA control (PE)

data_processing:
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/).
Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA;
PCR duplicates and reads of low quality were filtered;
Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold;
Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).

growth_protocol: ENCODE cell culture protocols

extract_protocol:
Nuclei were isolated and sonicated and lysates were cleared-up and applied for purification of RBP-DNA complexes with antibodies.
Libraries were constructed according to the instruction of the Illumina Preparing Samples for ChIP Sequencing.

value: Hepatocellular carcinoma


title: YY1_RBM25-KD ChIP-seq   rep2

description: ChIP-seq data (PE)

value: YY1 (Proteintech Cat# 66281-1-lg)


title: RNA-Seq of pseudomonas aeruginosa:SH2

description:
bacterial culture2
fpkm_SH2

tag: treatment


title: YY1_RBM25-KD ChIP-seq  rep1

description: ChIP-seq data (PE)


title: YY1_NC ChIP-seq Input  rep1

description: input DNA control (PE)


title: YY1_NC ChIP-seq rep2

description:
ChIP-seq data (PE)
YY1chip-NC-OPTIMAL_ppr.IDR0.02.filt.narrowPeak


title: PBMCs, 24HC1


title: PBMCs, 12HM1


title: RBM25_NC ChIP-seq Input  rep2

description: input DNA control (PE)


title: YY1_NC ChIP-seq rep1


title: RBM25_YY1-KD ChIP-seq Input  rep2

description: input DNA control (PE)


title: RBM25_YY1-KD ChIP-seq Input  rep1

description: input DNA control (PE)


title: RBM25_YY1-KD ChIP-seq  rep2

description: ChIP-seq data (PE)

value: RBM25 (Bethyl Cat# A301-068A)


title: RBM25_NC ChIP-seq rep2

description:
ChIP-seq data (PE)
RBM25chip-NC-OPTIMAL_ppr.IDR0.02.filt.narrowPeak


title: RBM25_NC ChIP-seq rep1


title: RBM25_YY1-KD ChIP-seq  rep1

description: ChIP-seq data (PE)


title: Control BL-HiC rep2

description: Hi-C data (PE)

data_processing:
Library strategy: HiC-Seq
The ChIA-PET2 software (Li et al., 2017a) was used for quality control and identification of chromatin interactions with the following parameter setting: -A ACGCGATATCTTATC -B AGTCAGATAAGATAT -s 1 -m 1 -t 4 -k 2 -e 1 -l 15 -S 500 -M "-q 0.05" –C 1.
PCA analysis is then applied to 40-kb resolution interaction matrix generated by HiC-Pro (Servant et al., 2015), and regions of continuous positive or negative PC1 values were used for the identification of A or B compartments (Heinz et al., 2010).
The interaction matrix was visualized by HiCPlotter (Akdemir and Chin, 2015).
High confident interactions were defined as those with >3 PET counts and q-value < 0.05 for downstream analysis.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: MICC

extract_protocol:
HepG2 cells were fixed with formaldehyde and isolated nuclei were digested by HaeIII. Proximity ligation was performed in the present of biotinylated bridge linker. After shearing by sonication, short DNA fragments ligated to bridge linker were purified by streptavidin beads.
Purified proximity ligation products on beads were A-tailed, adaptor-ligated, and PCR amplified. PCR products between 300-700 bp were purified as BL-Hi-C library using Ampure XP beads.
BL-HiC (Liang et al. 2017)

tag: source


title: RBM25-KD BL-HiC rep1

description: Hi-C data (PE)


title: Control BL-HiC rep1

description: Hi-C data (PE)


title: RBM25_NC ChIP-seq Input  rep1

description: input DNA control (PE)


title: RBM25-KD BL-HiC rep2

description: Hi-C data (PE)


title: YY1_RBM25-KD ChIP-seq Input   rep2

description: input DNA control (PE)


title: PBMCs, 6HC1


title: TSC B/C CTCF rep1

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

state: NC

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

description:
For processed data, reads from the two replicates were pooled to generate the wiggle files.
ctcf_101.wig

data_processing:
ChIP sequencing reads were aligned using bowtie2, using default parameters. All mm9 genome annotations were obtained from the UCSC genome browser (Casper J et al. Nucleic Acids Research 2018). Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/). Only reads that had a mapping quality greater than or equal to 30 were used.
hiddenDomains 3.0 (Starmer J, Magnuson T. BMC Bioinformatics 2016) was used to call peaks from H3K27me3 ChIP-Seq data, using input DNA sequenced from formaldehyde crosslinked TSCs or ESCs as a control. Default parameters plus max.read.count=10 were used in the main hiddenDomains.R script, and neighboring enriched bins were merged to generate the final set of H3K27me3 peaks. MACS2 (Zhang Y et al. Genome Biology 2008) was used to call peaks from all other ChIP-Seq datasets, with the same input used in hiddenDomains and parameters –broad –broad-cutoff 0.01.
CAST/EiJ pseudogenome creation and allele-specific read retention was performed as in (Calabrese et al. G3 2015; Calabrese et al. Cell 2012).
Genome_build: mm9
Supplementary_files_format_and_content: WIG files were generated from mm9 alignments, after filtering for mapping quality of greater than or equal to 30. Where indicated, the WIG file includes reads pooled from the two replicates.

source_name: F1 B/C trophoblast stem cells

growth_protocol: TSCs were cultured under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006). To deplete MEF feeder cells from TSCs prior to RNA isolation or crosslinking, TSCs were pre-plated for 40 minutes and cultured for three days in 70% MEF-conditioned TSC media supplemented with Fgf4 (25ng/ml; Invitrogen) and Heparin (1mg/ml; Sigma). This was done once for harvesting chromatin and twice before RNA isolation. For cortical neurons, embryonic day 13.5 (E13.5) to E16.5 mouse cortices were dissected and trypsinized with TrypLE express at 37 °C for 10 min. Dissociated neurons were cultured with Neurobasal medium with 5% fetal bovine serum, GlutaMAX (Invitrogen), B27 (Invitrogen) and Antibiotic-Antimycotic (Invitrogen) and changed into Neurobasal medium supplemented with 4.84 µg ml−1 uridine 5′-triphosphate (Sigma), 2.46 μg ml−1 5-fluoro-2′-deoxyuridine (Sigma,), GlutaMAX (Invitrogen), B27 (Invitrogen), and Antibiotic-Antimycotic (Invitrogen) at DIV1 and DIV3. Neurons were fixed in 10cm plates at DIV5. ESCs were cultured in media consisting of DMEM high glucose plus sodium pyruvate, 0.1 mM non-essential AA, 0.1 mM MTG, 2 mM L-glutamine, 1000 U/ml LIF (ESG1107, Millipore Sigma, St. Louis, MO) and 15% ES-qualified FBS. ESCs were maintained on gamma-irradiated feeders from CD1 embryos, plated approximately 1.5 million feeders per 10-cm plate. At the passage prior to harvesting cells for ChIP, ESCs were pre-plated for 40 minutes and cultured for two days in 70% MEF-conditioned media supplemented as above.

extract_protocol:
For all ChIPs except EZH2, cells were crosslinked in 0.6% formaldehyde. For Ezh2 ChIPs, cells were crosslinked in 1.5mM EGS (ethylene glycol bis(succinimidyl succinate); ThermoFisher Pierce) in PBS for 30 minutes and then in 0.6% formaldehyde. Whole cell lysates were sonicated and chromatin extracts were immunoprecipitated using the specified antibody.
Purified immunoprecipitated DNA was prepared for sequencing on the Illumina platform using Next Reagents (NEB).

treatment_protocol: see SAMPLES

tag: parent of origin

value: C57BL/6J mother X CAST/EiJ father

tag: passage number

tag: genotype/variation

value: wildtype

value: CTCF


title: Ctrl

city: Bethesda

first: Stefan

middle: A

last: Muljo

state: MD

address: 10 CENTER DR RM 11N306

institute: NIH/NIAID

data_processing:
Base-calling was performed with bcl2fastq v2.17
Reads were aligned to the mm10 (GRCm38) mouse reference genome using Bowtie v2.2.5 and TopHat v2.0.14 with default mapping parameters
Bigwigs coverage tracks were library-size normalized by reads per million (RPM)
Transcript expression and fold change values were calculated with Cuffdiff (Cufflinks v2.2.1) against the Ensembl GRCm38.p4 annotation
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized bigwig files and Cuffdiff tab-delimited fpkm_tracking output

source_name: 220-8 cell line, Ctrl

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center, Inc) per manufacturer's instructions.  RNA concentration was determined using the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen).  To confirm the concentration and determine the integrity of the RNA we used the Eukaryote Total RNA Nano Series II chip on a 2100 Bioanalyzer (Agilent).
RNA-seq library preparation was performed starting with 3.3 μg of total RNA using the TruSeq RNA sample prep kit following manufacturer’s protocol (Illumina)

tag: strain

value: BALB/c

value: 220-8 cell line

tag: cell line source

value: Bone Marrow-derived cell line

tag: genotype

value: WT (Puro empty vector)


title: TSC B/C CTCF rep2

tag: chip antibody


title: YY1_NC ChIP-seq Input  rep2

description: input DNA control (PE)

tag: cell type


title: KGli1_24h

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: Dropseq single cell RNA-seq

data_processing:
Paired-end sequencing reads were processed as previously described using the Drop-Seq Tools v1.12 software available in McCarroll’s lab (http://mccarrolllab.com/dropseq/). Briefly, each cDNA read (read2) was tagged with the cell barcode (the first 12 bases in read 1) and unique molecular identifier (UMI, the next 8 bases in read 1), trimmed of sequencing adaptors and poly-A sequences, and aligned to the mouse reference genome assembly (mm10) using STAR v 2.5.3a. Cell barcodes were corrected for possible bead synthesis errors using the DetectBeadSynthesisErrors program, and then collapsed to core barcodes if they were within an edit distance of 1. Digital gene expression (DEG) matrix was compiled by counting the number of unique UMIs for a given gene (as row) in a given cell (as column).
Genome_build: mm10
Supplementary_files_format_and_content: txt, UMI count matrix

source_name: Kidney Gli1+ cells

extract_protocol:
We used the DropSeq protocol described by Mackosco et al to generate the single cell transcriptomes. In brief, cells were diluted to a concentration of 100 cells/mL, and co-encapsulated with barcoded beads (ChemGenes #Macosko201110), which were diluted to a concentration of 120 beads/mL. Droplets of about 1 nL in size were generated using microfluidic polydimethylsiloxane (PDMS) co-flow devices (FlowJEM Drop-seq chips). Droplets were collected in a 50-mL RNase-free Falcon tube for a total run time of about 15 min. Droplet emulsion was aliquoted into 1 mL each of cells and beads and were broken promptly by perfluorooctanol, following which barcoded beads with captured transcriptomes were washed and spun down at 4 C. Hybridized RNA was reverse transcribed and exonuclease-treated. The beads from one run were then equally distributed into individual PCR tubes with populations of 8,000 beads/tube (~400 cells). PCR tubes were separately amplified for 4+9 PCR cycles, and the PCR products were purified by the addition of 0.6x Agencourt AMPure XP beads (Beckman Coulter #A63881). The quality of the amplified cDNA was evaluated by Bioanalyzer (Agilent 2100) on a High Sensitivity DNA chip. Only cDNA with average insertion size > 1200 bp were used for downstream library preparation and sequencing. cDNA from an estimated 5,000 cells were prepared and tagmented by Nextera XT (Illumina) using 600 pg of cDNA input. cDNA library was amplified (12 cycles) using custom primers as described (Macosko et al., 2015). Amplified libraries were purified with a 0.6x volume of AMPure XP beads and quality was measured by Bioanalyzer. Libraries with average length of ~500-700 bp were submitted to Genome Technology Access Center (GTAC) of Washington University in St. Louis and sequenced on HiSeq 2500 (Illumina).
DropSeq library preparation

treatment_protocol: Gli1+ cells were plated at a concentration of 3 × 105 cells into 10-cm3 dishes and allowed to attach overnight in regular media. The following day, cells were starved in serum-free αMEM media containing 1% pen/strep for 2 h. The cells were then treated with 1 ng/ml TGF-β for either 6 h, 12 h, or 24 h. Control cells without TGF-β were harvested after the 2-h starving period. The cells were harvested with TrypLE Select (Thermo Fisher Scientific) for 10 min at 37°C, and after 10 min, cells were further dispersed by gentle pipetting and filtered through a 40-µm cell strainer (pluriSelect). Single-cell suspension was visually inspected under a microscope, counted by hemocytometer (INCYTO C-chip), and resuspended in PBS + 0.01% BSA.

tag: gender

value: Male

value: TGF-beta, 24hrs


title: KGli1_12h

description: Dropseq single cell RNA-seq

tag: age

value: TGF-beta, 12hrs


title: KGli1_6h

description: Dropseq single cell RNA-seq

value: TGF-beta, 6hrs


title: CS3

city: London

first: Shiva

middle: M

last: Singh

state: ON

address: 1151 Richmond Street

department: Biology

institute: Western University

data_processing:
Base-calling was performed using CASAVA
Paired-end reads for each sample were quantified via pseudoalignment to version 38 of the Ensembl annotation of the mouse transcriptome using kallisto with 100 bootstrap samples taken
Differential analysis of gene expression was determined using sleuth via p-value aggregation
Genome_build: mm10
Supplementary_files_format_and_content: "tpmdata" contains the Sleuth object count matrix using normalized observations in transcripts per million for each transcript detected for sample as a comma separated values file

source_name: Hippocampus

extract_protocol:
Mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. Hippocampus was dissected, snap-frozen in liquid nitrogen, and stored at -80°C. RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) and stored at -80°C.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded total RNA Library Preparation protocol with rRNA depletion using RiboZero Gold.

treatment_protocol: C57BL/6 mice were exposed to ethanol via voluntary maternal continuous preference drinking of 10% ethanol in water throughout gestation (ethanol) or water only (control). Pups then were either exposed to maternal separation stress via 3 hours of daily isolation from dam and littermates from postnatal days 2-14 (separation) or left undisturbed with the dam (control). This protocol produced 4 experimental groups - control mice that had neither exposure (CC), mice that had just the prenatal ethanol exposure (EC), mice with just the postnatal separation (CS), and mice that had both the prenatal ethanol exposure and the postnatal separation (ES).

value: postnatal day 70

tag: prenatal treatment

tag: postnatal treatment

value: separation


title: CS2

value: control


title: CC3


title: EC3

value: ethanol


title: ES3


title: EC1


title: CC1


title: CC2


title: hLIN28A

source_name: 220-8 cell line, hLIN28A

tag: cell line


title: ES2


title: TruSeq_mRNA_experiment_3

city: Houston

first: Yue

last: Lu

state: TX

address: 1881 East Road

department: Epigenetics & Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Reads were mapped to rRNA sequences (GI numbers: 262231778, 120444901, 120444900, 328447215, 38176281 and Ensembl IDs: ENSMUST00000082388, ENSMUST00000082390, ENSMUST00000083988, ENSMUST00000157970) using Bowtie2 (version 2.1.0).
Reads that were not mapped to rRNAs were then mapped to the mouse genome (mm10) using TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M4 was enumerated using the htseq-count script within the HTSeq package (version 0.6.1) with options -m union and -s reverse.
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are the raw numer of fragments in each gene.

source_name: ES cell line

growth_protocol: Mouse ES cells were cultured in serum-containing ES cell medium on gelatin-coated plates without feeder cells.

extract_protocol:
Total RNA from mESCs was extracted using the QIAGEN RNeasy Mini kit with on-column DNase treatment following the manufacturer’s protocol.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol starting with 2 µg total RNA. Briefly, purified mRNAs (mRNA kit) were fragmented and converted to cDNA with reverse transcriptase. The resulting cDNAs were converted to double stranded cDNAs and subjected to end-repair, A-tailing, and adapter ligation. The constructed libraries were amplified using 8 cycles of PCR.

value: Zbtb24 knockout (1lox/1lox)

tag: tissue

value: mouse embryonic stem cells (mESCs)


title: TruSeq_mRNA_control_3

value: Zbtb24 wild-type (2lox/+)


title: SMARTer_experiment_100cells_2

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
Reads were mapped to rRNA sequences (GI numbers: 262231778, 120444901, 120444900, 328447215, 38176281 and Ensembl IDs: ENSMUST00000082388, ENSMUST00000082390, ENSMUST00000083988, ENSMUST00000157970) using Bowtie2 (version 2.1.0).
Reads that were not mapped to rRNAs were then mapped to the mouse genome (mm10) using TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M4 was enumerated using the htseq-count script within the HTSeq package (version 0.6.1) with options -m union and -s no.
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are the raw numer of fragments in each gene.

extract_protocol:
The cells were used directly without isolating total RNA in accordance with manufacturer recommendations.
mESCs were lysed in the reaction buffer included in the SMARTer Ultra Low RNA Kit v3 (TaKaRa, Japan). cDNA was then synthesized using the SMARTer Ultra Low RNA Kit followed by library construction using the Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA), according to the manufacturers’ protocols. We performed 10 cycles of PCR for 1000 cells (~10 ng RNA) (SMARTer 1000), and 18 cycles of PCR for 100 cells (~ 1 ng RNA) (SMARTer 100).

tag: number of cells


title: TruSeq_mRNA_control_2


title: KGli1_0h

description: Dropseq single cell RNA-seq

tag: treatment

value: TGF-beta, 0hr


title: TruSeq_mRNA_control_1


title: TruSeq_mRNA_experiment_2


title: SMARTer_experiment_100cells_1


title: ES1


title: Vivo heart_AMI_5day_VE-Cad-Cre-S1pr1 fl/fl_KO4_rep1

city: Shanghai

first: kuang

middle: ya

last: shu

state: Shanghai

address: 150 Jimo Rd, Pudong New District, Shanghai

department: Key Laboratory of Arrhythmias of the Ministry of Education of China, Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine

description: Gene expression profile in mouse hearts 5 days after myocardial infarction.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: heart, AMI, 5day, KO

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from hearts was extracted by Trizol (Invitrogen) following the manufacturer’s instructions. RNA quantity and quality were measured by NanoDrop ND-1000. Total RNA of hearts cells were used for high-throughput Gene Expression microarray (Agilent Technology).

treatment_protocol: The left anterior descending coronary arteries were ligated in WT and VE-Cad-Cre-S1pr1 fl/fl mice.

value: endothelial S1pr1 knock-out

value: male

value: heart

value: myocardial infarction

tag: time point

value: 5 days after myocardial infarction


title: Vivo heart_AMI_5day_WT1_rep1

source_name: heart, AMI, 5day, WT

value: WT


title: SMARTer_experiment_1000cells_2


title: EC2


title: SMARTer_control_100cells_1


title: SMARTer_control_100cells_2


title: Vivo heart_AMI_5day_WT3_rep1


title: CS1


title: SMARTer_experiment_1000cells_1


title: SMARTer_control_1000cells_2


title: SMARTer_control_1000cells_1


title: TruSeq_mRNA_experiment_1


title: ESCs replicate 2

city: Edinburgh

first: Shaun

middle: Michael

last: Webb

address: 2.21 Swann Building, Kings Buildings

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: Sample was rRNA-depleted (RiboZero, Epicentre); library was prepared using ScriptSeq (Epicentre) kit according to manual.

data_processing:
Align to mm9 genome with Tophat v1.41 and Bowtie 2.0.0.6
Extract properly paired, primary alignments
Separate alignments by strand in Samtools
Create bedgraph files with bedTools genomeCoverageBed
Conver to bigWig with wigToBigWig tool
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files of read coverage for forward and reverse strand

source_name: embryonic stem cells

extract_protocol:
Total RNA from brain extracted using TRIreagent and DNaseI treated (DNA-free, Ambion).
rRNA-depleted (RiboZero, Epicentre, for all samples except brain; RiboZero Gold, Epicentre for brain samples); library was prepared using  ScriptSeq (Epicentre) for all samples except brain, and ScriptSeqv2 (Epicentre) kit for brain according to manual and purified with 0.7vol AMPure beads as recommended by Epicentre; Samples were Illumina-sequenced (75bp, paired-end). Samples were rRNA-depleted (for details see SAMPLES); libraries were as stated in SAMPLES and purified with 0.7vol AMPure beads as recommended by Epicentre; Samples were Illumina-sequenced (75bp, paired-end, HiSeq).

value: embryonic stem cells


title: EBs replicate 2

source_name: embryoid bodies differentiated from embryonic stem cells

value: embryoid bodies


title: wt brain replicate 1

description: Sample was rRNA-depleted (RiboZero Gold, Epicentre); library was prepared using ScriptSeqv2 (Epicentre) kit according to manual.

source_name: total brain

value: total brain


title: neuronal cells replicate 1

source_name: neuronal cells differentiated from embryonic stem cells

value: neuronal cells


title: wt brain replicate 2


title: EBs replicate 1


title: ESCs replicate 1


title: Vivo heart_AMI_5day_VE-Cad-Cre-S1pr1 fl/fl_KO3_rep1


title: Brca1_tumor1

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description:
mRNA
Single cell RNA-Seq

data_processing:
Sample demultiplexing, barcode processing, and single cell 3’ gene counting were performed by the Cell Ranger pipelines (10X Genomics).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: TSV files with genes and barcode sequences corresponding to row and column indices, respectively.
Supplementary_files_format_and_content: matrix.mtx: Filtered gene-barcode matrix file (demultiplexed).

source_name: Cells from the tumor mass

extract_protocol:
YFP+ premalignant mammary epithelial cells or mammary tumor cells from Trp53L/L;Brca1L/L;R26Y mice post Ad-K8-Cre injection (at the indicated time points) were sorted into Dulbecco’s PBS + 0.04% BSA and retained on ice reagent.
Barcoded single cell RNA-seq libraries were generated as per the manufacturer’s instructions of 10× Chromium Single Cell 3’ v2 reagent kit (10× Genomics, Pleasanton, CA, USA).

tag: strain/background

value: Mixed genetic background

value: Female

value: Sorted DAPI- live cells from the tumor mass

tag: condition

value: Tumor #1 emerged in the mammary gland after Ad-K8-Cre intraductal injection


title: Chr2-cl KO B6/129 blood #C4693 (20 weeks)

first: Gernot

last: Wolf

state: Maryland

address: 6 Center Drive

department: NICHD

institute: NIH

data_processing:
Reads were aligned to the mouse reference genome using Tophat (--I 200000 --g 1)
Mapped reads were converted to bigwig files with DeepTools (--normalizeUsing RPKM --ignoreDuplicates).
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files

source_name: Blood

growth_protocol: ES cells were grown in DMEM supplemented with 20% FCS and LIF or in 2i media as indicated in the sample information.

extract_protocol:
Total RNA from ES cells was purified and depleted from genomic DNA using the RNeasy Plus minikit (Qiagen). Tissues were lysed using TRIzol reagent and RNA was purified after Isopropanol precipitation with RNeasy columns (Qiagen)
RNA libraries were prepared for sequencing using the TruSeq RNA Sample Prep Kit v2 (Illumina) or the SureSelect mRNA sequencing kit (Agilent) and polyA enrichment.

value: 20 weeks

value: Blood

tag: genotype/variation

value: Chr2-cl KO/KO

tag: media


title: Chr2-cl KO B6/129 brain #C4693 (16 weeks)

source_name: Brain

value: 16 weeks

value: Brain

tag: strain


title: RRBS Chr4-cl KO (2i + Vit. C)

data_processing:
Reads were processed using Trim Galore (--illumina --paired –rrbs) to trim bad quality bases and adaptors. Additionally, the first 5 nt of R2 and the last 3 nt of R1 and R2 were trimmed.
Reads were then mapped to the reference genome (mm9) using Bismark (Krueger and Andrews, 2011) to extract methylation calling results
Genome_build: mm9
Supplementary_files_format_and_content: Interval files with coordinates of CpG sites and methylation status

source_name: ES cells

growth_protocol: ES cells were grown in either standard ES cell media containing 20% FCS and LIF or for one week in 2i media containing vitamin C as described previously (Blaschke et al., 2013)

extract_protocol:
Genomic DNA was purified from WT and Chr4-cl KO ES cells using the Quick-gDNA purification kit (Zymo Research).
Libraries were constructed with the NEXTflex™ Bisulfite-Seq Kit (Bioo Scientific) using MspI digestion to fragment DNA.

value: ES cells

value: Chr4-cl KO

tag: growth condition

value: 2i + Vitamin C


title: Chr2-cl KO B6/129 blood #C4672 (20 weeks)


title: Chr2-cl WT B6/129 blood #C4673 (20 weeks)

value: Chr2-cl WT


title: Chr2-cl WT B6/129 blood #C4694 (20 weeks)


title: Chr2-cl WT B6/129 brain #C4694 (16 weeks)


title: Chr2-cl WT B6/129 brain #C4673 (16 weeks)


title: Chr2-cl KO B6/129 testis #C4695 (16 weeks)

source_name: Testis

value: Testis


title: Chr2-cl KO B6/129 testis #C4693 (16 weeks)


title: Chr2-cl WT B6/129 testis #C4673 (16 weeks)


title: Chr2-cl KO B6 ES cells #G11

source_name: Embryonic stem cells

value: Embryonic stem cells


title: Chr2-cl KO B6 ES cells #B10


title: Chr2-cl KO B6 ES cells #D10


title: neuronal cells replicate 2


title: Chr2-cl WT B6/129 testis #C4694 (16 weeks)


title: Chr2-cl KO B6/129 brain #C4695 (16 weeks)


title: Chr2-cl WT B6 ES cells #H7


title: Chr2-cl WT B6 ES cells #A8


title: RRBS Chr4-cl WT (serum)

value: Chr4-cl WT

value: serum


title: Chr4-cl KO B6 blood #T00524 (20 weeks)

value: Chr4-cl KO/KO


title: Chr2-cl WT B6 ES cells #E6


title: Chr4-cl KO B6 blood #T00415 (20 weeks)