title: siNup153-RNAseq-r2

description:
RNA-Seq of siNup153 treated U2OS cells replicate 2
processed data file: fpkm.txt.gz
strand specific polyA+ RNA

value: Nup153 RNAi


title: IMR90-H3K4me3-ChIPseq

status: Public on Nov 15 2016

type: SRA

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

country: USA

institute: University of California, San Diego (UCSD)

description:
ChIP-Seq of trimethylated H3K4me3 (IMR90 cells)
processed data file: H3K4me3-IMR90.peaks.bed.gz

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0) for DamID, ChIP-seq, and DNase-Seq. In the case of DNase-seq reads, 3' adapter sequences needed to be removed (starting with AGTCGTGATGTTCGTATGCCGTCTTC). STAR (v2.2.0c) was used for RNA-Seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.  DamID reads were further removed if the read was not preceeded by a GATC in the genome (read starting immediately after the GATC).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser. DamID peaks for Nup153 and Nup93 were found by merging replicates and using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 100" using the GFP DamID experiments as background. LBR-defined LADs are much more broad than other features and were defined by first creating a log2 normalized bedGraph of LBR-DamID vs. GFP-DamID smoothed over a range of 100 kb, then taking defining enriched regions with a log2 ratio greater 0.30.  Regions within 200 kb were merged to larger domains, and finally only regions greater than 200kb in size were considered as TADs to avoid noise. ChIP-Seq peaks were founding using the findPeaks program in HOMER using the paramter "-style histone" to find broad peaks for H3K4me3 and H3K9me2 peaks or "-style super" to find super enhancers from H3K27ac peaks using input as background.  CTCF peaks were found using the parameter "-style factor".    DNase-Seq peaks were found using HOMER findPeaks using the option "-style dnase".  For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: hg19
Supplementary_files_format_and_content: BED file Columns: (1) chr (2) start (3) end (4) peakName (5) peak score (6) strand.  FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: U2OS cells were cultured in DMEM (Gibco), 10% FBS. IMR90 cells in DMEM 20% FBS supplemented with nonessential aminoacids (Gibco) and low oxygen conditions (3%).

extract_protocol:
ChIP-seq: cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine. After sonication,chromatin was incubated with 5–10 μg of antibody at 4°C overnight. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG or sheep-anti-mouse IgG (Invitrogen). Subsequently, immuno-complexes were washed, decorsslinked and DNA was purified by QIAquick Spin columns (Qiagen).
ChIP-Seq and DamID-Seq libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) or the Kapa Hyper Prep Kit for Illumina Platforms followed by Illumina sequencing.

treatment_protocol: RNAi mediated gene silencing was performed using the following oligos (Invitrogen): control (Luc; 5’ UAUGCAGUUGCUCUCCAGC), Nup153 (5’-ACAUUUGGUAGAGUCUGCCUU) and Nup93 (5’-GCGCUAAUUUACUACUGCA) and delivered using siLenFect (Bio-Rad). For DamID-Seq experiments, the heat shock promoter, ecodam tag and RFC.1 region of the pLgw EcoDam-V5-RFC1 vector (a kind gift of Dr. Bas Van Steensel) was cloned into the polylinker of the pMSCV-puro vector yielding pMSCV-ED-puro.  Subsequently, cDNAs (GFP, Nup153, LBR, mNup93) were inserted using the Gateway cloning system (Thermofisher) and the final product was used to transduce the cells. 48 hours after transduction, puromycin (1μg/ml) was added to select transduced cells.

tag: cell line

tag: RNAi

tag: damid tagged factor

tag: antibody source


title: Cal-1 DMSO RNA Pol2

city: Bethesda

first: Louis

middle: M.

last: Staudt

state: MD

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

institute: National Cancer Institute

description: No additional information.

data_processing:
BRD4 and RNA Pol2 ChIP-Seq Analyses
Calculation Method: For BRD4 and RNA Pol2 ChIP-Seq analyses, 36 bp sequence tags were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. A maximum of two mismatches was allowed for each read. For each gene, a representative RefSeq was defined based on the RNA Pol2 ChIP-Seq data. In the case of multiple RefSeq deriving from alternative promoter usage, the RefSeq with highest RNA Pol2 promoter density (-+ 500 bp from TSS) was selected. In the case of multiple RefSeq sharing the same promoter but differing for exon composition, the RefSeq with the overall highest RNA Pol2 density was selected. Promoter peaks were defined as peaks whose apex was located within a -+ 2Kb window from a representative TSS. Upstream binding peaks were defined as peaks whose apex was located within a -15Kb to -2Kb window from the TSS. Gene body binding peaks were defined as peaks whose apex was located in a window starting at +2Kb from the TSS and ending with the end of the RefSeq. When multiple peaks were associated with the same representative RefSeq, the peak with the highest apex was used for further analyses. To compare the results of two experiments, ChIP-Seq data were normalized by total tags count.
Supplementary_files_format_and_content: wig file
Genome_build: hg18

source_name: Cal-1 DMSO RNA Pol2

growth_protocol:
Cal-1 Growth Protocol
Other: Cal-1 cells were cultured in RPMI-1640 medium supplemented with penicillin/streptomycin and 10% fetal bovine serum (Tet tested, Atlanta Biologicals). All cell lines were maintained in a humidified, 5% CO2 incubator at 37C.

extract_protocol:
RNA Pol2 Antibody Extraction
Other: For “Super-enhancer” ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of total RNA Pol2 antibody (Covance, 8WG16). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

treatment_protocol:
Agent: DMSO (Dimethyl sulfoxide)
Treatment time: 12 hours
In-vitro treatment: 1x10(8) exponentially growing cells were treated for 12 hours with DMSO.

tag: cell type

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells

tag: disease state


title: Mbd3abcKO_Dnmt1ChIP_rep1

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

organism: Mus musculus

source_name: murine embryonic stem cells

growth_protocol: E14 mouse embryonic stem cells (ESCs) were cultured on gelatin-coated dishes without feeder cells in high-glucose DMEM medium (Sigma) containing 10% serum (Corning) and LIF at 37°C with 5% CO2.

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Dnmt1 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: Untreated Mbd3abc KO E14 ES cells

value: E14 with Mbd3abc KO generated using CRISPR/Cas9


title: Tet1ci_Mbd2ChIP_rep1

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd2 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: Untreated Tet1c.i. E14 ES cells

value: E14 with two point mutations in catalytic domain of Tet1


title: Tet1ci_Mbd2ChIP_rep2


title: Gen2.2 JQ1 IgG Control

description: No additional information.

source_name: Gen2.2 JQ1 IgG Control

growth_protocol:
Gen2.2 Growth Protocol
Other: Gen2.2 cells were cultured in RPMI 1640 medium supplemented with non-essential amino acids, sodium pyruvate, penicillin/streptomycin and 10% fetal bovine serum. The mouse MS-5 stromal feeder cell line was used to support growth of Gen2.2 cells. All cell lines were maintained in a humidified, 5% CO2 incubator at 37C.

extract_protocol:
IgG Control Extraction
Other: For "Super-enhancer" ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of Negative Control antibody (anti-Flag-M2, Sigma). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

treatment_protocol:
Agent: JQ1
Treatment dose: 250 nM
Treatment time: 12 hours
In-vitro treatment: 1x10(8) exponentially growing cells were treated for 12 hours with 250 nM JQ1.

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)


title: Tet1ci_INPUT_rep1

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples.  Input DNA was diluted with 170 μl elution buffer and incubated at 65°C overnight to reverse crosslinking. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: Tet1ci_INPUT_rep2


title: IMR90-H3K27Ac-ChIPseq

description:
ChIP-Seq of acetylated H3K27ac (IMR90 cells)
processed data file: H3K27ac.IMR90.SE.bed.gz


title: Cal-1 DMSO BRD4

description: No additional information.

source_name: Cal-1 DMSO BRD4

extract_protocol:
BRD4 Antibody Extraction
Other: For “Super-enhancer” ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of BRD4 antibody (Bethyl, Cat No. A301-985A). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.


title: Cal-1 DMSO IgG Control

description: No additional information.

source_name: Cal-1 DMSO IgG Control


title: siNup153-RNAseq-r1

description:
RNA-Seq of siNup153 treated U2OS cells replicate 1
processed data file: fpkm.txt.gz
strand specific polyA+ RNA

library_source: transcriptomic

molecule: polyA RNA

extract_protocol:
RNA-Seq: RNA was extracted using Trizol (Ambion) and column purified using RNeasy kit (Qiagen).
RNA-Seq strand-specific polyA+ libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq Stranded RNA LT Kit (Illumina).


title: WT_Mbd3ChIP

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol: Cells were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd3 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: Untreated WT E14 ES cells


title: Cal-1 JQ1 RNA Pol2

description: No additional information.

source_name: Cal-1 JQ1 RNA Pol2


title: WT_INPUT


title: DNase-Seq-r1

description:
DNaseI hypersensitive sites  replicate 1
processed data file: DNase-Seq.r1.peaks.bed.gz

extract_protocol:
DNase-Seq: Isolated nuclei were subjected to DNaseI digestion and digested fragments were captured.
DNaseI-Seq libraries were constructed by the Crawford lab as in Song and Crawford, 2010.


title: WT_Mbd2ChIP


title: H3K9me2-ChIPseq

description:
ChIP-Seq of dimethylated H3K9me2
processed data file: H3K9me2.peaks.bed.gz


title: Tet1KD_Mbd3abc-FLAGChIP

extract_protocol: Cells were fixed, washed with PBS, and pelleted. After resuspention and incubation with Lysis buffers 1 (50 mM HEPES KOH pH 7.6, 140 mM NaC, 1 mM EDTA, 10% (w/v) glycerol, 0.5% NP-40, 0.25% Triton X100) l and 2, pellets were sheared in Lysis buffer 2  (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for sonication in a Bioruptor. Sheared chromatin was incubated at 4°C overnight with protein G magnetic beads (NEB) pre-blocked and coupled with anti-Flag M2 (Sigma F1804). Magnetic beads were washed, material was eluted at 65°C on a thermomixer, and the eluent was incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μL elution buffer (20 mM Tris-HCl pH 8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS) and treated similarly. Samples were treated with RNaseA/T1 (Ambion) followed by proteinase K (Ambion) and then PCI extracted. Ethanol precipitated ChIP-enriched DNA was then used for library construction or as a template for qPCR reactions. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.

treatment_protocol: One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection.

value: E14 with 6XHIS-3XFLAG tag on C terminus of endogenous Mbd3abc


title: Dnmt1KD_Mbd3abc-FLAGChIP


title: EGFPKD_Mbd3abc-FLAGChIP


title: Input-ChIPseq

description:
Input ChIP-seq sample
processed data file: none


title: H3K4me3-ChIPseq

description:
ChIP-Seq of trimethylated H3K4me3
processed data file: H3K4me3.peaks.bed.gz


title: CTCF-ChIPseq

description:
ChIP-Seq of CTCF
processed data file: CTCF.peaks.bed.gz


title: Tet1ci_Mbd3ChIP_rep1


title: H3K27ac-ChIPseq

description:
ChIP-Seq of acetylated H3K27ac
processed data file: H3K27ac.U2OS.SE.bed.gz


title: Tet1KD_Mbd3ChIP_rep2

data_processing:
Single-end fastq reads were split by barcode adapter sequences, adapter sequences were removed, and reads were mapped to the mm9 genome using bowtie, allowing up to three mismatches. Aligned reads were processed in HOMER (Heinz et al., 2010). Genome browser tracks (bedGraph files) were generated from mapped reads using the “makeUCSCfile” command. Peaks were called using the “findPeaks” command after reads were mapped, using INPUT libraries as a control. Peaks were called individually from replicate datasets and those peaks enriched in both datasets were retained. Mapped reads were aligned over specific regions using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window. Experiments were aligned over the following datasets: TSS reference sites (from HOMER software), intermediate CpG promoters (ICPs, defined in (Weber et al., 2007)), low methylated regions (LMRs, from (Stadler et al., 2011)), DNaseI hypersensitive sites (DHSs) from mouse ENCODE data (GSM1014154) with TSS locations removed, Mbd3 peaks (peaks called from both EGFP KD Mbd3 ChIP-seq libraries using HOMER) and Mbd2 peaks (peaks called from both EGFP KD Mbd2 ChIP-seq libraries using HOMER). After anchoring data over reference sites, aggregation plots were generated by averaging data obtained from biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd3 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: DNase-Seq-r2

description:
DNaseI hypersensitive sites  replicate 2
processed data file: DNase-Seq.r2.peaks.bed.gz


title: EGFPKD_Mbd3ChIP_rep2


title: EGFPKD_Mbd3ChIP_rep1


title: GFP-DamID-r2

description:
DamID-Seq mapping of GFP (control) interaction sites replicate 2
processed data file: none

data_processing:
Library strategy: DamID-seq
Basecalls performed using CASAVA version 1.8.2
Reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0) for DamID, ChIP-seq, and DNase-Seq. In the case of DNase-seq reads, 3' adapter sequences needed to be removed (starting with AGTCGTGATGTTCGTATGCCGTCTTC). STAR (v2.2.0c) was used for RNA-Seq. In all cases, only reads that mapped to a unique genomic locations (MAPQ > 10) were used for downstream analysis.  DamID reads were further removed if the read was not preceeded by a GATC in the genome (read starting immediately after the GATC).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser. DamID peaks for Nup153 and Nup93 were found by merging replicates and using the findPeaks program in HOMER with the following options "-style histone -o auto -size 2500 -minDist 2500 -tbp 0 -inputtbp 0 -fragLength 1 -inputFragLength 1 -F 2 -C 0 -ntagThreshold 100" using the GFP DamID experiments as background. LBR-defined LADs are much more broad than other features and were defined by first creating a log2 normalized bedGraph of LBR-DamID vs. GFP-DamID smoothed over a range of 100 kb, then taking defining enriched regions with a log2 ratio greater 0.30.  Regions within 200 kb were merged to larger domains, and finally only regions greater than 200kb in size were considered as TADs to avoid noise. ChIP-Seq peaks were founding using the findPeaks program in HOMER using the paramter "-style histone" to find broad peaks for H3K4me3 and H3K9me2 peaks or "-style super" to find super enhancers from H3K27ac peaks using input as background.  CTCF peaks were found using the parameter "-style factor".    DNase-Seq peaks were found using HOMER findPeaks using the option "-style dnase".  For RNA-Seq, Reads Per Kilobase of exon per milion mapped reads were calculated using HOMER (http://homer.salk.edu/homer/) across annotated gene exons (RefSeq).
Genome_build: hg19
Supplementary_files_format_and_content: BED file Columns: (1) chr (2) start (3) end (4) peakName (5) peak score (6) strand.  FPKM Tab delimited text file, Columns: (1) RefSeq acc (2) chr (3) start (4) end (5) strand (6) length (7) copies (8) annotation (9-) FPKM for each experiment

extract_protocol:
For DamID-Seq,  cells were harvested and gDNA was isolated using the Qiagen DNeasy Blood & Tissue Kit. gDNA was  digested with DpnI (NEB, 20 U/ μl) and ligated with the adaptor AdR, which was made by mixing and slowly annealing AdR-top (5’ CTAATACGACTCACTATAGGGCAGCGTGGTCGCGGCCGAGGA 3’) and AdR-bottom (5’ TCCTCGGCCG 3’). This ligation was completed using 1uL T4 Ligase (Roche, 5U/μl) for 2 hours at 16°C. The regions flanked by adaptors were amplified by PCR using the Bio-Adr-primer (5’ Bio-GGTCGCGGCCGAGGATC 3’) and purified using the Qiagen MinElute PCR purification kit. Amplified products were sonicated using a Bioruptor (Diagenode) to obtain DNA fragments of sizes between 100-500bp. MyOneC1 Streptavidin dynabeads (Invitrogen) were used to pull down the biotinylated ends of the sonicated PCR products. The bound DNA was removed off the beads by digestion with DpnII for 1 hour.
ChIP-Seq and DamID-Seq libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) or the Kapa Hyper Prep Kit for Illumina Platforms followed by Illumina sequencing.

value: GFP


title: INPUT_Mbd3ChIP_rep2

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples.  Input DNA was diluted with 170 μl elution buffer and incubated at 65°C overnight to reverse crosslinking. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: IMR90-GFP-DamID

description:
DamID-Seq mapping of GFP (control)  interaction sites (IMR90 cells)
processed data file: none


title: IMR90-Nup153-DamID

description:
DamID-Seq mapping of Nup153  interaction sites (IMR90 cells)
processed data file: Nup153-DamID-IMR90.toppeaks.bed.gz


title: Mbd2KD_Mbd3ChIP_rep1


title: Untagged_control_for_Mbd3abc-FLAGChIP

treatment_protocol: Untreated


title: Nup153-DamID-r3

description:
DamID-Seq mapping of Nup153  interaction sites replicate 3
processed data file: Nup153-DamID.peaks.bed.gz


title: Mbd3KD_Mbd2ChIP_rep2

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd2 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo-) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: LBR-DamID-r3

description:
DamID-Seq mapping of LBR  interaction sites replicate 3
processed data file: LBR-DamID.LADs.bed.gz

value: LBR


title: Tet1KD_Mbd3ChIP_rep1


title: Dnmt1KD_Mbd3ChIP_rep2


title: Nup153-DamID-r2

description:
DamID-Seq mapping of Nup153  interaction sites replicate 2
processed data file: Nup153-DamID.peaks.bed.gz


title: LBR-DamID-r1

description:
DamID-Seq mapping of LBR  interaction sites replicate 1
processed data file: LBR-DamID.LADs.bed.gz


title: Nup93-DamID-r2

description:
DamID-Seq mapping of Nup93  interaction sites replicate 2
processed data file: Nup93-DamID.peaks.bed.gz


title: Nup153-DamID-r1

description:
DamID-Seq mapping of Nup153  interaction sites replicate 1
processed data file: Nup153-DamID.peaks.bed.gz


title: GFP-DamID-forLBR

description:
DamID-Seq mapping of GFP (control) interaction sites (performed along with DamID for LBR)
processed data file: none


title: ZIKV-infected-rep3-IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: mRNA

data_processing:
For data analysis, after removing the adapter, the reads were mapped to human genome (hg38) and ZIKA genome (NC_012532) by using Tophat2 (Kim et al., 2013). The peak calling method was modified from the published method (Dominissini et al., 2012). To call m6A peaks, the longest isoform of each Human RefSeq gene (and the whole genome of ZIKV) was scanned using a 100 bp sliding window with 10 bp steps. To reduce bias from potential inaccurate gene structure annotation and the arbitrary use of the longest isoform, windows with read counts less than 1/20 of the top window in both m6A immunoprecipitate and input samples were excluded. For each gene, the read count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between immunoprecipitate and input samples by using the edgeR package (Robinson et al., 2010), combining information from all replicates in the two groups. The window was called as positive if the FDR was <1% and the log2 (enrichment score) was ≥1. Overlapping positive windows were merged. The following were calculated to obtain the enrichment score of each peak (or window): (a) read counts of the immunoprecipitated sample in the current peak/window, (b) median read counts of the immunoprecipitated sample in all 100 bp windows on the current mRNA, (c) read counts of the input sample in the current peak/window, and (d) median read counts of the input sample in all 100 bp windows on the current mRNA. The enrichment score of each window was calculated as ([a × d])/([b × c]).
Genome_build: Human hg38 ZIKA genome (NC_012532)
Supplementary_files_format_and_content: excel file containing processed m6A peak list from all samples

molecule: total RNA

source_name: human cell line

extract_protocol:
total RNA was extracted using Direct-zol (Zymo) from embryos homogenized in TRIzol. mRNA was further purified using Dynabeads mRNA DIRECT Kit. For IP samples, mRNA was sonicated and subjected to IP using m6A antibody (Synaptic Systems, 202003).
Libraries were constructed using TruSeq Stranded mRNA Library Prep Kit (Illumina).

tag: infection status

value: yes

tag: rna source

value: human cell line

tag: antibody

value: m6A antibody (Synaptic Systems, 202003)


title: Dnmt1KD_Mbd3ChIP_rep1


title: Tet1KD_Mbd2ChIP_rep2


title: GFP-DamID-r1

description:
DamID-Seq mapping of GFP (control) interaction sites replicate 1
processed data file: none


title: LBR-DamID-r2

description:
DamID-Seq mapping of LBR  interaction sites replicate 2
processed data file: LBR-DamID.LADs.bed.gz


title: INPUT_Mbd3ChIP_rep1


title: Mbd3KD_Mbd2ChIP_rep1


title: 18.4A

city: Boulder

first: Luis

last: Zea

state: Colorado

address: 429 UCB ECAE 1B02

institute: University of Colorado Boulder

data_processing:
Post-processing of the sequencing reads from RNA-seq experiments for each sample was performed using HudsonAlpha’s unique in-house RNA-seq data analysis pipeline. Briefly, quality control checks on raw sequence data for each sample were performed using FastQC (Babraham Bioinformatics, Cambridge, UK). Data-analysis was performed using the CLC Genomics Workbench (Version 7.5.1, CLC Bio, Aarhus, Denmark). The reference genome Escherichia coli (DH10B) sequence was downloaded from the UCSC genome browser. For read mapping, the following parameters were used: mismatch cost = 2, insertion and deletion cost = 3, length fraction: 0.8, similarity fraction = 0.8, global alignment = no, auto-detect paired distances = yes. Samples were grouped and differential expression of genes was calculated on the basis of fold changes (using the default cut-off ≥ ±2.0) observed in comparisons between defined conditions.
Genome_build: Escherichia coli (DH10B)
Supplementary_files_format_and_content: excel file include RPKM values for each Sample

organism: Escherichia coli

growth_protocol: Samples were sent to the International Space Station at 4C in FPAs, as described above. Temperature was increased to 37C and 23 hours later, the experiment was started by introducing the inoculum (E. coli ATCC 4157) into the growth medium (Medium E as described in Vogel & Bonner (1956) supplemented with 5 g/L glucose), yielding 3.25 mL of a culture with a starting cell concentration of 1.22e6 cell/mL.

extract_protocol:
Four ml of the bacterial suspension in RNALater II and Medium E growth medium were spun down at 200g for 5 min. The supernatant was discarded and the pellet were resuspended in 200ul PBS and mixed by pipetting. 100ul aliquots were taken out for DNA and RNA extraction from the same sample. RNA extraction was done using Qiagen RNeasy mini kit (Qiagen, Hilden, Germany) with on-column DNase digestion. Final elution was made in 30 μL dH2O. The concentration and integrity of the total RNA was estimated by Quant-iT™ RiboGreen® RNA Assay Kit  (ThermoFisher Scientific, Waltham, MA), and Agilent 2100 Bioanalyzer (Applied Biosystems, Carlsbad, CA), respectively.
Ribosomal RNA (rRNA) was removed using Ribo-Zero™ Gold (Yeast) kit (Epicenter, Madison, WI) using manufacturer's recommended protocol. Immediately after the rRNA removal the RNA was fragmented and primed for the first strand synthesis using the NEBnext First Strand synthesis module (New England BioLabs Inc., Ipswich, MA). Directional second strand synthesis was performed using NEBNExt Ultra Directional second strand synthesis kit. Following this the samples were taken into standard library preparation protocol using NEBNext® DNA Library Prep Master Mix Set for Illumina® with slight modifications. Briefly, end-repair was done followed by polyA addition and adapter ligation. Post-ligated materials were individually barcoded with primers and amplified through 12 cycles of PCR. Final library quantity was assessed by Quant-iT™ PicoGreen® dsDNA Assay Kit and the library quality was estimated on LabChip® GX (Caliper, PerkinElmer, Waltham, MA). Accurate quantification of the final libraries for sequencing applications was determined using the qPCR-based KAPA Biosystems Library Quantification kit (Kapa Biosystems, Inc., Woburn, MA). Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-End (PE) sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina, Inc.).

treatment_protocol: Nineteen hours after experiment start, antibiotic (Gentamicin Sulfate (MP Biomedical, Cat No. 1676045, Santa Ana, CA, USA)) was introducing into the cultures. Antibiotic concentration varied from one sample to the next from 0 to 150 ug/mL in 25 ug/mL steps. Thirty hours later, samples were fixed in RNA Later II ((ACROS, Cat. No. 41678, New Jersey, USA)). Samples were stored at -75C until return to Earth for analyses.

tag: strain

value: ATCC 4157

tag: location

value: Earth

tag: gentamycin concentration (ug/ml)


title: 18.2A


title: Mbd2KD_Mbd3ChIP_rep2


title: ZIKV-infected-rep2-IP

description: mRNA


title: Tet1KD_Mbd2ChIP_rep1

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4C overnight with constant rotation. Mbd2 antibody (bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: Dnmt1KD_Mbd2ChIP_rep2


title: ZIKV-infected-rep1-IP

description: mRNA


title: Nup93-DamID-r1

description:
DamID-Seq mapping of Nup93  interaction sites replicate 1
processed data file: Nup93-DamID.peaks.bed.gz


title: 17.8A


title: Dnmt1KD_Mbd2ChIP_rep1


title: 2.1A


title: ZIKV-uninfected-rep2-IP

description: mRNA

value: no


title: 2.3A


title: ZIKV-uninfected-rep3-IP

description: mRNA


title: ZIKV-uninfected-rep1-IP

description: mRNA


title: 1.5A


title: EGFPKD_Mbd2ChIP_rep1


title: 1.7A


title: 17.4A


title: INPUT_Mbd2ChIP_rep1

treatment_protocol:
One 10cm dish was transiently transfected with esiRNAs and lipofectamine 2000 and cultured 48 hours post transfection
esiRNA transient transfection with lipofectamine 2000.


title: INPUT_Mbd2ChIP_rep2


title: 1.3A


title: ZIKV-infected-rep3-input

description: mRNA

value: none (input)


title: 2.4A

value: Space


title: 1.1A


title: Endothelin-1 treated Mef2c neural crest conditional mutant (Sample 8)

city: San Francisco

first: Jianxin

last: Hu

address: 555 Mission Bay Blvd South

institute: CVRI

description: Endothelin-1 treated Mef2c conditional mutant neural crest cells

data_processing:
FASTQ files were first de-multiplexed (i.e., the barcode sequences were removed) using fastq-multx (part of the EA-UTILS software suite).
De-multiplexed FASTQ files were aligned to mm9 with Tophat 1.3.1 on Ubuntu. Minimum anchor: 5 bases. Segment length parameter: 25 bases. Allowed segment mismatches: 1. Allowed splicing mismatches: 0. Maximum multihits allowed: 15. No novel junctions allowed. Specified distance between mate pairs: 50 bases. Exact options were: -o TOPHAT_OUT --solexa-quals --min-anchor=5 --segment-length=25 --segment-mismatches=1 --splice-mismatches=0 --max-multihits=15 --no-novel-juncs --mate-inner-dist=50 GTF_FILE.gtf FILE1 FILE2
The Tophat "accepted_hits.bam" files were used as input to the program "OverdispersedRegionScanSeqs" (part of USeq), which aggregated reads into gene-level counts and calculated differential expression P-values.
The Tophat "accepted_hits.bam" files were also used as input to Cufflinks v1.3.0 and CuffDiff, which aggregated reads into gene and transcript-level counts and calculated differential expression P-values in an alternative fashion from USeq's method above.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file that contains expression profiling data presented as a matrix listing features of interest (such as gene, transcript, exon, miRNA) and normalized abundance measurements.

source_name: neural crest cells sorted from embryo culture

growth_protocol: 1) set up a 37°C warm plate by the dissection scope; 2) prepare fresh DMEM+1%FBS. aliquot 400ul DMEM+1%FBS to each well in a 24-well-plate(optional: add 1%antibiotics in DMEM); 3) prewarm the 24-well-plate with DMEM on the warm plate; 4) dissect E9.5 embryos in room temperature PBS (optional, save yolk sac for genotyping); 5) pinch off head (cut just above first branchial-arch) and tail (anywhere below hindlimb level is fine) with forceps; 6) transfer the embryo explant to the pre-warmed DMEM on a warm plate; 7) proceed to the next embryo until dissection is complete; 8) transfer the 24-well-plate to a cell culture incubator (37°C, 5% CO2) to recover for 1-hour; 9) check heartbeat under a dissection scope, make sure embryos are alive. Add drug(s) of interest and vehicle controls and return plate back to cell culture incubator; 10) culture 12-15 hours 11) check heart-beating again. Harvest "healthy" (-in terms of heart beating) embryo explants for further analysis.

extract_protocol:
RNA were extracted according to Qiagen's instructions (RNeasy Micro Kit, 74004)
Libraries were prepared according to Nugen's instructions (Ovation® RNA-Seq System V2, 7102; Encore Rapid DR Multiplex System 1–8, 0319). Barcode information: N11 GGACCC, N12 TTCAGC, N13 ACCC, N13 CGTA, E11 AAGGGA, E12 CCTTCA, E13 GAGT, E13 TTAG, EK11 CCTTCA, EK12 CCTCGG, EK13 TTCAGC.

treatment_protocol: Endothelin-1 is added at a concentration of10µM after 1 hour culture

tag: embryonic stage


title: ZIKV-infected-rep1-input

description: mRNA


title: 17.2A


title: ZIKV-uninfected-rep2-input

description: mRNA


title: Endothelin-1 treated Mef2c neural crest conditional mutant (Sample 7)


title: Endothelin-1 treated wild type (Sample 6)

description: Endothelin-1 treated wild type neural crest cells


title: ZIKV-infected-rep2-input

description: mRNA


title: 18.1A


title: 18.3A


title: EGFPKD_Mbd2ChIP_rep2

extract_protocol: Cells from RNAi-mediated KD were fixed, washed with ice-cold PBS, and pelleted. Cell pellets were lysed through sonication in a Bioruptor (UCD-200) and supernatants were saved. 30 μL of chromatin was stored overnight at 4°C for input samples while the remainder of the chromatin was combined with antibody coupled protein A magnetic beads (NEB) and incubated at 4°C overnight with constant rotation. Mbd2 antibody (Bethyl) coupled protein A magnetic beads (NEB) were blocked with 5 mg/ml BSA overnight at 4°C, prior to incubation with sheared chromatin. Magnetic beads were washed and material was eluted at 65°C on a thermomixer. Eluted material was transferred to a new microfuge tube, combined and incubated at 65°C overnight to reverse crosslinking. Input DNA was diluted with 170 μl elution buffer and treated similarly. Samples were treated with RNaseA/T1 (Ambion), proteinase K (Ambion), and then PCI extracted. Ethanol precipitated ChIP-encriched DNA was then used for library construction.  Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (exo minus) and dATP to yield a protruding 3- 'A' base for ligation of barcoded adapters which have a single 'T' base overhang at the 3’ end. DNA purification on Zymo Research PCR purification columns (Zymo, Irvine, CA) was performed following each enzyme reaction. The adaptor-ligated material was then PCR amplified with KAPA-HiFi polymerase using 16 cycles of PCR before size selection of 200-350 bp fragments on a 1% agarose gel. Libraries with different barcodes were pooled together and single-end sequencing was performed on an Illumina HiSeq2000.


title: Sample 2 of the RAS supplementation group

city: Chengdu

first: Tao

last: Zhong

state: Sichuan

address: No. 211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

data_processing:
Illumina Casava1.82 software was used for basecalling.
High-quality reads were obtained by discarding reads containing over 10% Ns, or overlapping at least 10 bp with adaptor sequences at mismatch rate equal to or less than 10%, or including over 50% bases with base quality score less than five, and then mapped to mouse genome using Tophat 2.0.9.
Cufflinks version 2.1.1 were applied to quantify gene expression and obtain FPKM expression values (denoted as the fragments per Kb of transcript per Mb mapped reads).
Genome_build: mouse genome
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Adipose tissue

extract_protocol:
Total RNA was purified with an RNeasy micro kit (QIAGEN, Germany) and an RNase-Free DNase Set (QIAGEN, Germany).
The sequencing RNA library of each sample was prepared using a TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina, San Diego, CA). mRNA was enriched with Oligo (dT) magnetic beads, and then randomly broken into short fragments of ~200 base pairs prior to cDNA synthesis. cDNA synthesis was performed using a SuperScript™ II Reverse Transcriptase (Invitrogen, Carlsbad, CA, USA) with random hexamer primers. cDNA was eluted after purification using AMPure XP beads (Beckman Coulter, Brea, CA, USA). Blunt-end cDNA was subsequently 3'-adenylated, ligated to sequencing adapters, and purified. Enrichment of cDNA amplification was carried out using Primer Cocktail , and purified with paramagnetic beads. Quality control and quantification of the constructed libraries were authenticated with a Qubit® dsDNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA) using a Qubit® 2.0 Fluorometer. Lastly, the libraries were sequenced utilizing an Illumina HiSeq™ 2500 Sequencing System.

treatment_protocol: The mice of DH group were fed a 10.00 g/kg•BW RAS supplementation

value: KM mice

tag: diet

value: 10.00 g/kg BW RAS supplementation


title: 1.6A


title: Endothelin-1 treated Mef2c neural crest conditional mutant (Sample 9)


title: ZIKV-uninfected-rep1-input

description: mRNA


title: Endothelin-1 treated wild type (Sample 5)


title: Sample 3 of the RAS supplementation group


title: PBS treated wild type (Sample 3)

description: PBS treated wild type neural crest cells


title: Endothelin-1 treated wild type (Sample 4)


title: 17.6A


title: ZIKV-uninfected-rep3-input

description: mRNA


title: Sample 3 of the control group

value: control


title: PBS treated wild type (Sample 2)


title: 1.4A


title: 17.3A


title: HCAFIS03_15S

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

data_processing:
Basecalls performed using CASAVA version 1.8.2
Individual FASTQ files for each sample were merged prior to the quality control & filtering steps
Quality control of the reads was carried out using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were filtered from the adapter sequences and their quality score using trim_galore software. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and only are retained those with at least 20 phred quality score.
Reads were mapped to hg19 (Homo sapiens) reference genome using Bowtie2 for paired end read alignments, allowing two mismatches (n = 2).
Resulting SAM aligment files were converted to BED format to be used in as input for peak calling software SPP v1.10 and further analyses were conducted via Diffbind and ChIPpeakAnno BioconductoR packages (https://bioconductor.org/packages/release/bioc/html/DiffBind.html; https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html ).
Genome_build: hg19
Supplementary_files_format_and_content: Peak calling results, obtained from SPP in encodePeak format. These tables are in tab separated plain text format.

growth_protocol: CD8+ T cell subsets were isolated from peripheral blood by fluorescence-activated cell sorting (FACS)

extract_protocol:
After sonication (Bioruptor, Diagenode), chromatin was immunoprecipitated with an iDeal ChIP-seq Kit (Diagenode)
TruSeq® ChIP Sample Preparation (Illumina Inc.)

tag: tissue

value: Blood

tag: subset

value: TEMRA


title: HCAFIS03_14S


title: Sample 1 of the RAS supplementation group


title: 17.5A


title: Cal-1 RNA-Seq

description: Processed data in Series supplementary file RNA-Seq_pDCs_vs_BPDCN_cell_lines_normalized.xlsx

data_processing:
RNA-Seq Analysis (HiSeq)
Calculation Method: Pair-end sequencing was performed on a HiSeq 2000 sequencer with v3 sequencing reagents (2x101 bp reads). To calculate Digital Gene Expression values, the pair-end reads were aligned to hg19 genome with STAR software. The total number of reads within each gene was counted using HTSeq software. Once the total number of reads within each gene was counted, we generated for each sample the 90% trimmed mean of the read counts (average of the read counts for the middle 90% of genes in that sample). We then normalized all counts in a given sample by dividing by the samples trimmed mean and multiplying by 500. Genes with normalized counts less than 1 were set equal to one. Finally we log2 transformed the normalized counts to generate the final gene expression values.
Supplementary_files_format_and_content: Excel spread sheet of log2 transformed normalized counts
Genome_build: hg19

extract_protocol:
AllPrep DNA/RNA Kit
Other: Total RNA from fresh samples was extracted with the AllPrep DNA/RNA kit (QIAGEN) according to the manufacturer's instructions.
Libraries were generated with the TruSeq RNA Sample Prep Kit-v2 (Illumina) according to the manufacturer's instructions.

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN) cell line


title: at-seed-agl62-30h_after_pollination-replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

data_processing:
Sequencing reads were aligned to the TAIR 10.0 version of the Arabidopsis reference genome (Col-0) using TopHat (Trapnell et al., 2009). Only uniquely mapping reads were used for further analysis. Differentially expressed genes were identified using the DESeq package (Anders and Huber, 2010).
Standard output from the DESEQ package with following column headers:
<id> feature identier
<baseMeanA> mean normalised counts from condition A
<baseMeanB> mean normalised counts from condition B
<foldChange fold> change from condition A to B
<log2FoldChange> the logarithm (to basis 2) of the fold change
<pval> p value for the statistical signicance of this change
<padj> p value adjusted for multiple testing with the Benjamini-Hochberg procedure (seethe R function p.adjust), which controls false discovery rate (FDR)
Genome_build: TAIR10

organism: Arabidopsis thaliana

source_name: agl62 seeds at 30 hrs after pollination, replicate 2

growth_protocol: Seeds were sterilized in 5% commercial bleach and 0.01% Tween-20 for 10 min and washed three times in sterile ddH2O. Sterile seeds were plated on ½ MS-medium (0.43% MS-salts, 0.8% Bacto Agar, 0.19% MES hydrate and 1% Sucrose; when necessary, the medium was supplemented with the appropriate antibiotics) and stratified at 4 ºC in the dark for 48 h. Plates were then transferred to a growth chamber (16 h light / 8 h dark; 110 μmol.s-1.m-2; 21ºC; 70% humidity). After 10 days seedlings were transferred to soil and grown in a growth chamber (16 h light / 8 h dark; 110 μmol.s-1.m-2; 21ºC; 70% humidity).

extract_protocol:
Seeds were harvested into RNA later (Sigma-Aldrich, St Louis, USA) and homogenized (Silamat S5; IvoclarVivadent, Ellwangen, Germany) using glass beads (1.25-1.55 mm; Carl Roth, Karlsruhe, Germany). RNA was extracted following a modified protocol for the RNAqueous kit (Ambion, Life Technologies). RNA was purified by Qiagen RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) after residual DNA removed by 2 uL DNaseI (Thermo-Scientific, Waltham, USA).
Libraries were prepared using the Truseq RNA Sample Preparation Kit (Illumina, San Diego, USA) and sequenced on an Illumina HiSeq2000 on two lanes in 100-bp paired-end mode.

treatment_protocol: agl62 and wild-type plants were emasculated 1-2 days prior to anthesis, hand-pollinated and seeds were harvested 30 h after pollination. Three biological replicates were generated per sample.

value: seed

tag: genotype/variation


title: Sample 1 of the control group


title: Sample 2 of the control group


title: PBS treated wild type (Sample 1)


title: 1.2A


title: 17.1A


title: Gen2.2 RNA-Seq

tag: cell line

value: blastic plasmacytoid dendritic cell neoplasm (BPDCN)


title: at-seed-WT-30h_after_pollination-replicate1

source_name: wild-type seeds at 30 hrs after pollination, replicate 1

value: wildtype


title: at-seed-agl62-30h_after_pollination-replicate1

source_name: agl62 seeds at 30 hrs after pollination, replicate 1


title: HCAFIS03_13S

value: EM


title: HCAFIS03_9S


title: HCAFIS03_8S


title: at-seed-WT-30h_after_pollination-replicate3

source_name: wild-type seeds at 30 hrs after pollination, replicate 3


title: HCAFIS03_12S


title: at-seed-WT-30h_after_pollination-replicate2

source_name: wild-type seeds at 30 hrs after pollination, replicate 2


title: HCAFIS03_11S

value: Naive


title: HCAFIS03_10S


title: ZIKV-vgRNA-rep3-IP

description: viral RNA

organism: Zika virus

source_name: virions

value: virions

value: m6A antibody (Synaptic Systems, 202003)


title: C [small RNA]

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University

description: small RNA ( < 200 nt)

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to tair 9.0 cDNA using BWA with parameters -e 0 -o 0 -M 1000 -k 0  -i 25 -q 10 -t 4
The 21-22 nt clean reads after adaptor-removal and filtering were mapped to the reference (main gene models, TAIR 9.0 release) using the BWA program. Stringent mapping of the short reads was performed with a mismatch penalty of 10000 and no gaps allowed.
Reads mapped to each gene model were counted, then followed by normalization and differential expression analysis
Genome_build: TAIR9
Supplementary_files_format_and_content: spreadsheets include numbers of mapped reads and RPKM values for each Sample

growth_protocol: Seeds pretreated with stratification for 2-4 days at 4°C were kept in the greenhouse for another 6 days (22°C, 16 h/8 h photoperiod) before transferring the seedlings to the soil for another 12 days.Aerial tissues were collected from the 18-day-old adult plants.

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and RNA was harvested using the microRNA Purification Kit (Norgen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 18-day-old adult plant

value: aerial tissue

tag: genotype


title: r [small RNA]

description: small RNA ( < 200 nt)


title: res [small RNA]

description: small RNA ( < 200 nt)


title: HCAFIS03_4S


title: Gen2.2 TCF4 mAb

description: No additional information.

data_processing:
TCF4 ChIP-Seq Analysis
Calculation Method: For TCF4 ChIP-Seq analysis, 36 bp sequence tags were aligned to human genome build 36 (hg18) with Bowtie software. Redundant reads were removed and reads uniquely mapping to reference genome were used for further analysis. A maximum of two mismatches was allowed for each read. To perform "peak calling", the genome was divided into "bins" of 25 bp. Each sequencing tag was associated with the bin of its start site and an additional extension of 7 bins (for a total of 200bp) along the direction of its read to match the average library size. For a given experiment, the number of "hits" in a bin was defined as the number of extended tags associated with that bin. Bins with fewer than 3 hits were removed. Peaks were defined by merging consecutive significant bins. The height of the peak was defined as the largest number of hits in any of the bins forming the peak. The "apex" of the peak was defined as the bin that had this largest number of hits. In the case of ties, the earliest such peak was chosen as the apex. A threshold of apex >30 tags/bin was used to define high-stringency TCF4 binding peaks. A Negative Control IP (anti-Flag antibody) experiment was included as specificity control for each cell line. Experimental peaks overlapping with a control bin with a tag count of 5 or greater were excluded from further analysis. To compare the results of two experiments, ChIP-Seq data were normalized by total tags count.
Supplementary_files_format_and_content: bed file
Genome_build: hg18

source_name: Gen2.2 TCF4 mAb

extract_protocol:
TCF4 mAb Extraction
Other: For the TCF4 ChIP-Seq, 5x10(7) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with rabbit monoclonal TCF4 antibody developed by Epitomics. The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm) cells


title: at-seed-agl62-30h_after_pollination-replicate3

source_name: agl62 seeds at 30 hrs after pollination, replicate 3


title: HCAFIS03_3S

source_name: TEMRA Input


title: es [small RNA]

description: small RNA ( < 200 nt)

source_name: ein5-1 ski2-3

value: ein5-1 ski2-3


title: HCAFIS03_7S


title: HCAFIS03_6S


title: HCAFIS03_1S

source_name: Naive Input


title: Cal-1 TCF4 mAb

description: No additional information.

source_name: Cal-1 TCF4 mAb

value: BPDCN (blastic plasmacytoid dendritic cell neoplasm)


title: ZIKV-vgRNA-rep1-IP

description: viral RNA


title: ZIKV-vgRNA-rep1-input

description: viral RNA

value: none (input)


title: ZIKV-vgRNA-rep3-input

description: viral RNA


title: Gen2.2 IgG Control

description: No additional information.

source_name: Gen2.2 IgG Control

extract_protocol:
IgG Control Extraction
Other: For "Super-enhancer" ChIP-Seq, 1x10(8) exponentially growing cells were collected by centrifugation, resuspended in room temperature RPMI without FBS ( 2x10(6) cells/ml) and cross-linked with 1% formaldehyde for 5 min at RT. Cross-linking was quenched by addition of 125 mM Glycine for 5 min at RT. Cross-linked cells were first washed with ice-cold PBS and then resuspended in ice-cold RIPA buffer (10mM Tris-HCl pH8, 140 mM NaCl, 1mM EDTA pH 8, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS and 0.1% Sodium Deoxycholate) to a final concentration of 5x10(6) cell/ml. DNA was sheared with a Misonix XL sonicator, by performing 12 x 45'' sonication cycles at power setting of 5. For the immune precipitation reaction, 2.0x10(7) chromatin cell equivalents were incubated overnight with 10 ug of Negative Control antibody (anti-Flag-M2, Sigma). The following day, chromatin/antibody complexes were incubated with 50 ul of Protein G magnetic beads (Invitrogen) for 4 h at 4C. Protein G bound complexes were washed 4 times with RIPA Buffer, once with LiCl Buffer (10 mM Tris-HCl pH8, 250 mM LiCl, 0.5% NP40, 0.5% Sodium Deoxycholate, 1 mM EDTA), once with TE pH 8.0 and finally resuspended in 100 ul TE pH8 containing RNAse A (0.2 ug/ul). Reverse cross-link was performed overnight at 65C, followed by treatment with 20 ug Proteinase K (Invitrogen) for 2 h at 50C. Final DNA purification was performed with QIAquick PCR Purification columns (QIAGEN).
ChIP DNA was used to generate ChIP-Seq libraries with the NEXTflexTM Illumina ChIP- Seq Library Prep Kit (Bio Scientific), according to manufacturer's instructions.


title: ZIKV-vgRNA-rep2-input

description: viral RNA


title: HCAFIS03_2S

source_name: EM Input


title: TPC_1_72h_neg_control

status: Public on Nov 14 2016

city: Nijmegen

first: Theo

middle: S

last: Plantinga

address: Geert Grooteplein Zuid 10

department: Department of Pathology

country: Netherlands

institute: Radboud University Medical Center

description: Barcode: TTAGGC

data_processing:
Illumina Casava software 1.8.2  used for basecalling of Hiseq2000 and NextSeq 500 data.
Library strategy: RNA-seq. Tuxedo Toolbox (Broad Institute) was used to infer gene expression levels by running TopHat and Cuffdiff. Reads were mapped to human gene annotation (Human Genome hg19).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: Human non-medullary thyroid carcinoma cell line

growth_protocol: All cell-culture was conducted in regular cell culture medium (BC-PAP in RPMI; FTC133 and TPC-1 in DMEM).

extract_protocol: Libraries were prepared according to Illumina's instructions.

tag: treatment protocol

value: TPC-1 cell line treated with DMSO vehicle for 72 hours


title: Cal-1 IgG Control

description: No additional information.

source_name: Cal-1 IgG Control

tag: cell type


title: TPC_1_48h_lanatoside

description: Barcode: ATCACG

value: TPC-1 cell line treated with 50 µM lanatoside C for 48 hours


title: TPC_1_72h_lanatoside

description: Barcode: ACTTGA

value: TPC-1 cell line treated with 50 µM lanatoside C for 72 hours


title: HCAFIS03_5S

value: Blood


title: FTC133_72h_digoxin

description: Barcode: GGTAGC

value: FTC133 cell line treated with 50 µM digoxin for 72 hours


title: TPC_1_48h_neg_control

description: Barcode: CTTGTA

value: TPC-1 cell line treated with DMSO vehicle for 48 hours


title: ZIKV-vgRNA-rep2-IP

description: viral RNA


title: FTC133_72h_proscillaridin

description: Barcode: ACAGTG

value: FTC133 cell line treated with 50 µM proscillaridin A for 72 hours


title: FTC133_72h_digoxigenin

description: Barcode: TGACCA

value: FTC133 cell line treated with 50 µM digoxigenin for 72 hours


title: FTC133_48h_digoxigenin

description: Barcode: GTGGCC

value: FTC133 cell line treated with 50 µM digoxigenin for 48 hours


title: FTC133_24h_proscillaridin

description: Barcode: ATGTCA

value: FTC133 cell line treated with 50 µM proscillaridin A for 24 hours


title: FTC133_48h_strophantin

description: Barcode: GTGAAA

value: FTC133 cell line treated with 50 µM strophantin K for 48 hours


title: FTC133_24h_digoxigenin

description: Barcode: AGTTCC

value: FTC133 cell line treated with 50 µM digoxigenin for 24 hours


title: FTC133_24h_digoxin

description: Barcode: GGCTAC

value: FTC133 cell line treated with 50 µM digoxin for 24 hours


title: FTC133_48h_digoxin

description: Barcode: GTCCGC

value: FTC133 cell line treated with 50 µM digoxin for 48 hours


title: FTC133_48h_neg_control

description: Barcode: CCGTCC

value: FTC133 cell line treated with DMSO vehicle for 48 hours


title: FTC133_72h_strophantin

description: Barcode: CGATGT

value: FTC133 cell line treated with 50 µM strophantin K for 72 hours


title: BC_PAP_72h_proscillaridin

description: Barcode: ACTTGA

value: BC-PAP

value: BC-PAP cell line treated with 50 µM proscillaridin A for 72 hours


title: FTC133_24h_neg_control

description: Barcode: GATCAG

value: FTC133 cell line treated with DMSO vehicle for 24 hours


title: BC_PAP_24h_proscillaridin

description: Barcode: ACAGTG

value: BC-PAP cell line treated with 50 µM proscillaridin A for 24 hours


title: FTC133_48h_proscillaridin

description: Barcode: GTTTCG

value: FTC133 cell line treated with 50 µM proscillaridin A for 48 hours


title: FTC133_72h_neg_control

description: Barcode: CGTACG

value: FTC133 cell line treated with DMSO vehicle for 72 hours


title: TPC_1_24h_neg_control

description: Barcode: GCCAAT

value: TPC-1 cell line treated with DMSO vehicle for 24 hours


title: TPC_1_24h_lanatoside

description: Barcode: CAGATC

value: TPC-1 cell line treated with 50 µM lanatoside C for 24 hours


title: Bach2_KO_Thn_Bach2_ChIP

city: Toon-shi

first: Makoto

last: Kuwahara

state: Ehime

address: Shitsukawa

department: Department of Immunology

country: Japan

institute: Graduate School of Medicine, Ehime University

description: Bach2-KO CD4 T cells

data_processing:
Illumina Casava1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7
peaks were called using MACS 1.0.0
Genome_build: mm9
Supplementary_files_format_and_content: WIG

source_name: Naïve CD4 T cells

growth_protocol: Naïve CD4 T (CD44lowCD62LhighCD25negative) cells were prepared using a CD4+CD62L+ T cell isolation kit II (Miltenyi Biotec).  Naïve CD4 T cells (1.5 × 10^6) were stimulated with immobilized anti-TCR-β mAb (3 μg ml-1, H57-597; BioLegend) and an anti-CD28 mAb (1 μg ml-1, 37.5; BioLegend) for two days under the conditions indicated.  Next, the cells were transferred to a new plate and cultured further in the presence of cytokines.  The cytokine conditions were as follows: Neutral (Thn) conditions, IL-2 (10 ng ml^-1), anti-IL-4 mAb (5 μg ml^-1, 11B11; BioLegend), and anti-IFN-γ mAb (5 μg ml-1, R4-6A2; BioLegend); Th2 conditions, IL-2 (10 ng ml-1), IL-4 (1 ng ml-1), and anti-IFN-γ mAb (5 μg ml-1, R4-6A2; BioLegend)

extract_protocol:
Lysates were clarified from sonicated nuclei and transcription factor- or histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP Sample Prep Kit.

value: Bach2 KO

value: spleen

value: CD4 T cells

tag: cell cultured conditions

value: Thn conditions (IL-2, anti-IFN-g, anti-IL-4)

tag: chip antibody

value: Bach2 (SIGMA, cat#:SAB2001201, lot#:QC10599


title: FTC133_24h_strophantin

description: Barcode: AGTCAA

value: FTC133 cell line treated with 50 µM strophantin K for 24 hours


title: Bach2_WT_Thn_Bach2_ChIP

description: Bach2-WT CD4 T cells

value: Bach2 WT


title: Bach2_WT_Thn_H3K27ac_ChIP

description: Bach2-WT CD4 T cells

value: H3K27ac (Active Motif, cat#:39133, lot#:105)


title: Bach2_KO_Thn_H3K27ac_ChIP

description: Bach2-KO CD4 T cells


title: Bach2_WT_Th2_H3K27ac_ChIP

description: Bach2-WT CD4 T cells

value: Th2 conditions (IL-2, IL-4, anti-IFN-g)


title: BC_PAP_24h_neg_control

description: Barcode: CGATGT

value: BC-PAP

value: BC-PAP cell line treated with DMSO vehicle for 24 hours


title: DCL4NLS

city: Zürich

first: Alexis

last: Sarazin

address: Universitätstrasse 2

country: Switzerland

institute: ETH

data_processing:
Basecalling pipeline: HiSeq Control Software 2.2.38 ; RTA 1.18.61.0 ; CASAVA-1.8.2
FASTQ file generation and demultiplexing and adapter removal was done by Fasteris.
Small RNA reads were filtered to 15-35nt long reads for analysis. Those were matched against the Arabidopsis thaliana genome (TAIR10) using MUMmer v3.0. Only reads with a perfect match over their entire length were analyzed further
Genome_build: TAIR10
Supplementary_files_format_and_content: For each sample, tab-delimited text files including distinct sequences and reads count values.

source_name: Siliques

growth_protocol: Plants were grown for 2 weeks in soil in a 12hr/12hr light/dark cycle, then moved into a 16hr/8hr chamber. Siliques analyzed in this work were harvested 5 days after pollination.

extract_protocol:
Total cellular RNA (10 µl, 200-300 ng/µL), extracted using TRIzol reagent (Invitrogen)
Extracted RNA was processed into sequencing libraries using adapted Illumina protocols and sequenced at Fasteris (http://www.fasteris.com, Switzerland) using the Illumina HiSeq sequencer

tag: ecotype

value: dcl4-2 mutant expressing nuclear DCL4 from Ubq10 promoter

value: siliques

tag: development stage

value: 5 days after pollination


title: BC_PAP_48h_neg_control

description: Barcode: GCCAAT

value: BC-PAP cell line treated with DMSO vehicle for 48 hours


title: BC_PAP_48h_proscillaridin

description: Barcode: CTTGTA

value: BC-PAP cell line treated with 50 µM proscillaridin A for 48 hours


title: WT

value: wild type


title: Bach2_KO_Th2_H3K27ac_ChIP

description: Bach2-KO CD4 T cells

tag: strain

value: Bach2 KO


title: cKI_Mx_pos_830 [Bisulfite-Seq]

city: New York

first: Barbara

last: Spitzer

state: NY

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequences and then mapped to mm10 using a whole genome bismark alignment software approach with a maximum of 2 mismatches in a directional manner allowed. Only uniquely aligned reads were retained. Reads which pass filter were considered for mapping. If both matched reads pass filter, the last base of R2 was compared to the first base of R1 (one base overlap); the base with the best quality score was retained and R1 was concatenated to R2 for use in alignment.
methylation score were determined for cytosines with at least 20 phred quality score and 10× coverage
Percentage of bisulfite converted Cytosines (Cs; representing unmethylated Cs) and non-converted Cs (representing methylated Cs) were recorded for each C position in a CpG context
Percent methylation values for CpG dinucleotides are calculated by dividing the number of methylated Cs by total coverage on that base (Cs and Ts).
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: tab-delimited text files include the number of methylated Cs and Ts per position (base) covered

source_name: bone marrow

extract_protocol:
bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Genomic DNA was purified from murine cells, digested with MspI restriction enzyme, subjected to end repair and adenylation followed by ligation to cytosine methylated paired-end Illumina adaptors. Fragments of 150-400 bp were isolated by size selection and subjected to bisulfite conversion and PCR amplification using paired-end Illumina primers.  Libraries were sequenced using an Illumina HiSeq2500 per manufacturer’s recommended protocol for 50bp single end read reads

treatment_protocol: Mx1-driven Cre-mediated recombination was induced by 5 IP injections of poly(I:C)

value: LSK


title: dcl4

value: dcl4-2 mutant


title: DCL4∆

value: dcl4-2 mutant expressing cytosplasmic DCL4 from Ubq10 promoter


title: cKI_Mx_pos_829 [Bisulfite-Seq]


title: Col-0 WT Rep2

data_processing:
The TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT.  Sequencing were performed on the Illumina HiSeq 2000 paired end at 2 X101 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA) . Base calling was done with CASAVA v1.8.
FASTQ files were generated by the Zurich Functional Genomics Center (www.fgcz.ch).
Sequenced reads were trimmed for adaptor sequence then mapped to TAIR10 genome using TopHat (v2.0.11) using the TAIR10 Ensembl genome index and genes annotation (http://ccb.jhu.edu/software/tophat/igenomes.shtml)
Bedgraph files have then be generated using deeptools (v1.5.11) on the accepted_hits.bam files generated by TopHat.
Genome_build: TAIR10
Supplementary_files_format_and_content: Bedgraph files generated using deeptools (v1.5.11)

source_name: Inflorescences

growth_protocol: Plants were grown for 2 weeks in soil in a 12hr/12hr light/dark cycle, then moved into a 16hr/8hr chamber.

extract_protocol:
RNA from inflorescences were extracted with the RNeasy mini kit (Qiagen) followed by Dnase treatment.
Sequencing was done at the Zurich Functional Genomics Center (www.fgcz.ch). The quality of the isolated RNA was determined with a Qubit® (1.0) Fluorometer (Life Technologies, California, USA) and a Bioanalyzer 2100 (Agilent, Waldbronn, Germany). Only those samples with a 260 nm/280 nm ratio between 1.8–2.1 and a 28S/18S ratio within 1.5–2 were further processed. The TruSeq Total RNA Sample Prep Kit v2 (Illumina, Inc, California, USA) was used in the succeeding steps. Briefly, total RNA samples (100-1000 ng) were ribo-depleted using Ribo Zero (Epicentre®, USA) then fragmented, end-repaired and polyadenylated before ligation of TruSeq adapters containing the index for multiplexing and reverse-transcription into double-stranded cDNA. Fragments containing TruSeq adapters on both ends were selectively enriched with  PCR.  The quality and quantity of the enriched libraries were validated using Qubit® (1.0) Fluorometer and the Caliper GX LabChip® GX (Caliper Life Sciences, Inc., USA).  The product is a smear with an average fragment size of approximately 260 bp. The libraries were normalized to 10nM in Tris-Cl 10 mM, pH8.5 with 0.1% Tween 20. The TruSeq PE Cluster Kit v3-cBot-HS (Illumina, Inc, California, USA) was used for cluster generation using 10 pM of pooled normalized libraries on the cBOT.  Sequencing were performed on the Illumina HiSeq 2000 paired end at 2 X101 bp using the TruSeq SBS Kit v3-HS (Illumina, Inc, California, USA).

value: Inflorescences


title: cKI_Mx_pos_827 [Bisulfite-Seq]


title: RNA-seq_Human_Week5_Heart_rep4

city: Hangzhou

first: Hongshan

last: Guo

state: Zhejiang Province

address: No.1369, Wenyixi Road

department: School of Medicine, Zhejiang University

institute: Liangzhu Laboratory

description: processed data file: merge.FPKM.human.txt

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
For NOMe-seq, bisulfte-converted reads were first alignned to the hg19 or mm9 refference using Bismark (v0.7.6), and unique mapped reads were retained to calculate the endogenous DNA methylation information, and also to deduce the chromatin accessbility at the same DNA molecule. FOr RNA-seq, sequencing reads were first aligned to the hg19 or mm9 refference using Tophat, and the expression level of protein-coding genes was quantified using cufflinks tool.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: bigWig file which contains the DNA methylation level of cytosine on WCG and GCH context, while .txt files contain the FPKM values of all the protein-coding genes in mouse and human.

extract_protocol:
For NOMe-seq, nuclei DNA was extracted using the Genomic DNA Clean & Concentrator™-10 Kit (Zymo Research), while for bulk RNA-seq, the total RNA was isolated using the Rneasy Mini kit (Qiagen), for single cell RNA-seq, the RNA was released after the single cell was picked into the lysis buffer.
For NOMe-seq, the nuclei was first treated with the GpC methyltransferase (M.CviPI), and the isolated DNA was bisulfite converted using MethylCode Bisulfite Conversion Kit (ThermoFisher), and NOMe-seq library was constructed using PBAT protocol.The single cell RNA-seq was performed using the protocol we developed in 2009 (Tang et al, 2009), while the bulk RNA-seq was performed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

value: heart

tag: age

tag: gender

value: unknown

tag: oct4-gfp knock-in (yes or no)

value: no

tag: bulk or single cell

value: bulk


title: RNA-seq_Human_Week5_Heart_rep3


title: BC_PAP_72h_neg_control

description: Barcode: ATCACG

value: BC-PAP

value: BC-PAP cell line treated with DMSO vehicle for 72 hours


title: wt_Mx_pos_825 [Bisulfite-Seq]


title: Col-0 WT Rep1

tag: tissue


title: RNA-seq_Human_Week5_Heart_rep1


title: wt_Mx_pos_823 [Bisulfite-Seq]


title: cKI_Mx_pos_824 [Bisulfite-Seq]


title: RNA-seq_Human_Week5_Heart_rep2


title: wt_Mx_pos_820 [Bisulfite-Seq]


title: RNA-seq_Human_Week26_male_Soma_single_cell7

value: gonadal somatic cell

value: male

value: single cell


title: cKI_Cre_neg_819 [Bisulfite-Seq]


title: RNA-seq_Human_Week26_male_Soma_single_cell6


title: cKI_Cre_neg_780 [Bisulfite-Seq]


title: RNA-seq_Human_Week26_male_Soma_single_cell5


title: RNA-seq_Mouse_E6.5_Epiblast_bulk2

description: processed data file: merge.FPKM.mouse.txt

value: epiblast


title: RNA-seq_Mouse_E16.5_male_Soma_bulk2

value: yes


title: RNA-seq_Human_Week26_male_Soma_single_cell4


title: RNA-seq_Mouse_E16.5_male_Soma_bulk1


title: RNA-seq_Mouse_E6.5_Epiblast_bulk1


title: RNA-seq_Human_Week26_male_Soma_single_cell1


title: RNA-seq_Human_Week26_male_Soma_single_cell3


title: mcm2-2A H3 ChIP G2M IP Rep2

city: Seattle

first: Laura

last: Lee

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

data_processing:
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) with Bowtie2
Mapped reads were filtered (-F 256)
Per-base coverage file was generated from mapped reads
Coverage files were normalized such that the average value at a genomic position of 1
Genome_build: Saccharomyces_cerevisiae.EF4.65
Supplementary_files_format_and_content: tab-delimited chromosome/position/normalized per-base coverage

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown to OD660 0.2. G1 cells were arrested with alpha-factor (5ug/ml final for BAR1+ strains; 1ug/mL final for bar1- strains). G2M cells were arrested with nocodazole (15ug/ml final). For cells in S phase, G1-arrested cells were filtered and washed, and released into fresh YPD.

extract_protocol:
Cells were disrupted with glass beads, then crosslinked DNA was sonicated to generate ~350bp fragments
Libraries were constructed using NuGEN Ovation UltraLow Library systems

treatment_protocol: Cells were fixed with 1% formaldehyde for 20 min.

tag: background strain

tag: growth conditions

value: 30 degrees C


title: RNA-seq_Human_Week26_male_Soma_single_cell2


title: RNA-seq_Human_Week26_male_PGC_single_cell6

value: primordial germ cell


title: RNA-seq_Mouse_E16.5_male_PGC_bulk1


title: mcm2-2A H3 ChIP G2M IP Rep1


title: RNA-seq_Mouse_E16.5_male_PGC_bulk3


title: RNA-seq_Human_Week26_male_PGC_single_cell7


title: RNA-seq_Mouse_E16.5_male_PGC_bulk2


title: RNA-seq_Human_Week26_male_PGC_single_cell4


title: mcm2-2A H3 ChIP G2M Input Rep1


title: RNA-seq_Mouse_E16.5_female_Soma_bulk2

value: female


title: RNA-seq_Mouse_E16.5_female_Soma_bulk1


title: mcm2-2A H3 ChIP G1 IP Rep1


title: mcm2-2A H3 ChIP G1 Input Rep1


title: mcm2-2A H3 ChIP G1 Input Rep2


title: RNA-seq_Human_Week26_male_PGC_single_cell3


title: RNA-seq_Human_Week26_male_PGC_single_cell2


title: mcm2-2A H3 ChIP G1 IP Rep2


title: mcm2-2A H3 ChIP G2M Input Rep2


title: mcm2-AID H3 ChIP G2M IP Rep1


title: mcm2-AID H3 ChIP G2M Input Rep2


title: RNA-seq_Mouse_E16.5_female_PGC_bulk2


title: RNA-seq_Mouse_E16.5_female_PGC_bulk1


title: mcm2-AID H3 ChIP G2M IP Rep2


title: RNA-seq_Mouse_E13.5_female_Soma_bulk1


title: RNA-seq_Human_Week26_male_PGC_single_cell1


title: RNA-seq_Human_Week26_male_PGC_bulk2


title: mcm2-AID H3 ChIP G1 IP Rep2


title: RNA-seq_Mouse_E13.5_male_Soma_bulk1


title: RNA-seq_Human_Week26_male_PGC_single_cell5


title: mcm2-AID H3 ChIP G1 IP Rep1


title: RNA-seq_Mouse_E13.5_female_PGC_bulk1


title: RNA-seq_Mouse_E11.5_Soma_bulk2


title: NOMe-seq_Human_Week7_male_Soma_rep2

description:
library strategy: NOMe-seq
bisulfite converted DNA


title: NOMe-seq_Human_Week7_male_Soma_rep1


title: mcm2-AID H3 ChIP G1 Input Rep1


title: RNA-seq_Mouse_E11.5_PGC_bulk2


title: orc1-161 BrdU ChIP IP rep1

value: BrdU

value: 24 degrees C


title: NOMe-seq_Human_Week7_male_PGC


title: RNA-seq_Mouse_E11.5_PGC_bulk1


title: orc1-161 BrdU ChIP IP rep2


title: orc1-161 BrdU ChIP Input


title: mcm2-AID H3 ChIP G2M Input Rep1


title: NOMe-seq_Human_Week5_female_Heart_rep1


title: NOMe-seq_Mouse_E6.5_Epiblast_rep2


title: RNA-seq_Mouse_E11.5_Soma_bulk1


title: orc1-161 H3 ChIP G2M IP Rep1


title: NOMe-seq_Human_Week26_male_Soma_rep1


title: NOMe-seq_Human_Week7_male_Soma_rep3


title: RNA-seq_Human_Week26_male_PGC_bulk1


title: NOMe-seq_Human_Week26_male_PGC_rep3


title: NOMe-seq_Mouse_E6.5_Epiblast_rep1


title: orc1-161 H3 ChIP G1 Input Rep1


title: NOMe-seq_Human_Week26_male_Soma_rep2


title: orc1-161 H3 ChIP G2M Input Rep1


title: NOMe-seq_Mouse_E16.5_female_Soma_rep3


title: NOMe-seq_Mouse_E6.5_Epiblast_rep3


title: NOMe-seq_Human_Week26_male_PGC_rep2


title: NOMe-seq_Mouse_E16.5_female_Soma_rep1


title: intestine_1year_input_DNA_R1

city: Paris

first: Yuvia

middle: Alheli

last: Perez Rico

address: 26 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
Basecalls were performed using CASAVA.
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2-2.1.0 configured for global alignment and allowing 1 mismatch in the seed alignment (seed size = 22). If a read aligned more than once in the genome, only the alignment with the best score was saved for further analyses. Aligned reads were saved in BAM format using samtools (version 0.1.8).
BAM files for biological replicates were merged with samtools and converted to BED format with bedtools (v2.24.0).
Peak calling was performed using SICER (V1.1) with the following parameters: redundancy threshold = 1, window size = 200, fragment size = 175 or 200, effective genome fraction = 0.7, gap size = 600 and FDR = 0.05.
After peak calling, peaks were discarded if 50% of the peak overlapped with the regions comprising 2 kb upstream and 2 kb downstream of TSSs (based on RefSeq annotations) and if the peak summit was within these regions.
To identify typical enhancers and super-enhancers the ROSE algorithm was applied (Whyte et al. 2013; Lovén et al. 2013), setting the -t parameter to 2000.
Genome_build: Zv9
Supplementary_files_format_and_content: BED files with annotations for typical enhancers and super-enhancers were generated using ROSE. Scores represent the H3K27ac density in each region.
Supplementary_files_format_and_content: WIG file with the H3K27ac profile generated by SICER and normalized by library size per million.

organism: Danio rerio

extract_protocol:
Whole brains, hearts, intestines and testis were dissected from adult male AB zebrafish (brains, hearts and testis = 10-month-old; hearts and intestines = 1-year-old). Two biological replicates were prepared from brain, heart (1-year-old), intestine and testis, whereas one biological replicate was prepared from 10-month-old heart. Each biological replicate was prepared using: 12 brains, 20 hearts, 5 intestines and 8 testis. All tissues were homogenized and cross-linked in 1% formaldehyde, washed and lysed. Chromatin was sheared using a Covaris S220 ultrasonicator to a DNA fragment size of 175 bp (10-month-old samples) or 200 bp (1-year-old samples). ChIP-seq was performed as previously described (Guenther et al. 2008) using 5 ug Abcam H3K27ac antibody (ab4729, lot# GR259887-1) bound to Dynal Protein A linked beads (Invitrogen). Reverse cross-linked and phenol:chloroform purified chromatin was used for single-end library preparation following standard Illumina protocols.
DNA fragments with an average size of 175 bp or 200 bp were used for single-end library preparation following standard Illumina protocols.

tag: strain background

value: AB

tag: genotype/variation

value: wild type

tag: Sex

value: adult

value: intestine


title: NOMe-seq_Mouse_E16.5_female_Soma_rep2

value: bulk


title: WT BrdU ChIP IP Rep1

tag: genotype

value: wild-type


title: NOMe-seq_Mouse_E16.5_male_PGC_rep2

tag: cell type


title: NOMe-seq_Mouse_E16.5_female_PGC_rep3


title: NOMe-seq_Mouse_E16.5_male_PGC_rep1


title: WT BrdU ChIP Input Rep1


title: NOMe-seq_Human_Week26_male_PGC_rep1

value: no


title: NOMe-seq_Human_Week17_male_Soma_rep2

value: gonadal somatic cell


title: NOMe-seq_Mouse_E16.5_female_PGC_rep1


title: NOMe-seq_Human_Week17_male_PGC_rep3

value: male


title: NOMe-seq_Human_Week26_male_Soma_rep3


title: intestine_1year_H3K27ac_ChIP-seq_R2

description:
processed data file
adult_1year_intestine_H3K27ac_drerio_super_enhancers.bed
adult_1year_intestine_H3K27ac_drerio_typical_enhancers.bed
adult_1year_intestine_drerio_H3K27ac_normalized.wig.gz

value: H3K27ac (Abcam ab4729)


title: WT H3 ChIP G2M IP Rep2


title: orc1-161 H3 ChIP G1 IP Rep1


title: WT H3 ChIP G2M IP Rep1


title: intestine_1year_input_DNA_R2


title: NOMe-seq_Mouse_E16.5_female_PGC_rep2


title: intestine_1year_H3K27ac_ChIP-seq_R1


title: NOMe-seq_Mouse_E13.5_male_PGC_rep2


title: WT H3 ChIP G1 IP Rep2


title: NOMe-seq_Human_Week17_male_PGC_rep1


title: NOMe-seq_Human_Week17_male_PGC_rep2


title: WT H3 ChIP G2M Input Rep2


title: WT H3 ChIP G2M Input Rep1


title: NOMe-seq_Human_Week17_male_Soma_rep1


title: heart_1year_input_DNA_R2

value: heart


title: heart_1year_input_DNA_R1


title: NOMe-seq_Mouse_E13.5_male_PGC_rep1

value: yes


title: heart_1year_H3K27ac_ChIP-seq_R2

description:
processed data file
adult_1year_heart_H3K27ac_drerio_super_enhancers.bed
adult_1year_heart_H3K27ac_drerio_typical_enhancers.bed
adult_1year_heart_drerio_H3K27ac_normalized.wig.gz


title: heart_1year_H3K27ac_ChIP-seq_R1


title: NOMe-seq_Human_Week17_male_Soma_rep3


title: NOMe-seq_Human_Week5_female_Heart_rep2


title: NOMe-seq_Human_Week12_male_PGC_rep2


title: NOMe-seq_Mouse_E13.5_male_PGC_rep3


title: mcm2-AID H3 ChIP G1 Input Rep2

value: 30 degrees C


title: NOMe-seq_Human_Week11_male_PGC_rep1

value: primordial germ cell


title: NOMe-seq_Human_Week12_male_PGC_rep1


title: heart_input_DNA_R1

description:
Processed data file: adult_heart_H3K27ac_drerio_super_enhancers.bed
Processed data file: adult_heart_H3K27ac_drerio_typical_enhancers.bed
Processed data file: adult_heart_drerio_H3K27ac_normalized.wig

data_processing:
Basecalls were performed using CASAVA.
ChIP-seq reads were aligned to the Zv9 genome assembly using Bowtie2-2.1.0 configured for global alignment and allowing 1 mismatch in the seed alignment (seed size = 22). If a read aligned more than once in the genome, only the alignment with the best score was saved for further analyses. Aligned reads were saved in BAM format using samtools (version 0.1.8).
BAM files from biological replicates were merged with samtools and converted to BED format with bedtools (v2.24.0).
Peak calling was performed using SICER (V1.1) with the following parameters: redundancy threshold = 1, window size = 200, fragment size = 175 or 200, effective genome fraction = 0.7, gap size = 600 and FDR = 0.05.
After peak calling, peaks were discarded if 50% of the peak overlapped with the regions comprising 2 Kb upstream and 2 Kb downstream of TSSs (based on RefSeq annotations) and if the peak summit was within these regions.
To identify typical enhancers and super-enhancers, the ROSE algorithm was applied (Whyte et al. 2013; Lovén et al. 2013), setting the -t parameter to 2000.
Genome_build: Zv9
Supplementary_files_format_and_content: BED files with annotations for typical enhancers and super-enhancers were generated using ROSE. Scores represent the H3K27ac density in each enhancer region.
Supplementary_files_format_and_content: WIG file with the H3K27ac profile generated by SICER and normalized by library size per million.

source_name: Adult heart, input

tag: strain/background


title: WT H3 ChIP G1 Input Rep2

tag: chip antibody


title: WT H3 ChIP G1 Input Rep1


title: NOMe-seq_Mouse_E13.5_female_PGC_rep2

value: female


title: testis_input_DNA_R2

description:
Processed data file: adult_testis_H3K27ac_drerio_super_enhancers.bed
Processed data file: adult_testis_H3K27ac_drerio_typical_enhancers.bed
Processed data file: adult_testis_drerio_H3K27ac_normalized.wig

source_name: Adult testis, input

value: testis


title: WT H3 ChIP G1 IP Rep1


title: NOMe-seq_Mouse_E11.5_Soma_rep2

value: unknown


title: NOMe-seq_Mouse_E13.5_female_PGC_rep3


title: testis_input_DNA_R1

value: AB


title: NOMe-seq_Mouse_E13.5_female_PGC_rep1


title: heart_H3K27ac_ChIP-seq_R1

source_name: Adult heart, H3K27ac ChIP

value: wild type


title: testis_H3K27ac_ChIP-seq_R2

source_name: Adult testis, H3K27ac ChIP

value: adult


title: NOMe-seq_Human_Week11_male_PGC_rep2


title: NOMe-seq_Mouse_E11.5_Soma_rep1