title: FOXA2 CDT1 CHIP Rep1

data_processing:
Sequencing read were aligned to human genome (hg19) using bowtie with default parameters
Peaks for TF ChIPs were called using MACS2 and IDR framework.
IDR called FOXA2 peaks from several tissues were further processed using in-house pipeline. Peaks from different cells were merged together if they were found to be overlapping. New peak summit for these merged peak was calcualted based on their relative contributions (heights) as a measure of distance. After calculating and assigning new peak summit to the merged peaks, peaks boundries were also redefined by extending them by 300 bps in both directions from the newly assigned peak summit.
These peaks were then used for downstream analysis. We calculated RPKM for these 600bp peaks. A meta table was created for these 600bp peaks with RPKM values for all TFs, histone marks as well as ATAC signal
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited file with coordinates and RPKM.

source_name: FOXA2 CDT1 CHIP Rep1

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were generated as previously described (Mikkelsen et al., 2010, Gifford et al., 2013) and Libraries were sequenced on a HiSeq 2500 at 11pmol.

tag: source cell tyep

tag: genotype/variation

value: Clonal FOXA2 doxycycline inducible cells

tag: chip antibody info.


title: FOXA2CDT1 CHIPBS Rep1

status: Public on Jan 29 2018

type: SRA

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

country: USA

institute: HSCRB

description: FOXA2 ChIP bisulfite sequencing in FOXA2-CDT1 fusion cells

library_source: genomic

data_processing:
library strategy: ChIP-BS-Seq
For the analysis of methylation changes associated with FOXA2 binding, we redefined binding sites to maximize overlap with our ChIP-BS-Seq data as bisulfite conversion on small amounts of input DNA results in . To do this, we combined FOXA2 ChIP-seq data from BJFOXA2 cells 4days and 10days post induction. The summit of each peak was determined using MACs, then the region 200bp either side was selected, and overlapping regions merged to generate a list of 113,398 sites. We then intersected these regions with BJ fibroblast WGBS and 4day BJFOXA2 ChIP-BS-Seq datasets and selected only CpGs covered by at least 3 reads in both samples, giving a total of 42,086 sites and 135,785 CpGs. We used these same regions to select matched CpGs covered at ≥3X in the ChIP-BS-Seq data from the BJFOXA2 mimosine treated and released samples (n = 13,494 sites and 18,429 CpGs).  We compared individual CpG and mean FOXA2 binding site methylation, generated CpG count and coverage plots and calculated the distances between the summit and nearest CpG using custom R scripts. For comparison to ATAC seq data (described above), we used HOMER (Heinz et al., 2010) to generate enrichment composite plots for 2kb either side of our peaks.
Genome_build: Hg19
Supplementary_files_format_and_content: Bed files contain regions surrounding FOXA2 peak summits (600bps), methylated CpGs over total CpGs and methylation ratio out of 1000

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Clonal FOXA2 doxycycline inducible cells lines were derived from an immortalized BJ foreskin fibroblast cell line from ATCC (BJ-5ta; CRL-4001).  Cells were cultured in MEM-Alpha (Life technologies: 32561-037) with 10% FBS, 1% pen-strep, .01mg/mL hygromycin B and 5ng/mL bFGF.  Derived BJFOXA2 lines were grown in the same conditions plus .5ug/mL Puromycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
To generate bisulfite converted DNA libraries following ChIP, we used Nugen Ovation UltraLow Methyl-seq Kit (0335-0336).  Bisulfite conversion was performed with EpiTect Bisulfite kit (Qiagen) with carrier DNA.  Libraries were sequenced on a HiSeq 2500 8pmol with 35% PhiX spike in.

treatment_protocol: Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night. To induce FOXA2, doxycycline was added at .5ug/mL.

tag: cell line

value: BJFOXA2 line

tag: source cell type

value: BJ Fibroblast


title: FOXA2_MIMOSINERelease ChIP-BS

description: FOXA2 ChIP bisulfite sequencing on cells halted in G1 with Mimosine treatment and then released back into normal cycling conditions


title: FOXA2 CDT1 CHIP Rep2

source_name: FOXA2 CDT1 CHIP Rep2


title: FOXA2 ChIP-BS

description: FOXA2 ChIP bisulfite sequencing

source_name: FOXA2 ChIP bisulfite sequencing


title: Mimosine FOXA2 ChIP

source_name: Mimosine FOXA2 ChIP


title: MimosineRelease FOXA2 ChIP

source_name: MimosineRelease FOXA2 ChIP


title: FOXA2 ATAC After Withdrawal

source_name: FOXA2 ChIP After Withdrwal

extract_protocol:
Tagmentation was performed on whole nuclei at 37C for 45 minutes as previously described in (Buenrostro et al., 2013).  DNA was isolated on PCR min-elute columns (Qiagen) and a small amount of the DNA was amplified for 9, 12 and 15 cycles to determine optimal cycling conditions.
Nextera amplified

treatment_protocol: Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment overnight. To induce FOXA2, doxycycline was added at .5ug/mL.


title: FOXA2 GATA4 CoExp FOXA2 ChIP Rep1

source_name: FOXA2 GATA4 CoExp FOXA2 ChIP Rep1


title: GATA4 ChIP

source_name: GATA4 ChIP


title: FOXA2 GATA4 CoExp FOXA2 ChIP Rep2

source_name: FOXA2 GATA4 CoExp FOXA2 ChIP Rep2


title: OCT ChIP BJ

source_name: OCT ChIP BJ


title: FOXA2 Mimosine ATAC Rep2

source_name: FOXA2 Mimosine ChIP


title: KO-cytoRNA-2.0_2nd 2.0 ng /ul Rnase A

city: Boston

first: Sun

last: Hur

state: MA

address: 3 Blackfan Circle, Boston, MA, 02115

department: Program in Cellular and Molecular Medicine (PCMM)

institute: Boston Children's Hospital

description:
cytoplasmic RNA
This 293T cell line does not express ADAR1 proteins

library_source: transcriptomic

data_processing:
Library strategy: RNA footprinting
Basecalls performed using RTA version 1.18.54
sequence data were trimmed by Trimmomatic 0.33
aligned against hg38 using STAR 2.5.2a
gene count analysis using htseq-count 0.6.1p1
repeat elements analysis using RepeatMasker
Genome_build: hg38
Supplementary_files_format_and_content: txt file with raw gene count & tbl.txt with Repeat element analysis

molecule: total RNA

source_name: HEK293T ADAR1KO cells_RNaseA-digested

growth_protocol: HEK293T ADAR1-KO cells are maintained in DMEM containing 10% FBS, 1% penicillin/streptomycin

extract_protocol:
cytoplasmic RNA was purified with hypotonic buffer, followed by douncing 50 times. RNA was purified using Qiagen RNeasy Mini Kit. RNAs were first incubated with recombinant  WT MDA5 proteins, then challenged by 2ng/ul of RNaseA. The reaction was terminated by TRIzol. RNA was recovered and rRNA was depleted using NEBNext rRNA depletion kit.
cDNA library was constructed using Clontech Smarter Stranded RNA-seq Kit. Mock-treated RNAs (cytoRNA-0.0) were fragmented by heating at 94C for 3min, RNaseA-digested RNA (cytoRNA-2.0) was fragmented by heating at 94C for 1min without First-strand Buffer. PCR cycles for cytoRNA-0.0 was 15, for cytoRNA-2.0 were 18. The Ampure Beads:DNA ratio was 0.8:1 (volume:volume) for DNA purification.

tag: cell type

value: human embryonic kidney cells grown in tissue culture

tag: passages

tag: mda5 protein status

value: recombinant wildtype

tag: hek293t genotype


title: KO-cytoRNA-0.0_1st 0.0 ng/ul RNase A

source_name: HEK293T ADAR1KO cells_mock


title: FOXA2 Mimosine Released ATAC Rep2

source_name: FOXA2 Mimosine Released ChIP


title: KO-cytoRNA-2.0_1st 2.0 ng/ul RNase A


title: KO-cytoRNA-0.0_2nd 0.0 ng/ul RNase A


title: FOXA2 GATA4 CoExp GATA4 ChIP

source_name: FOXA2 GATA4 CoExp GATA4 ChIP


title: cytoRNA-0.5_2nd 0.5 ng/ul RNase A

description: cytoplasmic RNA

data_processing:
Library strategy: RNA footprinting
Basecalls performed using RTA version 1.18.54
sequence data were trimmed by Trimmomatic 0.33
aligned against hg38 using STAR 2.5.2a
gene count analysis using htseq-count 0.6.1p1
repeat elements analysis using RepeatMasker
Genome_build: hg38
Supplementary_files_format_and_content: txt

source_name: HEK293T cells

growth_protocol: HEK293T cells are maintained in DMEM containing 10% FBS, 1% penicillin/streptomycin

extract_protocol:
cytoplasmic RNA was purified with hypotonic buffer, followed by douncing 50 times. RNA was purified using Qiagen RNeasy Mini Kit. RNAs were first incubated with recombinant  MDA5 proteins, then challenged by two concentrations of RNaseA. The reaction was terminated by TRIzol. RNA was recovered and rRNA was depleted using NEBNext rRNA depletion kit.
cDNA library was constructed using Clontech Smarter Stranded RNA-seq Kit. Mock-treated RNAs (cytoRNA-0.0) were fragmented by heating at 94C for 3min, RNaseA-digested RNAs (cytoRNA-0.5 and cytoRNA-2.0) were fragmented by heating at 94C for 1min without First-strand Buffer. PCR cycles for cytoRNA-0.0 was 15, for cytoRNA-0.5 and -2.0 were 18. The Ampure Beads:DNA ratio was 0.8:1 (volume:volume) for DNA purification.

treatment_protocol: No extra treatment to the cells.

value: recombinant G495R mutated form

value: wildtype


title: cytoRNA-2.0_1st 2.0 ng/ul RNase A

description: cytoplasmic RNA


title: THMYCN_139423_MYCN

first: James

last: Bradner

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Chromatin IP against MYCN in tumors from Th-MYCN mice

data_processing:
Sequenced reads were aligned to MM9 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: mm9
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

organism: Mus musculus

source_name: Th-MYCN mouse

growth_protocol: All experimental protocols were monitored and approved by The Institute of Cancer Research Animal Welfare and Ethical Review Body, in compliance with guidelines specified by the UK Home Office Animals (Scientific Procedures) Act 1986 and the United Kingdom National Cancer Research Institute guidelines for the welfare of animals in cancer research (Workman et al., 2010). Th-MYCN mice were genotyped to detect the presence of human MYCN transgene 27. Palpable intra-abdominal tumors or ganglia from Th-MYCN mice at 12-14 days of age were dissected and harvested for ChIP and immunohistochemistry.

extract_protocol:
For ChIP, tumors and ganglia were immediately flash frozen in liquid nitrogen and stored at -80°C. For immunohistochemistry, tumor and ganglia tissue were immediately fixed in 4% paraformaldehyde before being processed.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

tag: tissue

value: THMYCN tumor

tag: input

tag: treatment

tag: strain

value: Th-MYCN

tag: barcode

value: TTCCTGCT

tag: chip antibody

value: MYCN

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #


title: FOXA2_MIMOSINE ChIP-BS R1

description:
FOXA2 ChIP bisulfite sequencing on cells halted in G1 with Mimosine treatment
processed data file: 11_6PlusPlusMimo_oldFOXA2_ChipBS021616.bam.bed


title: cytoRNA-0.0_1st 0.0 ng/ul RNase A

description: cytoplasmic RNA


title: RNASeq Post-FOXA2 rep2

description: Induced Rep2

data_processing:
Sequencing reads were aligned to human genome (hg19) using TopHat with default parameters
RPKM calculations were performed using Cufflinnks
Genome_build: hg19

source_name: RNASeq Post-FOXA2

extract_protocol:
Rnseasy Qiagen
RNA was isolated with RNeasy columns (Qiagen) and non-stranded libraries were performed using Illumina’s standard Tru-Seq kit.  Libraries were sequenced on a HiSeq 2500 at 11pmol.

treatment_protocol:
To induce FOXA2, doxycycline was added at .5ug/mL.
Cells were halted in G1 by the addition of 200uM Mimosine (Sigma) treatment over night. To induce FOXA2, doxycycline was added at .5ug/mL.

tag: cell line background

value: immortalized BJ foreskin fibroblast cell line

value: FOXA2 doxycycline inducible cell line

tag: treated with

value: 0.5 ug/ml doxycycline


title: FOXA2 Mimosine ATAC Rep1

tag: genotype/variation


title: RNAseq Pre-FOXA2  rep2

description: Uninduced Rep2

source_name: RNAseq Pre-FOXA2

value: none (uninduced)


title: RNASeq Post-FOXA2 rep1

description: Induced Rep1


title: BJ_PlusMimosinePlus_FOXA2-FOXA2Chip0703.1

source_name: FOXA2 Mimo Plus ChIP

tag: cell line

value: FoxA2 Antibody

tag: chip antibody info.


title: BJ_PlusMimosineRelease_FOXA2-FOXA2Chip0703.1

source_name: FOXA2 Mimo Released ChIP


title: FOXA2 Mimosine Released ATAC Rep1

tag: source cell type

value: Clonal FOXA2 doxycycline inducible cells


title: cytoRNA-2.0_2nd 2.0 ng/ul RNase A

description: cytoplasmic RNA

tag: cell type

tag: passages


title: BJ_PlusMimosineRelease_FOXA2-FOXA2Chip0703.2


title: Foxa2_A549_Rep2.1

source_name: FOXA2 ChIP A549


title: Foxa2_A549_Rep1.1


title: FOXA2_dEN_WCE.1

source_name: WCE dEN

value: Definitive Endoderm (ES derived)


title: FOXA2_dEN_Rep1.1

source_name: FOXA2 ChIP dEN


title: FOXA2_KerCT_WCE.1

source_name: WCE Keratenocyte

value: KerCT


title: cytoRNA-0.0_2nd 0.0 ng/ul RNase A

description: cytoplasmic RNA

value: human embryonic kidney cells grown in tissue culture

tag: mda5 protein status

tag: hek293t genotype


title: FOXA2_KerCT_Rep1.1

source_name: FOXA2 ChIP Keratenocytes


title: FOXA2_KerCT_Rep2.1


title: BJ K4me2 Rep2

source_name: H3K4me2 ChIP

value: BJ Fibroblast


title: BJH_GATA4-V5chip0703.1

source_name: GATA4 ChIP


title: BJH_GATA4-V5chip0703.2


title: FOXA2_HepG2_WCE.1

source_name: WCE HEPG2


title: BJ K4me2 Rep1


title: BJ K27ac Rep2

source_name: H3K27ac ChIP


title: FOXA2_HepG2_Rep1.1

source_name: FOXA2 ChIP HEPG2


title: BJ K27ac Rep1


title: BJ_PlusMimosinePlus_FOXA2-FOXA2Chip0703.2


title: BJ FOXA2 ChIP Rep2

source_name: FOXA2 ChIP BJ


title: BJ FOXA2 ChIP Rep1


title: RNAseq Pre-FOXA2  rep1

description: Uninduced Rep1


title: BJ_ATAC_48h_R2

source_name: ATACseq Post-FOXA2


title: BJ_ATAC_R1

source_name: ATACseq Pre-FOXA2


title: THP1-shZFR-PMA-2

city: Bethesda

first: J

middle: Robert

last: Hogg

state: MD

address: 50 South Drive, #2239

department: Biochemistry and Biophysics Center

institute: National Heart, Lung and Blood Institute

data_processing:
Sequencing reads in FASTQ format were aligned to the reference genome hg19 using STAR aligner.
Differential gene expression analysis was performed using the DESEQ2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values and fold expression change.

growth_protocol: HEK-293TO cells were maintained in DMEM supplemented with 10% FBS , 100 U/ml of penicillin, 100 μg/ml streptomycin , and 0.3 mg/ml of L-glutamine at 37°C and 5% CO2. Human monocytic THP-1 cells (ATCC) were maintained in ATCC-formulated RPMI-1640 medium supplemented with 10% FBS (Gibco), 0.05 mM 2-mercaptoethanol (Sigma), and 100 U/mL of Penicillin, 100 μg/mL Streptomycin (Gibco).

extract_protocol:
Qiagen RNeasy Mini RNA isolation kit
One μg of total RNA was used per sample for library preparation. Ribosomal RNA was depleted from total RNA with the Ribo-Zero rRNA Removal Kit (Epicentre), and purified RNA was then converted to cDNA with the TruSeq RNA Library Preparation Kit (Illumina).

treatment_protocol: Monocyte-like THP-1 cells were differentiated into macrophage-like cells with 5 ng/mL of phorbol-12-myristate-13-acetate (PMA, Sigma) for 72 hr.

value: Transduced with ZFR-specific shRNA

value: ZFR knockdown


title: ChIPseq_nrpd1_antiNRPE1

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description:
ChIPseq of anti-NRPE1 in nrpd1.
Anti-NRPE1 antibody (Covance) were raised through recognizing the peptide NNCDKKNSETESDAAAWG-C as described before in Ream, T.S., et al. Molecular Cell, 33, 192-203 (2009).

data_processing:
GRO-seq: Qseq files from the sequencer were demultiplexed and converted to fastq format with a customized script for downstream analysis. For GRO-seq data, paired-end reads were first trimmed for Illumina adaptors and primers using Cutadapt (v 1.9.1). After trimming, reads less than 10bp long were removed with a customized Perl script. Paired-end reads were then separately aligned to the reference TAIR10 genome using Bowtie (v1.1.0) by allowing only unique hit (-m 1) and up to 3 mismatches (-v 3). Pair reads aligned to positions within 2000bp to each other were considered as correct read pairs using, and reads aligned to Watson or Crick strands were separated by a customized Perl script.
ChIP-seq: Reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie 1.0.0, allowing only uniquely mapping reads with less than two mismatches, and duplicated reads were combined into one read. NRPE1 ChIP-seq peaks were called using MACS2 (v 2.1.1.) with default parameters. ChIP-seq metaplots were plotted using NGSplot (v 2.41.4).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

organism: Arabidopsis thaliana

source_name: floral tissue, nrpd1-4, NRPE1 ChIP

growth_protocol: All plants were grown on soil under long day conditions (16 hours light, 8 hours dark). Inflorescence tissues were collected and used for the GRO-seq procedure.

extract_protocol:
GRO-seq: Approximately 10 grams of inflorescence and meristem tissue was collected from plants and immediate placed in ice cold grinding buffer (300 mM sucrose, 20 mM Tris, pH 8.0, 5 mM MgCl2, 5 mM KCl, 0.2% Triton X-100, 5 mM β-mercaptoethanol, 35% glycerol). Nuclei were isolated as described previously. Briefly, samples were ground with an OMNI International General Laboratory Homogenizer at 4°C until well homogenized, filtered through a 250µm nylon mesh, 100µm nylon mesh, miracloth, and finally a 40µm cell strainer before being split into 50ml conical tubes. Samples were spun for 10 minutes at 5250g, the supernatant was discarded, and the pellets were pooled and resuspended in 25ml of grinding buffer using a dounce homogenizer. The wash step was repeated at least once more and nuclei were resuspended in 1ml of freezing buffer (50 mM Tris, pH 8.0, 5 mM MgCl2, 20% glycerol, 5 mM β-mercaptoethanol). Approximately 5x10e6 nuclei in 200 µl of freezing buffer were run-on in 3x GRO-reaction buffer 16 with. Reactions were stopped after 5 minutes to minimize run on length (~5-15 nts) while still incorporating brUTP by addition of 750 µl Trizol LS and RNA purified according to the manual. Without fragmentation or Terminator treatment, nascent RNA was enriched twice for BrU by αBrdU (Santa Cruz Biotechnology sc-32323AC) and immunoprecipitated as described in Hetzel et al. 2016.
ChIP-seq: Chromatin immunoprecipitation was performed from 2 grams of formaldehyde crosslinked flower tissue as previously described, except that half of the input was immunoprecipitated with 3 µg of affinity purified anti-NRPE1 antibody (Covance) that recognizes the peptide N-CDKKNSETESDAAAWG- C49, and the other half was immunoprecipitated with pre-immune serum as control.
GRO-seq: Sequencing libraries were prepared from precipitated RNA using TruSeq Small RNA Library Prep kit following manufacturer instructions (Illumina). For GROseq in Col-0, nrpd1, nrpe1 and nrpd1/e1 double mutants, 14 cycles of PCR were used to amplify the libraries and the products ranging from 100 to 500bp were size selected by agarose gel. The libraries were sequenced on Illumina HiSeq 2000 platform by paired-end 100bp sequencing. For GROseq in spt5l, 14 cycles of PCR were used to amplify the libraries and the products were size selected by double SPRI bead purification (ratio of Ampure beads to library: 0.5:1 to 1.1:1).
ChIP-seq: DNA libraries for Illumina sequencing were generated using the Ovation Ultralow V2 system (Nugen).

tag: ecotype/background

value: Columbia

tag: tissue

value: floral

value: Anti-NRPE1 (Covance)


title: THP1-shZFR-PMA-1

tag: treatment


title: ChIPseq_nrpd1_preimmune

description: ChIPseq of pre-immune in nrpd1.

source_name: floral tissue, nrpd1-4, pre-immune ChIP

value: Pre-immune serum


title: THP1-shScr-PMA-3

value: Transduced with non-specific shRNA

value: control


title: THP1-shScr-PMA-2


title: ChIPseq_col_preimmune

description: ChIPseq of pre-immune in col.

source_name: floral tissue, wild type, pre-immune ChIP

value: Wild type


title: ChIPseq_col_antiNRPE1

description:
ChIPseq of anti-NRPE1 in col.
Anti-NRPE1 antibody (Covance) were raised through recognizing the peptide NNCDKKNSETESDAAAWG-C as described before in Ream, T.S., et al. Molecular Cell, 33, 192-203 (2009).

source_name: floral tissue, wild type, NRPE1 ChIP


title: THP1-shZFR-3

value: Undifferentiated monocyte like cell


title: GROseq_col_rep4

description: GROseq in Col (rep4)

data_processing:
Library strategy: GRO-Seq
GRO-seq: Qseq files from the sequencer were demultiplexed and converted to fastq format with a customized script for downstream analysis. For GRO-seq data, paired-end reads were first trimmed for Illumina adaptors and primers using Cutadapt (v 1.9.1). After trimming, reads less than 10bp long were removed with a customized Perl script. Paired-end reads were then separately aligned to the reference TAIR10 genome using Bowtie (v1.1.0) by allowing only unique hit (-m 1) and up to 3 mismatches (-v 3). Pair reads aligned to positions within 2000bp to each other were considered as correct read pairs using, and reads aligned to Watson or Crick strands were separated by a customized Perl script.
ChIP-seq: Reads were aligned to the Arabidopsis reference genome (TAIR10) with Bowtie 1.0.0, allowing only uniquely mapping reads with less than two mismatches, and duplicated reads were combined into one read. NRPE1 ChIP-seq peaks were called using MACS2 (v 2.1.1.) with default parameters. ChIP-seq metaplots were plotted using NGSplot (v 2.41.4).
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

source_name: floral tissue, wild type


title: GROseq_col_rep3

description: GROseq in Col (rep3)


title: THP1-shScr-PMA-1


title: BJ_ATAC_48h_R1

value: immortalized BJ foreskin fibroblast cell line

value: FOXA2 doxycycline inducible cell line

value: 0.5 ug/ml doxycycline


title: GROseq_idn2_rep1

description: GROseq in idn2 (rep1)

source_name: floral tissue, idn2-1


title: GROseq_idn2_rep2

description: GROseq in idn2 (rep2)


title: THP1-shScr-3


title: THP1-shZFR-PMA-3


title: THP1-shZFR-1


title: GROseq_aog4_rep2

description: GROseq in ago4 (rep2)

source_name: floral tissue, ago4-5


title: GROseq_ago4_rep1

description: GROseq in ago4 (rep1)


title: ZBTB2_KO_1

city: Zürich

first: Ino

last: Karemaker

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Biological replicate 1

data_processing:
Reads were mapped onto the reference mouse genome mm9 (NCBI build 37) using the Genomic Short-read Alignment Program
Differential gene expression was analysed with the Cufflinks v2.2.1 package
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample separately and the results of the statistical tests combining all samples

extract_protocol:
Total RNA was extracted with an RNeasy Mini Kit (Qiagen)
Libraries were prepared for Illumina sequencing using 5 ng of ChIP material with a Kapa Hyper Prep Kit (Kapa Biosystems), according to the manufacturer’s instructions, but with an additional incubation with USER enzyme (NEB) before library amplification to digest the second cDNA strand

tag: strain background

value: Embryonic stem cells

value: CRISPR-mediated Zbtb2 KO in IB10 ESCs


title: IB10_WT_1

description: Biological replicate 1

value: WT IB10 ESCs


title: GROseq_frg1/2_rep2

description: GROseq in frg1/2 (rep2)

source_name: floral tissue, frg1/2


title: BJ_ATAC_R2

value: none (uninduced)


title: IB10_WT_2

description: Biological replicate 2


title: THP1-shScr-2


title: WT_NPC

data_processing:
Reads were mapped onto the reference mouse genome mm9 (NCBI build 37), using the Burrows-Wheeler Alignment tool
Mapped reads were filtered on sequence quality, and PCR duplicates were removed, using samtools
Peak calling was performed using the MACS 2.0 tool with the indicated p-value against a merge of the 5% input and GFP ChIP in wildtype cells, which was randomly downscaled to match the number of reads of the GFP ChIP in the BAC line
Genome_build: mm9
Supplementary_files_format_and_content: Bed files contain called peaks

source_name: R1 ESC-derived NPCs

extract_protocol: Libraries were prepared for Illumina sequencing using 5 ng of ChIP material with a Kapa Hyper Prep Kit (Kapa Biosystems), according to the manufacturer’s instructions

value: Neural progenitor cells

value: R1 ESC-derived NPCs

tag: culture conditions

value: NPC medium

tag: chip antibody

value: GFP (Abcam, ab290)


title: Input_ZBTB2-GFP_NPC

source_name: ZBTB2-GFP BAC IB10 ESC-derived NPCs

value: ZBTB2-GFP BAC IB10 ESC-derived NPCs


title: GROseq_frg1/2_rep1

description: GROseq in frg1/2 (rep1)

value: Columbia

value: floral


title: GROseq_idn2/idnl1/idnl2_rep2

description: GROseq in idn2/idnl1/idnl2 (rep2)

source_name: floral tissue, idn2-1/idnl1-1/idnl2-1


title: THP1-shScr-1

value: Transduced with non-specific shRNA

value: control


title: ZBTB2-GFP_NPC


title: ZBTB2_KO_2

description: Biological replicate 2


title: Input_ZBTB2-GFP_ESC_2i

source_name: ZBTB2-GFP BAC IB10 ESCs

value: ZBTB2-GFP BAC IB10 ESCs

value: Serum/LIF + 2i


title: GROseq_suvr2_rep2

description: GROseq in suvr2 (rep2)

source_name: floral tissue, suvr2-1


title: GROseq_idn2/idnl1/idnl2_rep1

description: GROseq in idn2/idnl1/idnl2 (rep1)


title: WT_ESC

source_name: WT IB10 ESCs

value: Serum/LIF


title: ZBTB2-GFP_ESC_2i


title: GROseq_drm3_rep2

description: GROseq in drm3 (rep2)

source_name: floral tissue, drm3-1


title: ZBTB2-GFP_ESC


title: GROseq_suvr2_rep1

description: GROseq in suvr2 (rep1)


title: GROseq_drm3_rep1

description: GROseq in drm3 (rep1)


title: Input_ZBTB2-GFP_ESC


title: Cut-and-Run_human_K27_lo_(20170313_SH_HsSc_K27_lo_0306)

status: Public on Jan 28 2018

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description:
human dig cells K27me3 30 min digestion
Immunotargeting, cleavage and release

data_processing:
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to UCSC hg19.  2. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to UCSC sacCer3.  3. We extracted properly paired reads from both alignments (Supplementary files .bed.gz .SC.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to S.cervisiae) to create a normalized yeast track file (Supplementary file .bedgraph.gz).
genome_build: UCSC hg19
genome_build: UCSC sacCer3
Library strategy: Cut-and-Run

source_name: human K562 cells, anti-K27me3 Cell Signalling #9733

extract_protocol:
CUT-and-RUN_dig.rtf
PMID 25827087

value: human K562 cells


title: GROseq_nrpd1e1_rep2

description: GROseq in nrpd1/nrpe1 (rep2)

source_name: floral tissue, nrpd1-4/nrpe1-11


title: GROseq_nrpe1_rep1

description: GROseq in nrpe1 (rep1)

source_name: floral tissue, nrpe1-12


title: GROseq_nrpe1_rep2

description: GROseq in nrpe1 (rep2)


title: THP1-shZFR-2

value: Transduced with ZFR-specific shRNA

value: ZFR knockdown

value: Undifferentiated monocyte like cell


title: GROseq_nrpd1_rep2

description: GROseq in nrpd1 (rep2)

source_name: floral tissue, nrpd1-4


title: GROseq_col_rep1

description: GROseq in Col (rep1)

value: Wild type


title: Cut-and-Run_human_CENPA_lo_(20170313_SH_HsSc_CeAm_lo_0306)

description:
human dig cells CENP-A 30 min digestion
Immunotargeting, cleavage and release

source_name: human K562 cells, anti-CENP-A Abcam ab13939


title: GROseq_nrpd1_rep1

description: GROseq in nrpd1 (rep1)


title: GROseq_nrpd1e1_rep1

description: GROseq in nrpd1/nrpe1 (rep1)


title: GROseq_col_rep2

description: GROseq in Col (rep2)


title: Cut-and-Run_human_CENPB_lo_10min_(20170510_SH_HsSc_CeBlN10m0501)

description:
human nuclei CENP-B 10 min digestion
Immunotargeting, cleavage and release

source_name: human K562 cells, anti-CENP-B Abcam ab25734

extract_protocol:
Cut_and_Run_human.rtf
PMID 25827087


title: E6.75_Mesp1-GFP+_WT_172

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

country: United Kingdom

institute: University of Cambridge

data_processing:
library strategy: single cell RNA-seq
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

extract_protocol:
Bone marrow cells were isolated from the femurs, tibiae and iliac crest of 20 8-12 week old C57BL/6 mice.
The cells were lineage depleted and stained with antibodies to separate individual populations by FACS.
Single-cell sorting was done using a FACS Influx5 (BD Biosciences) using unstained cells and single-stained cells are gate-settng controls.
Cells were sorted directly into individual wells of a 96-well PCR plate containing lysis buffer.
Single-cell RNA-seq analysis was performed as described previously (Picelli et al., 2014).
Pooled libraries were run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: develpmental stage

value: Gastrulation

tag: age

value: Mesp1+ cells


title: E6.75_Mesp1-GFP+_WT_170


title: E6.75_Mesp1-GFP+_WT_171


title: E6.75_Mesp1-GFP+_WT_167


title: E6.75_Mesp1-GFP+_WT_169


title: E6.75_Mesp1-GFP+_WT_165


title: E6.75_Mesp1-GFP+_WT_166


title: E6.75_Mesp1-GFP+_WT_168


title: E6.75_Mesp1-GFP+_WT_160


title: E6.75_Mesp1-GFP+_WT_159


title: E6.75_Mesp1-GFP+_WT_164


title: E6.75_Mesp1-GFP+_WT_163


title: E6.75_Mesp1-GFP+_WT_158


title: E6.75_Mesp1-GFP+_WT_161


title: E6.75_Mesp1-GFP+_WT_157


title: E6.75_Mesp1-GFP+_WT_156


title: E6.75_Mesp1-GFP+_WT_154


title: E6.75_Mesp1-GFP+_WT_152


title: E6.75_Mesp1-GFP+_WT_155


title: E6.75_Mesp1-GFP+_WT_149


title: E6.75_Mesp1-GFP+_WT_153


title: E6.75_Mesp1-GFP+_WT_148


title: E6.75_Mesp1-GFP+_WT_147


title: E6.75_Mesp1-GFP+_WT_145


title: E6.75_Mesp1-GFP+_WT_162


title: E6.75_Mesp1-GFP+_WT_146


title: E6.75_Mesp1-GFP+_WT_140


title: E6.75_Mesp1-GFP+_WT_150


title: E6.75_Mesp1-GFP+_WT_144


title: E6.75_Mesp1-GFP+_WT_138


title: E6.75_Mesp1-GFP+_WT_133


title: E6.75_Mesp1-GFP+_WT_137


title: E6.75_Mesp1-GFP+_WT_143


title: E6.75_Mesp1-GFP+_WT_141


title: E6.75_Mesp1-GFP+_WT_139


title: E6.75_Mesp1-GFP+_WT_151


title: E6.75_Mesp1-GFP+_WT_131


title: E6.75_Mesp1-GFP+_WT_135


title: E6.75_Mesp1-GFP+_WT_136


title: E6.75_Mesp1-GFP+_WT_129


title: E6.75_Mesp1-GFP+_WT_132


title: E6.75_Mesp1-GFP+_WT_128


title: E6.75_Mesp1-GFP+_WT_127


title: E6.75_Mesp1-GFP+_WT_126


title: E6.75_Mesp1-GFP+_WT_142


title: E6.75_Mesp1-GFP+_WT_125


title: E6.75_Mesp1-GFP+_WT_122


title: E6.75_Mesp1-GFP+_WT_123


title: E6.75_Mesp1-GFP+_WT_121


title: E6.75_Mesp1-GFP+_WT_124


title: E6.75_Mesp1-GFP+_WT_119


title: E6.75_Mesp1-GFP+_WT_130


title: E6.75_Mesp1-GFP+_WT_134


title: E6.75_Mesp1-GFP+_WT_115


title: E6.75_Mesp1-GFP+_WT_112


title: E6.75_Mesp1-GFP+_WT_118


title: E6.75_Mesp1-GFP+_WT_113


title: E6.75_Mesp1-GFP+_WT_117


title: E6.75_Mesp1-GFP+_WT_116


title: E6.75_Mesp1-GFP+_WT_114


title: E6.75_Mesp1-GFP+_WT_109


title: E6.75_Mesp1-GFP+_WT_111


title: E6.75_Mesp1-GFP+_WT_108


title: E6.75_Mesp1-GFP+_WT_107


title: E6.75_Mesp1-GFP+_WT_106


title: E6.75_Mesp1-GFP+_WT_105


title: E6.75_Mesp1-GFP+_WT_104


title: E6.75_Mesp1-GFP+_WT_103


title: E6.75_Mesp1-GFP+_WT_101


title: E6.75_Mesp1-GFP+_WT_120


title: E6.75_Mesp1-GFP+_WT_100


title: E6.75_Mesp1-GFP+_WT_095


title: E6.75_Mesp1-GFP+_WT_096


title: E6.75_Mesp1-GFP+_WT_099


title: E6.75_Mesp1-GFP+_WT_097


title: E6.75_Mesp1-GFP+_WT_098


title: E6.75_Mesp1-GFP+_WT_094


title: E6.75_Mesp1-GFP+_WT_110


title: E6.75_Mesp1-GFP+_WT_093


title: E6.75_Mesp1-GFP+_WT_092


title: E6.75_Mesp1-GFP+_WT_091


title: E6.75_Mesp1-GFP+_WT_102


title: E6.75_Mesp1-GFP+_WT_090


title: E6.75_Mesp1-GFP+_WT_089


title: E6.75_Mesp1-GFP+_WT_088


title: E7.25_Mesp1-GFP+_WT_341


title: E6.75_Mesp1-GFP+_WT_087


title: E6.75_Mesp1-GFP+_WT_086


title: E7.25_Mesp1-GFP+_WT_339


title: E7.25_Mesp1-GFP+_WT_337


title: E6.75_Mesp1-GFP+_WT_085


title: E7.25_Mesp1-GFP+_WT_340


title: E7.25_Mesp1-GFP+_WT_338


title: E7.25_Mesp1-GFP+_WT_335


title: E7.25_Mesp1-GFP+_WT_336


title: E7.25_Mesp1-GFP+_WT_334


title: E7.25_Mesp1-GFP+_WT_333


title: E7.25_Mesp1-GFP+_WT_331


title: E7.25_Mesp1-GFP+_WT_332


title: E7.25_Mesp1-GFP+_WT_327


title: E7.25_Mesp1-GFP+_WT_326


title: E7.25_Mesp1-GFP+_WT_329


title: E7.25_Mesp1-GFP+_WT_325


title: E7.25_Mesp1-GFP+_WT_323


title: E7.25_Mesp1-GFP+_WT_328


title: E7.25_Mesp1-GFP+_WT_324


title: E6.75_Mesp1-GFP+_WT_084


title: E7.25_Mesp1-GFP+_WT_322


title: E7.25_Mesp1-GFP+_WT_320


title: E7.25_Mesp1-GFP+_WT_318


title: E7.25_Mesp1-GFP+_WT_317


title: E7.25_Mesp1-GFP+_WT_321


title: E7.25_Mesp1-GFP+_WT_315


title: E7.25_Mesp1-GFP+_WT_316


title: E7.25_Mesp1-GFP+_WT_313


title: E7.25_Mesp1-GFP+_WT_312


title: E7.25_Mesp1-GFP+_WT_311


title: E7.25_Mesp1-GFP+_WT_310


title: E7.25_Mesp1-GFP+_WT_308


title: E7.25_Mesp1-GFP+_WT_306


title: E7.25_Mesp1-GFP+_WT_307


title: E7.25_Mesp1-GFP+_WT_309


title: E7.25_Mesp1-GFP+_WT_305


title: E7.25_Mesp1-GFP+_WT_304


title: E7.25_Mesp1-GFP+_WT_303


title: E7.25_Mesp1-GFP+_WT_330


title: E7.25_Mesp1-GFP+_WT_301


title: E7.25_Mesp1-GFP+_WT_299


title: E7.25_Mesp1-GFP+_WT_302


title: E7.25_Mesp1-GFP+_WT_319


title: E7.25_Mesp1-GFP+_WT_298


title: E7.25_Mesp1-GFP+_WT_297


title: E7.25_Mesp1-GFP+_WT_295


title: E7.25_Mesp1-GFP+_WT_296


title: E7.25_Mesp1-GFP+_WT_314


title: E7.25_Mesp1-GFP+_WT_288


title: E7.25_Mesp1-GFP+_WT_292


title: E7.25_Mesp1-GFP+_WT_291


title: E7.25_Mesp1-GFP+_WT_287


title: E7.25_Mesp1-GFP+_WT_290


title: E7.25_Mesp1-GFP+_WT_294


title: E7.25_Mesp1-GFP+_WT_285


title: E7.25_Mesp1-GFP+_WT_286


title: E7.25_Mesp1-GFP+_WT_289


title: BE2C_H3K27AC

description: Chromatin IP against H3K27ac in BE(2)-C

data_processing:
Sequenced reads were aligned to HG19 referenece genome using bowtie2 with default parameters with the exception of '-k 1'
Peaks were called using MACS1.4.2 with  p-val =1e-9 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in wiggle format

growth_protocol: SK-N-AS, SH-SY5Y, NGP, BE(2)-C, and KELLY cells were kindly provided by Dr. Kimberly Stegmaier (Dana Farber Cancer Institute) and cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS. SHEP-21N cells were kindly provided by Dr. William Weiss (University of California, San Francisco) and cultured in RPMI supplemented with 10% Tetracycline-Free FBS (Clontech). Tet-Off MYCN shutdown was performed by addition of doxycycline (0.2μg/mL) to growth media

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the Rubicon Thruplex FD library preparation kit (cat#: 400427) per manufacturers instructions.

value: neuroblastoma cell line

tag: growth condition

value: 10% FBS, DMEM

tag: treated with

tag: chip antibody vendor

value: abcam

tag: chip antibody cat. #

tag: input

tag: barcode

value: ACTTGA


title: E7.25_Mesp1-GFP+_WT_281

tag: cell type


title: E7.25_Mesp1-GFP+_WT_280


title: E7.25_Mesp1-GFP+_WT_279


title: E7.25_Mesp1-GFP+_WT_278


title: E7.25_Mesp1-GFP+_WT_277


title: E7.25_Mesp1-GFP+_WT_284


title: E7.25_Mesp1-GFP+_WT_274


title: E7.25_Mesp1-GFP+_WT_271


title: E7.25_Mesp1-GFP+_WT_275


title: E7.25_Mesp1-GFP+_WT_273


title: E7.25_Mesp1-GFP+_WT_283


title: E7.25_Mesp1-GFP+_WT_272


title: E7.25_Mesp1-GFP+_WT_282


title: E7.25_Mesp1-GFP+_WT_269


title: E7.25_Mesp1-GFP+_WT_270


title: E7.25_Mesp1-GFP+_WT_268


title: E7.25_Mesp1-GFP+_WT_267


title: E7.25_Mesp1-GFP+_WT_266


title: E7.25_Mesp1-GFP+_WT_262


title: E7.25_Mesp1-GFP+_WT_260


title: E7.25_Mesp1-GFP+_WT_263


title: E7.25_Mesp1-GFP+_WT_264


title: E7.25_Mesp1-GFP+_WT_265


title: E7.25_Mesp1-GFP+_WT_276


title: E7.25_Mesp1-GFP+_WT_259


title: E7.25_Mesp1-GFP+_WT_261


title: E7.25_Mesp1-GFP+_WT_257


title: E7.25_Mesp1-GFP+_WT_293


title: E7.25_Mesp1-GFP+_WT_258


title: E7.25_Mesp1-GFP+_WT_256


title: E7.25_Mesp1-GFP+_WT_254


title: E7.25_Mesp1-GFP+_WT_251


title: E7.25_Mesp1-GFP+_WT_247


title: E7.25_Mesp1-GFP+_WT_249


title: E7.25_Mesp1-GFP+_WT_248


title: E7.25_Mesp1-GFP+_WT_245


title: E7.25_Mesp1-GFP+_WT_246


title: E7.25_Mesp1-GFP+_WT_244


title: E7.25_Mesp1-GFP+_WT_242


title: E7.25_Mesp1-GFP+_WT_243


title: E7.25_Mesp1-GFP+_WT_241


title: E7.25_Mesp1-GFP+_WT_240


title: E7.25_Mesp1-GFP+_WT_237


title: E7.25_Mesp1-GFP+_WT_234


title: E7.25_Mesp1-GFP+_WT_235


title: E7.25_Mesp1-GFP+_WT_255


title: E7.25_Mesp1-GFP+_WT_239


title: E7.25_Mesp1-GFP+_WT_238


title: E7.25_Mesp1-GFP+_WT_233


title: E7.25_Mesp1-GFP+_WT_232


title: E7.25_Mesp1-GFP+_WT_236


title: E7.25_Mesp1-GFP+_WT_253


title: E7.25_Mesp1-GFP+_WT_231


title: E7.25_Mesp1-GFP+_WT_250


title: E7.25_Mesp1-GFP+_WT_228


title: E7.25_Mesp1-GFP+_WT_230


title: E7.25_Mesp1-GFP+_WT_229


title: E7.25_Mesp1-GFP+_WT_226


title: E7.25_Mesp1-GFP+_WT_225


title: E7.25_Mesp1-GFP+_WT_224


title: E7.25_Mesp1-GFP+_WT_223


title: E7.25_Mesp1-GFP+_WT_222


title: E7.25_Mesp1-GFP+_WT_227


title: E7.25_Mesp1-GFP+_WT_221


title: E7.25_Mesp1-GFP+_WT_220


title: E7.25_Mesp1-GFP+_WT_219


title: E7.25_Mesp1-GFP+_WT_218


title: E7.25_Mesp1-GFP+_WT_211


title: E7.25_Mesp1-GFP+_WT_208


title: E7.25_Mesp1-GFP+_WT_213


title: E7.25_Mesp1-GFP+_WT_216


title: E7.25_Mesp1-GFP+_WT_215


title: E7.25_Mesp1-GFP+_WT_209


title: E7.25_Mesp1-GFP+_WT_212


title: E7.25_Mesp1-GFP+_WT_206


title: E7.25_Mesp1-GFP+_WT_205


title: E7.25_Mesp1-GFP+_WT_203


title: E7.25_Mesp1-GFP+_WT_200


title: E7.25_Mesp1-GFP+_WT_204


title: E7.25_Mesp1-GFP+_WT_202


title: E7.25_Mesp1-GFP+_WT_201


title: E7.25_Mesp1-GFP+_WT_198


title: E7.25_Mesp1-GFP+_WT_195


title: E7.25_Mesp1-GFP+_WT_192


title: E7.25_Mesp1-GFP+_WT_196


title: E7.25_Mesp1-GFP+_WT_193


title: E7.25_Mesp1-GFP+_WT_191


title: E7.25_Mesp1-GFP+_WT_190


title: E7.25_Mesp1-GFP+_WT_217


title: E7.25_Mesp1-GFP+_WT_214


title: E7.25_Mesp1-GFP+_WT_189


title: E7.25_Mesp1-GFP+_WT_207


title: E7.25_Mesp1-GFP+_WT_210


title: E7.25_Mesp1-GFP+_WT_184


title: E7.25_Mesp1-GFP+_WT_199


title: E7.25_Mesp1-GFP+_WT_185


title: E7.25_Mesp1-GFP+_WT_188


title: E7.25_Mesp1-GFP+_WT_187


title: E7.25_Mesp1-GFP+_WT_178


title: E7.25_Mesp1-GFP+_WT_183


title: E7.25_Mesp1-GFP+_WT_186


title: E7.25_Mesp1-GFP+_WT_182


title: E7.25_Mesp1-GFP+_WT_181


title: E7.25_Mesp1-GFP+_WT_180


title: E7.25_Mesp1-GFP+_WT_194


title: E7.25_Mesp1-GFP+_WT_179


title: E7.25_Mesp1-GFP+_WT_176


title: E6.75_Mesp1-GFP+_WT_083


title: E6.75_Mesp1-GFP+_WT_082


title: E7.25_Mesp1-GFP+_WT_197


title: E7.25_Mesp1-GFP+_WT_175


title: E6.75_Mesp1-GFP+_WT_081


title: E6.75_Mesp1-GFP+_WT_079


title: E6.75_Mesp1-GFP+_WT_077


title: E6.75_Mesp1-GFP+_WT_076


title: E6.75_Mesp1-GFP+_WT_078


title: E6.75_Mesp1-GFP+_WT_075


title: E6.75_Mesp1-GFP+_WT_074


title: E6.75_Mesp1-GFP+_WT_073


title: E6.75_Mesp1-GFP+_WT_080


title: E7.25_Mesp1-GFP+_WT_252


title: E6.75_Mesp1-GFP+_WT_072


title: E6.75_Mesp1-GFP+_WT_070


title: E6.75_Mesp1-GFP+_WT_071


title: E6.75_Mesp1-GFP+_WT_068


title: E7.25_Mesp1-GFP+_WT_300


title: E6.75_Mesp1-GFP+_WT_066


title: E6.75_Mesp1-GFP+_WT_065


title: E6.75_Mesp1-GFP+_WT_062


title: E6.75_Mesp1-GFP+_WT_064


title: E6.75_Mesp1-GFP+_WT_060


title: E6.75_Mesp1-GFP+_WT_063


title: E7.25_Mesp1-GFP+_WT_174


title: E6.75_Mesp1-GFP+_WT_058


title: E6.75_Mesp1-GFP+_WT_059


title: E6.75_Mesp1-GFP+_WT_061


title: E6.75_Mesp1-GFP+_WT_057


title: E6.75_Mesp1-GFP+_WT_056


title: E6.75_Mesp1-GFP+_WT_055


title: E6.75_Mesp1-GFP+_WT_054


title: E6.75_Mesp1-GFP+_WT_053


title: E6.75_Mesp1-GFP+_WT_050


title: E6.75_Mesp1-GFP+_WT_069


title: E6.75_Mesp1-GFP+_WT_049


title: E6.75_Mesp1-GFP+_WT_048


title: E6.75_Mesp1-GFP+_WT_047


title: E6.75_Mesp1-GFP+_WT_052


title: E6.75_Mesp1-GFP+_WT_067


title: E6.75_Mesp1-GFP+_WT_051


title: E6.75_Mesp1-GFP+_WT_040


title: E6.75_Mesp1-GFP+_WT_043


title: E6.75_Mesp1-GFP+_WT_042


title: E6.75_Mesp1-GFP+_WT_039


title: E6.75_Mesp1-GFP+_WT_046


title: E6.75_Mesp1-GFP+_WT_045


title: E6.75_Mesp1-GFP+_WT_038


title: E6.75_Mesp1-GFP+_WT_044


title: E6.75_Mesp1-GFP+_WT_037


title: E6.75_Mesp1-GFP+_WT_036


title: E6.75_Mesp1-GFP+_WT_032


title: E6.75_Mesp1-GFP+_WT_035


title: E6.75_Mesp1-GFP+_WT_034


title: E6.75_Mesp1-GFP+_WT_029


title: E6.75_Mesp1-GFP+_WT_030


title: E6.75_Mesp1-GFP+_WT_028


title: E6.75_Mesp1-GFP+_WT_027


title: E6.75_Mesp1-GFP+_WT_026


title: E6.75_Mesp1-GFP+_WT_024


title: E6.75_Mesp1-GFP+_WT_025


title: E6.75_Mesp1-GFP+_WT_023


title: E6.75_Mesp1-GFP+_WT_020


title: E6.75_Mesp1-GFP+_WT_022


title: E6.75_Mesp1-GFP+_WT_021


title: E6.75_Mesp1-GFP+_WT_041


title: E6.75_Mesp1-GFP+_WT_019


title: E6.75_Mesp1-GFP+_WT_018


title: E6.75_Mesp1-GFP+_WT_017


title: E6.75_Mesp1-GFP+_WT_015


title: E6.75_Mesp1-GFP+_WT_013


title: E6.75_Mesp1-GFP+_WT_012


title: E6.75_Mesp1-GFP+_WT_010


title: E6.75_Mesp1-GFP+_WT_016


title: E6.75_Mesp1-GFP+_WT_033


title: E6.75_Mesp1-GFP+_WT_011


title: E6.75_Mesp1-GFP+_WT_007


title: E6.75_Mesp1-GFP+_WT_009


title: E6.75_Mesp1-GFP+_WT_031


title: E6.75_Mesp1-GFP+_WT_005


title: E6.75_Mesp1-GFP+_WT_006


title: E6.75_Mesp1-GFP+_WT_008


title: E6.75_Mesp1-GFP+_WT_003


title: E6.75_Mesp1-GFP+_WT_002


title: E7.25_Mesp1-GFP+_WT_172


title: E7.25_Mesp1-GFP+_WT_170


title: E7.25_Mesp1-GFP+_WT_173


title: E6.75_Mesp1-GFP+_WT_004


title: E7.25_Mesp1-GFP+_WT_171


title: E7.25_Mesp1-GFP+_WT_169


title: E6.75_Mesp1-GFP+_WT_014


title: E7.25_Mesp1-GFP+_WT_167


title: E7.25_Mesp1-GFP+_WT_165


title: E7.25_Mesp1-GFP+_WT_164


title: E7.25_Mesp1-GFP+_WT_163


title: E7.25_Mesp1-GFP+_WT_161


title: E7.25_Mesp1-GFP+_WT_166


title: E7.25_Mesp1-GFP+_WT_158


title: E7.25_Mesp1-GFP+_WT_159


title: E7.25_Mesp1-GFP+_WT_160


title: E7.25_Mesp1-GFP+_WT_157


title: E7.25_Mesp1-GFP+_WT_156


title: E6.75_Mesp1-GFP+_WT_001


title: E7.25_Mesp1-GFP+_WT_151


title: E7.25_Mesp1-GFP+_WT_153


title: E7.25_Mesp1-GFP+_WT_152


title: E7.25_Mesp1-GFP+_WT_154


title: E7.25_Mesp1-GFP+_WT_150


title: E7.25_Mesp1-GFP+_WT_149


title: E7.25_Mesp1-GFP+_WT_168


title: E7.25_Mesp1-GFP+_WT_148


title: E7.25_Mesp1-GFP+_WT_155


title: E7.25_Mesp1-GFP+_WT_147


title: E7.25_Mesp1-GFP+_WT_145


title: E7.25_Mesp1-GFP+_WT_144


title: E7.25_Mesp1-GFP+_WT_177


title: E7.25_Mesp1-GFP+_WT_146


title: E7.25_Mesp1-GFP+_WT_142


title: E7.25_Mesp1-GFP+_WT_162


title: E7.25_Mesp1-GFP+_WT_139


title: E7.25_Mesp1-GFP+_WT_140


title: E7.25_Mesp1-GFP+_WT_143


title: E7.25_Mesp1-GFP+_WT_141


title: E7.25_Mesp1-GFP+_WT_138


title: E7.25_Mesp1-GFP+_WT_136


title: E7.25_Mesp1-GFP+_WT_134


title: E7.25_Mesp1-GFP+_WT_135


title: E7.25_Mesp1-GFP+_WT_133


title: E7.25_Mesp1-GFP+_WT_131


title: E7.25_Mesp1-GFP+_WT_130


title: E7.25_Mesp1-GFP+_WT_132


title: E7.25_Mesp1-GFP+_WT_129


title: E7.25_Mesp1-GFP+_WT_127


title: E7.25_Mesp1-GFP+_WT_125


title: E7.25_Mesp1-GFP+_WT_124


title: E7.25_Mesp1-GFP+_WT_128


title: E7.25_Mesp1-GFP+_WT_122


title: E7.25_Mesp1-GFP+_WT_123


title: E7.25_Mesp1-GFP+_WT_121


title: E7.25_Mesp1-GFP+_WT_119


title: E7.25_Mesp1-GFP+_WT_120


title: E7.25_Mesp1-GFP+_WT_118


title: E7.25_Mesp1-GFP+_WT_126


title: E7.25_Mesp1-GFP+_WT_116


title: E7.25_Mesp1-GFP+_WT_117


title: E7.25_Mesp1-GFP+_WT_115


title: E7.25_Mesp1-GFP+_WT_114


title: E7.25_Mesp1-GFP+_WT_137


title: E7.25_Mesp1-GFP+_WT_113


title: E7.25_Mesp1-GFP+_WT_112


title: E7.25_Mesp1-GFP+_WT_110


title: E7.25_Mesp1-GFP+_WT_107


title: E7.25_Mesp1-GFP+_WT_111


title: E7.25_Mesp1-GFP+_WT_109


title: E7.25_Mesp1-GFP+_WT_108


title: E7.25_Mesp1-GFP+_WT_106


title: E7.25_Mesp1-GFP+_WT_105


title: E7.25_Mesp1-GFP+_WT_104


title: E7.25_Mesp1-GFP+_WT_103


title: E7.25_Mesp1-GFP+_WT_101


title: E7.25_Mesp1-GFP+_WT_102


title: E7.25_Mesp1-GFP+_WT_099


title: E7.25_Mesp1-GFP+_WT_097


title: E7.25_Mesp1-GFP+_WT_100


title: E7.25_Mesp1-GFP+_WT_098


title: E7.25_Mesp1-GFP+_WT_096


title: E7.25_Mesp1-GFP+_WT_094


title: E7.25_Mesp1-GFP+_WT_095


title: E7.25_Mesp1-GFP+_WT_092


title: E7.25_Mesp1-GFP+_WT_090


title: E7.25_Mesp1-GFP+_WT_091


title: E7.25_Mesp1-GFP+_WT_087


title: E7.25_Mesp1-GFP+_WT_089


title: E7.25_Mesp1-GFP+_WT_088


title: E7.25_Mesp1-GFP+_WT_086


title: E7.25_Mesp1-GFP+_WT_085


title: E7.25_Mesp1-GFP+_WT_084


title: E7.25_Mesp1-GFP+_WT_083


title: E7.25_Mesp1-GFP+_WT_082


title: E7.25_Mesp1-GFP+_WT_081


title: E7.25_Mesp1-GFP+_WT_079


title: E7.25_Mesp1-GFP+_WT_080


title: E7.25_Mesp1-GFP+_WT_078


title: E7.25_Mesp1-GFP+_WT_075


title: E7.25_Mesp1-GFP+_WT_073


title: E7.25_Mesp1-GFP+_WT_093


title: E7.25_Mesp1-GFP+_WT_071


title: E7.25_Mesp1-GFP+_WT_070


title: E7.25_Mesp1-GFP+_WT_068


title: E7.25_Mesp1-GFP+_WT_072


title: E7.25_Mesp1-GFP+_WT_067


title: E7.25_Mesp1-GFP+_WT_066


title: E7.25_Mesp1-GFP+_WT_064


title: E7.25_Mesp1-GFP+_WT_065


title: E7.25_Mesp1-GFP+_WT_062


title: E7.25_Mesp1-GFP+_WT_063


title: E7.25_Mesp1-GFP+_WT_058


title: E7.25_Mesp1-GFP+_WT_057


title: E7.25_Mesp1-GFP+_WT_056


title: E7.25_Mesp1-GFP+_WT_055


title: E7.25_Mesp1-GFP+_WT_059


title: E7.25_Mesp1-GFP+_WT_054


title: E7.25_Mesp1-GFP+_WT_052


title: E7.25_Mesp1-GFP+_WT_053


title: E7.25_Mesp1-GFP+_WT_076


title: E7.25_Mesp1-GFP+_WT_049


title: E7.25_Mesp1-GFP+_WT_077


title: E7.25_Mesp1-GFP+_WT_047


title: E7.25_Mesp1-GFP+_WT_069


title: E7.25_Mesp1-GFP+_WT_046


title: E7.25_Mesp1-GFP+_WT_048


title: E7.25_Mesp1-GFP+_WT_044


title: E7.25_Mesp1-GFP+_WT_074


title: E7.25_Mesp1-GFP+_WT_042


title: E7.25_Mesp1-GFP+_WT_045


title: E7.25_Mesp1-GFP+_WT_043


title: E7.25_Mesp1-GFP+_WT_041


title: E7.25_Mesp1-GFP+_WT_060


title: E7.25_Mesp1-GFP+_WT_061


title: E7.25_Mesp1-GFP+_WT_038


title: E7.25_Mesp1-GFP+_WT_036


title: E7.25_Mesp1-GFP+_WT_037


title: E7.25_Mesp1-GFP+_WT_034


title: E7.25_Mesp1-GFP+_WT_051


title: E7.25_Mesp1-GFP+_WT_035


title: E7.25_Mesp1-GFP+_WT_050


title: E7.25_Mesp1-GFP+_WT_028


title: E7.25_Mesp1-GFP+_WT_039


title: E7.25_Mesp1-GFP+_WT_027


title: E7.25_Mesp1-GFP+_WT_031


title: E7.25_Mesp1-GFP+_WT_030


title: E7.25_Mesp1-GFP+_WT_026


title: E7.25_Mesp1-GFP+_WT_029


title: E7.25_Mesp1-GFP+_WT_032


title: E7.25_Mesp1-GFP+_WT_025


title: E7.25_Mesp1-GFP+_WT_023


title: E7.25_Mesp1-GFP+_WT_024


title: E7.25_Mesp1-GFP+_WT_022


title: E7.25_Mesp1-GFP+_WT_021


title: E7.25_Mesp1-GFP+_WT_016


title: E7.25_Mesp1-GFP+_WT_020


title: E7.25_Mesp1-GFP+_WT_018


title: E7.25_Mesp1-GFP+_WT_033


title: E7.25_Mesp1-GFP+_WT_014


title: E7.25_Mesp1-GFP+_WT_013


title: E7.25_Mesp1-GFP+_WT_012


title: E7.25_Mesp1-GFP+_WT_007


title: E7.25_Mesp1-GFP+_WT_011


title: E7.25_Mesp1-GFP+_WT_009


title: E7.25_Mesp1-GFP+_WT_006


title: E7.25_Mesp1-GFP+_WT_005


title: E7.25_Mesp1-GFP+_WT_008


title: E6.75_Mesp1-GFP+_KO_084


title: E7.25_Mesp1-GFP+_WT_002


title: E7.25_Mesp1-GFP+_WT_001


title: E6.75_Mesp1-GFP+_KO_083


title: E7.25_Mesp1-GFP+_WT_004


title: E6.75_Mesp1-GFP+_KO_085


title: E7.25_Mesp1-GFP+_WT_003


title: E6.75_Mesp1-GFP+_KO_080


title: E6.75_Mesp1-GFP+_KO_082


title: E6.75_Mesp1-GFP+_KO_076


title: E6.75_Mesp1-GFP+_KO_077


title: E6.75_Mesp1-GFP+_KO_081


title: E6.75_Mesp1-GFP+_KO_079


title: E7.25_Mesp1-GFP+_WT_015


title: E6.75_Mesp1-GFP+_KO_078


title: E6.75_Mesp1-GFP+_KO_073


title: E7.25_Mesp1-GFP+_WT_019


title: E6.75_Mesp1-GFP+_KO_072


title: E6.75_Mesp1-GFP+_KO_075


title: E6.75_Mesp1-GFP+_KO_071


title: E6.75_Mesp1-GFP+_KO_074


title: E6.75_Mesp1-GFP+_KO_066


title: E6.75_Mesp1-GFP+_KO_065


title: E6.75_Mesp1-GFP+_KO_062


title: E6.75_Mesp1-GFP+_KO_070


title: E6.75_Mesp1-GFP+_KO_067


title: E6.75_Mesp1-GFP+_KO_069


title: E6.75_Mesp1-GFP+_KO_063


title: E6.75_Mesp1-GFP+_KO_061


title: E6.75_Mesp1-GFP+_KO_058


title: E6.75_Mesp1-GFP+_KO_060


title: E6.75_Mesp1-GFP+_KO_059


title: E6.75_Mesp1-GFP+_KO_057


title: E6.75_Mesp1-GFP+_KO_055


title: E6.75_Mesp1-GFP+_KO_056


title: E6.75_Mesp1-GFP+_KO_053


title: E6.75_Mesp1-GFP+_KO_054


title: E6.75_Mesp1-GFP+_KO_050


title: E6.75_Mesp1-GFP+_KO_049


title: E6.75_Mesp1-GFP+_KO_052


title: E6.75_Mesp1-GFP+_KO_047


title: E6.75_Mesp1-GFP+_KO_051


title: E6.75_Mesp1-GFP+_KO_068


title: E6.75_Mesp1-GFP+_KO_048


title: E6.75_Mesp1-GFP+_KO_044


title: E6.75_Mesp1-GFP+_KO_042


title: E6.75_Mesp1-GFP+_KO_064


title: E6.75_Mesp1-GFP+_KO_037


title: E6.75_Mesp1-GFP+_KO_043


title: E6.75_Mesp1-GFP+_KO_033


title: E6.75_Mesp1-GFP+_KO_034


title: E6.75_Mesp1-GFP+_KO_039


title: E6.75_Mesp1-GFP+_KO_041


title: E6.75_Mesp1-GFP+_KO_035


title: E6.75_Mesp1-GFP+_KO_031


title: E6.75_Mesp1-GFP+_KO_036


title: E6.75_Mesp1-GFP+_KO_032


title: E6.75_Mesp1-GFP+_KO_038


title: E6.75_Mesp1-GFP+_KO_027


title: E6.75_Mesp1-GFP+_KO_045


title: E6.75_Mesp1-GFP+_KO_030


title: E6.75_Mesp1-GFP+_KO_046


title: E6.75_Mesp1-GFP+_KO_029


title: E6.75_Mesp1-GFP+_KO_024


title: E6.75_Mesp1-GFP+_KO_028


title: E6.75_Mesp1-GFP+_KO_019


title: E6.75_Mesp1-GFP+_KO_025


title: E6.75_Mesp1-GFP+_KO_018


title: E6.75_Mesp1-GFP+_KO_026


title: E6.75_Mesp1-GFP+_KO_023


title: E6.75_Mesp1-GFP+_KO_022


title: E6.75_Mesp1-GFP+_KO_012


title: E6.75_Mesp1-GFP+_KO_021


title: E6.75_Mesp1-GFP+_KO_011


title: E6.75_Mesp1-GFP+_KO_040


title: E6.75_Mesp1-GFP+_KO_020


title: E6.75_Mesp1-GFP+_KO_006


title: E6.75_Mesp1-GFP+_KO_005


title: E6.75_Mesp1-GFP+_KO_008


title: E6.75_Mesp1-GFP+_KO_003


title: E6.75_Mesp1-GFP+_KO_004


title: E6.75_Mesp1-GFP+_KO_001


title: E6.75_Mesp1-GFP+_KO_016


title: E6.75_Mesp1-GFP+_KO_017


title: KO_5

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young

department: Pathology

institute: UCLA

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23
All fastq files were mapped using bowtie2 and reads were removed if they were non-unique, in duplicate, mapped to mitochondrial genome, or mapped to un-mapped  contiguous sequences. Only the remaining reads following these filters were used for subsequent analysis.
bedGraph files were geenrated from sorted bam files using makeTagDirectories and makeUCSCfile with -fragLength 60 -o auto -fsize 1e50 -res 1
MACS2 was used to perform peak calling with the following parameters:--nomodel -g mm --keep-dup all -q .01 --llocal 1000. Peaks from all samples were collapsed and merged together. Reads were quantified using Seqmonk over all peaks and converted to Reads Per Million by dividing the reads by the the total number of reads per sample while normalizing for the length of the peak.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

source_name: Adipose

extract_protocol:
Adipocyte nuclei were isolated according to methods previously described (Church 2014). Briefly, 250,000 cells from filtered adipocyte suspension were washed once with PBS prior to addition of cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. For SVF, 50,000 cells were used for nuclei isolation according to standard protocol. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 10x concentration Tn5 (Nextera) for primary adipose and standard concentration for SVF.
All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 100-1000bp, were quantified with qPCR and Qubit, and sequenced 50bp, single-end sequencing.

tag: strain

tag: genotype

tag: stimulus

tag: sample type

value: chromatin


title: KO_4


title: Day5_Cont_R3

data_processing:
RNA-seq fastq files were aligned to the mouse genome using Tophat v1.3.3 with the following options: -p 4 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-firststrand --no-novel-indels --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2 --s. Only uniquely mapped reads were kept for downstream analysis.
All aligned reads were imported to SeqMonk. mRNA RPKM values were calculated using Seqmonk’s mRNA quantitation pipeline (http://www.bioinformatics.bbsrc.ac.uk/projects/seqmonk/).
Bedgraph files were generated from aligned BAM files using the Bedtools suite: genomeCoverageBed -bg -split, using the mouse mm9 reference genome.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files for each sample represent the read coverage at each genomic position.

source_name: iBAd Cell Line

extract_protocol:
Cells were resuspended in TriReagent and RNA purified using Rneasy columns (Qiagen).
mRNA libraries were generated using the Illumina Truseq stranded kit.

value: With Isoproterenol

tag: time


title: WT_4

value: WT


title: Day5_Cont_R2


title: E6.75_Mesp1-GFP+_KO_007


title: Cut-and-Run_AGM_K27_lo_(20170713_SH_CaSc_K27Lo_0630)

description:
AGM dig cells K27 30 min digestion
Immunotargeting, cleavage and release

data_processing:
1. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the 25bp paired-end Illumina reads to NCBI AC239401.3, alphasat array clone CH252_365N9 of Chlorocebus aethiops.  2. We used Bowtie2 2.2.5 with options "--end-to-end --very-sensitive --no-overlap --no-dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same 25bp paired-end Illumina reads to UCSC sacCer3.  3. We extracted properly paired reads from both alignments (Supplementary files .bed.gz .SC.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to S.cervisiae) to create a normalized yeast track file (Supplementary file .bedgraph.gz).
genome_build: NCBI AC239401.3
genome_build: UCSC sacCer3
Library strategy: Cut-and-Run

organism: Chlorocebus aethiops

source_name: African green monkey Cos-7 cells, anti-K27me3 Cell Signalling #9733

tag: tissue

value: African green monkey Cos-7 cells


title: WT_2


title: FSK_IL10

source_name: SVF


title: E7.25_Mesp1-GFP+_WT_017


title: IWAT_KO

source_name: iWAT Tissue

value: Unstimulated


title: E6.75_Mesp1-GFP+_KO_015


title: E7.25_Mesp1-GFP+_WT_040


title: Cut-and-Run_AGM_CENPB_lo_(20170713_SH_CaSc_CeBLo_0630)

description:
AGM dig cells CENP-B 30 min digestion
Immunotargeting, cleavage and release

source_name: African green monkey Cos-7 cells, anti-CENP-B Abcam ab25734


title: E6.75_Mesp1-GFP+_KO_014


title: Day0

data_processing:
Library strategy: ATAC-Seq
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23
All fastq files were mapped using bowtie2 and reads were removed if they were non-unique, in duplicate, mapped to mitochondrial genome, or mapped to un-mapped  contiguous sequences. Only the remaining reads following these filters were used for subsequent analysis.
bedGraph files were geenrated from sorted bam files using makeTagDirectories and makeUCSCfile with -fragLength 60 -o auto -fsize 1e50 -res 1
MACS2 was used to perform peak calling with the following parameters:--nomodel -g mm --keep-dup all -q .01 --llocal 1000. Peaks from all samples were collapsed and merged together. Reads were quantified using Seqmonk over all peaks and converted to Reads Per Million by dividing the reads by the the total number of reads per sample while normalizing for the length of the peak.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

extract_protocol:
50,000 iBAd cells on Day 0 and Day 5 of differentiation were centrifuged and washed once with PBS prior to addition of 50uL cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 2.5uL Tn5 (Nextera) in a 50uL reaction volume and placed in a 37C waterbath for 30 minutes.
All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 100-1000bp, were quantified with qPCR and Qubit, and sequenced 50bp, single-end sequencing.

tag: time point


title: Cut-and-Run_AGM_CENPA_lo_(20170713_SH_CaSc_CeALo_0630)

description:
AGM dig cells CENP-A 30 min digestion
Immunotargeting, cleavage and release

source_name: African green monkey Cos-7 cells, anti-CENP-A Abcam ab13939


title: E6.75_Mesp1-GFP+_KO_010


title: Day5_IL10

value: With IL-10 and Isoproterenol


title: E6.75_Mesp1-GFP+_KO_009


title: E6.75_Mesp1-GFP+_KO_013


title: Day0_R1


title: Day0_R3


title: Sox17 Control-2

status: Public on Jan 27 2018

city: Daejeon

first: Chan Soon

last: Park

address: 291 Daehak-ro, Yu-seong gu

department: graduate school of medical science and engineering

country: South Korea

institute: KAIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: endothelial cells from high grade glioma

growth_protocol: housed in a pathogen-free animal facility

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: strain background

tag: genotype/variation

value: Sox17 control


title: Cut-and-Run_AGM_IgG_lo_(20170713_SH_CaSc_IgGLo_0630)

description:
AGM dig cells IgG 30 min digestion
Immunotargeting, cleavage and release

source_name: African green monkey Cos-7 cells, anti-rabbit Antibodies online ABIN101961


title: Sox17 ECKO-1

value: endothelial cells from high grade glioma


title: E6.75_Mesp1-GFP+_KO_002

tag: develpmental stage

tag: age


title: Day5_IL10_R3


title: Sox17 Control-1


title: Day5_IL10_R2


title: Sox7 ECKO-2


title: Sox7 Control-2

value: Sox7 control


title: Day5_IL10_R1


title: Day5_Cont_R1


title: IWAT_WT


title: FSK

value: FSK


title: Day0_R2


title: ChIP-seq_K562_Hub_KO_TAL1_rep2

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

institute: St. Jude Children's Research Hospital

description: ChIP DNA

data_processing:
ChIP-seq raw reads were aligned to the hg19 genome assembly using Bowtie2 with the k=1.
Wig files were generated according to standard format using variableStep and span=20.  Each data value was normalized using total read counts. Then wig files were converted to bigwig using wigToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig file

source_name: Human K562 cells

growth_protocol: K562 cells were cultured in RPMI1640 medium supplemented with 10% FBS and 1% penicillin-streptomycin.

extract_protocol: For ChIP-seq analysis using the Illumina NextSeq500, 1-10 ng of ChIP DNA was processed for library generation using the NEBNext Ultra II DNA Library Prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.

tag: cell line

value: MYO1D Hub KO

tag: chip antibody

value: Santa Cruz Biotechnology,sc-12984,C1315


title: ChIP-seq_K562_Hub_KO_H3K27ac_rep1

description: ChIP DNA


title: ChIP-seq_K562_Hub_KO_GATA1_rep2

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_Input_rep2_S21

description: ChIP DNA

value: MYO1D Non-hub KO

value: none (input)


title: Day5_Cont


title: Sox17 Control-3


title: Sox17 ECKO-3


title: Sox17 ECKO-2


title: E7.25_Mesp1-GFP+_WT_010

value: Gastrulation

value: Mesp1+ cells


title: ChIP-seq_K562_Hub_KO_Input_rep2_S17

description: ChIP DNA


title: Sox7 Control-1


title: ChIP-seq_K562_Hub_KO_GATA1_rep1

description: ChIP DNA


title: ChIP-seq_K562_Hub_KO_H3K27ac_rep2

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_TAL1_rep1

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_Input_rep1_S9

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_TAL1_rep2

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_H3K27ac_rep1

description: ChIP DNA


title: B1

city: Shenyang City

first: Xining

last: Pang

address: 77 Puhe Street, Shenbei New District

department: Department of Stem Cells and Regenerative Medicine

institute: China Medical University

data_processing:
Base-calling were performed by the Illumina Genome Analyzer Sequencing Control Software (SCS) v2.8.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Genome_build: GRCH38
Supplementary_files_format_and_content: text files include small RNA counts for each sequence

source_name: Keratinocytes

growth_protocol: Full-thickness skin samples were incubated at 4°C overnight in Dispase II (Roche Applied Science, Indianapolis, IN, USA), and the dermal components were then removed through collagenase digestion. After 0.25% trypsin digestion, cultures of the released primary KCs from the epidermis were initiated using tissue culture flasks coated with collagen (Becton Dickinson Labware, Bedford, MA, USA) in EpilifeTM growth medium (Invitrogen Ltd, Paisley, UK) supplemented with 1% human KC growth supplement (Invitrogen Ltd).

extract_protocol:
The total RNA from the cells was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.
For cDNA libraries construction and NGS, 4 ug RNA from each sample was prepared using the Illumina TruSeq Small RNA Sample Preparation Kit according to the manufacturer’s instructions. Briefly, 4 ug of total RNA were ligated with the 5’ and 3’ adapters successively. An RT reaction is then used to create single stranded cDNA. The cDNA is PCR amplified by 12 cycles using a common primer and a primer containing one of 48 index sequences. The introduction of the index sequence at the PCR step separates the indexes from the RNA ligation reaction. This design allows for the indexes to be read using a second read and significantly reduces bias compared to designs which include the index within the first read. The protocol allows use of different index tags to make use of the Illumina multiplexing capability for analysis of directional and small RNA samples, by employing six-base indices to distinguish different samples from one another in a single lane of a flowcell. A gel purification procedure was carried out to select the fragments sized from 140 to 160 bp to produce the library for cluster generation and sequencing. The libraries were qualified using the Agilent 2100 High-Sensitivity DNA kit and quantified using the KAPA SYBR FAST qPCR Kit.

value: epidermis

tag: developmental stage

value: fetus

value: gestational age 33 weeks

tag: Sex

value: female

value: Keratinocytes


title: A1

value: gestational age 22 weeks


title: B3

value: male


title: A3

value: gestational age 23 weeks


title: ChIP-seq_K562_Non-hub_KO_H3K27ac_rep2

description: ChIP DNA


title: B2

value: gestational age 36 weeks


title: ChIP-seq_K562_TAL1_rep2

description: ChIP DNA

value: wildtype


title: ChIP-seq_K562_GATA1_rep2

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_GATA1_rep2

description: ChIP DNA


title: ChIP-seq_K562_H3K27ac_rep2

description: ChIP DNA


title: ChIP-seq_K562_H3K27ac_rep1

description: ChIP DNA


title: ChIP-seq_K562_Non-hub_KO_GATA1_rep1

description: ChIP DNA


title: Sox7 ECKO-1

value: endothelial cells from high grade glioma


title: A2


title: ChIP-seq_K562_Hub_KO_TAL1_rep1

description: ChIP DNA

value: MYO1D Hub KO


title: ChIP-seq_K562_Hub_KO_Input_rep1_S5

description: ChIP DNA


title: ChIP-seq_K562_Input_rep1_S1

description: ChIP DNA


title: ChIP-seq_K562_TAL1_rep1

description: ChIP DNA

value: Santa Cruz Biotechnology,sc-12984,C1315


title: ChIP-seq_K562_Input_rep2_S13

description: ChIP DNA


title: ChIP-seq_K562_GATA1_rep1

description: ChIP DNA


title: VC_2 [small RNA]

status: Public on Jan 26 2018

city: Salt Lake City

first: Leslie

middle: Ellen

last: Sieburth

state: UT

address: 257 South 1400 East

department: Biology

institute: University of Utah

data_processing:
FastQC was used to evaluate read quality.
cutadapt v.1.8.3 with Python 2.6.6 used to trim adapter sequences and filter reads < 21 nt.
Bowtie v.1.1.2 used to align small RNA reads.
R/Bioconductor package "GenomicAlignments" used to calculate read counts per exon from input Bowtie BAM files.
R/Bioconductor package "mirbase.db" used to count reads aligning to annotated miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: DESeq2 genotype pairwise comparison results (default column output from package) and DESeq2-normalized reads (columns) for 21-24 nt length small RNAs, sense and antisense orientation, for each genotype and replicate, for each AGI gene identifier (rows).

source_name: VC_5d whole seedling

growth_protocol: Seedlings were grown vertically on 0.5X MS growth media with 0.5% sucrose on 0.8% agar plates, at 22˚C, and in constant light for 5 d.

extract_protocol:
Invitrogen Plant RNA Reagent + Dnase treatment
NEBNext Small RNA Library Prep for Illumina

treatment_protocol: Segregating mutants were collected from GM plates then tissue immediately frozen with liquid nitrogen and stored at -80˚C until RNA extraction.

value: vcs sov (aka vcs-7)

tag: biological replicate

value: 5 d whole seedling

tag: molecule subtype

value: small RNA


title: VS_3 [small RNA]

source_name: VS_5d whole seedling

value: vcs (vcs-7 [SOV-L.er])


title: VC_3 [small RNA]


title: VC_1 [small RNA]


title: VS_1 [small RNA]


title: CS_2 [small RNA]

source_name: CS_5d whole seedling

value: VCS SOV (Col-0 [SOV-L.er])


title: CS_1 [small RNA]


title: CO_3 [small RNA]

source_name: CO_5d whole seedling

value: sov  (aka Col-0)


title: CS_3 [small RNA]


title: VS_240_r4

data_processing:
FastQC was used to summarize read quality.
Bowtie2 version 2.2.3 & TopHat2 v2.0.12 were used to align reads to the genome yeilding BAM files.
samtools version 0.1.19-44428cd was used for indexing and sorting BAM files.
HTSeq 0.6.1 was used to summarize read counts by gene.
R version 3.1.0 was used to normalize read counts.
Genome_build: TAIR10
Supplementary_files_format_and_content: Library nomalized read counts (reads per million) are provided for each AGI gene identifier (rows) and for all 128 libraries (columns).

source_name: VS_240_5d whole seedling

extract_protocol:
Omega Bio-Tek EZ RNA column extraction + Dnase I treatment
Plant RiboZero & Illumina TruSeq Stranded Kits

treatment_protocol: Transcriptional arrest by vacuum infiltration. 50-60 seedlings per genotype per replicate treated in 3 mL 1 mM cordycepin with swirling.

tag: time after transcription inhibition (min)

tag: biological replicate no.


title: VS_480_r4

source_name: VS_480_5d whole seedling


title: CO_1 [small RNA]


title: CO_2 [small RNA]


title: VS_30_r4

source_name: VS_30_5d whole seedling


title: VS_120_r4

source_name: VS_120_5d whole seedling


title: VS_07_r4

source_name: VS_07_5d whole seedling


title: VS_15_r4

source_name: VS_15_5d whole seedling


title: VS_2 [small RNA]


title: VC_240_r4

source_name: VC_240_5d whole seedling


title: VC_120_r4

source_name: VC_120_5d whole seedling


title: VC_30_r4

source_name: VC_30_5d whole seedling


title: VC_480_r4

source_name: VC_480_5d whole seedling


title: VC_15_r4

source_name: VC_15_5d whole seedling


title: VS_00_r4

source_name: VS_00_5d whole seedling


title: VC_07_r4

source_name: VC_07_5d whole seedling


title: VC_60_r4

source_name: VC_60_5d whole seedling


title: VC_00_r4

source_name: VC_00_5d whole seedling


title: CS_240_r4

source_name: CS_240_5d whole seedling


title: CS_120_r4

source_name: CS_120_5d whole seedling


title: CS_60_r4

source_name: CS_60_5d whole seedling


title: CS_30_r4

source_name: CS_30_5d whole seedling


title: CS_480_r4

source_name: CS_480_5d whole seedling


title: CS_15_r4

source_name: CS_15_5d whole seedling


title: CS_00_r4

source_name: CS_00_5d whole seedling


title: CO_480_r4

source_name: CO_480_5d whole seedling


title: VS_60_r4

source_name: VS_60_5d whole seedling


title: CO_60_r4

source_name: CO_60_5d whole seedling


title: CO_240_r4

source_name: CO_240_5d whole seedling


title: CO_07_r4

source_name: CO_07_5d whole seedling


title: CO_30_r4

source_name: CO_30_5d whole seedling


title: VS_120_r3

source_name: VS_120_5d whole seedling


title: VS_240_r3

source_name: VS_240_5d whole seedling


title: VS_60_r3

description: Note: raw file name sequence (i.e. 11119X21,11119X29) is out of order to correct swapped sample tubes prior to sequencing


title: CO_00_r4

source_name: CO_00_5d whole seedling


title: VS_480_r3

source_name: VS_480_5d whole seedling


title: VS_30_r3

source_name: VS_30_5d whole seedling


title: VS_15_r3

source_name: VS_15_5d whole seedling


title: VS_00_r3

source_name: VS_00_5d whole seedling


title: VS_07_r3

source_name: VS_07_5d whole seedling


title: VC_120_r3

source_name: VC_120_5d whole seedling


title: VC_240_r3

source_name: VC_240_5d whole seedling


title: VC_480_r3

source_name: VC_480_5d whole seedling


title: CO_120_r4

source_name: CO_120_5d whole seedling


title: CO_15_r4

source_name: CO_15_5d whole seedling


title: CS_07_r4

source_name: CS_07_5d whole seedling


title: VC_30_r3

source_name: VC_30_5d whole seedling


title: VC_15_r3

source_name: VC_15_5d whole seedling


title: VC_00_r3

source_name: VC_00_5d whole seedling


title: CS_480_r3

source_name: CS_480_5d whole seedling


title: CS_240_r3

source_name: CS_240_5d whole seedling


title: CS_120_r3

source_name: CS_120_5d whole seedling


title: VC_60_r3

source_name: VC_60_5d whole seedling


title: CS_15_r3

source_name: CS_15_5d whole seedling


title: CS_00_r3

source_name: CS_00_5d whole seedling


title: CS_30_r3

source_name: CS_30_5d whole seedling


title: CO_60_r3

source_name: CO_60_5d whole seedling


title: CO_480_r3

source_name: CO_480_5d whole seedling


title: CO_120_r3


title: CO_240_r3

source_name: CO_240_5d whole seedling


title: CO_07_r3

source_name: CO_07_5d whole seedling


title: VS_480_r2

source_name: VS_480_5d whole seedling


title: CO_30_r3

source_name: CO_30_5d whole seedling


title: CO_00_r3

source_name: CO_00_5d whole seedling


title: CO_15_r3

source_name: CO_15_5d whole seedling


title: VS_120_r2

source_name: VS_120_5d whole seedling


title: VS_240_r2

source_name: VS_240_5d whole seedling


title: VC_07_r3

source_name: VC_07_5d whole seedling


title: VS_07_r2

source_name: VS_07_5d whole seedling


title: VS_30_r2

source_name: VS_30_5d whole seedling


title: VS_15_r2

source_name: VS_15_5d whole seedling


title: VS_00_r2

source_name: VS_00_5d whole seedling


title: VC_480_r2

source_name: VC_480_5d whole seedling


title: VC_120_r2

source_name: VC_120_5d whole seedling


title: VC_60_r2

source_name: VC_60_5d whole seedling


title: CS_60_r3

source_name: CS_60_5d whole seedling


title: VC_240_r2

source_name: VC_240_5d whole seedling


title: CS_07_r3

source_name: CS_07_5d whole seedling


title: VC_30_r2

source_name: VC_30_5d whole seedling


title: VC_07_r2


title: VC_00_r2

source_name: VC_00_5d whole seedling


title: CS_240_r2

source_name: CS_240_5d whole seedling


title: CS_480_r2

source_name: CS_480_5d whole seedling


title: CS_120_r2

source_name: CS_120_5d whole seedling


title: CS_30_r2

source_name: CS_30_5d whole seedling


title: CS_15_r2

source_name: CS_15_5d whole seedling


title: CO_120_r2

source_name: CO_120_5d whole seedling


title: VS_60_r2

source_name: VS_60_5d whole seedling


title: CO_240_r2

source_name: CO_240_5d whole seedling


title: CS_07_r2


title: VC_15_r2

source_name: VC_15_5d whole seedling


title: CO_15_r2

source_name: CO_15_5d whole seedling


title: CS_60_r2


title: CS_00_r2

source_name: CS_00_5d whole seedling


title: CO_07_r2

source_name: CO_07_5d whole seedling


title: CO_60_r2

source_name: CO_60_5d whole seedling


title: VS_480_r1

source_name: VS_480_5d whole seedling


title: CO_480_r2

source_name: CO_480_5d whole seedling


title: CO_30_r2

source_name: CO_30_5d whole seedling


title: VS_60_r1


title: VS_30_r1

source_name: VS_30_5d whole seedling


title: VS_07_r1

source_name: VS_07_5d whole seedling


title: CO_00_r2

source_name: CO_00_5d whole seedling


title: VS_120_r1

source_name: VS_120_5d whole seedling


title: VS_240_r1

source_name: VS_240_5d whole seedling


title: VC_240_r1

source_name: VC_240_5d whole seedling


title: VC_480_r1

source_name: VC_480_5d whole seedling


title: VC_120_r1

source_name: VC_120_5d whole seedling


title: VS_00_r1

source_name: VS_00_5d whole seedling


title: VC_30_r1

source_name: VC_30_5d whole seedling


title: VC_15_r1

source_name: VC_15_5d whole seedling


title: VC_07_r1

source_name: VC_07_5d whole seedling


title: CS_60_r1

source_name: CS_60_5d whole seedling


title: CS_120_r1

source_name: CS_120_5d whole seedling


title: CS_480_r1

source_name: CS_480_5d whole seedling


title: CS_240_r1

source_name: CS_240_5d whole seedling


title: CS_07_r1

source_name: CS_07_5d whole seedling


title: CS_00_r1

source_name: CS_00_5d whole seedling


title: CO_480_r1

source_name: CO_480_5d whole seedling


title: CO_120_r1

source_name: CO_120_5d whole seedling


title: CO_60_r1

source_name: CO_60_5d whole seedling


title: CO_240_r1

source_name: CO_240_5d whole seedling


title: Macrophage (GW3965)

first: David

last: Casero

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

description: PTTSmmMPGW

data_processing:
Reads were aligned to the Mus musculus genome (mm10 build) using STAR v2.3.0 (Dobin et al. doi:10.1093/bioinformatics/bts635) in supervised mode using the Ensemble GRCm38.71 gene annotation as template. Relevant alignment parameters are: --outFilterMultimapScoreRange 0.75  --outFilterMultimapNmax 100 --outFilterMismatchNmax 25 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 --outFilterMismatchNoverLmax 0.25 --sjdbOverhang 99
HTSeq-count v0.5.4p3 (Simon Anders, http://www-huber.embl.de/users/anders/HTSeq/) was used to compute the matrix of raw counts (relevant paramters: --mode=intersection-strict). Gene expression estimates were generated after normalizing for sequencing depth and effective gene length
Genome_build: GRCm38.71/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: peritoneal macrophage

extract_protocol:
Total RNA was isolated using Qiagen miRNAeasy micro kit
RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits from Illumina on RNA isolated from macrophages treated with or without GW3965.

tag: cell type

value: peritoneal macrophage

tag: strain

value: Pooled male and female

tag: developmental stge


title: KO_gw4

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23
All fastq files were mapped using bowtie2 and reads were removed if they were non-unique, in duplicate, mapped to mitochondrial genome, or mapped to un-mapped  contiguous sequences. Only the remaining reads following these filters were used for subsequent analysis.
bedGraph files were geenrated from sorted bam files using makeTagDirectories and makeUCSCfile with -fragLength 60 -o auto -fsize 1e50 -res 1
MACS2 was used to perform peak calling with the following parameters:--nomodel -g mm --keep-dup all -q .01 --llocal 1000. Peaks from all samples were collapsed and merged together. Reads were quantified using Seqmonk
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

source_name: Peritoneal macrophages

extract_protocol:
Primary peritoneal macrophages were isolated four days after thioglycollate injection. Cells were treated for 3 hours and 50,000 cells were centrifuged and washed once with PBS prior to addition of 50uL cold hypotonic lysis buffer containing 0.1% Igepal to yield nuclei. The lysis reaction was centifuged and the supernatant was discarded. Isolated nuclei were incubated with 2.5uL Tn5 (Nextera) in a 50uL reaction volume and placed in a 37C thermomixer for 30 minutes at 300rpm agitation.
All ATAC datasets were generated using Tn5 from Nextera with previously published protocols with minor adjustments (Buenrostro et al, Curr.Protoc. Mol. Biol. 2015). Transposed DNA was cleaned up with a Qiagen MinElute PCR Purification Kit and amplified with a non-saturating PCR to enrich for Transposed DNA. The reaction was size selected on a gel for fragments 100-1000bp, were quantified with qPCR and Qubit, and sequenced 50bp, single-end sequencing.

tag: genotype

value: KO

tag: stimulus

tag: time

value: 3 Hours


title: KO_gw2


title: KO_gw3


title: KO_gw1


title: CO_00_r1

source_name: CO_00_5d whole seedling

tag: genotype/variation

tag: tissue


title: CO_15_r1

source_name: CO_15_5d whole seedling


title: CO_07_r1

source_name: CO_07_5d whole seedling


title: VC_60_r1

source_name: VC_60_5d whole seedling


title: CO_30_r1

source_name: CO_30_5d whole seedling


title: KO_dmso3

value: DMSO


title: KO_dmso2


title: CS_30_r1

source_name: CS_30_5d whole seedling


title: CS_15_r1

source_name: CS_15_5d whole seedling


title: EM_IL15 Sample 36

city: Cleveland

first: AARTHI

last: TALLA

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University School of Medicine

data_processing:
samples were demutliplexed using 'bcl2fastq.1.8.4'
The sequencing raw reads were trimmed off adapter sequence contaminants using Trimmomatic 0.32
The trimmed reads mapped onto the Ensembl version of the human genome (Ensembl - Grch38), using the STAR 2.4.0f1 aligner
The transcript abundance was then estimated by counting the number of reads mapping to the exons that are unique to the transcripts of a gene using HTSeq
The obtained transcript counts were normalized by TMM (Trimmed Mean of M-values) by correcting for the library size and differential expressed genes were determined using the edgeR Bioconductor package
Genome_build: Ensembl - Grch38
Supplementary_files_format_and_content: Tab delimited text files of the counts per million (CPM) of every transcript per sample

source_name: primary sorted memory CD4+ T cell subsets derived from PBMCs

extract_protocol:
Qiagen RNeasy Micro Kit
Clontech SMARTer Ultra Low Input RNA Kit for Sequencing [converting from RNA to cDNA] and Nextera XT DNA [DNA library prep]

tag: infection status

value: HIV, Successfully treated

tag: donorid

tag: cd4+ t cell memory subset

value: EM

tag: lra used for stimulation


title: EM_Bryostatin Sample 35

value: primary sorted memory CD4+ T cell subsets derived from PBMCs

value: Bryostatin


title: VC_00_r1

source_name: VC_00_5d whole seedling


title: EM_PMA_Ionomycin Sample 33


title: WT_gw1

value: WT


title: EM_Unstimulated Control Sample 34

value: Unstimulated Controls


title: WT_gw4


title: KO_dmso1


title: WT_gw3


title: TM_IL15 Sample 32

value: TM


title: WT_gw2


title: WT_dmso3


title: KO_dmso4


title: VS_15_r1

source_name: VS_15_5d whole seedling

value: 5 d whole seedling


title: Macrophage (DMSO)

description: PTTSmmMPDMSO

tag: Sex


title: WT_dmso2


title: TM_Unstimulated Control Sample 30


title: WT_dmso1


title: Pkd2f_P7_WT2_miRNA-seq

city: Seoul

first: Jong Hoon

address: Cheongpa-ro 47-gil 100, Yongsan-gu,

institute: Sookmyung Women's university

data_processing:
Basecalls performed using CASAVA v1.8.2
the low-quality-reads were filtered by NGSQCToolkit_v2.3.3
The reads were aligned to the miRBase v21 & mm10 genome using miRdeep2
Read counts of representative genes and their isoforms were measured by HTSeq
Genome_build: mm10

extract_protocol:
Kidneys were removed and total RNA was harvested using Trizol reagent from each indicated time points of two ADPKD mice models.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

tag: age

value: Post natal day 7

value: kidney


title: Pkd2f_P7_WT1_miRNA-seq


title: Pkd2f_P7_KO1_miRNA-seq


title: CM_IL15 Sample 28

value: CM


title: Pkd2f_P3_KO3_miRNA-seq

value: Post natal day 3


title: Pkd2f_P7_KO3_miRNA-seq


title: TM_PMA_Ionomycin Sample 29


title: Pkd2f_P3_KO1_miRNA-seq


title: Pkd2f_P7_WT3_miRNA-seq


title: Pkd2f_P3_KO2_miRNA-seq


title: CM_Bryostatin Sample 27


title: CM_Unstimulated Control Sample 26


title: WT_dmso4


title: Pkd2f_P3_WT2_miRNA-seq


title: Pkd2f_P3_WT3_miRNA-seq


title: Pkd2f_P3_WT1_miRNA-seq


title: CM_PMA_Ionomycin Sample 25


title: Pkd2f_P1_KO3_miRNA-seq

value: Post natal day 1


title: EM_IL15 Sample 24


title: Pkd2f_P1_KO2_miRNA-seq


title: EM_Bryostatin Sample 23


title: TM_Bryostatin Sample 31


title: Pkd2f_P1_WT3_miRNA-seq


title: Pkd2f_P7_KO2_miRNA-seq


title: EM_Unstimulated Control Sample 22


title: Pkd2f_P1_WT1_miRNA-seq


title: Pkd1f_P7_KO3_miRNA-seq


title: Pkd2f_P1_WT2_miRNA-seq


title: TM_IL15 Sample 20


title: Pkd1f_P7_KO2_miRNA-seq


title: TM_Bryostatin Sample 19


title: EM_PMA_Ionomycin Sample 21


title: Pkd1f_P7_WT1_miRNA-seq


title: Pkd1f_P3_KO1_miRNA-seq


title: Pkd1f_P3_KO3_miRNA-seq


title: Pkd1f_P3_KO2_miRNA-seq


title: Pkd1f_P7_KO1_miRNA-seq


title: Pkd1f_P3_WT3_miRNA-seq


title: TM_PMA_Ionomycin Sample 17


title: TM_Unstimulated Control Sample 18


title: CM_Bryostatin Sample 15


title: Pkd2f_P1_KO1_miRNA-seq


title: CM_IL15 Sample 16


title: Pkd1f_P1_KO3_miRNA-seq


title: Pkd1f_P1_KO2_miRNA-seq


title: Pkd1f_P1_KO1_miRNA-seq


title: Pkd1f_P3_WT1_miRNA-seq


title: CM_Unstimulated Control Sample 14


title: Pkd1f_P1_WT3_miRNA-seq


title: Pkd1f_P1_WT2_miRNA-seq


title: Pkd1f_P1_WT1_miRNA-seq


title: Pkd1f_P7_WT3_miRNA-seq


title: CM_PMA_Ionomycin Sample 13


title: Pkd2f_P7_KO3_RNA-seq

data_processing:
Basecalls performed using CASAVA v1.8.2
the low-quality-reads were filtered by NGSQCToolkit_v2.3.3
The reads were aligned to the mm10 genome using TopHat v2.1.0
Read counts of representative genes and their isoforms were measured by HTSeq
Genome_build: mm10


title: Pkd2f_P7_WT3_RNA-seq


title: Pkd1f_P3_WT2_miRNA-seq


title: Pkd2f_P7_KO2_RNA-seq


title: EM_Unstimulated Control Sample 10


title: Pkd2f_P7_KO1_RNA-seq


title: Pkd2f_P7_WT1_RNA-seq


title: Pkd2f_P3_KO2_RNA-seq


title: EM_Bryostatin Sample 11


title: Pkd2f_P3_WT3_RNA-seq


title: Pkd2f_P3_KO3_RNA-seq


title: Pkd2f_P3_KO1_RNA-seq


title: TM_IL15 Sample 8


title: EM_IL15 Sample 12


title: Pkd2f_P3_WT2_RNA-seq


title: Pkd2f_P3_WT1_RNA-seq


title: TM_Unstimulated Control Sample 6


title: TM_Bryostatin Sample 7


title: Pkd2f_P1_KO1_RNA-seq


title: TM_PMA_Ionomycin Sample 5


title: Pkd2f_P1_WT3_RNA-seq


title: Pkd2f_P7_WT2_RNA-seq


title: Pkd2f_P1_WT2_RNA-seq


title: EM_PMA_Ionomycin Sample 9


title: Pkd1f_P7_KO1_RNA-seq


title: CM_IL15 Sample 4


title: Pkd2f_P1_WT1_RNA-seq


title: Pkd1f_P7_WT3_RNA-seq


title: Pkd1f_P7_KO2_RNA-seq


title: CM_Bryostatin Sample 3


title: Pkd1f_P7_KO3_RNA-seq


title: Pkd1f_P7_WT2_RNA-seq


title: EM_d14 Sample 33

value: HIV

tag: timepoint


title: Pkd2f_P1_KO3_RNA-seq


title: CM_Unstimulated Control Sample 2


title: TM_d14 Sample 32


title: Pkd1f_P3_WT2_RNA-seq


title: Pkd1f_P3_WT3_RNA-seq


title: Pkd1f_P7_WT1_RNA-seq


title: Pkd1f_P3_KO1_RNA-seq


title: CM_PMA_Ionomycin Sample 1


title: Pkd1f_P3_KO3_RNA-seq


title: Pkd2f_P1_KO2_RNA-seq


title: Pkd1f_P3_WT1_RNA-seq


title: Pkd1f_P1_KO3_RNA-seq


title: CM_d14 Sample 31


title: Pkd1f_P1_KO2_RNA-seq


title: EM_d14 Sample 30


title: Pkd1f_P3_KO2_RNA-seq


title: Pkd1f_P1_KO1_RNA-seq


title: Pkd1f_P1_WT3_RNA-seq


title: TM_d14 Sample 29


title: Pkd1f_P1_WT2_RNA-seq


title: Pkd1f_P1_WT1_RNA-seq


title: EM_d14 Sample 27


title: TM_d14 Sample 26


title: CM_d14 Sample 25


title: CM_d14 Sample 28


title: CM_d0 Sample 18

value: Healthy


title: CM_d0 Sample 14


title: TM_d0 Sample 15


title: Naive_d0 Sample 17

value: Naive


title: CM_d0 Sample 22


title: Naive_d0 Sample 13


title: EM_d0 Sample 20


title: EM_d14 Sample 12


title: EM_d0 Sample 24


title: Naive_d0 Sample 21


title: EM_d14 Sample 9


title: TM_d0 Sample 23


title: TM_d14 Sample 11


title: CM_d14 Sample 7


title: EM_d0 Sample 16


title: TM_d0 Sample 5


title: EM_d0 Sample 6


title: CM_d0 Sample 4


title: EM_d0 Sample 3


title: TM_d0 Sample 2


title: CM_d0 Sample 1


title: TM_d0 Sample 19


title: CM_d14 Sample 10


title: RNA-seq of mouse liver + LNA-negative_6 days_male3_G153_M16

status: Public on Jan 25 2018

middle: J.

last: Waxman

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene. Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics),
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing normalized read counts and 12 pair-wise differential expression results.

source_name: live_LNA-negative_6 days_male

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was depleted of rRNA using the NEBNext Poly(A) mRNA Magnetic isolation module (NEB, Ipswich, MA, Cat# E7490S). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: To inhibit miR-1948-5p and miR-802-5p function in mouse liver in vivo, LNA constructs complementary to these miRNAs and a negative control were purchased from Exiqon and injected into male and female 9 wk ICR mice (mmu-miR-1948-5p:GGCAGAATACTCATA; mmu-miR-802-5p: GAATCTTTGTTACTG; negative control: ACGTCTATACGCCCA).  Mice were given two subcutaneous injections of the LNA in 1X PBS solution at 25 mg/kg on Day 0 and again on Day 1. Mice were killed and euthanized on Day 3 or Day 6, to give a total of three days or six days of LNA exposure in vivo.  Injections were carried out in the morning between 10 am - 12 pm. LNA-miR-1948 was injected into male mice; LNA-miR-802 was injected into female mice; LNA-negative control was injected into both male and female mice for both 3 day and 6 day exposures, and served as controls.  At the end of the 3 day or 6 day treatments, mice were killed by cervical dislocation, and livers were harvested for RNA extraction and RNA-seq library construction from poly(A) enriched mRNAs.  For each sex and at each time point, N=5 mice received LNA-anti-miRNA, and N=3 mice received scrambled LNA (negative controls).

value: 10 weeks

value: Male

tag: treatment

value: Scrambled LNA (negative control) for 6 days

value: liver


title: RNA-seq of mouse liver + LNA-negative_6 days_male1_G153_M14


title: TM_d14 Sample 8

tag: cell type

value: primary sorted memory CD4+ T cell subsets derived from PBMCs


title: RNA-seq of mouse liver + LNA-negative_6 days_male2_G153_M15

tag: strain


title: RNA-seq of mouse liver + LNA-miR1948_6 days_male3_G153_M11

source_name: live_LNA-miR1948_6 days_male

value: LNA inhibition of miR-1948-5p for 6 days


title: RNA-seq of mouse liver + LNA-miR1948_6 days_male4_G153_M12


title: RNA-seq of mouse liver + LNA-miR1948_6 days_male2_G153_M10


title: PC3_tumor_130

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4.
Graft and host derived reads were separated using xenome. Reference sequences for xenome were created using TopHat2 with parameters --transcriptome-index and -G.
Human derived reads were mapped using TopHat2.
Counting of reads per gene was done using featureCounts
Counts were normalized to RPM and RPKM values as described in Mortazavi et al. (2008) taken gene lengths into account given by  featureCounts
Genome_build: human: hg19, RefSeq annotation from 2014-11-07; mouse: mm10, RefSeq annotation from 2014-06-08
Supplementary_files_format_and_content: .txt files containing read counts per gene, rpms and rpkms

source_name: human prostate cancer cell line (PC3) xenograft, A2M

extract_protocol:
Total RNA was extracted using the prepGold total RNA kit.
Around 1 μg of total RNA was used for library preparation using Illumina TruSeq RNA sample prep kit v2 following the manufacturer's description.

tag: cell line

value: PC3 (PC-3) human prostate cancer cell line

tag: xenograft host

value: mouse


title: RNA-seq of mouse liver + LNA-negative_6 days_female1_G153_M6

source_name: live_LNA-negative_6 days_female

value: Female


title: RNA-seq of mouse liver + LNA-miR1948_6 days_male1_G153_M9


title: PC3_tumor_112


title: PC3_tumor_131


title: RNA-seq of mouse liver + LNA-miR802_6 days_female5_G153_M5

source_name: live_LNA-miR802_6 days_female

value: LNA inhibition of miR-802-5p for 6 days


title: PC3_tumor_128


title: PC3_tumor_129


title: RNA-seq of mouse liver + LNA-miR802_6 days_female3_G153_M3


title: RNA-seq of mouse liver + LNA-miR802_6 days_female2_G153_M2


title: RNA-seq of mouse liver + LNA-miR802_6 days_female4_G153_M4


title: RNA-seq of mouse liver + LNA-miR802_6 days_female1_G153_M1


title: RNA-seq of mouse liver + LNA-miR1948_6 days_male5_G153_M13


title: RNA-seq of mouse liver + LNA-negative_6 days_female1_G153_M7


title: RNA-seq of mouse liver + LNA-negative_3 days_male3_G152_M16

source_name: live_LNA-negative_3 days_male

value: Scrambled LNA (negative control) for 3 days


title: PC3_tumor_127

source_name: human prostate cancer cell line (PC3) xenograft, PBS

value: PBS


title: PC3_tumor_132


title: RNA-seq of mouse liver + LNA-negative_3 days_male1_G152_M14


title: PC3_tumor_125


title: RNA-seq of mouse liver + LNA-negative_3 days_male2_G152_M15


title: PC3_tumor_126


title: RNA-seq of mouse liver + LNA-negative_6 days_female1_G153_M8


title: PC3_tumor_124


title: RNA-seq of mouse liver + LNA-miR1948_3 days_male4_G152_M12

source_name: live_LNA-miR1948_3 days_male

value: LNA inhibition of miR-1948-5p for 3 days


title: RNA-seq of mouse liver + LNA-miR1948_3 days_male5_G152_M13


title: PC3_tumor_123


title: HEK293_adeno_miR1948_2_G144_M12

data_processing:
Adapter sequences were removed from reads using the TrimGalore software.
Small RNA sequence reads corresponding to mmu-miR-1948-5p (ATGAGTATTCTGCCTAA) and mmu-miR-1948-3p (TAGGCAGAGCACTCGTAC) were counted.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file containing read count statistics for mmu-miR-1948-5p and mmu-miR-1948-3p derived from adenovirus infected HEK293 cells.

extract_protocol:
RNA was extracted from the infected cells using Trizol per the manufacturer's instructions.
strand-specific, small RNA library; 1 μg of total RNA was used in NEBNext Small RNA library prep set for Illumina (NEB, Cat# E7330) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335), according to the manufacturer's instructions.

treatment_protocol: HEK293 cells were cultured to 80% confluence in 12 well plates and infected with 4-7 x 10(6) infectious units of adenovirus harboring a CMV-driven GFP reporter fused with a 200 nt sequence flanking the miR-1948 hairpin structure, or with GFP only as control.  These adenoviral constructs were designed and expressed in adenovirus serotype 5 by Applied Biological Materials, British Columbia, Canada (ABM; control adenovirus Cat. # m009; adeno-mmu-miR-1948, custom designed).  Adenovirus seed stocks were propagated in HEK293A cells and titered by plaque assays using standard protocols (Green and Loewenstein, 2006). Cells were infected with adenovirus for ~30 hr to achieve a cytopathic effect and strong GFP fluorescence. Total RNA was then extracted and used for small RNA-seq library preparation.

value: adenovirus infected

tag: molecule subtype

value: small RNA (~21 bp)


title: RNA-seq of mouse liver + LNA-miR1948_3 days_male3_G152_M11


title: HEK293_adeno_miR1948_1_G144_M11


title: HEK293_adeno_GFP_G143_M14


title: RNA-seq of mouse liver + LNA-miR1948_3 days_male2_G152_M10


title: KSHV ΔmiR-K12-11 infected BR3

city: Gainesville

first: Rolf

last: Renne

address: 2033 Mowry Road

institute: University of Florida

description: Biological Replicate 3

data_processing:
Library strategy: qCLASH
Adapter sequences were removed and low-quality reads were discarded using Trimmomatic.
Reads were analyzed using Hyb, a program which aligns reads to a transcript database and identifies RNA-RNA hybrids.
miRNA-mRNA hybrids were analyzed for the origin of the mRNA (5' UTR, CDS, or 3' UTR) using a custom script.
The binding characteristics of the miRNA portion of the hybrid with the mRNA portion were analyzed using a custom script.
Supplementary_files_format_and_content: .hyb files contain the read sequence, the energy of the hybrid folding, the read and genomic location of each RNA component of the hybrid, the alignment score of each  RNA component of the hybrid, and the identity of each RNA.  Column headers are (from left to right): Unique sequence identifier, read sequence, predicted binding energy in kcal/mol, name of matched transcript (first fragment), read start site (first fragment), read end  site (first fragment), transcript start site (first fragment), transcript end site (first fragment), mapping score (first fragment), name of matched transcript (second fragment), read start site (second fragment), read end  site (second fragment), transcript start site (second fragment), transcript end site (second fragment), mapping score (second fragment).

source_name: TIVE-EX-LTC cells

growth_protocol: TIVE-EX-LTC cells were were maintained in DMEM containing 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
Protein G Dynabeads were coated with 2A8, a mouse monoclonal antibody against Argonaute (Ago).  Cells were lysed and treated with DNase and RNase T1.  The cell lysates were added to the antibody-coated beads and allowed to incubate overnight.  After immunoprecipitation, Ago-bound RNAs were phosphorylated.  Ago-RNA complexes were incubated overnight with RNA ligase.  This was followed by dephosphorylation and ligation of the miRCat-33 3’-linker (5’-TGGAATTCTCGGGTGCCAAGG-3’).  After the complexes were eluted from the beads, the samples were treated with proteinase K.  The RNA was phosphorylated and ligated to the Illumina TruSeq® Small RNA Sample Prep Kits RA5 5' adapter.
RNA was reverse-transcribed using Illumina TruSeq® Small RNA Sample Prep Kits RTP and then amplified through 19-24 PCR cycles with Illumina TruSeq® Small RNA Sample Prep Kits RP1 and one of the following barcoded primers: RPI1, RPI2, or RPI3.  WT_BR1, UI_BR1, and D11_BR1 received RPI1, WT_BR2, UI_BR2, and D11_BR2 received RPI2, and WT_BR3, UI_BR3, and D11_BR3 received RPI3.  PCR products were incubated with PEG-8000 and DNA was extracted from the supernatants.

treatment_protocol: TIVE-EX-LTC cells were expanded in 15 cm plates until they reached approximately 80-90% confluence. Cells were trypsinized, resuspended in medium, and rinsed twice with PBS. After the second rinse the cells were resuspended in 10 mL PBS and transferred to a clean 10 cm cell culture plate on ice. Cells were UV-irradiated in a crosslinker at a wavelength of 250 nm, receiving a total energy of 600 joules/cm2. After crosslinking, the cells were counted using a hemocytometer and distributed into aliquots of 50 million cells. The cells were pelleted at 4° C, supernatants were removed, and the cells were frozen at -80° C until further use.

value: derived from Telomerase-Immortalized human umbilical Vein Endothelial cells, Long-Term Culture (TIVE-LTC)

value: infected with KSHV ΔmiR-K12-11


title: RNA-seq of mouse liver + LNA-negative_3 days_female3_G152_M8

source_name: live_LNA-negative_3 days_female

value: 10 weeks


title: KSHV ΔmiR-K12-11 infected BR2

description: Biological Replicate 2


title: RNA-seq of mouse liver + LNA-negative_3 days_female2_G152_M7


title: RNA-seq of mouse liver + LNA-negative_3 days_female1_G152_M6


title: wt KSHV infected BR3

description: Biological Replicate 3

value: infected with wild type KSHV


title: KSHV ΔmiR-K12-11 infected BR1

description: Biological Replicate 1