title: BT188_OV

type: RNA

city: Warsaw

first: Klaudia

last: Kiel

address: Adolfa Pawińskiego 5

country: Poland

institute: Mossakowski Medical Research Centre Polish Academy of Sciences

description: Gene expression after 12hr from treatment in GSC

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

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

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

source_name: glioblastoma

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

growth_protocol: 3D culture in Neurobasal medium

extract_protocol: Total RNA was extracted from G cells by using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: Cells were treated with either mock or OV  and harvested after 12h.

tag: disease

value: glioblastoma patient derived cells

tag: agent

value: oncolitic virus


title: Brain_non-stroke_rep1

status: Public on Jul 29 2020

type: SRA

city: Albuquerque

first: Tamara

last: Roitbak

address: 1 University of New Mexico

country: USA

institute: University of New Mexico

description: Brain_non-stroke_rep1. Source: Temporal lobe biopsy samplescollected  from the tissue adjacent to the tumor, or tissue removed when accessing a deep tumor.  Identified by the pathologist as “normal”, based on the absence of gliosis, necrosis, or tumor cells.

library_source: transcriptomic

data_processing:
Each sequencing library was analyzed by CLC Genomics Workbench (version20.0.2) using the QIAseq miRNA Quantification workflow and RNA-seq Analysis tool
Briefly, sequence reads were trimmed for adapter sequence, grouped by Unique Molecular Identifiers (UMIs), mapped to miRBase (v22) and miRNA expression calculated by counting the number of distinctive UMI reads corresponding to each miRBase -annotated miRNA
Genome_build: miRBase(v22) - mature.fa
Supplementary_files_format_and_content: tab demlimited text file containing raw counts for all samples
Supplementary_files_format_and_content: GSE155257_Normalized_Counts_All_Samples.xlsx: Excel file includes normalized counts for all samples; whole transcriptome analysis data.
Supplementary_files_format_and_content: GSE155257_Diff_gene_expression.xlsx: Excel file includes differential gene expression in human stroke brain tissue versus control samples.

molecule: total RNA

organism: Homo sapiens

source_name: temporal lobe

growth_protocol: Tissue specimens were cut longitudinally to obtain two mirror samples from the same tissue block. One portion of the brain tissue was fixed in 10% neutral buffered formalin and subjected to sectioning and histological staining, followed by morphological evaluation. Another “mirror” part of each sample was stored in RNA later and subsequently frozen at -70o C, for further gene and microRNA analysis.

extract_protocol:
Each sample was stored in RNA later and subsequently frozen at -70°C.
miRNA was isolated using the QIAseq miRNA Library kit and sequenced on Illumina NextSeq500

tag: tissue

value: brain

tag: disease state

value: normal

tag: age

tag: Sex

value: Male


title: 786-O_USP37_sg9_Rep3

status: Public on May 27 2020

city: Boston

first: Jeremy

last: Simon

state: MA

address: 450 Brookline Ave

department: Department of Data Science

institute: Dana-Farber Cancer Institute

data_processing:
Reads were filtered for adapter contamination using cutadapt (Martin, 2011) and filtered such that at least 90% of bases of each read had a quality score > 20.
Reads were aligned to the reference genome (hg19) using STAR version 2.5.2b retaining only primary alignments (Dobin et al., 2013). Reads overlapping blacklisted regions of the genome were then removed.
Transcript abundance was then estimated using salmon (Patro et al., 2017b). Differential expression was detected and Variance-stabilizing transformed (VST) expression values were computed using DESeq2 (Love et al., 2014)
Genome_build: hg19
Supplementary_files_format_and_content: Batch corrected, VST-normalized expression values from DESeq2

molecule: polyA RNA

source_name: 786-O cells

growth_protocol: 786-O cells were cultured in DMEM containing 10% fetal bovine serum (FBS) plus 1% penicillin streptomycin. For lentivirus packaging and infection, following lentivirus infection, cells were maintained in the presence of blasticidin (10 μg/ml) or puromycin (2 μg/ml) depending on the vector. All cells were maintained at 37°C with 5% CO2.

extract_protocol:
Total RNA from 786-O cells (triplicates) was extracted by using RNeasy kit with on column DNase digestion (Qiagen)
Libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer’s instructions. Samples were sequenced on an Illumina HiSeq2500 with paired-end 150 bp reads

treatment_protocol: SgRNA sequences targeting USP37 and HIF2a were cloned into pLenti CRISPR-V2 puro. 293T packaging cell line was used for lentivirus generation. Lentiviral infection was performed as previously described (25). Briefly, post-transfection with lipofectamine 3000, medium containing viruses was collected twice after 48 and 72 hours. After passing through 0.45 μM filters, an appropriate amount of virus was used to infect target cells in the presence of 8 μg/ml polybrene (sc-134220, Santa Cruz). After incubation for additional one day, target cell lines were selected with appropriate antibiotic.

tag: cell line

value: 786-O cells

tag: treatment


title: G61557_mock


title: 786-O_USP37_sg9_Rep1


title: Brain_stroke_rep4

description: Brain_stroke_rep4  Temporal lobe tissue removed during chemicraniectomy/stroke-ectomy procedure. Patient with malignant hemispheric stroke.

value: stroke


title: 786-O_USP37_sg9_Rep2


title: 786-O_HIF2a_sgscr_Rep3


title: 786-O_HIF2a_sgscr_Rep1


title: 786-O_HIF2a_sgscr_Rep2


title: G88_OV


title: 786-O_HIF2a_sg6_Rep3


title: G61557_OV


title: Brain_stroke_rep1

description: Brain_stroke_rep1  Temporal lobe tissue removed during chemicraniectomy/stroke-ectomy procedure. Patient with malignant hemispheric stroke.

value: Female


title: G157_OV


title: G157_mock


title: BT188_mock


title: G44_OV


title: G107_mock


title: 786-O_USP37_sgscr_Rep2


title: 786-O_USP37_sg3_Rep1


title: G107_OV


title: 786-O_HIF2a_sg4_Rep1


title: 786-O_USP37_sg3_Rep3


title: 786-O_USP37_sg3_Rep2


title: 786-O_HIF2a_sg6_Rep2


title: G44_mock


title: 786-O_HIF2a_sg6_Rep1


title: 786-O_HIF2a_sg4_Rep3


title: D7_R2

status: Public on May 01 2020

city: Berlin

first: Marco

last: Preussner

address: Takustrasse 6

country: Germany

institute: FU berlin

description: Ribo-Seq

data_processing:
Sequencing reads from both input and riboseq were aligned to the mouse reference genome (mm10) using STAR. For the riboseq data —outFilterScoreMinOverLread and —outFilterMatchNminOverLread were both set to 0.3 to allow mapping of short fragments.
RNASeQC was used for calculating gene-wise TPM values for each sequenced replicate using the aligned reads
GENCODE release M21 (GRCm38.p6) was supplied as annotation for gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: TPM

organism: Mus musculus

source_name: EL4 +U2af26DE7

growth_protocol: EL4 cells were cultivated in RPMI medium containing 10% FCS (Biochrom) and 1% Penicillin/Streptomycin (Biowest).

extract_protocol:
RNA was extracted using RNATri (Bio&Sell) followed by DNaseI digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For generation of stable EL4 cells 5 µg of linearized pCMV-U2AF26ΔE7-Flag plasmid was transfected into 2x106 EL4 cells by electroporation with the Nucleofector II (Amaxa Biosytems) electroporation system following the manufacturer’s protocol. 48 hours after transfection, clones were selected with 4 mg/ml G418 (Sigma) in RPMI and clones were expanded.

tag: cell type

tag: genotype

tag: sample type

value: ribo-seq


title: 786-O_HIF2a_sg4_Rep2


title: G88_mock


title: D7_B36_2

description: total RNA (polyA+)

value: input


title: Set2_Y149F_60_RNA_Rep2

status: Public on Apr 29 2020

description: rRNA depleted

data_processing:
Reads were trimmed and filtered of adapter sequencing using cutadapt, and required to have at least 90% of bases with quality scores exceeding 20
Reads were then aligned to the reference yeast genome (sacCer3) using STAR
Base-by-base signals (of aligned reads) were analyzed over sets of genomic features of interest.
Genome_build: sacCer3
Supplementary_files_format_and_content: bed files with BAM-aligned reads on both strands

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae BY4741

growth_protocol: The indicated yeast strains were grown to saturation in YPD before being diluted to an OD600 of 0.2 and grown to an OD600 of ~1. Cells were isolated, washed with water, and then resuspended in SD media (Cheung et al., 2008).

extract_protocol:
Ten ODs of cells were collected at each time point and RNA was isolated by acid phenol extraction. Five μg RNA was treated with DNase (Promega) and purified (RNeasy column, QIAGEN). Two and a half μg RNA was then processed using yeast-specific rRNA depletion beads (Illumina).
Strand-specific bar-coded sequencing libraries were then prepared (TruSeq Stranded Total RNA Library Preparation Kit, Illumina). Libraries were pooled and sequenced across two lanes (Hi-Seq 4000, Illumina).

tag: background strain

tag: set2 genotype

tag: nutrient stress timepoint

value: 60 min

tag: replicate


title: Set2_null_60_RNA_Rep3

description: rRNA depleted


title: D7_B36_1

description: total RNA (polyA+)


title: WT_B37_2

description: total RNA (polyA+)

source_name: EL4 WT

value: WT


title: WT_B37_1

description: total RNA (polyA+)


title: D7_R1

description: Ribo-Seq


title: R3

description: Ribo-Seq


title: R2

description: Ribo-Seq


title: D7_R3

description: Ribo-Seq


title: R1

description: Ribo-Seq


title: Set2_H199L_0_RNA_Rep1

description: rRNA depleted

value: 0 min


title: Set2_H199L_60_RNA_Rep3

description: rRNA depleted


title: Set2_Y149F_60_RNA_Rep1

description: rRNA depleted


title: Set2_F234Y_60_RNA_Rep1

description: rRNA depleted


title: Set2_F234Y_60_RNA_Rep2

description: rRNA depleted


title: Set2_Y149F_0_RNA_Rep3

description: rRNA depleted


title: Set2_F234Y_0_RNA_Rep3

description: rRNA depleted


title: Set2_null_60_RNA_Rep1

description: rRNA depleted


title: Set2_Y149F_0_RNA_Rep2

description: rRNA depleted


title: Set2_null_0_RNA_Rep3

description: rRNA depleted


title: Set2_Y149F_60_RNA_Rep3

description: rRNA depleted


title: Set2_null_0_RNA_Rep1

description: rRNA depleted


title: Set2_H199L_60_RNA_Rep2

description: rRNA depleted


title: Set2_H199L_60_RNA_Rep1

description: rRNA depleted


title: BY4741_WT_0_RNA_Rep2

description: rRNA depleted


title: Set2_H199L_0_RNA_Rep3

description: rRNA depleted


title: BY4741_WT_0_RNA_Rep3

description: rRNA depleted


title: BY4741_WT_0_RNA_Rep1

description: rRNA depleted


title: Set2_H199L_0_RNA_Rep2

description: rRNA depleted


title: Set2_F234Y_60_RNA_Rep3

description: rRNA depleted


title: Set2_Y149F_0_RNA_Rep1

description: rRNA depleted


title: ChIP-Seq_CtrA(Totalinput)_H.neptuniumLE670_(GHA-430)

status: Public on Mar 29 2020

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

library_source: genomic

data_processing:
Base calling: HiSeq Control Software 2.2.38, RTA 1.18.61.0, CASAVA-1.8.2
Alignment: Bowtie-0.12.9, samtools-0.1.18
Peak calling and refinement: MACS2 Software (Galaxy Version 2.1.1.20160309.0)
Peak annotation: SeqMonk Software v1.40.0 (Braham Bionformatics Institute)
Genome_build: Hyphomonas neptunium LE670 (ATCC15444) : NC_008358
Supplementary_files_format_and_content: The xls file reporting CtrA and GcrA ChIP-Seq peaks (described in the paper) was generated by MACS2 and SeqMonk softwares. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length coordinates (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue); column 10: DNA sequences (+/-75pb window surrounding the peak summit).

molecule: genomic DNA

organism: Hyphomonas neptunium

growth_protocol: Overnight saturated cultures of Hyphomonas neptunium LE670 strains were freshly diluted in Difco Marine Broth 2216 media and cultures were grown at 28°C with aeration to mid-log phase (O.D.580nm~0.5).

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 2% of each pre-cleared lysate was kept as total input samples (negative control samples). The rest of the pre-cleared lysates was incubated overnight at 4°C with polyclonal antibodies targeting CtrAHN (this work) or GcrACC (Holtzendorff et al., 2004) (1:1,000 dilution). The immuno-complexes were captured after incubation with Protein-A agarose (pre-saturated with BSA) during a 2 h incubation at 4°C and they were washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted from the Protein-A agarose beads with two times 250 μl elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.

treatment_protocol: H. neptunium wildtype cells were treated with formaldehyde (1% final concentration) in 10 uM sodium phosphate buffer (pH 7.6) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were frozen in liquid nitrogen and stored at -80°C.

tag: strain

value: Wild type

tag: antibody


title: ChIP-Seq_GcrA(Totalinput)_H.neptuniumLE670_(GHA-466)


title: ChIP-Seq_CtrA_H.neptuniumLE670_(GHA-428)

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37Â°C, according to the manufacturer's instructions. Lysates were sonicated (BioruptorÂ® Pico) at 4Â°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4Â°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 Î¼l of protein-A agarose (Roche, www.roche.com) and 100 Î¼g BSA. 2% of each pre-cleared lysate was kept as total input samples (negative control samples). The rest of the pre-cleared lysates was incubated overnight at 4Â°C with polyclonal antibodies targeting CtrAHN (this work) or GcrACC (Holtzendorff et al., 2004) (1:1,000 dilution). The immuno-complexes were captured after incubation with Protein-A agarose (pre-saturated with BSA) during a 2 h incubation at 4Â°C and they were washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted from the Protein-A agarose beads with two times 250 Î¼l elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65Â°C to reverse the crosslinks. The samples were then treated with 2 Î¼g of Proteinase K for 2 h at 45Â°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 Î¼g of glycogen as a carrier and resuspended in 50 Î¼l of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.
-His6-CtrA(HN) antibody (polyclonal) was raised in rabbit against purified His6-CtrA (H. neptunium) protein.
-His6-CtrA(HN) protein purification:
To purify His6-CtrA(HN), E. coli Rosetta2 (DE3) pLysS was transformed with plasmid pOL145 (CtrAHN), and grown at 37°C in LB medium supplemented with 0.5% glucose. When the culture had reached an OD580 of 0.5-0.7, expression of the His6-CtrA(HN) protein was induced with 0.5 mM IPTG. Cells were harvested after the culture had reached an OD580 of 2.5 by centrifugation for 10 min at 4500g. Cells were washed twice in buffer A (50 mM Na2HPO4, 300 mM NaCl, 10 mM imidazole, pH 8.0 HCl) and stored at -80°C. After cells were thawed on ice and resuspended in the above-mentioned buffer containing 10g/ml DNase I and 100g/ml PMSF, they were disrupted by two to four passages through the French press at 16,000 psi. After centrifugation at 30,000g for 30 to 60 min at 4°C to remove cell debris, the supernatant was applied to a 5 ml HisTrap HP column (GE Healthcare) which was equilibrated with the above-mentioned buffer prior to use. The column was washed with 5 column volumes (CV) of buffer A and elution of the protein was obtained with a linear imidazole gradient of buffer A and B (50 mM Na2HPO4, 300 mM NaCl, 500 mM imidazole, pH 8.0 - HCl) at a flow rate of 1 ml/min using an Äkta purifier 10 (GE Healthcare). Elution fractions were checked by SDS-PAGE and a second step of purification was performed using size exclusion chromatography: Fractions were loaded onto a 120 ml Superdex 200 16/60 (GE-Healthcare, USA) equilibrated with buffer C (50 mM Na2HPO4, 300 mM NaCl, pH 8.0 - HCl) and the protein was eluted with 1 CV of buffer C using a flow rate of 0.5 ml/min. Fractions that contained a high concentration of His6-CtrA(HN) protein (as visualized by SDS PAGE) were pooled and dialyzed with buffer D (50 mM Na2HPO4, 300 mM NaCl, 5% glycerol, pH 8.0 -HCl). Protein solution was then snap-frozen in liquid nitrogen and stored at -80 °C until further use. Polyclonal antibody against His6-CtrA(HN) were raised in rabbits (Eurogentec, Belgium).
-GcrA(Cc) antibody (polyclonal) was raised in rabbit against purified GcrA (C. crescentus) protein. The production of this GcrA antibody was previously described and published in Holtzendorff et al., 2004 (Science) (https://www.ncbi.nlm.nih.gov/pubmed/15087506)

value: CtrA


title: Negative_control_Caulobacter_crescentus_NA1000(WT)(GHA-354)

status: Public on Mar 20 2020

data_processing:
Base calling: HiSeq Control Software 2.0.12.0, RTA 1.17.21.3, CASAVA-1.8.2
Alignment: Map with Bowtie for illumina (Galaxy Version 1.1.2), Samtools (http://samtools.sourceforge.net/)
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.45.1 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting MipZ ChIP-Seq normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature; column 5: Description; column 6, 7, 8 and 9: MipZ ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Caulobacter vibrioides

source_name: negative control

growth_protocol: Overnight cultures of C. crescentus NA1000 (negative control sample), BH64 (MipZWT-eYFP), BH99 (MipZD42A-eYFP) and BH100 (MipZK13A-eYFP) strains grown in PYE supplemented with vanillate (50μM) were harvested and washed 3 times with PYE, and then restarted in 80ml of PYE medium (starting O.D.660nm~0.05) for 5h at 30°C. Then, 0.3% xylose was added (induction of MipZ-eYFP fusions from the Pxyl promoter) and cultures were incubated for an additional 1h at 30°C.

extract_protocol:
After resuspension of the cell pellets in Dilution buffer (GFP-Trap®_A for Immunoprecipitation of GFP-Fusion Proteins, ChromoTek, Germany; 10 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 150 mM NaCl), they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using Dilution buffer supplemented with protease inhibitors (Roche). Cleared lysates were incubated 2h at 4°C with GFP-Trap®_A agarose beads (pre-washed 3 times with Dilution buffer). Beads were then washed subsequently with Dilution buffer, twice with high salt Wash buffer (10 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 500 mM NaCl) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The captured immuno-complexes were eluted from the GFP-Trap®_A agarose beads with two times 250 μL of Elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.

treatment_protocol: Cultures (final O.D.660nm~0.6) were supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.


title: Set2_null_0_RNA_Rep2

description: rRNA depleted


title: ChIP-Seq_MipZ_Caulobacter_crescentus_NA1000(WT)(GHA-28)

description: processed data file: MipZ_ChIP-Seq_profiles_RPM_normalized.xlsx

data_processing:
Base calling: RTA SCS.2.6, GERALD.1.5.1
Alignment: Map with Bowtie for illumina (Galaxy Version 1.1.2), Samtools (http://samtools.sourceforge.net/)
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.45.1 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting MipZ ChIP-Seq normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature; column 5: Description; column 6: MipZ ChIP-Seq profiles (normalized Read Per Million unit, RPM)

source_name: MipZ

growth_protocol: Overnight cultures in PYE of C. crescentus NA1000(WT) were restarted in 80ml of PYE (starting O.D.660nm~0.05) and incubated at 30°C.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. The pre-cleared lysates was then incubated overnight at 4°C with polyclonal rabbit antibodies targeting MipZ (1:500 dilution). The immuno-complexes were captured after incubation with Protein-A agarose beads (pre-saturated with BSA) during a 2 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A agarose beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the Chrysalis 36cycles v 4.0 Sequencing Kit following manufacturer instructions.

treatment_protocol: Cultures (final O.D.660nm~0.5) were supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.


title: ChIP-Seq_MipZD42A-eYFP_Caulobacter_crescentus_BH99(GHA-350)


title: Set2_F234Y_0_RNA_Rep2

description: rRNA depleted


title: Set2_F234Y_0_RNA_Rep1

description: rRNA depleted


title: HiC_CTCF-AID_NPC_d4_ctl_rep1

status: Public on Mar 06 2020

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
Hi-C reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (HIC) were generated useing juicebox pre (Neva et al., 2016).

source_name: neural precursor cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol:
Hi-C experiments were conducted using Mbo1 according to previous publication (Rao et al., 2014).
Hi-C library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24 or 48 hours after stating auxin treatment. Neural cell differentiation treatment was performed with or without auxin treatment, and the neural precursor cells were harvested on day 4 or 2 days after washing out auxin from the day 4 sample.

value: F123 mouse neural precursor cell


title: BY4741_WT_60_RNA_Rep3

description: rRNA depleted


title: TG003_35_3

status: Public on Feb 14 2020

data_processing:
For alignment and quantification of gene.tpm files we used the Whippet-quant function of Whippet v0.6.4. This aligns and quantifies in one step
Genome_build: hg38

growth_protocol: HEK293 cells were cultured in DMEM High glucose (Biowest) containing 10% FCS (Biochrom) and 1% Penicillin/Streptomycin (Biowest).

treatment_protocol: Confluent HEK293 cells were incubated at 39°C for 12 hours. Cells were then treated with 50 µM TG003 (or DMSO as solvent control) and after further 30 minutes at 39°C, samples were incubated for 6 hours at either 39°C or 35°C.

tag: temperature


title: TG003_39_1


title: DMSO_39_1

value: DMSO


title: DMSO_39_3


title: TG003_35_2


title: Set2_null_60_RNA_Rep2

description: rRNA depleted


title: BY4741_WT_60_RNA_Rep1

description: rRNA depleted


title: BY4741_WT_60_RNA_Rep2

description: rRNA depleted


title: ChIP-Seq_MipZK13A-eYFP_Caulobacter_crescentus_BH100(GHA-353)


title: ChIP-Seq_MipZWT-eYFP_Caulobacter_crescentus_BH64(GHA-352)

source_name: MipZWT-eYFP


title: ChIP-Seq_GcrA_H.neptuniumLE670_(GHA-465)

value: GcrA


title: DMSO_35_2


title: DMSO_35_1


title: SFMBT1_input

status: Public on Feb 04 2020

data_processing:
Reads were then trimmed and filtered of adapter sequencing using cutadapt, and required to have at least 90% of bases with quality scores exceeding 20. Duplicated sequences were then capped at a maximum of 5 occurrences
Reads were then aligned to the reference human genome (hg19) using STAR
Reads overlapping blacklisted regions of the genome were then removed. Reads were then extended in silico to a fragment size of 250 bp, and regions of significant enrichment relative to input control were identified using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized RNA abundance matrix
Supplementary_files_format_and_content: Nornalized ChIP signal in bigWig format

growth_protocol: 786-O cells were cultured in DMEM supplemented with 10% fetal bovine serum plus 1% penicillin–streptomycin and were maintained at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol:
ChIP was performed with SFMBT1 antibody (Bethyl, A303-221A) as previously described (Zhang et al., 2018).
ChIP-seq libraries (Illumina) were prepared according to manufacturer’s recommendations and sequenced at the UNC High Throughput Genomic Sequencing facility using single-end 50bp reads


title: SFMBT1_ChIP


title: SFMBT1_si1_Rep2

data_processing:
Reads were then trimmed and filtered of adapter sequencing using cutadapt, and required to have at least 90% of bases with quality scores exceeding 20
Reads were then aligned to the reference human genome (hg19) using STAR, and transcript abundance was estimated using Salmon
Differential expression between each siRNA and control was analyzed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Normalized RNA abundance matrix
Supplementary_files_format_and_content: Nornalized ChIP signal in bigWig format

extract_protocol:
RNA was extracted from 786-O cells using RNeasy kit with on-column DNase digestion (Qiagen)
Libraries were constructed and sequenced at BGI as single-end 50 bp reads

treatment_protocol: SFMBT1 siRNA1/2 were obtained from Dharmacon. Target sequences were as follows:  SFMBT1 si1: TGGCAGACGTTGTGCGGTT  SFMBT1 si2: GGAAAGAGTTATCGGGCTA


title: SFMBT1_si2_Rep2


title: SFMBT1_si2_Rep1


title: SFMBT1_si1_Rep3


title: SFMBT1_si1_Rep1


title: HiC_CTCF-AID_NPC_d4_auxin_rep1


title: HiC_CTCF-AID_NPC_d4_auxin_rep2


title: SFMBT1_siCtrl_Rep3

value: siScrambled


title: TG003_39_2


title: SFMBT1_siCtrl_Rep2


title: DMSO_39_2


title: Total-Input_RpoD_Caulobacter_crescentus_NA1000(Expo)_GHA-599

status: Public on Jan 11 2020

data_processing:
Base calling: HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2
Alignment: Map with Bowtie for illumina (Galaxy Version 1.2.0), SAM-to-BAM (Galaxy Version 2.1.1)
Peak calling and refinement: MACS2 Callpeak (Galaxy Version 2.1.1.20160309.6)
Peak annotation: SeqMonk Software v1.45.1 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting CdnL and RpoD ChIP-Seq peaks was generated by MACS2 software. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length coordinates (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue). Common peaks between CdnL and RpoD datasets are highlighted in green.

growth_protocol: Overnight saturated cultures of Caulobacter crescentus strains were freshly diluted in PYE media and cultures were grown at 30°C to mid-log phase (O.D.660nm~0.5).

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37 °C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4 °C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. Five percent of the pre-cleared lysates were kept as total input samples (negative control samples). The rest of the pre-cleared lysates was then incubated overnight at 4 °C with polyclonal rabbit antibodies targeting CdnL (1:1,000 dilution) or monoclonal mouse antibodies targeting RpoD/Sigma70 (1:250 dilution ; Neoclone #WP004), respectively.
CdnL antibody used in our ChIP-seq was specifically raised for this study; His6-SUMO-CdnL was overproduced in Rosetta (DE3) pLysS E.coli cells from pEG1129 by inducing for 3 hr at 30C with 0.5 mM IPTG at OD600 of 0.5. Cells were harvested by centrifugation, resuspended in lysis buffer (50 mM Tris-HCl, pH 8.0, 300 mM KCl, 20 mM imidazole, and 10% glycerol), lysed with 1 mg/mL lysozyme, sonicated and centrifuged at 4 oC for 30 min at 15000 x g. Supernatant was loaded onto a HisTrap FF 1 mL column (GE Life Sciences) and eluted with lysis buffer with 300 mM imidazole, cleaved with His6-Ulp1 (SUMO protease) at 1:500 (protease: fusion) molar ratio overnight while dialyzing into lysis buffer. Sample was reloaded onto HisTrap FF 1mL and flow through collected to separate His6-SUMO and His6-Ulp1 from CdnL. CdnL fraction was dialyzed into PBS prior to antibody production. CdnL antisera was generated by immunizing a rabbit with CdnL purified as above (Pocono Rabbit Farm & Laboratory). Specificity was determined using cell lysates with deleted or overexpressed CdnL.
The immuno-complexes were captured after incubation with Protein-A (CdnL) or Protein-G (RpoD/Sigma70) agarose beads (pre-saturated with BSA) during a 2 h incubation at 4 °C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A or Protein-G agarose beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like the total input samples, incubated overnight with 300 mM NaCl at 65 °C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45 °C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) according to the manufacturer's instructions.

treatment_protocol: Cultures of exponentially growing (OD660nm of 0.5, 80 ml culture in PYE per sample) C. crescentus NA1000 WT strain were supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.

tag: genotype/variation


title: TG003_35_1


title: HiC_CTCF-AID_NPC_d4_ctl_rep2


title: ChIP-Seq_RpoD_Caulobacter_crescentus_NA1000(Expo)_GHA-589

tag: chip antibody

value: monoclonal mouse antibodies targeting RpoD/Sigma70 (Neoclone #WP004)


title: DMSO_35_3


title: TG003_39_3


title: ChIP-Seq_CtrA_DptsP DspoTrpoB*_C.crescentus_Exp phase(AIYT-20)

status: Public on Nov 25 2019

data_processing:
Base calling: HiSeq Control Software 2.2.38, RTA 1.18.61.0, CASAVA-1.8.2
Alignment: Map with Bowtie for illumina (Galaxy Version 1.2.3), SAM-to-BAM (Galaxy Version 2.1.1)
Peak calling and refinement: MACS2 Callpeak (Galaxy Version 2.1.1.20160309.6)
Peak annotation: SeqMonk Software v1.45.1 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting CtrA ChIP-Seq peaks in WT and mutants in exponential and stationary phase (as described in the paper) was generated by MACS2 software. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length coordinates (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue).

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus NA1000 culture

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 2% of each pre-cleared lysate was kept as total input samples (negative control samples). The rest of the pre-cleared lysates was incubated overnight at 4°C with rabbit polyclonal antibodies targeting CtrA (Sanselicio and Viollier,2015) (1:1,000 dilution). The immuno-complexes were captured after incubation with Protein-A agarose (pre-saturated with BSA) during a 2 h incubation at 4°C and they were washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted from the Protein-A agarose beads with two times 250 μl elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.

treatment_protocol: C. crescentus wildtype and mutant cells were treated with formaldehyde (1% final concentration) in 1 uM sodium phosphate buffer (pH 7.6) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were frozen in liquid nitrogen and stored at -80°C.

value: ptsP spoT rpoB*

tag: tissue

value: Caulobacter crescentus NA1000 culture


title: Total-Input_CtrA_C.crescentus_(AIYT-24)


title: SFMBT1_si2_Rep3


title: ChIP-Seq_CtrA_CtrA401SS_C.crescentus_Exp phase(AIYT-23)

value: ctrA401SS (ctrAT168IT170I)


title: SFMBT1_siCtrl_Rep1


title: ChIP-Seq_CtrA_WT_C.crescentus_Exp phase(GHA-490)


title: ChIP-Seq_CtrA_CtrA401_C.crescentus_Exp phase(AIYT-22)

value: ctrA401 (ctrAT170I)


title: Total-Input_CdnL_Caulobacter_crescentus_NA1000(Expo)_GHA-604


title: ChIP-Seq_CdnL_Caulobacter_crescentus_NA1000(Expo)_GHA-600

value: polyclonal rabbit antibodies targeting CdnL


title: ChIP-Seq_CtrA_DptsP DspoT_C.crescentus_Exp phase(AIYT-19)

value: ptsP spoT


title: hMDM-CD14-DR-D7-2

status: Public on Oct 31 2019

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

description:
sample name in processed data file:
hMDM3
GroupA_vsd.txt

data_processing:
RNA-seq reads were aligned to the hg38 reference genome assembly using STAR v2.6.0
The raw counts were normalized using variance stabilizing transformation (VST) method after excluded a minimum count of 1.0 in all of the samples.
Differentiall expressed genes were calculated using DESeq package in R
Genome_build: hg38 (GRCh 38)
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts

source_name: monocyte

growth_protocol: The H9 hESC line was obtained from WiCell (Madison, WI, USA) and cultured in feeder-free TeSR-E8 or mTeSR-1 medium (STEMCELL Technologies, Vancouver, Canada) on tissue culture plates coated with Vitronectin (Gibco, Grand Island, NY, USA) or Matrigel hESC-qualified Matrix (Corning Inc., Corning, NY, USA), and were mechanically passaged. For differentiation into macrophage-like cells, hESCs were transitioned into Growth Factor-Reduced Matrigel (Corning Inc.) in mTeSR-1 medium at a density of 5–8 colonies/35-mm dish. Mesodermal differentiation was induced with APEL2 medium supplemented with 1× insulin-transferrin-selenium-X (Gibco) and BMP4. HSPC production was induced by treatment with APEL2 medium containing VEGF4 and SCF for 2 days, followed by SCF, IL-3 and IL-6 and TPO and Flt-3L. After 12-20 days, floating HSPCs were further differentiated into iMAC using macrophage M-CSF and RPMI1640 medium supplemented with 10% fetal bovine serum.     THP-1 pro-monocyte cells were maintained in RPMI1640 containing 10% FBS and 5% penicillin/streptomycin. For differentiation into macrophages, THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA, 100 ng/ml for 48 h). To generate hMDMs, we sorted CD14+ blood monocytes from hPBMCs using magnetic CD14 microbeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and cultured the cells in the presence of M-CSF (100 ng/ml).

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Briefly, cells were homogenized and transferred directly into a spin column. Tubes were centrifuged 2 min at maximum speed. Homogenized lysate were then transfered into spin column and centrifuged for 30min at 8000g, and save the flow-through and add 1 volume of 70% EtOH. Transfer 700 ul of sample into RNeasy spin column and centrifuged for 15s at 8000g. After 15s, 700 ul RPE buffer was added to spin column and centrifuged 15s at 8000g. Next, 500 ul RPE buffer was added to spin column and centrifuged 2min at 8000g. After 2min, transfer spin column in a new 1.5 ml collection tube and added 50ul RNase free water directly to the membrane and centrifuged for 1min at 8000g.
The library was prepared using Truseq stranded mRNA prep kit (Illumina, San Diego, CA, USA) and run on a HiSeq2500 sequencer (Illumina) with a 101-bp paired-end read length. Raw data were processed using STAR v.2.6 to align genome reads against human Reference genome (hg38) and differentially expressed genes were identified using DESeq21 after raw count data were normalized using variance stabilizing transformation (VST) method. Multidimensional scaling (MDS) and clustering analysis were calculated based on Poisson model. Spearman correlation coefficients between pairs of samples were computed.

treatment_protocol: Macrophages were infected with H37Rv-GFP Mtb at the desired multiplicity of infection (MOI) for 2h with mild shacking (120 rpm) at 37°C. For the high-throughput screening, a MOI of 5 was used. Infected cells were washed twice with fresh medium.

value: hMDM

tag: infection status

value: not infected


title: ChIP-Seq_CtrA_WTrpoB*_C.crescentus_Exp phase(AIYT-21)

value: rpoB*


title: ChIP-Seq_CtrA_DptsP_C.crescentus_Stat phase(GHA-493)

value: ptsP


title: ChIP-Seq_CtrA_WT_C.crescentus_Stat phase(GHA-491)

value: Wild type


title: H9-MAC-D20-1

description:
sample name in processed data file:
iMAC_D20-1
GroupA_vsd.txt

source_name: Embryonic stem cell

value: human ES-derived macrophage

tag: time

value: day 20


title: ChIP-Seq_CtrA_DspoT_C.crescentus_Stat phase(GHA-494)

value: spoT


title: WT stress replicate 2 20190223

status: Public on Oct 01 2019

city: Taipei City

first: Paul

last: Verslues

address: No.128, Sec.2, Academia Rd., Nangang Dist.

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

description: seedlings grown for seven days under unstressed control conditions, transferred to low water potential (-0.7 MPa) for 96 hours before sample collection

data_processing:
Illumina CASAVA-Bcl2fastq version 1.8.4 for basecalling and demultiplexing
RNAseq reads were trimmed using trimmomatic v0.35 with parameters ILLUMINACLIP:Trimmomatic-0.35/adapters/TruSeq3-PE-2.fa:2:30:10:8:true CROP:151 MINLEN:100
trimmed reads were mapped to the TAIR10 genome using Bowtie2 and BLAT with default parameters
RPKM values were computed using Rackj (http://rackj.sourceforge.net/)
expression comparisons were performed using DESeq2
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: comma-separate text files made by DESeq2

organism: Arabidopsis thaliana

source_name: WT stress

growth_protocol: seeds were sown on agar plates containing half strength Murashige-Skoog media with 2 mM MES buffer (pH 5.7) and stratified for 3 days at 4ᵒC. Plates were then positioned vertically in a rack and and kept under continuous light (80-100 micromol photons m-2sec-1 ) at 23ᵒC in a controlled environment chamber. Note that no sugar was added to any of the growth media used.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Plant Mini Kit according to the manufacturer’s protocol.  RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and run on 2% agarose gel with post-run staining.
TruSeq Stranded Total RNA Library Prep Kit; input 3 ug total RNA, poly-A RNA were purified by oligo-dT beads; USER digest treatment was done to the adaptor ligation product; final library was amplified by 10 cycles of PCR using KAPA HiFi Mastermix. Library concentrations were normalized using KAPA Library Quantification Kit for Illumina.
Stranded-specific RNA-seq with oligo-dT purification.

treatment_protocol: After seven days of growth, seedlings were transferred to either fresh control plates (-0.25 MPa) or to agar plates infused with polyethylene glycol 8000 (PEG) to impose low water potential (-0.7MPa) stress.  Plaese were returned to the growth chamber and all samples were collected 96 h after transfer (control and stress treatments).

value: stress -0.7MPa

value: wild type Col-0

value: whole seedling


title: pEG100 HIN1 control replicate 2 20190223

description: seedlings grown for elevent days under unstressed control conditions

source_name: pEG100 HIN1 control

value: unstressed control -0.25MPa

value: 35S:HIN1stable transgenic line


title: WT stress replicate 3 20190223


title: WT control replicate 3 20190223

source_name: WT control


title: pEG100 HIN1 stress replicate 2 20190223

source_name: pEG100 HIN1 stress


title: H9-MAC-D60-2

description:
sample name in processed data file:
iMAC_D60-2
GroupA_vsd.txt

value: day 60


title: H9-MAC-D60-1

description:
sample name in processed data file:
iMAC_D60-1
GroupA_vsd.txt


title: hMDM-CD14-DR-D0

description:
sample name in processed data file:
hMDM1
GroupA_vsd.txt


title: pEG100 HIN1 control replicate 3 20190223


title: WT control replicate 2 20190223


title: pEG100 HIN1 control replicate 1 20190223


title: WT control replicate 1 20190223


title: WT stress replicate 1 20190223


title: hMDM-CD14-DR-D7-1

description:
sample name in processed data file:
hMDM2
GroupA_vsd.txt


title: pEG100 HIN1 stress replicate 1 20190223


title: pEG100 HIN1 stress replicate 3 20190223


title: H9-MAC-D20-2

description:
sample name in processed data file:
iMAC_D20-2
GroupA_vsd.txt


title: Day_40_rep3

status: Public on Sep 13 2019

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

hyb_protocol: A total of 600 ng of Cy3-labelled cRNA was hybridized to Agilent 8x60 K-Human Genome Microarrays using Agilent Gene Expression Hybridization Kit, according to the manufacture's instructions (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: The microarrays were read on the Agilent DNA Microarray SureScan Scanner using the FeatureExtraction program (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The raw reads were filtered using a custom-made Perl script to retain only probes detected above background in at least 3 of the 24 samples. Processed reads were log2 transformed and quantile normalized using Expander 7.0 software.

source_name: Wycell, WA09 (H9), day 40, replicate 3

label_protocol: A total of 40 ng of RNA was processed and fluorescently labeled using Agilent Low Input Quick Amp Labeling Kit, according to the manufacture's instructions (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Human pluripotent stem cells (hPSC) were maintained and differentiated as in Shelton et al. (2016) Methods 101:73-84.

extract_protocol: Total RNA was purified using Total RNA Mini Kit, according to the manufacture's instructions (FroggaBio, Toronto, ON, Canada).

treatment_protocol: Briefly, the differentiation of pluripotent hPSCs was initiated by culturing cells in E6 medium supplemented with high concentrations (7.5 or 10 µM) of CHIR99021 for 2 days. Cells were then cultured in E6 without CHIR99021 until day 12, at which point medium was changed to StemPro-34 supplemented with 5 ng/mL FGF2 until day 20. Cells were returned to E6 medium from days 20 to 35, and then cultured in N2-ITS medium from days 35 to 50. Addtional day 2 cultures were generated with low concentrations (3 µM) of CHIR99021 for 2 days, with or without 0.1 µM LDN193189.

tag: day of differentiation

value: Human pluripotent stem cells (hPSC)


title: Day_2_Low_rep2

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, replicate 2


title: HCT116-WT-Input-4

status: Public on Aug 20 2019

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: fragmented genomic DNA

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19  using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

value: colorectal cancer cells

tag: passages

value: Low passages (6-10)


title: HCT116-C14-Input

description:
fragmented genomic DNA
Cells knocked out of ZIC2 gene by CRISPR/Cas9

tag: cell type


title: HCT116-WT-ZIC2

description: fragmented genomic DNA

value: ZIC2 (Abcam)


title: Day_2_Low_rep1

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, replicate 1


title: Day_2_Low_LDN_rep3

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, LDN193189, replicate 3


title: Day_25_rep1

source_name: Wycell, WA09 (H9), day 25, replicate 1


title: HCT116-C3-ZIC2


title: HCT116-C3-Input


title: Day_8_rep3

source_name: Wycell, WA09 (H9), day 8, replicate 3


title: Day_2_Low_LDN_rep1

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, LDN193189, replicate 1


title: Day_40_rep2

source_name: Wycell, WA09 (H9), day 40, replicate 2


title: Day_2_High_rep1

source_name: Wycell, WA09 (H9), day 2, high CHIR99021, replicate 1


title: Day_50_rep1

source_name: Wycell, WA09 (H9), day 50, replicate 1


title: Day_25_rep3

source_name: Wycell, WA09 (H9), day 25, replicate 3


title: Day_25_rep2

source_name: Wycell, WA09 (H9), day 25, replicate 2


title: Day_8_rep2

source_name: Wycell, WA09 (H9), day 8, replicate 2


title: Day_2_Low_rep3

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, replicate 3


title: Day_50_rep2

source_name: Wycell, WA09 (H9), day 50, replicate 2


title: Day_2_Low_LDN_rep2

source_name: Wycell, WA09 (H9), day 2, low CHIR99021, LDN193189, replicate 2


title: Day_8_rep1

source_name: Wycell, WA09 (H9), day 8, replicate 1


title: Day_2_High_rep2

source_name: Wycell, WA09 (H9), day 2, high CHIR99021, replicate 2


title: Day_0_rep3

source_name: Wycell, WA09 (H9), day 0, replicate 3


title: Day_2_High_rep3

source_name: Wycell, WA09 (H9), day 2, high CHIR99021, replicate 3


title: Day_50_rep3

source_name: Wycell, WA09 (H9), day 50, replicate 3


title: Day_0_rep1

source_name: Wycell, WA09 (H9), day 0, replicate 1


title: Day_0_rep2

source_name: Wycell, WA09 (H9), day 0, replicate 2


title: Day_40_rep1

source_name: Wycell, WA09 (H9), day 40, replicate 1


title: HCT116-C14-ZIC2


title: HCT116-C18-Input-3

description:
fragmented genomic DNA
Cells knocked out of ZIC5 gene by CRISPR/Cas9


title: HCT116-WT-Input-3

description: fragmented genomic DNA


title: HCT116-C16-Input-3


title: HCT116-sc1-input

description:
fragmented genomic DNA
Cells treated with non-targeting dsRNA


title: HCT116-shTCF7L2-ZIC5

description:
fragmented genomic DNA
Cells treated with TCF7L2 dsRNA

value: ZIC5CT289 (homemade)


title: HCT116-shCTNNB1-ZIC5

description:
fragmented genomic DNA
Cells treated with CTNNB1 dsRNA


title: HCT116-sc2-TCF7L2


title: HCT116-C18-ZIC5FL290

value: ZIC5FL290 (homemade)


title: HCT116-C16-PolII

value: PolII (CST)


title: HCT116-WT-Input-1

description: fragmented genomic DNA


title: HCT116-C18-Input-2


title: HCT116-GFP-Zic5-GFP

description:
fragmented genomic DNA
Cells overexpressed with GFP-Zic5

value: GFP (DSHB)


title: HCT116-C18-TCF7L2

value: TCF7L2 (CST)


title: HCT116-sc1-CTNNB1


title: HCT116-sc2-input


title: HCT116-WT-Input-2

description: fragmented genomic DNA


title: HCT116-WT-TCF7L2

description: fragmented genomic DNA


title: HCT116-C16-TCF7L2


title: HCT116-sc1-ZIC5


title: HCT116-sc2-ZIC5


title: HCT116-WT-ZIC5FL290

description: fragmented genomic DNA


title: HCT116-C18-PolII


title: HCT116-C16-Input-1


title: HCT116-C18-Input-1


title: HCT116-WT-H3K4me3

description: fragmented genomic DNA

value: H3K4me3 (homemade)


title: HCT116-C16-H3K4me3


title: HCT116-C18-ZIC5CT289


title: HCT116-C18-H3K4me3


title: HCT116-WT-PolII

description: fragmented genomic DNA


title: HCT116-C16-ZIC5CT289


title: HCT116-WT-ZIC5CT289

description: fragmented genomic DNA


title: C18-shZic2-3-R1

description:
total RNA
Cells knocked out of ZIC5 gene by CRISPR/Cas9, and treated with Zic2 dsRNA


title: C18-shZic2-3-R2


title: HCT116-C16-R1

description:
total RNA
Cells knocked out of ZIC5 gene by CRISPR/Cas9


title: C18-shZic2-1-R2


title: Human PH7 rep1

status: Public on May 29 2019

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

data_processing:
Base-calling was performed using Illumina's NextSeq control software RTA
Quality control:QC was carried out by MIT BMC/BCC in house pipeline including sequencing error rate estimation, sequencing reads complexity estimation, fastqc report, sample contamination estimation, intergenic reads percentile calculation, intronic reads percentile calculation, UTR reads percentile calculation, gene coding reads percentile calculation, and rRNA contamination estimation. Besides, sense to antisense reads ratio was calculated to indicate strand specificity. Hierarchical clustering and heatmap creation were carried out by TIBCO Spotfire 7.6.1.17 basing on log2(fpkm+1) values of the expressed coding genes to observe sample relationship and to detect outliers.
RNA-Seq mapping: against GRCm38/mm10 reference for mouse sequences and GRCh38/hg38 reference for human sequences using STAR/2.5.3
Gene expression was quantitated using RSEM v. 1.3.0
Exon level qualitfication was performed by DEXSeq v.1.22.0
Genome_build: GRCm38/mm10, GRCh38/hg38
Supplementary_files_format_and_content: txt file with, for each gene and each sample (from RSEM);for each exon and each sample (from DEXSeq)

source_name: 231 cell line

growth_protocol: Cells at passage 4 were plated at 70% confluency in either pH6.4 medium or pH7.4 medium for 48 hours.

extract_protocol:
Total RNA from cell lines was extracted using RNeasy Plus Mini Kit (Qiagen), following manufacturer instruction
KAPA Hyper Prep Kit (Kapa Biosystems) was used for library preparation. Short read sequencing was performed on NextSeq500 platform using 75bp paired-end method and Nextseq150nt kit.

treatment_protocol: Upon 48 hours of exposure to pH7.4 or pH6.4 cells were harvested for RNA extraction.

tag: exposure length

value: 48 hours in pH7.4 medium


title: Human PH7 rep2


title: Human PH6 rep2

value: 48 hours in pH6.4 medium


title: C18-shZic2-2-R1


title: C18-shZic2-2-R2


title: C18-shZic2-1-R1


title: HCT116-WT-R2

description:
total RNA
Cells treated with non-targeting dsRNA


title: Mouse PH7 rep2

source_name: 4T1 cell line


title: HCT116-C16-R2


title: C18-shCtrl-R2

description:
total RNA
Cells knocked out of ZIC5 gene by CRISPR/Cas9, and treated with non-targeting dsRNA


title: HiC-TCC_NCAPH2_Rep1

status: Public on May 05 2019

first: Nezar

last: Abdennur

description:
NCAPH2.1000.cool
NCAPH2.20000.cool
NCAPH2.40000.cool
NCAPH2.100000.cool
NCAPH2.1000.mcool

data_processing:
Hi-C: Hi-C datasets were processed using a portable pipeline called distiller, available at https://github.com/mirnylab/distiller-nf. Briefly, Hi-C sequencing reads were mapped to the mouse reference assembly mm9 using bwa mem (Li 2013) with flags -SP. Alignments were parsed, filtered for duplicates and pairs were classified using the pairtools package (https://github.com/mirnylab/pairtools). Hi-C pairs were aggregated into contact matrices in the cooler format using the cooler package (https://github.com/mirnylab/cooler) at multiple resolutions. fter binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. All contact matrices were normalized using the iterative correction procedure (Imakaev et al., 2012) such that the genome-wide sum of contact probability for each row/column equals 1.0.
RNA-seq: We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq  with the “union” option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler files (extension .cool for single-resolution, .mcool for multi-resolution) contain contact matrices and were generated using the cooler Python package; RNA-seq bigWig files were generated using STAR in units of RPM; The xlsx file contains estimated transcript abundances and differential expression statistics between TAM control and the Ncaph2 mutant. The TAM control Samples are in Series GSE93431 listed as GSM2453295, GSM2453296, GSM2453297, and GSM2453298.

source_name: Liver

extract_protocol:
Liver was dissected and the left lateral lobe was prepped for a two-step perfusion adapted from (Li et al 2010 & Goncalves et al 2007): First, the liver was perfused with an EDTA-containing buffer to remove Ca2+ from the tissue in order to weaken the integrity of the desmosomes, which were subsequently digested using a Ca2+ rich buffer containing collagenase. The freed hepatocytes were rinsed through a cell strainer and washed four times with ice-cold Ca2+ rich buffer without collagenase. For each wash, the cells were spun at low centrifugal force (60g for 1min) to enrich intact hepatocytes and reduce non-mesenchymal debris. Part of each sample was fixed with 1% PFA for 10 minutes at room temperature. Fixed and unfixed hepatocytes were aliquoted and frozen in liN2 for later use.
Hi-C: Roughly 100 million fixed hepatocytes per sample were processed according to (Kalhor et al, 2012) using HindIII. TCC libraries were PCR-amplified (12 cycles) and size selected. Equimolar pools of libraries were sequenced; RNA-seq: RNA integrity was tested with Bioanalyzer (Agilent RNA Nano Kit) and ribosomal RNA was removed using Ribo-Zero rRNA Removal Kit (Illumina) prior to library preparation.  Strand-specific libraries were prepared with NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®. After amplification and size selection with Agencourt AMPure XP beads (Beckmann Coulter) their size-distributions were determined with Bioanalyzer. Equimolar pools of libraries were sequenced with Illumina HiSeq2000 (50bp, single end).
Tethered Chromosome Capture (TCC) variant of Hi-C; RNA-seq

treatment_protocol: Treated 12 week old mice were injected with 1mg Tamoxifen (100μl of 10mg/ml Tamoxifen in corn oil) on 5 consecutive days. After keeping these mice for another 5 days without injection, they were sacrificed and the hepatocytes were harvested.

tag: genotype

tag: treatment

value: tamoxifen

tag: age

value: 12 weeks

value: liver


title: HCT116-C18-R1


title: Mouse PH6 rep1


title: Mouse PH7 rep1


title: HiC-TCC_NCAPH2_Rep2

data_processing:
Hi-C: Hi-C datasets were processed using a portable pipeline called distiller, available at https://github.com/mirnylab/distiller-nf. Briefly, Hi-C sequencing reads were mapped to the mouse reference assembly mm9 using bwa mem (Li 2013) with flags -SP. Alignments were parsed, filtered for duplicates and pairs were classified using the pairtools package (https://github.com/mirnylab/pairtools). Hi-C pairs were aggregated into contact matrices in the cooler format using the cooler package (https://github.com/mirnylab/cooler) at multiple resolutions. fter binning, low-coverage bins were removed using a maximum allowed median absolute deviation (MAD) filter on log genomic coverage, set to five MADs. All contact matrices were normalized using the iterative correction procedure (Imakaev et al., 2012) such that the genome-wide sum of contact probability for each row/column equals 1.0.
RNA-seq: We mapped the RNA-seq data to mm9 reference mouse genome assembly and GENCODE vM1 transcriptome using STAR v.2.5.0a and adapted scripts from the ENCODE RNA-Seq pipeline [https://www.encodeproject.org/pipelines/ENCPL002LSE/]. To obtain the tracks of local transcription, we aggregated the uniquely mapped reads into RPKM-normalized bigWig files using the built-in STAR functionality. To find differentially expressed genes, we aggregated the read counts at the gene level using HTSeq  with the “union” option and called DE genes with DESeq2. Alignment with STAR v2.5.0.a was done using parameters: --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMunmapped Within --outFilterType BySJout --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1. Signal tracks were generated using STAR with parameters: --runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Stranded  --outWigReferencesPrefix chr.
Genome_build: mm9
Supplementary_files_format_and_content: Cooler files (extension .cool for single-resolution, .mcool for multi-resolution) contain contact matrices and were generated using the cooler Python package; RNA-seq bigWig files were generated using STAR in units of RPM; The xlsx file contains estimated transcript abundances and differential expression statistics between TAM control and the Ncaph2 mutant.


title: C18-shCtrl-R1


title: 12570_PCW17_input

status: Public on Apr 02 2019

city: Berkeley

first: Axel

last: Visel

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: input chromatin

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline)
Genome_build: hg38
Supplementary_files_format_and_content: *replicated.broadPeak, peaks called by MACS2 with a q-value <= 0.05

source_name: fetal left ventricle, input ChIP

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen left ventricle tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp.  Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated  with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2500 or 4000.

value: left ventricle

tag: developmental stage

tag: disease


title: 12570_PCW17_H3K27ac

description: Chromatin IP against H3K27ac

source_name: fetal left ventricle, H3K27ac ChIP

value: anti-H3K27ac (Active motif, 39133)


title: 14H133

status: Public on Jan 01 2019

city: Montreal

first: Guy

last: Sauvageau

state: QC

address: 2950, Chemin de Polytechnique

institute: Institute for Research in Immunology and Cancer

data_processing:
Basecalls performed using CASAVA 1.8.2
Sequenced reads were masked for sequencing adapters and mapped to the reference genome using CASAVA 1.8.2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CASAVA 1.8.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample. Columns are: Chromosome, Start location, Stop location, Gene, RPKM, base count.

source_name: acute promyelocytic leukemia

extract_protocol:
TriZol + RNeasy mini Kit (Qiagen, #74106)
KAPA Stranded RNA-Seq PolyA (KAPA Biosystems)

value: Blood

value: acute promyelocytic leukemia


title: 14H071

value: Bone marrow


title: 14H018


title: 13H162


title: 12570_LV_PCW17_RNA

description: Stranded (first-strand synthesis)

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC RNA-seq pipeline (https://github.com/ENCODE-DCC/rna-seq-pipeline)
Gene-wise counts were computed using htseq-count from the HTSeq package (PMID: 25260700; v0.9.1) with -s set to no.
Genome_build: hg38
Supplementary_files_format_and_content: *.counts.txt, HTseq quantifications

source_name: fetal left ventricle, total RNA

extract_protocol:
RNA was isolated from homogenized left ventricle using the TRIzol Reagent (Thermo Fisher Scientific). RNA samples were DNase-treated with the TURBO DNA-free Kit (Thermo Fisher Scientific), and then RNA quality was assessed via 2100 Bioanalyzer (Agilent) and an RNA 6000 Nano Kit (Agilent).
RNA-seq libraries were generated via the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina), according to manufacturer protocols.
RNA-seq libraries were subjected to additional purification steps to remove remaining high molecular weight products.


title: HCT116-C18-R2

value: colorectal cancer cells

value: Low passages (6-10)


title: 13H126


title: Human PH6 rep1


title: HCT116-WT-R1


title: 13H071


title: 11H043


title: 10H023


title: 10H110


title: 09H035


title: 10H059


title: 09H073


title: 09H053


title: 07H052


title: EZH2-null TFH, biological rep1 [ATAC-seq]

status: Public on Dec 31 2018

first: Jun

last: Huang

address: Eckhardt, 5640 S Ellis Ave

department: Institute for Molecular Engineering

institute: University of Chicago

description:
KOTFH_Rep1
processed data file: KOTFH.final.bigwig
processed data: KO_WT_TFH.txt

data_processing:
ATAC-seq:
Raw sequencing reads were first trimmed for both adapters and quality and filtered for quality using Trim Galore! v0.4.4, which is a wrapper based on CutAdapt v1.14 and FastQC v0.11.5.
Paired-end reads which passed quality control (QC) were then aligned against mm10 using Bowtie2 v2.2.9.
The resultant BAM files were then filtered again to remove unmapped reads, mate-unmapped reads, non-primary aligned reads, reads that fail platform quality checks and PCR duplicate reads using SAMtools v1.4.1 ( -F 1804). In addition, reads mapped to ChrM were also removed and PCR duplicate reads were further marked up and removed using Picard v2.16.0 MarkDuplicates. The insert size distribution were then calculated using Picard v2.16.0 CollectInsertSizeMetrics.
Since Tn5 transposase binds as a dimer and insert two adaptors separated by 9bp, all aligned reads were shifted +4 bp on the positive strand and -5bp on the negative strand using deepTools v2.5.2 alignmentSieve.
Following that, peak calling was performed using MACS2 v2.1.1 with a q-value threshold of 0.01. Peaks that overlap with the Encode black list regions were then removed using bedtools v2.26.0 intersect. We then merged peaks from all replicates and filtered peaks that are not reproducible, using Irreproducible Discovery Rate (IDR) (IDR < 0.005), across at least one pair of replicates in each sample group. Subsequently, depending on the comparisons required for different purposes, filtered peaks from multiple sample groups were merged using bedtools v2.26.0 merge to create an atlas of genome wide accessible chromatin regions for further analysis.
For each analysis that compares across multiple sample groups, all required shifted BAM files of all replicates of those samples were used to generate an accessibility matrix by counting the normalized reads (by reads per million, RPM) within each peak region of the corresponding atlas peak file, using deepTools v.2.5.4 multiBamSummary in BED-mode. The resulting matrix was passed to DESeq2 v1.16.1 to calculate the differential accessibility of the peaks of the relevant pairs. PCA was then plotted using DESeq2 v1.16.1.
ChIP-seq:
Similar to the above ATAC-seq analysis, briefly, the raw sequencing reads from ChIP-seq were first trimmed and filtered with Trim Galore! v0.4.4, and then aligned in single-end mode and against mm10 using Bowtie2 v2.2.9.
The reads were then filtered using samtools to remove low quality reads and unmapped reads. Duplicate reads were also filtered using Picard v2.16.0 MarkDuplicates.
Peak calling was done by MACS2 v2.1.1 with a q-value threshold of 0.01 and the --SPMR flag. The resultant bedgraph files were used to build coverage plot using MACS2 v2.1.1 bdgcmp with a logLR method and a p value of 1e-5.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Bigwig: Coverage plots (Replicates FDR filtered and combined; 1 per sample group).
Supplementary_files_format_and_content: narrowPeak: Peak calling results from MACS2 (1 per sample).
Supplementary_files_format_and_content: txt: Raw counts matrix of reads per atlas peak (1 per analysis group).

source_name: EZH2-null mice, LCMV Armstrong D8

extract_protocol:
ATAC-seq:
50,000 sorted cells were treated with lysis buffer and then centrifuged. The nuclei preparation was harvested after discarding the supernatant.
Libraries were prepared with the Nextera DNA Sample Preparation Kit (FC-121-1030, Illumina). Briefly, the nuclei preparation was labeled with Nextera enzyme and immediately amplified by PCR of 9-10 cycles with barcoded primers and sequenced on NextSeq500 in a 150 bp/150 bp or 76 bp/76 bp paired end run.
ChIP-seq:
DNA-protein complexes of target cells were extracted and fixed with the Simple ChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (#9003; Cell Signaling Technology) according to the manufacturer's instruction.
Chromatin fragments were immunoprecipitated with anti-H3K27me3 (Cell Signaling Technology, #9733, Clone number: C36B11) with ChIP Grade Protein G magnetic Beads (#9006; Cell Signaling Technology). The Illumina’s TruSeq indexed pair-ended DNA library preparation protocol was performed automatically on the SPRIworks system (Beckman Coulter). By using cartridge and method card specific to Illumina sequencing system, a fragment library can be prepared for Illumina sequencers. After individual libraries were constructed, qualities and band-sizes were assessed using Bioanalyzer High Sensitivity Chip (Agilent Technologies) and Qubit (Life Technologies). Libraries were also quantified by qPCR using the Library Quantification Kit for Illumina sequencing platforms (KAPA Biosystems), using an ABI 7900HT Real-Time PCR System (Life Technologies). Libraries were normalized to a working concentration of 10 nM, using the molarity calculated from qPCR and adjusted for fragment size with the Bioanalyzer analysis.

tag: strain/background

value: TFH

value: LCMV Armstrong infection

tag: time point

value: Day 8


title: EZH2-null TH1, biological rep2 [ATAC-seq]

description:
KOTH1_Rep2
processed data file: KOTH1.final.bigwig


title: KO Naive, biological rep1 [ChIP-seq]

description:
KO_Naive_Rep1
processed data file: KO_Naive.final.bigwig
processed data: KO_WT_TFH_Naive.txt

source_name: EZH2-null mice

value: CD4+ T cells

value: Naive


title: H3K27me3-ChIP Naive-Input [ChIP-seq]

source_name: WT mice, naïve

value: WT


title: KO Naive, biological rep2 [ChIP-seq]

description:
KO_Naive_Rep2
processed data file: KO_Naive.final.bigwig
processed data: KO_WT_TFH_Naive.txt


title: Naive CD4+ Cells, biological rep2 [ATAC-seq]

description:
Naive_Rep2
processed data file: Naive.final.bigwig
processed data: KO_WT_TFH_and_Naive.txt


title: Naive CD4+ Cells, biological rep1 [ATAC-seq]

description:
Naive_Rep1
processed data file: Naive.final.bigwig
processed data: KO_WT_TFH_and_Naive.txt


title: KO Naive, biological rep3 [ChIP-seq]

description:
KO_Naive_Rep3
processed data file: KO_Naive.final.bigwig
processed data: KO_WT_TFH_Naive.txt


title: H3K27me3-ChIP TH1-Input [ChIP-seq]

description:
H3K27me3_TH1_input
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.

source_name: SMARTA chimera mice, LCMV Armstrong D3

value: SMARTA

value: Day 3


title: H3K27me3-ChIP TH1 [ChIP-seq]

description:
H3K27me3_TH1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: H3K27me3_TH1.final.bigwig


title: H3K27me3-ChIP Naive [ChIP-seq]

description:
H3K27me3_Naive
processed data file: H3K27me3_Naive.final.bigwig


title: Naive_2 CD4+ Cells, biological rep3 [ATAC-seq]

description:
Naive_2_Rep3
processed data file: Naive_2.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: Naive_2 CD4+ Cells, biological rep2 [ATAC-seq]

description:
Naive_2_Rep2
processed data file: Naive_2.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: H3K27me3-ChIP TFH [ChIP-seq]

description:
H3K27me3_TFH
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: H3K27me3_TFH.final.bigwig


title: 10H017


title: WT TFH, biological rep1 [ATAC-seq]

description:
WTTFH_Rep1
processed data file: WTTFH.final.bigwig
processed data: KO_WT_TFH.txt

source_name: WT mice, LCMV Armstrong D8


title: WT TH1, biological rep1 [ATAC-seq]

description:
WTTH1_Rep1
processed data file: WTTH1.final.bigwig


title: EZH2-null TH1, biological rep1 [ATAC-seq]

description:
KOTH1_Rep1
processed data file: KOTH1.final.bigwig


title: WT TH1, biological rep2 [ATAC-seq]

description:
WTTH1_Rep2
processed data file: WTTH1.final.bigwig


title: EZH2-null TFH, biological rep2 [ATAC-seq]

description:
KOTFH_Rep2
processed data file: KOTFH.final.bigwig
processed data: KO_WT_TFH.txt


title: WT TFH, biological rep2 [ATAC-seq]

description:
WTTFH_Rep2
processed data file: WTTFH.final.bigwig
processed data: KO_WT_TFH.txt


title: Naive_2 CD4+ Cells, biological rep1 [ATAC-seq]

description:
Naive_2_Rep1
processed data file: Naive_2.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D8 SMARTA TFH, biological rep3 [ATAC-seq]

description:
D8TFH_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt

source_name: SMARTA chimera mice, LCMV Armstrong D8


title: D8 SMARTA TH1, biological rep2 [ATAC-seq]

description:
D8TH1_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D8 SMARTA TFH, biological rep2 [ATAC-seq]

description:
D8TFH_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D8 SMARTA TH1, biological rep1 [ATAC-seq]

description:
D8TH1_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D5 SMARTA TH1, biological rep3 [ATAC-seq]

description:
D5TH1_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt

source_name: SMARTA chimera mice, LCMV Armstrong D5

value: Day 5


title: D5 SMARTA TH1, biological rep2 [ATAC-seq]

description:
D5TH1_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D8 SMARTA TFH, biological rep1 [ATAC-seq]

description:
D8TFH_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D5 SMARTA TFH, biological rep1 [ATAC-seq]

description:
D5TFH_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D5 SMARTA TH1, biological rep1 [ATAC-seq]

description:
D5TH1_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TH1, biological rep3 [ATAC-seq]

description:
D2TH1_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt

source_name: SMARTA chimera mice, LCMV Armstrong D2

value: Day 2


title: D5 SMARTA TFH, biological rep3 [ATAC-seq]

description:
D5TFH_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: H3K27me3-ChIP TFH-Input [ChIP-seq]

description:
H3K27me3_TFH_input
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.


title: D5 SMARTA TFH, biological rep2 [ATAC-seq]

description:
D5TFH_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D5TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D8 SMARTA TH1, biological rep3 [ATAC-seq]

description:
D8TH1_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D8TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TH1, biological rep2 [ATAC-seq]

description:
D2TH1_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TFH, biological rep1 [ATAC-seq]

description:
D2TFH_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TFH, biological rep3 [ATAC-seq]

description:
D2TFH_Rep3
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TFH, biological rep2 [ATAC-seq]

description:
D2TFH_Rep2
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TFH.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: D2 SMARTA TH1, biological rep1 [ATAC-seq]

description:
D2TH1_Rep1
SMARTA: Transgenic mouse carrying a T-cell receptor specific for LCMV epitope of glycoprotein amino acids 66-77.
processed data file: D2TH1.final.bigwig
processed data: D2-D8_WT_TFH_TH1_and_Naive_2.txt


title: WT control replicate 2 20180324

status: Public on Jul 20 2018

description: seedlings grown for elevent days under unstressed control conditions

data_processing:
Illumina CASAVA-Bcl2fastq version 1.8.4 for basecalling and demultiplexing
RNAseq reads were mapped to the TAIR10 genome using Bowtie2 and BLAT with default parameters
RPKM values were computed using Rackj (http://rackj.sourceforge.net/)
expression comparisons were performed using DESeq2
Genome_build: TAIR10 (ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: comma-separate text files made by DESeq2

source_name: whole seedling

growth_protocol: seeds plated on agar plates containing half strength Murashige-Skoog media with 2 mM MES buffer (pH 5.7) and stratified for 3 days at 4ᵒC.  Plates were then positioned vertically in a rack and and kept under continuous light (80-100 micromol photons m-2sec-1 ) at 23ᵒC in a controlled environment chamber.  Note that no sugar was added to any of the growth media used.

treatment_protocol: After seven days of growth, seedlings of control condition (-0.25 MPa) continue grow until day elevent and seven days old stress treated seedlings were transfered to agar plates infused with polyethylene glycol 8000 (PEG) to impose low water potential (-0.7MPa) stress.  All samples were collected 96 h after transfer (control and stress treatments).

value: unstressed control -0.25MPa

value: wild type Col-0

value: whole seedling


title: ahl10-1 control replicate 3 20180324


title: WT stress replicate 2 20180324

description: seedlings grown for seven days under unstressed control conditions, transferred to low water potential (-0.7 Mpa) for 96 h before sample collection

value: stress -0.7MPa


title: ahl10-1 stress replicate 2 20180324


title: ahl10-1 control replicate 2 20180324


title: ahl10-1 stress replicate 3 20180324


title: ahl10-1 stress replicate 1 20180324


title: WT stress replicate 1 20180324


title: WT stress replicate 3 20180324


title: ahl10-1 control replicate 1 20180324


title: WT control replicate 3 20180324


title: NFkB-p65_input_Rep1

status: Public on Jul 19 2018

data_processing:
ChIP and input control FASTQ files for ZHX2 and NF-κB–p65 were filtered requiring a quality score of ≥20 in at least 90% of nucleotides, and adapter contaminated reads were removed with TagDust (40). Additionally, no more than five reads with identical sequences were retained. Non-filtered reads were aligned with GSNAP (41) to the hg19 human reference genome (parameter set: -k 15, -m 1). Post-alignment filtering was performed using blacklists created by ENCyclopedia Of DNA Elements (ENCODE) (42).
Peaks were identified for each sample using MACS2, comparing ChIP to matched input control.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of raw ChIP-seq signal

growth_protocol: 786-0 cells were cultured in DMEM containing 10% fetal bovine serum plus 1% penicillin–streptomycin. Cells were maintained in an incubator at 37°C and 5% CO2

extract_protocol:
ChIP was performed with ZHX2 (Genetex, 112232) or p65 (Santa Cruz Biotechnology, sc-372-x) antibodies as previously described (37, 38).
TruSeq libraries were constructed as per manufacturer's recommendations.

tag: cell line

value: clear cell renal cell carcinoma (ccRCC) cell line

value: none (input)


title: NFkB-p65_ChIP_Rep1

value: p65 (Santa Cruz Biotechnology, sc-372-x)


title: ZHX2_input_Rep1


title: ZHX2_ChIP_Rep1

value: ZHX2 (Genetex, 112232)


title: ZHX2_ChIP_Rep2


title: WT control replicate 1 20180324


title: ZHX2_input_Rep2


title: SAM19655388 M 97 AD IV

status: Public on Dec 20 2017

city: South San Francisco

first: Brad

middle: A

last: Friedman

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: RNA from fusiform gyrus

extract_protocol: RNA was extracted from frozen tissue sections. RIN scores ranged from 5 to 8.5.

value: fusiform gyrus

tag: Sex

value: M

tag: age at death

tag: diagnosis

value: Alzheimer's disease

tag: braak score

value: IV

tag: caseid


title: SAM19655459 F 88 AD VI

tag: tissue

value: F

value: VI


title: SAM19655461 M 82 AD VI


title: SAM19655486 M 81 CON IV

value: control


title: SAM19655479 M 97 CON III

value: III


title: SAM19655484 M 80 CON III


title: SAM19655406 F 93 AD IV


title: SAM19655404 M 87 AD IV


title: SAM19655390 F 82 AD IV


title: SAM19655454 M 84 AD V

value: V


title: SAM19655482 M 91 CON III


title: SAM19655380 F 96 AD IV


title: SAM19655383 F 94 AD IV


title: SAM19655471 M 87 AD VI


title: SAM19655381 M 77 AD IV


title: SAM19655491 M 79 CON II

value: II


title: SAM19655433 F 87 AD V


title: SAM19655483 F 97 CON IV


title: SAM19655472 M 87 AD VI


title: SAM19655416 M 89 AD IV


title: SAM19655425 M 82 AD IV


title: SAM19655398 F 89 AD III


title: SAM19655445 F 87 AD VI


title: SAM19655496 M 81 CON IV


title: mESCs_WT_day0_rep2

status: Public on Dec 31 2017

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and 100 ul of the mixture was hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then air dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, No XDR, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain greenProcessed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were filtered out. Raw data were further filtered to retain only present probes (probes for which at least two of the eight samples are present). Probes with null expression values are those excluded because of these two filtering steps. Data were further processed in Expander 7, where greenProcessed signals were quantile-normalized and log2-transformed.

source_name: mES cells, WT, day 0

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 300ng RNA using the Quick Amp Labeling Kit, one-color kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from the cells was extracted using E.Z.N.A. ® Micro-elute Total RNA Kit I according to manufacturer's instructions.

treatment_protocol: Differentiation of ES cells was induced through formation of embryoid bodies (EBs) as described previously (PMID 23168335). Concisely, EBs were formed in mESC media without LIF in hanging drops containing 800 cells per 20µL droplet on the lid of a petri dish and cultured for two days. EBs were then collected from the droplets and cultured for 3 days in suspension culture in petri dishes. At day 5, EBs were plated on 0.1% gelatin coated coverslips for 24 hours.

value: wild type

tag: days of differentiation


title: mESCs_Nkx25R141C_day6_rep2

source_name: mES cells, Nkx25R141C, day 6

value: heterozygous Nkx25 R141C


title: mESCs_Nkx25R141C_day0_rep2

source_name: mES cells, Nkx25R141C, day 0


title: mESCs_WT_day6_rep1

source_name: mES cells, WT, day 6


title: SAM19655423 M 90 AD III


title: SAM19655411 F 91 AD IV


title: SAM19655408 M 89 AD III


title: SAM19655415 M 85 AD IV


title: SAM19655514 M 76 CON I

value: I


title: mESCs_Nkx25R141C_day6_rep1


title: SAM19655508 F 90 CON IV


title: mESCs_Nkx25R141C_day0_rep1


title: mESCs_WT_day6_rep2


title: SAM19655443 M 75 AD V


title: mESCs_WT_day0_rep1


title: SAM19655599 M 87 AD III


title: SAM19655401 M 96 AD IV


title: SAM19655419 F 95 AD IV


title: SAM19655475 F 71 AD VI


title: SAM19655444 M 86 AD V


title: SAM19655476 M 73 AD V


title: SAM19655418 M 82 AD IV


title: SAM19655502 M 87 CON IV


title: SAM19655451 F 66 AD VI


title: SAM19655448 M 89 AD V


title: SAM19655513 M 78 CON III