title: met2set25_Hi-C

city: Berkeley

first: Barbara

middle: J.

last: Meyer

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

data_processing:
Library strategy: Hi-C
Libraries were sequenced with Illumina's HiSeq 4000 Platform using 100 bp paired end reads. Reads were mapped to the ce11 reference genome, binned at 50 kb, and iteratively corrected using scripts derived from those available at https://bitbucket.org/mirnylab/hiclib as in Brejc et al 2017. For each genotype, interaction frequencies after iterative correction from the replicates were combined.
To correct for experimental variation in the decay of chromatin contacts with genomic distance, we calculated Hi-C Z scores using a LOESS method (Imakaev et al 2012) with scripts available at https://github.com/dekkerlab/cworld-dekker
Compartments were quantified using principal component analysis with scripts available at https://github.com/dekkerlab/cworld-dekker
To quantify TAD boundaries, we calculated insulation scores from the Hi-C interaction data as in Crane et al 2015 using the following parameters: insulation square 500000, insulation delta span 200000, insulation mode mean, and noise threshold 0.1.
Genome_build: ce11
Supplementary_files_format_and_content: .matrix files are tab-delimited tables of genome-wide interaction frequencies iteratively corrected and normalized for read depth as in Crane et al 2015.
Supplementary_files_format_and_content: .zScore.matrix files are tab-delimited tables of Z scores.
Supplementary_files_format_and_content: .compartment files give the eigenvector values and eigenvalues for the first three principal components
Supplementary_files_format_and_content: .insulation files give the insulation score and delta vector for each 50 kb bin in the genome, as defined in Crane et al 2015

organism: Caenorhabditis elegans

source_name: mixed stage embryos

growth_protocol: Worms were grown on NGM plates with concentrated HB101 bacteria until gravid.  Adults were collected and bleached to release mixed-stage embryos.

extract_protocol:
We purfied, sheared, and size-selected DNA and pulled down biotinylated fragments as in Brejc et al 2017.
We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Brejc at al 2017.

treatment_protocol: We isolated nuclei, digested with DpnII restriction enzyme, filled in the restriction overhangs with biotinylated nucleotides, and ligated as in Brejc et al 2017.

tag: genotype

value: mixed stage embryos


title: cec4_Hi-C

status: Public on Apr 21 2020

type: SRA

state: CA

country: USA

library_source: genomic

molecule: genomic DNA

tag: strain

tag: tissue


title: IFNg2LPS1_REP2_GCN5

type: protein

city: Boston

first: Trevor

last: Siggers

state: MA

address: 24 Cummington Mall

department: Department of Biology

institute: Boston University

hyb_protocol: Microarray DNA double stranding and PBM protocols are as previously described (Berger et al., 2006, Siggers et al., 2015, and Mohaghegh et al., 2019).

scan_protocol: Microarrays were scanned with a GenePix 4400A scanner and fluorescence was quantified using GenePix Pro 7.2

data_processing:
Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006).
Processed data corresponds to z-scores normalized against the fluorescence distribution obtained  at sets of random background probes

label: alexa fluor conjugated antibody

molecule: protein

organism: Homo sapiens

label_protocol: The array was incubated with nuclear extract for one hour in the dark in a binding reaction buffer (20mM HEPES, pH 7.9, 100mM NaCl, 1mM DTT, 0.2mg/mL BSA, 0.02% Triton X-100, 0.4mg/mL salmon testes DNA (Sigma-Aldrich, Catalogue #D7656). The array was then rinsed in a HBS bath containing 0.1% Tween-20 and subsequently de-wetted in a HBS bath. After the protein incubation, the array was incubated for 20 minutes in the dark with 20ug/mL primary antibodies for the TF or COF of interest. The primary antibodies were diluted in 2% milk in HBS. After the primary antibody incubation, the array was first rinsed in a HBS bath containing 0.1% Tween-20 and subsequently de-wetted in a HBS bath. Microarrays were then incubated with 10ug/mL of either alexa488 or alexa647 conjugated secondary antibody for 20 minutes in the dark. The secondary antibody was diluted in 2% milk in HBS. Excess antibody was removed by washing the array twice for 3 minutes in 0.05% Tween-20 in HBS and once for 2 minutes in HBS in coplin jars as described above. After the washes, the array was de-wetted in a HBS bath.

growth_protocol: THP-1 cells, a human monocyte cell line, were obtained from ATCC (TIB-202). The cells were grown in suspension in RPMI 1640 Glutamax media (Thermofisher Scientific, Catalogue #72400120) with 10% heat-inactivated fetal bovine serum (Thermofisher Scientific, Catalogue #11360070) and 1mM sodium pyruvate (Thermofisher Scientific, Catalogue #16140071). T175 (Thermofisher Scientific, Catalogue #132903) non-treated flasks were used when culturing THP-1 cells for experiments.Cells were grown in 50mL of media when being cultured in T175 flasks. To differentiate THP-1 cells into adherent macrophages, cells were grown to a density of 8.0 x 105 cells/mL and treated with 25ng/mL Phorbol 12-Myristate 13-Acetate (PMA) (Sigma-Aldrich, Catalogue #P8139) for 4 days. Following the 4 days of PMA treatment, the media was replaced with fresh RPMI media with 10% heat-inactivated fetal bovine serum and 1mM sodium pyruvate. The cells rested for two days in the fresh media before being stimulated with various reagents.

extract_protocol: To harvest nuclear extracts from THP-1 cells, the media was aspirated off and the cells were washed once with 1X PBS (Thermofisher Scientific, Catalogue #100010049). Once the 1X PBS used to wash the cells was aspirated off, enough 1X PBS was mixed with 1X Protease Inhibitor (Sigma-Aldrich, Catalogue #P8340) to cover the cells was added to each flask. A cell scraper was then used to dislodge the cells from the flask. The cells were collected in a falcon tube and placed on ice. To pellet the cells, the cell volume was centrifuged at 500xg for 5 minutes at 4°C. Once the cells were pelleted, the supernatant was aspirated off. The pellet was resuspended in Buffer A and incubated for 10 minutes on ice (10mM HEPES, pH 7.9, 1.5mM MgCl, 10mM KCl, 0.1mM Protease Inhibitor, Phosphatase Inhibitor (Santa-Cruz Biotechnology, Catalogue #sc-45044), 0.5mM DTT (Sigma-Aldrich, Catalogue #4315) to lyse the plasma membrane. After the 10 minute incubation, a final concentration of 0.1% Igepal detergent was added to the cell and Buffer A mixture and vortexed for 10 seconds. To separate the cytosolic fraction from the isolated nuclei, it was centrifuged at 500xg for 5 minutes at 4°C. The cytosolic fraction was collected into a separate eppendorf tube. The pelleted nuclei were then resuspended in Buffer C (20mM HEPES, pH 7.9, 25% Glycerol, 1.5mM MgCl, 0.2mM EDTA, 0.1mM Protease Inhibitor, Phosphatase Inhibitor, 0.5mM DTT, and 420mM NaCl) and then vortexed for 30 seconds. The nuclei are incubated in Buffer C while mixing at 4°C. To separate the nuclear extract from the nuclear debris, the mixture was centrifuged at 21,000xg for 20 minutes at 4°C. The nuclear extract was collected in a separate eppendorf tube and flash frozen using liquid nitrogen. Nuclear extracts were stored at -80°C until being used for experiments.

treatment_protocol: THP-1 cells differentiated with PMA were treated with either Lipopolysaccharide (LPS) (Sigma-Aldrich, L3024), Interferon gamma (IFN-γ) (Thermofisher Scientific, Catalogue #PHC4031), or IFN-γ in combination with LPS. PMA treated THP-1 cells were left untreated (UT), treated with 1ug/mL of LPS for 45 minutes (LPS45), or with 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1). For each condition, nuclear lysates were harvested. For all nuclear lysates assayed using PBM experiments, the expression levels of COFs and TFs profiled with CASCADE were confirmed with western blot.

tag: treatment

tag: target protein

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32728)

tag: secondary antibody concentration


title: HUES64_WT_RNA_rep1

city: Cambridge

first: Jocelyn

last: Charlton

address: 7 Divinity Avenue

department: Stem Cell and Regenerative Biology

institute: Harvard University

library_source: transcriptomic

data_processing:
Data was aligned using STAR aligner followed by stringtie v1.3 to the hg19 genome.
Genome_build: hg19
Supplementary_files_format_and_content: *_abundance.txt: Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM.

molecule: total RNA

source_name: ESCs

growth_protocol: HUES 64 and HUES8 cells were grown in feeder-free conditions using Geltrex (Thermo Fisher Scientific) and mTeSR (STEMCELL Technologies).

extract_protocol: Libraries were prepared using the TruSeq RNA Sample Prep v2 HS Protocol.

tag: knockout

tag: cell type

value: ESCs

tag: cell line


title: IFNg2LPS1_REP1_GCN5

value: 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1)


title: KI-96 rep4

city: Guangzhou

first: Su

last: Yang

address: Huangpu Avenue

country: China

institute: Jinan University

data_processing:
Sequencing adapters were trimmed by BBduk (minlen=100 ktrim=r k=23 mink=11 hdist=1 tpe tbo; http://jgi.doe.gov/data-and-tools/bb-tools/). Reads with length under 100 bp after trimming were discarded.
lipped reads were aligned to mouse genome GRCm38 (primary assembly) by STAR aligner with default settings. Read counts for genes were obtained by using HTSeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes gene counts for all samples

organism: Mus musculus

extract_protocol:
Mice were sacrificed and decapitated. Striatal tissues were dissected from the brain. RNAs were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CRISPR-Cas9 to truncate full-length mutant Htt in HD140Q knock-in (KI)

tag: strain background

tag: age

tag: genotype/variation

value: KI-96 (expressing an N-terminal Huntingtin fragment shorter than KI-571)

value: striatum


title: IFNg2LPS1_REP2_HDAC1

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: Sample 85: Monocyte from healthy

type: RNA

city: Medellín

first: LELIA

last: LAVALETT

state: Antioquia

department: Antioquia

country: Colombia

institute: Universidad de antioquia

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were extracted with Illumina GenomeStudio v2011.1  software. Probes signal value was transformed by logarithm and normalized by Z-ratio method. The data were normalised using quantile normalisation with Lumi package in R

label: biotin

source_name: Human monocyte

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Peripheral blood

tag: agent

tag: disease state

value: Healthy control


title: Sample 91: Monocyte from healthy

description: replicate 2


title: cec4_IgG_ChIP

description: ChIP-seq with IgG antibody

data_processing:
Adapters were trimmed using cutadapt version 1.2.1 (Martin, 2011), and reads were then aligned to the ce11 genome using bowtie2 version 2.3.0 (Langmead and Salzberg, 2012) with default settings.
Reads were sorted using SAMtools version 1.3.1 (Li et al., 2009) and read coverage in bigwig files was calculated by normalizing the read number in each 50 bp bin to the total read number using the bamCoverage function in deepTools version 2.5.0.1 (Ramírez et al., 2016) with the “normalizeUsingRPKM” option.
Genome_build: ce11
Supplementary_files_format_and_content: bigWig files contain reads normalized by the total read number (RPKM) in 50 bp bins

source_name: mixed-stage embryos

growth_protocol: met-2 set-25 (two biological replicates) and cec-4 (one biological replicate) mutant mixed-stage embryos were grown on NGM plates with concentrated HB101 bacteria until gravid.  Adults were collected and bleached to release mixed-stage embryos.

extract_protocol:
Embryos were washed, dounced, and sheared as in Anderson et al 2019, except that no sarkosyl was added before shearing. Protein A Dynabeads (50 μL) (ThermoFisher Scientific, 10002D) were washed once in 1 mL FA buffer with protease inhibitors (150 mM NaCl, 50 mM HEPES-KOH pH 7.6, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 5 mM DTT, protease inhibitor cocktail, 1 mM PMSF). Beads were then incubated with 6.6 μg rat polyclonal anti-SDC-3 antibody (rb3779) for 90 min at room temperature in a total volume of 1 mL FA buffer plus protease inhibitors, and the supernatant was removed. Embryo extract containing approximately 2 mg of total protein was then added to the beads and incubated at room temperature for 90 min in a total volume of 1 mL FA buffer plus protease inhibitors. Beads were washed and DNA eluted as in Kruesi et al 2013.
We performed end repair, A-tailing, ligation of NEXTflex DNA Barcodes, and amplification as in Kruesi et al 2013.

treatment_protocol: Approximately 0.5 g of embryos were washed once in M9 buffer and then fixed for 10 min in 50 mL 2% formaldehyde in M9 buffer.

tag: genotype

value: mixed-stage embryos


title: IFNg2LPS1_REP1_HDAC1


title: cec4_SDC3_ChIP

description: ChIP-seq with anti-SDC-3 antibody

tag: strain


title: Sample 94: Monocyte from healthy

description: replicate 3

tag: tissue


title: KI-96 rep3


title: Sample 31: Monocyte from healthy

description: replicate 1


title: met2set25_2_IgG_ChIP

description: ChIP-seq with IgG antibody


title: HUES64_WT_RNA_rep3


title: LS04_pres_ALL

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

country: Germany

institute: University Medical Center Freiburg

data_processing:
fastq conversion (bcl2fastq 1.8.4)
alignment and transcript abundance estimation: Salmon (0.8.2)
gene-level abundance estimation: Tximport (1.4.0)
batch effect minimisation: RUVSeq on upper-quartile normalized counts
differential gene expression analysis: DESeq2 (1.16.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited file contains per-gene normalised read count values resulted from RUVr normalization

source_name: PBMC

growth_protocol: All patient samples were collected at the point of diagnosis, remission following treatment or relapse and stored with written informed consent for research in one of four centres (Newcastle Haematology Biobank, Newcastle, UK; University Hospital Schleswig-Holstein, Kiel, Germany; Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia; Haematological Malignancy Diagnostic Service, Leeds, UK). Mononuclear cells were isolated from bone marrow or peripheral blood by density centrifugation followed by immediate extraction of DNA or RNA, or cryopreservation in the presence of 10% v/v DMSO.

extract_protocol:
Total RNA was extracted with AllPrep DNA/RNA Mini Kit (Qiagen), innuPREP DNA/RNA Mini Kit (Analytik Jena), or TRIzol (Thermo Fisher Scientific) followed by RNeasy Mini Kit (Qiagen) from either bone marrow or peripheral blood, according to manufacturers’ instructions. Messenger RNA was captured using the NEBNext poly(A) mRNA Magnetic Isolation Module.
Libraries were prepared using the NEBNext Ultra Directional RNA Kit according to manufacturer's instruction, and submitted for paired-end 100, 150 or 75 bp sequencing on Illumina HiSeq 2000, 4000 and NextSeq 500 instruments, respectively.

value: PBMC

value: presentation ALL patient


title: IFNg2LPS1_REP1_p65

tag: treatment


title: IFNg2LPS1_REP2_p65

tag: target protein


title: KI-96 rep2


title: LS03_pres_ALL


title: WT rep7

source_name: wild type_striatum

value: wild type


title: met2set25_2_SDC3_ChIP

description: ChIP-seq with anti-SDC-3 antibody


title: met2set25_1_IgG_ChIP

description: ChIP-seq with IgG antibody


title: WT rep6


title: HUES8_PKO_RNAseq

data_processing:
Data was aligned using STAR aligner followed by stringtie v1.3 to the hg19 genome.
Genome_build: hg19
Supplementary_files_format_and_content: *_RNAseq.txt: Gene ID, Gene Name, Reference, Strand, Start, End, Coverage, FPKM, TPM.

source_name: HUES8 embryonic stem cells

growth_protocol: HUES8 cells were grown in feeder-free conditions using Geltrex (Thermo Fisher Scientific) and mTeSR (STEMCELL Technologies).

value: TET1, TET2, TET3, DNMT3B, DNMT3A


title: IFNg2LPS1_REP1_PU1

tag: primary antibody


title: LS04_relapse_AML

value: relapse AML patient


title: KI-96 rep1


title: WT rep5


title: IFNg2LPS1_REP2_RBBP5

tag: primary antibody concentration

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11034)


title: HUES8_TKO_RNAseq

value: TET1, TET2, TET3


title: IFNg2LPS1_REP1_RBBP5

tag: secondary antibody


title: WT rep4


title: LS03_relapse_AML


title: HUES8_WT_RNAseq


title: IFNg2LPS1_REP2_TBL1XR1

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)

tag: secondary antibody concentration


title: WT rep3


title: HUES64_DKO_RNAseq

source_name: HUES64 embryonic stem cells

growth_protocol: HUES64 and HUES8 cells were grown in feeder-free conditions using Geltrex (Thermo Fisher Scientific) and mTeSR (STEMCELL Technologies).

tag: knockout

value: DNMT3A, DNMT3B


title: IFNg2LPS1_REP2_PU1

value: 100ng/mL IFN-γ for 2 hours followed by 1ug/mL LPS for 1 hour (IFNg2LPS1)


title: oxWGBS_HUES64_WT_ESCs

data_processing:
Raw sequencing reads were trimmed using cutadapt and aligned against human or mouse genome using BSMAP.
Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: hg19
Supplementary_files_format_and_content: chr, start, end, ratio (0 to 1), number of reads.

extract_protocol:
DNA was extracted using the Zymo Quick-DNA Universal Kit following the manufacturer's instructions.
DNA was sonicated, bisulfite converted using the Qiagen Epitect Fast kit and prepped using the Swift Accel-NGS Methyl-seq DNA library kit.

tag: cell type

value: embryonic stem cell


title: WGBS_HUES8_PKO_TET3_rescue


title: WGBS_HUES8_PKO_TET2_rescue


title: WT rep2


title: WGBS_HUES8_PKO_control_tfx


title: met2set25_1_SDC3_ChIP

description: ChIP-seq with anti-SDC-3 antibody


title: HUES8_QKO_RNAseq

value: TET1, TET2, TET3, DNMT3B

tag: cell line


title: IFNg2LPS1_REP1_TBL1XR1


title: WGBS_HUES8_DKO_P6


title: WT rep1

tag: strain background

value: striatum


title: WGBS_HUES8_PKO_P20


title: HUES8_PKO_WGBS

data_processing:
Raw sequencing reads were trimmed using cutadapt and aligned against human or mouse genome using BSMAP.
Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: hg19
Supplementary_files_format_and_content: Bed format, columns: chr, start, end, ratio (0 to 1), number of reads.


title: IFNg2LPS1_REP2_SMARCA4

value: SMARCA4 (sc17796)


title: cyclized a6A-IP mRNA 2

city: Hangzhou

first: Jie

last: Cao

address: Zheda Road 38

department: Department of Polymer Science and Engineering

institute: Zhejiang University

data_processing:
adapter, low quality reads and short reads were trimed with fastp v0.19.7 with following parameters: -f 10 -F 10 -x --detect_adapter_for_pe -l 25
clean reads were aligned with mm10 genome using hisat2 v2.1.0 with parameters: --rna-strandness RF
a6A peaks were called following Ma et al., Genome Research. 2017, in short: to call a6A peaks, the longest isoform of each human gene was scanned using a 100-bp sliding window with 10-bp steps. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. A negative binomial model was used to identify the differential windows between IP and input samples by using the edgeR package (Robinson et al. 2010), combining information from all replicates in the two groups. The window was called as positive if the FDR < 1% and Fold Change ≥ 1.5. Overlapping positive windows were merged.
mutation was called by samtools mpileup v1.9 with parameters:  -BQ 0 -d 10000000 -l H2.35.allyl.peaks.bed
Genome_build: mm10
Supplementary_files_format_and_content: bed file contains a6A and m6A peak regions in a6A/m6A-IP product relative to input samples in our method, H2.35.allyl.pileup.txt file contains mutations called from a6A-IP-cyclized samples using samtools

molecule: polyA RNA

source_name: H2.35 cells

growth_protocol: H2.35 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM)/high-glucose media(HyCloneSH30243.01) supplemented with 10% fetal bovine serum (FBS; Gibco 10270) , 1% 100× Pen Strep (HyClone SV30010) and 200nM Dexamethasone at 37 °C with 5 % CO2

extract_protocol:
RNA was extracted with Triozl Reagent(invitrogene), mRNA was extracted with GenElute™ Direct mRNA Miniprep Kits(sigma), IP and cyclized products were precipitated with isopropanol
Libraries were constructed following illumina's instructions except using HIV/RevertAid Reverse Transcriptase for reverse transcription in a6A-associated sequencing, superscript Ⅱwas used for m6A-seq

treatment_protocol: H2.35 cells were starved in methionine deficient medium supplemented with 1 mM L-cysteine for 30min then treated with 1mM allyl-L-selenohomocysteine for 16h

tag: reverse transcriptase

value: HIV


title: WGBS_EpiSC_DKO_P4

data_processing:
Raw sequencing reads were trimmed using cutadapt and aligned against human or mouse genome using BSMAP.
Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: mm9
Supplementary_files_format_and_content: Bed format, columns: chr, start, end, ratio (0 to 1), number of reads.

source_name: EpiSCs

value: EpiSCs


title: IFNg2LPS1_REP1_SMARCA4


title: m6A-IP mRNA

value: SuperScript II


title: IFNg2LPS1_REP2_p300


title: WGBS_EpiSC_WT


title: WGBS_HUES64_DKO_CloneB_P3


title: m6A-input mRNA


title: TBX5_Input

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

description:
Pooled_TBX5_FE.bw
Pooled_TBX5_peaks.bed
Pooled_TBX5_peaks.narrowPeak

data_processing:
Raw sequencing reads were aligned to the mm10 genome using Bowtie2 (Langmead and Salzberg 2012, Nat Methods) and SAMtools (Li et al 2009 Bioinformatics, Li 2011 Bioinformatics) requiring a minimum mapping quality of 40 (-q 40).
Pooled peak calling was performed using default settings of MACS2 callpeak (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc) with a q-value set to 0.05 (-q 0.05).
A fold-enrichment track was generated using MACS2 using the bdgcmp function (-m FE) for visualization on the genome browser (Zhang et al 2008 Genome Biol, Feng et al 2012 Nat Protoc).
Peaks overlapping ENCODE blacklist sites (Amemiya et al. 2019; ENCODE Project Consortium 2012) were removed from the final set of peaks.
Peaks were annotated to genes using the R package ChIPSeeker (Yu et al 2015, Bioinformatics). Promoter designation was a TBX5 summit overlapping with +/- 2000bp of the TSS.
Peaks were annotated to histone peaks using the ChIPpeakAnno (Zhu L et al 2010 BMC Bioinformatics; Zhu L 2013; “Integrative analysis of ChIP-chip and ChIP-seq dataset.” In Lee T, Luk ACS (eds.), Tilling Arrays, volume 1067, chapter 4, -19. Humana Press.) findOverlapsOfPeaks function using the options: maxgap=200, minoverlap=1, ignore.strand=T, connectedPeaks="merge". Peaks were annotated to TBX3 peaks using the options: maxgap=0, minoverlap=1, ignore.strand=T, connectedPeaks="merge".
Genome_build: mm10
Supplementary_files_format_and_content: .bw files are bigWig files generated by MACS2 of the fold enrichment. The .bed and .narrowPeak file are from MACS2 output following removal of ENCODE blacklist sites. SupplementaryDataset.txt contains all TBX5 peaks with information from the .narrowPeak file, whether they overlap with any of the histone or TBX3 peaks, if they were annotated as promoter proximal or distal, and the Type designation/predicted activity (e.g. Active Promoter).

source_name: Heart

extract_protocol:
Chromatin extract was prepared from hearts dissected from E14.5 CD-1 mouse embryos (2 replicates) obtained from Charles River. Extracts were cross-linked in PBS containing 1% formaldehyde at 25°C for 10 minutes and quenched by 125 mM glycine. The cross-linked samples were incubated in LB1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA; 10% Glycerol; 0.5% NP-40; 0.25% Triton X-100) with protease and phosphatase inhibitors on ice for 10 minutes. The samples were then sonicated in LB3 (10 mM Tris-HCl, pH 8.0; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% sodium deoxycholate; 0.5% N-lauroyl sarcosine; 1% Triton X-100) with protease and phosphatase inhibitors. Chromatin extract was then cleared by centrifugation at 14,000g, 4°C for 10 minutes. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516) at 4°C for >12 hours in a total volume of 200 μL. The immune-complexes were captured by Protein G-conjugated magnetic beads (Life Technologies, 1003D), washed in sequence by LB3, LB3 with 1 M NaCl, LB3 with 0.5 M NaCl, LB3, and TE (10 mM Tris-HCl, pH 8.0; 1 mM EDTA). The captured chromatin was eluted in ChIP Elution Buffer (10 mM Tris-HCl, pH 8.0; 1 mM EDTA; 1% SDS; 250 mM NaCl) at 65°C. After RNase and proteinase K treatment and reverse cross-linking, DNA were purified.
Libraries from ChIP and input DNA were prepared using NEBNext Ultra DNA Library Prep Kit (E7370S). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Sera-Mag magnetic beads (GE, 6515-2105-050-250). DNA libraries were sequenced using Illumina Hi-seq instruments (single-end 50 base) by the Genomics Core Facility at the University of Chicago.

tag: developmental stage

value: Heart


title: IFNg2LPS1_REP1_p300


title: REPL2_LPS45_PMA_p300

value: 1ug/mL of LPS for 45 minutes (LPS45)


title: WGBS_HUES64_DKO_CloneA_P3


title: HUES64_WT_RNAseq


title: a6A-IP mRNA 2

value: RevertAid Reverse Transcriptase


title: TBX5_ChIP_2

tag: antibody


title: REPL2_UT_PMA_p300

value: untreated


title: RNA_MN_day60_rep2

source_name: In vitro derived motor neurons

value: In vitro derived motor neurons


title: LPS45_PMA_IRF3

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32733)


title: TBX5_ChIP_1


title: WGBS_HUES8_PKO_TET1s_rescue


title: a6A-input mRNA


title: UT_PMA_IRF3


title: LPS45_PMA_p65


title: RNA_MN_day16_rep2


title: UT_PMA_p65


title: RNA_MN_day16_rep1


title: PAO1_T2.5_rep2

city: Singapore

first: Micheal

last: Mac Aogain

address: 308232, 11 Mandalay Rd, Singapore

department: Lee Kong Chian School of Medicine

country: Singapore

institute: Nanyang Technological University

description: RRNA-depleted RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to PAO1 genome (NC_002516) and assessed using the Rockhopper RNAseq analysis pipline (Tjaden et al 2013, Genome biology)
Genome_build: PAO1 NC_002516
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each experimental condition.

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial culture

growth_protocol: PAO1 was cultured for 24 hours in TSB broth.

extract_protocol:
1ml of culture was treated with RNAprotect reagent and total RNA extracted using the Rneasy kit. Ribosomal RNA was depleted using the Ribo-Zero rRNA removal kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PAO1 was exposed to the presence of 2.5 um testosterone or vehicle control (EtOH).

value: wild type


title: PAO1_T2.5_rep1

description: RRNA-depleted RNA


title: RNA_MN_day60_rep1


title: oxWGBS_MN_day60

description: oxidative whole genome bisulfite sequencing

data_processing:
Library strategy: oxidative Bisulfite-seq
Raw sequencing reads were trimmed using cutadapt and aligned against human or mouse genome using BSMAP.
Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: hg19
Supplementary_files_format_and_content: Bed format, columns: chr, start, end, ratio (0 to 1), number of reads.


title: PAO1_control_rep1

description: RRNA-depleted RNA


title: LPS45_PMA_RBBP5

value: Goat anti-rabbit IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11034)


title: UT_PMA_RBBP5


title: oxWGBS_MN_day16


title: REPL1_LPS45_PMA_p300

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 488 (A11029)


title: peritoneal macrophage from WT mouse 2

city: Incheon

first: Hyun Jin

last: Jung

address: 317 College of Pharmacy, 191 Hambangmoe-ro,  Yeonsu-gu

country: South Korea

institute: Seoul National University

description: Gene expression data from peritoneal macrophages from wild-type mouse

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: WT (wild-type) mouse peritoneal macrophage

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Peritoneal macrophages were harvested from the peritoneal cavity using a syringe. The cells were incubated at 37°C for 40 min in cell culture plates. After non-adherent cells were washed, the adherent cells were collected.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: gender

value: Female

tag: cell

value: peritoneal macrophages


title: WGBS_HUES64_WT_ESCs

value: embryonic stem cell


title: WGBS_MN_day16


title: PAO1_control_rep2

description: RRNA-depleted RNA

tag: strain

tag: genotype


title: HUES64_DKO_P28_WGBS

data_processing:
Raw sequencing reads were trimmed using cutadapt and aligned against human genome using BSMAP. Duplicate reads were removed using Picard tools. Methylation calls were made using MOABS mcall module.
Genome_build: hg19
Supplementary_files_format_and_content: *_WGBS.bed: Bed format, columns: chr, start, end, ratio (0 to 1), number of reads.

value: DNMT3A, DNMT3B


title: REPL1_UT_PMA_p300

tag: treatment


title: UT_PMA_IRF8

tag: target protein

value: Donkey anti-goat IgG (H+L) Cross-Absorbed Secondary Antibody, Alexa Fluor 488 (A11055)


title: PorcineCL_DP14_biorep4

city: Olsztyn

first: Monika

middle: M

last: Kaczmarek

address: Tuwima 10

country: Poland

institute: Institute of Animal Reproduction and Food Research, Polish Academy of Sciences

description: microRNA expression in D14 pregnant porcine corpus luteum

hyb_protocol: Dried (MiVac DNA Concentrator, Genevac, USA) samples were resuspended in nuclease free water with addition of 10x GE Blocking Agent and 2x Hi-RPM Hybridization Buffer, and incubated at 100°C for 5 minutes. Afterwards cooled mixtures were hybridized to Agilent miRNA microarrays for 20 h at 55°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 5 minutes at room temperature with GE Wash Buffer 1 (Agilent) and 5 minutes with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x15 K array slides (Scan resolution 5 µm, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent Technologies) using default parameters (protocol miRNA_107_Sep09 and Grid: 074558_D_F_20150412) to obtain background subtracted and spatially detrended Processed Signal intensities. Baseline transformation to the median of all samples was applied, and then data were normalized among the samples by quantile method. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies for miRNA arrays and using the standard Flag criteria in the GeneSpring GX 14.9 Software (Agilent).

organism: Sus scrofa

source_name: Porcine corpus luteum, Day 14 of pregnancy, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled RNA was prepared from 100 ng RNA fallowing the manufacturer’s instructions supplied with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Waldbronn, Germany). First sample was dephosphorylated in 37°C for 30 minutes in a reaction volume of 4 µl containing 1x Calf Intestinal Phosphatase Buffer and Calf Intestinal Phosphatase. On completion of the dephosphorylation 2.8 µl of 100% DMSO was added and incubated at 100°C for 10 minutes. Labelling was accomplished by addition of 10x T4 RNA Ligase Buffer, Cyanine3-pCp, and T4 RNA ligase to the abovementioned mixture and incubation at 16°C for 2 hours, followed by Micro BioSpin 6 column (Bio-Rad, USA) purification.

growth_protocol: Crossbred gilts of similar age (6-8 months) and genetic background from one commercial herd were either inseminated 12 and 24 hours after detection of the second estrus (pregnant) or not inseminated at all (cyclic).

extract_protocol: Total RNA was isolated with the miRVana miRNA isolation kit (Ambion, Life Technologies, USA) according to the manufacturer’s instructions. The protocol includes sample disruption in lysis buffer, acid phenol:chloroform extraction and an on-column RNA isolation. Quality and quantity of RNA was determined using UV spectrophotometry (NanoDrop 1000). RNA with RNA Integrity number higher than 8 (Agilent 2100 Bioanalyzer, Agilent Technologies, Santa Clara, CA) was used for microarray analysis of each individual sample.

treatment_protocol: Luteal tissue was collected post mortem on day (D) 14 (n=4/status) of either the estrous cycle or pregnancy, snap-frozen in liquid nitrogen and stored at -80°C.

tag: tissue

value: corpus luteum

tag: breed

value: crossbreed

tag: day

value: Day 14

tag: status

value: pregnancy


title: LPS45_PMA_IRF8

data_processing:
Exported fluorescence data from GenePix Pro 7.2 were normalized with MicroArrary LINEar Regression (Berger et al, 2006).
Processed data corresponds to z-scores normalized against the fluorescence distribution obtained  at sets of random background probes

value: 1ug/mL of LPS for 45 minutes (LPS45)

tag: primary antibody

tag: primary antibody concentration

tag: secondary antibody

tag: secondary antibody concentration


title: HUES8_TKO_WGBS

tag: knockout

value: TET1, TET2, TET3


title: HUES8_QKO_WGBS

value: TET1, TET2, TET3, DNMT3B


title: PorcineCL_DP14_biorep2

source_name: Porcine corpus luteum, Day 14 of pregnancy, replicate 2


title: A14-5-3

status: Public on Apr 20 2020

city: Shanghai

first: Yang

last: Wang

address: Dongan road 131

institute: Fudan University

data_processing:
illumina GApipeline1.6 used for base calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence by cutadapt (v1.9.1）then mapped to hg19 whole genome using Hisat2(v2.0.1)
Reads Per Kilo basesof per exon per Million reads(RPKM) were calculated using a protocol from Mortazavi, A., B. A. Williams, et al. Nature methods, 2008.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: HBV-infected HepG2-NTCP cells

growth_protocol: The HepG2-NTCP cell line (kindly provided by Prof. Stephan Urban) was maintained in Dulbecco`s modified Eagle`s medium (DMEM) supplemented with 10% FBS; the cells were plated on 24-well plates.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2-NTCP cells were infected with HBV virions at 200 viral genome equivalents (vge) per cell in the presence of 4% PEG8000 for 16 hours and then washed by PBS. 6 days later, cells were treated with IFN-α2 or IFN-α14 for 6 h.

value: hepatic carcinoma

tag: cell type

value: Human hepatoma cell

tag: cell line


title: A14-5-2


title: UT_PMA_IRF2

value: untreated

value: Goat anti-mouse IgG (H+L) Highly Cross-absorbed Secondary Antibody, Alexa Fluor 647 (A32728)


title: A14-5-1


title: LPS45_PMA_IRF2


title: HUES8_WT_WGBS


title: WGBS_MN_day60

value: In vitro derived motor neurons


title: HUES8_PKO_P6_WGBS

value: TET1, TET2, TET3, DNMT3B, DNMT3A


title: A2-5-2


title: PorcineCL_DP14_biorep3

source_name: Porcine corpus luteum, Day 14 of pregnancy, replicate 3


title: PorcineCL_DC14_biorep4

description: microRNA expression in D14 cyclic porcine corpus luteum

source_name: Porcine corpus luteum, Day 14 of estrous cycle, replicate 4

value: estrous cycyle


title: PorcineCL_DC14_biorep3

source_name: Porcine corpus luteum, Day 14 of estrous cycle, replicate 3


title: PorcineCL_DP14_biorep1

source_name: Porcine corpus luteum, Day 14 of pregnancy, replicate 1


title: PorcineCL_DC14_biorep1

source_name: Porcine corpus luteum, Day 14 of estrous cycle, replicate 1


title: A2-5-1


title: NC-2

value: mock


title: NC-3


title: NC-1


title: PorcineCL_DC14_biorep2

source_name: Porcine corpus luteum, Day 14 of estrous cycle, replicate 2


title: ntl_control_3

first: Xue

middle: Huan

last: Liu

state: Shanghai

address: NO.2005 Songhu Road

department: School of Life Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: http://rice.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Oryza sativa

source_name: seedling

extract_protocol:
Seedlings were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Nipponbare

tag: age

value: 8 days after germination

value: seedling


title: ntl_heat_3


title: ntl_heat_2


title: ntl_control_2


title: ntl_control_1


title: NIP_heat_2

value: wild type


title: NIP_heat_1


title: NIP_control_3


title: A2-5-3


title: NIP_control_1


title: LUCAT1_KD_Async_rep2

first: Manashree

last: Damle

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

description:
nascent RNA
Strand-specific RNA-SEQ (LUCAT1 knockdown Asynchronous)

data_processing:
Reads were aligned to the hg38 genome using STAR v2.5.3
Reads in the whole gene body were counted using featureCounts v1.6.1
Gene annotations were obtained from Ensembl
EdgeR was used for gene filtering and RPKM calculations. Genes with atleast 1 read count in atleast 2 samples were further used to calculate library sizes, counts per million (cpm) and finally RPKM values and fold-changes
Genome_build: hg38
Supplementary_files_format_and_content: Genome browser tracks were generated using Homer v4.10.3
Supplementary_files_format_and_content: BIGWIG and RPKM

source_name: RPE1 cells

growth_protocol: hTERT-RPE1 cells were grown in regular RPE1 medium at 37° C, 5% CO2

extract_protocol:
hTERT-RPE1 cells were collected in Trizol reagent, extracted with chloroform and precipitated with isopropanol. DnaseI treated RNA samples were then extracted using RNA clean & concentrator kit, Zymo Research
Library is constructed as described before (Bowman et al., 2013 - Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics. 2013;14:466. Published 2013 Jul 9. doi:10.1186/1471-2164-14-466)

treatment_protocol: hTERT-RPE1 cells were transfected with 130-150 pmol LNA GapMeRs with the facilitation of Lipofectamine RNAiMax in Opti-MEM

value: RPE1 cells

value: LUCAT1 knockdown Asynchronous


title: LUCAT1_KD_Async_rep1


title: Control_Async_rep1

description:
nascent RNA
Strand-specific RNA-SEQ (Control Asynchronous)

value: Control Asynchronous


title: MIAT_KD_Async_rep1

description:
nascent RNA
Strand-specific RNA-SEQ (MIAT knockdown Asynchronous)

value: MIAT knockdown Asynchronous


title: LUCAT1_KD_Async_rep3


title: LINC00704_KD_Async_rep3

description:
nascent RNA
Strand-specific RNA-SEQ (LINC00704 knockdown Asynchronous)

value: LINC00704 knockdown Asynchronous


title: LINC00704_KD_Async_rep1


title: MIAT_KD_Async_rep3


title: MIAT_KD_Async_rep2


title: LINC00704_KD_Async_rep2


title: Control_Async_rep2


title: ntl_heat_1


title: iEC-2_Smoke_6h_rep3

city: Rockville

first: David

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

department: Division of Preclinical Innovation

institute: NCATS/NIH

data_processing:
Alignment of paired end reads was performed by STAR aligner to produce BAM alignment files.
HTSeq-count was used to produce counts per genomic feature using the BAM files and a gtf file for GRCh38.p7
DESeq package in R was used to normalize gene read counts prior to statistical analysis and principle components analysis.
Genome_build: Ensembl GRCh38 build 85 (corresponds to patch 7)
Supplementary_files_format_and_content: Processing produced two matrix files, one with raw read counts and one containing normalized read counts.

source_name: iEC

growth_protocol: Primary endothelial cells (human aorta (HAEC), coronary artery (HCAEC), and umbilicus (HUVEC)) were purchased from Lonza and cultured in EGMTM-2. Induced pluripotent stem cells (iEC-1 and iEC-2, cell lines NC6-1 and NC6-2) were generated from fibroblasts from a healthy normal donor as described8. iEC lines NC6-1 and NC6-2 were differentiated from iPSC lines that were derived independently from a single healthy patient. The iPSCs were maintained and propagated on Matrigel-coated plates in TeSR-E8 medium (Stemcell Technologies, Vancouver, Canada) as described previously8, including Recombinant Human (RH-) proteins. iPSCs reaching ~80% confluence were passaged and seeded at low density.  After 24 hours culture, cells were induced for five days to become mesoderm progenitors in MDM (Iscove’s modified Dulbecco’s medium (IMDM, Invitrogen, Catalog#: 21056-023), Ham's F-12 Nutrient Mix, GlutaMAX™ (Catalog#: Invitrogen, 31765-035) at 1:1 ratio supplemented with Albucult (RH-Albumin) (5 mg/mL/ml,  Novozymes Delta), and a-Monothioglycerol (a-MTG; 3.9 ml per 100 ml; 350–450 µM, Sigma-Aldrich, Catalog#: M6145), Protein-free hybridoma mixture II (PFHMII) (5%) (Invitrogen, Catalog#:12040-077), Ascorbic acid 2 phosphate (50 µg/ml, Sigma-Aldrich, Catalog#: A 8960), Penicillin/streptomycin (50 U Pen G/50 mg streptomycin sulfate, Invitrogen, Catalog#: 15140122), Insulin Transferrin Selenium-X Supplement (Invitrogen, Catalog#: 515000560), RH-Vascular endothelial growth factor (RH-VEGF, 10 ng/ml, Invitrogen, Catalog#: PHC9394), and RH-Basic fibroblast growth factor (RH-bFGF, 10 ng/ml, Pepro Tech, Catalog#: 100-18B), and RH-Bone Morphogenetic Protein 4 (BMP4, 10 ng/ml R&D system, Catalog# 314-BP-050). The medium was replaced with Endothelial Cell Growth Medium-2 (EGMTM-2, Lonza, Catalog# CC-3162) at day 6 to commit cells to the endothelial lineage. At seven days of induction, 50-70% PECAM1+ mesoderm progenitor cells were generated. PECAM1+ cells were selected using magnetic beads coated with anti-PECAM1 antibodies (Miltenyi Biotec, Catalog# 130-091-935) according to manufacturer’s instructions. The PECAM1+ cells were further cultured and expended in Collagen I coated plates or dishes ( Corning, Catalog# 356240) with endothelial culture medium containing human endothelial-SFM (Invitrogen, Catalog#11111044) and EGMTM-2 at 1:1 ratio for endothelial cells maturation  and proliferation (Fig 1). As these iPSC-derived endothelial cells (iECs) became confluent, they were passaged into fresh Collagen I coated plates or dishes every 4-5 days.

extract_protocol:
Total RNA samples were prepared from cultured cells using Qiaquick kit (Qiagen, Hilden Germany) and selected for polyA+ transcripts using the Qiagen Oligotex midi kit. Resulting samples were depleted of ribosomal sequences using two rounds of RiboZero Gold™, Illumina Inc.
TruSeq Protocol (NHLBI/NIH Seq. Core, Bethesda, MD)

treatment_protocol: Samples used to characterize tobacco smoke toxicity were exposed to a tobacco smoke extract or appropreiate vehicle control solution for 6 hours. Tobacco smoke extract was prepared by bubbling air from burning cigarettes through cell growth medium containing 10% DMSO, then filtering to remove insoluble tar. Eight University of Kentucky 3R4F reference cigarettes11 were burned in succession and the smoke was pulled by vacuum through a glass frit submerged in 50 mL of growth medium plus 10% DMSO at a flow rate of ~20 cm3 per minute. Each cigarette yields approximately 30.6 mg tar per cigarette11, so this smoke extract stock contains approximately 245mg tar/50 mL. Insoluble tar was removed by filtration through a 0.45 mm filter and the resulting (4.96 mg/mL tar equivalents) smoke extract stock solution was used to treat cells approximately 2 hours after preparation. This smoke extract stock solution was diluted 1:10 into 100 microliters per well of a 96-well microplate for cytotoxicity or cytokine assays, or into 1 mL per well of a 12-well microplate for gene expression studies resulting in treatments using 0.5 mg/mL tar equivalents.

value: Smoke

value: iEC

tag: cell long name

value: Induced Endothelial Cell

tag: iec clone

tag: study arm

value: Response to Smoke


title: iEC-2_Smoke_6h_rep1

tag: treatment


title: iEC-2_Control_6h_rep3

value: Control

value: Response to Smoke, and Cell Line Characterization


title: iEC-2_Control_6h_rep2


title: iEC-2_Smoke_6h_rep2


title: iEC-1_Smoke_6h_rep3


title: iEC-1_Smoke_6h_rep2


title: iEC-1_Smoke_6h_rep1


title: iEC-1_Control_6h_rep3


title: NIP_control_2

tag: genotype

tag: tissue


title: iEC-1_Control_6h_rep2


title: NIP_heat_3


title: iEC-1_Control_6h_rep1


title: HUVEC_Smoke_6h_rep3

source_name: HUVEC

value: HUVEC

value: Human Umbilical Vein Endothelial Cell


title: HUVEC_Smoke_6h_rep1


title: HUVEC_Smoke_6h_rep2


title: HUVEC_Control_6h_rep3


title: HUVEC_Control_6h_rep2


title: HCAEC_Control_6h_rep3

source_name: HCAEC

value: HCAEC

value: Human Coronary Artery Endothelial Cell


title: HCAEC_Smoke_6h_rep1


title: HCAEC_Smoke_6h_rep3


title: HCAEC_Smoke_6h_rep2


title: HAEC_Smoke_6h_rep3

source_name: HAEC

value: HAEC

value: Human Aorta Endothelial Cell


title: HAEC_Smoke_6h_rep2


title: HAEC_Control_6h_rep3


title: iEC-2_Control_6h_rep1


title: HAEC_Control_6h_rep2


title: HCAEC_Control_6h_rep2


title: HAEC_Smoke_6h_rep1


title: iPSC_Control_rep3

source_name: iPSC

value: iPSC

value: Induced Pluripotent Stem Cell

value: Cell Line Characterization


title: Fibroblast_Control_rep3

source_name: Fibroblast

value: Fibroblast


title: iPSC_Control_rep1


title: Fibroblast_Control_rep2


title: H3K27Ac

description: ChIP-seq

data_processing:
RNA-seq:
Reads were aligned to the hg38 genome using STAR v2.5.3.
Reads in the whole gene body were counted using featureCounts v1.6.1.
Gene annotations were obtained from Ensembl.
EdgeR was used for gene filtering and RPKM calculations. Genes with at least 1 read count in at least 2 samples were further used to calculate library sizes, counts per million (cpm) and finally RPKM values.
ChIP-seq and Cut&Run:
Reads were aligned to the hg38 genome using bowtie 2 v2.3.4.3.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bigWig: Genome browser tracks were generated using Homer v4.10.3.
Supplementary_files_format_and_content: *_RPKMs.txt: Tab-delimited text files includes RPKM values.

growth_protocol: hTERT-RPE1 cells were grown in regular RPE1 medium at 37° C, 5% CO2.

extract_protocol:
RNA-seq: hTERT-RPE1 cells were collected in Trizol reagent, extracted with chloroform and precipitated with isopropanol. DNaseI treated RNA samples were then extracted using RNA clean & concentrator kit, Zymo Research.
ChIP-seq: hTERT-RPE1 cells were washed once with PBS and crosslinked with 1% Formaldehyde for 10 min at room temparature for ChIP experiments. Chromatin was extracted in 1% SDS containg lysis buffer and sonicated.
Cut&Run: hTERT-RPE1 cells were washed once with PBS and crosslinked with 1% Formaldehyde for 10 min at room temperature and Cut&Run protocol was performed as described in Skene PJ et al., 2017.
Library is constructed as described before (Bowman et al., 2013 - Bowman SK, Simon MD, Deaton AM, Tolstorukov M, Borowsky ML, Kingston RE. Multiplexed Illumina sequencing libraries from picogram quantities of DNA. BMC Genomics. 2013;14:466. Published 2013 Jul 9. doi:10.1186/1471-2164-14-466).

treatment_protocol:
hTERT-RPE1 cells were synchronized with 400 uM Mimosine treatment for 22hrs.
hTERT-RPE1 cells were transfected with 130-150 pmol LNA GapMeRs with the facilitation of Lipofectamine RNAiMax in Opti-MEM.

tag: antibody


title: H3K4me1

description: ChIP-seq


title: H3K27me3

description: Cut-n-run seq

data_processing:
Library strategy: CUT&RUN-sequencing
RNA-seq:
Reads were aligned to the hg38 genome using STAR v2.5.3.
Reads in the whole gene body were counted using featureCounts v1.6.1.
Gene annotations were obtained from Ensembl.
EdgeR was used for gene filtering and RPKM calculations. Genes with at least 1 read count in at least 2 samples were further used to calculate library sizes, counts per million (cpm) and finally RPKM values.
ChIP-seq and Cut&Run:
Reads were aligned to the hg38 genome using bowtie 2 v2.3.4.3.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.bigWig: Genome browser tracks were generated using Homer v4.10.3.
Supplementary_files_format_and_content: *_RPKMs.txt: Tab-delimited text files includes RPKM values.


title: Fibroblast_Control_rep1


title: H3K4me3

description: ChIP-seq


title: iPSC_Control_rep2


title: HUVEC_Control_6h_rep1


title: Input

description: ChIP-seq


title: LUCAT1_KD_S6_rep1

description:
Strand-specific RNA-SEQ (LUCAT1 knockdown)
Nascent RNA
processed data file: Control_LUCAT1_RPKMs.txt

tag: lincrna

value: LUCAT1 LNA


title: LUCAT1_KD_S6_rep2


title: LUCAT1_KD_S4_rep2


title: LUCAT1_KD_S4_rep1


title: HAEC_Control_6h_rep1


title: LUCAT1_KD_S0_rep1


title: HCAEC_Control_6h_6h_rep1


title: LUCAT1_KD_S2_rep2


title: LUCAT1_KD_S0_rep2


title: MIAT_KD_S4_rep2

description:
Strand-specific RNA-SEQ (MIAT knockdown)
Nascent RNA
processed data file: Control_MIAT_RPKMs.txt

value: MIAT LNA


title: MIAT_KD_S6_rep2


title: MIAT_KD_S4_rep1


title: LUCAT1_KD_S2_rep1


title: MIAT_KD_S6_rep1


title: MIAT_KD_S2_rep2


title: MIAT_KD_S2_rep1


title: MIAT_KD_S0_rep2


title: LINC00704_KD_S4_rep2

description:
Strand-specific RNA-SEQ (LINC00704 knockdown)
Nascent RNA
processed data file: Control_LINC00704_RPKMs.txt

value: LINC00704 LNA


title: LINC00704_KD_S0_rep2


title: LINC00704_KD_S2_rep1


title: LINC00704_KD_S2_rep2


title: LINC00704_KD_S0_rep1


title: LINC00704_KD_S4_rep1


title: LINC00704_KD_S6_rep1


title: Control_S6_rep2

description:
Strand-specific RNA-SEQ (Control)
Nascent RNA
processed data file: Control_LINC00704_RPKMs.txt
processed data file: Control_MIAT_RPKMs.txt
processed data file: Control_LUCAT1_RPKMs.txt

value: Control LNA


title: Control_S6_rep1


title: Control_S4_rep2


title: Control_S2_rep2


title: Control_S2_rep1


title: Control_S0_rep1


title: MIAT_KD_S0_rep1


title: Nuc_input_T8-10_rep2

description:
Nascent RNA-SEQ (Nuclear input)
Nascent RNA
processed data file: Nuclear_input_RPKMs.txt

tag: time point


title: Nuc_input_T4-6_rep1


title: Nuc_input_T2-4_rep2


title: Nuc_input_T8-10_rep1


title: LINC00704_KD_S6_rep2


title: Nuc_nascent_T8-10_rep2

description:
Nascent RNA-SEQ (Nuclear nascent)
Nascent RNA
processed data file: Nuclear_nascent_RPKMs.txt


title: Nuc_input_T0-2_rep1


title: Nuc_input_T6-8_rep1


title: Nuc_input_T0-2_rep2


title: Nuc_input_Async_rep1

value: Asynchronized


title: Nuc_input_Async_rep2


title: Nuc_input_T6-8_rep2


title: Nuc_input_T2-4_rep1


title: Nuc_nascent_T6-8_rep1


title: Nuc_nascent_T4-6_rep2


title: Nuc_nascent_T4-6_rep1


title: Nuc_nascent_T8-10_rep1


title: Control_S0_rep2


title: Nuc_nascent_T6-8_rep2


title: Nuc_nascent_T2-4_rep2


title: Nuc_nascent_T0-2_rep1


title: Nuc_nascent_T2-4_rep1


title: Control_S4_rep1


title: WC_input_T8-10_rep2

description:
Nascent RNA-SEQ (Whole cell input)
Nascent RNA
processed data file: Whole_cell_input_RPKMs.txt


title: Nuc_nascent_T0-2_rep2


title: WC_input_T8-10_rep1


title: Nuc_input_T4-6_rep2


title: WC_input_T6-8_rep1


title: WC_input_T4-6_rep2


title: WC_input_T2-4_rep2


title: WC_input_T4-6_rep1


title: Nuc_nascent_Async_rep1


title: WC_input_T6-8_rep2


title: WC_input_T0-2_rep1


title: WC_input_T0-2_rep2


title: WC_input_Async_rep2


title: WC_nascent_T8-10_rep2

description:
Nascent RNA-SEQ (Whole cell nascent)
Nascent RNA
processed data file: Whole_cell_nascent_RPKMs.txt


title: WC_nascent_T8-10_rep1


title: WC_input_Async_rep1


title: WC_input_T2-4_rep1


title: WC_nascent_T6-8_rep2


title: WC_nascent_T4-6_rep2


title: WC_nascent_T4-6_rep1


title: WC_nascent_T6-8_rep1


title: WC_nascent_T2-4_rep2


title: WC_nascent_T0-2_rep2


title: WC_nascent_T0-2_rep1


title: WC_nascent_Async_rep2


title: WC_nascent_Async_rep1


title: C53_MX2_dox0_rep3

first: Tongwu

last: Zhang

address: 9609 Medical Center Drive

department: Division of Cancer Epidemiology & Genetics

institute: National Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling and The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Additional quality control was performed by the MultiQC RNA-Seq module
Quasi-mapping algorithm Salmon was used to provide fast and bias-aware quantification of transcript expression using Gencode human transcripts database (release 29 based on GRCh38.p12)
differentially expressed genes (DEGs) were calculated with DESeq2 adjusting for cell line, biological replicate, and library construction batch.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files of Salmon quantificiation include normalized TPM and read count values for each Sample.

source_name: Primary cultured melanocytes

growth_protocol: Melanocytes were grown in Medium M254 with supplements (Invitrogen) at 37C with 5% CO2, and infected with the lentiviral system using MX2 cDNA cloned into pINDUCER20 or empty vector, followed by drug selection (1mg/ml Geneticin)

extract_protocol:
Total RNA was isolated using a miRNeasy Mini kit (217004, Qiagen). To reduce melanin carryover, cell lysate in QIAzol reagent was heated at 65°C for 5 minutes before the addition of chloroform and phase separation.
Sequencing library was constructed following Illumina TruSeq Standard mRNA Library protocol for 150bp paired-end sequencing

treatment_protocol: Following drug selection, cells were treated with 0 or 100ng/ml doxycycline for 72hrs before being harvested for RNA isolation.

tag: individual id

tag: lentiviral vector

value: pINDUCER20-MX2 cDNA

tag: doxycycline

value: 0 ng/ml

value: Primary cultured melanocytes


title: C53_MX2_dox100_rep3

value: 100 ng/ml


title: C53_Empty_dox100_rep3


title: Nuc_nascent_Async_rep2


title: C53_MX2_dox100_rep2


title: C53_Empty_dox100_rep2


title: C53_MX2_dox100_rep1


title: C53_Empty_dox100_rep1


title: C53_MX2_dox0_rep1


title: C29_Empty_dox100_rep3


title: C29_MX2_dox0_rep3


title: C29_MX2_dox0_rep2


title: C29_MX2_dox0_rep1


title: C29_MX2_dox100_rep2


title: WC_nascent_T2-4_rep1


title: C23_MX2_dox100_rep3


title: C23_MX2_dox0_rep3


title: C29_Empty_dox100_rep1


title: C23_Empty_dox100_rep2


title: C23_MX2_dox0_rep2


title: C23_MX2_dox100_rep1


title: C23_Empty_dox100_rep1


title: C23_MX2_dox0_rep1


title: C23_MX2_dox100_rep2


title: C53_MX2_dox0_rep2


title: RNA-Seq_WT rep2

city: milano

first: Saverio

last: Minucci

address: via Adamello 16

country: Italy

institute: European Institute of Oncology

description:
processed data file:
LSD1_KO_table.txt

data_processing:
basecall was performed using CASAVA v1.8
Sequenced reads were mapped to hg18 using TopHat v2.0.10 for LSD1 KO and LSD1 WT,  while Tophat 1.3.1 for all the other LSD1 treatment
Reads counts and differential expressed genes were calculated using Cufflinks and CuffDiff
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include cuffidiff output with RPKM values for each Sample

source_name: Leukemia cell line NB4

growth_protocol: NB4 cells were grown in RPMI medium containing 10% FBS and supplemented with 2mM L-Glutamine, penicillin (50 units/ml) and streptomycin (100 mg/ml).

extract_protocol:
Total RNA was extracted from NB4 cells with Trizol (Invitrogen) and then purified using the RNeasy kit (Quiagen).
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: NB4 cells were plated at 500000 cells/ml and treted as indicated in each sample for 24 hours.

value: Leukemia cell line

value: not treated

value: WT


title: RNA-Seq_KO rep1

description:
processed data file:
LSD1_KO_table.txt

value: LSD1 KO


title: RNA-Seq_KO rep2

description:
processed data file:
LSD1_KO_table.txt


title: ChIP-Seq_input2

data_processing:
for GFI1 ChIP Basecalls was performed using bcl2fastq software v2 and quality check  performed with fastqc version 0.11.5. for all the other LSD1 ChIP basecall was performed using CASAVA v1.8 and quality check with fastqc 0.10.0
ChIP-seq reads were aligned to the hg18 genome assembly using bowtie v1.0.1 with the option (-m 1 –v 2)
peaks were called using MACS version 1.4.1 with threshold of 10-5
Genome_build: hg18
Supplementary_files_format_and_content: bed file containing chromosome coordinates of peaks and MACS score

extract_protocol:
Cells were cross-linked in culture medium with 1% formaldehyde in PBS and the reaction was stopped after 10 min at RT by adding 0.125 M glycine for 5 min at 4°C. The cells were washed twice with PBS and collected by centrifugation. Pellets were stored at -80° in SDS buffer (50 mM Tris•HCl pH 8.1, 0.33% SDS, 150mM NaCl, 5 mM EDTA, and protease inhibitor cocktail) or directly processed. Fixed cells were resuspended in IP buffer (100mM tris ph 8.6 0.3% SDS 1.7% TRITON x-100 and 5mM EDTA). Chromatin was then fragmented to obtain ~300 bp in average size length by using a Branson Sonifier 250. Chromatin pre-clearing was obtained with protein A-sepharose beads (Amersham). Then, the supernatant was immunoprecipitated overnight in the presence of 30-50 µl of protein G magnetic beads. For histone modification 1 ml corresponding to 3x106 cells per each IP and 4ug/ml primary antibody were used; for LSD1, GFI1 and PML Chip-Seq 40x106 cells per each IP; 10ug/ml. Before IP 2.5% of input was stored prior to the decrosslinking procedure. Decrosslinking was performed for all the IP samples and corresponding inputs, overnight in 0.1%SDS and 0.1% NaCOH3. The day after, the enriched DNA was treated with proteinase K at 56°C for 40 min and purified with a DNA purification kit (Qiagen).
The obtained DNA was then quantified by picogreen and processed for ChIP-Seq library preparation (as described for the Illumina protocol). For libraries preparation, 2ng of immunoprecipitated DNA was used.

treatment_protocol: NB4 cells were plated at 500000 cells/ml and treated as indicated in each sample for 24 hours.

value: Not treated

tag: antibody used

value: No Antibody


title: ChIP-Seq_GFI1

tag: cell type


title: C29_MX2_dox100_rep3


title: RNA-Seq_WT rep1

description:
processed data file:
LSD1_KO_table.txt

tag: cell line


title: ChIP-Seq_LSD1_MC_2580


title: ChIP-Seq_LSD1_DMSO

value: DMSO


title: C29_Empty_dox100_rep2


title: ChIP-Seq_H3K27ac_MC_2580_+_RA_0.01µM


title: ChIP-Seq_H3K27ac_MC_2580


title: ChIP-Seq_H3K27ac_RA_0.01

value: RA 0.01uM


title: ChIP-Seq_H3K4me3_MC_2580_+_RA_1µM

value: H3K4me3 (Activ Motif #39159)


title: ChIP-Seq_H3K27ac_DMSO


title: ChIP-Seq_H3K4me3_RA_1µM

value: RA 1uM


title: ChIP-Seq_H3K4me3_MC_2580


title: ChIP-Seq_H3K4me3_RA_0.01µM


title: ChIP-Seq_H3K4me3_DMSO


title: ChIP-Seq_H3K4me_RA_1µM


title: ChIP-Seq_H3K4me_MC_2580_+_RA_0.01µM


title: C29_MX2_dox100_rep1


title: ChIP-Seq_H3K4me_RA_0.01µM


title: C23_Empty_dox100_rep3


title: RNA-Seq_RA_0.01µM

description:
processed data file:
RNA_seq_LSD1_treatment_table.txt


title: RNA-Seq_RA_1µM


title: ChIP-Seq_H3K4me_DMSO


title: RNA-Seq_MC_2580_+_RA 0.01µM


title: ChIP-Seq_H3K4me_MC_2580


title: RNA-Seq_MC_2580


title: ChIP-Seq_H3K27ac_RA_1µM


title: CONTROL Line2 Rep2

first: Stephanie

last: Rollmann

department: Biological Sciences

institute: University of Cincinnati

data_processing:
Raw sequencing data were filtered for adapter contamination using the program Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore), allowing for a maximum error rate of zero.
The Cutadapt program was then used to trim low quality sequences that have Phred scores below 20 as well as remove reads shorter than 30 bp from the analysis (Martin 2011).
The remaining RNA-seq reads were then aligned using STAR (Dobin et al. 2013).
Genome_build: Drosophila melanogaster reference genome (version 6.10; Attrill et al. 2016)
Supplementary_files_format_and_content: Each text file includes the gene symbol, FlyBase gene ID, and read count for each sample.

organism: Drosophila melanogaster

source_name: CONTROL_whole head

extract_protocol:
Whole heads were removed, flash frozen on dry ice, and RNA was harvested using RNeasy Mini Kit (Qiagen, Valencia, CA).
Total RNA was sent to the Weill Cornell Medical College Genomics Resources Core Facility for RNA sequencing using standard protocols. There, cDNA libraries were generated from each sample and then sequenced using Illumina HiSeq4000 to generate 100 bp reads.

tag: Sex

value: Female

tag: selection regime

value: unselected control

tag: selection treatment

value: Control

value: whole head

tag: biological replicate


title: ChIP-Seq_input


title: CONTROL Line3 Rep1


title: ChIP-Seq_H3K4me2_MC_2580_+_RA_0.01µM


title: CONTROL Line2 Rep1


title: ChIP-Seq_H3K4me2_RA_1µM


title: ChIP-Seq_H3K4me2_RA_0.01µM


title: CONTROL Line1 Rep2


title: CONTROL Line1 Rep1


title: ChIP-Seq_H3K4me2_DMSO


title: CYC Low Line3 Rep2

source_name: CYC Low_whole head

value: cyclohexanone (CYC)

value: PI-


title: ChIP-Seq_H3K4me2_MC_2580


title: CYC Low Line3 Rep1


title: CYC Low Line2 Rep2


title: CONTROL Line3 Rep2


title: CYC Low Line2 Rep1


title: CYC Low Line1 Rep2


title: CYC High Line3 Rep2

source_name: CYC High_whole head

value: PI+


title: RNA-Seq_DMSO

value: Leukemia cell line


title: CYC Low Line1 Rep1


title: CYC High Line3 Rep1


title: AB8111

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

source_name: Spinal cord

growth_protocol: All mice were maintained under specific pathogen-free conditions

extract_protocol:
Mice were perfused with 5 ml PBS via the left ventricle and spinal cord samples were harvested from individual mice. CNS tissues were cut into small pieces and homogenized through a 100m mesh filter without tissue digestion. After washing, the cell pellet was resuspended in 40% Percoll and the myelin fraction was separated from mononuclear cells by density centrifugation (2200rpm, 20 min at 14ºC with low acceleration and no brake).
Samples were flow sorted either using AriaII, AriaIII or Aria-Fusion (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

treatment_protocol: Mice were immunized subcutaneously with 200μg of MOG35-55 peptide emulsified in CFA containing 1mg of Mycobacterium tuberculosis as described previously. Mice received intraperitonal injections of 250ng pertussis toxin at the time of immunization and 48 hours later.

tag: strain

tag: organ

value: Spinal cord

tag: selection marker

value: GFP+

tag: eae status

value: acute (day 16 post immunization; median EAE score 2.9)

value: Adoptive transfer of monocytes from GFP mice 6 days post EAE immunization

tag: mouse age

value: 8-12 weeks


title: AB8112

tag: treatment

value: Adoptive transfer of cMoPs from GFP mice


title: AB6019

value: GFP-CD45.2- or GFP+CD45.2+

value: Adoptive transfer of MDPs from CD45.1/1 mice and monocytes from GFP mice


title: AB6017

value: CD45+ Ly6G-

value: Treatment with MC21 blocking antibody

tag: replicate id


title: AB6016


title: CYC High Line2 Rep2

value: Female

tag: tissue


title: AB6018


title: CYC High Line2 Rep1


title: CYC High Line1 Rep2


title: AB6015


title: AB6012

value: CD44+ Ly6G- CD11b+ CX3CR1low/int


title: CYC High Line1 Rep1

value: whole head


title: AB6014


title: AB6013


title: AB6011

value: Treatment with MC21 blocking antibody isotype control


title: BUT Low Line3 Rep1

source_name: BUT Low_whole head

value: 2,3-butanedione (BUT)

value: PI-


title: AB6009


title: BUT Low Line2 Rep2


title: AB7789

value: Adoptive transfer of GMPs from GFP mice


title: BUT Low Line2 Rep1


title: BUT Low Line1 Rep1


title: AB6008

value: Spinal cord


title: AB6007


title: BUT Low Line1 Rep2


title: AB6006


title: AB5814


title: BUT High Line3 Rep2

source_name: BUT High_whole head

value: PI+


title: BUT High Line2 Rep2


title: AB5805

value: C57BL/6 Zbtb46-GFP

value: chronic (day 30 post immunization, median score 2.2)


title: AB5806

value: 8-12 weeks


title: AB5800

value: acute (day 16 post immunization; median EAE score 2.9)


title: BUT High Line1 Rep2


title: AB5810


title: BUT High Line1 Rep1


title: BUT Low Line3 Rep2


title: AB5801


title: AB1945


title: AB1946


title: AB6010


title: AB1944


title: AB1943


title: AB1942


title: Sample 8C_RsmA_delhfq_ChIP

city: Iowa City

first: Michael

middle: J

last: Gebhardt

state: IA

address: 431 Newton Road, 200A EMRB

department: Department of Microbiology and Microbiology

institute: University of Iowa

data_processing:
Paired ChIP-Seq reads corresponding to fragment sizes of either 200 or 400 bp (see SAMPLES section) were aligned to the PAO1 genome using bowtie2 (version 2.3.1) allowing 1 mismatch in a 28 bp seed region with no discordant or unpaired alignments.
The program samtools (version 1.2) was used to extract read 1 from each mapped read pair.
For the RsmA-V +/- rifampicin experiments (samples 1-2): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from exponential-phase wild-type cells (sample 3) with the following settings: KDE = 50,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2
For Hfq +/- ∆rsmAF (Samples 4 and 5) ChIP Experiment: Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from log-phase wild-type cells (Sample 9) with the following settings: KDE = 45,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.
For RsmA +/- ∆hfq (Samples 7 and 8) ChIP Experiment: Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from log-phase wild-type cells (Sample 9) with the following settings: KDE = 30,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.
Bed files for each experimental replicate were created by QuEST and the final processed bed files were generated by identifying the largest overlapping peak region which statisfy the following conditions: (1) peak regions must have a positive peak shift, (2) peak regions must have a positive strand correlation, (3) peak regions must have a q-value of less than 0.01, and (4) peak regions must be shared by two or more experimental replicates.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: wig files were generated using QuEST; Scores represent normalized smoothed read density
Supplementary_files_format_and_content: bed intervals reflect regions with signicant (as defined above in data processing steps) enrichment of reads in the experimental condition in comparision to the mock control condition.

growth_protocol: Bacterial cultures were started from single colonies, grown overnight, and back-diluted in LB media

extract_protocol:
DNA associated with proteins of interest were immunoprecipitated from lysates with anti-VSVG monocolonal antibody
Immunoprecipitated DNA was not size-selected during library construction
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions.

treatment_protocol: As indicated above, a subset of the samples were treated with rifampicin (150 µg/mL) for 30 minutes prior to the ChIP protocol,

tag: genotype/variation

value: RsmA-VSVG {delta}hfq

value: Bacterial cells grown to OD 0.5

tag: treatment protocol

value: no rifampicin treatment

tag: chip antibody

value: Agarose-immobilized anti-VSVG (Sigma-Aldrich, Cat.# A1970, monoclonal antibody clone P5D4)

tag: input/mock used

value: Sample 9_PAO1_3


title: Sample 9_PAO1_3

description: mock IP:  IP with the anti-VSVG antibody on lysates from cells lacking the target epitope

value: wild-type

tag: cell type


title: AB1941

value: CD44+ Ly6G- CD11b+ CX3CR1low/int


title: BUT High Line3 Rep1

tag: Sex

value: Female

value: whole head


title: AB1939


title: PAO1 WT rep1

city: Winnipeg

first: Kangmin

last: Duan

state: MB

address: 66 Chancellors Cir

country: Canada

institute: University of Manitoba

data_processing:
After RNA-Sequencing, the obtained raw data were filtered according to the following standards: 1) removing reads with ≥ 10 % unidentified nucleotides (N); 2) removing reads with > 50 % bases having Phred quality scores of ≤ 20; 3) removing reads aligned to the barcode adapter using FASTP (https://github.com/OpenGene/fastp).
Quality trimmed reads were aligned using Bowtie2 (Langmead and Salzberg, 2012)  (version 2.2.8) to the P. aeruginosa PAO1 reference genome to identify known genes and calculated gene expression by RSEM (Li and Dewey, 2011).
The gene expression level was calculated and further normalized by using the fragments per kb of transcript per million (FPKM) mapped reads method to eliminate the influence of different gene lengths and amount of sequencing data on the calculation of gene expression.
The edgeR package (http://www.r-project.org/) was used to identify differentially expressed genes (DEGs) across samples with fold changes ≥ 2 and a false discovery rate-adjusted P (q value) < 0.05.
Go terms and KEGG pathway were defined as being significantly enriched when the q value ≤ 0.05.
Genome_build: Pseudomonas aeruginosa PAO1

source_name: wild-type PAO1

growth_protocol: liquid culture in LB (Luria-Bertani) medium

extract_protocol:
Strains were grown overnight at 37 °C followed by sub-culturing into fresh medium and grown to mid-exponential phase. Total RNA was extracted by TRIzol-based method (Life Technologies, CA, USA). In brief, the cultures were centrifuged at 12, 000 g for 5 minutes. The supernatant was discarded, cell pellets were resuspended in 1 ml of TRIzol and then incubated at room temperature for 5 minutes to permit complete dissociation of nucleoproteins complex. Followed by adding 0.2 ml chloroform into the tube and mix well, the samples were centrifuged (12, 000 g at 4 °C for 15 minutes) to form three layers. The upper aqueous phase was transferred to a fresh tube and added by 0.5 ml cold isopropanol to precipitate RNA. After centrifugation, the supernatant was removed, and the pellet was suspended in 1 ml 75% ethanol. Samples were centrifuged and the supernatant was discarded, air-dried RNA pellet was resolved in 50 µL RNase-free Water.
RNA integrity was measured using Bioanalyzer 2100 (Agilent, Santa Clara, CA) and rRNA was removed from 1 mg of total RNA with Ribo-Zero Magnetic Gold Kit (Epicentre Biotechnologies, Madison, WI, USA). To construct the RNA-Seq library, TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) was used. rRNA-depleted RNA was fragmented into small pieces using Elute Prime Fragment Mix. First-strand cDNA was synthesized with First Strand Master Mix and Super Script II reverse transcriptase (Invitrogen, Carlsbad, CA, USA). Following purification by Agencourt RNAClean XP beads (Beckman Coulter, CA, USA), the second-strand cDNA library was synthesized using Second Strand Master Mix and dATP, dGTP, dCTP, dUTP mix. Purified fragmented cDNA was end repaired (30 minutes at 37 °C) prior to ligating sequencing adapters. Amplified RNA-Seq libraries were purified by using AMPureXP Beads.

treatment_protocol: grow until mid-exponential phase in LB

value: wild type


title: Sample 8B_RsmA_delhfq_ChIP


title: PAO1 clpV3-KO rep1

value: clpV3 deletion mutant


title: Sample 8A_RsmA_delhfq_ChIP


title: PAO1 WT rep2


title: PAO1 clpV3-KO rep2


title: BUT High Line2 Rep1

tag: selection regime

value: 2,3-butanedione (BUT)


title: AB1937

value: Spinal cord


title: Sample 7B_RsmA_ChIP

value: RsmA-VSVG


title: AB1935

value: chronic (day 30 post immunization, median score 2.2)


title: Sample 7C_RsmA_ChIP


title: Sample 5 C_Hfq_delAF_ChIP

value: Hfq-VSVG {delta}rsmA {delta}rsmF

value: Sample 6_PAO1_2


title: AB1936

value: 8-12 weeks


title: 24h AT3 rep.3

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

data_processing:
Demultiplexing
FastQ quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX (v0.11.7)
Size filtering: discarding reads shorter than 20 nt (via READemption v0.4.3)
Read mapping via READemption (v0.4.3)
Counting of reads per gene via READemption (v0.4.3)
Genome_build: Mus muculus: GRCm38.p6 (ENSEMBL)
Supplementary_files_format_and_content: CSV (tab separated) of gene count per gene per sample

source_name: immortalized murine cell line

growth_protocol: Cells were seeded in six-well plates 2 days prior to infection and kept in an oxygen-controlled incubator at 1% oxygen. The complete DMEM media was exchanged after 24h for complete DMEM without antibiotic.

extract_protocol:
Cells were washed 1x with PBS before total RNA extraction using the mirVana kit (Ambion) following the manufacturer's instructions
input of 500ng total RNA for oligo-dT capture beads for poly-A-mRNA enrichment for TruSeq Stranded mRNA Library Preparation Kit (Illumina) following manufacturer's instructions
TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: AT3 cell were infected at a m.o.i. of 10 with F. nucleatum ATCC 23726 for 24h

tag: cell line

value: AT-3 Mouse Mammary Carcinoma Cell Line

tag: infection

value: control


title: Sample 7A_RsmA_ChIP

value: Bacterial cells grown to OD 0.5

value: no rifampicin treatment

value: Agarose-immobilized anti-VSVG (Sigma-Aldrich, Cat.# A1970, monoclonal antibody clone P5D4)


title: 24h AT3 rep.1


title: 24h Fn-AT3 rep.3

value: F. nucleatum


title: 24h AT3 rep.2


title: Sample 5 A_Hfq_delAF_ChIP


title: Sample 5 B_Hfq_delAF_ChIP


title: Sample 4C_Hfq_ChIP

value: Hfq-VSVG


title: Sample 4B_Hfq_ChIP


title: 24h Fn-AT3 rep.2


title: AB1940

tag: strain

value: CD44+ Ly6G- CD11b+ CX3CR1low/int


title: Sample 4A_Hfq_ChIP


title: SC104746

city: Durham

first: Li

address: 111 T.W. Alexander Dr

institute: NIH

description:
104746_m_merged.report.csv
104746_m_merged.genematrix.csv

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq
Supplementary_files_format_and_content: txt,raw counts of RNA-seq
Supplementary_files_format_and_content: xlsx,log fold change of RNA-seq

source_name: cardiomyocytes

extract_protocol:
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes
RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific). One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.

tag: co-cultured cell type

value: co-cultured cell

value: cardiomyocytes


title: SC104827

description:
104827_m_merged.report.csv
104827_m_merged.genematrix.csv

source_name: fibroblasts

value: fibroblasts


title: Sample 2B_RsmA_ChIPPAR_Rif

value: sample taken 30 minutes after treatment with 150 ug/mL rifampicin

value: Sample 3_PAO1_midlog


title: m_NCM_AF1

description:
RNAseq_genecountsraw.txt
RNAseq_logFC_cafNCMmcnfNCM.xlsx

value: adult fibroblasts


title: m_NCM_NF2

value: neonatal fibroblasts


title: Sample 3_PAO1_midlog

value: wild-type


title: m_NCM_NF1


title: Sample 6_PAO1_2


title: Sample 2A_RsmA_ChIPPAR_Rif

value: RsmA-VSVG


title: Sample 1A_RsmA_ChIPPAR

value: sample taken prior to rifampicin treatment


title: P1_SC100349

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm9/mm10/rn6 genome via STAR v2.5.2b
Reads were assigned to Ensembl genes by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10 for mouse RNASeq; rn6 for rat RNASeq; mm9 for ChIPSeq
Supplementary_files_format_and_content:
csv,gene expression matrix for single cell RNASeq
txt,raw counts of RNA-seq
xlsx,log fold change of RNA-seq
bedGraph, read intensity of ChIPSeq samples

extract_protocol:
Cell suspension was centrifuge (100 x g, 2min) three times to separate the cardiomyocytes and non-cardiomyocytes
RNA was extracted from cells using the GeneJet RNA Purification Kit (Thermo Scientific). One µg of RNA was used for generation of sequencing library using the TruSeq RNA Library Prep Kit V2 (Illumina) according to the manufacturer’s instructions.
Mouse CMs were fixed using 1% formaldehyde for 10 min, and 0.125 M glycine was added to stop fixation. Cells were harvested, and DNA was fragmented to 300–500 bp by sonication with Covaris S220 sonicator. Immunoprecipitation was performed with antibodies conjugated to Dynabeads Protein G beads (Life Technology). ChIP DNA was eluted, reverse cross-linked, extracted by phenol/chloroform, and precipitated.

treatment_protocol: For Single cell RNA-Seq for one-day, four-day and seven-day mice, ventricles close to auricle and far away auricle and cardiac apex were chopped into small pieces respectively and digested with Pierce™ Primary Cardiomyocyte Isolation Kit (Thermo, 88281).For 14-day and 28-day mice, hearts were digested by using langendorff perfusion technique, following with heart dissociation enzyme stock solution to digest heart.

tag: developmental stage

tag: tissue/cell type

value: heart


title: RNA-seq_Arid1a-cKO_rep3

city: Zibo

first: Dai

middle: Shang

last: Kun

state: Shandong

address: 266 Xincun West Road

department: School of Life Sciences and Medicine

institute: Shandong University of Technology

data_processing:
ATAC-seq reads were aligned to the mouse GRCm38 reference genome (vM23 from GENCODE) using Bowtie 2 (v. 2.3.5.1) with default parameters. MACS (v. 2.2.5) was used to call peaks (-f BAMPE -g mm --keep-dup all -p 0.01).High-quality reads of RNA-seq were quantified using Salmon (v.1.0.0) and differential gene expression analysis was conducted using DESeq2(v1.26.0).
Genome_build: GRCm38

source_name: Retinal ganglion cells

extract_protocol:
The dissected retinas were dissociated in EBSS containing papain and DNase (Worthington) for 20min at 37℃, with gentle shaking every 5min, then digestion was stopped by adding Ovomucoid/EBSS (Worthington). The dissociated retinal cells were incubated with FC block antibody (1:100, BD Biosciences 553141), and then stained with Thy1.2-PE antibody (1:100, Invitrogen 12-0902-82) and DAPI. FACS sorting was performed with a BD FACSAria IIIu instrument.
RNA-seq libraries from the purified RGCs were prepared using the Illumina RNA-Seq Preparation Kit. Total RNA sample QC was measured by Agilent 2100 Bioanalyzer.

value: Retina

tag: age

value: 8-10 weeks

tag: genotype

value: Arid1a del/del


title: Sample 1B_RsmA_ChIPPAR

value: Bacterial cells grown to OD 0.5

value: Agarose-immobilized anti-VSVG (Sigma-Aldrich, Cat.# A1970, monoclonal antibody clone P5D4)


title: m_NCM_AF2


title: P14_SC100379


title: Sample 2C_RsmA_ChIPPAR_Rif


title: P7_SC100303


title: RNA-seq_Arid1a-WT_rep3

value: Arid1a fl/fl


title: RNA-seq_Arid1a-cKO_rep2


title: P4_SC100327


title: 24h Fn-AT3 rep.1

value: AT-3 Mouse Mammary Carcinoma Cell Line

value: F. nucleatum


title: Sample 1C_RsmA_ChIPPAR


title: RNA-seq_Arid1a-WT_rep2


title: RNA-seq_Arid1a-cKO_rep1


title: NELF_Input

city: Beijing

last: Yu

address: Medicial Science Building, Tsinghua University

department: The Institution of Immunology

institute: Tsinghua University

data_processing:
Basecal was performed using CASAVA 1.8
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 1.1.2
Reads were filtered as the unsure bases less than 10% and low quality (I<10) bases less than 50%.
Peaks were called using findPeaks program in HOMER (v4.7.2) with the following setting: FDR < 0.001)
Genome_build: mm10

source_name: Macrophages

growth_protocol: Bone marrows cells from C57BL/6 mice were cultured for 5 days in DMEM supplemented with 10% FBS and 10% L929 cell supernatant as conditioned medium providing macrophage colony stimulating factor to generate BMDMs

extract_protocol:
Lysates were clarified from sonicated nuclei and NELFE-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for indicated time.

value: Bone marrow-derived macrophages

tag: antibody

tag: treatment


title: NELF_L60_rep2

value: anti-NELF

value: LPS for 60 min


title: RNA-seq_Arid1a-WT_rep1

tag: tissue


title: ATAC-seq_Arid1a-cKO_rep2

extract_protocol:
The dissected retinas were dissociated in EBSS containing papain and DNase (Worthington) for 20min at 37℃, with gentle shaking every 5min, then digestion was stopped by adding Ovomucoid/EBSS (Worthington). The dissociated retinal cells were incubated with FC block antibody (1:100, BD Biosciences 553141), and then stained with Thy1.2-PE antibody (1:100, Invitrogen 12-0902-82) and DAPI. FACS sorting was performed with a BD FACSAria IIIu instrument.
ATAC-seq libraries were prepared from the purified RGCs using TruePrep DNA Library Prep Kit V2 for Illumina.


title: NELF_L30_rep2

value: LPS for 30 min


title: NELF_UT_rep2

value: untreated


title: WT single cell enterocytes

city: Philadelphia

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description:
WT_mm10
WT_9365033471_S2

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.
Genome_build: mm10
Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample

source_name: enterocyte - ileum

extract_protocol:
Cells were loaded on to a GemCode instrument (10X Genomics) to produce single-cell bar-coded droplets using 10X Single Cell 3’ v2 chemistry.
Libraries generated were sequenced across at least one lane on the Illumina Illumina HiSeq 2500 instrument with the HiSeq Rapid SBS kit.

treatment_protocol: Enteroids were isolated vio EDTA and enzymatically digested with Collagenase and Dispase to become a single cell suspension.

tag: strain background

value: wild type

value: 8 weeks

value: enterocyte - ileum


title: TNFAIP8 single cell enterocytes

description:
Tko_mm10
Tko_2207317113_S1


title: ATAC-seq_Arid1a-WT_rep2


title: NELF_L60_rep1


title: ATAC-seq_Arid1a-WT_rep1


title: NELF_L30_rep1


title: NELF_UT_rep1


title: Nelfb_KO_L30

first: Bin

address: Zheng Yutong Building room D311

description: nuclear-run-on RNA

data_processing:
Basecal was performed using CASAVA 1.8
The reverse (-2) reads of paired-end reads were used for analysis. Reads were trimed to 51 bp from end, and adaptor sequence were further filtered out from reads.
Trimmed PRO-seq reads from two sequencing runs for each condotion were pooled and aligned to the mm10 genome assembly using Bowtie version 1.1.2, and uniquely mapped reads with mismatch less than 2 were kept for further analysis.
Visualized bedgraph files were generated by using HOMER software package (v4.7.2) with strand specificity.
Genome_build: mm10

extract_protocol:
Nuclei of cells from each condition were isolated and subjected to Run-on experiment with biotin-CTP and -UTP supplement to label nascent RNA. RNA was isolated and hydrolyzed. Then two biotin enrichment processes were preformed with interval of adding -OH group in 3' end and removing 5' cap of enriched RNA fragments. Enriched biotin-labeled RNA were used for further library construction.
RNA libraries were prepared by using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, cat.no.E7300). After quality control, libraries were subjected to sequencing with standard Illumina protocols.
PRO-Seq

treatment_protocol: BMDMs were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for indicated time.


title: Nelfb_KO_UT

description: nuclear-run-on RNA


title: Nelfb_KO_30min rep3

data_processing:
Basecal was performed using CASAVA 1.8
Tophat (v2.1.0) was used for pair-end reads alignment with the following parameters:  -i 70 -g 1 --no-novel-indels
Gene expression level were quantified by using Cufflinks (v2.2.1), and Cufflinks was also used for further differential expression analysis
Genome_build: mouse (mm10)
Supplementary_files_format_and_content: Excel file contains quantified gene expression level as FPKM and adjusted p-value for differentail expression analysis.

extract_protocol:
RNA was isolated using Qiagen RNA-easy kit and total RNA was polyA enriched.
RNA libraries were prepared for sequencing using TruSeq mRNA-seq Sample Preparation Kit(Illunima)
none provided by the submitter


title: CDK9_UT

extract_protocol:
Lysates were clarified from sonicated nuclei and CDK9-DNA complexes were isolated with antibody
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMDMs  were left untreated or exposed to 10 ng/ml cell culture grade LPS (Escherichia coli 0111:B4, InvivoGen) for 1 hour.


title: WT_L30

description: nuclear-run-on RNA


title: WT_UT

description: nuclear-run-on RNA


title: Nelfb_KO_30min rep2


title: Nelfb_KO_0min rep3


title: Nelfb_KO_0min rep2


title: Nelfb_KO_0min rep1


title: Sample 17: Rat1_1

city: Edinburgh

first: Clementine

last: Delan-Forino

address: Michael Swann Building 5.1, King's Buildings, Mayfield Road

country: United Kingdom

institute: University of Edinburgh - WTCCB

description: RNA bound to protein of interest

data_processing:
Library strategy: CRAC
CRAC Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped. (For the raw reads uploaded here barcodes were not clipped)
CRAC Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
CRAC Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
CRAC Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
CRAC Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign and counts over each genomic features calculated using pyReadCounters from pyCRAC package
RNAseq Demultiplexing: Reads were indexed during library preparation and demultiplexed by the sequencing platform
RNAseq Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
RNAseq Reverse Complement: Reads were reverse complemented
RNAseq Sequences filtration: Low complexity sequences were filtered out before genome alignment
RNAseq Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign, all reads mapping to non RNA polymerase II transcripts were filtered out, and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gff format

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: S.cerevisiae strains expressing C-terminal HTP or N-terminal FTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.

extract_protocol:
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
CRAC (as described in Delan-Forino et al, MiMB, in press) and RNA seq (Lexogen Sense mRNA kit)

treatment_protocol: Protein-RNA complexes were stabilised by in-vivo UV crosslinking.

tag: tag

value: HISx6-TEV proteas cleavage site-protA

value: yeast culture

tag: barcode name

value: clipped

tag: barcode sequence


title: Sample 8: Mtr4-arch_1

description: RNA bound to protein of interest

value: Ac

value: NNNGCGCAGC


title: Sample 15: Rrp44_Mtr4-arch_1

description: RNA bound to protein of interest

value: Ab

value: NNNATTAGC


title: Sample 9: Mtr4-arch_2

description: RNA bound to protein of interest

value: Bd

value: NNNTCTCTAGC


title: ATAC-seq_Arid1a-cKO_rep1

value: Retina

value: 8-10 weeks

value: Arid1a del/del


title: Sample 16: Rrp44_Mtr4-arch_2

description: RNA bound to protein of interest

value: Bb

value: NNNGTGAGC


title: WT_60min rep2

tag: cell type

value: Bone marrow-derived macrophages


title: Sample 2: Air1_2

description: RNA bound to protein of interest


title: Sample 1: Air1_1

description: RNA bound to protein of interest

value: Ca

value: NNNCTAGC


title: WT_30min rep3


title: WT_60min rep1


title: WT_30min rep2