title: Human HS_20A_PAC-1

value: GD_RNA_18 and 28


title: LnCaP_Control_Replicate1

status: Public on Aug 18 2020

type: SRA

city: Belfast

first: Rebecca

middle: Elizabeth

last: Steele

address: 97 Lisburn Road

department: CCRCB

country: United Kingdom

institute: Queen's University Belfast

library_source: transcriptomic

data_processing:
Two biological replicates of each condition were used for the assay
Samples were multiplexed and paired-end sequenced with 150bp read length
Sequencing reads were aligned to Hg19 (GRCh37) using STAR
Raw counts of reads were mapped to genes using HTSeq counts
Normalised counts were generated using DESeq2
Genome_build: Hg19 (GRCh37)

molecule: total RNA

organism: Homo sapiens

source_name: LnCaP Cell Line

extract_protocol:
RNA was isolated with Illustra RNAspin Minikit (GE healthcare, cat num. 25-0500-72)
Libraries for sequencing were prepared by the Norwegian High Throughput Sequencing Centre using Strand-specific TruSeq RNA-seq library prep kit.

treatment_protocol: LNCaP cells were treated with control, 40mM OSMI-2-only, 0.5mM AT7519-only and 0.5mM AT7519+40mM OSMI-2, for 4 hours prior to harvesting

tag: cell line

value: LnCaP

tag: treatment

value: Control


title: Control-2-1

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

country: USA

institute: UCSD

description: processed data file: RNAseq_set2_RPKM.csv

data_processing:
RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i). Reads did not map to repetitive elements were then mapped to the human genome (hg19). Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
Differential expression was calculated using DESeq2 version 1.10.1
The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.
Genome_build: Homo sapiens UCSC hg19

growth_protocol: HEK293T cells were grown in standard cell culture in 10% FBS in DMEM

extract_protocol:
Total and polysome derived RNA were extracted using Trizol reagent
Strand-specific RNA sequencing libraries were prepared from 0.5-3 µg total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina).

treatment_protocol: Polysome cells were treated with cycloheximide (CHX) at 100 µg/ml for 5 min at 37°C.

tag: tissue

value: HEK293T cells


title: PSPPH_3241_cycle3_Rep1

city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt

library_source: genomic

data_processing:
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using a custom script and used for further analyses.
Autoseed software was used for motif analysis.
Use R ggseqlogog package to build motif logos.
Genome_build: Pseudomonas savastanoi pv. phaseolicola 1448A  (GCF_000012205.01)
Supplementary_files_format_and_content: xls file was summary of position weight matrix for all motifs; txt file was genome wide target sites result of TFs.

molecule: genomic DNA

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 12 ml buffer A and lysed by sonication at ten seconds interval for 20 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA column was eluted with 30 ml gradient from 60 to 500 mM imidazole prepared in buffer A gradually.
HT-SELEX was performed by using selection ligands containing an 8 bp barcode before and after the 40 bp randomized region for Illumina system or a 10 bp barcode after the 40 bp randomized region for BGI system, respectively. The ligand libraries were produced by PCR amplification using the primers in Supplementary TableX and 40 bp randomized oligo as template. The libraries were sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer to analyze the uniformity of each base (A, T, C, G). Then, 100-200 ng protein and 5 ul selection ligands were added into Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1 mM DTT, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC (Sigma P4929)) until the total volume reached 25 ul. After incubating for 30 min at room temperature, the 150 ul promega buffer (without poly-dIdC) containing 10 ul Ni Sepharose 6 Fast Flow resin (GE Healthcare 17-5318-01) equilibrated in binding buffer was added into the mixture and incubated for 60 min with a gentle shaking at room temperature. After binding, the resin beads were consecutively washed with a gentle shaking for 12 times with 200 μl of Promega binding buffer (without poly-dIdC). It took 5 min for each washing. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound DNA was re-suspended by using 200 uL double-distilled water. Finally, about 20 uL bound DNA was performed for PCR amplification using Phusion DNA polymerase (NEB M0530L) with the primers in Supplementary TableX, and the resulting PCR products were used as selection ligands for the next cycle of HT-SELEX. This process was repeated four times. After each cycle, the purified PCR products from each HT-SELEX cycle were pooled and sequenced using Illumina HiSeq Xten or BGI MGISEQ 2000 sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce each TF expression at 16 °C for 16 h.

tag: genotype

value: wide type

tag: growth phase

value: exponential phase


title: PSPPH_3241_cycle2_Rep1

organism: Pseudomonas savastanoi pv. phaseolicola 1448A


title: Human HS_PAC-1

city: Montreal

first: Genevieve

last: Deblois

state: Quebec

address: 2950, chemin de Polytechnique

country: Canada

institute: Université de Montréal

data_processing:
Reads were aligned to hg19 using tophat (2.0.8) with default parameters
Transcripts were merged using cufflinks (2.1.1) and differential expression computed for all relevant contrasts with default parameters
Genome_build: hg19
Supplementary_files_format_and_content: csv file showing mean FPKM value for all identified transcripts

source_name: HS 578T

growth_protocol: MDA-MB-436 and HS 578T cells were grown in DMSO supplemented with 10%FBS and Penicilin/Streptomycin (100 U/mL Penicilium and 100 μg/mL. Streptomycin). Taxane-resistant cells were generated upon long-term exposure to increasing concentrations of paclitaxel at a starting concentration 0.05 nM with increments (dose and time adjusted to the growth and survival of adapting cells), until the cytotoxic concentration of 10 to 20 nM was reached with the resistant cells growing at a similar rate than the parental cells (>6 months).

extract_protocol:
RNA was extracted using the qiaquick purification kit according to manufacturer's protocol
RNA samples were quantified by qubit (Life Technologies) and quality by Agilent Bioananlyzer. All samples had RIN score >8 were library prepared using TruSeq Stranded mRNA kit (Illumina). Two hundred nanograms total RNa from  30 RNA samples were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads , following purification the RNA was fragmented. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” based were added and adapter ligated followed by purification and enrichment with PCR to create cDNA libraries.
Final cDNA libraries were size validated using Agilent Bioanalyzer and concentration validated by qPCR (Kapa Biosystems/Roche). All libraries were normalized to 10nM and pooled together, denatured with 0.2N NaOH and diluted to a final concentration of 8 pM. Pooled libraries were loaded onto cBot (Illumina) for cluster generation. Clustered flow cell was then sequenced Paired-end 100 cycles V3 using Illumina Hiseq2000 to achieve ~30 million reads per sample.

treatment_protocol: Taxol-resistant cells were grown in presence of 20nM of Paclitaxel at all time. Parental cells (MDA-MB-436 and Hs 578T) were grown in DMEM with 1:1000 DMSO at all time.

tag: cell type

value: TNBC

tag: paclitaxel sensitivity

value: parental taxol-sensitive  treated with paclitaxel 72h

tag: replicate

value: GD_RNA_17 and 27

tag: agent

value: 20nM Paclitaxel, 72h


title: PSPPH_3241_cycle1_Rep1


title: Human HS_DMSO-1

value: parental taxol-sensitive

value: GD_RNA_16 and 26


title: AIMP1-sh2-2

description:
processed data file: RNAseq_set2_RPKM.csv
The control samples are Control-2-1/ Control-2-2


title: Human 436_20C_PAC-1

value: Taxol-resistant

value: GD_RNA_15 and 25

value: 20nM Paclitaxel


title: AIMP1-sh1-2


title: sRNA_Blade_S5_rep2

city: Wuhan

first: Chang

last: Liu

address: Shizishan Street

institute: Huazhong Agricultural University

description: small RNA

data_processing:
Basecalls performed using CASAVA
Adaptor sequences, contamination, and low-quality reads were removed from the raw reads. Mapping of the clean data to the reference genome and de novo MIRNA identification were performed with ShortStack (v 3.8.2; parameter set: --dicermin 18 --dicermax 26 --foldsize 400)
The reads counts of mature miRNAs identifed by ShortStack or reported in miRBase (rice) were collected for each library
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include miRNA raw counts for each sample of small RNA-seq
Supplementary_files_format_and_content: FASTA file with the miRNA sequences for each tag* ID

organism: Oryza sativa

source_name: blade

growth_protocol: The seeds were soaked in distilled water at room temperature for 1 day and imbibed for 2 days in water at 37°C in a constant temperature incubator (referred to as the first and second day after germination, respectively). The water was changed twice daily. The germinated seeds were transferred to 96-well plates with cut bottoms and grown in water under a 16 h (light, 28°C)/8 h (dark, 25°C) cycle.

extract_protocol:
LJ and blade tissue form the first complete leaves of seedlings were separately cut and collected on the 4th, 5th, 6th, 7th, and 9th day after germination, the length of LJ were less than 1 mm, and the length of blade was less than 10 mm. The collected tissues were immediately frozen in liquid nitrogen and subjected to total RNA extraction with TRIzol (Invitrogen). The total RNAs were sent to BGI (Shenzhen, China) for small RNA library construction.
Small RNA libraries were prepared for sequencing using standard protocols

value: blade

tag: developmental stage


title: PSPPH_3079_cycle3_Rep1


title: sRNA_Blade_S4_rep2

description: small RNA


title: LnCaP_Control_Replicate2


title: PSPPH_3079_cycle2_Rep1


title: Human 436_20B_PAC-1

value: GD_RNA_14 and 24


title: sRNA_Blade_S4_rep1

description: small RNA


title: UBAP2L-sh2-2

description:
processed data file: RNAseq_set1_RPKM.csv
The control samples are Control-1-1/ Control-1-2


title: PSPPH_3079_cycle1_Rep1


title: Human 436_20A_PAC-1

value: GD_RNA_13 and 23


title: UBAP2L-sh2-1


title: sRNA_Blade_S3_rep2

description: small RNA


title: PSPPH_3066_cycle4_Rep1


title: PSPPH_3079_cycle4_Rep1


title: UBAP2L-sh1-2


title: PSPPH_3066_cycle3_Rep1


title: sRNA_Blade_S2_rep2

description: small RNA


title: Human 436_PAC-1

value: GD_RNA_12 and 22


title: sRNA_Blade_S5_rep1

description: small RNA


title: PSPPH_3066_cycle1_Rep1


title: PSPPH_3066_cycle2_Rep1


title: sRNA_Blade_S2_rep1

description: small RNA


title: sRNA_Blade_S3_rep1

description: small RNA


title: Control-1-2

description: processed data file: RNAseq_set1_RPKM.csv


title: Human 436_DMSO-1

value: GD_RNA_11 and 21


title: Human_436_20C_2_H3K27me3

description: ChIP_29_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

data_processing:
Reads were filtered for quality (phred33 score >=30) and length (n>=32) trimming using FASTX Toolkit 0.0.13.1
Filtered reads were aligned to the reference assembly hg19 using bwa v.0.5.9. Only uniquely mapped reads were retained for further analysis. Redundant reads were removed using SAMtools v0.1.18
Number of reads were downsampled to the lowest number of reads of the samples to be compared together
Peaks were called using MACS2.0 with default values (mfold[10,30], p-value 1e-03) and BigWig files were obtained with MACS2.0 default.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig (bw) files showig average reads intensity to be displayed in the genome browser

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody

value: H3K27me3 (Diagenode C15410069)

value: paclitaxel


title: AIMP1-sh2-1

value: HEK293T cells


title: sRNA_Blade_S1_rep2

description: small RNA


title: PSPPH_3048_cycle3_Rep1

value: wide type

value: exponential phase


title: Human_436_20C_2_H3K27ac

description: ChIP_28_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: H3K27ac (Abcam Ab4729)


title: CNOT7-sh-2-2


title: Control-1-1


title: sRNA_Blade_S1_rep1

description: small RNA


title: sRNA_LJ_S5_rep2

description: small RNA

source_name: lamina joint

value: lamina joint


title: AIMP1-sh1-1


title: PSPPH_3048_cycle4_Rep1


title: CNOT7-sh2-1


title: Human_436_20C_2_H3K4me1

description: ChIP_26_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K4me1 (Abcam Ab8895)


title: PSPPH_3048_cycle2_Rep1


title: Human_436_20C_2_input

description: ChIP_25_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: Taxol-resistant


title: PSPPH_3048_cycle1_Rep1


title: sRNA_LJ_S4_rep2

description: small RNA


title: UBAP2L-sh1-1


title: CNOT7-sh1-1


title: sRNA_LJ_S5_rep1

description: small RNA


title: PSPPH_3004_cycle4_Rep1


title: sRNA_LJ_S4_rep1

description: small RNA


title: Human_436_20B_2_H3K27me3

description: ChIP_23_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: Human_436_20B_2_H3K4me3

description: ChIP_21_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K4me3 (Millipore 05-1339)


title: Human_436_20B_2_H3K27ac

description: ChIP_22_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: sRNA_LJ_S3_rep2

description: small RNA


title: PSPPH_3004_cycle3_Rep1


title: CLK3-sh1-2


title: CLK3-sh1-1


title: PSPPH_3004_cycle2_Rep1


title: sRNA_LJ_S3_rep1

description: small RNA


title: sRNA_LJ_S2_rep2

description: small RNA


title: EC_Poly_KO9_2


title: PSPPH_3004_cycle1_Rep1


title: Human_436_20C_2_H3K4me3

description: ChIP_27_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: PSPPH_2733_cycle4_Rep1


title: Human_436_20B_2_input

description: ChIP_19_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: EC_Poly_KO1_2


title: EC_Poly_KO9_1


title: sRNA_LJ_S2_rep1

description: small RNA


title: Human_436_20A_2_H3K27ac

description: ChIP_16_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: PSPPH_2733_cycle3_Rep1


title: Human_436_20A_2_H3K4me3

description: ChIP_15_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: Human_436_20B_2_H3K4me1

description: ChIP_20_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: EC_Poly_KO1_1


title: CNOT7-sh1-2


title: PSPPH_2733_cycle2_Rep1


title: sRNA_LJ_S1_rep1

description: small RNA


title: Human_436_20A_2_H3K27me3

description: ChIP_17_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: EC_Poly_293T_2


title: PSPPH_2733_cycle1_Rep1

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt


title: Human_436_20A_2_H3K4me1

description: ChIP_14_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: sRNA_LJ_S1_rep2

description: small RNA


title: EC_Poly_293T_1


title: PSPPH_2720_cycle4_Rep1


title: sc_male_tail_rep3

city: Irvine

first: Ali

last: Mortazavi

state: CA

address: 2300 Biological Sciences 3

department: Developmental and cell biology

institute: University of California, Irvine

description: PolyA RNA  unstranded, paired-end, read_length= 43 bp

data_processing:
Unstranded, paired-end 43 bp RNA-seq reads for each worm were mapped to the S. carpocapsae genome using Bowtie 1.0.0 with the following options: -X 1500 -a -m 200 --S -- seedlen 25 -n 2 --offrate 1 -p 64 -v 3  (Langmead et al. 2009). After Bowtie, gene expression was quantified with RSEM with the following options: rsem-calculate-expression -- bam -- paired-end. Gene expression for S. carpocapsae were performed as previously described (Lu et al. 2017) and reported in Transcripts Per Million (TPM). We used counts for differential gene expression analysis.
The Transcript per million (TPM) generated by rsem-calculate-expression for S. carpocapsae samples were normalized according to groups using the R package limma (Ritchie et al., 2015) because samples were collected, processed and sequenced in different batches.

organism: Steinernema carpocapsae

source_name: activated in lawn of Xenorhabdus nematophila

growth_protocol: For S.carpocapse as described in Serra L, Chang DZ, Macchietto M, et al. Adapting the Smart-seq2 Protocol for Robust Single Worm RNA-seq. Bio-protocol. 2018;8(4). doi:10.21769/BioProtoc.2729. For C.elegans as described in Brenner S. The genetics of Caenorhabditis elegans. Genetics. 1974;77(1):71-94. http://www.ncbi.nlm.nih.gov/pubmed/4366476.

extract_protocol:
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.
as described in Serra L., Chang D., Macchietto M., Williams K., Murad R., Lu D., *Dillman A.R., & *Mortazavi A. 2018. Adapting the Smart-seq2 protocol for robust single worm RNA-seq. Bio-protocol 8(4): e2729.

treatment_protocol: S. carpocapsae IJs were cultured with Xenorhabdus nematophila and collected at the IJ or young adult stage. C. elegans strain him-8 young adults were grown on Escherichia coli (op50) and collected at young adult stage. C.elegans strain N2 dauers were starved for 16 weeks at 25° C, confirmed phenotypically and collected.

tag: strain

value: ALL

value: wildtype

value: young adult

value: tail


title: EC_Input_KO9_2


title: sc_male_tail_rep2


title: Human_436_DMSO_2_H3K27me3

description: ChIP_5_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: parental taxol-sensitive

value: DMSO


title: PSPPH_2720_cycle3_Rep1


title: EC_Input_KO9_1


title: sc_male_tail_rep1


title: PSPPH_2720_cycle2_Rep1


title: Human_436_DMSO_2_H3K27ac

description: ChIP_4_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: sc_male_head_rep3

value: head


title: PSPPH_2720_cycle1_Rep1


title: sc_male_head_rep1


title: Human_436_DMSO_2_H3K4me3

description: ChIP_3_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: EC_Input_293T_2


title: PSPPH_2693_cycle4_Rep1


title: Human_436_DMSO_2_input

description: ChIP_1_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: Human_436_DMSO_2_H3K4me1

description: ChIP_2_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: EC_Input_KO1_1


title: PSPPH_2693_cycle3_Rep1


title: EC_Input_293T_1


title: sc_male_whole_rep3

value: whole body


title: PSPPH_2693_cycle2_Rep1


title: sc_male_whole_rep2


title: PSPPH_2693_cycle1_Rep1


title: IR-64 Fluoride Stress

city: Kolkata

first: Aditya

last: Banerjee

state: West Bengal

address: 30, Mother Teresa Sarani

department: Biotechnology

country: India

institute: St. Xavier's College

data_processing:
The sequence data was processed using Fastp to remove adapter sequences and low quality reads and single nucleotide repeats. The QC passed reads were further processed to remove rRNA reads using bbduck module of BBMap package and rRNA sequences obtained from Rfam database.
The processed data was used for assemble de novo transcriptome using Trinity v2.8.3 with default parameters. The reads were assembled into 158,411 transcripts/contigs  and 122,337 genes.
The transcripts were translate using TransDecoder and proteins with longest open reading frame from each transcript were retained. The protein sequences were used for  homology search against Uniref100 and Uniprot databases using Diamond’s blastp module with 0.001 and default e value thresholds respectively. The pfam annotations were obtained using hmmscan against pfam database.
The annotation information was used to refine the ORF prediction using the TransDecoder. After refinement only 70,578 transcripts were retained and 68,009 of  transcripts had at least one hit form any of the three data bases (Uniref100, Uniprot and pfam). To obtain KEGG enzyme annotations the proteins were submitted to  KEGG Automate Annotation Server (KAAS). Gene Ontology information was obtained from UnprotKB.
Transcript expression values were obtained as reads counts using FeatureCounts program. The expression values were normalized using DeSeq2 default normalization algorithms (Relative Log Normal Expression). The normalized reads were used for The differential expression analysis was performed after retaining transcripts with > 5 reads in any of the sample. After filtering 38,900 samples were retained and any transcript with absolute log2 fold change 2 or more and pvalue < 0.05 were considered as significantly differentially expressed. Overall 1396 transcripts were significantly differentially expressed and majority of then are over expressed in treated sample when compared to the control.
Genome_build: De novo assembly (Trinity v2.8.3 with default parameters)
Supplementary_files_format_and_content: tab-delimited text files and Read counts mapped to each transcript

source_name: Total seedling

growth_protocol: Seeds of IR-64 were sown in pots containing soilrite and grown in standard greenhouse conditions.

extract_protocol:
Freshly harvested leaves and roots were frozen in liquid nitrogen and total RNA was extracted using TriZol reagent following the standardized protocol of the laboratory. RNA quality and concentration was checked by Bioanalyzer and Qubit spectrophotometer respectively.
RNA libraries were prepared for sequencing using NEB Next ULTRA RNA II library preperation kit for illumina

treatment_protocol: One set of pots were regularly watered with double distilled water (control) and the other set was supplemented with aqeous solution containing 25 mg L-1 NaF.

tag: subspecies

value: Indica

tag: cultivar

value: Shoots and roots (total seedling)

tag: age

value: 25 days

tag: growth medium

value: Soilrite supplemented with 25 mg L-1 NaF

value: Wild type


title: Human_436_20A_2_input

description: ChIP_13_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: paclitaxel


title: Human_436_20C_1_H3K27me3

description: ChIP_29_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: Taxol-resistant

value: H3K27me3 (Diagenode C15410069)


title: Human_436_20C_1_H3K27ac

description: ChIP_28_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K27ac (Abcam Ab4729)


title: sc_male_whole_rep1

value: ALL

value: wildtype


title: PSPPH_2689_cycle4_Rep1

value: wide type

value: exponential phase


title: IR-64 Control

value: Soilrite supplemented with double distilled water


title: EC_Input_KO1_2

value: HEK293T cells


title: sc_female_tail_rep3

value: young adult

value: tail


title: ∆lsd1; cat null hda-1 H3K9me3 ChIP-seq rep2

city: Eugene

first: Eric

middle: U

last: Selker

state: OR

address: 1229 University of Oregon; 1318 Franklin Blvd.

department: Biology, Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are tdf or bigwig files generated using IGV or DeepTools (Ramirez et al., 2016) respectively, using a window size of 25bp.

organism: Neurospora crassa

source_name: germinated conidia

extract_protocol: Cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32oC. Mycelia were washed in PBS prior to crosslinking. Mycelia were cross-linked for 10 min in 0.5% formaldehyde, glycine (125mM final concentration) was added for 5 minutes and tissue was washed with PBS.  Tissue was added to ChIP lysis buffer (50mM Hepes pH 7.5, 90mM NaCl, 1mM EDTA, 1% triton + proteinase inhibitors) and disrupted by sonication for thirty pulses before chromatin was sheared using a Bioruptor (Diagenode) for 15 min with a cycle of 30 sec on followed by 30 sec off, at high power. Lysates were cleared by centrifugation, 1/20th Input was saved, and H3K9me3 antibody was added (3µL) and samples were rotated overnight at 4oC. The next day, equilibrated Protein A/G agarose (Santa Cruz Biotechnology) was added to bind the antibody, incubated for 3 hours at 4˚C, and washed twice in cold ChIP Lysis buffer, once with ChIP Lysis buffer + 0.5M NaCl, once with LiCl buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% NP40), and DNA/protein was eluted with TES buffer (50mM Tris pH 8.0, 10mM EDTA, 1% SDS) and incubated at 65˚C.  Samples (IP and input) were decrosslinked at 65˚C overnight.  The next day, samples were proteinase K treated for 2 hours at 50˚C, and DNA was purified using the QIAquick PCR purification kit and eluted in 30 μl of water.  Approximately 10 ng of DNA was used to generate ChIP-Seq libraries.  Each library was prepared using the NEB Next DNALibrary Prep Kit for Illumina according to the manufacturer’s instructions.  “Invisible” fragments between 250-400 bp were excised and purified using the MinElute gel extraction kit (Qiagen, 28606).  Final libraries were PCR-amplified using one cycle at 98˚C for 30 sec, 10 cycles at 98˚C for 10 sec, 60˚C for 30 sec and 72˚C for 30 sec and a final extension at 72˚C for 5 min.

value: germinated conidia

tag: chip antibody

value: his-3::hda-1*-3xFLAG; delta_lsd1::nat-1; delta_hda-1::hph (*=D263N)


title: Human_436_20C_1_H3K4me3

description: ChIP_27_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K4me3 (Millipore 05-1339)

tag: cell line


title: PSPPH_2689_cycle3_Rep1


title: sc_male_head_rep2

value: head


title: sc_female_tail_rep2


title: Human_436_20C_1_H3K4me1

description: ChIP_26_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: H3K4me1 (Abcam Ab8895)


title: PSPPH_2689_cycle2_Rep1


title: ∆lsd1; cat null hda-1 H3K9me3 ChIP-seq rep1


title: Human_436_20C_1_input

description: ChIP_25_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: Taxol-resistant

value: paclitaxel


title: sc_female_tail_rep1


title: Human_436_20B_1_H3K27me3

description: ChIP_23_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K27me3 (Diagenode C15410069)


title: sc_female_head_rep3

value: ALL


title: PSPPH_2689_cycle1_Rep1


title: catalytic null lsd1 H3K9me3 ChIP-seq rep2


title: PSPPH_2563_cycle4_Rep1


title: catalytic null lsd1 H3K9me3 ChIP-seq rep1


title: sc_female_head_rep2

value: wildtype


title: ∆lsd1; dim-2 cat null H3K9me3 ChIP-seq

data_processing:
ChIP-seq processing: All sequencing reads were mapped to the corrected N. crassa OR74A (NC12 genome) (Galazka et al., 2016) using Bowtie2 (Langmead and Salzberg, 2012). ChIP-seq read coverage was averaged, normalized, and analyzed using tools available from deepTools2 on the open-source platform Galaxy (Afgan et al., 2016). Sequencing tracks are displayed as 25-nt-window bigWig files with the Integrative Genomics Viewer (IGV) (Robinson et al., 2011).
RNA-seq processing: Tools available on Galaxy (Afgan et al., 2018) were used to map mRNA-sequencing reads (intron size < 1kb) (Dobin et al, 2012) against the corrected N. crassa OR74A (NC12) genome (Galazka et al., 2016), count the number of reads per gene (Dobin et al., 2012) and determine differentially expressed genes with DESeq2 (Love et al, 2014).
Bisulfite-seq processing: The BRAT-BW software package (compbio.cs.ucr.edu/brat/; Harris et al, 2012) was used to prepare and map the reads to the N. crassa OR74A (annotation NC12) genome, which was converted to a four stranded reference genome to permit bisulfite mapping. BRAT-BW acgt-count “-B” option cytosine-only files produced for the forward and reverse strand reads were merged. The average 5mC level was determined for 25bp step-wise window size across the genome using the Methpipe program (http://smithlabresearch.org/software/methpipe/). The resulting file was renamed with a “.igv” file extension to allow display on the Integrated Genome Viewer (IGV; www.broadinstitute.org/igv/)
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: ChIP-seq processed data files are bigwig files generated using DeepTools (Ramirez et al., 2016) using a window size of 25bp.
Supplementary_files_format_and_content: RNA-seq processed data files are txt files containing normalized counts for 2 replicates each of wild type (Klocko et al. 2016; GSE82222) and ∆lsd1 and the output file from DESeq2 (Love et al., 2014) with pairwise comparisons of 2 biological replicates from each genotype.
Supplementary_files_format_and_content: Bisulfite-seq processed data files are .igv files displaying the % methylation over 25bp windows where a score of 0 is a DNA region that has no cytosine methylation and a score of 1.0 is DNA where all of the cytosines are methylated in the region.  Values in between 0 and 1.0 represent partial methylation of a region.

value: mat a his-3::dim-2C926A delta_lsd1::nat-1; delta_dim-2::hph


title: Human_436_20B_1_H3K4me3

description: ChIP_21_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: PSPPH_2563_cycle3_Rep1

value: wide type

value: exponential phase


title: sc_female_head_rep1


title: PSPPH_2563_cycle2_Rep1


title: sc_female_whole_rep3

value: whole body


title: Human_436_20B_1_H3K4me1

description: ChIP_20_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: ∆lsd1 N7985 bisulfite-seq

extract_protocol: Cultures were grown in Vogel's medium and 1.5% sucrose (standard minimal medium), shaking for 18 hours at 32˚C. Genomic DNA was isolated using a protocol modified from (Pomraning et al, 2009). Genomic DNA (1µg) was treated with bisulfite and libraries were prepared for sequencing using the NEBNext Ultra DNA Library Prep Kit for Illumina (E7370; NEB) and EpiMark Bisulfite Conversion Kit (E3318; NEB). The library was purified with Agencourt AMPure XP beads (Beckman Coulter), quantified using a Qubit HS Assay (Life Technologies), visualized on the Fragment AnalyzerTM (Advanced Analytical), and sequenced on a Illumina HiSeq 4000

value: mat ? delta_lsd1::hph


title: PSPPH_2563_cycle1_Rep1

description:
all_motifs_pwm_summary.xls
all_TF_PWM_genome_wide_target_sites_filtered_results.txt


title: sc_female_whole_rep2

value: young adult


title: PSPPH_2539_cycle4_Rep1


title: Human_436_20A_1_H3K27me3

description: ChIP_17_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: PSPPH_2539_cycle3_Rep1


title: Human_436_20B_1_H3K27ac

description: ChIP_22_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K27ac (Abcam Ab4729)


title: PSPPH_2539_cycle2_Rep1


title: Human_436_20A_1_H3K27ac

description: ChIP_16_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw


title: ∆lsd1 N7979 bisulfite-seq

value: germinated conidia


title: sc_female_whole_rep1

description: PolyA RNA  unstranded, paired-end, read_length= 43 bp


title: sc_naïve_tail_rep2

source_name: not activated Infective Juvenile(IJ)

value: Infective Juvenile (IJ)

value: tail


title: ∆lsd1 N5555 bisulfite-seq rep2

value: mat a delta_lsd1::hph


title: Human_436_20A_1_H3K4me1

description: ChIP_14_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: H3K4me1 (Abcam Ab8895)


title: Human_436_20A_1_H3K4me3

description: ChIP_15_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: Taxol-resistant

value: H3K4me3 (Millipore 05-1339)

value: paclitaxel


title: PSPPH_2539_cycle1_Rep1


title: sc_naïve_tail_rep1

value: ALL

value: wildtype


title: 750s-to-380_r2_RNA.fastq

city: Los Angeles

middle: Alva

last: Webb

address: 3616 Trousdale Parkway

institute: University of Southern California

description: Cells growing semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years were transferred to the same medium but now under 380 µatm CO2. Cells were allowed to acclimate for 2 weeks (~5 generations) before sampling. Samples for WGBS were taken in the middle of the photoperiod (i.e. midday)

data_processing:
Raw read files were downloaded from the UC San Diego IGM Genomics Center
Trimmomatic version 0.35 was used to quality trim and filter with the following settings: SE -threads 35 -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35.
Quality processed reads were mapped onto Trichodesmium IMS101 genes (per Integrated Microbial Genomes (JGI) annotation) using Bowtie2 v2.2.6 with default settings. Counts per gene were enumerated using the sam2counts.py script (https://github.com/vsbuffalo/sam2counts).
Genome_build: Trichodesmium erythraeum IMS101 (https://img.jgi.doe.gov/cgi-bin/w/main.cgi?section=TaxonDetail&page=taxonDetail&taxon_oid=637000329)
Supplementary_files_format_and_content: Tab-delimited file with raw counts per gene as rows and individual biological replicates as columns

organism: Trichodesmium erythraeum IMS101

source_name: cell population

growth_protocol: See description in the SAMPLES section

extract_protocol:
Cultures were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until RNA extraction.
RNA was extracted with the Ambion MirVana microRNA isolation kit (Thermo Fisher Scientific) in an RNase-free environment in accordance with the manufacturer’s instructions, followed by two incubations with Ambion’s Turbo DNA-free kit to degrade trace amounts of DNA. Then the Ribo-Zero rRNA Removal Kit (Illumina) was used to remove rRNA.
RNA was then submitted to the UC San Diego IGM Genomics Center for library construction and sequencing using the TruSeq Stranded mRNA Library Prep kit (Illumina). Multiplexed libraries were sequenced by using Illumina Hi-Seq4000, yielding single-end 50-bp read libraries.

tag: environment

value: cell culture

tag: co2 concentration

value: 380 µatm

tag: medium

value: Aquil medium w/o fixed nitrogen

tag: location

value: University of Southern California, Los Angeles


title: 750s-to-380_r1_RNA.fastq


title: ∆lsd1; ∆dim-2 H3K9me3 ChIP-seq

tag: genotype

value: mat a delta_lsd1::hph; delta_dim-2::hph

tag: tissue


title: Human_436_20A_1_input

description: ChIP_13_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

tag: cell type

tag: paclitaxel sensitivity

tag: replicate


title: sc_naïve_head_rep3

tag: developmental stage

value: head


title: Human_436_20B_1_input

description: ChIP_19_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

tag: antibody

tag: agent


title: ∆lsd1 N7983 bisulfite-seq

value: mat ? delta_lsd1::hph

value: germinated conidia


title: PPRV -3

city: Yangling

first: Xuefeng

last: Qi

state: Shaanxi

address: Taicheng Road

institute: Northwest A&F University

data_processing:
Filter small RNA:Separate RNA segment of different size by PAGE gel,select18-30 nt stripe and recycle.
3'adaptor ligation:link 5-adenylated,3-blocked single-stranded DNA adapter to 3'of selected small RNAs in step(1).
Reverse primer annealing:The RT primer is added to (2) system,and is crossed to the RNA 3' and excessive free 3' adapter.
5'adaptor ligation:5'adaptor is linked to 5'end of the product in step(3).Since the connection attached to the single-stranded molecule first,but not connected to 3'adaptor and RT primer hybridchain.It greatly reduce the self-ligation.
Strand cDNA synthesis:reverse extend of the RT primer in step(3)to synthetise strand cDNA.
PCR amplification:use high-ping polymerase to amplify cDNA,enrich cDNA with both 3'and 5'adaptor.
Library fragment selection:Separate PCR product of100~120bp by PAGE gel to eliminate primer-dimer and other byproducts.
Genome_build: Library quantitative and pooling cyclization.
Supplementary_files_format_and_content: XLSX

organism: Capra aegagrus

source_name: Peripheral blood mononuclear cells

growth_protocol: Total RNA extracted using Trizol following manufacturer's instructions

extract_protocol: none provided by the submitter

treatment_protocol: Peripheral blood mononuclear cells were infected with Nigeria 75/1 vaccine virus for 24h.

value: Peripheral blood mononuclear cells

tag: treatment


title: Human_436_DMSO_1_H3K27me3

description: ChIP_5_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: parental taxol-sensitive

value: H3K27me3 (Diagenode C15410069)

value: DMSO


title: 750-selected_r2_RNA.fastq

description: Cells were grown semi-continuously in Aquil medium with replete nutrients in 750 µatm CO2 for 4.5 years. Samples for RNA were taken in the middle of the photoperiod (i.e. midday)

value: 750 µatm


title: PPRV -2

value: Peripheral blood mononuclear cells were infected with Nigeria 75/1 vaccine virus for 24h.


title: Human_436_DMSO_1_H3K27ac

description: ChIP_4_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: H3K27ac (Abcam Ab4729)


title: 750-selected_r1_RNA.fastq


title: sc_naïve_tail_rep3

tag: strain

value: ALL

value: wildtype

value: Infective Juvenile (IJ)

value: tail


title: Human_436_DMSO_1_H3K4me3

description: ChIP_3_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: H3K4me3 (Millipore 05-1339)


title: sc_naïve_whole_rep3

value: whole body


title: sc_naïve_head_rep1

value: head


title: Control-3

value: untreated


title: PSPPH_2469_cycle4_Rep1

value: wide type

tag: growth phase

value: exponential phase


title: sc_naïve_whole_rep2


title: Human_436_DMSO_1_input

description: ChIP_1_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: parental taxol-sensitive


title: sc_naïve_whole_rep1


title: sc_naïve_head_rep2


title: Control-1

value: Peripheral blood mononuclear cells


title: 20E_smallRNA

status: Public on Aug 17 2020

city: Amherst

first: Lawrence

middle: M

last: Schwartz

state: MA

address: 211 Morrill Science Center, 611 North Pleasant Street

department: Department of Biology

institute: University of Massachusetts

data_processing:
For RNA-seq analysis, reads in each RNA-seq library were mapped to the reference Manduca genome (Msex 1.0) using the TopHat2 (version 2.0.10) allowing 2 mismatches (“-v 2”). To detect transposon expression, we allowed reads to map to multiple locations (”-g 45,000”) by taking into account 44,487 copies of SINE families in M. sexta. All reads were apportioned by the number of times mapped to the genome. RPKM values for each gene and transposon were calculated after mapping.
For small RNA-seq analysis, adapter sequences (5´-CTGTAGGCACCAT-3´ for small RNA-seq, 5´-TGGAATTCTCGGG-3´ for oxidized small RNA-seq) were removed from the 3´-ends of the reads. Reads shorter than 18nt were discarded, and the remaining reads were collapsed. The collapsed reads were aligned to the Msex 1.0 genome assembly using Bowtie (version 1.0.0) without mismatch. To identify potential piRNAs, small RNAs that were longer than 25 nt and not annotated as miRNAs or other non-coding RNAs were extracted as piRNAs. The reads of piRNAs that mapped to multiple loci in the genome were apportioned over these loci, and piRNA reads were normalized by the total number of genome mapping reads excluded other non-coding RNAs (rRNA, tRNA etc.).
Genome_build: Msex1.0
Supplementary_files_format_and_content: RNA-seq: tab-delimited files containing mapped read counts for each gene and transposon locus
Supplementary_files_format_and_content: small RNA-seq: tab-delimited files containing collapsed small RNA sequences

organism: Manduca sexta

source_name: intersegmental muscle

extract_protocol:
Intersegmental muscles of 3-4 animals per developmental time point (eight time points in total: days 13, 14, 15, 16, 17, 18, and 1-hour post-eclosion (PE); plus 20-hydroxyecdysone injection on day 17: 20E) were homogenized and total RNA was isolated using a mirVana RNA Isolation kit (Life Technologies).
For RNA-seq library construction, directional and random primed cDNA libraries were constructed with poly(A)+ RNA, analyzed with a Bioanalyzer (Agilent Technologies; Santa Clara, CA) and 50 nt single-end sequencing was performed. We prepared three biological replicates of RNA-seq libraries for 7 timepoints (day 13-18, and 20E). For small RNA-seq library construction, 50 ug of total RNA was fractionated by 15% urea polyacrylamide gel electrophoresis and the 18-30 nt fraction extracted for library construction. 3´ and 5´ adaptors were ligated to the small RNA and the cDNA reverse transcribed and PCR amplified. The libraries were purified by polyacrylamide gel electrophoresis, and subjected to 50 nt single-end sequencing on an Illumina HiSeq™ 2000 (San Diego, CA) by Beijing Genomics Institute (Hong Kong). For oxidized small RNA-seq library construction, we performed the β-elimination protocol (Ghildiyal et al. 2008 Science) and sequenced the library at the Deep Sequencing Core Facility at the UMass Medical School.

value: intersegmental muscle during pupal-adult development

value: 20-hydroxyecdysone treated day 17


title: D16_smallRNA

value: day 16


title: D17_smallRNA

value: day 17


title: PE_smallRNA

value: 1-hour post-eclosion


title: PPRV -1

value: Peripheral blood mononuclear cells were infected with Nigeria 75/1 vaccine virus for 24h.


title: D15_smallRNA

value: day 15


title: D18_smallRNA

value: day 18


title: Human_436_DMSO_1_H3K4me1

description: ChIP_2_Concat.fastq.gz.output.hg19.bam.downsamp.bam.bdgcmp.sorted.bedgraph.bw

value: TNBC

value: H3K4me1 (Abcam Ab8895)

value: DMSO


title: p53

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Single-stranded DNA libraries containing transcription factor binding site sequences and all possible single base variants were commercially synthesized on microarray chips (Agilent). Double-stranded DNA was generated on the chip by hybridization with the wild-type reverse complement oligonucleotides in solution (variant complements were absent from the hybridization solution). For each wild-type sequence, the solution contained ~2.5 μM (large excess) unlabeled HPLC-purified oligonucleotides and ~0.25 μM FAM/Cy3-labelled HPLC-purified oligonucleotides (Integrated DNA Technologies). The reaction buffer mixture for the hybridization step was 100 μl 10x reaction buffer (260 mM Tris-HCl, pH 9.5, 65 mM MgCl2) in a total volume of 1000 μl, similarly to 20. The chip was incubated with reaction mixture in a hybridization oven using a pre-warmed stainless-steel chamber and gasket cover slip. After a 5-hour incubation (85 °C for 10 min, 75 °C for 10 min, 65 °C for 60 min, 60 °C for 120 min, and 55 °C for 100 min), the hybridization chamber was disassembled in a glass staining dish in 500 ml phosphate buffered saline (PBS) / 0.01% Triton X-100 at 37°C. The chip was transferred to a second staining dish, washed for 10 min in PBS / 0.01% Triton X-100 at 37°C, washed once more for 3 min in PBS at room temperature, similarly to 20. The fluorescent signal (Cy3/FAM) of hybridized oligonucleotides was measured using a GenePix 4400A microarray scanner to confirm that the hybridization was successful and reproducible, and that no significant cross-hybridization occurred. Protein binding and antibody steps were performed similarly to protein-binding microarray (PBM) assays (Berger et al, Nature Biotechnology 2006). The fluorescent signal of bound transcription factor for each DNA spot was measured using a GenePix 4400A microarray scanner.

scan_protocol: Protein-bound arrays were scanned to detect Alexa-488-conjugated or Alexa-647-conjugated (detected at 635nm wavelength) antibody using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots of interest. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescent signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots.

label: Alexa 488

molecule: protein

organism: synthetic construct

source_name: Human p53

label_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manucript, for each tested protein.

tag: transcription factor

tag: protein concentration

value: Protein concentration:100nM


title: D13_oxidized_smallRNA

value: day 13


title: 20E_mRNA_rep2

molecule: polyA RNA


title: D13_smallRNA


title: D14_smallRNA

value: day 14


title: 20E_mRNA_rep3


title: Control-2

value: untreated


title: GR

source_name: Human GR

extract_protocol: Cell growth, protein extraction, and protein labelling protocols are described in detail in the manucript, for each tested protein.

value: GR


title: Ets1

source_name: Human Ets1

value: Protein concentration:15nM


title: D17_mRNA_rep3

value: intersegmental muscle during pupal-adult development


title: D17_mRNA_rep1


title: D18_mRNA_rep1


title: D18_mRNA_rep3


title: D17_mRNA_rep2


title: D18_mRNA_rep2


title: Cbf1

source_name: Yeast Cbf1

value: Protein concentration:8000nM


title: D16_mRNA_rep2

value: day 16


title: D16_mRNA_rep1


title: 20E_mRNA_rep1

value: 20-hydroxyecdysone treated day 17


title: D15_mRNA_rep3


title: D8-BDD2-C8+_94

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
The libraries were mapped to hg19 genome using STAR aligner allowing up to 3 mismatches and discarding any read mapping to more than one loci in the genome.
Gene quantification was performed using cuffquant and libraries were normalized using cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text table cotaining the FPKM values of all genes in each library

source_name: BJ Fibroblasts

growth_protocol: Reprogramming cells were cultured with BJ medium, containing 10% FBS supplemented with DMEM high gucose medium,at the first five days. At day 5, reprogramming cells were trypsinized to single cells and 50,000 of which were replated onto matrigel coated plates. From day 5 onwards, reprogramming cells were cultured using hES medium, containing 20% KOSR supplemented with DMEM/F12.

extract_protocol:
Cells were harvested and single cell RNA-seq libraries were prepared using STRT-seq protocol (Islam et al., 2014).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: BJ cells were infected with O2S and K2M lentivirus in the presence of 4 mg/mL polybrene. The supernatant with lenvirus was replaced with BJ medium on the following day. The dye was added at day 8 at 0.05 micromole final concentration and the cells were sorted based on the intensity of the dye.

value: BJ fibroblasts 8 days post induced viral expression of OSKM

tag: bdd2-c8 enrichment

value: Positive


title: D15_mRNA_rep2

value: day 15


title: D13_mRNA_rep3


title: D15_mRNA_rep1


title: D14_mRNA_rep2


title: D14_mRNA_rep3


title: D13_mRNA_rep2


title: D14_mRNA_rep1


title: D8-BDD2-C8+_96


title: D8-BDD2-C8+_92


title: D8-BDD2-C8+_93


title: D13_mRNA_rep1


title: D8-BDD2-C8+_95


title: D8-BDD2-C8+_91


title: D8-BDD2-C8+_90


title: D8-BDD2-C8+_9


title: D8-BDD2-C8+_85


title: D8-BDD2-C8+_87


title: D8-BDD2-C8+_89


title: D8-BDD2-C8+_86


title: D8-BDD2-C8+_88


title: D8-BDD2-C8+_83


title: D8-BDD2-C8+_82


title: D8-BDD2-C8+_84


title: D16_mRNA_rep3


title: D8-BDD2-C8+_81


title: D8-BDD2-C8+_80


title: D8-BDD2-C8+_8


title: D8-BDD2-C8+_78


title: D8-BDD2-C8+_72


title: D8-BDD2-C8+_74


title: D8-BDD2-C8+_77


title: D8-BDD2-C8+_73


title: D8-BDD2-C8+_76


title: D8-BDD2-C8+_75


title: D8-BDD2-C8+_67


title: D8-BDD2-C8+_65


title: D8-BDD2-C8+_66


title: D8-BDD2-C8+_70


title: D8-BDD2-C8+_61


title: D8-BDD2-C8+_69


title: D8-BDD2-C8+_60


title: D8-BDD2-C8+_59


title: D8-BDD2-C8+_68


title: D8-BDD2-C8+_7


title: D8-BDD2-C8+_57


title: D8-BDD2-C8+_56


title: D8-BDD2-C8+_55


title: D8-BDD2-C8+_58


title: D8-BDD2-C8+_54


title: D8-BDD2-C8+_64


title: D8-BDD2-C8+_63


title: D8-BDD2-C8+_53


title: D8-BDD2-C8+_50


title: D8-BDD2-C8+_52


title: D8-BDD2-C8+_5


title: D8-BDD2-C8+_49


title: D8-BDD2-C8+_6


title: D8-BDD2-C8+_79


title: D8-BDD2-C8+_48


title: D8-BDD2-C8+_45


title: D8-BDD2-C8+_44


title: D8-BDD2-C8+_47


title: D8-BDD2-C8+_42


title: D8-BDD2-C8+_46


title: D8-BDD2-C8+_40


title: D8-BDD2-C8+_43


title: D8-BDD2-C8+_41


title: D8-BDD2-C8+_4


title: D8-BDD2-C8+_39


title: D8-BDD2-C8+_38


title: D8-BDD2-C8+_37


title: D8-BDD2-C8+_35


title: D8-BDD2-C8+_36


title: D8-BDD2-C8+_34


title: D8-BDD2-C8+_51


title: D8-BDD2-C8+_71


title: D8-BDD2-C8+_32


title: D8-BDD2-C8+_33


title: D8-BDD2-C8+_30


title: D8-BDD2-C8+_62


title: D8-BDD2-C8+_29


title: D8-BDD2-C8+_3


title: D8-BDD2-C8+_27


title: D8-BDD2-C8+_31


title: D8-BDD2-C8+_24


title: D8-BDD2-C8+_25


title: D8-BDD2-C8+_28


title: D8-BDD2-C8+_23


title: D8-BDD2-C8+_21


title: D8-BDD2-C8+_20


title: D8-BDD2-C8+_22


title: D8-BDD2-C8+_17


title: D8-BDD2-C8+_2


title: D8-BDD2-C8+_15


title: D8-BDD2-C8+_14


title: D8-BDD2-C8+_11


title: D8-BDD2-C8+_10


title: D8-BDD2-C8+_12


title: D8-BDD2-C8+_13


title: D8-BDD2-C8+_26


title: D8-BDD2-C8-_96

value: Negative


title: D8-BDD2-C8+_1


title: D8-BDD2-C8-_94


title: D8-BDD2-C8-_95


title: D8-BDD2-C8-_93


title: D8-BDD2-C8-_90


title: D8-BDD2-C8-_91


title: D8-BDD2-C8-_92


title: D8-BDD2-C8+_18


title: D8-BDD2-C8-_89


title: D8-BDD2-C8-_84


title: D8-BDD2-C8-_88


title: D8-BDD2-C8-_87


title: D8-BDD2-C8-_80


title: D8-BDD2-C8-_81


title: D8-BDD2-C8+_19


title: D8-BDD2-C8-_86


title: D8-BDD2-C8-_83


title: D8-BDD2-C8-_8


title: D8-BDD2-C8-_82


title: D8-BDD2-C8+_16


title: D8-BDD2-C8-_76


title: D8-BDD2-C8-_74


title: D8-BDD2-C8-_9


title: D8-BDD2-C8-_78


title: D8-BDD2-C8-_77


title: D8-BDD2-C8-_85


title: D8-BDD2-C8-_7


title: D8-BDD2-C8-_68


title: D8-BDD2-C8-_65


title: D8-BDD2-C8-_73


title: D8-BDD2-C8-_64


title: D8-BDD2-C8-_70


title: D8-BDD2-C8-_75


title: D8-BDD2-C8-_72


title: D8-BDD2-C8-_71


title: D8-BDD2-C8-_67


title: D8-BDD2-C8-_69


title: D8-BDD2-C8-_61


title: D8-BDD2-C8-_66


title: D8-BDD2-C8-_79


title: D8-BDD2-C8-_57


title: D8-BDD2-C8-_63


title: D8-BDD2-C8-_53


title: D8-BDD2-C8-_54


title: D8-BDD2-C8-_62


title: D8-BDD2-C8-_60


title: D8-BDD2-C8-_59


title: D8-BDD2-C8-_58


title: D8-BDD2-C8-_56


title: D8-BDD2-C8-_52


title: D8-BDD2-C8-_48


title: D8-BDD2-C8-_51


title: D8-BDD2-C8-_50


title: D8-BDD2-C8-_5


title: D8-BDD2-C8-_6


title: D8-BDD2-C8-_49


title: D8-BDD2-C8-_43


title: D8-BDD2-C8-_40


title: D8-BDD2-C8-_4


title: D8-BDD2-C8-_47


title: D8-BDD2-C8-_44


title: D8-BDD2-C8-_41


title: D8-BDD2-C8-_55


title: D8-BDD2-C8-_45


title: D8-BDD2-C8-_37


title: D8-BDD2-C8-_42


title: D8-BDD2-C8-_46


title: D8-BDD2-C8-_39


title: D8-BDD2-C8-_33


title: D8-BDD2-C8-_38


title: D8-BDD2-C8-_32


title: D8-BDD2-C8-_36


title: D8-BDD2-C8-_35


title: D8-BDD2-C8-_3


title: D8-BDD2-C8-_30


title: D8-BDD2-C8-_34


title: D8-BDD2-C8-_27


title: D8-BDD2-C8-_31


title: D8-BDD2-C8-_25


title: D8-BDD2-C8-_29


title: D8-BDD2-C8-_24


title: D8-BDD2-C8-_23


title: D8-BDD2-C8-_20


title: D8-BDD2-C8-_22


title: D8-BDD2-C8-_2


title: D8-BDD2-C8-_26


title: D8-BDD2-C8-_19


title: D8-BDD2-C8-_18


title: D8-BDD2-C8-_16


title: D8-BDD2-C8-_17


title: D8-BDD2-C8-_14


title: D8-BDD2-C8-_12


title: D8-BDD2-C8-_13


title: D8-BDD2-C8-_15


title: D8-BDD2-C8-_11


title: D8-BDD2-C8-_1


title: D8-BDD2-C8-_10


title: D16_TRA-1-60-negative_mRNA_92

data_processing:
Reads were aligned to hg19 genome assembly using STAR aligner. Reads that uniquely map to hg19 and contain less than 3 mismatches were kept for further Processing. Cells that showed below 10000 uniquely mapped reads were filtered out.
Gene quantification was performed using Cuffquant.
Expression levels were then normalized using Cuffnorm.
Genome_build: hg19
Supplementary_files_format_and_content: Tables containing normalized expression levels (FPKM) of genes in high quality scRNA-Seq libraries.

growth_protocol: BJ fibroblasts were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies).

extract_protocol:
Cells were trypsinized and single cell suspensions were harvested for STRT seq Scripts run using C1 Fluidigm mRNA-seq chips (10-17um).
cDNA is harvesed from Fluidigm chips, and concentration of cDNA is measured by high sensitivity bioanalyzer chips and diluted to required range of cDNA for following library preparation steps. cDNA libraries were prepared using Nextera XT DNA Library Preparation Kit (FC-131-1096) following the manufacture's instruction.
Single-cell

tag: cell line

value: BJ Fibroblasts

value: BJ fibroblasts 16 days post induced viral expression of OSKM


title: D16_TRA-1-60-negative_mRNA_94


title: D16_TRA-1-60-negative_mRNA_93


title: D16_TRA-1-60-negative_mRNA_96


title: D16_TRA-1-60-negative_mRNA_95


title: D16_TRA-1-60-negative_mRNA_91


title: D16_TRA-1-60-negative_mRNA_90


title: D8-BDD2-C8-_28


title: D8-BDD2-C8-_21


title: D16_TRA-1-60-negative_mRNA_86


title: D16_TRA-1-60-negative_mRNA_85


title: D16_TRA-1-60-negative_mRNA_89


title: D16_TRA-1-60-negative_mRNA_80


title: D16_TRA-1-60-negative_mRNA_81


title: D16_TRA-1-60-negative_mRNA_88


title: D16_TRA-1-60-negative_mRNA_87


title: D16_TRA-1-60-negative_mRNA_77


title: D16_TRA-1-60-negative_mRNA_84


title: D16_TRA-1-60-negative_mRNA_74


title: D16_TRA-1-60-negative_mRNA_82


title: D16_TRA-1-60-negative_mRNA_78


title: D16_TRA-1-60-negative_mRNA_83


title: D16_TRA-1-60-negative_mRNA_73


title: D16_TRA-1-60-negative_mRNA_72


title: D16_TRA-1-60-negative_mRNA_79


title: D16_TRA-1-60-negative_mRNA_70


title: D16_TRA-1-60-negative_mRNA_76


title: D16_TRA-1-60-negative_mRNA_75


title: D16_TRA-1-60-negative_mRNA_65


title: D16_TRA-1-60-negative_mRNA_63


title: D16_TRA-1-60-negative_mRNA_62


title: D16_TRA-1-60-negative_mRNA_69


title: D16_TRA-1-60-negative_mRNA_71


title: D16_TRA-1-60-negative_mRNA_67


title: D16_TRA-1-60-negative_mRNA_66


title: D16_TRA-1-60-negative_mRNA_59


title: D16_TRA-1-60-negative_mRNA_64


title: D16_TRA-1-60-negative_mRNA_61


title: D16_TRA-1-60-negative_mRNA_58


title: D16_TRA-1-60-negative_mRNA_56


title: D16_TRA-1-60-negative_mRNA_55


title: D16_TRA-1-60-negative_mRNA_57


title: D16_TRA-1-60-negative_mRNA_54


title: D16_TRA-1-60-negative_mRNA_50


title: D16_TRA-1-60-negative_mRNA_48


title: D16_TRA-1-60-negative_mRNA_51


title: D16_TRA-1-60-negative_mRNA_46


title: D16_TRA-1-60-negative_mRNA_47


title: D16_TRA-1-60-negative_mRNA_45


title: D16_TRA-1-60-negative_mRNA_68


title: D16_TRA-1-60-negative_mRNA_43


title: D16_TRA-1-60-negative_mRNA_42


title: D16_TRA-1-60-negative_mRNA_41


title: D16_TRA-1-60-negative_mRNA_60


title: D16_TRA-1-60-negative_mRNA_40


title: D16_TRA-1-60-negative_mRNA_38


title: D16_TRA-1-60-negative_mRNA_39


title: D16_TRA-1-60-negative_mRNA_34


title: D16_TRA-1-60-negative_mRNA_35


title: D16_TRA-1-60-negative_mRNA_36


title: D16_TRA-1-60-negative_mRNA_29


title: D16_TRA-1-60-negative_mRNA_32


title: D16_TRA-1-60-negative_mRNA_49


title: D16_TRA-1-60-negative_mRNA_53


title: D16_TRA-1-60-negative_mRNA_30


title: D16_TRA-1-60-negative_mRNA_52


title: D16_TRA-1-60-negative_mRNA_31


title: D16_TRA-1-60-negative_mRNA_25


title: D16_TRA-1-60-negative_mRNA_26


title: D16_TRA-1-60-negative_mRNA_28


title: D16_TRA-1-60-negative_mRNA_44


title: D16_TRA-1-60-negative_mRNA_27


title: D16_TRA-1-60-negative_mRNA_24


title: D16_TRA-1-60-negative_mRNA_21


title: D16_TRA-1-60-negative_mRNA_23


title: D16_TRA-1-60-negative_mRNA_22


title: D16_TRA-1-60-negative_mRNA_17


title: D16_TRA-1-60-negative_mRNA_16


title: D16_TRA-1-60-negative_mRNA_14


title: D16_TRA-1-60-negative_mRNA_18


title: D16_TRA-1-60-negative_mRNA_37


title: D16_TRA-1-60-negative_mRNA_33


title: D16_TRA-1-60-negative_mRNA_15


title: D16_TRA-1-60-negative_mRNA_11


title: D16_TRA-1-60-negative_mRNA_12


title: D16_TRA-1-60-negative_mRNA_10


title: D16_TRA-1-60-negative_mRNA_9


title: D16_TRA-1-60-negative_mRNA_7


title: D16_TRA-1-60-negative_mRNA_8


title: D16_TRA-1-60-negative_mRNA_5


title: D16_TRA-1-60-negative_mRNA_4


title: D16_TRA-1-60-negative_mRNA_3


title: D16_TRA-1-60-negative_mRNA_6


title: D16_TRA-1-60-positve_mRNA_96


title: D16_TRA-1-60-positve_mRNA_95


title: D16_TRA-1-60-negative_mRNA_20


title: D16_TRA-1-60-negative_mRNA_1


title: D16_TRA-1-60-positve_mRNA_92


title: D16_TRA-1-60-negative_mRNA_19


title: D16_TRA-1-60-positve_mRNA_93


title: D16_TRA-1-60-positve_mRNA_91


title: D16_TRA-1-60-positve_mRNA_87


title: D16_TRA-1-60-positve_mRNA_89


title: D16_TRA-1-60-positve_mRNA_90


title: D16_TRA-1-60-negative_mRNA_13


title: D16_TRA-1-60-positve_mRNA_88


title: D16_TRA-1-60-positve_mRNA_85


title: D16_TRA-1-60-positve_mRNA_86


title: D16_TRA-1-60-positve_mRNA_83


title: D16_TRA-1-60-positve_mRNA_84


title: D16_TRA-1-60-positve_mRNA_82


title: D16_TRA-1-60-positve_mRNA_81


title: D16_TRA-1-60-negative_mRNA_2


title: D16_TRA-1-60-positve_mRNA_79


title: D16_TRA-1-60-positve_mRNA_80


title: D16_TRA-1-60-positve_mRNA_74


title: D16_TRA-1-60-positve_mRNA_77


title: D16_TRA-1-60-positve_mRNA_94


title: D16_TRA-1-60-positve_mRNA_76


title: D16_TRA-1-60-positve_mRNA_73


title: D16_TRA-1-60-positve_mRNA_75


title: D16_TRA-1-60-positve_mRNA_78


title: D16_TRA-1-60-positve_mRNA_70


title: D16_TRA-1-60-positve_mRNA_72


title: D16_TRA-1-60-positve_mRNA_67


title: D16_TRA-1-60-positve_mRNA_71


title: D16_TRA-1-60-positve_mRNA_68


title: D16_TRA-1-60-positve_mRNA_69


title: D16_TRA-1-60-positve_mRNA_65


title: D16_TRA-1-60-positve_mRNA_64


title: D16_TRA-1-60-positve_mRNA_63


title: D16_TRA-1-60-positve_mRNA_62


title: D16_TRA-1-60-positve_mRNA_61


title: D16_TRA-1-60-positve_mRNA_59


title: D16_TRA-1-60-positve_mRNA_60


title: D16_TRA-1-60-positve_mRNA_58


title: D16_TRA-1-60-positve_mRNA_57


title: D16_TRA-1-60-positve_mRNA_54


title: D16_TRA-1-60-positve_mRNA_53


title: D16_TRA-1-60-positve_mRNA_55


title: D16_TRA-1-60-positve_mRNA_52


title: D16_TRA-1-60-positve_mRNA_50


title: D16_TRA-1-60-positve_mRNA_51


title: D16_TRA-1-60-positve_mRNA_49


title: D16_TRA-1-60-positve_mRNA_47


title: D16_TRA-1-60-positve_mRNA_45


title: D16_TRA-1-60-positve_mRNA_46


title: D16_TRA-1-60-positve_mRNA_66


title: D16_TRA-1-60-positve_mRNA_41


title: D16_TRA-1-60-positve_mRNA_43


title: D16_TRA-1-60-positve_mRNA_42


title: D16_TRA-1-60-positve_mRNA_39


title: D16_TRA-1-60-positve_mRNA_40


title: D16_TRA-1-60-positve_mRNA_38


title: D16_TRA-1-60-positve_mRNA_37


title: D16_TRA-1-60-positve_mRNA_36


title: D16_TRA-1-60-positve_mRNA_35


title: D16_TRA-1-60-positve_mRNA_34


title: D16_TRA-1-60-positve_mRNA_56


title: D16_TRA-1-60-positve_mRNA_33


title: D16_TRA-1-60-positve_mRNA_32


title: D16_TRA-1-60-positve_mRNA_31


title: D16_TRA-1-60-positve_mRNA_30


title: D16_TRA-1-60-positve_mRNA_28


title: D16_TRA-1-60-positve_mRNA_27


title: D16_TRA-1-60-positve_mRNA_25


title: D16_TRA-1-60-positve_mRNA_26


title: D16_TRA-1-60-positve_mRNA_23


title: D16_TRA-1-60-positve_mRNA_44


title: D16_TRA-1-60-positve_mRNA_22


title: D16_TRA-1-60-positve_mRNA_18


title: D16_TRA-1-60-positve_mRNA_15


title: D16_TRA-1-60-positve_mRNA_14


title: D16_TRA-1-60-positve_mRNA_16


title: D16_TRA-1-60-positve_mRNA_20


title: D16_TRA-1-60-positve_mRNA_24


title: D16_TRA-1-60-positve_mRNA_48


title: D16_TRA-1-60-positve_mRNA_19


title: D16_TRA-1-60-positve_mRNA_21


title: D16_TRA-1-60-positve_mRNA_29


title: D16_TRA-1-60-positve_mRNA_8


title: D16_TRA-1-60-positve_mRNA_10


title: D16_TRA-1-60-positve_mRNA_17


title: D16_TRA-1-60-positve_mRNA_4


title: D16_TRA-1-60-positve_mRNA_9


title: LnCaP_OSMI2_Replicate2

value: LnCaP

value: OSMI2 treated


title: D16_TRA-1-60-positve_mRNA_3


title: D16_TRA-1-60-positve_mRNA_13


title: D16_TRA-1-60-positve_mRNA_1


title: D16_TRA-1-60-positve_mRNA_12


title: D16_TRA-1-60-positve_mRNA_6


title: D16_TRA-1-60-positve_mRNA_7


title: D16_TRA-1-60-positve_mRNA_11


title: D8_mRNA_95


title: D8_mRNA_90


title: D8_mRNA_88


title: D8_mRNA_89


title: D8_mRNA_87


title: D16_TRA-1-60-positve_mRNA_5


title: D8_mRNA_81


title: D8_mRNA_83


title: D8_mRNA_84


title: D16_TRA-1-60-positve_mRNA_2


title: D8_mRNA_94


title: D8_mRNA_93


title: D8_mRNA_82


title: D8_mRNA_92


title: D8_mRNA_74


title: D8_mRNA_85


title: D8_mRNA_75


title: D8_mRNA_76


title: D8_mRNA_72


title: D8_mRNA_79


title: D8_mRNA_80


title: D8_mRNA_77


title: D8_mRNA_69


title: D8_mRNA_96


title: D8_mRNA_66


title: D8_mRNA_73


title: D8_mRNA_71


title: D8_mRNA_62


title: DDX6-sh1-1

description:
processed data file: RNAseq_set2_RPKM.csv
The control samples are Control-2-1/ Control-2-2

value: HEK293T cells


title: D8_mRNA_61


title: D8_mRNA_91


title: D8_mRNA_70


title: D8_mRNA_68


title: D8_mRNA_86


title: D8_mRNA_65


title: D8_mRNA_78


title: D8_mRNA_59


title: D8_mRNA_58


title: D8_mRNA_54


title: D8_mRNA_56


title: D8_mRNA_57


title: D8_mRNA_60


title: D8_mRNA_52


title: D8_mRNA_63


title: D8_mRNA_53


title: D8_mRNA_49


title: D8_mRNA_55


title: D8_mRNA_67


title: D8_mRNA_45


title: D8_mRNA_48


title: D8_mRNA_51


title: D8_mRNA_47


title: D8_mRNA_64


title: D8_mRNA_46


title: D8_mRNA_37


title: D8_mRNA_43


title: D8_mRNA_42


title: D8_mRNA_39


title: D8_mRNA_40


title: D8_mRNA_36


title: D8_mRNA_38


title: D8_mRNA_44


title: D8_mRNA_34


title: D8_mRNA_50


title: D8_mRNA_41


title: D8_mRNA_32


title: D8_mRNA_33


title: D8_mRNA_31


title: D8_mRNA_29


title: D8_mRNA_30


title: D8_mRNA_28


title: D8_mRNA_27


title: D8_mRNA_25


title: D8_mRNA_23


title: D8_mRNA_22


title: D8_mRNA_21


title: D8_mRNA_20


title: D8_mRNA_19


title: D8_mRNA_26


title: D8_mRNA_17


title: D8_mRNA_18


title: D8_mRNA_15


title: D8_mRNA_35


title: D8_mRNA_14


title: D8_mRNA_16


title: D8_mRNA_12


title: D8_mRNA_11


title: D8_mRNA_13


title: D8_mRNA_10


title: D8_mRNA_6


title: D8_mRNA_5


title: D8_mRNA_9


title: D8_mRNA_8


title: D8_mRNA_7


title: D8_mRNA_3


title: D8_mRNA_4


title: D8_mRNA_2


title: D8_mRNA_24


title: D8_mRNA_1


title: D2_mRNA_94

value: BJ fibroblasts 2 days post induced viral expression of OSKM


title: D2_mRNA_95


title: D2_mRNA_91


title: D2_mRNA_92


title: D2_mRNA_90


title: D2_mRNA_88


title: D2_mRNA_87


title: D2_mRNA_89


title: D2_mRNA_86


title: D2_mRNA_85


title: D2_mRNA_84


title: D2_mRNA_81


title: D2_mRNA_83


title: D2_mRNA_79


title: D2_mRNA_82


title: D2_mRNA_80


title: D2_mRNA_78


title: D2_mRNA_77


title: D2_mRNA_76


title: D2_mRNA_75


title: D2_mRNA_93


title: D2_mRNA_72


title: D2_mRNA_71


title: D2_mRNA_74


title: D2_mRNA_68


title: D2_mRNA_70


title: D2_mRNA_69


title: D2_mRNA_65


title: D2_mRNA_66


title: D2_mRNA_64


title: D2_mRNA_61


title: D2_mRNA_67


title: D2_mRNA_63


title: D2_mRNA_58


title: D2_mRNA_57


title: D2_mRNA_60


title: D2_mRNA_59


title: D2_mRNA_56


title: D2_mRNA_54


title: D2_mRNA_52


title: D2_mRNA_53


title: D2_mRNA_50


title: D2_mRNA_55


title: D2_mRNA_49


title: D2_mRNA_73


title: D2_mRNA_51


title: D2_mRNA_47


title: D2_mRNA_44


title: D2_mRNA_45


title: D2_mRNA_48


title: D2_mRNA_62


title: D2_mRNA_43


title: D2_mRNA_46


title: D2_mRNA_42


title: D2_mRNA_40


title: D2_mRNA_96


title: D2_mRNA_37


title: D2_mRNA_41


title: D2_mRNA_36


title: D2_mRNA_39


title: D2_mRNA_35


title: D2_mRNA_32


title: D2_mRNA_31


title: D2_mRNA_33


title: D2_mRNA_30


title: D2_mRNA_29


title: D2_mRNA_28


title: D2_mRNA_27


title: D2_mRNA_25


title: D2_mRNA_22


title: D2_mRNA_24


title: D2_mRNA_23


title: D2_mRNA_21


title: D2_mRNA_20


title: D2_mRNA_19


title: D2_mRNA_38


title: D2_mRNA_16


title: D2_mRNA_17


title: D2_mRNA_18


title: D2_mRNA_14


title: D2_mRNA_12


title: D2_mRNA_13


title: D2_mRNA_10


title: D2_mRNA_11


title: D2_mRNA_34


title: D2_mRNA_5


title: D2_mRNA_6


title: D2_mRNA_4


title: D2_mRNA_26


title: D2_mRNA_3


title: D2_mRNA_7


title: D2_mRNA_2


title: BJ_mRNA_94

value: WT


title: BJ_mRNA_96


title: BJ_mRNA_91


title: BJ_mRNA_92


title: BJ_mRNA_93


title: D2_mRNA_15


title: BJ_mRNA_90


title: BJ_mRNA_89


title: BJ_mRNA_87


title: BJ_mRNA_88


title: BJ_mRNA_86


title: D2_mRNA_8


title: BJ_mRNA_85


title: BJ_mRNA_80


title: BJ_mRNA_82


title: BJ_mRNA_79


title: BJ_mRNA_84


title: BJ_mRNA_81


title: BJ_mRNA_83


title: D2_mRNA_9


title: BJ_mRNA_76


title: BJ_mRNA_78


title: D2_mRNA_1


title: BJ_mRNA_73


title: BJ_mRNA_74


title: BJ_mRNA_72


title: BJ_mRNA_95


title: BJ_mRNA_69


title: BJ_mRNA_71


title: BJ_mRNA_68


title: BJ_mRNA_67


title: BJ_mRNA_66


title: BJ_mRNA_64


title: BJ_mRNA_65


title: BJ_mRNA_63


title: BJ_mRNA_62


title: BJ_mRNA_61


title: BJ_mRNA_60


title: BJ_mRNA_77


title: BJ_mRNA_58


title: BJ_mRNA_59


title: BJ_mRNA_53


title: BJ_mRNA_55


title: BJ_mRNA_57


title: BJ_mRNA_52


title: BJ_mRNA_56


title: BJ_mRNA_54


title: BJ_mRNA_48


title: BJ_mRNA_51


title: BJ_mRNA_50


title: BJ_mRNA_45


title: BJ_mRNA_47


title: BJ_mRNA_49


title: BJ_mRNA_43


title: BJ_mRNA_46


title: BJ_mRNA_42


title: BJ_mRNA_44


title: BJ_mRNA_70


title: BJ_mRNA_41


title: BJ_mRNA_75


title: BJ_mRNA_39


title: BJ_mRNA_40


title: BJ_mRNA_38


title: BJ_mRNA_36


title: BJ_mRNA_35


title: BJ_mRNA_37


title: BJ_mRNA_34


title: BJ_mRNA_32


title: BJ_mRNA_33


title: BJ_mRNA_31


title: BJ_mRNA_29


title: BJ_mRNA_30


title: BJ_mRNA_27


title: BJ_mRNA_24


title: BJ_mRNA_23


title: BJ_mRNA_22


title: BJ_mRNA_20


title: BJ_mRNA_19


title: BJ_mRNA_18


title: BJ_mRNA_26


title: BJ_mRNA_16


title: BJ_mRNA_15


title: BJ_mRNA_17


title: BJ_mRNA_14


title: BJ_mRNA_12


title: BJ_mRNA_13


title: BJ_mRNA_11


title: BJ_mRNA_8


title: BJ_mRNA_10


title: BJ_mRNA_9


title: BJ_mRNA_7


title: BJ_mRNA_6


title: BJ_mRNA_28


title: BJ_mRNA_5


title: BJ_mRNA_3


title: BJ_mRNA_2


title: BJ_mRNA_1


title: BJ_mRNA_25


title: D16_TRA-1-60-negative_95

data_processing:
Library strategy: ATAC-seq
Paired-end fastq files: The high standard deviation is due to the fact that the libraries are ATAC-Seq and have nucleosomal patterns
Reads were aligned to hg19 genome assembly using STAR aligner with the option –alignIntronMatrix set to 1. Only reads that uniquely maps to hg19 and contain less than 3 mismatches were kept for further processing.
Duplicates were removed using PICARD tools
Group information was added for each library using PICARD tools
Reads in each library were ordered lexicographically using PICARD tools. ChrM and amibiguiously mapped reads were removed during this step
Coverage of each library over regions of interest was measured using GATK v3.5
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files of merged mapped files belonging to a particular time-point generated using makeUCSCfile script of HOMER.

growth_protocol: BJ fibroblasts were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. BJ human neonatal fibroblast was routinely tested for Mycoplasma and was negative in all instances. hES cells and iPSCs clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromolar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol:
C1 Single-Cell Auto Prep System with its Open App™ program (Fluidigm, Inc.) is used for scATAC-seq library preparation. Briefly, cells were trypsinized into single cells. Cells at a concentration of 300-350 cells/μL were combined with C1 Cell Suspension Reagent at a ratio of 3:2.5 μL , and loaded on to the C1 Single-Cell Auto Prep IFC microfluidic chips with the “ATACseq: Cell Load and Stain (1862x)” scripts. Following experiments were performed according to the scripts, including cell viability assay, cell lysis, transposition, fragment release and quench, and fragment extension.
96 libraries were harvested from fluidigm chip and dual index were integrated by additional 14 cycle PCR. The PCR products were pooled and purified on a single MinElute PCR purification column (Qiagen). Bioanalyzer is used for library size measurement, and KAPA Library Quantification kit(Kapa Biosystems) is used for library concentration measurement.
Single-cell ATAC-Seq

value: induced viral expression of OSKM

tag: time

value: 16 days post induced viral expression of OSKM

tag: tra-1-60 status


title: D16_TRA-1-60-negative_96


title: D16_TRA-1-60-negative_94


title: BJ_mRNA_21


title: D16_TRA-1-60-negative_93


title: D16_TRA-1-60-negative_91


title: D16_TRA-1-60-negative_92


title: D16_TRA-1-60-negative_87


title: D16_TRA-1-60-negative_88


title: D16_TRA-1-60-negative_89


title: D16_TRA-1-60-negative_86


title: D16_TRA-1-60-negative_84


title: D16_TRA-1-60-negative_82


title: D16_TRA-1-60-negative_80


title: D16_TRA-1-60-negative_83


title: D16_TRA-1-60-negative_79


title: D16_TRA-1-60-negative_78


title: BJ_mRNA_4


title: D16_TRA-1-60-negative_77


title: D16_TRA-1-60-negative_81


title: D16_TRA-1-60-negative_76


title: D16_TRA-1-60-negative_75


title: D16_TRA-1-60-negative_71


title: D16_TRA-1-60-negative_70


title: D16_TRA-1-60-negative_72


title: D16_TRA-1-60-negative_73


title: D16_TRA-1-60-negative_90


title: D16_TRA-1-60-negative_68


title: D16_TRA-1-60-negative_67


title: D16_TRA-1-60-negative_74


title: D16_TRA-1-60-negative_69


title: D16_TRA-1-60-negative_65


title: D16_TRA-1-60-negative_66


title: D16_TRA-1-60-negative_85


title: D16_TRA-1-60-negative_63


title: D16_TRA-1-60-negative_61


title: D16_TRA-1-60-negative_60


title: D16_TRA-1-60-negative_64


title: D16_TRA-1-60-negative_58


title: D16_TRA-1-60-negative_59


title: D16_TRA-1-60-negative_57


title: D16_TRA-1-60-negative_54


title: D16_TRA-1-60-negative_55


title: D16_TRA-1-60-negative_52


title: D16_TRA-1-60-negative_49


title: D16_TRA-1-60-negative_51


title: D16_TRA-1-60-negative_47


title: D16_TRA-1-60-negative_62


title: D16_TRA-1-60-negative_45


title: D16_TRA-1-60-negative_46


title: D16_TRA-1-60-negative_44


title: D16_TRA-1-60-negative_41


title: D16_TRA-1-60-negative_43


title: D16_TRA-1-60-negative_38


title: D16_TRA-1-60-negative_39


title: D16_TRA-1-60-negative_40


title: D16_TRA-1-60-negative_37


title: D16_TRA-1-60-negative_33


title: D16_TRA-1-60-negative_34


title: D16_TRA-1-60-negative_32


title: D16_TRA-1-60-negative_35


title: D16_TRA-1-60-negative_30


title: D16_TRA-1-60-negative_53


title: D16_TRA-1-60-negative_50


title: D16_TRA-1-60-negative_48


title: D16_TRA-1-60-negative_28


title: D16_TRA-1-60-negative_27


title: D16_TRA-1-60-negative_24


title: D16_TRA-1-60-negative_23


title: D16_TRA-1-60-negative_25


title: D16_TRA-1-60-negative_26


title: D16_TRA-1-60-negative_22


title: D16_TRA-1-60-negative_21


title: D16_TRA-1-60-negative_42


title: D16_TRA-1-60-negative_19


title: D16_TRA-1-60-negative_18


title: D16_TRA-1-60-negative_16


title: D16_TRA-1-60-negative_56


title: D16_TRA-1-60-negative_17


title: D16_TRA-1-60-negative_15


title: D16_TRA-1-60-negative_36


title: D16_TRA-1-60-negative_14


title: D16_TRA-1-60-negative_31


title: D16_TRA-1-60-negative_12


title: D16_TRA-1-60-negative_13


title: D16_TRA-1-60-negative_10


title: D16_TRA-1-60-negative_29


title: D16_TRA-1-60-negative_9


title: D16_TRA-1-60-negative_8


title: D16_TRA-1-60-negative_11


title: D16_TRA-1-60-negative_6


title: D16_TRA-1-60-negative_5


title: D16_TRA-1-60-negative_7


title: D16_TRA-1-60-negative_2


title: D16_TRA-1-60-negative_4


title: D16_TRA-1-60-positve_96


title: D16_TRA-1-60-positve_95


title: D16_TRA-1-60-negative_1


title: D16_TRA-1-60-negative_20


title: D16_TRA-1-60-positve_93


title: D16_TRA-1-60-positve_94


title: D16_TRA-1-60-positve_90


title: D16_TRA-1-60-positve_92


title: D16_TRA-1-60-positve_86


title: D16_TRA-1-60-positve_89


title: D16_TRA-1-60-positve_87


title: D16_TRA-1-60-positve_88


title: D16_TRA-1-60-positve_91


title: D16_TRA-1-60-positve_84


title: D16_TRA-1-60-positve_81


title: D16_TRA-1-60-positve_85


title: D16_TRA-1-60-positve_79


title: D16_TRA-1-60-negative_3


title: D16_TRA-1-60-positve_83


title: D16_TRA-1-60-positve_76


title: D16_TRA-1-60-positve_78


title: D16_TRA-1-60-positve_77


title: D16_TRA-1-60-positve_75


title: D16_TRA-1-60-positve_82


title: D16_TRA-1-60-positve_74


title: D16_TRA-1-60-positve_73


title: D16_TRA-1-60-positve_72


title: D16_TRA-1-60-positve_70


title: D16_TRA-1-60-positve_71


title: D16_TRA-1-60-positve_67


title: D16_TRA-1-60-positve_64


title: D16_TRA-1-60-positve_68


title: D16_TRA-1-60-positve_69


title: D16_TRA-1-60-positve_66


title: D16_TRA-1-60-positve_63


title: D16_TRA-1-60-positve_62


title: D16_TRA-1-60-positve_60


title: D16_TRA-1-60-positve_61


title: D16_TRA-1-60-positve_80


title: D16_TRA-1-60-positve_59


title: D16_TRA-1-60-positve_58


title: D16_TRA-1-60-positve_56


title: D16_TRA-1-60-positve_57


title: D16_TRA-1-60-positve_54


title: D16_TRA-1-60-positve_55


title: D16_TRA-1-60-positve_51


title: D16_TRA-1-60-positve_53


title: D16_TRA-1-60-positve_49


title: D16_TRA-1-60-positve_48


title: D16_TRA-1-60-positve_50


title: D16_TRA-1-60-positve_46


title: D16_TRA-1-60-positve_42


title: D16_TRA-1-60-positve_41


title: D16_TRA-1-60-positve_45


title: D16_TRA-1-60-positve_39


title: D16_TRA-1-60-positve_36


title: D16_TRA-1-60-positve_43


title: D16_TRA-1-60-positve_44


title: D16_TRA-1-60-positve_40


title: D16_TRA-1-60-positve_52


title: D16_TRA-1-60-positve_32


title: D16_TRA-1-60-positve_65


title: D16_TRA-1-60-positve_33


title: D16_TRA-1-60-positve_37


title: D16_TRA-1-60-positve_31


title: D16_TRA-1-60-positve_29


title: D16_TRA-1-60-positve_34


title: D16_TRA-1-60-positve_30


title: D16_TRA-1-60-positve_28


title: D16_TRA-1-60-positve_25


title: D16_TRA-1-60-positve_27


title: D16_TRA-1-60-positve_47


title: D16_TRA-1-60-positve_26


title: D16_TRA-1-60-positve_22


title: D16_TRA-1-60-positve_24


title: D16_TRA-1-60-positve_21


title: D16_TRA-1-60-positve_23


title: D16_TRA-1-60-positve_20


title: D16_TRA-1-60-positve_38


title: D16_TRA-1-60-positve_18


title: D16_TRA-1-60-positve_19


title: D16_TRA-1-60-positve_17


title: D16_TRA-1-60-positve_15


title: D16_TRA-1-60-positve_16


title: D16_TRA-1-60-positve_12


title: D16_TRA-1-60-positve_35


title: D16_TRA-1-60-positve_14


title: D16_TRA-1-60-positve_13


title: D16_TRA-1-60-positve_7


title: D16_TRA-1-60-positve_11


title: D16_TRA-1-60-positve_10


title: D16_TRA-1-60-positve_8


title: D16_TRA-1-60-positve_6


title: D16_TRA-1-60-positve_9


title: D16_TRA-1-60-positve_5


title: D16_TRA-1-60-positve_2


title: D16_TRA-1-60-positve_3


title: D16_TRA-1-60-positve_4


title: D16_TRA-1-60-positve_1


title: D8_94

value: 8 days post induced viral expression of OSKM


title: D8_96


title: D8_93


title: D8_92


title: D8_91


title: D8_95


title: D8_89


title: D8_88


title: D8_87


title: D8_85


title: D8_86


title: D8_84


title: D8_83


title: D8_82


title: D8_81


title: D8_80


title: D8_79


title: D8_73


title: D8_77


title: D8_75


title: D8_76


title: D8_71


title: D8_70


title: D8_69


title: D8_90


title: D8_65


title: D8_67


title: D8_64


title: D8_66


title: D8_62


title: D8_59


title: D8_57


title: D8_58


title: D8_61


title: D8_63


title: D8_54


title: D8_52


title: D8_50


title: D8_56


title: D8_78


title: D8_53


title: D8_74


title: D8_72


title: D8_51


title: D8_68


title: D8_49


title: D8_46


title: D8_47


title: D8_42


title: D8_44


title: D8_45


title: D8_60


title: D8_41


title: D8_40


title: D8_39


title: D8_38


title: D8_55


title: D8_37


title: D8_36


title: D8_34


title: D8_35


title: D8_33


title: D8_32


title: D8_29


title: D8_30


title: D8_28


title: D8_27


title: D8_26


title: D8_25


title: D8_24


title: D8_48


title: D8_23


title: D8_22


title: D8_21


title: D8_43


title: D8_19


title: D8_18


title: D8_17


title: D8_16


title: D8_15


title: D8_13


title: D8_11


title: D8_12


title: D8_14


title: D8_10


title: D8_7


title: D8_9


title: D8_31


title: D8_5


title: D8_4


title: D8_8


title: D8_6


title: D8_3


title: D8_2


title: D2_95

value: 2 days post induced viral expression of OSKM


title: D8_1


title: D2_96


title: D2_94


title: D2_90


title: D2_91


title: D2_93


title: D2_92


title: D8_20


title: D2_87


title: D2_88


title: D2_89


title: D2_86


title: D2_83


title: D2_85


title: D2_84


title: D2_82


title: D2_81


title: D2_78


title: D2_77


title: D2_73


title: D2_70


title: D2_72


title: D2_75


title: D2_71


title: D2_69


title: D2_67


title: D2_66


title: D2_74


title: D2_68


title: D2_64


title: D2_62


title: D2_63


title: D2_60


title: D2_59


title: D2_65


title: D2_58


title: D2_80


title: D2_55


title: D2_79


title: D2_54


title: D2_51


title: D2_76


title: D2_52


title: D2_53


title: D2_61


title: D2_50


title: D2_47


title: D2_48


title: D2_49


title: D2_43


title: D2_42


title: D2_44


title: D2_45


title: D2_41


title: D2_40


title: D2_39


title: D2_57


title: D2_36


title: D2_37


title: D2_38


title: D2_34


title: D2_35


title: D2_33


title: D2_32


title: D2_31


title: D2_29


title: D2_30


title: D2_28


title: D2_23


title: D2_27


title: D2_25


title: D2_26


title: D2_24


title: D2_46


title: D2_22


title: D2_21


title: D2_19


title: D2_20


title: D2_15


title: D2_16


title: D2_10


title: D2_13


title: D2_11


title: D2_7


title: D2_9


title: D2_14


title: D2_8


title: D2_5


title: D2_6


title: D2_3


title: D2_4


title: D2_2


title: HUVEC_H_T7d_2_iMARGI

first: Sheng

last: Zhong

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California San Diego

description: in situ ligation of nuclear RNA and genomic DNA

data_processing:
Illumina Casava (1.8) software used for base calling
Paired-end read pair duplicates were removed using FastUniq (1.1)
Paired-end read pairs were aligned to the hg38 genome assembly using STAR (2.5.4b)
Samtools (1.6) and in-house script were used to parse the mapped read pairs
Genome_build: hg38
Supplementary_files_format_and_content: The processed BEDPE file shows the valid RNA-DNA interaction read pairs. BEDPE format (https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format), the 1,2,3 and 9 colums show the genomic coordinate of RNA end (Read 1), and the 4, 5, 6, and 10 columns show that of DNA end (Read 2).

source_name: Human umbilical Vein Endothelial Cells treatment combining high glucose (HG, to mimic hyperglycemia) and TNFα (to mimic inflammation) for 7 days

growth_protocol: HUVECs were grown following the manufacturer's protocol

extract_protocol:
Approximately 5 million cells were used for construction of an iMARGI sequencing library. Cells were crosslinked in 1% formaldehyde at room temperature (RT) for 10 minutes with rotation. Crosslinking reaction was quenched with glycine at 0.2 M concentration and incubated at RT for 10 minutes. Cells were pelleted, washed using 1 × PBS and aliquoted into ~ 5 million in each tube. To prepare nuclei, crosslinked cells was incubated in 1 mL of cell lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% Nonidet P-40, 1× protease inhibitor) on ice for 15 minutes and homogenized with dounce homogenizer pestle A for 20 strokes on ice. Nuclei were pelleted and weighed to estimate the pellet volume (10 mg of nuclei pellet was estimated to be about 10 µL). Nuclei pellet were incubated with SDS buffer (0.5× Cutsmart buffer, 0.5% SDS) with 1:3 volume ratio at 62 °C for 10 minutes with mixing and immediately quenched with a final of 1% Triton X-100. To digest chromatin, washed nuclei pellet was re-suspended in AluI chromatin digestion mix (2.3 U/µL AluI (NEB), 0.3 U/µL RNasinPlus, 1× Cutsmart buffer) and incubated at 37 °C overnight with mixing. After chromatin digestion, 1 µL of RNase I (1:10 diluted in 1× PBS) was directly added to the reaction mixture and incubated at 37 °C for 3 minutes to fragment RNA. Nuclei were pelleted and washed twice using PNK wash buffer (20 mM Tris-HCl pH 7.5, 10 mM MgCl2). To prepare the RNA and DNA ends for linker ligation, nuclei were incubated in 200 µL RNA 3´ end dephosphorylation reaction mix (0.5 U/µL T4 PNK (NEB), 0.4 U/µL RNasinPlus, 1× PNK phosphatase buffer pH 6.5) at 37°C for 30 minutes with mixing. Nuclei were washed twice with PNK buffer, resuspended in 200 µL DNA A-tailing mix (0.3 U/µL Klenow fragment 3´-5´ exo- (NEB), 0.1 mM dATP, 0.1% Triton X-100, 1× NEB buffer 2) and incubated at 37°C for 30 minutes with mixing. The same linker sequence as described in the previous MARGI paper was used. For in situ RNA-linker ligation, nuclei were resuspended in 200 µL ligation mix (38 µL adenylated and annealed linker, 10 U/ µL T4 RNA ligase 2-truncated KQ (NEB), 1× T4 RNA ligase reaction buffer, 20% PEG 8000, 0.1% Triton X-100, 0.4 U/µL RNasinPlus) and incubated at 22°C for 6 hour and then 16°C overnight with mixing. After ligation, the nuclei were washed five times with PNK buffer to remove excess free linker. For in situ RNA-DNA proximity ligation, nuclei were resuspended in 2 mL of proximity ligation mixture (4 U/µL T4 DNA ligase (NEB), 1× DNA ligase reaction buffer, 0.1% Triton X-100, 1 mg/mL BSA (NEB), 0.5 U/µL RNasinPlus) and incubated at 16 °C overnight.
To reverse crosslinking, nuclei were washed twice with 1× PBS, resuspended in 250 µL of extraction buffer (1 mg/mL Proteinase K [NEB], 50 mM Tris-HCl pH 7.5, 1% SDS, 1 mM EDTA, 100 mM NaCl) and incubated at 65 °C for 3 hours. DNA and RNA were extracted by adding an equal volume of Phenol:Chloroform:Isoamyl Alcohol (pH 7.9, Ambion) followed by ethanol precipitation. The subsequent steps including removal of biotin from non-proximity ligated linkers, pulldown of RNA-DNA chimera, reverse transcription of RNA, DNA denaturation, circularization, oligo annealing and BamHI (NEB) digestion and sequencing library generation were performed as previously described. iMARGI libraries were subsequently subject to pair-end 100-cycle sequencing on Illumina HiSeq 4000. The circularization and library construction strategy can phase RNA and DNA ends into Read 1 and Read 2. Since AluI restriction enzyme recognizes "AGCT" sequence and leaves "CT" at the 5´ end of the cut, we expect the first two bases of DNA end (Read 2) to be enriched with "CT".

treatment_protocol: HUVECs were treated with 25mM Mannitol in the control group; Cells in the H_T groups were treated with 25mM D-Glucose and 5ng/mL TNFalpha for 7 days (7d)

value: HUVEC

tag: assay

value: iMARGI


title: BJ_96

value: WT control


title: HUVEC_control_2_iMARGI

source_name: Human umbilical Vein Endothelial Cells cultured under osmotic control (25 mM mannitol)


title: BJ_95


title: BJ_94


title: D2_18


title: D2_17


title: Aptamer21-txomePEARL-control-2

city: Waltham

first: Lee

last: Vandivier

address: 830 Winter St

institute: Arrakis Therapeutics

data_processing:
Reads were stitched with Paired-End reAd mergeR (PEAR) requiring a minimum assembled length of at least 10 nucleotides (nt)
PEARL-seq reads were trimmed with Cutadapt (at least 5-nt of overlap and a maximum of 20% mismatches), DMS-MaP and SHAPE-MaP reads were trimmed with Trimmomatic (LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30)
Targeted experiment reads were aligned with Bowtie2. Transcriptome-wide experiments were aligned with STAR
Mutation rates (MaP) and RT stalls (PEARL-seq) were called using an in-house pipeline (https://bitbucket.org/arrakistx/pearl-seq/src/master/)
Genome_build: hg38 + Aptamer21 spikein
Supplementary_files_format_and_content: *_mut_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC, Reactivity
Supplementary_files_format_and_content: *_stall_rate.txt.gz generated with our in-house pipeline. Columns are: Sequence, Position, Base, Coverage, Sample, Mutation.Rate, Control.Mutation.Rate, Mutation.FC, Mutation.Log2FC
Supplementary_files_format_and_content: *_10ntBinCounts.txt (Transcriptome-wide experiments only) tabulating stalls across genomic 10nt bins. 0-count bins are not reported

source_name: HepG2 + In vitro transcription

extract_protocol:
All Aptamer 21 derivatives were produced by in vitro transcription (IVT) from linearized plasmid templates, using the HiScribe IVT kit (New England Biolabs) according to the manufacturer’s standard protocol with 33.5 ng/µL template. Total RNA was extracted from 12 samples of 2x10^5 to 1.5x10^6 HepG2 cells using the ReliaPrep RNA cell miniprep system (Promega) according to the manufacturer’s standard protocol.
Libraries were produced using standard Illumina protocols.

tag: library type

value: PEARL-seq

tag: scale

value: Transcriptome

tag: platform

value: HiSeq 4000


title: Aptamer21-txomePEARL-control-1


title: Aptamer21-txomePEARL-Cmpd4-3


title: D2_12

value: BJ Fibroblasts


title: Aptamer21-txomePEARL-Cmpd4-2


title: Aptamer21-txomePEARL-Cmpd4-1


title: Aptamer21-txomePEARL-Cmpd2d-3


title: BJ_88


title: BJ_89


title: D2_1


title: Aptamer21-txomePEARL-control-3


title: BJ_86


title: Aptamer21-txomePEARL-Cmpd2d-1


title: BJ_84


title: BJ_87


title: BJ_85


title: HCT116_ctl_rep3

city: Bethesda

first: Lorinc

last: Pongor

state: MD

address: 37 Convent Dr,

department: DTB

institute: NIH

description: Cells were transduced with lentivirus pLVX, and selected with 1ug/mL of puromyocin

data_processing:
Sequenced reads were aligned to the human hg19 genome version using the STAR aligner
Differential gene expression was quantified using RSEM and DESeq2
Genome_build: hg19

source_name: HCT-116 Human colon adenocarcinoma

growth_protocol: Cells were maintained according to ATCC's instructions in Dulbecco's modified Eagle's medium

extract_protocol:
Total RNA was extracted using RNeasy mini plus kit (Qiagen, 74134)
Samples were sequenced on HiSeq4000 using 150 (2 x 150 cycles), Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

tag: genotype

value: control


title: HCT116_FOXA1_overexpressed_rep1

description: Cells were transduced with lentivirus pLVX-FOXA1-FLAG, and selected with 1ug/mL of puromyocin

value: FOXA1 overexpressed


title: BJ_83


title: BJ_92


title: HCT116_FOXA1_overexpressed_rep2


title: HCT116_ctl_rep2


title: BJ_82


title: HCT116_FOXA1_overexpressed_rep3


title: BJ_93


title: HCT116_ctl_rep1


title: BJ_81


title: BJ_91


title: LS180_siFOXA1_rep3

description: Cells reverse-transfected using Lipofectamine 2000 transfection reagent (Life technology Invitrogen) at a final concentration of 20 nM for two 48 hour periods with OnTarget siRNA SMARTpool for FOXA1 (ThermoFisher Scientific, Dharmacon)

source_name: LS180 Human colon adenocarcinoma


title: LS180_siFOXA1_rep2


title: BJ_80


title: BJ_90


title: BJ_79


title: BJ_78


title: LS180_siFOXA1_rep1


title: LS180_ctl_rep2

description: Cells reverse-transfected using Lipofectamine 2000 transfection reagent (Life technology Invitrogen) at a final concentration of 20 nM for two 48 hour periods with Allstars Negative control (Qiagen)


title: LS180_ctl_rep3


title: LS180_ctl_rep1


title: BJ_76


title: BJ_75


title: BJ_74


title: BJ_71


title: SW1222_siFOXA1_rep3

source_name: SW1222 Human colon adenocarcinoma


title: BJ_72


title: BJ_73


title: SW1222_ctl_rep2


title: SW1222_siFOXA1_rep1


title: SW1222_ctl_rep1


title: SW1222_siFOXA1_rep2


title: BJ_70


title: BJ_69


title: SW1222_ctl_rep3


title: BJ_66


title: Undeveloped left heart fetal left ventricle vascular endothelial cadherin (CD144/CDH5) positive cells

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
10X Genomics: Barcodes and UMI are in the R1 file: 1-16 (barcode), 17-26 (UMI)
Cell Ranger
Seurat
TrimGalore
STAR
featureCounts
Genome_build: hg38
Supplementary_files_format_and_content: raw read counts

source_name: Fetal heart tissue

growth_protocol: Cardiogenic differentiation of human iPSC was performed using a chemically defined protocol using activator and inhibitors of the Wnt signaling pathway.

extract_protocol: Total RNA was isolated using Direct-zol RNA MiniPrep Plus (Zymo Research) in accordance to manufacturer’s instructions, followed by DNAse treatment.

tag: tissue

value: Fetal heart tissue

tag: cell type

value: Endothelial cells


title: BJ_65


title: Undeveloped left heart fetal left ventricle vascular endothelial cadherin (CD144/CDH5) negative cells

value: Cardiac cells


title: BJ_67


title: Aptamer21-txomePEARL-Cmpd2d-2


title: Undeveloped left heart fetal right ventricle vascular endothelial cadherin (CD144/CDH5) negative cells


title: Undeveloped left heart fetal right ventricle vascular endothelial cadherin (CD144/CDH5) positive cells


title: BJ_64


title: Normal fetal left ventricle vascular endothelial cadherin (CD144/CDH5) negative cells


title: BJ_77


title: Normal fetal left ventricle vascular endothelial cadherin (CD144/CDH5) positive cells


title: BJ_63


title: BJ_62


title: Normal fetal right ventricle vascular endothelial cadherin (CD144/CDH5) positive cells


title: Normal fetal right ventricle vascular endothelial cadherin (CD144/CDH5) negative cells


title: BJ_68


title: BJ_61


title: BJ_58


title: BJ_57


title: BJ_59


title: Control

source_name: Peripheral blood mononuclear cells (PBMCs)

value: Induced pluripotent stem cell-derived endothelial cells (iPSC-ECs)


title: Hypoplastic left heart syndrome (HLHS) patient

value: Peripheral blood mononuclear cells (PBMCs)


title: BJ_56


title: BJ_55


title: BJ_54


title: CD13+_Tead4

data_processing:
The libraries were mapped using STAR aligner to hg19 genome, allowing up to 3 mismatches in each read and discarding reads that map to more than one locus. The options –alignIntronMax and –alignEndsType were set to 1 and EndToEnd respectively.
GEM was used to call peaks with the following parameters --f SAM --k_min 6 --k_max 13 --outHOMER --outBED
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed files containing loci bound by D8 CD13+ TEAD4 and D8 CD13- TEAD4 as per GEM.

growth_protocol: BJ fibroblasts were infected with lentivirus carrying O2S and K2M polycistronic construct, and cultured in 10% Fetal Bovine Serum (Gibco) for the first 5 days. Cells were passaged at D4 and transferred onto Matrigel coated plates. From D6 till D8, reprogramming cells were cultured with hESC medium, composed of 20% knockout serum replacement (KOSR, Life Technologies), 2mM Glutamine (Life Technologies), 1x non-essential amino acids solution (NEAA, Life Technologies), 8 mg mL-1 bFGF (Life Technologies), and 55 mM Beta-mercaptoethanol in DMEM/F12 (Life Technologies).

extract_protocol:
Cells were harvested following previously published protocol (Yang et al., 2015).
ChIP-seq libraries were prepared following previously published protocol (Yang et al., 2015). Briefly, ChIP DNA was end-repaired. Then poly-A tail was added followed by ligation with adaptors. Finally, the fragments were amplified using 12 cycles of PCR. The amplified ChIP DNA was purified using Ampure beads. The concentration and size range of ChIP-seq library were measured by Agilent 2000 bioanalyzer kit.

treatment_protocol: For CD13 sorting, cells were trypsinized and filtered with 40um cell mesh to devoid of cell clumps. Single cells were re-suspended with 1% FBS (Sigma) at a concentration of 25 million/ml, and incubated with Anti human-CD13-FITC (Miltenyi Biotec, Cat. No.: 130-103-732) at a dilution of 1:11, at fridge for 15 min. Next, cells were incubated with Anti-FITC MicroBeads (Miltenyi Biotec) in a 1:5 dilution, at fridge for 20 min. Cells were then separated into positively and negatively stained population by the magnetic separator according to the manufacturer's instructions.

value: BJ

value: Fibroblasts

tag: cd13 sorting

value: Positive

tag: antibody

value: Anti-TEAD4 antibody - ChIP Grade (Abcam, ab58310)


title: CD13-_Tead4

tag: treatment

value: 8 days post induced viral expression of OSKM

value: Negative


title: BJ_51

value: WT control


title: BJ_53


title: CD13-_Input


title: BJ_50


title: CD13+_Input


title: BJ_49


title: D8_CD13+_CD201+_Rep2

description:
CD13pos_CD201pos_R2_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt

data_processing:
Reads were aligned to hg19 genome assembly using STAR aligner. Reads that uniquely map to hg19 and contain less than 3 mismatches were kept for further processing.
Gene quantification was performed using Cuffquant with the options -u and -b
Expression levels were then normalized using Cuffnorm using the classic-fpkm mode.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: D8_FPKM.txt: Tab-delimited text file containing the FPKM values for each gene in every sample.

extract_protocol:
RNA was extracted by the conventional methods using Trizol. Extracted RNA was treated with DNase I to get rid of the contaminant DNA, and purified with the RNeasy mini kit from Qiagen thereafter.
RNA-seq libraries were prepared using the TruSeq® Stranded mRNA Library Prep kit following manual guide of the kit. Briefly, mRNA was enriched by the beads conjugated with Poly-T oligo, fragmentized, and reverse transcribed to cDNA. After ligating adaptors, cDNA was further amplified by 15 cycles of PCR. The library was sequenced on HiSeq 4000 sequencer.

treatment_protocol: For sorting using surface markers, cells were trypsinized and filtered with 40um cell mesh to devoid of cell clumps. Single cells were re-suspended with 1% FBS (Sigma) at a concentration of 25 million/ml, and incubated with Anti human-CD13-FITC (Miltenyi Biotec, Cat. No.: 130-103-732) and CD201 (EPCR)-PE, human (Miltenyi Biotec, Cat. No.: 130-105-298) at a dilution of 1:11, at fridge for 15 min. Sorting was performed using MoFlo XDP Cell Sorter (Beckman Coulter).

tag: cd13 profile

tag: cd201 profile


title: D8_CD13-_CD201-_Rep2

description:
CD13neg_CD201neg_R2_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt


title: D8_CD13+_CD201+_Rep1

description:
CD13pos_CD201pos_R1_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt


title: BJ_47


title: BJ_46


title: D8_CD13-_CD201-_Rep1

description:
CD13neg_CD201neg_R1_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt


title: BJ_45


title: D8_CD13-_CD201+_Rep2

description:
CD13neg_CD201pos_R2_0
mRNA-seq
PolyA RNA
processed data file: D8_FPKM.txt


title: D2_56

value: induced viral expression of OSKM

value: 2 days post induced viral expression of OSKM