title: Input/screening-library-WG

description:
plasmid DNA
input, baseline library
processed data file: none

data_processing:
Library strategy: STARR-seq
Reads from Illumina Hiseq2000 were aligned to human genome hg19 by bowtie. Reads that are mapped to more than one location to the genome were filtered out.  Only distinct fragments were used as output by Picard.  data from two biological replicates and called enhancer peaks by MACS2 (default setting, q-value = 0.05) (Zhang et al. 2008). The genome coverage of the plasmid library was used as input when calculating the enrichment of STARR-Seq reads. We took the enrichment score reported by MACS2 as enhancer activity.
genome build: hg19
processed data files format and content: no processed data file for the input library

growth_protocol: LNCap cells (ATCC) were cultured in RPMI 1640 medium (ThermoFisher Scientific) supplemented with 10% heat-inactivated FBS (Gemini) and 1% antibiotic-antimycotic (ThermoFisher Scientific) prior to transfection.

extract_protocol:
Total RNA was extracted from transfected LNCap cells using PerfectPure RNA Cultured Cell Kit (5PRIME), and followed by poly (A) tail mRNA isolation using Dynabeads® Oligo (dT) kit (ThermoFisher Scientific). mRNA was treated with TURBOTM DNase (ThermoFisher Scientific) and purified by Agencourt RNAClean XP beads (Beckman Coulter).
Target-specific first strand cDNA synthesis was performed with SuperScript III (ThermoFisher Scientific; 1.5 ug mRNA/reaction) to specifically reverse transcribe Enhancer-seq mRNAs (RT primer: 5’- CAAACTCATCAATGTATCTTATCATG-3’). After reverse transcription, reactions were treated with RNase A+H and subjected to final PCR. In the final PCR amplification, 5 ul cDNA reaction was used as template in every 50 ul PCR reaction using Q5 High-Fidelity DNA polymerase (NEB) using the following program: 98°C for 30s; 20 cycles of 98°C for 10s, 65°C for 30s and 72°C for 30s. Illumina HiSeq platform compatible primers were used (forward: 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’; reverse: 5’-CAAGCAGAAGACGGCATACGAGAT-index-GTGACTGGAGTTCAGACGTG-3’). PCR products were cleaned up by AmPure XP beads (Beckman Coulter; beads/reaction ratio = 0.8). Input library for sequencing was generated using similar PCR setup. Products from 8 PCR reactions were pooled (10 ng plasmid/reaction, 10 cycles of PCR).

treatment_protocol: Input plasmid library was electroporated into cells using the NucleofectorTM platform (Lonza) according to manufacturer’s protocol (1 ug DNA/1 million cells). A total of 300 million cells were electroporated in each replicate and two replicates were generated. After transfection, cells were plated in phenol red free RPMI 1640 medium (ThermoFisher Scientific) supplemented with 10% charcoal:dextran stripped FBS (Gemini) and 1% antibiotic-antimycotic (ThermoFisher Scientific) for 72 hours until harvest.


title: Rep1-WG-STARR-seq

status: Public on Mar 02 2017

type: SRA

city: Chicago

first: Kevin

last: White

state: IL

address: 900 E 57th Street

department: Institute for Genomics and Systems Biology

country: USA

institute: University of Chicago

description:
total RNA
Replicate 1 of WHG-STARR-seq
processed data file: enhancer_overlap_dnase.txt, enhancer_not_overlapped_dnase.txt

library_source: transcriptomic

data_processing:
Library strategy: STARR-seq
Reads from Illumina Hiseq2000 were aligned to human genome hg19 by bowtie. Reads that are mapped to more than one location to the genome were filtered out.  Only distinct fragments were used as output by Picard.  data from two biological replicates and called enhancer peaks by MACS2 (default setting, q-value = 0.05) (Zhang et al. 2008). The genome coverage of the plasmid library was used as input when calculating the enrichment of STARR-Seq reads. We took the enrichment score reported by MACS2 as enhancer activity.
genome build: hg19
processed data files format and content: BED files of peak calls, and for RNA-seq differential expression, a gene list with associated log(fold change), log(CPM), and p-values fore each gene
processed data files format and content: enhancer_overlap_dnase.txt: WG-STARR-Seq enhancers that are in DHS sites. enhancer_not_overlapped_dnase.txt: WG-STARR-Seq enhancers that are not in DHS sites

molecule: total RNA

organism: Homo sapiens

source_name: human prostate adenocarcinoma cells

tag: cell line

value: LNCaP

tag: treatment


title: Rep3-TSA-ATAC-seq

description:
genomic DNA
Replicate 3 of TSA treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2249-2250-2251_bff_100_fseq_35bp_map_pool.sorted.top40995.bed

library_source: genomic

data_processing:
Library strategy: ATAC-seq
Cutadapt was used to trim adapter sequeces from paired ends. We used Bowtie and Bowtie2(Langmead and Salzberg 2012) for each library to do a two-round alignment to the hg19 human genome. In the first round, Bowtie was used and only uniquely mappable reads were kept and unmappable reads were gathered as the input for the second round.  We removed potential PCR duplicates by running Picard.  All uniquely mappable reads aligning to the plus strand were offset by +4-bp, and those aligning to the minus strand were offset −5-bp. used Fseq (Boyle et al. 2008) at default parameters (http://fureylab.web.unc.edu/software/fseq/) to call peaks in both vehicle condition and TSA treatment. We then merged peaks across conditions and counted the ATAC-seq reads number for each peak in each condition. Genomic regions showing differential accessibility after TSA treatment were called by EdgeR (we treated each region as if it was a gene, GLM tagwise dispersion used, q-value < 0.05).
genome build: hg19
processed data files format and content: BED files of peak calls, and for RNA-seq differential expression, a gene list with associated log(fold change), log(CPM), and p-values fore each gene
processed data files format and content: 160505_TSA_diff_ATAC_Seq.txt: LNCaP differential ATAC-Seq sites by TSA treatment. 2015-2249-2250-2251_bff_100_fseq_35bp_map_pool.sorted.top40995.bed: LNCaP TSA 24hr ATAC-Seq sites.

molecule: genomic DNA

growth_protocol: 1.0X105 cells per well were seeded in 6-well plates in phenol red free RPMI 1640 medium (ThermoFisher Scientific) supplemented with 10% charcoal:dextran stripped FBS (Gemini) and 1% antibiotic-antimycotic (ThermoFisher Scientific) for 72 hours before treatment.

extract_protocol:
Nuclei from 50,000 TSA/DMSO treated cells were freshly extracted and incubated with Tn5 transposase (Illmina).
ATAC-seq was performed as previously described (Buenrostro JD et al., 2013). Transposed DNA was extracted from nuclei, and PCR amplified using NEBNext High-Fidelity DNA polymerase (NEB) and customized Nextera PCR primers.

treatment_protocol: Cells were treated with either 100 ng/ml TSA (Sigma Aldrich) or DMSO for 24 hours before harvest to achieve three biological replicates.

value: TSA 24h @ 100 ng/ml


title: Rep1-TSA-ATAC-seq

description:
genomic DNA
Replicate 1 of TSA treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2249-2250-2251_bff_100_fseq_35bp_map_pool.sorted.top40995.bed


title: Rep2-TSA-ATAC-seq

description:
genomic DNA
Replicate 2 of TSA treated
processed data file: 160505_TSA_diff_ATAC_Seq.txt, 2015-2249-2250-2251_bff_100_fseq_35bp_map_pool.sorted.top40995.bed


title: ChIP_H3K27ac_shCEBP-beta_IFNg_4h

city: Milano

first: Viviana

last: Piccolo

state: Milano

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: European Institute of Oncology (IEO)

description: Chromatin IP against H3K27ac

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm10 reference genome using Bowtie2  v.2.2.6 (PMID: 22388286)  with "--very-sensitive" parameter. Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using SICER v1.1  (PMID: 24743992) using a redundancy threshold of 1,  a window size of 200 bp, a gap size of 600 bp and a False Discovery Rate (FDR)  cutoff of 1 × 10−3. Fragment size was set to 150 and the effective genome fraction to 0.80.
Genome_build: mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: Summary file of significant islands with requirement of FDR=0.01 detected with SICER. It is a bed format with the end position included : chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

organism: Mus musculus

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: ChIP lysates were generated from 2x10^8 cells. Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 10ug of antibody. Antibodies were pre-bound overnight to 100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: Macrophages were subjected to different treatments (see individual samples for details)

tag: strain

tag: cell type

value: BMDM cells (7th day of differentiation)

tag: antibody

value: Anti-H3K27ac (Abcam # ab4729)

value: IFNg (100 ng/ml) for 4hrs


title: ChIP_H3K27ac_shJunB_IFNg_4h

description: Chromatin IP against H3K27ac


title: ChIP_H3K27ac_shJunB_UT

description: Chromatin IP against H3K27ac

value: No treatment


title: ChIP_wt_MYC_IL4_IFNg_4h

description: Chromatin IP against Myc

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm10 reference genome using Bowtie2  v.2.2.6 (PMID: 22388286)  with "--very-sensitive" parameter. Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using MACS2 v.2.1.0.20150731 (PMID: 18798982)   with added parameters   -B --SPMR  --bw 100 -q 0.01
Genome_build: mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: MACS2 narrowPeak bed file: chrom, start, end, name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start.

value: Anti-Myc (Santa-Cruz sc-764)

value: IFNg (100 ng/ml) and IL4 (10ng/ml) for 4hrs


title: ChIP_H3K27ac_shCEBP-beta_UT

description: Chromatin IP against H3K27ac


title: ChIP_H3K27ac_scramble_UT

description: Chromatin IP against H3K27ac


title: ChIP_H3K27ac_scramble_IFNg_4h

description: Chromatin IP against H3K27ac


title: ChIP_wt_MYC_IL4_IFNg_2h

description: Chromatin IP against Myc

value: IFNg (100 ng/ml) and IL4 (10ng/ml) for 2hrs


title: ChIP_wt_MYC_IL4_4h

description: Chromatin IP against Myc

value: IL4 (10ng/ml) for 4hrs


title: ChIP_wt_MYC_UT

description: Chromatin IP against Myc


title: Rep2-WG-STARR-seq

description:
total RNA
Replicate 2 of WHG-STARR-seq
processed data file: enhancer_overlap_dnase.txt, enhancer_not_overlapped_dnase.txt


title: ChIP-Seq H3K27ac_IL4_4h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IL4 (10 ng/ml) for 4hrs
Chromatin IP against H3K27ac

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm10 reference genome using Bowtie2  v.2.2.6 (PMID: 22388286)  with "--very-sensitive" parameter. Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using SICER v1.1  (PMID: 24743992) using a redundancy threshold of 1,  a window size of 200 bp, a gap size of 600 bp and a False Discovery Rate (FDR)  cutoff of 1 × 10−3. Fragment size was set to 150 and the effective genome fraction to 0.80.
Genome_build: mm10 (Genome Reference Consortium GRCm38
Supplementary_files_format_and_content: Summary file of significant islands with requirement of FDR=0.01 detected with SICER. It is a bed format with the end position included : chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

treatment_protocol: Macrophages were subjected to different treatment (see individual samples for details)


title: ChIP-Seq H3K27ac_IFNg_4h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IFNg (100 ng/ml) for 4hrs
Chromatin IP against H3K27ac


title: ChIP-Seq H3K27ac_IFNg_IL4_4h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 4hrs
Chromatin IP against H3K27ac


title: ChIP_wt_MYC_IL4_2h

description: Chromatin IP against Myc

value: IL4 (10ng/ml) for 2hrs


title: ChIP_wt_IRF1_IFNg_4h

description: Chromatin IP against IRF1

value: Anti-IRF1 (Santa Cruz sc-640)


title: ChIP-Seq H3K27ac_UT

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: No treatment
Chromatin IP against H3K27ac


title: ChIP_wt_JunB_UT

description: Chromatin IP against JunB

value: Anti-JunB (Santa Cruz sc-46x)


title: ChIP_wt_JunB_IFNg_IL4_4h

description: Chromatin IP against JunB


title: ChIP-Seq H3K27ac_IFNg_IL4_2h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 2hrs
Chromatin IP against H3K27ac


title: ChIP_wt_JunB_IFNg_4h

description: Chromatin IP against JunB


title: ChIP_wt_C/EBP-beta_UT

description: Chromatin IP against CEBPB

value: Anti-CEBPb (Santa Cruz sc-150X)


title: ChIP_wt_C/EBP-beta_IFNg_IL4_4h

description: Chromatin IP against CEBPB


title: ChIP_wt_IRF1_IFNg_IL4_4h

description: Chromatin IP against IRF1


title: ChIP-Seq STAT6_IL4_2h

description:
antibody: Anti-STAT6 (Santa Cruz sc-981)
treatment: IL4 (10 ng/ml) for 2hrs
Chromatin IP against STAT6

data_processing:
Reads quality filtered according to the Illumina pipeline
Reads were mapped to the UCSC mm10 reference genome using Bowtie2  v.2.2.6 (PMID: 22388286)  with "--very-sensitive" parameter. Subsequently, only uniquely mapping reads were considered in the analysis.
Peaks were called using using MACS2 v.2.1.0.20150731 (PMID: 18798982)   with added parameters "  -B --SPMR  --bw 100 -q 0.01
Genome_build: mm10 (Genome Reference Consortium GRCm38)
Supplementary_files_format_and_content: MACS2 narrowPeak bed file: chrom, start, end, name, score, strand, fold-change, -log10pvalue, -log10qvalue, relative summit position to peak start.


title: ChIP_wt_STAT1_IFNg_2h

description: Chromatin IP against STAT1

value: Anti-STAT1 (Santa Cruz sc-592)

value: IFNg (100 ng/ml) for 2hrs


title: ChIP-Seq H3K27ac_IL4_2h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IL4 (10 ng/ml) for 2hrs
Chromatin IP against H3K27ac


title: ChIP_wt_STAT1_IFNg_4h

description: Chromatin IP against STAT1


title: ChIP-Seq STAT6_IL4_IFNg_2h

description:
antibody: Anti-STAT6 (Santa Cruz sc-981)
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 2hrs
Chromatin IP against STA6


title: ChIP-Seq STAT1_IFNg_IL4_2h

description:
antibody: Anti-STAT1 (Santa Cruz sc-592)
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 2hrs
Chromatin IP against STAT1


title: ChIP_wt_IRF1_UT

description: Chromatin IP against IRF1


title: ChIP-Seq STAT1_IFNg_2h

description:
antibody: Anti-STAT1 (Santa Cruz sc-592)
treatment: IFNg (100 ng/ml) for 2hrs
Chromatin IP against STAT1


title: ChIP-Seq  input

description:
antibody: Not needed
treatment: No treatment
whole extract


title: 9_E62_6h_N

city: Molndal

first: Elisabeth

last: Israelsson

address: Pepparedsleden 1

department: Translational Biology

country: Sweden

institute: AstraZeneca, IMED RIA

description:
counts_1n2_combined.tsv
batch1_combined.counts
S9.E62.6h.N_S9_R1_001

data_processing:
Base calling were done by bcl2fastq from Illumina
Reads were mapped with HiSat2 (2.0.4 )
Counts were generated with featurecounts (1.4.4) using Ensembl version 78
TPMs were generated using Sailfish (0.10.1)
All processing was wrapped together with bcbio 0.9.9
Genome_build: hg38
Supplementary_files_format_and_content: batch1_combined.counts: A .COUNT file containing the counts obtained from pipeline specified above for batch 1. Ensembl version 78
Supplementary_files_format_and_content: batch2_combined.counts: A .COUNT file containing the counts obtained from pipeline specified above for batch 2. Ensembl version 78
Supplementary_files_format_and_content: counts_1n2_combined.tsv: A tab separated file containing the combined counts obtained from pipeline specified above for batch 1 and 2. Ensembl version 78

molecule: polyA RNA

source_name: alveolar macrophages

growth_protocol: Human alveolar macrophages were derived from tissue lung resection or transplant tissue by flushing tissue with sterile Ca2+ Mg2+ -free PBS (Life Technologies) using a 19 gauge needle (BD). For functional assays, cells were seeded at a density of 200,000 cells per well in a 96-well tissue-culture grade flat bottom plate (Costar). Following plating, non-adherent cells were removed by copious washing with serum-free RPMI (Life Technologies) after an hour’s rest. After the final wash, the cells were incubated overnight in XVivo10 media (Lonza) supplemented with 4mM L-glutamine (Sigma) and 1% penicillin-streptomycin (Sigma).

extract_protocol:
RNeasy Mini kit with on-column DNA digestion (QIAGEN, Hilden, Germany) and eluted in 50 ul Rnase-free water
RNA was diluted to 5ng/ul and used as input to create RNA libraries using TruSeq Stranded mRNA kit (Illumina, CA, USA) following standard instructions. Libraries were validated on the BioAnalyzer (Agilent, CA, USA) using DNA1000 chip and the concentration was determined using Quant-iT dsDNA High Sensitivity assay kit on the Qubit fluorometer (Thermo Fisher, MA, USA). Sample libraries were pooled in equimolar concentrations and diluted and denatured according to Illumina guidelines. The pool was then sequencing using a High Output 2 x 76 bp kit on an Illumina NextSeq500

treatment_protocol: AM were incubated with JQ1 for 1h at 37°C and subsequently challenged with 100ng/ml LPS from E. coli (serotype 026:B6, Sigma) for 6h or 24 h at 37°C in CO2 incubator. DMSO-treated cells were used as a vehicle control.

tag: sample number

tag: stimulation

value: unstim

value: DMSO

tag: stimulation treatment

tag: timepoint

tag: stimulation treatment time

tag: donor

tag: batch


title: ChIP_wt_C/EBP-beta_IFNg_4h

description: Chromatin IP against CEBPB


title: 8_E62_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S8.E62.6h.L_S8_R1_001

value: LPS

tag: stimulation concentration


title: ChIP-Seq H3K27ac_IFNg_2h

description:
antibody: Anti-H3K27ac (Abcam # ab4729)
treatment: IFNg (100 ng/ml) for 2hrs
Chromatin IP against H3K27ac

value: BMDM cells (7th day of differentiation)


title: 5_E62_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S5.E62.24h.L_S5_R1_001


title: 4_E62_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S4.E62.24h.LC_S4_R1_001

tag: treatment concentration


title: 6_E62_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S6.E62.24h.N_S6_R1_001


title: 33_E80_6h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S33.E80.6h.N_S33_R1_001


title: 35_E80_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S35.E80.6h.L_S35_R1_001


title: 7_E62_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S7.E62.6h.LC_S7_R1_001


title: 32_E80_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S32.E80.6h.L_S32_R1_001


title: 30_E80_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S30.E80.24h.N_S30_R1_001


title: 34_E80_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S34.E80.6h.LC_S34_R1_001


title: 2_E62_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S2.E62.24h.L_S2_R1_001


title: 27_E80_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S27.E80.24h.N_S27_R1_001


title: 29_E80_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S29.E80.24h.L_S29_R1_001


title: 19_E66_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S19.E66.24h.LC_S19_R1_001


title: 16_E66_6h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S16.E66.6h.N_S16_R1_001


title: 21_E66_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S21.E66.24h.N_S21_R1_001


title: 24_E66_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S24.E66.24h.N_S24_R1_001


title: 23_E66_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S23.E66.24h.L_S23_R1_001


title: 36_E80_6h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S36.E80.6h.N_S36_R1_001


title: 20_E66_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S20.E66.24h.L_S20_R1_001


title: 17_E66_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S17.E66.6h.L_S17_R1_001


title: 28_E80_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S28.E80.24h.LC_S28_R1_001


title: 25_E80_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S25.E80.24h.LC_S25_R1_001


title: 3_E62_24h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S3.E62.24h.N_S3_R1_001


title: 18_E66_6h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S18.E66.6h.N_S18_R1_001


title: 22_E66_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S22.E66.24h.LC_S22_R1_001


title: 15_E66_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S15.E66.6h.LC_S15_R1_001


title: ChIP_wt_STAT1_UT

description: Chromatin IP against STAT1


title: 14_E66_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S14.E66.6h.L_S14_R1_001


title: 26_E80_24h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S26.E80.24h.L_S26_R1_001


title: 31_E80_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S31.E80.6h.LC_S31_R1_001


title: 13_E66_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S13.E66.6h.LC_S13_R1_001


title: 12_E62_6h_N

description:
counts_1n2_combined.tsv
batch1_combined.counts
S12.E62.6h.N_S12_R1_001


title: 11_E62_6h_L

description:
counts_1n2_combined.tsv
batch1_combined.counts
S11.E62.6h.L_S11_R1_001


title: 10_E62_6h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S10.E62.6h.LC_S10_R1_001


title: 1_E62_24h_LC

description:
counts_1n2_combined.tsv
batch1_combined.counts
S1.E62.24h.LC_S1_R1_001


title: D3_R2_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2023_D3_R2_24h_LPS_DMSO_AD_69


title: H2A.W.7 IP

city: Vienna

first: Zdravko

last: Lorkovic

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
Sequencing reads were aligned to the Arabidopsis genome (TAIR10) with up to two mismatches allowed.
coverage plots (log2ratio(Chip/input)) bin size: 100 kb.
Regions enriched in H2A.W.7 were defined using deepTools2.0, R/3.2.2, and bedtools software with the input DNA used as a control.
For plotting H2A.W.7 and H2A.W.6 over H2A.W.7-rich regions we defined the log2ratio(ChipH2A.W.7/input) coverage with a bin size of 5 bp.
Next, we selected all regions with scores >0 and finally, from resulting regions, only those with enrichment scores ≥1 and a width ≥200 (both had to be true) were selected.
Genomic features were defined by CEAS annotation software.
The profile of H3K9me2 S2 from reference S2 was used to define heterochromatic regions.
Genome_build: Tair10
Supplementary_files_format_and_content: bw: bigwig-files (binary format) - coverage as log2-ratio of Chip over input; bed: regions with chr start and end

organism: Arabidopsis thaliana

extract_protocol:
For MNase digestion followed by immunoprecipitation, nuclei were isolated from 4 grams of 2-3 weeks old leaves. Isolated nuclei were washed once in 1 ml of N buffer (15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, 250 mM sucrose, 1 mM DTT, 10 mM ß-glycerophosphate) supplemented with protease inhibitors (Roche). After spinning for 5 min at 1,800 × g at 4oC nuclei were re-suspended in N buffer to a volume of 1 ml. Twenty microliters of MNase (0.1 u/μl) (SigmaAldrich) were added to each tube and incubated for 15 min at 37oC and during the incubation nuclei were mixed 4 times by inverting the tubes. MNase digestion was stopped on ice by addition of 110 μl of MNase stop solution (100 mM EDTA, 100 mM EGTA). Nuclei were lysed by addition of 110 μl of 5 M NaCl (final concentration of 500 mM NaCl). The suspension was mixed by inverting the tubes and they were then kept on ice for 15 min. Extracts were cleared by centrifugation for 10 min at 20,000 × g at 4C. Supernatants were collected and centrifuged again as above. For each immunoprecipitation extract, an equivalent of 4 g of leaf material was used, usually in a volume of 1 ml. To control MNase digestion efficiency, 200 μl of the extract were kept for DNA extraction. Antibodies, including non-specific IgG from rabbit, were bound to protein A magnetic beads (GE Healthcare) and then incubated with MNase extracts over night at 4oC. Beads were washed two times with N buffer without sucrose, containing 300 mM NaCl, followed by three washes with N buffer containing 500 mM NaCl and one wash with N buffer without sucrose, containing 150 mM NaCl. Beads were re-suspended in 120 μl of N buffer containing 150 mM NaCl and mixed with 35 μl of 5 × loading buffer.
DNA was phenol/chloroform extracted from H2A.W.6 and H2A.W.7 immunoprecipitates and Illumina libraries were generated using the TruSeq Nano DNA Library prep kit (Illumina), and the libraries were sequenced with a 50 bp paired-end protocol. Sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at).

tag: age

value: 2-3 weeks old

tag: tissue

value: leaf


title: H2A.W.6 IP


title: D3_R2_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2021_D3_R2_24h_unst_DMSO_AD_67


title: D3_R1_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2018_D3_R1_24h_LPS_10JQ1_AD_64


title: JSC211_041814

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: single cell in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: lung cancer xenograft derived primary tumor cell

extract_protocol:
Briefly, 300,000 MGH134 (a patient-derived non-small cell lung cancer line [Pubmed ID 25758528]) cells stably expressing luciferase and GFP were introduced into the lung by percutaneous injection. Mice blood samples were collected 7-8 weeks after injection, and CTCs were isolated using the CTC iChip [Pubmed ID 23552373]. Primary tumors were digested into single cells by collagenase and hyaluronidase (Stemcell Technologies). A total of 10 GFP-positive single CTCs and 6 single primary tumor cells were individually micromanipulated using a 10 μm transfer tip on an Eppendorf TransferMan NK 2 micromanipulator.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers


title: JSC204_102413

description: single cell in lysis buffer

source_name: lung cancer xenograft derived CTC

value: lung cancer xenograft derived CTC


title: JSC201_101613

description: single cell in lysis buffer


title: JSC212_041814

description: single cell in lysis buffer

value: lung cancer xenograft derived primary tumor cell


title: JSC203_101613

description: single cell in lysis buffer


title: JSC207_022114

description: single cell in lysis buffer


title: JSC209_041814

description: single cell in lysis buffer


title: JSC210_041814

description: single cell in lysis buffer


title: JSC194_100213

description: single cell in lysis buffer


title: JSC202_101613

description: single cell in lysis buffer


title: JSC208_041814

description: single cell in lysis buffer


title: JSC214_041814

description: single cell in lysis buffer


title: JSC197_101613

description: single cell in lysis buffer


title: D3_R1_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2017_D3_R1_24h_LPS_DMSO_AD_63


title: JSC193_100213

description: single cell in lysis buffer


title: Case6_Normal

city: Cincinnati

first: Minzhe

last: Guo

state: OH

address: 3333 BURNET AVENUE

department: Pulmonary Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Adapter sequences were removed using cutadapt (v1.2.1).
Sequenced reads were aligned to the human genome build hg19. Only high-quality reads were included in the analysis, following removal of multiply-mapped reads, reads with base quality <=30, and zero 'N's allowed per read.
FPKM (fragments per kilobase of transcript per million mapped reads) values were calculated using cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Adjacent normal lung tissues

growth_protocol: Not applicable

extract_protocol:
RNA was obtained according to Muley T, Herth FJF, Schnabel P, Dienemann H, Meister M. From tissue to molecular phenotyping: Pre-analytical requirements Heidelberg Experience. Transl Lung Cancer Res 2012;1(2):111-121. DOI: 10.3978/j.issn.2218-6751.2011.12.07
Libraries were prepared using Illumina TruSeq preparation kit per Illumina's protocols.

treatment_protocol: Not applicable

tag: subject status

value: invasive mucinous adenocarcinoma (IMA) patient

tag: subject/case id

value: lung

tag: tissue subtype

value: Adjacent normal lung tissues


title: D3_R2_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R2_6h_unst_DMSO_AD_55

tag: treatment


title: Case4_Normal


title: D1_R2_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2022_D3_R2_24h_unst_10JQ1_AD_68


title: JSC195_100213

description: single cell in lysis buffer

tag: cell type


title: JSC192_100213

description: single cell in lysis buffer


title: RNA-Seq__shMyc_IL-4_4h_R2

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm10 genome and transcripts using TopHat v2.1.0  (PMID: 23618408),  option --b2-very-sensitive  -g 1
Transcripts abundance were quantified using HTSeq (PMID: 25260700), option -s no
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm10 (Genome Reference Consortium GRCm38), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained with edgeR

growth_protocol: Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 10ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol).

extract_protocol: TruSeq RNA kit (Illumina) starting from polyA mRNA

tag: strain

value: IL4 (10 ng/ml) for 4hrs


title: Control


title: RNA-Seq__scramble_IL-4_4h_R2


title: D3_R2_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2024_D3_R2_24h_LPS_10JQ1_AD_70

tag: sample number


title: Case5_Normal


title: Case3_Normal


title: RNA-Seq__shMyc_IL-4_2h_R2

value: IL4 (10 ng/ml) for 2hrs


title: Case2_Normal


title: RNA-Seq__shMyc_IL-4_4h_R1


title: D3_R2_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R2_6h_LPS_DMSO_AD_57

tag: stimulation


title: RNA-Seq__shMyc_UT_R1

value: No treatment


title: Case1_Normal


title: D3_R1_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_6h_LPS_DMSO_AD_51

tag: stimulation treatment


title: D3_R1_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_6h_unst_DMSO_AD_49

tag: timepoint


title: RNA-Seq__scramble_UT_R2


title: RNA-Seq__scramble_IL-4_2h_R2


title: RNA-Seq__scramble_IL-4_2h_R1


title: RNA-Seq__shMyc_UT_R2


title: RNA-Seq__scramble_IL-4_4h_R1


title: D3_R2_6h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R2_6h_LPS_10JQ1_AD_58

tag: stimulation treatment time


title: Case6_Tumor

source_name: Invasive mucinous adenocarcinoma of the lung


title: Case5_Tumor

value: Invasive mucinous adenocarcinoma of the lung


title: D3_R1_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_6h_unst_10JQ1_AD_50

tag: donor


title: RNA-Seq__scramble_UT_R1


title: RNA-Seq_shCEBP-beta_IFNg_4h_R2

value: IFNg (100 ng/ml) for 4hrs


title: Case4_Tumor


title: RNA-Seq_shJunB_IFNg_4h_R2


title: D1_R2_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R2_6h_unst_10JQ1_AD_56

tag: batch


title: Case3_Tumor


title: D3_R1_6h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_6h_LPS_10JQ1_AD_52

tag: stimulation concentration


title: RNA-Seq_scramble_IFNg_4h_R2


title: RNA-Seq_shCEBP-beta_UT_R2


title: D3_R1_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_24h_unst_DMSO_AD_61


title: RNA-Seq_shJunB_UT_R2


title: Case2_Tumor


title: RNA-Seq_shCEBP-beta_IFNg_4h_R1


title: RNA-Seq_scramble_UT_R2


title: Case1_Tumor


title: D2_R2_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_6h_unst_DMSO_AD_31


title: RNA-Seq_shJunB_IFNg_4h_R1


title: D2_R2_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_6h_unst_10JQ1_AD_32

tag: treatment concentration


title: RNA-Seq_shJunB_UT_R1


title: poly(A) mRNA IFNg_IL4_4h_R3

description:
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 4hrs
Processed data file: CPM.TABLE.READS.txt

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm10 genome and transcripts using TopHat v2.1.0  (PMID: 23618408), allowing up to two mismatches and the option --b2-very-sensitive
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm10 (Genome Reference Consortium GRCm38), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained with edgeR

extract_protocol: Used TruSeq RNA kit (Illumina) starting from polyA mRNA


title: D2_R2_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_6h_LPS_DMSO_AD_33


title: RNA-Seq_scramble_UT_R1


title: poly(A) mRNA IFNg_4h_R3

description:
treatment: IFNg (100 ng/ml) for 4hrs
Processed data file: CPM.TABLE.READS.txt


title: A549_SPDEF_ChIPseq_rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Adapter sequences were removed using cutadapt (v1.2.1).
For each read, 5 end bases were trimmed using fastx_trimmer (v1.0.0). Reads were further trimmed using  fastq_quality_filter (v1.0.0) if more than 10% of bases with a quality score <20.
The remaining reads were aligned against human genome build hg19 using bowtie2 (v2.2.6) with "sensitive end-to-end" mode. Alignments with MAPQ quality score >=10 were included in the peak calling.
Peaks were called using MACS2 (v.2.1.0) with the following parameters: --gsize 2451960000 --bw=300 --ratio 1.0 --slocal 1000 --llocal 10000 --keep-dup 1 --bdg --qvalue 0.05. Each bed file contains the following 5 tab-delimited columns: chromosome name, start position of peak, end position of peak, peak name assigned by MACS2, integer score for display.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files containing narrow peaks generated by MACS2.

growth_protocol: A549 cells were cultured according to ATCC culture method.

extract_protocol:
ChIP was performed as described in Maeda et al., J Clin Invest. (2012) doi: 10.1172/JCI64048
Illumina sequencing libraries were prepared as described in Maeda et al., J Clin Invest. (2012) doi: 10.1172/JCI64048

treatment_protocol: A549 cells were infected with NKX2-1 and/or SPDEF-expressing lentivirus.

tag: cell line background

value: lung carcinoma cells

tag: infected with

value: lentivirus expressing NKX2-1

tag: chip antibody

value: SPDEF antibody

tag: chip antibody vendor

value: Santa Cruz Biotechnology (Santa Cruz, CA)

tag: chip antibody cat. #

tag: chip antibody lot #


title: RNA-Seq_shCEBP-beta_UT_R1

tag: cell type

value: BMDM cells (7th day of differentiation)

tag: treatment


title: RNA-Seq_scramble_IFNg_4h_R1

tag: strain


title: D2_R2_6h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_6h_LPS_10JQ1_AD_34

tag: sample number

tag: stimulation

value: LPS


title: poly(A) mRNA IL4_4h_R3

description:
treatment: IL4 (10 ng/ml) for 4hrs
Processed data file: CPM.TABLE.READS.txt


title: A549_SPDEF_ChIPseq_rep1


title: RNA-Seq__shMyc_IL-4_2h_R1


title: poly(A) mRNA IFNg_IL4_2h_R3

description:
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 2hrs
Processed data file: CPM.TABLE.READS.txt


title: A549_NKX2-1_input_rep2

value: none (input)


title: D2_R2_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_24h_unst_10JQ1_AD_44

value: unstim

tag: stimulation treatment

tag: timepoint


title: poly(A) mRNA IFNg_2h_R3

description:
treatment: IFNg (100 ng/ml) for 2hrs
Processed data file: CPM.TABLE.READS.txt


title: poly(A) mRNA IL4_2h_R3

description:
treatment: IL4 (10 ng/ml) for 2hrs
Processed data file: CPM.TABLE.READS.txt


title: D3_R1_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D3_R1_24h_unst_10JQ1_AD_62

tag: stimulation treatment time

tag: donor


title: A549_SPDEF_input_rep2


title: poly(A) mRNA UT_R3

description:
treatment: No treatment
Processed data file: CPM.TABLE.READS.txt


title: A549_SPDEF_input_rep1


title: D2_R2_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_24h_LPS_10JQ1_AD_46

tag: stimulation concentration

tag: batch


title: poly(A) mRNA IL4_4h_R2


title: D2_R2_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_24h_LPS_DMSO_AD_45

value: DMSO


title: poly(A) mRNA IFNg_IL4_2h_R2


title: D2_R1_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_6h_unst_DMSO_AD_25


title: A549_NKX2-1_SPDEF_rep3

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Adapter sequences were removed using cutadapt (v1.2.1).
For each read, 5 end bases were trimmed suing fastx_trimmer (v1.0.0). Reads were further trimmed using  fastq_quality_filter (v1.0.0) if more than 10% of bases with a quality score <20.
The remaining reads were aligned against human genome build hg19 using bowtie2 (v2.2.5) and Tophat (v2.1.0) with following parameters: --read-mismatches 2 --read-edit-dist 2 --read-realign-edit-dist 1000 -a 8 -m 0 -i 70 -I 500000 -g 20 --min-segment-intron 50 --max-segment-intron 500000 --segment-mismatches 2 --segment-length 25 --library-type fr-unstranded --max-insertion-length 3 --max-deletion-length 3.
Counts were generated using htseq-count (v0.6.1) with the following parameters: mode (union), stranded (no), minimum alignment quality (10), feature type (exon), and ID attribute (gene_id).
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing abundance measurements in raw counts

extract_protocol:
RNA was extracted using Trizol Reagent (ThermoFisher, cat# 15596026) and purified using Rneasy MinElute Cleanup Kit (Qiagene, cat# 74204).
Libraries were prepared using Illumina TruSeq preparation kit per Illumina's protocols.

treatment_protocol: A549 cells expressing NKX2-1 were infected with pGK control, pGK.SPDEF or pGK.FOXA3-expressing lentivirus.

tag: cell line background

tag: genotype/variation

value: expressing NKX2-1

value: SPDEF-expressing lentivirus


title: poly(A) mRNA IL4_2h_R2


title: D2_R2_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R2_24h_unst_DMSO_AD_43


title: A549_NKX2-1_SPDEF_rep2

tag: infected with


title: D2_R1_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_6h_unst_10JQ1_AD_26

tag: treatment concentration


title: poly(A) mRNA IFNg_IL4_4h_R1


title: poly(A) mRNA IFNg_4h_R1


title: D2_R1_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_6h_LPS_DMSO_AD_27


title: A549_NKX2-1_SPDEF_rep1


title: A549_NKX2-1_ChIPseq_rep2

tag: chip antibody

value: NKX2-1 (TTF-1) antibody

tag: chip antibody vendor

value: Seven Hills Bioreagents (Cincinnati, OH)

tag: chip antibody cat. #


title: poly(A) mRNA IFNg_IL4_2h_R1

tag: cell type


title: A549_NKX2-1_FOXA3_rep3

value: FOXA3-expressing lentivirus


title: poly(A) mRNA IL4_4h_R1

tag: strain


title: poly(A) mRNA IFNg_2h_R1


title: D2_R1_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_24h_unst_DMSO_AD_37

tag: sample number

tag: treatment


title: poly(A) mRNA IFNg_IL4_4h_R2

description:
treatment: IFNg (100 ng/ml) and IL4(10ng/ml) for 4hrs
Processed data file: CPM.TABLE.READS.txt


title: A549_NKX2-1_ChIPseq_rep1

tag: chip antibody lot #


title: A549_NKX2-1_FOXA3_rep2


title: poly(A) mRNA IFNg_2h_R2


title: poly(A) mRNA UT_R2


title: A549_NKX2-1_input_rep1


title: poly(A) mRNA IL4_2h_R1


title: A549_NKX2-1_pGK_rep3

value: Control (pGK)-expressing lentivirus


title: D2_R1_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_24h_LPS_DMSO_AD_39

tag: stimulation

tag: stimulation treatment

tag: timepoint


title: A549_NKX2-1_pGK_rep2


title: A549_NKX2-1_pGK_rep1


title: D3_R2_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_6h_unst_10JQ1_AD_08

tag: stimulation treatment time

tag: donor


title: A549_NKX2-1_FOXA3_rep1

tag: cell line background


title: D1_R2_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_6h_unst_DMSO_AD_07

tag: batch


title: poly(A) mRNA UT_R1


title: D2_R1_6h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_6h_LPS_10JQ1_AD_28

tag: stimulation concentration


title: RNA-seq of Vehicle-TGFb treated HSC rep 2

first: Chan

last: Zhou

state: Massachusetts

address: 55 Fruit Street

department: gastroenterology

institute: Mass General Hospital, Harvard Medical School

data_processing:
Raw RNA-seq data were mapped into human reference genome (hg19) with bowtie2 (v2.1.0). Furthermore, HTSeq (v0.6.1) was used to quantify expression of coding genes in HSCs under different conditions. The mapped reads in bam format were converted into BigWig.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; text fileswith the number of reads mappped into the coding and noncoding genes from the RNA-seq

source_name: Hepatic stellate cells (HSC) with vehicle and TGF-beta treatment

growth_protocol: HSC myofibroblasts were cultured ex vivo in DMEM with 10% FCS.

extract_protocol:
Total RNA was extracted with TRIzol reagent, treated with DNAse I and cleaned using an acid-phenol:chloroform extraction. RNA quality was checked using an Agilent TapeStation 2200. All samples had a RIN score greater than 9.
RNA-seq libraries were prepared from 600 ng of total RNA according to the manufacturer’s instructions for the Illumina TruSeq Stranded mRNA Kit and barcoded for sequencing.

treatment_protocol: HSC myofibroblasts were treated with either ethanol vehicle or nortriptyline (27 uM) for 48 hours prior to RNA extraction. Prior to TGF-beta stimulation, HSCs were serum starved in media containing DMEM with 0.2% bovine serum albumin (BSA) for 48 hours.  Cells were then treated with TGF-β (2.5ng/ml) and either ethanol vehicle or nortriptyline (27 uM) for 16 hours prior to harvest.

value: adult HSC myofibroblasts

tag: passage

value: passage 7-8

value: serum starved for 48 hours before receiving TGF-beta (2.5ng/ml) ethanol vehicle for 16 hours


title: D2_R1_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_24h_unst_10JQ1_AD_38

tag: treatment concentration


title: D1_R2_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_6h_LPS_DMSO_AD_09


title: RNA-seq of Vehicle-TGFb treated HSC rep 1


title: RNA-seq of Nortriptyline-TGFb treated HSC rep 2

source_name: Hepatic stellate cells (HSC) with Nortriptyline and TGF-beta treatment

value: serum starved for 48 hours before receiving TGF-beta (2.5ng/ml) and nortriptyline (27 uM) for 16 hours


title: D1_R2_6h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_6h_LPS_10JQ1_AD_10


title: D2_R1_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D2_R1_24h_LPS_10JQ1_AD_40


title: D1_R2_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_24h_LPS_DMSO_AD_21


title: RNA-seq of Vehicle treated HSC rep 2

source_name: Hepatic stellate cells (HSC) with vehicle treatment

value: ethanol vehicle for 48 hours


title: RNA-seq of Vehicle treated HSC rep 1


title: D1_R2_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_24h_unst_DMSO_AD_19


title: RNA-seq of Nortriptyline-TGFb treated HSC rep 1


title: D3_R2_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_24h_unst_10JQ1_AD_20


title: D1_R1_6h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_6h_unst_DMSO_AD_01


title: RNA-seq of Nortriptyline treated HSC rep 2

source_name: Hepatic stellate cells (HSC) with Nortriptyline treatment

value: nortriptyline 27uM for 48 hours


title: D1_R1_6h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_6h_unst_10JQ1_AD_02


title: D1_R2_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R2_24h_LPS_10JQ1_AD_22


title: RNA-seq of Nortriptyline treated HSC rep 1


title: wt rep2

city: Göttingen

first: Björn

last: Schwalb

address: Fassberg 11

country: Germany

institute: MPI

data_processing:
Acquisition of data obtained from 4tU-Seq experiments was performed as described (Schulz et al., 2013), with minor modifications. Briefly, paired-end 50 base reads with additional 6 base reads of barcodes were obtained for labeled RNA. Reads were demultiplexed and aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using STAR (version 2.3.0) (Dobin et al., 2013). SAMTools was used to quality filter SAM files (Li et al., 2009). Alignments with MAPQ smaller than 7 (-q 7) were skipped and only proper pairs (-f99, -f147, -f83, -f163) were selected. Further processing of the data was carried out using R/Bioconductor (Gentleman et al., 2004; Ihaka and Gentleman, 1996).
We used a spike-in (RNAs) normalization strategy essentially as described before in (Schwalb et al., 2016) to allow observation of global shifts in 4sU-seq signal. Read counts for all spike-ins necessary to that end were calculated using HTSeq (Anders et al., 2015). Those size factors were used to correct for library size and sequencing depth variations.
Piled-up counts for every genomic position were summed up over replicates, using fragment coverage i.e. counting both sequenced bases covered by reads and unsequenced bases spanned between proper mate-pair reads.
Genome_build: S. cerevisiae genome (sacCer3, Version R64-1-1, released 03Feb2011, http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/S288C_reference_genome_R64-1-1_20110203.tgz)
Supplementary_files_format_and_content: tabular containing read counts according to Sc.cerevisiae.feature.anno_Steinmetz_2013.gtf

organism: Saccharomyces cerevisiae BY4741

source_name: wt

growth_protocol: inoculate strain from O/N culture at OD600 0.1, grow at 30C in YPD to OD600 0.8, label with 5mM 4thiouracil final conc. for 6 minutes, spin 1 min, discard supernatant, freeze in lN2

extract_protocol:
add spike-ins before cell lysis, extract total RNA with phenol/chloroform, purify labeled RNA
using NUGen Ovation Universal RNA-Seq System starting with 100 ng RNA input

tag: genotype

value: wt


title: D1_R1_6h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_6h_LPS_DMSO_AD_03

value: LPS


title: wt rep1

treatment_protocol: label with 5mM 4thiouracil final conc. for 6 minutes


title: D1_R1_24h_unst_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_24h_unst_DMSO_AD_13


title: D1_R1_24h_unst_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_24h_unst_10JQ1_AD_14


title: rtf1 ko rep1


title: rtf1 ko rep2


title: D1_R1_24h_LPS_DMSO

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_24h_LPS_DMSO_AD_15


title: paf1 ko rep2


title: paf1 ko rep1


title: D1_R1_24h_LPS_10JQ1

description:
counts_1n2_combined.tsv
batch2_combined.counts
iBET_hAM_2016_D1_R1_24h_LPS_10JQ1_AD_16


title: Input time point 0 no UV

status: Public on Mar 01 2017

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

description: small RNA seq

data_processing:
basecalling performed by FASTERIS company (HiSeq Control Software 2.2.38 - RTA 1.18.61.0 - CASAVA 1.8.2)
3' adapter removal performed by FASTERIS company
mapping performed on Arabidopsis genome (TAIR10) with bowtie (parameters -t -q -y -e 50 -n 0 -a --best --strata)
suppress reads overlapping miR coordinates (with bedtools intersectbed -f 0.9)
filtering reads of 21, 22-23, 24-25, 26-30, 31-40 nt with awk script
Genome_build: TAIR10
Supplementary_files_format_and_content: gff files contain the number of reads. Header names for the gff files : 1. Chromosome, 2. Source, 3. Region, 4. Start, 5. End, 6. Number of reads, 7. Strand, 8. Frame, 9. Annotation

source_name: Input time point 0 no UV

growth_protocol: 16/8 photoperiod (light/dark)

extract_protocol:
Total RNA were prepared using Trizol (Sigma)
According to FASTERIS company

treatment_protocol: UV-C treatment (3000 J/m2). Harvest 30 min after UV-C exposure

tag: developmental stage

value: 2 week-old plants

tag: growth condition

value: in vitro

tag: ip antibody

value: no UV

tag: time

value: time point 0

tag: tissue

value: seedlings


title: RIP DDB2 time point 0 no UV

description: DDB2 IP and small RNA seq

source_name: RIP DDB2 time point 0 no UV

value: ANTI-FLAG M2 affinity gel (Sigma A2220)

tag: treatment


title: RIP AGO1 time point 15 min after UV

description: AGO1 IP and small RNA seq

source_name: RIP AGO1 time point 15 min after UV

value: UV

value: time point 15 min


title: Input time point 15 min after UV

description: small RNA seq

source_name: Input time point 15 min after UV


title: RIP DDB2 time point 15 min after UV

description: DDB2 IP and small RNA seq

source_name: RIP DDB2 time point 15 min after UV


title: RIP AGO1 time point 0 no UV

description: AGO1 IP and small RNA seq

source_name: RIP AGO1 time point 0 no UV


title: Sample PBMC-RPMI capture replicate 2 with 10.0 ng cDNA input

city: Nijmegen

first: Kees

last: Albers

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Medical Center

description:
Isolation and stimulation of peripheral blood mononuclear cells (PBMC) was performed as previously described (van de Veerdonk et al). In short, venous blood was collected into EDTA tubes and primary blood mononuclear cells (PBMCs) were isolated by density centrifugation of blood diluted 1:1 in PBS over Ficoll-Paque (Pharmacia Biotech AB, Uppsala, Sweden). Cells were washed three times in PBS and resuspended in RPMI 1640 (Dutch modified) supplemented with 50 mg/L gentamicin, 2 mM l-glutamine, and 1 mM pyruvate. Cells were counted in a Coulter Counter Z (Beckman Coulter, Mijdrecht, the Netherlands) and adjusted to 5x10^6 cells/mL. Mononuclear cells (5x10^7) in a 2 mL volume were added to round-bottom 6-well plates (Greiner, Alphen a/d Rijn, the Netherlands) and incubated with either culture medium (negative control) or heat killed (HK) Candida (1x106/mL) for 24 hours before isolation of RNA using RNeasy mini kit (Qiagen, Venlo, The Netherlands).
processed data file:
all_samples_molecule_counts.txt
cdna_mips_geuvadis.txt

data_processing:
Match each read pair to a designed smMIP probe (allowing two mismatches);
Remove likely extension-ligation dimers;
For all reads assigned to a given smMIP probe, identify the molecule counts from the unique molecular identifiers;
Determine the read-dependent threshold for UMIs due to sequencing errors;
Estimate normalized expression levels from error-corrected molecule counts integrating replicates using a dedicated Bayesian model.
Genome_build: Reads for the HEK/K562 allelic ratio experiment were mapped to hg19. For all other experiments, no read mapping was performed.
Supplementary_files_format_and_content:
Tab-delimited file with molecule counts for each smMIP and sample, corrected and uncorrected for sequencing errors in the molecular identifiers.
all_samples_molecule_counts.txt: txt file with molecule counts for all experiments
cdna_mips_ercc.txt: txt file with probe design for ERCC experiments
cdna_mips_geuvadis.txt: txt file with probe design for PBMC and EBV experiments
cdna_mips_ase-K562-HEK293.txt: txt file with probe design for allelic ratio experiments

source_name: Peripheral blood mononuclear cells

growth_protocol: Primary cells and cell lines were grown according to the description provided for each sample.

extract_protocol:
The isolated total RNA was quantified using the Qubit RNA HS assay kit (Thermo Fisher Scientific, Waltham, MA, USA). cDNA synthesis of 2-5 µg of RNA was performed with iScript (BIO-RAD, Hercules, CA, USA) reverse trancriptase. After cDNA synthesis, the cDNA was purified using Qiaquick (Qiagen, Venlo, The Netherlands) purification columns, and cDNA quantity was measured using the Qubit ssDNA assay kit (Thermo Fisher Scientific).
Single-molecule inversion probes applied to cDNA. Main steps are 1) MIP phosphorylation 2) MIP capture 3) Exonuclease treatment; 4) PCR amplification
Targeted RNA-Seq using cDNA-smMIPs

treatment_protocol: Except for the PBMC stimulation experiment, cells were not stimulated. In the PBMC experiment, cells were stimulated with heat-killed Candida Albicans.

tag: cell type

value: PBMC

tag: amount cdna (ng) input used for smmip capture

tag: number of pcr cycles

tag: cdna sample id


title: Sample PBMC-RPMI capture replicate 1 with 50.0 ng cDNA input


title: Sample PBMC-RPMI capture replicate 1 with 10.0 ng cDNA input


title: Sample PBMC-RPMI capture replicate 2 with 50.0 ng cDNA input


title: Sample PBMC-RPMI capture replicate 2 with 100.0 ng cDNA input


title: poly(A) mRNA IFNg_4h_R2

description:
treatment: IFNg (100 ng/ml) for 4hrs
Processed data file: CPM.TABLE.READS.txt

source_name: Primary bone marrow-derived macrophages (BMDM)

tag: strain

value: BMDM cells (7th day of differentiation)


title: Sample PBMC-CAN capture replicate 2 with 50.0 ng cDNA input


title: Sample PBMC-CAN capture replicate 2 with 10.0 ng cDNA input


title: Sample PBMC-CAN capture replicate 2 with 100.0 ng cDNA input


title: Sample K562HEK-9 capture replicate 2 with 10.0 ng cDNA input

description:
Culturing of HEK cell line: HEK293T cells (ECACC 12022001) were cultured in 100mm tissue-culture treated culture dishes (Corning, New York, USA) in DMEM medium containing 10% (vol/vol) Fetal Bovine Serum 1% penicillin/streptomycin and 1% sodium pyruvate (all Sigma-Aldrich, St. Louis, USA). At passage 12, cells were detached using 0.25% Trypsin (BD Biosciences, San Jose, USA) after which ~3 million cells were used for RNA isolation. Culturing of K562 cell line: K562 cells (ECACC 89121407) were cultured in 75 cm2 cell culture flasks (Corning, New York, USA) in RPMI 1640 medium containing 15% Fetal Bovine Serum, 2% HEPES and 1% penicillin/streptomycin (all Sigma-Aldrich, St. Louis, USA). ~6 million cells were used for RNA isolation. Allelic ratio dilution curve: cDNA of K562 and HEK293T cells was combined in a serial dilution. cDNA of K562 and HEK293T cells was diluted to a final concentration of 1 ng/ul. The serial dilution started with 75% K562 cDNA and 25% HEK293T cDNA. For the following steps of the serial dilution, 75% of the cDNA from the previous step was combined with 25% HEK293T cDNA. This resulted in a series of 8 cDNA samples of which the concentration K562 cDNA exponentially decreased and the HEK293T cDNA increased accordingly. One sample with only K562 cDNA and one sample with only HEK293T cDNA were also included in the experiment. Subsequently, samples were divided into two 10 ul duplicates containing 10 ng cDNA each. Capture was performed using the allelic-ratio smMIPS.
processed data file:
all_samples_molecule_counts.txt
cdna_mips_ase-K562-HEK293.txt

source_name: K562 and HEK293 cell line


title: Sample PBMC-CAN capture replicate 1 with 100.0 ng cDNA input


title: Sample PBMC-CAN capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-9 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-8 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-7 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-7 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-6 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-6 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-5 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-4 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-3 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-4 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-3 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-1 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-2 capture replicate 2 with 10.0 ng cDNA input


title: Sample K562HEK-2 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-5 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-10 capture replicate 1 with 10.0 ng cDNA input


title: Sample K562HEK-10 capture replicate 2 with 10.0 ng cDNA input


title: Sample EBV3 capture replicate 2 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 1

description:
Human B-lymphoblast cells of two anonymized healthy individuals were immortalized by transformation with the Eppstein?Barr virus. Cells were cultured in RPMI1640 medium (Sigma, St Louis, MO) containing 10% (vol/vol) Fetal Bovine Serum (Sigma), 1% 10?U/ul penicillin and 10 ug/ul streptomycin (Sigma), at a density of 0.5x10^6 cells/ml. Fresh medium was supplied twice a week.
processed data file:
all_samples_molecule_counts.txt
cdna_mips_geuvadis.txt

source_name: EBV-transformed lymphocytes (LCLs)

value: LCL


title: Sample EBV3 capture replicate 1 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 1


title: Sample K562HEK-1 capture replicate 1 with 10.0 ng cDNA input


title: Sample PBMC-CAN capture replicate 1 with 50.0 ng cDNA input


title: Sample EBV2 capture replicate 1 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 1


title: Sample EBV3 capture replicate 2 with 50.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 2 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 1


title: Sample EBV3 capture replicate 2 with 5.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample K562HEK-8 capture replicate 2 with 10.0 ng cDNA input


title: Sample EBV3 capture replicate 2 with 10.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV3 capture replicate 1 with 50.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV3 capture replicate 1 with 5.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 2 with 50.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV3 capture replicate 1 with 10.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 1 with 50.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 2 with 5.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 1 with 5.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV2 capture replicate 2 with 10.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV3 capture replicate 2 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 2


title: Sample EBV3 capture replicate 1 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 2


title: Sample EBV2 capture replicate 1 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 2


title: Sample EBV3 capture replicate 2 with 50.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV3 capture replicate 1 with 5.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample PBMC-RPMI capture replicate 1 with 100.0 ng cDNA input


title: Sample EBV3 capture replicate 2 with 5.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 1 with 50.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV3 capture replicate 1 with 10.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 2 with 5.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 2 with 50.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV3 capture replicate 2 with 10.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 1 with 10.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV3 capture replicate 1 with 50.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 2 with 10.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 1 with 5.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV3 capture replicate 1 with 10.0 ng cDNA input in experiment 1


title: Sample EBV3 capture replicate 2 with 100.0 ng cDNA input in experiment 1


title: Sample EBV3 capture replicate 2 with 10.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 1 with 10.0 ng cDNA input in experiment 2 by experimentalist 1


title: Sample EBV3 capture replicate 1 with 100.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 1 with 50.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 2 with 50.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 2 with 10.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 1 with 10.0 ng cDNA input in experiment 1


title: Sample EBV2 capture replicate 2 with 5.0 ng cDNA input in experiment 2 with 23 PCR cycles by experimentalist 2


title: Sample EBV3 capture replicate 1 with 50.0 ng cDNA input in experiment 2 by experimentalist 2


title: Sample EBV2 capture replicate 1 with 100.0 ng cDNA input in experiment 1


title: A549 PARP3-/- pyridostatin_RNA-seq 3

city: Brookline

first: Tovah

middle: A

last: Day

address: 450 Brookline Avenue

institute: Dana Farber Cancer Institute

description: TD12; 20161103_12_TD3584_S12

data_processing:
Illumina Bcl2fastq v2.16
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample 1-12 in a matrix

source_name: A549 PARP3-/- cells

growth_protocol: A549 lung adenocarcinoma cells were maintained under standard conditions in DMEM with 10% FBS and pen/strep.

extract_protocol:
Total RNA was isolated from wild-type and PARP3-/- A549 cells using the Qiagen RNeasy Mini Kit according to the manufacturer’s specifications.
RNA was subjected to Illumina-based RNA-seq using a TruSeq Stranded mRNA Library Prep Kit (Illumina) as per the manufacturer’s recommendations. RNA-seq libraries were sequenced with an Illumina NextSeq 500 using single end 75 base pair sequencing.

treatment_protocol: Cells were either treated with vehicle (DMSO) or 1 micromolar pyridostatin for 24 hr before isolation of RNA.

tag: cell line

tag: genotype/variation

tag: treated with

value: 1 micromolar pyridostatin for 24 hr


title: A549 PARP3-/- pyridostatin_RNA-seq 1

description: TD10; 20161103_10_TD3584_S10


title: A549 PARP3-/- pyridostatin_RNA-seq 2

description: TD11; 20161103_11_TD3584_S11


title: A549 WT pyridostatin_RNA-seq 3

description: TD9; 20161103_9_TD3584_S9

source_name: A549 WT cells

value: wild type


title: Sample EBV3 capture replicate 2 with 50.0 ng cDNA input in experiment 1


title: A549 PARP3-/- vehicle_RNA-seq 3

description: TD6; 20161103_6_TD3584_S6

value: vehicle


title: A549 WT pyridostatin_RNA-seq 1

description: TD7; 20161103_7_TD3584_S7


title: A549 WT pyridostatin_RNA-seq 2

description: TD8; 20161103_8_TD3584_S8


title: A549 PARP3-/- vehicle_RNA-seq 1

description: TD4; 20161103_4_TD3584_S4


title: A549 WT vehicle_RNA-seq 1

description: TD1; 20161103_1_TD3584_S1


title: A549 WT vehicle_RNA-seq 3

description: TD3; 20161103_3_TD3584_S3


title: A549 PARP3-/- vehicle_RNA-seq 2

description: TD5; 20161103_5_TD3584_S5


title: A549 WT vehicle_RNA-seq 2

description: TD2; 20161103_2_TD3584_S2


title: 293FT + ZIKV

city: La Jolla

first: Tariq

last: Rana

state: CA

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
The reads were aligned to UCSC hg19 reference genome using TopHat (v 1.4.1).
DUST scores were calculated with PRINSEQ Lite (v 0.20.3), and low-complexity reads (DUST >4) were removed from the BAM files.
The alignment results were parsed via the SAMtools to generate SAM files.
Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) using the “union” option.
After removing absent features (zero counts in all samples), the raw counts were imported into R/Bioconductor package DESeq2 to identify differentially expressed genes among the samples.
P values for differential expression were calculated using binomial test for differences between the base means of two conditions. The p values were adjusted for multiple test correction using the Benjamini–Hochberg algorithm to control the false discovery rate.
Genome_build: hg19
Supplementary_files_format_and_content: processed_file.xlsx is an excel file that contains the read count and analysis result from DESeq2

growth_protocol: Microglia, THP-1, BJ, and 293FT cells were maintained under standard culture conditions at 37°C in a 5% CO2 atmosphere. THP-1 cells, a human leukemia monocytic cell line, were cultured in RPMI 1640 medium supplemented with 10% FBS and 50 μM β- mercaptoethanol (Sigma). THP-1 cells were differentiated into macrophages by treatment with 5 ng/ml phorbol-12-myristate-13-acetate (PMA) overnight. The following day, the medium was replaced with fresh medium without PMA. 293FT human embryonic kidney cells and the human fibroblast cell line BJ were cultured in DMEM (Invitrogen) supplemented with 10% FBS. The human microglial cell line (kindly provided by Dr. Jon Karn lab at the Case Western Reserve University, Ohio, USA) was cultured in DMEM medium with high glucose supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA was extracted from the cell lines using an RNeasy Mini Kit (Qiagen), following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ZIKV prototype MR766 was propagated in the low passage Vero cell line. Vero cells were infected with virus at a MOI of 1 in EMEM medium supplemented with 10% FBS. The medium was replaced with fresh medium 24 h after infection and the viral supernatant was collected at 48 h post-infection. Viral titers were assessed using iScript One-Step RT-PCR kit (Bio-Rad) and the viral copy number was calculated from a standard curve of in vitro transcribed viral RNA transcripts. For infection, cell lines were seeded in 6-well culture plates at a density of 1 × 106 cells per well. ZIKV, diluted to the desired multiplicity of infection (MOI:1), was added to the cells and the plates were incubated at 37°C in a 5% CO2 atmosphere for 6, 12, 24, or 48 h. As controls, cells were incubated with culture supernatants from uninfected Vero cells (mock-infected controls). At the indicated times post-infection, cell supernatants were collected for determination of viral copy number.

tag: cell

value: ZIKV


title: Sample EBV2 capture replicate 2 with 100.0 ng cDNA input in experiment 1


title: THP-1


title: BJ

source_name: BJ

value: BJ


title: BJ + ZIKV


title: TCPS - SkBr3

city: Amherst

first: Alyssa

middle: D

last: Schwartz

address: 686 N pleasant St, Goessmann 159

department: Chemical Engineering

institute: University of Massachusetts Amherst

description: Associated genes.fkpm_tracking header: q12

data_processing:
Reads were mapped to the reference genome using Tophat2 with a bowtie aligner
Normalized read counts were determined using cufflinks
Differential expression was determined with Cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking file was generated using cufflinks to identify Fragments Per Kilobase of transcript per Million mapped reads

source_name: Human Breast Cancer Cell Line

growth_protocol: Cells were grown in DMEM with 10% FBS and 1% pen/strep

extract_protocol:
Total RNA was collected using  GenElute Mammalian total RNA miniprep kit (Sigma)
Libraries were prepared following the protocol for the TRUseq LT kit

treatment_protocol: Cells were seeded onto TCPS or 2D biomaterials, encapsulated into 3D gels as single cells, grown into spheroids in PEG-polyNIPAAM for 14 days before encapsulation into 3D  gels, or cells were disociated back onto TCPS after being grown into spheroids for 14 days in PEG-polyNIPAAM

tag: subtype

value: HER2-overexpressing Breast Cancer

tag: material platform

value: TCPS

tag: growth protocol

value: SkBr3 cells cultured on TCPS


title: Microglia

source_name: Microglia

value: Microglia


title: Microglia + ZIKV


title: Spheroids - 231

description: Associated genes.fkpm_tracking header: q9

value: Triple Negative Breast Cancer

value: Spheroids in polyNIPAAM

value: MDA-MB-231 cells grown into spheroids for 14 days


title: Spheroids-to-TCPS - 231

description: Associated genes.fkpm_tracking header: q7

value: Spheroids dissociated onto TCPS

value: MDA-MB-231 cells grown into spheroids for 14 days, then replated onto TCPS


title: TCPS - 231

description: Associated genes.fkpm_tracking header: q11

value: MDA-MB-231 cells cultured on TCPS


title: THP-1 + ZIKV


title: 293FT


title: Mouse - SkBr3

description: Associated genes.fkpm_tracking header: q6

value: Mouse Xenograft

value: SkBr3 cells in vivo


title: 2D Stiff - 231

description: Associated genes.fkpm_tracking header: q4

value: 2D Gel - 33 kPa

value: MDA-MB-231 cells cultured on a stiff 2D gel


title: 2D Stiff - SkBr3

description: Associated genes.fkpm_tracking header: q2

value: SkBr3 cells cultured on a stiff 2D gel


title: 2D Soft - 231

description: Associated genes.fkpm_tracking header: q3

value: 2D Gel - 10 kPa

value: MDA-MB-231 cells cultured on a soft 2D gel


title: 2D Soft - SkBr3

description: Associated genes.fkpm_tracking header: q1

value: HER2-overexpressing Breast Cancer

value: SkBr3 cells cultured on a soft 2D gel


title: RNA_Seq_BE2C_control_2

city: Cologne

first: Yulia

last: Kargapolova

address: Robert-Koch-Straße 21

department: CMMC

institute: Cologne University

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the human reference assembly, version hg19, using STAR
Normalized bedGraph files were generated using bedtools
differentiation gene expression was assessed by edgeR Bioconductor package
Genome_build: hg19

source_name: brain; derived from metastatic site: bone marrow; cell line

growth_protocol: BE(2)-C cells were passaged in Dulbecco’s Modified Eagle’s Medium (high glucose) with the following components added: heat inactivated fetal bovine serum at a final concentration 10% and Penicillin-Streptomycin at a final concentration 1%.

extract_protocol:
Total RNA was isolated using Qiagen miRNeasy Kit
Total RNA was ribo-depleted, IlIiumina stranded total RNA library Prep kit was used to create the libraries.

treatment_protocol: For siRNA transfection 100,000 cells were seeded in 12 well plates 12-16 hours before transfection.  Next they were transfected wih siRNAs against CSTF2tau or unrelated control, using Roti-Fect siRNA transfection kit. RNA was isolated 72 hours after transfection.

tag: genotype

value: WT

value: control siRNA


title: RNA_Seq_BE2C_CSTF2tau_KD_2

source_name: brain; derived from metastatic site: bone marrow;cell line

value: CSTF2tau siRNA


title: RNA_Seq_BE2C_control_1


title: MCF7_RUNX2_NoDOX_dup1_RNAseq

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

state: NY

department: School of Medicine

institute: New York University

description: processed data file: MCF7_RUNX2_NoDOX_v_DOX_raw_countmat.csv

data_processing:
ChIP-seq: ChIP-seq reads were aligned using bowtie
ChIP-seq: Peaks were called using MACS2 with default parameters, including a q value < 0.001
ChIP-seq: bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
ChIP-seq: A binding intensity matrix was generated using bamliquidator
ChIP-seq: Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
RNA-seq: RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
RNA-seq: Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
RNA-seq: Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
RNA-seq: Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
RNA-seq: All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
Genome_build: hg19
Supplementary_files_format_and_content: bed files for ER ChIP
Supplementary_files_format_and_content: Count Matrix Files for two separate experiments, one for MCF7 Parental and Tamoxifen Resistant lines, and anotherr for RUNX2 with and without DOX

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.

extract_protocol: Cell lines were extracted using the Rneasy (Qiagen # 74104) kit with the substitution of Trizol instead of Buffer RLT. Preparation for sequaencing is done using the Illumina Truseq RNAseq v2 kit (15025063)

tag: cell subtype

value: RUNX2 DOX inducible model

tag: condition

value: Full Medium


title: MCF7_RUNX2_NoDOX_dup2_RNAseq


title: MCF7_RUNX2_DOX_dup3_RNAseq

value: Full Medium + Doxycycline


title: MCF7_RUNX2_NoDOX_dup3_RNAseq


title: MCF7_RUNX2_DOX_dup2_RNAseq


title: Spheroids-to-TCPS - SkBr3

description: Associated genes.fkpm_tracking header: q8

value: Spheroids dissociated onto TCPS

value: SkBr3 cells grown into spheroids for 14 days, then replated onto TCPS


title: Spheroids - SkBr3

description: Associated genes.fkpm_tracking header: q10

value: Spheroids in polyNIPAAM

value: SkBr3 cells grown into spheroids for 14 days


title: MCF7_RUNX2_DOX_dup1_RNAseq


title: MCF7_Par_dup2_RNAseq

description: processed data file: MCF7_Parental_v_TAMresistant_raw_countmat.csv

value: Parental


title: MCF7_TAMR_dup1_RNAseq

value: Tamoxifen Resistance


title: MCF7_Par_dup1_RNAseq


title: MCF7_LTED_E2_ER_ChIPseq

extract_protocol: Cell lines before ChIP were then either introduced to White Medium DMEM with or without supplemental E2 or Doxycycline, Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit

value: Long Term Estrogen Deprivation

value: White Medium + E2


title: MCF7_RUNX2_DOX_HA_ChIPseq_dup2


title: MCF7_TAMR_dup2_RNAseq


title: MCF7_RUNX2_DOX_HA_ChIPseq_dup1


title: PE1B_ER_ChIPseq

source_name: patient derived Pleaural Effusion

value: Patient

value: Pleural Effusion


title: MCF7_TAMR_E2_ChIPseq


title: MCF7_LTED_noE2_ER_ChIPseq

value: White Medium


title: MCF7_TAMR_noE2_ER_ChIPseq


title: Mouse - 231

description: Associated genes.fkpm_tracking header: q5

value: Triple Negative Breast Cancer

value: Mouse Xenograft

value: MDA-MB-231 cells in vivo


title: MCF7_E2_ER_ChIPseq

value: Wild Type


title: RNA_Seq_BE2C_CSTF2tau_KD_1

value: WT

value: CSTF2tau siRNA


title: Baf53afl- EtOH rep1

city: Stanford

first: Erik

last: Miller

address: 279 Campus Drive

institute: Stanford University

description: ATAC-seq

data_processing:
Raw reads were mapped to the mm9/NCBI37 Mus musculus genome using Bowtie (version 0.12.9).
Nuclear ATAC-seq fragments smaller than 235 bp were used to call accessible sites. Accessible sites and ChIP-seq peaks were called by Model-based Analysis for ChIP-seq 2 (MACS2) (version 2.1.0). Peaks overlapping ENCODE “blacklist” regions were discarded.
To determine which peaks are significantly altered in knockout/treated cells versus wild-type/control cells, we merged peaks from both cell types and all replicates. Non-redundant read/fragment counts was calculated over the set of merged peaks that are common to all replicates by counting overlapping fragments (for paired-end). Non-redundant fragment depth was used as normalization factors for edgeR (version 3.12.1) analysis of differential peak density17. Peaks were deemed altered between samples if the False Discovery Rate (FDR) < 10%.
Genome_build: mm9
Supplementary_files_format_and_content: bed files generated using MACS2

source_name: Baf53afl/- ES cells

growth_protocol: We passaged 2-3 x 10^6 ES cells onto gelatin-coated 10 cm plates every two days and changed media every day. The cells were grown in serum-LIF ES cell media.

extract_protocol:
Cells were stained with Annexin V-FITC (eBioscience) and 7-AAD (BD Biosciences) and 50,000 viable cells were FACS sorted. Those cells were washed with PBS and then with RSB Buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2). Nuclei were obtained by re-suspending cells in 0.5 ml Lysis Buffer (0.1% Tween-20/RSB Buffer) and incubated for 10 minutes on ice.
Nuclei were pelleted by centrifuging for 10 minutes at 500xg, re-suspended in 50 µl of Transposition Mix (1X Tagmentation DNA Buffer, 2.5 µl Tagment DNA Enzyme (Illumina)), and incubated for 30 minutes at 37 ºC. DNA was purified with a MinElute PCR Purification Kit (QIAGEN) and libraries were amplified by PCR with barcoded Nextera primers (Illumina). Libraries were size selected using Agencourt AMPure XP (Beckman Coulter) for fragments between ~50 – 1000 bp according to the manufacturer’s instructions. Libraries were paired-end sequenced on a NextSeq Desktop Sequencer (Illumina).

treatment_protocol: Wild-type ES cells were treated 1 µM ICRF-193 or the equivalent volume of DMSO for 24 hours. Conditional knockout cells were treated with 0.8 µM tamoxifen or the equivalent volume of ethanol for 24 hours and then media was changed to media without tamoxifen or ethanol and cells were grown for another 48 hours.

tag: tissue

value: embryonic stem cells


title: Baf53afl- Tax rep2

description: ATAC-seq


title: Brgflfl Tax rep2

description: ATAC-seq

source_name: Brg1fl/fl ES cells


title: Baf53afl- EtOH rep2

description: ATAC-seq


title: Brgflfl EtOH rep2

description: ATAC-seq


title: Brgflfl EtOH rep1

description: ATAC-seq


title: Brgflfl Tax rep1

description: ATAC-seq


title: DMSO 1h rep3

description: ATAC-seq

source_name: WT ES cells

value: wild type


title: DMSO 1h rep2

description: ATAC-seq


title: ICRF 1h rep2

description: ATAC-seq


title: ICRF 1h rep3

description: ATAC-seq


title: DMSO 1h rep1

description: ATAC-seq


title: ICRF 24h rep2

description: ATAC-seq


title: DMSO 24h rep2

description: ATAC-seq


title: ICRF 24h rep1

description: ATAC-seq


title: Baf53afl- Tax rep1

description: ATAC-seq


title: DMSO 24h rep1

description: ATAC-seq


title: V16397/HHQ-HBV-8h_L5

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Clipping adapters and low-quality bases.
STAR
RSEM
edgeR
limma
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene level counts from RSEM output

source_name: PHH

extract_protocol:
On-column DNase I treatment was performed during RNA isolation with the RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).

value: liver

value: primary human hepatocyte

tag: donor number

tag: infection

value: HBV

tag: time

tag: treatment


title: V16397/HHQ-Mock-D8_L2

tag: cell type

value: Mock


title: CDH1+/THY1+ WT1

city: Bloomington

first: Aaron

last: Buechlein

state: IN

address: 1001 E 3rd St

department: Center for Genomics and Bioinformatics

institute: Indiana University

data_processing:
Sequenced reads were trimmed using Trimmomatic V 0.32 for adaptor sequence and low-quality sequence.   Remaining paired reads were then mapped to GRCm38.p4 whole genome using tophat2 v2.1.1 with parameters --b2-very-sensitive --read-edit-dist 2 --max-multihits 100
Mapped reads were quantified using featureCounts from the Subread v1.5.0-p3 package, with the following parameters: -p -t exon -g gene_id -s 2 -T 32 and gencode vM9 as the annotation.
DESeq2 V1.12.3 (R  version 3.3.1) was used to perform fold-change analysis on the raw counts table.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: tab-delimited text file includes the DESeq2 fold-change results

source_name: male germline stem cells

growth_protocol: GSCs were cultured on DR4 MEFs. GSC medium was used for GSCs maintenance, including StemPro-34 (Gibco), StemPro supplement (1X, Gibco); MEM vitamin solution (1X, Gibco); non-essentialamino acid solution (1X, Gibco); Antibiotic-Antimycotic (1X, Gibco); L-glutamine (1X, Hyclone); estradiol (Sigma), 30 ng/ml; progesterone (Sigma), 60ng/ml; fetal bovine serum (Hyclone), 1%; transferrin (Sigma), 100 ug/ml; insulin (Gibco), 25 ug/ml; Rat GDNF (peprotech), 10 ng/ml; human FGF (peprotech), 10 ng/ml; putrescine (Sigma),60 um; selenite (Sigma), 30 nM; pyruvic acid (Sigma), 30 ug/ml; lactic acid, 0.06% (Sigma), b-mercaptoethanol (Sigma), 50 uM; ascorbic acid (Sigma), 100 uM; D-biotin (Sigma), 10 ug/ml; D-glucose (Sigma), 6 mg/ml; BSA (Calbiochem), 5 mg/ml.

extract_protocol:
RNAs were isolated using RNeasy-plus micro kit (74034, Qiagen).
Libraries for each sample were constructed using the Illumina TruSeq Stranded Total RNA Library Prep Kit / Ribo-Zero Gold kit as per manufacturer’s instructions. Libraries were quantified using an Agilent 2200 TapeStation, pooled equimolar and sequenced on an Illumina NextSeq500 instrument using a NextSeq150-v2 Mid Output reagent kit and flowcells.

tag: passage

value: 6 to 8

tag: strain

tag: age

value: 5 weeks

tag: gender

value: male


title: V16397/8181-Mock1-D13_L4


title: CDH1+/THY1+ RP7

value: OCT4/GFP; Dox-OCT4

value: 8 weeks


title: CDH1+/THY1+ RP5

value: 19 days


title: CDH1-/THY1+ RP7


title: CDH1-/THY1+ RP5


title: CDH1-/THY1+ WT1


title: V16397/8181-HBV-D10_L3


title: V16397/8181-Mock-D8_L1


title: H44443/8181-Mock-D10_L1.D711


title: C15_+Zn_KP

city: Tsukuba

first: Amrit Kaur

last: Nanda

state: Ibaraki

address: 1-1 Ohwashi

department: Crop Livestock and Environment

country: Japan

institute: Japan International Research Center for Agricultural Sciences

description:
processed data file:
DESeq2_MinusZn.Inefficient_vs_PlusZn.Inefficient.csv
DESeq2_PlusZn.Inefficient_vs_PlusZn.Efficient.csv
DESeq2_Inefficient_vs_Efficient.csv
DESeq2_MinusZn_vs_PlusZn.csv

data_processing:
Samples were sequenced using Illumina HiSeq 2500, generating in average 15.5 million paired-end reads of 150 bases per sample.
The sequencing company (Novogene) performed an initial cleaning by removing reads containing adapters, reads containing N > 10% and reads containing low quality (Qscore <= 5) bases over 50 % of the total bases.
Following check with FastQC v0.11.5, the first 10 bases of all reads were trimmed, as well as low-quality bases from both ends (Qscore < 20) and low-quality regions from both ends (sliding window of 4 bases with Qscore < 15), using Trimmomatic v0.36.
Paired-reads of less than 100 bases were removed.
Paired reads were aligned against the Nipponbare reference genome (IRGSP-1.0, assembly GCA_001433935.1) from the EnsemblPlants database, using Hisat2 v2.0.4 with the options --no-mixed and --no-discordant.
Gene counting was performed at the gene feature level using featureCounts from the Subread package v1.5.0-p3 , with the parameters: -p -B -C -T 10 -t "gene"
Differential expression analysis was performed on the raw fragment counts using the R DESeq2 package v1.12.3, with the options - betaPrior = FALSE and - lfcThreshold = 1.
Genome_build: Oryza_sativa.IRGSP-1.0.31.dna_sm.genome.fa (Oryza sativa EnsemblPlants assembly IRGSP-1.0, INSDC Assembly GCA_001433935.1).
Supplementary_files_format_and_content: DESeq2 results files ("DESeqResults object") from various differential expression analyses, with annotations from the reference genome.

organism: Oryza sativa

source_name: Zn-Inefficient_media with Zn

growth_protocol: Rice seeds were sown in nutrient solution containing 12 μM FeEDTA and 0.1 mM CaCl2. After 1 week, solution was change to half strength Yoshida nutrient solution and solution was renewed every 3-4 days. Two-week-old plants were transferred to full strength Yoshida nutrient solution with 1 mM KHCO3 and 0.1% agar, containing Zn (+Zn) or not (-Zn).

extract_protocol:
Total RNA was extracted from crown tissue using the Qiagen RNeasy Plant Mini Kit, according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Plants were grown in full strength Yoshida nutrient solution containing 0.1% agar, 1 mM KHCO3 and 0 or 1.5 μM ZnSO4 for 8 days.

tag: genotype/variation

value: Kinandang Patong

tag: phenotype

value: Zn-Inefficient

tag: exposed to

value: +Zn

value: Crown

tag: time point

value: 8 days of treatment


title: C13_+Zn_IR74


title: H44443/8181-HBV-D8_L1.D710


title: ICRF 1h rep1

description: ATAC-seq

value: embryonic stem cells

tag: genotype


title: C12_+Zn_Nipponbare

description:
processed data file:
DESeq2_MinusZn.Efficient_vs_PlusZn.Efficient.csv
DESeq2_PlusZn.Inefficient_vs_PlusZn.Efficient.csv
DESeq2_Inefficient_vs_Efficient.csv
DESeq2_MinusZn_vs_PlusZn.csv

source_name: Zn-Efficient_media with Zn

value: Nipponbare

value: Zn-Efficient


title: H44442/HHQ-pIC-8h_L6.D711

value: liver

value: primary human hepatocyte

value: pIC


title: H44442/HHQ-pIC-4h_L5.D707

value: Mock


title: H44442/HHQ-pIC-24h_L7.D705


title: C11_+Zn_IR64


title: H44442/HHQ-Mock2-D13_L8.D707


title: C6_-Zn_RIL46

description:
processed data file:
DESeq2_MinusZn.Efficient_vs_PlusZn.Efficient.csv
DESeq2_MinusZn.Inefficient_vs_MinusZn.Efficient.csv
DESeq2_Inefficient_vs_Efficient.csv
DESeq2_MinusZn_vs_PlusZn.csv

source_name: Zn-Efficient_media without Zn

value: -Zn; Zn deficiency


title: C7_-Zn_KP

description:
processed data file:
DESeq2_MinusZn.Inefficient_vs_PlusZn.Inefficient.csv
DESeq2_MinusZn.Inefficient_vs_MinusZn.Efficient.csv
DESeq2_Inefficient_vs_Efficient.csv
DESeq2_MinusZn_vs_PlusZn.csv

source_name: Zn-Inefficient_media without Zn


title: H44442/HHQ-Mock-D6_L7.D711


title: H44442/HHQ-Mock-D3_L7.D709


title: C14_+Zn_RIL46


title: C2_-Zn_IR55179


title: H44442/HHQ-Mock-8h_L6.D709


title: H44442/HHQ-Mock-4h_L5.D705


title: H44442/HHQ-Mock-24h_L6.D703


title: H44442/HHQ-Mock-12h_L6.D701


title: C5_-Zn_IR74


title: H44442/HHQ-Mock1-D13_L8.D705


title: C4_-Zn_Nipponbare


title: C10_+Zn_IR55179


title: H44442/HHQ-HBV2-D13_L8.D708

value: HBV


title: H44442/HHQ-Mock-D10_L8.D703


title: H44442/HHQ-HBV1-D13_L8.D706


title: H44442/HHQ-HBV-D8_L8.D702


title: H44442/HHQ-HBV-D6_L7.D712


title: H44442/HHQ-IFN-4h_L5.D708

value: IFN


title: C3_-Zn_IR64


title: H44442/HHQ-HBV-D3_L7.D710


title: H44442/HHQ-HBV-D10_L8.D704


title: H44442/HHQ-IFN-24h_L7.D706


title: H44442/HHQ-HBV-D2_L7.D708


title: H44442/HHQ-HBV-4h_L5.D706


title: H44442/HHQ-IFN-8h_L6.D712


title: H44442/HHQ-HBV-24h_L6.D704


title: H44442/HHQ-HBV-12h_L6.D702


title: H44442/8181-pIC-8h_L3.D707


title: H44442/HHQ-Mock-D2_L7.D707


title: H44442/8181-pIC-24h_L4.D701


title: H44442/8181-Mock2-D13_L5.D703


title: H44442/8181-Mock-D3_L4.D705


title: H44442/8181-Mock-8h_L3.D705


title: H44442/8181-Mock-D6_L4.D707


title: H44442/8181-Mock-4h_L2.D701


title: H44442/8181-Mock-D2_L4.D703


title: H44442/8181-Mock-24h_L3.D711


title: H44442/8181-Mock-12h_L3.D709


title: H44442/8181-IFN-4h_L2.D704


title: H44442/8181-IFN-24h_L4.D702


title: H44442/8181-HBV2-D13_L5.D704


title: H44442/8181-HBV1-D13_L5.D702


title: H44442/8181-HBV-D3_L4.D706


title: H44442/8181-HBV-D2_L4.D704


title: H44442/8181-pIC-4h_L2.D703


title: Ku1919 clone 2 GSK343

city: Singapore

first: Xiaoran

last: Chai

state: Singapore

address: 60 Biopolis Street, Genome, #02-01

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Illumina Casava1.9 software was used for basecalling
Sequenced reads were trimmed for adaptor sequence,, then mapped to hg19 whole genome using STAR-2.3.0e with parameters --outSAMstrandField intronMotif
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks-2.1.1 with parameters -b -u --max-bundle-frags 100000000
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample

source_name: Ku1919 clone 2 GSK343

growth_protocol: Urothelial bladder carcinoma cell lines were maintained under 10% FBS contained culture medium

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

treatment_protocol: Urothelial bladder carcinoma cel lnese were treated with GSK343 (1 uM) for 14 days prior RNA extraction

value: Urothelial Bladder Carcinoma Cell line

value: wildtype


title: H44442/8181-HBV-8h_L3.D706


title: H44442/8181-HBV-4h_L2.D702


title: Ku1919 clone 1 GSK343

source_name: Ku1919 clone 1 GSK343


title: control-treated HeLa cells

city: Shanghai

first: Feng

last: Wang

state: Shanghai

address: Yueyang Road 320

department: State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science

country: China

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Map the single-end reads to human reference genome (GRCh38) using TopHat with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using GFOLD (v1.1.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: control-treated HeLa cells

growth_protocol: HeLa cells were maintained in Dulbecco’s Modified Eagle’s medium supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA were isolated using TRIzol (Invitrogen, USA)
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina) and then applied to sequencing on Illumina HiSeq 2000 in CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai.
Total RNAs were processed for single-end (1x100 nt) RNA-seq on an Illumina HiSeq2000 platform according to manufacturer’s instruction.

treatment_protocol: (1) HeLa cells were first starved for 12 hr followed by adding EGF (50 ng/ml) for 4hrs; (2) Stable knock-down of hnRNP A1 using retrovirus system was established in HeLa cells according to manufacturer’s instruction (Clontech)

tag: cell line

value: HeLa

value: control


title: hnRNP A1-knockdown HeLa cells

source_name: hnRNP A1-knockdown HeLa cells

value: hnRNP A1-knockdown


title: Ku1919 clone 2

source_name: Ku1919 clone 2


title: EGF-treated HeLa cells

source_name: EGF-treated HeLa cells

value: EGF


title: Ku1919 clone 1

source_name: Ku1919 clone 1


title: Ku1919 GSK343 rep 3_14days

value: Mutant


title: Ku1919 parental

source_name: Ku1919 parental


title: Ku1919 GSK343 rep 2_14days


title: Ku1919 control rep 3_14days

source_name: Ku1919 control


title: Ku1919 control rep 2_14days


title: Ku1919 GSK343 rep 1_14days


title: H44442/8181-HBV-D6_L4.D708


title: Ku1919 GSK343 rep 3_7days


title: Ku1919 GSK343 rep 2_7days


title: H44442/8181-IFN-8h_L3.D708


title: Ku1919 GSK343 rep 1_7days


title: H44442/8181-HBV-24h_L3.D712


title: Ku1919 control rep 2_7days


title: H44442/8181-HBV-12h_L3.D710


title: Ku1919 control rep 3_7days


title: RT4 control rep 2_14days

source_name: RT4 control


title: RT4 control rep 3_14days


title: RT4 GSK343 rep 1_14days

source_name: RT4 GSK343


title: Ku1919 control rep 1_7days


title: RT4 GSK343 rep 3_7days


title: RT4 control rep 2_7days


title: RT4 control rep 3_7days


title: RT4 GSK343 rep 1_7days


title: RT4 control rep 1_7days


title: KDM6A Mut rep 9

source_name: KDM6A Mut

value: Urothelial Bladder Carcinoma


title: KDM6A Mut rep 10


title: KDM6A Mut rep 6


title: Ku1919 control rep 1_14days


title: KDM6A Mut rep 2


title: KDM6A Mut rep 3


title: KDM6A Mut rep 7


title: RT4 GSK343 rep 2_14days


title: RT4 GSK343 rep 2_7days


title: KDM6A WT rep 9

source_name: KDM6A WT


title: RT4 GSK343 rep 3_14days


title: KDM6A WT rep 7


title: KDM6A WT rep 6


title: KDM6A Mut rep 4


title: KDM6A WT rep 4


title: KDM6A Mut rep 8


title: KDM6A WT rep 2


title: KDM6A WT rep 5


title: KDM6A WT rep 1


title: KDM6A Mut rep 5