title: QuantSeq_RNAseq_PMC14_2hours_DMSO

description:
RNAseq_Counts_PMC14_featureCounts_unnormalized.txt
PMC14-DMSO

data_processing:
For 3'-mRNA-seq (QuantSeq), Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0).
Fo 3'-mRNA-seq (QuantSeq), Read counting across genomic features was performed using featureCounts prior to differential gene expression analysis using limma voom. Gene set enrichment analyses were performed using GSEA software (Broad Institute) and enrichment plots were plotted using replotGSEA.R.
For Total RNA-seq, Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were trimmed using cutadapt (v1.7) and aligned to the human reference genome (Hg19) using HISAT2 (v2.1.0). Read counting across genomic features was performed using featureCounts v1.5.0 (Liao et al., 2014) prior to differential gene expression analysis using limma voom (Law et al., 2014).
For Total RNA-seq, Pre-ranked gene set enrichment analyses were performed using GSEA software (Broad Institute) against the Molecular Signatures Database (MSigDB) collection, and enrichment plots were plotted using replotGSEA.R (part of the Rtoolbox R package).Analysis of core transcriptional regulatory circuitries was performed by using MM1.S and HeLa specific gene sets previously described (Huang et al., 2018) and normalized RNA-seq count (normalized CPM) values in Rstudio.
Genome_build: HG19
Supplementary_files_format_and_content: Gene Expression Counts

source_name: CD138-selected Bone Marrow Mononuclear Cells

growth_protocol: Cells were grown in vitro under standard culture conditions

extract_protocol:
For 3'-mRNA-seq (QuantSeq), Cells were collected and washed once with ice-cold PBS prior to resuspension in TRIzol™ (ThermoFisher Scientific, 15596026). RNA was isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052) according to the manufacturers instructions. Sequencing libraries were prepared from 500ng RNA using the QuantSeq 3’-mRNA Seq Library Prep Kit for Ilumina (Lexogen, Vienna, Austria). Libraries were sequenced on the Illumina NextSeq 500 to obtain 75 b.p. single-end reads.
For Total RNA-seq, Total RNA was immediately extracted using TRIzol reagent (ThermoFisher Scientific, 15596026) and isolated using the Direct-zol RNA MiniPrep kit (Zymo Research, R2052). Libraries were prepared with NEBNext Ultra II Directional RNA Library Prep Kit for Ilumina (NEB, E7760S) with ribosomal RNA depletion and sequenced on an Ilumina NextSeq 500 with 75 b.p. single-end reads.

treatment_protocol: Samples were treated in biological duplicate or triplicate in the presence of small molecule inhibitors, as indicated.

tag: ectopic expression

tag: rna library prep

value: 3'-mRNA (QuantSeq)


title: QuantSeq_RNAseq_PMC09_2hours_A485

status: Public on May 11 2021

type: SRA

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

country: USA

institute: AbbVie

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
PMC09-A485

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: timepoint

value: 2 hours

tag: treatment+dose


title: TU0064_LTBI_CD4m

city: La Jolla

first: Julie

last: Burel

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample91_CD4m

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Genome_build: GRCh38.gencode.v27B
Supplementary_files_format_and_content: read count matrix with rows as genes and columns as cells

molecule: polyA RNA

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 T cells sorted using BD Aria 3 cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease group

value: LTBI

tag: geographic location

value: USA:San Diego

tag: cell subset

value: Memory CD3+CD4+CD8- T cells


title: TU0057_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample88_CD4m

value: TBneg


title: QuantSeq_RNAseq_PMC09_2hours_DMSO

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
PMC09-DMSO

value: DMSO


title: TTseq_MM1S_2hours_DMSO

data_processing:
Library strategy: TT-seq
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5). Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function. BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1). For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
BigWig files were imported into Integrative Genomics Viewer (IGV, v2.7.0) for visualization of specific loci. Using Deeptools (v3.0.0), average profile plots and heatmaps were generated by computing read average read density (from BigWig files) across defined genomic intervals using computeMatrix, which we subsequently plot using plotProfile and plotHeatmap, respectively.
Genome_build: Hg19
Supplementary_files_format_and_content: bigWig

source_name: Multiple Myeloma

growth_protocol: MM1.S cells were grown under standard in vitro culture conditions.

extract_protocol:
Cells were lysed in in TRIzol. Chloroform (1/5th volume) was added and samples were vortexed and centrifuged at 4°C (13000g, 15 minutes). The aqueous phase was isolated and total RNA was extracted by isopropanol precipitation at room temperature (10 minutes) followed by centrifugation at 4°C (13000g, 10 minutes). The isolated RNA pellet was washed with 70 percent ethanol followed by centrifugation at 4°C (13000g,15 minutes). The RNA pellet was dissolved in 100μL nuclease-free H2O and denatured at 65ºC for 10 minutes. 150μg total RNA per treatment condition (pl 883 us 15μg D.melanogaster S2 RNA spike-in) in 100μL final volume were sonicated in microTUBE AFA Fiber screw cap tubes (6 x 16mm, Covaris, 520096) using the Covaris S220 Focused Ultrasonicator at maximum power for 15 seconds. Thiol-specific biotinylation of fragmented RNA was performed by adding 750μL volume nuclease free water followed by incubatation with 10mM TRIS (pH 7.4), 1mM EDTA, 200 μg/mL dimethylformamide (DMF; Sigma Aldrich, 227056) and 300μg EZ-LinkTM HPDP-Biotin (ThermoFisher Scientific, 21341) at room temperature for 1.5 hours with constant rotation (1500μL final volume – ‘biotin labelling reaction’). One volume chloroform was added to the biotin-labelling reaction and the reaction was vortexed and centrifuged at 4°C (20000g, 5 minutes). The aqueous phase was isolated and the chloroform isolation was repeated twice. NaCl (to 0.5M) and one volume isopropanol was added to the aqueous phase and fragmented RNA was isolated by centrifugation at 4°C (20000g, 20 minutes). The RNA pellet was washed with 75 percent ethanol, centrifuged at 4°C (20000g, 20 minutes) and dissolved in nuclease-free water (1μL per 1μg input RNA). Fragmented RNA was denatured at 65°C for 10 minutes prior to incubation with streptavidin beads (μMACs Streptavidin Kit, Miltenyi Biotec, Bergisch Gladbach Germany, 130-074-101) at room temperature for 15 minutes with constant rotation. Biotinylated RNA was isolated using μMACs columns that had been pre-equillibrated with room temperature wash buffer (100mM Tris-HCl pH 7.4, 10mM EDTA, 1M NaCl, 0.1% v/v Tween20). Following incubation with biotinylated RNA / streptavidin beads the columns were washed with 5 times each with 0.9mL pre-warmed (65ºC) and room-temperature wash buffer. Biotinylated RNA was eluted through two additions of 100μL 100mM dithiothreitol (DTT) 3 minutes apart and collected into 700μL RLT buffer from the RNeasy MinElute Cleanup Kit (Qiagen, Hilden Germany, 74204). Biotinylated RNA was isolated using the Qiagen RNeasy MinElute Cleanup Kit using 12μL elution buffer to elute RNA. RNA was quantified using the Agilent Tapestation High Sensitivity RNA kit (Agilent, 5067-5576).
Sequencing libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: 30e6 MM1.S cells per treatment condition were incubated with 1mM 4-thiouridine (Sigma Aldrich, 877 T4509) for the final 10 minutes of A-485 or DMSO treatment (2 hours).


title: TU0059_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample89_CD4m


title: TU0056_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample87_CD4m


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_DMSO_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-DMSO-3

value: 6 hours

value: FU-Cas9-Cherry + Scrambled sgRNA


title: ATACseq_MM1S_A485_2hours_Replicate2

library_source: genomic

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1)
For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Genome_build: HG19, Dm3
Supplementary_files_format_and_content: bigWig

molecule: genomic DNA

growth_protocol: Cells were grown in vitro under standard culture conditions.

extract_protocol:
Cells were washed once in ice-cold PBS and lysed in ATAC lysis buffer (0.1% Tween-20, 0.1% NP-40, 3mM MgCl2, 10mM NaCl, 10mM Tris HCl pH 7.4). Tagmentation was performed with Tn5 transposase and 2x TD Buffer (Nextera DNA Library Prep Kit, Ilumina) for 30 minutes at 37°C.
Tagmented DNA was purified using a MinElute colum (Qiagen, 28004) and amplified for 12 cycles using 2x KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602). The amplified libraries were purified using MinElute columns (Qiagen) and sequenced on an NextSeq 500.

treatment_protocol: Cells were treated with A-485, A-241, or DMSO at indicated concentrations for indicated time-points.


title: TU0054_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample86_CD4m


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_DMSO_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-DMSO-2


title: TU0035_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample83_CD4m


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_DMSO_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-DMSO-1


title: TU0046_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample85_CD4m


title: TU0036_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample84_CD4m


title: TU0025_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample81_CD4m


title: QuantSeq_RNAseq_PMC14_2hours_A485

description:
RNAseq_Counts_PMC14_featureCounts_unnormalized.txt
PMC14-A485


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_DMSO_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-DMSO-2

value: FU-Cas9-Cherry + NCOR1 sgRNA


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_A485_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-A485-1


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_A485_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-A485-2


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_DMSO_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-DMSO-3


title: TU0024_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample80_CD4m


title: TU0033_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample82_CD4m


title: QuantSeq_RNAseq_MM1S_scrambled_sgRNA_A485_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-SCR-A485-3


title: TU0023_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample79_CD4m


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_A485_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-A485-1


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_A485_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-A485-2


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_DMSO_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-DMSO-3


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_A485_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-A485-3


title: TU0005_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample74_CD4m


title: TU0011_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample76_CD4m


title: TU0010_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample75_CD4m


title: TU0022_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample78_CD4m


title: TU0124_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample101_CD4m


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA2_DMSO_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-2-DMSO-1


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_DMSO_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-DMSO-1


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_DMSO_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-DMSO-2


title: TT0121_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample72_CD4m

value: South Africa


title: TT0121_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample73_CD4m


title: TT0120_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample70_CD4m


title: TT0119_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample69_CD4m


title: TT0117_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample66_CD4m


title: TT0117_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample67_CD4m


title: QuantSeq_RNAseq_ALF11_2hours_DMSO

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF11-DMSO


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_A485_6hours_replicate2

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-A485-2


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_A485_6hours_replicate1

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-A485-1


title: QuantSeq_RNAseq_ALF03_2hours_DMSO

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF04-DMSO


title: TT0119_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample68_CD4m


title: QuantSeq_RNAseq_ALF03_2hours_A485

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF04-A485


title: QuantSeq_RNAseq_ALF11_2hours_A485

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF11-A485


title: QuantSeq_RNAseq_MM1S_NCOR1_sgRNA1_A485_6hours_replicate3

description:
RNAseq_Counts_MM1S_NCOR1_KO_featureCounts_unnormalized.txt
MM1-NCOR1-1-A485-3


title: TU0013_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
Sample77_CD4m


title: TT0116_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample65_CD4m


title: TT0116_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample64_CD4m


title: QuanSeq_RNAseq_MM1S_16hours_A485_6hour_washout_Replicate2

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-6h-2

value: 16 hours

value: A-485, 1µM, then 6 hour washout


title: TT0114_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample62_CD4m


title: QuanSeq_RNAseq_MM1S_16hours_A485_30min_washout_Replicate2

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-30m-2

value: A-485, 1µM, then 0.5hour washout


title: QuanSeq_RNAseq_MM1S_16hours_A485_30min_washout_Replicate1

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-30m-1


title: QuantSeq_RNAseq_ALF02_2hours_DMSO

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF02-A485


title: TT0112_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample61_CD4m


title: TT0120_ATB_V1_CD4m_2

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample71_CD4m


title: TT0111_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample59_CD4m


title: QuanSeq_RNAseq_MM1S_16hours_A485_2hour_washout_Replicate2

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-2h-2

value: A-485, 1µM, then 2 hour washout


title: TT0112_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample60_CD4m


title: QuantSeq_RNAseq_ALF02_2hours_A485

description:
RNAseq_Counts_Primary_MM_featureCounts_unnormalized.txt
ALF02-DMSO


title: TT0109_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample56_CD4m


title: TT0107_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample53_CD4m


title: QuanSeq_RNAseq_MM1S_16hours_A485_2hour_washout_Replicate1

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-2h-1


title: QuanSeq_RNAseq_MM1S_16hours_A485_Replicate2

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-T0-2


title: Total_RNAseq_MM1S_JQ1_2hours_Replicate3

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-JQ1-3

value: Total mRNA


title: Total_RNAseq_MM1S_DMSO_Replicate3

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-UT-3


title: TT0109_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample57_CD4m


title: TT0111_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample58_CD4m


title: Total_RNAseq_MM1S_JQ1_2hours_Replicate2

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-JQ1-2


title: TT0114_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample63_CD4m


title: Total_RNAseq_MM1S_DMSO_Replicate2

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-UT-2


title: TT0108_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample55_CD4m


title: QuanSeq_RNAseq_MM1S_16hours_A485_Replicate1

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-T0-1


title: TT0107_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample52_CD4m


title: Total_RNAseq_MM1S_DMSO_Replicate1

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-UT-1


title: QuanSeq_RNAseq_MM1S_16hours_A485_6hour_washout_Replicate1

description:
RNAseq_Counts_MM1S_Washout_featureCounts_unnormalized.txt
MM1-WO-6h-1


title: Total_RNAseq_MM1S_JQ1_2hours_Replicate1

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-JQ1-1


title: TT0105_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample50_CD4m


title: TT0105_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample49_CD4m


title: TT0108_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample54_CD4m


title: TT0070_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample47_CD4m


title: TT0075_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample48_CD4m


title: Total_RNAseq_MM1S_A485_6hours_Replicate1

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-6h-1


title: Total_RNAseq_MM1S_A485_6hours_Replicate2

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-6h-2


title: Total_RNAseq_MM1S_A485_2hours_Replicate3

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-2h-3


title: TT0106_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample51_CD4m


title: Total_RNAseq_MM1S_A485_2hours_Replicate2

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-2h-2


title: TT0070_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample46_CD4m


title: TT0058_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample41_CD4m


title: TT0059_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample43_CD4m


title: TT0059_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample42_CD4m


title: TT0069_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample45_CD4m


title: Total_RNAseq_MM1S_A485_6hours_Replicate3

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-6h-3


title: TT0050_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample38_CD4m


title: TT0069_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample44_CD4m


title: P60

city: Moscow

first: Alex

last: Nik

address: Orekhoviy bulvar, 28

country: Russia

institute: FSCC

data_processing:
Adaptors were trimmed with Cutadapt; the resulting FASTQ files were then mapped to the human genome (GRCh37 assembly) with bowtie2
FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to visualize different quality control measurements.
For each sample, sequences were annotated using human pre-miRNA and mature miRNA databases provided by the miRbase (http://microrna.sanger.ac.uk/sequences/) in SeqBuster.
The resulting count data was analyzed in DESeq2 to obtain differentially expressed microRNAs.
Cluster analysis was performed for miRNAs with more than 10 read counts.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw counts for every mirna and every sample

source_name: plasma

extract_protocol:
Total RNA isolation was carried out using a miRNeasy Serum/Plasma Kit (Qiagen) on an automatic QIAcube station (Qiagen) according to the manufacturer protocol. One unit of RiboLock RNase Inhibitor (Thermo Fisher Scientific) was added per 1.0 μL of RNA solution to prevent degradation.
The libraries were prepared with Illumina TruSeq Small RNA Library Prep Kit following the manufacturer standard protocols

treatment_protocol: Blood samples were collected in EDTA tubes from fasting subjects at 0800-0900 h. Samples were immediately centrifuged at +5°С and 3000 rpm for 20 minutes, aliquoted and stored at -80°C until further analysis.

tag: tissue

value: plasma

tag: Sex

value: female

tag: age

tag: disease state

value: control


title: 147.1

value: acromegaly


title: 133.1


title: P40


title: TT0057_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample40_CD4m


title: 191.1


title: 154.1


title: 131.1


title: TT0048_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample36_CD4m

value: LTBI


title: Total_RNAseq_MM1S_A485_2hours_Replicate1

description:
RNAseq_Counts_MM1S_A485_JQ1_featureCounts_unnormalized.txt
MM1-2h-1

value: 2 hours


title: TT0049_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample37_CD4m

value: Memory CD3+CD4+CD8- T cells


title: TT0047_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample35_CD4m

value: TBneg


title: TT0046_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample34_CD4m


title: Be


title: Ba


title: K5P


title: TT0041_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample32_CD4m


title: Ku


title: TT0044_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample33_CD4m


title: K2P


title: TT0036_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample29_CD4m


title: TT0036_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample28_CD4m


title: TT0033_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample26_CD4m


title: K1P


title: 160.1


title: 134.1


title: TT0033_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample27_CD4m


title: 144.1


title: K3P


title: P64


title: TT0032_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample25_CD4m


title: TT0030_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample24_CD4m


title: TT0029_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample23_CD4m


title: 127.1


title: 138.1


title: TT0028_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample22_CD4m


title: TT0040_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample31_CD4m


title: P42


title: 201.1


title: TT0039_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample30_CD4m


title: K4P


title: TT0027_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample21_CD4m


title: TT0026_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample19_CD4m


title: TT0022_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample18_CD4m


title: PROseq_MM1S_2hours_A485_Replicate2

data_processing:
Library strategy: PRO-seq
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1).
For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Genome_build: HG19
Supplementary_files_format_and_content: bigWig

growth_protocol: MM1.S were grown in vitro under standard culture conditions in the presence of DMSO or A-485 (1µM) for 2 hours.

extract_protocol:
For nuclear run-on, cells were incubated with one volume of 2X Nuclear run-on reaction master-mix containing biotin 11-CTP (1.4mM Tris-HCl pH 8, 0.7mM MgCl2, 0.14mM DTT, 42mM KCl, 0.05mM biotin 11-CTP (Perkin Elmer NEL544001EA), 2.5M CTP, 0.25mM ATP, 0.25mM GTP, 0.25mM UTP, 40U SUPERaseIn, 1% Sarkozyl (Sigma-Aldrich L5125)) at 37°C for three minutes with gentle agitation, prior to the addition of LRIzol-LS (ThermoFisher, 10296010). Following mixture with chloroform, the aqueous phase was isolated by centrifugation. 1L GlycoBlue and 2.5 volumes of 100% ethanol was added to the aqueous phase fir RNA precipitation (incubation for 10 minutes at room temperature). Precipitated RNA was washed with 70% ethanol and resuspended in nuclease-free water. RNA was subsequently denatured by incubation at 65°C fir 40 seconds, prior to incubation with 0.2M NaOH on ice for 12.5 minutes followed by addition of 1 volume of 1M Tris-HCl (pH 6.8). Base hydrolyzed RNA was exchanged to 10mM Tris solution using a Micro Bio-Spin 30 column (Biorad, 7326250) according to the manufacturers instructions. For enrichment of biotin-tagged RNA, hydrolyzed RNA was incubated with Dynabeads M-280 Streptavidin (ThermoFisher Scientific, 11206D) in PRO-Seq Binding Buffer (10mM Tris-HCl pH 7.4, 300mM NaCl, 0.1% v/v TritonX-100) at room temperature for 20 minutes with gentle rotation. Streptavidin beads were washed (1 minute with rotation per wash) three times each in High Salt Wash Buffer (50mM Tris-HCl pH 7.4, 2M NaCl, 0.5% v/v TritonX-100), Binding Buffer and Low Salt Wash Buffer (5mM Tris-HCl pH 7.4, 0.1% TritonX-100) and then resuspended in TRIzol. Following incubation at room temperature for 3 minutes, TRIzol samples were mixed with chloroform and the aqueous phase was isolated after centrifugation. TRIzol/chloroform treatment of washed Streptavidin beads was repeated once and beads were incubated with chloroform for 3 minutes at room temperature prior to centrifugation. 1μL GlycoBlue and 900μL ethanol was added to the pooled aqueous phase solution and samples were incubated at room temperature for 10 minutes prior to centrifugation.
Precipitated biotin-enriched RNA was washed with 70% ethanol and resuspended in nuclease free water. Samples (AS cell lines) underwent ribo-depletion using the NEBNext® rRNA Depletion Kit and sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and 75 single end base pair reads were sequenced Illumina NextSeq 500.

treatment_protocol: Cells were washed once in ice-cold PBS and then re-suspended in Permeabilization buffer (1mL/106 cells; 10mM Tris-HCl pH 7.4, 200mM sucrose, 10mM KCl, 5mM MgCl2, 1mM EDTA, 0.05% v/v Tween20, 0.15% v/v NP-40, 0.5mM DTT, 2U/mL SUPERaseIn, containing Roche cOmplete protease inhibitors) for 5 minutes on ice. Following two sequential washes in Permeabilization buffer (0.5mL/106 cells), cells were re-suspended in Storage buffer (10mM Tris-HCl pH 8, 25% glycerol, 5mM MgCl2, 0.1mM EDTA, 5mM DTT).


title: TT0051_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample39_CD4m


title: PROseq_MM1S_2hours_A485_Replicate1


title: TT0022_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample17_CD4m


title: PROseq_MM1S_2hours_DMSO_Replicate2

value: DMSO


title: TT0020_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample16_CD4m


title: TT0019_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample15_CD4m


title: PROseq_MM1S_2hours_DMSO_Replicate1


title: TT0016_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample13_CD4m


title: TT0017_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample14_CD4m


title: TT0013_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample12_CD4m


title: ChIPseq_H3K27ac_HeLa_6hours_DMSO_Control

data_processing:
Sequencing files were demultiplexed using Bcl2fastq (v2.17.1.14) to generate Fastq files on which QC was performed using FASTQC (v0.11.5).
Sequencing reads were then aligned to custom reference genome consisting the human genome (Hg19) and the Drosophila melanogaster genome (Dm3) using Bowtie2 (v2.3.3).
The resulting SAM files were converted to BAM files using Samtools (v1.4.1) using the view command, which were subsequently sorted, indexed, and potential PCR duplicates removed using the rmdup function.
BAM files were converted into BigWig files using the bamCoverage function (Deeptools, v3.0.0) using the following settings (--normalizeUsing CPM --smoothLength 150 --binSize 50 -e 200 scaleFactor 1).
For experiments with external normalization, the reads mapping to either Hg19 or Dm3 genomes were quantified using FeatureCounts (Subread package, v1.5.0) and the percentage of mapped Dm3 reads as a total of total mapped Dm3+Hg19 reads was calculated. A scale factor was then calculated as the ratio of Dm3 reads in the control treatment condition and the treatment sample, which was then applied as the scaleFactor in the bamCoverage function.
Genome_build: HG19
Supplementary_files_format_and_content: bigWig

source_name: Cervical adenocarcinoma

extract_protocol:
Cells were washed once in ice-cold PBS prior to crosslinking. For crosslinking, 1/10th volume of fresh formaldehyde solution (11% formaldehyde, 0.05mM EGTA, 1mM EDTA, 100mM NaCl, 50mM Hepes-KOH pH 7.5) was added and incubated for 20 minutes at room temperature with rotation. Crosslinking was quenched by addition of 1/20th volume of 2.5M glycine and incubated for 5 minutes at room temperature with rotation. For isolation of nuclei, cell pellets were washed once in ice-cold PBS and then resuspended in ice-cold nuclear extraction buffer (0.5% NP-40, 2mM EDTA, 10mM NaCl, 20mM Tris-HCl pH 8) and incubated for 5 minutes on ice. Following three sequential incubations in nuclear extraction buffer, cell nuclei were pelleted and resuspended in sonication buffer (0.3% SDS, 1% NP-40, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 7.5) at a concentration equivalent to 50e6 cells per mL. Samples were sonicated in 12x24mm Covaris tubes using the Covaris S2 instrument for 18 minutes using the following settings: 20% Duty Cycle, 1000 cycles/burst, and 10 Intensity. Prior to immunoprecipitation, sheared chromatin was diluted 1:1 in ChIP dilution buffer (1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8) and quantified using Qubit dsDNA HS assay kit. For ChIP-Rx, sheared Drosophila chromatin from S2 cells was spiked into immunoprecipitations at 1:40 ratio of Drosophila:human and processed as a single sample until ChIP-Rx normalization following DNA sequencing. Immunoprecipitations were performed overnight (12-16 hours, 4°C, with rotation) using Protein A and Protein G Dyna beads (Invitrogen) and the indicated antibody. Samples were washed once with ChIP dilution buffer, wash buffer 1 (0.1% SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), wash buffer 2 (0.5% deoxycholate, 0.5% NP-40, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8), and TE buffer (1mM EDTA, 10mM Tris-HCl pH 7.5) prior to incubation in reverse crosslinking buffer (200mM NaCl, 100mM NaHCO3, 1% SDS, 300μg/mL Proteinase-K) for 4 hours at 55°C with shaking. Finally, the supernatant was reverse-crosslinked overnight (12-16 hours) at 65°C prior to ChIP DNA isolation using Zymogen ChIP DNA Clean and Concentrator Kit (Zymo Research, D5205).
Libraries were generated from ChIP DNA using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645) and sequenced on an Illumina NextSeq 500 with 75 b.p. single-end reads.

treatment_protocol: Cells were treated with A-485, A-241, RGFP966, or DMSO at indicated concentrations for indicated time-points.

value: HeLa

value: 6 hours

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: ChIPseq_H3K27ac_HeLa_6hours_A485


title: ChIPseq_H3K27me3_MM1S_40hours_A485

value: 40 hours

value: H3K27me3 (Millipore, 07449)


title: TT0027_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample20_CD4m

value: South Africa


title: ChIPseq_H3K27ac_HeLa_2hours_A485


title: TT0011_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample10_CD4m


title: PROseq_MM1S_Input


title: ChIPseq_H3K27me3_MM1S_32hours_A485

value: 32 hours


title: ChIPseq_H3K27me3_MM1S_Untreated

value: Untreated


title: TT0010_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample9_CD4m


title: TT0008_TBneg_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample8_CD4m


title: TT0006_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample6_CD4m


title: ChIPseq_H3K27ac_MM1S_32hours_A485


title: TT0007_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample7_CD4m


title: ChIPseq_H3K27ac_MM1S_2hours_A241


title: ChIPseq_H3K27ac_MM1S_6hours_A241


title: TT0005_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample5_CD4m


title: ChIPseq_H3K27ac_MM1S_Control_DMSO


title: TT0003_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample3_CD4m


title: TT0001_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample2_CD4m


title: ChIPseq_UTX_MM1S

value: UTX (Bethyl, A302-374A)


title: MDA-MB-231 cells, Control_2

city: Charlestown

first: Yang

last: Sun

state: MA

address: 149 13th Street, CBRC 3050E

department: CBRC

institute: Massachusetts General Hospital

data_processing:
"Qphred" represents base quality values of Illunima, the Qphred=-10log10(e). Base Quality and Phred score relationship in illumina Casava 1.8
GC-content is used to detect potential AT/GC separation.
The Sequenced Reads/raw reads often contain low quality reads or reads with adaptors. Raw reads filtering conditions are as follows: (1) Remove reads containing adaptors; (2) Remove reads containing N > 10% (N represents base that could not be determined);(3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Novogene use STAR to accomplish the mapping. For the spieces(Human and mice) whose gene annotation information are more completed, if only need the differential expression significant genes, can map reads to the transcriptome directly. If research the study of alternative splicing, variation, the fusion gene, the alignment should be carried out at the genome level. In order to avoid losing a lot of effective junction reads, Novogene use STAR software to alignment for RNA-seq sequencing data analysis, the junction reads can be positioned precisely
Reads will be mapped to exon, intron and intergenic.
After getting the information about distribution of mapped reads on genome area, we will focus the distribution of mapped reads on chromosome. On one hand we can get insight into how many regions on chromosome is covered, on the other hand we can get the information about transcription activity on chromosome.We calculate mapped reads density on every chromosome , then plot based on the mapped reads density. In general, the longer the chromosome is, the more reads will be mapped to the chromosome. The statistics of reads mapped to chromosome indicates the relationship between chromosome length and reads number.
Genome_build: hg19
Supplementary_files_format_and_content: processed data-fpkm.txt

source_name: breast cancer

growth_protocol: MDA-MB-231 cells were culture in DMEM supplied with 10% FBS and Penicillin-Streptomycin

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen 74104)
mRNA from Eukaryote organisms is purified from total RNA using poly-T oligo-attached magnetic beads (For prokaryotes, mRNA was purified through the removal of rRNA by using kit). The mRNA is first fragmented randomly by addition of fragmentation buffer.Then first strand cDNA is synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis is subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA is purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization(1). In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments are purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is gotten by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: Cells were treated with vehicle control or MGH-CP1 for 24 hours

tag: cell type

value: breast cancer cells

tag: treatment

value: vehicle control


title: MDA-MB-231 cells, MGH-CP1-1

value: MGH-CP1 10μM 24 hours


title: ChIPseq_Pol2_MM1S_2hours_DMSO

value: RNA Polymerase II (Millipore, 05-623)


title: MDA-MB-231 cells, Control_1


title: RB 135_Rep_2

type: genomic

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

description: Methylation

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Methylation Analysis: Raw data files generated by the iScan array scanner were read and preprocessed by using “minfi” Bioconductor package.

label: Cy3 and Cy5

source_name: O-PDX

label_protocol: standard Illumina protocol

extract_protocol: Dneasy Blood and Tissue Kit: Qiagen #65904 was used to extract genomic DNA

value: xenograft

tag: protocol

value: Dneasy Blood and Tissue kit


title: RB 134-2

description: Methylation


title: ChIPseq_H3K27ac_MM1S_2hours_DMSO_Replicate2

value: 2 hours


title: ChIPseq_H3K27ac_MM1S_2hours_DMSO_Replicate1

value: DMSO


title: ChIPseq_P300_MM1S_2hours_A485

value: P300 (SantaCruz, sc-585)


title: RB 133_Rep_2

description: Methylation


title: primary LSECs infected with siAirn1_2, biological rep2

city: Tianjin

first: chen

last: ting

state: Tianjin

address: 22 Meteorological Tai Road, Heping District, Tianjin, China

department: School of Basic Medical Sciences

country: China

institute: Tianjin Medical University

data_processing:
basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads"
Mapping clean reads to hg19 whole genome using BWA
Bowtie2 was used to get mapping ratio
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

growth_protocol: mouse Primary LSECs cultured 24h

extract_protocol:
Primary LSECs were isolated by pronase/collagenase perfusion digestion from the 8-week-old Balb/c mice liver, subsequently Primary LSECs (1x106/well) were seeded in collagen–coated 6-well plates and transfected with siAirns and siRNA-control for 48 h, RNA of cells were harvested and isolated useing Trizol reagent. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer
The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: mouse Primary LSECs infected with two separated siAirn for 48h

value: liver

tag: Stage

value: primary LSECs at day 3

tag: strain

value: balb/c

tag: genotype

value: siAirn


title: ChIPseq_P300_MM1S_2hours_DMSO

tag: cell line

tag: ectopic expression


title: TT0001_ATB_V1_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample1_CD4m

value: South Africa

value: Memory CD3+CD4+CD8- T cells


title: RB 130_Rep_2

description: Methylation


title: ChIPseq_H3K27ac_MM1S_2hours_A485_Replicate1

tag: timepoint

tag: treatment+dose

value: H3K27ac (Abcam, ab4729)


title: primary LSECs infected with siAirn1_1, biological rep1


title: RB 138_Rep_2

description: Methylation


title: ChIPseq_H3K27ac_MM1S_6hours_A485_Replicate2

value: 6 hours


title: ChIPseq_H3K27ac_MM1S_6hours_A485_Replicate1


title: RB 129_Rep_2

description: Methylation


title: ChIPseq_H3K18ac_MM1S_2hours_DMSO

value: H3K18ac (Abcam, ab1191)


title: primary LSECs infected with NC-control, biological rep2

value: NC


title: ChIPseq_H3K27ac_MM1S_2hours_A485_Replicate2


title: RB 128_Rep_2

description: Methylation


title: primary LSECs infected with NC-control, biological rep1


title: ChIPseq_BRD4_MM1S_2hours_A485


title: ChIPseq_BRD4_MM1S_2hours_DMSO


title: RB 122_Rep_2

description: Methylation


title: ChIPseq_H3K18ac_MM1S_2hours_A485


title: RB 124_Rep_2

description: Methylation


title: ChIPseq_H3K27ac_MM1S_16hours_A485

value: 16 hours


title: ChIPseq_H3K27ac_MM1S_washout_input

value: none (INPUT)


title: Fah-/- tumor rep3

city: chengdou

first: ji

middle: hong

last: jie

address: 37 Guoxue Road, Chengdu, China

institute: West China Hospital

data_processing:
The filtered data was compared with reference sequence by software HISAT and Bowtie2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: liver

growth_protocol: WT liver(WT1-WT3) and Alb-Cre:Hdac3−/− liver (0d(Ha-Hc), 7d(Hd-Hg), 21d(Hh-Hk), 50d(Hl-Hn)) receiving successive PH(sPH),  Alb-Cre:Hdac3−/− tumor tissues(HCC1-HCC3) and adjacent non-tumor tissues(N1-N3), spontaneous liver cancers of Alb-Cre:Hdac3-/- mice (HCC1-HCC3) and liver tumor of recipient Fah-/- mice (HCCa-HCCc)

extract_protocol:
Livers were collected, 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: Liver tissues were collected at defined points

value: Fah-/-

value: 12 mohths


title: Fah-/- tumor rep2


title: ChIPseq_H3K27ac_MM1S_16hours_A485_30min_washout

value: A-485, 1µM, then 0.5hour washout


title: RB 121-2

description: Methylation

value: xenograft

value: Dneasy Blood and Tissue kit


title: ChIPseq_H3K27ac_MM1S_16hours_A485_6hour_washout

value: A-485, 1µM, then 6 hour washout


title: ChIPseq_H3K27ac_MM1S_16hours_A485_2hour_washout

value: A-485, 1µM, then 2 hour washout


title: ChIPseq_H3K27ac_MM1S_sgNCOR1_sgRNA2_DMSO_6hours

value: DMSO

value: FU-Cas9-Cherry + NCOR1 sgRNA


title: Fah-/- tumor rep1


title: 198.1

value: plasma

value: female

value: acromegaly


title: ChIPseq_H3K27ac_MM1S_RGFP966_2hours

value: 2 hours

value: H3K27ac (Abcam, ab4729)


title: adjacent non-tumor rep3

value: 10 mohths


title: ChIPseq_H3K27ac_MM1S_sgNCOR1_sgRNA2_A485_6hours

value: 6 hours


title: ChIPseq_BRD2_MM1S_2hours_A485

value: BRD2 (Cell Signalling, 5848)


title: RB 138_Rep_1

description: Methylation


title: H9CR Tumor

description: Methylation

source_name: Retinal Organoid-Derived Retinoblastoma

value: organoid derived tumor


title: TT0003_ATB_V2_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample4_CD4m

tag: disease group

tag: geographic location

value: South Africa

value: Memory CD3+CD4+CD8- T cells


title: adjacent non-tumor rep1


title: ChIPseq_H3K27ac_MM1S_sgNCOR1_sgRNA1_A485_6hours


title: adjacent non-tumor rep2


title: ChIPseq_H3K27ac_MM1S_sgScrambled_A485_6hours

value: FU-Cas9-Cherry + Scrambled sgRNA


title: CRISPRscreen_MM1S_T0_ScreenEnd

description: Tend

data_processing:
Reads were demultiplexed with Bcl2fastq (v2.17.1.14)
The sequencing reads were subsequently trimmed using cutadapt (v1.7) to remove vector-derived sequences, yielding only 20b.p. sequences corresponding to sgRNAs.
The enrichment of sgRNAs and statistical analyses was performed with MAGeCK (v0.5.6).
Data visualized was performed in Rstudio using the ggplot2 package.
Genome_build: Hg19
Supplementary_files_format_and_content: sgRNA counts file

growth_protocol: MM cell lines were engineered to express the Cas9 endonuclease by transduction with the FUCas9Cherry vector and subsequent selection for mCherry-positive cells.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, 69504) and the sequencing libraries were generated by PCR amplification, as previously described.
The libraries were sequenced on the NextSeq 500 (Ilumina) to generate 75b.p. single-end reads.
CRISPR/Cas9 Screen

treatment_protocol: For genome-scale screening, MM1.S cells expressing the Cas9 were transduced with a genome-wide sgRNA from Brunello (75,000 sgRNAs)-Gecko (120,000 sgRNA) library at a MOI of 0.3, aiming for 200-fold representation of each guide.  Puromycin selection at 500ng/mL was performed with the optimized dose and split into relevant treatment conditions (vehicle vs. A-485). Puromycin resistant cells were subsequently cultured in IC50-70 concentrations of A-485 (125nM, increased to 250nM), or DMSO vehicle, over 6 weeks (to allow for approximately 21 cell divisions) to select for resistant populations.


title: ChIPseq_H3K27ac_MM1S_sgScrambled_DMSO_6hours


title: CRISPRscreen_MM1S_A485_Replicate2


title: CRISPRscreen_MM1S_T0_ScreenStart


title: RB 116-2

description: Methylation

tag: tissue

value: xenograft

value: Dneasy Blood and Tissue kit


title: SJRB-iPSC-8CR Tumor

description: Methylation


title: Hdac3−/− tumor rep3


title: SJRB-iPSC-1CR Tumor

description: Methylation


title: ChIPseq_Pol2_MM1S_2hours_A485

value: RNA Polymerase II (Millipore, 05-623)


title: TT0012_LTBI_CD4m

description:
Microscaled (SmartSeq2) cDNA amplification - RNA seq
The submitter declares that the raw data cannot be made available via any mechanism due to patient privacy concerns
Sample11_CD4m

value: LTBI

tag: cell subset


title: Hdac3−/− tumor rep2

tag: age


title: SJRB-iPSC-6CR Tumor

description: Methylation


title: E38-6h-CI

city: Linköping

first: Rada

last: Ellegård

state: Ostergotlands Lan

address: Vallmogatan 16

country: Sweden

institute: Linköping University

data_processing:
trimmomatic
STAR
featureCounts
Genome_build: GRCh38
Supplementary_files_format_and_content: counts

source_name: endocervix biopsy

extract_protocol:
MinElute Reaction Cleanup Kit (Qiagen)
Ovation RNA-Seq V2 kit (Tecan)

tag: donor

tag: condition

value: complement and antibody opsonized HIV

tag: time


title: E38-6h-C

value: complement opsonized HIV


title: Hdac3−/− tumor rep1


title: E38-6h-F

value: free HIV


title: E38-6h-CO

value: mock


title: Hdac3-/- 50d rep3

value: 50 day after sPH (2-3 mohths-old)


title: E37-6h-C


title: Hdac3-/- 50d rep2


title: SJRB-iPSC-15

description: Methylation

source_name: induced pluripotent stem cell

value: iPSC line


title: H9

description: Methylation

source_name: human embryonic stem cell

value: ESC line


title: E37-6h-F


title: SJRB-iPSC-14

description: Methylation


title: E37-6h-CI


title: Hdac3-/- 50d rep1


title: E36-6h-F


title: E36-6h-CI


title: E37-6h-CO


title: SJRB-iPSC-13

description: Methylation


title: Hdac3-/- 21d rep4

value: 21 day after sPH (2-3 mohths-old)


title: CRISPRscreen_MM1S_A485_Replicate1

value: 6 hours


title: E22-6h-CI


title: Hdac3-/- 21d rep3


title: SJRB-iPSC-12

description: Methylation


title: E22-6h-C


title: Hdac3-/- 21d rep2


title: SJRB-iPSC-11

description: Methylation


title: E22-6h-F


title: SJRB-iPSC-10

description: Methylation


title: SJRB-iPSC-9

description: Methylation


title: C26-6h-C

source_name: ectocervix biopsy


title: C26-6h-CI


title: C26-6h-CO


title: C26-6h-F


title: SJRB-iPSC-8

description: Methylation


title: Hdac3-/- 7d rep4

value: 7 day after sPH (2-3 mohths-old)


title: Hdac3-/- 21d rep1


title: Hdac3-/- 7d rep3


title: C25-6h-CO


title: Hdac3-/- 7d rep2


title: SJRB-iPSC-7

description: Methylation


title: C25-6h-CI


title: E36-6h-CO


title: SJRB-iPSC-6

description: Methylation


title: Hdac3-/- 7d rep1


title: C22-24h-F


title: E22-6h-CO


title: C22-24h-C


title: C25-6h-F


title: C22-24h-CI


title: SJRB-iPSC-5

description: Methylation


title: Hdac3-/- 0d rep2

value: 0 day after sPH (2-3 mohths-old)


title: C11-24h-F


title: SJRB-iPSC-4

description: Methylation


title: C11-24h-CI


title: C11-24h-CO


title: C25-6h-C


title: Hdac3-/- 0d rep1


title: WT rep3

value: WT(Wile Type)

value: 2-3 mohths


title: SJRB-iPSC-2

description: Methylation


title: C8-24h-F


title: SJRB-iPSC-3

description: Methylation


title: C11-24h-C


title: C8-24h-CO


title: C8-24h-C


title: C8-24h-CI


title: Hdac3-/- 0d rep3


title: WT rep2


title: WT rep1


title: RB_045

description: Methylation

value: xenograft


title: c12 17q #+6 HU exp5

city: Ghent

first: Kaat

last: Durinck

address: Corneel Heymanslaan 10

department: Biomolecular Medicine

country: Belgium

institute: Center for Medical Genetics

description:
biological replicate 2
Sample 52

data_processing: On average 7.0 ± 1.9M high-quality reads were generated per samples. For each sample, gene-level read counts were generated upon mapping to the Homo sapiens reference genome (GRCh38) using STAR. Counts were normalized using edgeR and differential gene expression profiling was performed using DeSeq2. Gene Set Enrichment Analysis (GSEA)(Subramanian et al., 2005) was performed using the c1 and c2 curated gene collection of MSigDB. Three criteria were handled in selecting genesets, only genesets belonging to the (i) top 20 of highest NES, (ii) top 20 of significant p-values ánd (iii) characterized by a FDRq value <0.25 were selected for further consideration.

growth_protocol: Naive UGENT-11/60 hESCs (referred to as C12) were cultured as described previously (Warrier et al., 2017). In brief, naive hESCs were cultured on inactivated (by irradiation) Mouse Embryonic Fibroblasts (MEFs; A34180, Fisher Scientific). MEFs were seeded at a density of 200 000 cells per well of a 6-well plate in MEF media consisting of DMEM 1x (41965-039, Invitrogen) supplemented with 10% fetal calf serum, 1% L-glutamine (25030-025, Invitrogen) and 1% Penicillin/Streptomycin (15140-122, Invitrogen). Cells were allowed to attach and spread prior to use. hESC were subsequently seeded on the attached MEF. Basal naive hESC medium consisted of Knockout DMEM (10829-018, Invitrogen) containing 20% knockout serum replacement (10828-028, Invitrogen), 2mM L-glutamine, 1% Penicillin/Streptomycin, 1% non-essential amino acids (11140-050, Invitrogen), and 0.1mM β-mercapto-ethanol (31350-010, Invitrogen). This basal naive hESC medium is supplemented with 12ng/ml bFGF (100–18B, Peprotech) and 1000U recombinant human LIF (300-05, Sigma) and the small molecules 1μM PD0325903 (13034, Sanbio), 3μM CHIR99021 (1386, Axon Medchem), 10μM Forskolin (F6886, Sigma) and 50ng/ml ascorbic acid (A8960, Sigma) and used as complete media. Naive hESCs were maintained in hypoxic conditions of 5% O2 and 5% CO2 conditions at 37°C. MEF depletion in the hESC culture at passaging was done by discarding the 0.05% trypsin/EDTA (25300-054, Invitrogen) applied to the culture after an incubation of 5min at room temperature. Next, loosened hESC colonies and remaining MEF were resuspended in complete hESC media. Naive colonies were passaged as single cells at a density of 35 000 cells per well of a 6-well plate every three days and were re-plated on inactivated MEFs.

extract_protocol:
RNA sequencing was carried out on samples collected of C12-cl28 and C12-cl32 under normal growing conditions (PBS) and conditions of RS (150µM HU), for six consecutive passages (passage 1-6) during two independent cultures (n=12 biological replicates per condition). Total RNA was isolated using the miRNeasy micro kit (217084, Qiagen) according to manufacturer’s instructions, including on-column DNase treatment.
Next, libraries for mRNA sequencing were prepared using the QuantSeq 3’ mRNA FWD kit (Lexogen) prior to sequencing on the Nextseq500 (High output, SR75, Illumina).
Lexogen quantseq 3' mRNA-seq

treatment_protocol: The cells were seeded in complete media either supplemented with 150µM hydroxyurea (HU; H8627-1G, Sigma) or equal amounts of PBS (14190-094, Invitrogen) as control condition.

tag: cell type

value: hESC

tag: cell line subclass

tag: pluripotency level

value: naive

tag: feederlayer

value: MEF

tag: treatment

value: HU

tag: passage


title: RB_057

description: Methylation

tag: protocol

value: Dneasy Blood and Tissue kit


title: ArgSer_7a

city: London

first: Matthew

last: Berg

state: Ontario

address: 1151 Richmond St

department: Biochemistry

country: Canada

institute: University of Western Ontario

data_processing:
Sequence reads were obtained from Genewiz (South Plainfield, NJ)
Sequenced reads were trimmed for adaptor sequence and then mapped to Saccharomyces cerevisiae S288C reference genome (release R64-2-1_20150113) using STAR v2.5.4b
Raw counts for each sample were obtained using featureCounts v1.6.0
Differentially expressed genes were determined using DESeq2 v1.26.0
Genome_build: Saccharomyces cerevisiae S288C reference genome (release R64-2-1_20150113)
Supplementary_files_format_and_content: Raw gene counts table for every gene and every sample
Supplementary_files_format_and_content: Normalized counts text files for each gene for each sample

organism: Saccharomyces cerevisiae

source_name: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 YCplac33-tRNA-Ser(UCU, G26A)

growth_protocol: Overnight cultures were diluted to an OD600 = 0.1 in synthetic complete media and grown to an OD600 of ~ 2.0

extract_protocol:
RNA samples were then extracted using the MasterPure Yeast RNA Purification Kit (Epicentre) following manufacturer's protocol
Stranded Illumina TruSeq cDNA libraries with poly dT enrichment were prepared from high quality total RNA (RIN > 8)

tag: strain

tag: genotype

value: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 YCplac33-tRNA-Ser(UCU, G26A)


title: c12 WT #+6 HU exp5

description:
biological replicate 2
Sample 50

tag: cell line


title: c12 17q #+6 PBS exp5

description:
biological replicate 2
Sample 51

value: PBS


title: c12 WT #+6 PBS exp5 (new sample)

description:
biological replicate 2
Sample 53


title: MAST 116-1

description: Methylation


title: c12 17q #+5 HU exp5

description:
biological replicate 2
Sample 48


title: c12 17q #+5 PBS exp5

description:
biological replicate 2
Sample 47


title: ArgSer_6a


title: ArgSer_5a


title: SJRB-iPSC-1

description: Methylation


title: ProAla_4a

source_name: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 YCplac33-tRNA-Pro(G3:U70)

value: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 YCplac33-tRNA-Pro(G3:U70)


title: RB_042

description: Methylation


title: c12 WT #+5 PBS exp5

description:
biological replicate 2
Sample 45


title: c12 17q #+4 HU exp5

description:
biological replicate 2
Sample 44


title: c12 17q #+4 PBS exp5

description:
biological replicate 2
Sample 43


title: ProAla_3a


title: c12 WT #+4 HU exp5

description:
biological replicate 2
Sample 42


title: RB_041

description: Methylation


title: c12 WT #+4 PBS exp5

description:
biological replicate 2
Sample 41


title: c12 17q #+6 HU exp4

description:
biological replicate 1
Sample 40


title: RB_043

description: Methylation


title: RB_044

description: Methylation


title: WT_16a

source_name: MATα his3Δ1 leu2Δ0 lys2Δ0 ura3Δ0 YCplac33

value: MAT{alpha} his3{delta}1 leu2{delta}0 lys2{delta}0 ura3{delta}0 YCplac33


title: c12 WT #+5 HU exp5

description:
biological replicate 2
Sample 46


title: WT_15a


title: RB_052

description: Methylation


title: RB_040

description: Methylation


title: ChIPseq_BRD2_MM1S_2hours_DMSO

tag: timepoint

value: 2 hours

tag: treatment+dose

value: DMSO

tag: ectopic expression

tag: chip antibody

value: BRD2 (Cell Signalling, 5848)


title: c12 17q #+5 HU exp4

description:
biological replicate 1
Sample 36


title: c12 WT #+6 PBS exp4

description:
biological replicate 1
Sample 37


title: c12 17q #+5 PBS exp4

description:
biological replicate 1
Sample 35


title: WT_13a


title: c12 WT #+5 PBS exp4

description:
biological replicate 1
Sample 33


title: ProAla_2a


title: c12 17q #+4 HU exp4

description:
biological replicate 1
Sample 32


title: L.acidophilus + FK506 3

city: Seoul

first: Mi-La

last: Cho

address: 222,Banpo-daero, Seocho-gu

country: South Korea

institute: The Catholic University of Korea

description:
4-3
LAFK_3
Normalized_FPKM.txt

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Normalized_FPKM.txt: Tab-delimited text file includes FPKM, TPM, and read count values for each Sample.

source_name: cell from spleen

growth_protocol: CD4+ T cell isolated from normal Balb/c mice were stimulated with anti-CD3 (0.5ug/ml) for 3 days in complete culture medium (RPMI 1640 supplemented with 10% [v/v]).

extract_protocol:
RNA was harvested using standard QIAGEN RNeasy mini kit protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: CD4+ T cell isolated from normal Balb/c mice were stimulated with anti-CD3 (0.5ug/ml) in the presence of L. acidophilus or FK506 alone or combined L. acidophilus and FK506 for 3 days.

value: Balb/c

value: wild type

tag: age

value: 7 weeks

value: CD4+ T cells

value: L. acidophilus + FK506


title: RB_054

description: Methylation

tag: tissue

value: xenograft


title: c12 17q #+6 PBS exp4

description:
biological replicate 1
Sample 39

value: hESC

value: naive


title: c12 17q #+4 PBS exp4

description:
biological replicate 1
Sample 31

value: MEF


title: c12 WT #+6 HU exp4

description:
biological replicate 1
Sample 38

value: HU


title: L.acidophilus + FK506 2

description:
4-2
LAFK_2
Normalized_FPKM.txt


title: MDA-MB-231 cells, MGH-CP1-2

value: breast cancer cells

value: MGH-CP1 10μM 24 hours


title: c12 WT #+4 HU exp4

description:
biological replicate 1
Sample 30


title: RB_063

description: Methylation

value: Dneasy Blood and Tissue kit


title: L.acidophilus + FK506 1

description:
4-1
LAFK_1
Normalized_FPKM.txt


title: SJRB-iPSC-15_D45

description: Methylation

source_name: Retinal Organoid

value: Day 45 organoid


title: c12 17q #+3 PBS exp5

description:
biological replicate 2
Sample 27

value: PBS


title: c12 17q #+3 HU exp5

description:
biological replicate 2
Sample 28


title: c12 WT #+5 HU exp4

description:
biological replicate 1
Sample 34


title: RB_055

description: Methylation


title: c12 WT #+3 PBS exp5

description:
biological replicate 2
Sample 25


title: FK506 3

description:
3-3
FK_3
Normalized_FPKM.txt


title: c12 WT #+3 HU exp5

description:
biological replicate 2
Sample 26


title: FK506 2

description:
3-2
FK_2
Normalized_FPKM.txt


title: c12 17q #+2 HU exp5

description:
biological replicate 2
Sample 24


title: SJRB-iPSC-13_D45

description: Methylation


title: c12 WT #+2 HU exp5

description:
biological replicate 2
Sample 22


title: FK506 1

description:
3-1
FK_1
Normalized_FPKM.txt


title: c12 17q #+2 PBS exp5

description:
biological replicate 2
Sample 23


title: SJRB-iPSC-12_D45

description: Methylation


title: c12 WT #+2 PBS exp5

description:
biological replicate 2
Sample 21


title: L.acidophilus 3

description:
2-3
LA_3
Normalized_FPKM.txt

value: L. acidophilus


title: c12 WT #+4 PBS exp4

description:
biological replicate 1
Sample 29


title: c12 17q #+1 HU exp5

description:
biological replicate 2
Sample 20


title: SJRB-iPSC-11_D45

description: Methylation


title: L.acidophilus 2

description:
2-2
LA_2
Normalized_FPKM.txt


title: c12 WT #+1 HU exp5

description:
biological replicate 2
Sample 18


title: SJRB-iPSC-10_D45

description: Methylation


title: SJRB-iPSC-14_D45

description: Methylation


title: SJRB-iPSC-9_D45

description: Methylation


title: aCD3 3

description:
1-3
aCD3_3
Normalized_FPKM.txt


title: SJRB-iPSC-8_D45

description: Methylation


title: ChIPseq_H3K27ac_MM1S_sgNCOR1_sgRNA1_DMSO_6hours

value: 6 hours

value: DMSO

value: FU-Cas9-Cherry + NCOR1 sgRNA

value: H3K27ac (Abcam, ab4729)


title: ChIPseq_H3K27ac_MM1S_RGFP966_6hours


title: c12 17q #+3 PBS exp4

description:
biological replicate 1
Sample 13


title: L.acidophilus 1

description:
2-1
LA_1
Normalized_FPKM.txt

value: Balb/c

value: wild type

value: 7 weeks

value: CD4+ T cells


title: c12 WT #+1 PBS exp5

description:
biological replicate 2
Sample 17

value: hESC

value: naive


title: c12 17q #+3 HU exp4

description:
biological replicate 1
Sample 14

value: MEF

value: HU


title: c12 17q #+2 HU exp4

description:
biological replicate 1
Sample 10


title: SJRB-iPSC-7_D45

description: Methylation


title: aCD3 2

description:
1-2
aCD3_2
Normalized_FPKM.txt


title: aCD3 1

description:
1-1
aCD3_1
Normalized_FPKM.txt


title: c12 WT #+3 PBS exp4

description:
biological replicate 1
Sample 11


title: c12 17q #+1 PBS exp5

description:
biological replicate 2
Sample 19


title: c12 WT #+2 HU exp4

description:
biological replicate 1
Sample 8


title: c12 WT #+2 PBS exp4

description:
biological replicate 1
Sample 7


title: SJRB-iPSC-4CR Tumor

description: Methylation

value: organoid derived tumor


title: c12 17q #+1 HU exp4

description:
biological replicate 1
Sample 6


title: KO5_LUNG

city: Buffalo

first: Ding

last: Xu

state: NY

address: 3435 Main St.

department: Oral Biology

institute: University at Buffalo

data_processing:
base calling with Casava
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Paired-end clean reads were aligned to mm10 using the Spliced Transcripts Alignment to a Reference (STAR) software.
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: tables with lists of gene counts, normalized raw counts per sample, DEGs

source_name: Lung

extract_protocol:
LPS-induced leucocytes (> 95% PMNs) were collected from air pouch  and used for RNA extraction. Lungs were perfused, removed, flash frozen in liquid nitrogen, and RNA was harvested using RNeasy Mini Kit (QIAGEN) following the protocol.
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA)  was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: For PMN isolation, 3 ml of sterile air was injected under the dorsal skin of mice. Three days later, the pouch was refilled with 2 ml of sterile air. On the seventh day, 1 μg of LPS from Escherichia coli O111:B4 (sigma) in 0.5% solution of carboxymethyl cellulose (sodium salt; Sigma) was injected into the air pouch. After 4 hours, mice were euthanized by isoflurane inhalation and the cells in the pouch were collected by washing with PBS.

value: Lung

value: RAGE-/-


title: SJRB-iPSC-5_D45

description: Methylation

value: Day 45 organoid

value: Dneasy Blood and Tissue kit


title: c12 17q #+1 PBS exp4

description:
biological replicate 1
Sample 5

value: PBS


title: SJRB-iPSC-6_D45

description: Methylation


title: ChIPseq_NCOR1_MM1S

source_name: Multiple Myeloma

value: NCOR1 (Diagenode, C15410341)


title: c12 WT #+3 HU exp4

description:
biological replicate 1
Sample 12


title: KO4_LUNG


title: SJRB-iPSC-4_D45

description: Methylation


title: C22-24h-CO

tag: donor

tag: condition

value: free HIV

tag: time


title: c12 WT #+1 HU exp4

description:
biological replicate 1
Sample 4

tag: cell type

tag: cell line subclass

tag: pluripotency level


title: SJRB-iPSC-3_D45

description: Methylation


title: KO2_LUNG


title: Anti-146a rep3

city: Montreal

first: Gerardo

last: Ferbeyre

state: Qc

address: 2900 Boul. Édouard-Montpetit

department: Biochimie

institute: Université de Montréal

data_processing:
Sequences were trimmed for sequencing adapters and low quality 3' bases using Trimmomatic v0.35
Data was aligned to human reference genome GRCh38 (Gencode v26 and Ensembl v88) using STAR v2.5.1b
DESeq2 v1.22.2 was used to generate normalized gene readcounts
Genome_build: GRChg38 (Gencode v26 and Ensembl v88)
Supplementary_files_format_and_content: Tab-delimited text files include normalized read counts values for each samples and fold changes

source_name: Normal lung fibroblast cells

growth_protocol: Cells were cultured in DMEM (Wisent, Montreal, QC) supplemented with 10% fetal bovine serum (FBS; Wisent), 1% penicillin G/streptomycin sulfate (Wisent) and 2 mM L-Glutamine (Wisent).

extract_protocol:
Cells were harvested in trizol and total RNA was extracted following the manufacturer's instructions up until the isopropanol step. RNA was then bound on Qiagen Rnase easy mini kit (Qiagen, cat#74104) and further purified according to the manufacturer's instructions.
Total RNA extract were rRNA depleted and libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche, cat#08098140702)

treatment_protocol: Cells were retrovirally infected with either an empty vector or a vector expressing RASV12. Cells were selected  with puromycin (1.5 ug/ml) for 3 days. Day 10 post-infection, they were seeded at 8x10^6 and 24 hours later, transfected with antagomirs (CTL or anti-146a). Cells were harvested in Trizol 24 post-transfection.

tag: genotype/variation

value: Expressing RASV12 and a antagomir against miR-146a


title: Anti-146a rep2


title: SJRB-iPSC-2_D45

description: Methylation

tag: protocol


title: c12 17q #+2 PBS exp4

description:
biological replicate 1
Sample 9

tag: feederlayer

tag: treatment

tag: passage


title: KO1_LUNG

tag: strain

tag: genotype


title: Anti-146a rep1

tag: cell line


title: AHA4_LUNG

value: RAGE knock-in


title: Control rep1

value: Expressing RASV12 and a control antagomir


title: Control rep2


title: H9_D45

description: Methylation


title: AHA3_LUNG


title: SJRB-iPSC-1_D45

description: Methylation


title: miR-CLIP rep3

extract_protocol:
An IP against AGO2 was preformed and RNA was extracted using Trizol. Biotin/streptavidin affinity purification was performed on this extracted RNA and a second RNA isolation was done using Trizol.
Total RNA extract were rRNA depleted and libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche, cat#08098140702)

treatment_protocol: Cells were retrovirally infected with either an empty vector or a vector expressing RASV12. Cells were selected  with puromycin (1.5 ug/ml) for 3 days. Day 10 post-infection, they were seeded at 8x10^6 and 24 hours later, transfected with a miR-146 mimic modified with and internal psoralen and biotin or and unmodified miR-146a mimic. Cells were harvested in Trizol 24 post-transfection.

value: Expressing RASV12 and a modified mIR-146a (psoralen and biotin)

tag: antibody


title: miR-CLIP rep2


title: AHA2_LUNG


title: miR-CLIP rep1


title: RB_062

description: Methylation

value: xenograft


title: AHA1_LUNG


title: Input rep2


title: RB_060

description: Methylation


title: Input rep1


title: c12 WT #+1 PBS exp4

description:
biological replicate 1
Sample 3

value: hESC


title: RB_061

description: Methylation


title: WT3_LUNG

value: wild type


title: WT2_LUNG


title: RB_058

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L6_ACTGAT

city: Groningen

first: Xiaojing

last: Chu

state: Groningen

address: Antonius Deusinglaan 1

department: Genetics

country: Netherlands

institute: University medical center Groningen

data_processing:
Alignment was performed with HISAT2 using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
Raw counts were calculated with StringTie using a standard protocol described in Pertea, Mihaela, et al. Nature protocols 11.9 (2016): 1650.
VST normalization and diffentially expressed genes identification were performed with an R package DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file including VST normalized gene expression value of each sample

source_name: Candida albicans_24h

growth_protocol: For PBMCs: Blood from healthy individuals were collected in EDTA tubes (BD vacutainer) and isolated by Ficoll.  Gradient centrifugation was performed for 30 minutes at 400g, using no break. After centrifugation, the layer containing PBMCs was collected using a Pasteur pipette. PBMCs were washed twice with PBS, counted (BioRad cell counter) and adjusted to reach the final concentration of 2 million cells/ml in RPMI 1640 (Gibco, ThermoFisher Scientific), supplemented with 10% heat-inactivated Fetal Cow Serum (Gibco, ThermoFisher Scientific), gentamicin 10mg/ml, L-glutamine 10mM and pyruvate 10mM. Cells were seeded into wells to settle overnight before stimulation.  For HUVECs: Pooled donor-HUVECs were purchased (Lonza) and cultured in EBM-2TM medium (Lonza) supplemented with EGM-2 MV SingleQuot Kit Supplements & Growth Factors (Lonza) at 37oC, 5% CO2 and saturating humidity. Passage 3-5, confluent cells were used for all experiments.

extract_protocol:
Cells were harvested and lysed in lysis buffer of MirVanva MagMax RNA isolation kit. RNA was isolated according to the manufactures instructions. RNA concentration was measured based on Optical density (OD260) using the Nanodrop machine (NanoDrop Technologies). RNA integrity was determined using the Bioanalyzer (Agilent D2000). All samples had RIN score >9.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 1) PBMC stimulation: PBMCs were stimulated with various pathogens, including heat-killed Streptococcus pneumonia  at 1 million cells/ml, heat-killed Candida albicans (at 1 million cells/ml, heat-killed  Aspergillus fumigatus at 1 million cells/ml, Mycobacterium tuberculosis  at 1 million cells/ml, heat-killed Pseudomonas aeruginosa at 1 million cells/ml 30. Cells were also stimulated with only RPMI 1640 a negative control.  RNA  was isolated from the PBMCs at 4 and 24 hours after stimulation. 2) HUVEC direct stimulation:  HUVECs were stimulated with either Heat-killed Streptococcus Pneumonia ( 1 million cells/ml), Heat-killed Candida albicans( 1milllion cells/ml), LPS  at 1000ng/ml, IL-1β at 10ng/ml, TNF-αat 10ng/ml for 6 or 24 hours. 3) Supernatant effect on HUVEC: The supernatants from activated PBMCs were thawed overnight at 4oC and warmed up shortly to 37oC. Polymyxin B was added to the supernatants at the final concentration of 100µg/ml to neutralize residual LPS 9. The supernatants were then added to HUVECs. To study the effect of IL-1 and TNF-α secreted by activated PBMCs on endothelial cells, LEAF-purified TNF-α Antibody and/or IL-1RA  were added to the supernatants at the final concentration of 4µg/ml and 300ng/ml, respectively, incubated at 37oC for 1 hour before adding to HUVECs. HUVECs were incubated with the supernatants from stimulated PBMCs 6 and 24 hours.

value: PBMC

value: healthy donor

tag: donor id


title: WT1_LUNG

tag: tissue


title: 140516_SN163_0555_AC3VYAACXX_L5_GTGGCC


title: 140516_SN163_0555_AC3VYAACXX_L3_AGTCAA

source_name: Mycobacterium tuberculosis_4h


title: KO6_PMN

source_name: PMN

value: PMN

value: air pouch, LPS


title: RB 153

description: Methylation

source_name: O-PDX


title: RB 154

description: Methylation


title: KO4_PMN

value: RAGE-/-


title: Input rep3


title: RB_050

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L5_CCGTCC

source_name: Candida albicans_4h


title: hESC derived SkMC_TFC_2

city: Sydney

first: Travis

last: Ruan

address: Parramatta Road

country: Australia

institute: University of Sydney

data_processing:
RNASeq data aligned using STAR to hg38 assembly
Reads quantified using featureCounts
Differential expression evaluated using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: read counts

source_name: GENEA016 hESC

growth_protocol: Growth protocol is described in Caron et al., 2016, Stem Cells Transl Med

extract_protocol:
RNA extracted using commercial RNA extraction kit
Library prepared by commercial sequencing provider (Novogene)

treatment_protocol: Cells were treated for 4 days, starting at D20 at the same time as they were induced to differentiate into myotubes

value: hESC derived SkMC

value: TFC Treated


title: hESC derived SkMC_TFC_1


title: RB 143

description: Methylation

value: Dneasy Blood and Tissue kit


title: 140516_SN163_0555_AC3VYAACXX_L2_GCCAAT

source_name: Aspergillus fumigatus_4h


title: 140516_SN163_0555_AC3VYAACXX_L4_TAGCTT


title: 140424_SN163_0548_AC3TJNACXX_L7_ACTGAT


title: AHA6_PMN


title: hESC derived SkMC_C_3

value: Cocktail of Myokines Treated


title: hESC derived SkMC_C_2


title: RB 144

description: Methylation


title: AHA4_PMN


title: RB_046

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L5_ACAGTG


title: 140516_SN163_0555_AC3VYAACXX_L3_AGTTCC


title: hESC derived SkMC_C_1


title: RB 145

description: Methylation


title: AHA2_PMN


title: 140606_SN163_0558_AC4E0YACXX_L6_GTGAAA

source_name: Aspergillus fumigatus_24h


title: 140424_SN163_0548_AC3TJNACXX_L5_GTTTCG

source_name: Streptococcus pneumoniae_24h


title: hESC derived SkMC_TFC_3


title: hESC derived SkMC_F_3

value: Follistatin Treated


title: 140424_SN163_0548_AC3TJNACXX_L8_GTTTCG


title: RB 149

description: Methylation


title: WT3_PMN


title: WT2_PMN


title: KO1_PMN


title: 140516_SN163_0555_AC3VYAACXX_L7_GTTTCG


title: hESC derived SkMC_F_2


title: 140424_SN163_0548_AC3TJNACXX_L8_ATTCCT


title: hESC derived SkMC_F_1


title: RB 139

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L4_GAGTGG


title: RB_049

description: Methylation


title: hESC derived SkMC_T_3

value: Testosterone Treated


title: treg_Bach2-cKO rep3

city: Shanghai

first: Heng

last: Zhang

address: No.227 Sounth Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: Regulatory T cells

growth_protocol: Sorted fresh B220-CD4+YFP+cells from WT and Bach2 KO mice spleen

extract_protocol:
Cells were havest and RNA was extract by Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 0.1-1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated sorted cells with plate-bound CD3 and CD28 for 24h

value: lymphocytes

tag: cell subtype

value: Regulatory T cells

value: CD3 and CD28 stimulation in vitro for 24h


title: WT1_PMN


title: RB 134-1

description: Methylation

value: xenograft


title: treg_Bach2-cKO rep2


title: 140424_SN163_0548_AC3TJNACXX_L5_GATCAG


title: 140516_SN163_0555_AC3VYAACXX_L2_CGATGT

source_name: Pseudomonas aeruginosa_24h


title: hESC derived SkMC_T_1


title: hESC derived SkMC_T_2


title: 140606_SN163_0558_AC4E0YACXX_L6_TTAGGC

source_name: Mycobacterium tuberculosis_24h


title: RB_053

description: Methylation


title: hESC derived SkMC_NTC_3

value: Untreated


title: treg_Bach2 WT rep3

value: WT


title: treg_Bach2-cKO rep1


title: RB_056

description: Methylation


title: 140424_SN163_0548_AC3TJNACXX_L8_CCGTCC

value: PBMC


title: hESC derived SkMC_NTC_2


title: treg_Bach2 WT rep2


title: 140516_SN163_0555_AC3VYAACXX_L5_GTTTCG

value: healthy donor


title: RB_059

description: Methylation


title: hESC derived SkMC_NTC_1


title: treg_Bach2 WT rep1


title: MAST 232-2

description: Methylation


title: 140516_SN163_0555_AC3VYAACXX_L2_ATCACG


title: MAST 232-1

description: Methylation


title: RB_051

description: Methylation


title: ChIPseq_H3K27ac_S2_2hours_A485

organism: Drosophila melanogaster

source_name: Embryonic

tag: timepoint

value: 2 hours

tag: treatment+dose

tag: ectopic expression

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: 140516_SN163_0555_AC3VYAACXX_L1_CAGATC

tag: cell type


title: ChIPseq_H3K27ac_S2_6hours_DMSO_Control

value: 6 hours

value: DMSO


title: 140516_SN163_0555_AC3VYAACXX_L1_CGATGT


title: RB_033

description: Methylation


title: RB_034

description: Methylation


title: RNA-seq-HPPT_untreated_rep6

city: Bethesda

first: Hye Kyung

last: Lee

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq counts from RNA-seq samples

growth_protocol: Primary Human Renal Proximal Tubule Epithelial Cells (ATCC® PCS-400-010™) were cultured in low-serum medium consisting of Renal Epithelial Cell Basal Medium (ATCC® PCS-400-030™) with Renal Epithelial Cell Growth Kit (ATCC® PCS-400-040™), Penicillin-Streptomycin-Amphotericin B Solution (ATCC® PCS-999-002™) and Phenol Red (ATCC® PCS-999-001™) added.

extract_protocol:
Total RNA was isolated from the cytokine-stimulated cells using PureLink™ RNA Mini Kit (Invitrogen) and libraries for sequencing were prepared according to the manufacturer’s instructions with TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina, RS-122-2301).
Libraries for sequencing were prepared using standard Illumina protocols.

treatment_protocol: human primary proximal tubule (HPPT) cells were stimulated with IFNβ, JAK inhibitor (Ruxolitinib) and the combination of IFNb and Ruxolitinib for 12 hours in concentration of 10 ng/ml.

value: human primary proximal tubule cells

value: untreated


title: 140424_SN163_0548_AC3TJNACXX_L7_ATGTCA


title: RB_035

description: Methylation

value: Dneasy Blood and Tissue kit


title: RNA-seq-HPPT_untreated_rep5


title: 140424_SN163_0548_AC3TJNACXX_L5_TGACCA


title: RNA-seq-HPPT_untreated_rep4


title: Control-replicate2

city: Tokyo

first: Noboru

last: Mizushima

address: 7-3-1 Hongo

country: Japan

institute: The University of Tokyo

data_processing:
Library strategy: Amplicon sequencing
Basecalls performed using Illumina bcl2fastq version 1.8.4
Sequenced reads were trimmed for adaptor sequence and random primer sequences using in-house pipeline
The number of reads that completely matched the GeCKO v2 library sequence was calculated
Supplementary_files_format_and_content: tab-delimited text files include read count for each target

growth_protocol: HEK293T cells expressing the GFP-LC3-RFP autophagy flux reporter and Cas9 (HEK293T GFP-LC3-RFP cells) were cultured in 10% fetal bovine serum (S1820-500; biowest) supplemented DMEM (D6546; Sigma-Aldrich). HEK293T GFP-LC3-RFP cells were transfected the GeCKOv2 library at a multiplicity of infection (MOI) of 0.3–0.5 and selected with puromycin. Cells were cultured and expanded for two weeks, and sorted using a cell sorter (MoFlo AstriosEQ; Beckman Coulter). After sorting, the cells were expanded for roughly two weeks. The sorting was repeated four times.

extract_protocol:
Genomic DNA was extracted using Blood & Cell Culture Midi kit (13343; QIAGEN).
A total of 100 - 240 µg genomic DNA (varying between replicates) was extracted, and sgRNA sequences were amplified by PCR using Herculase II Fusion DNA polymerase (600675; Agilent Technologies). Next, the amplicons were subjected to the second PCR to attach Illumina adaptors and barcode samples. The primers used in the first PCR were as follows: F1, 5'-AATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCG-3', and R1, 5'-CTTTAGTTTGTATGTCTGTTGCTATTATGTCTACTATTCTTTCC-3'. The primers used in the second PCR were as follows: F2, 5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-(variable-length sequence, up to 8 bp)-TCTTGTGGAAAGGACGAAACACCG-3'  R2, 5'-CAAGCAGAAGACGGCATACGAGAT-(8-bp barcode)-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTCTACTATTCTTTCCCCTGCACTGT-3'. DNA was sequenced on a HiSeq 2500 (Illumina) sequencer. After data acquisition, the number of reads that completely matched the GeCKO v2 library sequence was calculated.

treatment_protocol: Cells were resuspended with HBSS containing 10% FBS, penicillin and streptomycin. Autophagy-activated cells were collected using a cell sorter (MoFlo AstriosEQ; Beckman Coulter).

tag: sorts

value: Homo sapiens

tag: sequenced molecule

value: Genomic DNA amplicon


title: Control-replicate1


title: AutophagyActivated-replicate2


title: 140516_SN163_0555_AC3VYAACXX_L8_GGCTAC


title: RB_036

description: Methylation

tag: protocol


title: Leaflet sample V15

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Illumina software BaseCaller was used to generate BCL files, which were demultiplexed using CASAVA-1.8.2
STAR version 2.5.2a was used to align the reads to the hg38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in hg38 version 97
Genome_build: hg38 gene version 97
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: NGS 11, Hancock®, leaflet

extract_protocol:
Conduits for NGS were explanted from the patients during surgical procedures and immediately transferred to RNAlater® (Sigma Aldrich) to inhibit RNA-degradation. Explants were then dissected to isolate the thickened material of the conduit-wall and one of the three valve-leaflets for RNA-isolation. RNA-isolation was performed in an RNase free area using the TRIzol® reagent (ThermoFisher, 15596026) according to manufacturer’s recommendations. Briefly, small tissue-pieces were frozen in liquid nitrogen and then powered using the TissueLyser® (Qiagen). The resulting 50 – 100 mg tissue-powder was lysed in 1mL TRIzol reagent. Then, the lysate was mixed with 0,2 mL Chloroform and centrifuged to create three phases with the RNA accumulating in the upper aqueous phase. RNA was precipitated using isopropylalcohol and washed twice using 75% Ethanol. DNase treatment was performed on RNeasy mini-columns according to the manufacturer’s protocols (Qiagen). RNA quality was evaluated using the NanoDrop (ThermoFisher) and a fragment analyzer.
RNA-seq libraries were performed using 500 ng total RNA of a non stranded RNA Seq, massively-parallel mRNA sequencing approach from Illumina (TruSeq stranded total RNA Library Preparation , Illumina)

value: tissue from Conduit leaflet


title: Leaflet sample V14

source_name: NGS 10, Hancock®, leaflet


title: 140424_SN163_0548_AC3TJNACXX_L6_CGTACG