title: Reanalysis PCa_H75


title: ATAC-seq - ASEL #3

status: Public on Oct 06 2020

type: SRA

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology (IMP)

description: Batch 2 ASEL 1.5k cells

library_source: genomic

data_processing:
For ChIP-seq, the single-end raw reads of ChIP-seq dataset were mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). Uniquely mapped reads were retained and duplicated reads were marked and discarded using SAMtools (v0.1.18). For visualization, the coverage tracks (i.e. bigWig files) were generated from bam files using kent-ucsc (v2.79). Sharp peaks were identified with macs2 (v2.1.0) against the pooled control samples with default parameters.
For ATAC-seq, the paired-end raw reads of ATAC-seq data were trimmed with Cutadapt (v1.18) and mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). For all samples, multi-mapped reads were filtered with SAMtools (v0.1.20) and duplicate reads were marked and discarded with Picard-tools (v2.18.27; Broad Institute). For visualization, the normalized coverage tracks (i.e. bigWig files) were generated from bam files using with R packages GenomicRanges (v1.38.0) and rtracklayer (v1.46.0) with paired-end option.
Genome_build: ce11
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million

molecule: genomic DNA

organism: Caenorhabditis elegans

source_name: ASEL

extract_protocol:
ChIP assays were performed as previously described in (Askjaer et al., 2014) with minor modifications. ATAC-seq libraries were prepared as described in (Corces et al., 2017) with minor modifications.
ChIP-seq: NEBNext® Ultra II DNA Library Prep Kit. ATAC-seq: Nextera DNA Library Prep Kit

tag: strain

tag: genotype

value: otIs252[lsy-6::YFP (fosmid); rol-6(su1006)] II;  otIs235[che-1p::mChopti; rol-6(su1006)] V

tag: developmental stage

value: Embryo - 350 minutes

tag: cell type

value: ASEL


title: Reanalysis PCa_G65

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Prostate adenocarcinoma from Caucasian men

hyb_protocol: Samples were hybridized to oligonucleotide glass arrays with sequences representing probes for 866 human and 89 human viral miRNAs from the Sanger miRBase (release 12.0) (Human miRNA Microarray V3, Agilent Technologies). After 20 hours slides were washed and scanned.

scan_protocol: Slides were scanned with the dual-laser Agilent scanner G2505B

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze miRNA expression profiles in normal prostates and prostate cancer tissues. Raw intensity values were background subtracted (method = subtract with an offset of 20) and normalized using the quantile method. Duplicated probes were averaged.

molecule: total RNA

organism: Homo sapiens

source_name: Prostate Cancer

label_protocol: MiRNA expression profiling was carried out using the one-colour labelling method. Labelling, hybridization, washing and slide scanning were performed following the manufacturers protocol (Agilent Technologies). Briefly, 100 ng of totRNA were dephosphorylated and denaturated; then a ligation and labeling step with Cy3 was performed.

extract_protocol: TotRNA was isolated following standard TriReagent protocol (Sigma-Aldrich) and DNAse treatment was performed (TURBO Dnase Free, Life Technologies). totRNA quality and quantity were checked by means of bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific) respectively.

tag: tissue

value: Tumor


title: Kidney_STARTinput1

city: La Jolla

first: Nathan

middle: E

last: Lewis

state: California

address: 9500 Gilman Dr

department: Pediatrics

country: USA

institute: UCSD

description:
normalized_TSS_counts.tsv
eTSS_NCBI_picr.bed.gz
eTSS_NCBI_picr.meta.tsv.gz
eTSS_syn20999279_picr.bed.gz
eTSS_syn20999279_picr.meta.tsv.gz
peaks_location.tsv

library_source: transcriptomic

data_processing:
5' and control processing: cutadapt (Martin, 2011) was used to trim adapter sequences and low quality bases from the reads. Reads were aligned to the Chinese Hamster genome assembly PICR (Rupp et al., 2018) and annotation GCF_003668045.1, part of the NCBI Annotation Release 103. Sequence alignment was accomplished using the STAR aligner v2.5.3a. Reads mapped to multiple locations were removed from analysis. Tags were then made using Homer v4.11 command "makeTagDirectory {o_dir} -genome {g} -checkGC -single {bam}"
5' and control processing: Peaks for 5'GRO-seq csRNA-seq was done using Homer v4.11 with input GRO-Seq, using "findPeaks {tss_tag_file} -style tss -i {control_tag_file} -norm 1000000"
5' and control processing: Peaks were then merged using homer command "mergePeaks -d 150 -strand {in_files} > {out}"
Ribosome-depleted RNA: Alignment performed using STAR v2.5.3a with default parameters and removing reads mapped to multiple locations. Quantification performed using htseq-count, with the command "htseq-count -f bam -s reverse -t exon -i gene {bam_f} {annotation} > {out)}"
ATAC-seq: ATAC-seq was processed using the pipeline here: https://github.com/kundajelab/atac_dnase_pipelines . Briefly, the reads were trimmed using cutadapt v1.9.1. Reads were aligned using Bowtie v2.2.4. Peaks were called using Macs2 v2.1.3 with a p-value of 0.01, and replicates were merged using irreproducible discovery rate (IDR) (Li et al., 2011) of 0.1. The fold-change value is the number of normalized counts over the local background, taken as 10,000 kb surrounding.
TSS called using custom Python scripts and thresholding based on distance to NCBI annotation.
Bedgraph were generated by constructing single-nucleotide resolution bedGraph files based on 5' read positions using HOMER. TSS peak files contain TSS cluster positions defined using HOMER's findPeaks.pl command (tab-delimited text files). Normalized to 1e7 uniquely aligned reads.
RNA bedgraph files, which was strand agnostic, created first by making the tag directory , with command  "makeTagDirectory {tag_dir} {bam_file} -read2 -single". Then, bedgraph file was made using "makeUCSCfile {tag_dir} -o {bedgraph_file} -style rnaseq". Normalized to 1e7 uniquely aligned reads.
Genome_build: PICR GCF_003668045.1
Genome_build: [genome annotation]  PICR NCBI Annotation 103
Genome_build: [genome annotation]  picr_proteogenomics.gff (https://www.synapse.org/#!Synapse:syn20999279)
[normalized_TSS_counts.tsv]  Counts-per-million (CPM) matrix, n-by-m matrix, where n is the number of TSS, and m is the number of samples. Each column has a header that names after the title column above, and there is an ID column which gives an ID for each peak.
[peaks_location.tsv]  tsv file of locations of the peaks, along with average CPM.
[eTSS_NCBI_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by NCBI Refseq.
[eTSS_NCBI_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[eTSS_syn20999279_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by Synapse.org ID syn20999279.
[eTSS_syn20999279_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[ATAC_peaks.bed.gz]  A tsv file outputted from Homer mergePeaks on bed files outputted from macs2 using the aforementioned pipeline. The Stat column is the averaged 10*log10qvalue over the samples that contained the peak. This is a modified bed file with a header and a column that indicates which samples contained the open-chromatin position.

organism: Cricetulus griseus

source_name: Kidney

growth_protocol: See paper for complete protocol details. Female Chinese hamsters (Cricetulus griseus) were generously provided by George Yerganian (Cytogen Research and Development, Inc) and housed at the University of California San Diego animal facility on a 12h/12h light/dark cycle with free access to normal chow food and water. All animal procedures were approved by the University of California San Diego Institutional Animal Care and Use Committee in accordance with University of California San Diego research guidelines for the care and use of laboratory animals. None of the used Hamsters were subject to any previous procedures and all of them were used naive without any previous exposure to drugs. Euthanized hamsters were quickly chilled in a wet ice/ethanol mixture (~50/50), organs were isolated, placed into Trizol LS, flash frozen in liquid nitrogen and stored at -80C for later use. CHO-K1 cells were grown on F-K12 media at 37 Â°C with 5 % CO2 (GIBCO-Invitrogen, carlsbad, CA, USA). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018). Hamster bone marrow-derived macrophages (BMDMs) were generated as detailed previously (Link et al., 2018).

extract_protocol:
[RNA-seq]  RNA was extracted from organs that were homogenized in Trizol LS using an Omni Tissue homogenizer. After incubation at RT for 5 minutes, samples were spun at 21.000g for 3 minutes, supernatant transferred to a new tube and RNA extracted following manufacturerâs instructions. Strand-specific total RNA-seq libraries from ribosomal RNA-depleted RNA were prepared using the TruSeq kit Stranded Total RNA Library kit (Illumina) according to the manufacturer-supplied protocol.
[csRNA-seq]  Capped small RNA-sequencing was performed identically as described by (S. H. Duttke et al., 2019). Briefly, total RNA was size selected on 15% acrylamide, 7M UREA and 1x TBE gel (Invitrogen EC6885BOX), eluted and precipitated over night at -80Â°C. Given that the RIN of the tissue RNA was often as low as 2, essential input libraries were generated to facilitate accurate peak calling. csRNA libraries were twice cap selected prior to decapping, adapter ligation and sequencing. Input libraries were decapped prior to adapter ligation and sequencing to represent the whole repertoire of small RNAs with 3â-OH.
[sRNA-seq]  Similar to csRNA-seq, without the decapping.
[5'GRO-seq and GRO-seq]  Global nuclear run-on sequencing (GRO-seq (Core et al., 2008) and 5âGRO-seq (Core et al., 2008; Lam et al., 2013)) were performed as described below. Nuclei from hamster tissues were isolated as described in (Hetzel et al., 2016). Hamster BMDM nuclei were isolated using hypotonic lysis [10 mM Tris-HCl pH 7.5, 2 mM MgCl2, 3 mM CaCl2; 0.1% IGEPAL] and flash frozen in GRO-freezing buffer [50 mM Tris-HCl pH 7.8, 5 mM MgCl2, 40% Glycerol]. 0,5-1 x 106 BMDM nuclei were run-on with BrUTP-labelled NTPs as described (S. H. C. Duttke et al., 2015) with 3x NRO buffer [15mM Tris-Cl pH 8.0, 7.5 mM MgCl2, 1.5 mM DTT, 450 mM KCl, 0.3 U/Âµl of SUPERase In, 1.5% Sarkosyl, 366 ÂµM ATP, GTP (Roche) and Br-UTP (Sigma Aldrich) and 1.2 ÂµM CTP (Roche, to limit run-on length to ~40 nt)]. Reactions were stopped after five minutes by addition of 750 Âµl Trizol LS reagent (Invitrogen), vortexed for 5 minutes and RNA extracted and precipitated as described by the manufacturer.
[GRO-seq]  RNA pellets were fully resuspended in 18 Âµl ddH2O + 0.05% Tween (dH2O+T). Subsequently, 2 Âµl fragmentation mix [100 mM ZnCl2, 10 mM Tris-HCl pH 7.5] was added and the samples incubated at 70Â°C for 15 minutes. RNA fragmentation was stopped by placing samples on ice and addition of 2.5 Âµl 100 mM EDTA p.H. 8.0 and 500 Î¼l cold GRO binding buffer [GRO-BB; 0.25Ãsaline-sodium-phosphate-EDTA buffer (SSPE), 0.05% (vol/vol) Tween, 37.5 mM NaCl, 1 mM EDTA p.H. 8.0]. BrU enrichment was performed using a BrdU Antibody (Sigma B8434-200 Âµl Mouse monoclonal BU-33) coupled to Protein G (Dynal 1004D) beads. Per run on reaction, 3x 20 Âµl of Protein G beads were washed twice in DPBS+0.05% Tween 20 (DPBS+T) and then the antibody coupled in a total volume of 1 ml DPBS+%T under gentle rotation. 1 Âµl of antibody was used per 8 Âµl of beads. After one hour at RT, the beads were collected using a magnet and the supernatant saved for future coupling reactions. Coupled beads were washed twice with GRO-BB prior to use. It is recommended to pre-chill beads to 4áµC prior to the IP as traces of RNase may be observed. RNase activity can be monitored e.g. using IDTâs RNaseAlertÂ®. No crosslinking is required and worked best in our hands followed by DMP >>> Bs3. To each reaction of fragmented NRO-RNA with added GRO-BB, 20 Î¼l equilibrated Î±BrdU beads were added and the samples slowly rotated at 4 Â°C for 80 minutes. Beads were subsequently collected on a magnet and the IP reaction washed twice with 500 Î¼l GRO binding buffer before RNA was eluted by incubation of the beads in 500 Î¼l Trizol LS (Thermo Fisher) under medium agitation for 5 minutes. 120 Î¼l of TET [10 mM Tris-HCl pH 7.5, 1 mM EDTA p.H. 8.0, 0.05 % Tween20] was added to increase the supernatant and RNA extracted as described by the manufacturer. For end-repair and decapping, RNA pellets were dissolved in 8 Âµl TET by vigorous vortexing, heated to 70Â°C for 2 minutes and placed on ice. After a quick spin, 22 Âµl Repair MM [3 Âµl 10x PNK buffer, 15.5 Âµl dH2O+T, 0.5 Âµl SUPERase-In RNase Inhibitor (10 U, Ambion), 2 Âµl PNK (20U, Enzymatics Y904L), 1 Âµl RppH (5U, NEB)] was added, mixed by flicking and incubated at 37Â°C for 1 hour. To phosphorylate the 5âend, 1 Âµl 10 mM ATP was subsequently added and the reactions were incubated for another 45 minutes at 37Â°C (the high ATP concentration is advised to quench RppH activity). Following end repair, 2.5 Âµl 50 mM EDTA was added, reactions mixed and then heated to 70Â°C for 2 minutes before being placed on ice. A second BrdU enrichment was performed as detailed above. For library preparation, RNA pellets were dissolved in 2.75 Âµl TET + 0.25 Âµl Illumina TruSeq 3âAdapter (10 mM), heated to 70Â°C for 2 minutes and placed on ice. 7 Âµl of 3âMM [4.75 Âµl 50% PEG8000, 1 Âµl 10x T4 RNA ligase buffer (NEB), 0.25 Âµl SUPERase-In, 1 Âµl T4 RNA Ligase 2 truncated (200U; NEB)] was added, mixed well by flicking and reactions incubated at 20Â°C for 1 hour. Reactions were diluted by addition of 10 Âµl TET + 2 Âµl 50 mM EDTA, heated to 70Â°C for 2 minutes, placed on ice and a third round of BdUTP enrichment was performed. RNA was transferred as a pellet to PCR strips during the 75% ethanol wash and dried. Samples were dissolved in 4 Âµl TET [10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 0.05% Tween 20] + 1 Âµl 10 mM reverse transcription (RT) primer. To anneal the RT-primer, the mixture was incubated at 75Â°C for 5 minutes, 37Â°C for 15 minutes and 25Â°C for ~10 minutes.  To ligate the 5â Illumina TruSeq adapter, 10 Âµl 5âMM [1.5 Âµl ddH2O + 0.2% Tween20, 0.25 Âµl denaturated 5âTruSeq adapter (10 mM), 1.5 Âµl 10x T4 RNA ligase buffer, 0.25 Âµl SUPERase-In, 0.2 Âµl 10 mM ATP, 5.8 Âµl 50% PEG8000, 0.5 Âµl T4 RNA ligase 1 (5U; NEB)] was added and reactions were incubated at 25Â°C for 1 hour. Reverse transcription was performed using Protoscript II (NEB) [4 Âµl 5x NEB FirstStrand buffer (NEB; E7421AA), 0.25 Âµl SUPERase-In, 0.75 Âµl Protoscript II (150U; NEB)] at 50Â°C for 1 hour. After addition of 30 Âµl PCR MM [25 Âµl 2x LongAmp Taq 2X Master Mix (NEB), 0.2 Âµl 100 mM forward primer, 2.8 Âµl 5 M Betaine and 2 Âµl 10 mM individual barcoding primer], mixtures were amplified for 13 cycles. PCR reactions were cleaned up using 1.5 volumes of SpeedBeadsâ¢ (GE Healthcare) in 2.5 M NaCl/20%PEG8000 and the libraries size selected on a PAGE/TBE gels to 150â225 bp. Gel slices were shredded by spinning through a 0.5 ml perforated PCR tube placed on top of a 1.5 ml tube. 150 Âµl Gel EB [0.1% LDS, 1M LiCl, 10 mM Tris-HCl pH 7.8] was added and the slurry incubated under agitation overnight. To purify the eluted DNA, 800 Âµl Zymogen ChIP DNA binding buffer (D5205) was added into the 1.5 ml tube containing the shredded gel slice and the Gel EB, mixed by pipetting and the slurry transferred to a ZymoMiniElute column. Samples were first spun at 1000g for 3 minutes, then 10k g for 30 seconds. Flow through was removed, and samples washed with 200 Âµl Zymo WashBuffer (with EtOH). Gel remainders were removed by flicking and columns washed by addition on another 200 Âµl Zymo WashBuffer. Flow through was removed, columns spun dry by centrifugation at 14k g for 1 minute and DNA eluted by addition of 20 Âµl pre-warmed Sequencing TET [10 mM Tris-HCl pH 8.0, 0.1 mM EDTA, 0.05% Tween 20]. Libraries were sequenced on an Illumina NextSeq 500 at using 75 cycles single end.
[5' GRO-seq]  RNA pellets were resuspendend in 10 Âµl TET, heated to 70Â°C for 2 minutes and placed on ice. 10 Âµl of dephosporylation MM [2 Âµl 10x CutSmart, 6.75 Âµl dH2O+T, 1 Âµl Calf Intestinal alkaline Pho

tag: treatment

tag: Sex

value: Female

value: Kidney

tag: assay

value: total short RNA (20-65nt)

tag: molecule


title: ATAC-seq - ASER #2

description: Batch 1 sort 2 ASER 1k cells

source_name: ASER

value: ASER


title: ATAC-seq - ABp 90 minutes (delta150) #2

description: 90min ABp delta150 #2 - MLC2309 - no tbx binding site

source_name: Embryo (ABp) - 90 minutes (delta150)

value: lucIs39[tbx-37p::mNeonGreen::2xNLS::tbx-37 3'UTR; pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR; med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR)]; lsy-6(luc160[lsy-6::d150]) V

value: Embryo - 90 minutes

value: ABp


title: ATAC-seq - ASEL #2

description: Batch 1 sort 2 ASEL 1k cells


title: Reanalysis PCa_W25


title: Reanalysis PCa_W28


title: Heart_STARTinput1

source_name: Heart

value: Heart


title: Reanalysis PCa_X40


title: ATAC-seq - ASER #1

description: Batch 1 sort 1 ASER 1k cells


title: FemaleReproductive_STARTinput1

source_name: FemaleReproductive

value: FemaleReproductive


title: ATAC-seq - ASEL #1

description: Batch 1 sort 1 ASEL 1k cells


title: ATAC-seq - ABa 90 minutes (delta150) #1

description: 90min ABa delta150 #1  - MLC2309  - no tbx binding site

source_name: Embryo (ABa) - 90 minutes (delta150)

value: ABa


title: Reanalysis PCa_V18


title: Sample 6 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG6_S87]

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA).
Sequenced raw FASTQ files were trimmed for adapters and contaminants such as ribosomal DNA, mitochondrial DNA, unclassified sequences using Bowtie 2 aligner and kraken database, respectively.
Trimmed reads were mapped to the reference genome hg38 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using hg38 assembly and Ensemble transcripts release 91
Transcripts were later filtered for regions fully or partially spanned within exon regions. Normalization was done to remove over or under represented genes and further normalized to baseline (no silencing cells without rhTGF-β1 treatment). Gene enrichment analysis was then performed for comparisons of differentially expressed genes between SDC-1 silenced cells with rhTGF-β1 or SDC-4 silenced cells with rhTGF-β1 versus Control siRNA silenced cells co-cultured with rhTGF-β1. Differentially regulated genes were filtered for statistical group differences with p-value <0.05, fold change >-2/+2, and total read counts >10. Enriched gene-set on above comparisons were explored for treatment effect using hierarchical clustering and pathway enrichment via KEGG analysis tools.
Genome_build: hg38
Supplementary_files_format_and_content: Normalized CPM Counts for genes in a txt format

growth_protocol: Patient derived CD90+CD73+CD105+mesenchymal stromal cells from endometrioma were cultured with DMEM F/12 medium with 10% Fetal bovine serum medium. They were passaged for 2-3 generations or until cells reach about 2 million cells for each sample.

extract_protocol:
Invaded 3D spheroids were lysed using TRIzol reagent (Ambion® Thermo Fisher Scientific, Waltham, USA) and subsequent RNA extraction was performed using Ethanol precipitation method.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014), tagmentation step was accomplished using Nextera XT kit (Illumina) and sequencing was done in Nextseq 550® at the bioinformatics expression analysis facility at Karolinska University hospital, Sweden.

treatment_protocol:
Gene Silencing: 20nM negative control siRNA (catalog no. 4390843) or SDC-1 siRNA (catalog no. 4392420) or SDC-4 siRNA (catalog no. 4392420, all obtained from Ambion® Thermo Fisher Scientific, Waltham, USA) were suspended in Opti-MEM medium (Gibco® Thermo Fisher Scientific, Waltham, USA) and incubated for five minutes. Similarly, DharmaFECT 1 (catalog no. T-2001-03, DharmaconTM Horizon discovery, Waterbeach, UK) was suspended in Opti-MEM medium and incubated for 5 minutes according to the manufacturer’s protocol. Later, RNA silencer and transfection solution were mixed and allowed to incubate for 30 minutes to form a complex containing silencer and transfection reagent. The above mixture was added to Patient derived CD90+CD73+CD105+mesenchymal stromal cells from endometrioma, cultured in adherent culture plates and incubated for 12 hours. Later, the silencing media were replaced with DMEM F/12 medium with 10% Feta bovine serum medium to 48 hours. Later, cells were harvested, counted and subjected to TGF-b treatment, mentioned below.
TGF-B treatment within 3D-invasion assay: Patient derived mesenchymal stromal cell markers CD90+CD73+CD105+ (plated at 5,000 cells/well), silenced with either control siRNA, siRNA against SDC1 or SDC4 were mixed with spheroid enrichment medium containing growth factors EGF, bFGF (10ng/ml each, Invitrogen® Thermo Fisher Scientific, Waltham, USA), B27 supplement (Gibco® Thermo Fisher Scientific, Waltham, USA), insulin-transferrin-selenium (Gibco® Thermo Fisher Scientific, Waltham, USA), and 50µg/ml progesterone (Sigma Aldrich, USA) in phenol-free DMEM/F12 medium (Gibco® Thermo Fisher Scientific, Waltham, USA). The cell suspension was mixed with ECM matrix ( provided in commercial available kit, Cultrex® 3D-spheroid invasion assay kit (catalog no. 3500-096-K, Trevigen Inc., USA) and plated onto 96 well ultra lo attachment plates (triplicates for each sample and each treatments. 3D spheroids were allowed to form for 48 hours.Then, invasion media provided in kit were added, followed by spheroid enrichment mdium with and without 2ng/ml recombinant human (rh)TGF-β1 (catalog no. T7039-50UG, Sigma-Aldrich, USA) were added to the corresponding wells.  3D spheroids were  allowed to incubate for another 96 hours.

tag: source subject status

value: ASRM Stage III-IV ovarian endometriosis

value: CD90+CD73+CD105+ mesenchymal stromal cells from endometrioma

tag: genotype and treatment


title: Brain_STARTinput2

source_name: Brain

value: Brain


title: Sample 5 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG5_S86]

source_name: CD90+CD73+CD105+mesenchymal stromal cells from endometrioma


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 48h-rep2

city: Cheongju-si

first: Yong-Soon

last: Park

state: Chungcheongbuk-do

address: Cheongju

department: Biotechnology Research  Institute

country: South Korea

institute: Chungbuk National University

data_processing:
Illumina Hiseq 2000, Casava1.7 software
Sequenced reads were trimmed for adaptor sequence, and trimmed for low-quality sequence, then mapped to Arabidopsis thaliana whole genome using HISAT2 v 2.1.0 with default parameters and '--max-intronlen 2000'
The number of mapped clean reads for each gene was counted using HTSeq v. 0.11.0 and then normalized with DESeq package in R to avoid bias due to different of sequencing amount.
Genome_build: Arabidopsis reference genome: TAIR 10.0; Vibrio reference genome: accession number GCA_000186585.1
Supplementary_files_format_and_content: Tab-delimited text files include normalized values with DESeq package in R for each Sample.  Mmatrix table counts.txt with raw gene counts for expressed gene and every sample.  Only the transcripts of Arabidopsis thaliana are represented.

organism: Arabidopsis thaliana

source_name: leaf tissue

growth_protocol: Arabidopsis plants were grown at 24 ± 2 °C under a 8 h light/16 h dark photoperiod and fluorescent light (7,000 lux light intensity) for 3 weeks.

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq Stranded Total RNA LT (with Ribo-Zoro-Plant) Set A (Illumina, CA, USA) according to manufacturer’s protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: V. vulnificus MO6-24/O (OD600 = 1) was infiltrated onto the 3-week-old Arabidopsis plants along with PBS as a negative control.

tag: ecotype

value: V.vulnificus MO6-24/O

tag: time

value: leaf


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 48h-rep1


title: Reanalysis PCa_P60


title: Arabidopsis leaf infiltrated by PBS 48h-rep1

value: phosphate-buffer saline


title: Arabidopsis leaf infiltrated by PBS 48h-rep2


title: Reanalysis PCa_Q70

value: Tumor


title: Brain_STARTinput1

value: Female


title: Sample 4 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG4_S85]


title: Reanalysis PCa_CC8


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 24h-rep2


title: Spleen_START2

value: Spleen; blood

value: capped short RNA (20-65nt)

value: capped short total RNA (20-65nt)


title: Sample 3 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG3_S84]


title: Reanalysis PCa_CC75


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 24h-rep1


title: Spleen_START1


title: CHO_STARTinput1

source_name: CHO

tag: cell line

value: CHO

value: total short RNA (20-65nt)


title: Arabidopsis leaf infiltrated by PBS 24h-rep2


title: Reanalysis PCa_CC62


title: Sample 2 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG2_S83]


title: Reanalysis PCa_CC41


title: Sample 1 with SDC-4 siRNA silencing and 2ng/ml TGF-β stimulation [SG1_S82]


title: Pancreas_START2

source_name: Pancreas

value: Pancreas


title: Pancreas_START1


title: Arabidopsis leaf infiltrated by PBS 24h-rep1


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 12h-rep2


title: Sample 4 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF4_S79]


title: Sample 5 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF5_S80]


title: Arabidopsis leaf infiltrated by PBS 12h-rep2


title: Arabidopsis leaf infiltrated by PBS 12h-rep1


title: Reanalysis PCa_CC3


title: Reanalysis PCa_CC17


title: Muscle_START2

source_name: Muscle

value: Muscle


title: Reanalysis PCa_CC35


title: MiscOrgans_START2

source_name: Whole Organism

value: Whole Organism


title: Muscle_START1


title: Reanalysis PCa_C27


title: MiscOrgans_START1


title: Sample 2 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF2_S77]


title: Reanalysis PCa_BB5


title: Sample 1 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF1_S76]


title: Lung_START2

source_name: Lung

value: Lung


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 6h-rep2


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 6h-rep1


title: Sample 6 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF6_S81]

value: ASRM Stage III-IV ovarian endometriosis


title: Sample 6 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE6_S75]

value: CD90+CD73+CD105+ mesenchymal stromal cells from endometrioma


title: Lung_START1


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 12h-rep1


title: Reanalysis PCa_B17


title: Liver_START2

source_name: Liver

value: Liver


title: Sample 5 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE5_S74]


title: Arabidopsis leaf infiltrated by PBS 6h-rep2


title: Reanalysis PCa_B11


title: Arabidopsis leaf infiltrated by PBS 6h-rep1


title: Reanalysis PCa_B12


title: Sample 3 with SDC-1 siRNA silencing and 2ng/ml TGF-β stimulation [SF3_S78]


title: Liver_START1


title: Reanalysis PCa_C25


title: Sample 3 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE3_S72]


title: Sample 2 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE2_S71]


title: Sample 4 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE4_S73]


title: Kidney_START2

value: Kidney


title: Reanalysis PCa_AA97


title: Sample 1 with control siRNA silencing and 2ng/ml TGF-β stimulation [SE1_S70]


title: Kidney_START1


title: Arabidopsis leaf infiltrated by PBS 3h-rep1

value: leaf


title: Heart_START2

value: Heart


title: Sample 6 with SDC-4 siRNA silencing and no TGF-β stimulation [SD6_S69]


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 0h-rep2

value: V.vulnificus MO6-24/O


title: FemaleReproductive_START2

value: Female

value: FemaleReproductive


title: Heart_START1

value: capped short RNA (20-65nt)


title: Reanalysis PCa_AA69

value: Tumor


title: FemaleReproductive_START1

value: capped short total RNA (20-65nt)


title: Sample 5 with SDC-4 siRNA silencing and no TGF-β stimulation [SD5_S68]


title: Arabidopsis leaf infiltrated by PBS 0h-rep2

value: phosphate-buffer saline


title: Reanalysis PCa_CC91


title: Sample 4 with SDC-4 siRNA silencing and no TGF-β stimulation [SD4_S67]


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 0h-rep1


title: Reanalysis PCa_D40


title: Sample 3 with SDC-4 siRNA silencing and no TGF-β stimulation [SD3_S66]


title: Reanalysis PCa_CC87


title: Reanalysis PCa_D37


title: CHO_START1

value: CHO


title: Arabidopsis leaf infiltrated by PBS 0h-rep1


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 3h-rep2


title: Brain_START3

value: Brain


title: Reanalysis PCa_CC83


title: Brain_START2


title: Sample 1 with SDC-4 siRNA silencing and no TGF-β stimulation [SD1_S64]


title: Sample 2 with SDC-4 siRNA silencing and no TGF-β stimulation [SD2_S65]


title: Brain_START1


title: Reanalysis PCa_AA65


title: MCF-7 cells expressing shPOLE and vector control, replicate 1

city: New York

first: Richard

last: Possemato

state: NY

address: 550 First Avenue

department: Pathology

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.4
Sequenced reads were checked for contaminations using fastqscreen v0.5.2 and were mapped to mm10 referece genome using STAR aligner v2.5.3a d with default parameters.
Raw read counts were obtained using featureCounts from subread package v1.4.6-p3
Normalization and differential gene exrpression analysis was performed using DESeq2 v1.14.0
Genome_build: hg19
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

source_name: MCF7 shPOLE_1 VC_1

extract_protocol:
RNeasy Plus Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: shRNA infection of cell lines with stable expression of POLE or control, 5 days prior to extraction

tag: replicate

value: shRNA targeting DNA Polymerase epsilon (POLE)


title: MCF-7 cells expressing shPOLE and vector control, replicate 2

source_name: MCF7 shPOLE_1 VC_2


title: Arabidopsis leaf infiltrated by V. vulnificus MO6-24/O 3h-rep1


title: Reanalysis PCa_AA90

source_name: Prostate Cancer


title: Sample 6 with SDC-1 siRNA silencing and no TGF-β stimulation [SC6_S63]


title: Sample 5 with SDC-1 siRNA silencing and no TGF-β stimulation [SC5_S62]


title: Arabidopsis leaf infiltrated by PBS 3h-rep2


title: MCF-7 cells expressing shPOLE and POLE cDNA, replicate 1

source_name: MCF7 shPOLE_1 Rescue_1

value: Vector Control


title: Reanalysis PCa_A9


title: CAMA-1 cells expressing shPOLE and vector control, replicate 2

source_name: CAMA-1 shPOLE_1 VC_2


title: Sample 4 with SDC-1 siRNA silencing and no TGF-β stimulation [SC4_S61]

value: ASRM Stage III-IV ovarian endometriosis


title: Liver_GROCap1

data_processing:
Library strategy: GRO-Seq
5' and control processing: cutadapt (Martin, 2011) was used to trim adapter sequences and low quality bases from the reads. Reads were aligned to the Chinese Hamster genome assembly PICR (Rupp et al., 2018) and annotation GCF_003668045.1, part of the NCBI Annotation Release 103. Sequence alignment was accomplished using the STAR aligner v2.5.3a. Reads mapped to multiple locations were removed from analysis. Tags were then made using Homer v4.11 command "makeTagDirectory {o_dir} -genome {g} -checkGC -single {bam}"
5' and control processing: Peaks for 5'GRO-seq csRNA-seq was done using Homer v4.11 with input GRO-Seq, using "findPeaks {tss_tag_file} -style tss -i {control_tag_file} -norm 1000000"
5' and control processing: Peaks were then merged using homer command "mergePeaks -d 150 -strand {in_files} > {out}"
Ribosome-depleted RNA: Alignment performed using STAR v2.5.3a with default parameters and removing reads mapped to multiple locations. Quantification performed using htseq-count, with the command "htseq-count -f bam -s reverse -t exon -i gene {bam_f} {annotation} > {out)}"
ATAC-seq: ATAC-seq was processed using the pipeline here: https://github.com/kundajelab/atac_dnase_pipelines . Briefly, the reads were trimmed using cutadapt v1.9.1. Reads were aligned using Bowtie v2.2.4. Peaks were called using Macs2 v2.1.3 with a p-value of 0.01, and replicates were merged using irreproducible discovery rate (IDR) (Li et al., 2011) of 0.1. The fold-change value is the number of normalized counts over the local background, taken as 10,000 kb surrounding.
TSS called using custom Python scripts and thresholding based on distance to NCBI annotation.
Bedgraph were generated by constructing single-nucleotide resolution bedGraph files based on 5' read positions using HOMER. TSS peak files contain TSS cluster positions defined using HOMER's findPeaks.pl command (tab-delimited text files). Normalized to 1e7 uniquely aligned reads.
RNA bedgraph files, which was strand agnostic, created first by making the tag directory , with command  "makeTagDirectory {tag_dir} {bam_file} -read2 -single". Then, bedgraph file was made using "makeUCSCfile {tag_dir} -o {bedgraph_file} -style rnaseq". Normalized to 1e7 uniquely aligned reads.
Genome_build: PICR GCF_003668045.1
Genome_build: [genome annotation]  PICR NCBI Annotation 103
Genome_build: [genome annotation]  picr_proteogenomics.gff (https://www.synapse.org/#!Synapse:syn20999279)
[normalized_TSS_counts.tsv]  Counts-per-million (CPM) matrix, n-by-m matrix, where n is the number of TSS, and m is the number of samples. Each column has a header that names after the title column above, and there is an ID column which gives an ID for each peak.
[peaks_location.tsv]  tsv file of locations of the peaks, along with average CPM.
[eTSS_NCBI_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by NCBI Refseq.
[eTSS_NCBI_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[eTSS_syn20999279_picr.bed.gz]  Updated TSS annotation in bed format where the TSS are adjusted based on our analysis and informed by Synapse.org ID syn20999279.
[eTSS_syn20999279_picr.meta.tsv.gz]  Additional info on eTSS bed file. A tab-separated-value file where each row is a TSS corresponding to the TSS in the bed file. In the file the columns are (1) The name of the TSS that corresponds to the bed file IDs (2) Comma-separated list of biosamples that express the TSS (3) Confidence score with three binary values, where the leftmost bit is one if the maximum CPM is greater or equal to 2 CPM, the second bit is if there were more than one biosample with the TSS, and the third bit is 1 if it is considered a stable TSS, meaning there was total-RNA reads present there as well. (4) The location of the the CHO ATAC region, if there is one near the TSS (5) Corresponding gene (6) Corresponding transcript (7) If this TSS was annotated from the current paper or was from the previous annotation, (which is only there if there was no experimental TSS seen for that transcript) 8) Binary value if there was an open-chromatin region near the TSS in any of the samples.
[ATAC_peaks.bed.gz]  A tsv file outputted from Homer mergePeaks on bed files outputted from macs2 using the aforementioned pipeline. The Stat column is the averaged 10*log10qvalue over the samples that contained the peak. This is a modified bed file with a header and a column that indicates which samples contained the open-chromatin position.

value: Capped global nuclear run on (5' GRO-Seq)

value: capped nascent RNA


title: Reanalysis PCa_A3


title: CAMA-1 cells expressing shPOLE and vector control, replicate 1

source_name: CAMA-1 shPOLE_1 VC_1


title: Sample 3 with SDC-1 siRNA silencing and no TGF-β stimulation [SC3_S60]

value: CD90+CD73+CD105+ mesenchymal stromal cells from endometrioma


title: Reanalysis PCa_A2


title: Sample 2 with SDC-1 siRNA silencing and no TGF-β stimulation [SC2_S59]


title: Kidney_GROCap1

source_name: Kidney

value: Kidney


title: CHO_GROCap2


title: Sample 1 with SDC-1 siRNA silencing and no TGF-β stimulation [SC1_S58]


title: Sample 6 with control siRNA silencing and no TGF-β stimulation [SB6_S57]


title: CHO_GROCap1


title: MCF-7 cells expressing shPOLE and POLE cDNA, replicate 2

source_name: MCF7 shPOLE_1 Rescue_2


title: Lung_GROCap1

value: Lung


title: Brain_GROCap1

source_name: Brain


title: MDA-MB-231 cells expressing shPOLE and vector control, replicate 2

source_name: MDA-MB-231 shPOLE_1 VC_2


title: Reanalysis PCa_A5


title: MDA-MB-231 cells expressing shPOLE and vector control, replicate 1

source_name: MDA-MB-231 shPOLE_1 VC_1


title: MDA-MB-231 cells expressing shPOLE and POLE cDNA, replicate 2

source_name: MDA-MB-231 shPOLE_1 Rescue_2


title: Sample 4 with control siRNA silencing and no TGF-β stimulation [SB4_S55]

source_name: CD90+CD73+CD105+mesenchymal stromal cells from endometrioma


title: CAMA-1 cells expressing shPOLE and POLE cDNA, replicate 2

source_name: CAMA-1 shPOLE_1 Rescue_2


title: MDA-MB-231 cells expressing shPOLE and POLE cDNA, replicate 1

source_name: MDA-MB-231 shPOLE_1 Rescue_1


title: Sample 3 with control siRNA silencing and no TGF-β stimulation [SB3_S54]


title: BMDM1hKLA_GROCap1

source_name: Bone marrow-derived macrophages

value: 1-hour KLA treatment

value: Bone marrow-derived macrophages


title: CAMA-1 cells expressing shPOLE and POLE cDNA, replicate 1

source_name: CAMA-1 shPOLE_1 Rescue_1


title: BMDMwt_GROCap1

value: Female


title: Sample 5 with control siRNA silencing and no TGF-β stimulation [SB5_S56]


title: Lung_GRO1

source_name: Lung

value: Global nuclear run on

value: nascent RNA


title: Sample 2 with control siRNA silencing and no TGF-β stimulation [SB2_S53]


title: Sample 1 with control siRNA silencing and no TGF-β stimulation [SB1_S52]


title: Sample 6C

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina bcl2fastq
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 2.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: RNA-seq LV-shSOX2

growth_protocol: Fresh tissue was enzymatically digested with 20 μg/ml DNase I (Roche Applied Science, Basel, Switzerland) and 1 mg/ml collagenase A in Dulbecco's modified Eagle's medium (DMEM)-F12 (Euroclone, Milan, Italy) and filtered. Patient-derived SSM2c cells were cloned from the original metastases (SSM2) by plating one cell per well. Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Euroclone, Milan, Italy) containing 10% fetal bovine serum (FBS), 1% penicillin/streptomycin (PS) and 1% Glutamine, and maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted with RNeasy mini kit (Qiagen) and quantified by using Nanodrop 8000.
cDNA libraries were prepared following Illumina RNA-Seq preparation protocol. The cDNA fragments were amplified by polymerase chain reaction (PCR) and sequenced at both ends using an Illumina Genome Analyzer IIx. Rna-seq and ChIP-seq data was analyzed using MAP-RSEQ (http://bioinformaticstools.mayo.edu/), respectively, high-throughput packages designed by the Mayo Clinic Bioinformatics Program for these purposes.

treatment_protocol: Melanoma cells were transduced with lentivectors targeting SOX2 3’ untranslated region (UTR) (targeting sequence 5’-CTGCCGAGAATCCATGTATAT-3’) (LV-shSOX2), GLI1 (UTR) (targeting sequence 5’-CCTGATTATCTTCCTTCAGAA-3’) (LV-shGLI1) or non-targeting region (LV-c).

value: Metastatic melanoma cells

tag: source

value: patient-derived melanoma cells

tag: passage

value: subcutaneous melanoma metastasis

value: shRNA mediated knockdown of SOX2


title: Sample 6B


title: Sample 6 with no silencing and no TGF-β stimulation [SA6_S51]

value: no silencing and no TGF-β stimulation


title: Sample 5C

source_name: RNA-seq LV-c

value: Control vector for shRNA mediated knockdowns in Sample 6A-C


title: Sample 5 with no silencing and no TGF-β stimulation [SA5_S50]

value: ASRM Stage III-IV ovarian endometriosis


title: Liver_GRO1

source_name: Liver

value: Liver


title: Sample 4 with no silencing and no TGF-β stimulation [SA4_S49]


title: Sample 3 with no silencing and no TGF-β stimulation [SA3_S48]


title: Sample 5B


title: Sample 6A


title: Sample 2C

source_name: RNA-seq RV-c/LV-shGLI1

value: shRNA mediated knockdown of GLI1


title: Kidney_GRO1


title: Brain_GRO1

value: Brain


title: CHO_GRO2

source_name: CHO

value: CHO


title: CHO_GRO1


title: Sample 2 with no silencing and no TGF-β stimulation [SA2_S47]

value: CD90+CD73+CD105+ mesenchymal stromal cells from endometrioma


title: Spleen_ATAC1

description:
ATAC_peaks.bed.gz
eTSS_NCBI_picr.meta.tsv.gz
eTSS_syn20999279_picr.meta.tsv.gz

value: Spleen; blood

value: ATAC

value: accessible DNA


title: BMDMwt_GRO1

value: 1-hour KLA treatment

value: Bone marrow-derived macrophages

value: Female

value: Global nuclear run on


title: Sample 1 with no silencing and no TGF-β stimulation [SA1_S46]


title: BMDM1hKLA_GRO1

value: Global nuclear run on (GRO-Seq)

value: nascent RNA


title: Sample 5A

value: Metastatic melanoma cells

value: patient-derived melanoma cells

value: subcutaneous melanoma metastasis


title: Lung_ATAC1

value: Lung


title: Sample 2B

value: shRNA mediated knockdown of GLI1


title: Sample 2A


title: Liver_ATAC1

value: Liver


title: Sample 1C

source_name: RNA-seq RV-c/LV-c

value: Control vector for shRNA mediated knockdowns in Sample 2A-C


title: ∆prfA rep 3

city: Ithaca

first: Martin

last: Wiedmann

address: 341 Stocking Hall

department: Food Science

institute: Cornell University

data_processing:
Sequence reads were aligned to the L. monocytogenes 10403S genome using the BWA-MEM algorithm, version 0.7.3a (Oliver et al., 2010)
The data for coverage per base on the sense and antisense strands were analyzed separately using SAMtools (Li et al., 2009)
Differential expression of genes in each strain comparison (wt/∆prfA, wt/prfA*, and prfA*/∆prfA) were analyzed using the baySeq package for R version 2.2.0 (Hardcastle and Kelly, 2010)
Genome_build: CP002002.1
Supplementary_files_format_and_content: Differential expression of genes in each strain comparison

organism: Listeria monocytogenes

source_name: ∆prfA rep 3

growth_protocol: Three L. monocytogenes strains were used for this study: (i) wt (10403S), (ii) prfA* mutant (G145S), and (iii) ∆prfA mutant. All strains were maintained in brain heart infusion (BHI; Difco, Becton Dickinson and Co., Sparks, MD) stocks, stored at -80°C in 15% glycerol. Strains were streaked from frozen glycerol stocks, onto BHI agar plates, followed by incubation at 37°C for 24 h. A single colony from these plates was subsequently inoculated into 5 mL of BHI broth in 16 mm tubes, followed by incubation at 37°C with shaking (230 rpm) for 16 h (Series 25 Incubator, New Brunswick Scientific, Edison, NJ). After 16 h, 100 μL BHI culture was inoculated into fresh 10 mL Luria Bertani (LB)-MOPS broth pre-treated with 0.2% activated charcoal, which was filtered prior to supplementation with 25 mM G1P to induce prfA transcription and PrfA activity and grown to mid-log phase (approximately OD600 0.4) at 37°C, prior to RNA extraction.

extract_protocol:
For each sample, 10 mL of RNAprotect bacteria reagent (Qiagen, Valencia, CA) was added to 10 mL of bacterial culture. The mixture was then incubated at room temperature for 10 min to ensure that the bacterial RNA was stabilized. Cells were pelleted by centrifugation (4,637 × g, 30 min) at 4°C and then lysed with 25 mg/ml proteinase K (Thermo Fisher Scientific, Waltham, MA) and 50 mg/ml lysozyme (Thermo Fisher Scientific) at 37°C for 30 min. Cell lysates were subsequently mixed with 1 mL of Tri Reagent (Ambion, Austin, TX), transferred into bead-beating tubes that contained 3 mL of 0.1 mm zirconium beads, followed by adjustment (with Tri Reagent) to a final volume of 5 mL. The lysates were processed in the bead-beater at maximum speed for 4 min. After bead-beating, samples were centrifuged (4,637 × g, 10 min) at 4°C. Supernatants were separated from the beads, transferred into a new tube, and mixed with 500 μL of bromo-chloro-propane (BCP). After incubation with BCP for 10 min, samples were centrifuged at 14,637 × g for 15 min at 4°C. The aqueous layer was collected, and nucleic acids were precipitated overnight at 80°C using 2.5 volumes of 100% ice-cold isopropanol. Nucleic acids were pelleted, washed with 75% ethanol, as resuspended in 100 μL nuclease free water. Total RNA was incubated with Turbo DNase (Life Technologies) to remove remaining DNA in the presence of RNasin (Promega). Subsequently, RNA was purified using phenol-chloroform/chloroform extractions, followed by precipitation and resuspension. Quality of RNA was assessed using a 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA) (all samples had RNA integrity numbers > 5). Efficiency of the DNase treatment was determined using qRT-PCR for the housekeeping gene rpoB (all samples showed Ct > 35, indicating absence of DNA contamination at relevant levels). All experiments were performed in biological triplicate.
Preparation of directional cDNA fragment libraries was performed using the ScriptSeq Complete Kit (Bacteria) (Illumina, San Diego, CA). 16S and 23S rRNA was removed from total RNA with Ribo-Zero rRNA Removal Reagents (Bacteria) and Magnetic Core Kit. rRNA-depleted samples were run on the 2100 Bioanalyzer (Agilent Technology) to confirm reduction of 16S and 23S rRNA and followed by purification using Agencourt RNAClean XP Kit (Beckman Coulter Inc, Brea, CA). The Cornell Core Facility for RNA-sequencing prepared and sequenced indexed RNA-seq libraries (ScriptSeq Complete Kit, Illumina). Sequencing was carried out on a NextSeq 500 (single-end, 75 bp per read).

tag: strain

value: deltaprfA


title: Kidney_ATAC1

source_name: Kidney

value: Kidney


title: Sample 1B


title: CHO_ATAC3

value: CHO

value: ATAC


title: Sample 1A


title: WT rep3

source_name: WT rep3

tag: genotype

value: wild type


title: CT40-iHIOs_S23

city: Cleveland

first: Emina

last: Huang

state: OH

address: 9500 Euclid Ave

department: Stem Cell

institute: Lerner Research Institute/Cleveland Clinic

description: UC3 iHIOs RNA-Seq

data_processing:
RNA-seq data was sequenced using Illumina HiSeq 2500
FastQC (version 0.9.5) was used to check the quality of reads (*.FASTQ) --> no need of trimming
STAR (version 2.5.3a) was used for alignment. HG19 reference genome and Gencode V19 annotation were used.
FeatureCounts of Subread package (version 1.5.2) was used for counting mapping reads for genes.
DESeq2 was used for differentially expressed genes analysis
Genome_build: HG19, gencode V19 annotation
Supplementary_files_format_and_content: Read count table compressed by gzip

source_name: Primary adult intestinal FBs

growth_protocol: Generating human intestinal tissue from pluripotent stem cells in vitro, Nat Protoc. 2011 Nov 10; 6(12): 1920–1928.

extract_protocol:
iPSCs, DE, Spheroids and iHIOs (NL n=3 CT n=3) were isolated/propagated and harvested prior to RNA extraction and standard sequencing/processing
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: no treatment

tag: tissue origin

value: Reprogrammed FBs cultivated from patient-derived colitic colon mucosa

tag: passages

value: Passage 0

value: induced human intestinal organoids (iHIOs)


title: CHO_ATAC1

value: Female

tag: tissue

value: accessible DNA


title: Brain_ATAC1

source_name: Brain

tag: treatment

value: Brain


title: ∆prfA rep 2

source_name: ∆prfA rep 2


title: prfA* rep 3

source_name: prfA* rep 3

value: prfA*


title: CT35-iHIOs_S24

description: UC2 iHIOs RNA-Seq


title: BMDMwt_ATAC2

tag: cell type

value: Bone marrow-derived macrophages

tag: Sex


title: prfA* rep 2

source_name: prfA* rep 2


title: CT5-iHIOs_S22

description: UC1 iHIOs RNA-Seq


title: 4153-OxBS_IDH1 wildtype

type: genomic

city: Toronto

first: Paul

middle: N

last: Kongkham

state: ON

address: 399 Bathurst St, WW4-450

department: Surgery

country: Canada

institute: University of Toronto

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 4153

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version 1.20.0). BS data represents 5mC plus 5hmC. OxBS data represents 5mC alone. 5hmC beta values were calculated by subtracting OxBS data from BS data for each probe across all samples.

label: Cy5 and Cy3

source_name: Primary fresh-frozen human high grade glioma

label_protocol: 200 ng of BS or OxBS converted DNA was used as input, and labelled as per standard Illumina protocols.

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens using the PureLink Genomic DNA Kit (Invitrogen). DNA for each sample (1 g/sample) was processed in parallel using bisulfite conversion alone (BS) or oxidative bisulfite conversion (OxBS) using the TrueMethyl® Array kit (Cambridge Epigenetix) as per the manufacturer’s instructions, optimized for downstream analysis using the Illumina BeadChip array.

treatment_protocol: During sample processing, genomic DNA from each specimen was processed in parallel using both Bisulfite (BS) conversion and Oxidative Bisulfite (OxBS) conversion.

value: glioma

tag: idh1 mutation status

value: wild-type


title: NL34-iHIOs_S20

description: NL3 iHIOs RNA-Seq

value: Reprogrammed FBs cultivated from normal colon mucosa


title: 4143-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 4143


title: WT rep2

source_name: WT rep2


title: BMDM1hKLA_ATAC2

source_name: Bone marrow-derived macrophages

value: 1-hour KLA

tag: assay

tag: molecule


title: BMDMwt_ATAC1


title: NL33-iHIOs_S21

description: NL2 iHIOs RNA-Seq


title: 2846-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 2846


title: 4148-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 4148


title: ∆prfA rep 1

source_name: ∆prfA rep 1

value: deltaprfA


title: BMDM1hKLA_ATAC1


title: 4148-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 4148


title: 4153-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 4153


title: prfA* rep 1

source_name: prfA* rep 1


title: 4167-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 4167

value: mutant


title: 3966-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 3966


title: 3966-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 3966


title: CGGAGCCTCCGGCA_Lane2_iCXCR5KO_Th1_4

city: Bonn

first: Dirk

last: Baumjohann

state: NRW

address: Venusberg-Campus 1

department: Medical Clinic III

country: Germany

institute: University Hospital Bonn

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to the Mouse (mm10) Genome with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (GRCm38.75)
Genome_build: Mouse: mm10, Ensembl 75
Supplementary_files_format_and_content: sample (columns) and gene (rows) -wise UMI expression table

organism: Mus musculus

source_name: murine spleen

extract_protocol:
secondary lymphoid organs were removed, single cell suspensions and antibody stainings for flow cytometry and cell sorting were prepared on ice. Cells were sorted directly into lysis buffer and immediately spun down and frozen on dry ice. RNA was isolated using magnetic beads
Libraries were constructed using a bulk adjusted mcSCRB-seq protocol.

treatment_protocol: mice were treated with tamoxifen to induce the CreERT2-mediated knockout of Bcl6 or CXCR5 in CD4 T cells

tag: celltype

value: CD4 T cell

value: SMARTA Cd4-CreERT2+ CXCR5fl/fl CD45.1/2


title: 2619-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 2619


title: 2846-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 2846


title: WT rep1

source_name: WT rep1

value: wild type


title: 4187-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 4187


title: 3591-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 3591


title: 4070-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 4070


title: 1541-iHIOs_S19

description: NL1 iHIOs RNA-Seq

source_name: cell line

value: Reprogrammed CRL1541 FBs


title: 3D7/DDGFP-PfAP2-HC OFF, time point 5 (40-48 hours post-invasion)

city: Basel

first: Till

middle: Steffen

last: Voss

address: Socinstrasse 59

department: Medical Parasitology and Infection Biology

country: Switzerland

institute: Swiss Tropical and Public Health Institute

description: DDGFP-AP2-HC TP5 OFF

hyb_protocol: Microarray hybridizations were carried out as described in (Painter HJ, Altenhofen LM, Kafsack BF, Llinás M: Whole-genome analysis of Plasmodium spp. Utilizing a new Agilent technologies DNA microarray platform. Methods Mol Biol. 2013;923:213-9). In short, 400ng Cy5-labeled test cDNA and 400ng Cy3-labeled reference pool cDNA were hybridized on a P. falciparum 8x15K Agilent gene expression microarray (GEO platform ID GPL15130) for 16 hours at 65°C in an Agilent hybridisation oven (G2545A).

scan_protocol: Microarrays were scanned as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: The raw microarray data representing relative transcript abundance ratios between each test sample and the reference pool (Cy5/Cy3 log2 ratios) were subjected to lowess normalization and background filtering as implemented by the Acuity 4.0 program (Molecular Devices). Flagged features and features with either Cy3 or Cy5 intensities lower than two-fold the background were discarded.

organism: Plasmodium falciparum

source_name: 3D7/DDGFP-PfAP2-HC OFF parasites

label_protocol: Labeling was carried out as described in [Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5]

growth_protocol: 3D7/DDGFP-PfAP2-HC parasites cultured in presence of Shield-1 were synchronised with sorbitol to obtain an eight-hour growth window (16-24 hpi) and again in the next generation after RBC invasion at 0-8 hpi. The culture was then split at 8-16 hpi and one half was maintained in the presence of Shield-1 (+Shield-1) and the other half was cultured in the absence of Shield-1 (-Shield-1) to achieve DDGFP-PfAP2-HC depletion. In the subsequent generation, parasites from the paired populations were harvested for total RNA extraction at the following time points: TP1 (8-16 hpi), TP2 (16-24 hpi), TP3 (24-32 hpi), TP4 (32-40 hpi) and TP5 (40-48 hpi).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) following manufacturer's instructions.

value: conditional mutant 3D7/DDGFP-PfAP2-HC

tag: culture conditions

value: OFF

tag: developmental stage

value: late schizonts (40-48 hours post-invasion)

value: whole organism

source_name: reference pool RNA

value: wild type parasites (8-48hpi)


title: 4122-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 4122


title: GCGTAGTACCGAGG_Lane2_iCXCR5KO_Th1_3


title: 3591-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 3591


title: 4143-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 4143


title: CT35-Spheroids_S18

description: UC2 Sph RNA-Seq

value: Reprogrammed FBs cultivated from patient-derived colitic colon mucosa

value: Passage 0

value: Spheroids (Sph)


title: CT5-Spheroids_S16

description: UC1 Sph RNA-Seq


title: ACTCGCTACCCAGC_Lane2_iCXCR5KO_Th1_1


title: GGAGCTACCCCCTG_Lane2_iCXCR5KO_Th1_2


title: 4167-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 4167

value: glioma


title: 4187-OxBS_IDH1 wildtype

description:
Oxidative bisulfite converted sample
Methylation IDH1 wild-type 4187

value: wild-type


title: NL34-Spheroids_S14

description: NL3 Sph RNA-Seq

value: Reprogrammed FBs cultivated from normal colon mucosa


title: AAGAGGCATTCCTC_Lane2_iCXCR5KO_Tfh4


title: 3D7/DDGFP-PfAP2-HC OFF, time point 4 (32-40 hours post-invasion)

description: DDGFP-AP2-HC TP4 OFF

value: early schizonts (32-40 hours post-invasion)


title: GTAGAGGATAGTGG_Lane2_iCXCR5KO_Tfh3


title: 4070-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 4070


title: NL33-Spheroids_S15

description: NL2 Sph RNA-Seq


title: 3D7/DDGFP-PfAP2-HC OFF, time point 2 (16-24 hours post-invasion)

description: DDGFP-AP2-HC TP2 OFF

value: late ring stages (16-24 hours post-invasion)


title: 2619-BS_IDH1 wildtype

description:
Bisulfite converted sample
Methylation IDH1 wild-type 2619


title: GCTCATGAGTACAC_Lane2_iCXCR5KO_Tfh2

value: CD4 T cell


title: CT40-DE_S11

description: UC3 DE RNA-Seq

value: Definitive Endoderm (DE)


title: 1541-Spheroids_S13

description: NL1 Sph RNA-Seq


title: 3D7/DDGFP-PfAP2-HC OFF, time point 3 (24-32 hours post-invasion)

description: DDGFP-AP2-HC TP3 OFF

value: trophozoites (24-32 hours post-invasion)


title: 3D7/DDGFP-PfAP2-HC OFF, time point 1 (8-16 hours post-invasion)

description: DDGFP-AP2-HC TP1 OFF

value: early ring stages (8-16 hours post-invasion)


title: 3D7/DDGFP-PfAP2-HC ON, time point 5 (40-48 hours post-invasion)

description: DDGFP-AP2-HC TP5 ON

source_name: 3D7/DDGFP-PfAP2-HC ON parasites

value: conditional mutant 3D7/DDGFP-PfAP2-HC

value: 675nM Shield-1 (ON)


title: TAGGCATGTTGATT_Lane2_Ctrl_Th1_5

value: SMARTA Cd4-CreERT2+ CXCR5+/+ CD45.1/2


title: CTCTCTACTTCAAT_Lane2_Ctrl_Th1_4


title: 3D7/DDGFP-PfAP2-HC ON, time point 4 (32-40 hours post-invasion)

description: DDGFP-AP2-HC TP4 ON

value: whole organism


title: 3797-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 3797

value: mutant


title: CT35-DE_S12

description: UC2 DE RNA-Seq

value: Reprogrammed FBs cultivated from patient-derived colitic colon mucosa


title: 3D7/DDGFP-PfAP2-HC ON, time point 3 (24-32 hours post-invasion)

description: DDGFP-AP2-HC TP3 ON

value: wild type parasites (8-48hpi)


title: NL34-DE_S8

description: NL3 DE RNA-Seq

value: Passage 0


title: CT5-DE_S10

description: UC1 DE RNA-Seq


title: 4235-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 4235

value: glioma


title: NL33-DE_S9

description: NL2 DE RNA-Seq


title: 3D7/DDGFP-PfAP2-HC ON, time point 2 (16-24 hours post-invasion)

description: DDGFP-AP2-HC TP2 ON


title: 1730-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 1730


title: 4122-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 4122


title: 1541-DE_S7

description: NL1 DE RNA-Seq

value: Reprogrammed CRL1541 FBs


title: 3797-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 3797


title: CGAGGCTGTTAAAG_Lane2_Ctrl_Th1_1


title: GGACTCCTTACTTA_Lane2_Ctrl_Tfh5


title: 3D7/DDGFP-PfAP2-HC ON, time point 1 (8-16 hours post-invasion)

description: DDGFP-AP2-HC TP1 ON


title: ATCTCAGGGCTTAC_Lane2_iCXCR5KO_Tfh1

value: SMARTA Cd4-CreERT2+ CXCR5fl/fl CD45.1/2


title: CT40-Spheroids_S17

description: UC3 Sph RNA-Seq

value: Spheroids (Sph)


title: CGTACTAGTAAATG_Lane2_Ctrl_Tfh2


title: CT35-iPSCs_S6

description: UC2 iPSCs RNA-Seq

value: 3-5 passages

value: induced pluripotent stem cells (iPSCs)


title: CT5-iPSCs_S4

description: UC1 iPSCs RNA-Seq


title: TAAGGCGAGTTTTA_Lane2_Ctrl_Tfh1

value: CD4 T cell


title: CT40-iPSCs_S5

description: UC3 iPSCs RNA-Seq


title: CAGAGAGGTTATAC_Lane2_Ctrl_Th1_3


title: NL34-iPSCs_S2

description: NL3 iPSCs RNA-Seq

value: Reprogrammed FBs cultivated from normal colon mucosa


title: 1730-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 1730


title: RANK-/- vs RANK+/+ MMTV-PYMT tumor cells Array 1B

city: Hospitalet de Llobregat

first: Eva

last: González-Suárez

state: Barcelona

address: Hospital Duran i Reynals - 3a planta -Gran Via de l'Hospitalet, 199

department: Epigenetics and Cancer Biology

country: Spain

institute: Institut d'Investigació Biomèdica de Bellvitge

description: Technical replicate 2

hyb_protocol: Microarrays were hybridized and washed according to manufacturer's protocol (version 6.5).

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

source_name: RANK-/-

label_protocol: Two-color microarray-based LowInput QuickAmp Labeling (Agilent)

growth_protocol: One million MMTV-PyMT late carcinoma tumor cells (either RANK+/+ or RANK-/-) were orthotopically transplanted into syngeneic C57BL/6 mice.

extract_protocol: Grown tumors were enzymatically disaggregated and live CD45- cells were sorted using MoFlo Astrios.

value: Flow cytometry-sorted CD45- MMTV-PYMT tumor cells

value: RANK-/-

source_name: RANK+/+

value: RANK+/+


title: Infantile Pompe-rhGAA treated - C

city: Durham

first: Wei

last: Chen

state: NC

address: 101 Science Drive

department: Center for Genomic and Computational Biology

institute: Duke University

description:
rhGAA_vs_untreated-Pompe_expression_matrix.csv
treated-gaa-ip3

data_processing:
Illumina NovaSeq 6000 reads were processed using the TrimGalore toolkit v0.4.1 to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads.  Only reads that were 20nt or longer after trimming were kept for further analysis. Read quality was checked for each sample using FastQC v0.11.2.
Reads were mapped to the GRCh38v93 version of the human genome and transcriptome using the STAR RNA-seq alignment tool v2.5.0c.  Reads were kept for subsequent analysis if they mapped to a single genomic location.
Gene counts were compiled using the HTSeq tool v0.6.1.  Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 Bioconductor package v1.16.1 with the R statistical programming environment v3.4.1_3.
Genome_build: GRCh38v93
Supplementary_files_format_and_content: normalized expression matrix in csv format

source_name: 3D engineered tissue, myobundle

growth_protocol: Primary muscle cells were isolated from biopsies using the outgrowth method, expanded for 5 passages in T175 flasks, and used to construct 3D myobundles. 3D myobundles were cultured for 4 days in 3D growth media followed by 2 weeks of 3D differentiation.

extract_protocol:
RNeasy Fibrous Tissue Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: engineered skeletal muscle

tag: culture age

value: 2 weeks of 3D differentiation culture

value: Treated with 2ug/ml rhGAA (from Sanofi Genzyme) every other day during second week of 3D differentiation


title: RANK+/+ vs RANK-/- MMTV-PYMT tumor cells Array 3A

description: Technical replicate 1


title: RANK+/+ vs RANK-/- MMTV-PYMT tumor cells Array 2B

description: Technical replicate 2


title: GGACTCCTTACTTA_Lane1_iCXCR5ko_Tf5

source_name: murine popliteal lymph node

value: Cd4-CreERT2+ CXCR5fl/fl


title: RANK+/+ vs RANK-/- MMTV-PYMT tumor cells Array 3B

description: Technical replicate 2


title: Infantile Pompe-rhGAA treated - B

description:
rhGAA_vs_untreated-Pompe_expression_matrix.csv
treated-gaa-ip2


title: GCTACGCTTTACAT_Lane2_Ctrl_Th1_2

value: SMARTA Cd4-CreERT2+ CXCR5+/+ CD45.1/2


title: RANK-/- vs RANK+/+ MMTV-PYMT tumor cells Array 1A

description: Technical replicate 1


title: RANK+/+ vs RANK-/- MMTV-PYMT tumor cells Array 2A

description: Technical replicate 1


title: NL33-iPSCs_S3

description: NL2 iPSCs RNA-Seq

source_name: Primary adult intestinal FBs


title: TAGGCATGTAGTTT_Lane1_iCXCR5ko_Tf6


title: AGGCAGAATAAGTA_Lane1_iCXCR5ko_Tf3


title: Infantile Pompe-untreated - C

description:
Pompe_vs_healthy-expression_matrix.csv
disease-ip3


title: 3921-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 3921

value: mutant


title: 3734-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 3734

value: glioma


title: Gene expression IDH1 wild-type 4187

hyb_protocol: 5.5 micrograms of cRNA were hybridized for 16 hr at 45 degrees Celcius on the Affymetrix Human Gene 2.0 ST array platform. Gene chips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: Affymetrix CEL files were loaded and analyzed using Partek® Genomics Suite™ version 6.6. Quantile Normalization and RMA Background Correction were performed using this package.

label: biotin

source_name: Fresh-frozen primary human high grade glioma

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocols.

extract_protocol: Extraction of RNA was performed using the Ambion WT Kit as per the manufacturer's protocol

tag: idh1 status

value: wild-type


title: RNAseq_RRFKD_60min [ks22]

city: Baltimore

first: Allen

middle: R

last: Buskirk

state: MD

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

data_processing:
The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Cells were cultured in LB+0.2% arabinose @ 37 C to OD = 0.2. The media was changed to LB+0.2% glucose and the cells were cultured at 37 C for 10 min. The media was changed one more time to fresh LB+0.2% glucose and the cells were cultured at 37 C and harvested after 5 min, 15 min, or 60 min by filtration.

extract_protocol:
Cell pellets were cryogenically pulverized in a Spex 6870 freezer mill; 5 cycles of 1 min at 5 Hz with 1 min cooling. Cell lysates were clarified by centrifugation. For standard ribosome profiling (StRP), lysates were digested with nucleases, and monosomes were purified over a sucrose gradient. For high salt ribosome profiling (HighSaltRP), ribosomes were pelleted by sucrose cushion and then resuspended. Purified ribosomes were treated with nucleases, and monosomes were purified over a sucrose gradient.
For StRP and HighSaltRP, ribosome footprints were PAGE purified. Afterword, for all library types, RNA was ligated to a linker using RNA ligase T2, converted to DNA using RT, circularized, and PCR amplified.

tag: genotype/variation

value: RRFKD

tag: rna source

value: whole cell lysate

tag: growth condition

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 60 min

tag: molecule subtype

value: mRNA


title: CGTACTAGTAAATG_Lane1_iCXCR5ko_Tf2

value: CD4 T cell

tag: genotype

tag: strain


title: TCCTGAGCTAATTC_Lane1_iCXCR5ko_Tf4


title: 4238-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 4238

source_name: Primary fresh-frozen human high grade glioma

tag: tissue


title: RNAseq_RRFKD_15min [ks21]

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 15 min


title: 1541-iPSCs_S1

description: NL1 iPSCs RNA-Seq

tag: tissue origin

value: Reprogrammed CRL1541 FBs

tag: passages

value: 3-5 passages

value: induced pluripotent stem cells (iPSCs)


title: 3734-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 3734

tag: idh1 mutation status


title: Gene expression IDH1 wild-type 4153


title: Infantile Pompe-rhGAA treated - A

description:
rhGAA_vs_untreated-Pompe_expression_matrix.csv
treated-gaa-ip1

value: engineered skeletal muscle

tag: treatment


title: 4238-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 4238


title: TAAGGCGAGTTTTA_Lane1_iCXCR5ko_Tf1


title: Gene expression IDH1 wild-type 2846


title: RNAseq_RRFKD_5min [ks20]

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 5 min


title: Infantile Pompe-untreated - A

description:
Pompe_vs_healthy-expression_matrix.csv
disease-ip1

value: 2 weeks of 3D differentiation culture


title: ATCTCAGGTTCCTC_Lane1_Ctrl_nonTfh4

value: Cd4-CreERT2+ CXCR5+/+


title: RNAseq_WT_60min [ks19]

value: wild type


title: Healthy-s116-4

description:
Pompe_vs_healthy-expression_matrix.csv
healthy-s116

value: wildtype


title: GCTCATGATAGTGG_Lane1_Ctrl_nonTfh3


title: 4235-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 4235

value: glioma

value: mutant


title: RNAseq_WT_5min [ks17]


title: Gene expression IDH1 wild-type 4148

value: wild-type


title: 3690-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 3690


title: RNAseq_WT_15min [ks18]

value: whole cell lysate


title: Gene expression IDH1 wild-type 4070


title: Healthy-s111-2

description:
Pompe_vs_healthy-expression_matrix.csv
healthy-s111


title: Healthy-s110-1

description:
Pompe_vs_healthy-expression_matrix.csv
healthy-s110


title: AAGAGGCATTGATT_Lane1_Ctrl_nonTfh1


title: CGAGGCTGTTCAAT_Lane1_Ctrl_Tfh4


title: HighSaltRP_RRFKD_15min [ks15]

data_processing:
library strategy: ribosome profiling
The linker sequence was trimmed and reads mapping to rRNA or tRNA sequences were discarded. The remaining reads were mapped to the E. coli K-12 MG1655 genome.
Genome_build: NC_000913.2
Supplementary_files_format_and_content: WIG files of ribosome occupancy, assigned to the 3'-end of reads, normalized by the total number of reads in the library.

value: RRFKD

value: monosome fraction

value: mRNA:ribosome footprints


title: Gene expression IDH1 wild-type 3966


title: 3690-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 3690


title: HighSaltRP_RRFKD_60min [ks16]

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 60 min


title: CoVi17_4_MS_24_9P_TCR

city: San Diego

first: Pandurangan

last: Vijayanand

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description: Single-cell RNA-seq with 10x Genomics v1 V(D)J

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Genome_build: GRCh38-alts-ensembl-2.0.0 from Cell Ranger
Genome_build: GRCh37 (hg19-3.0.0 from Cell Ranger)
Supplementary_files_format_and_content: cd4t24_annotation.txt.gz meta data for 31341 cells
Supplementary_files_format_and_content: cd4t24_umi.txt.gz UMI count data matrix for 31341 cells
Supplementary_files_format_and_content: cd4t6_annotation.txt.gz meta data for 91140 cells
Supplementary_files_format_and_content: cd4t6_umi.txt.gz UMI count data matrix for 91140 cells
Supplementary_files_format_and_content: cd4t0n6_annotation.txt.gz meta data for 123001 cells
Supplementary_files_format_and_content: cd4t0n6_umi.txt.gz UMI count data matrix for 123001 cells

molecule: polyA RNA

source_name: PBMC

growth_protocol: Not applicable

extract_protocol:
For combined single-cell RNA-seq and TCR-seq assays (10x Genomics), a maximum of 60,000 virus-reactive memory CD4+ T cells from up to 8 donors were pooled by sorting into low retention 1.5mL collection tubes, containing 500 µL of a1:1 solution of PBS:FBS supplemented with RNAse inhibitor (1:100). Following sorting, ice-cold PBS was added to make up to a volume of 1400 µl. Cells were then centrifuged for 5 minutes (600 g at 4 ˚C) and the supernatant was carefully removed leaving 5 to 10 µl. 25 µl of resuspension buffer (0.22 µm filtered ice-cold PBS supplemented with ultra-pure bovine serum albumin; 0.04 %, Sigma-Aldrich) was added to the tube and the pellet was gently but thoroughly resuspended. Following careful mixing, 33 µl of the cell suspension was transferred to a PCR-tube for processing as per the manufacturer’s instructions (10x Genomics).
Single-cell RNA-seq using 10x genomics platform was performed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol

treatment_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from up to 80ml of anti-coagulated blood by density centrifugation over Lymphoprep (Axis-Shield PoC AS, Oslo, Norway) and cryopreserved in 50% decomplemented human antibody serum, 40% complete RMPI 1640 medium and 10% DMSO.
To determine the specificity and molecular features of such T cells, expressing activation markers ex vivo, we isolated CD38high HLA-DRhigh PD-1+ memory CD4+ T cells from hospitalized COVID-19 patients and performed single-cell transcriptome and TCR sequence analysis
PBMCs from each donor, were thawed, washed, plated in 6-well culture plates at a concentration of 5 x 106 cells/ml in 1 ml of serum-free TexMACS medium (Miltenyi Biotec) and left overnight (5 % CO2, 37 ˚C). Cells were stimulated by the addition of individual virus-specific peptide polls (1 µg/ml) for 6 h in the presence of a blocking CD40 antibody (1 µg/ml; Miltenyi Biotec). For subsequent MACS-based enrichment of CD154+, cells were sequentially stained with fluorescence-labeled surface antibodies, Cell-hashtag TotalSeq™-C antibody (0.5 µg/condition), and a biotin-conjugated CD154 antibody (clone 5C8; Miltenyi Biotec) followed by anti-biotin microbeads (Miltenyi Biotec). Labelled cells were added to MS columns (Miltenyi Biotec) and positively selected cells (CD154+) were eluted and used for FACS sorting of CD154+ memory CD4+ T cells. The flow-through from the column was collected and re-plated for harvesting cells responding 24 h after peptide stimulation.
Analogous to enrichment for CD154+, CD137-expressing CD4+ memory T cells cells were positively selected by staining with biotin-conjugated CD137 antibody (clone REA765; Miltenyi Biotec) followed by anti-biotin MicroBeads and applied to a new MS column. Following elution, enriched populations were immediately sorted using a FACSAria Fusion Cell Sorter (Becton Dickinson) based on dual expression of CD154 and CD69 for 6-hour stimulation condition, and CD137 and CD69 for 24-hour stimulation condition.

value: Blood

tag: cell type

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: HighSaltRP_RRFKD_5min [ks14]


title: HighSaltRP_WT_60min [ks13]


title: GCTACGCTTTATAC_Lane1_Ctrl_Tfh3

tag: celltype

value: CD4 T cell


title: CoVi16_4_M_6_9P_TCR


title: 2475-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 2475


title: CAGAGAGGTTACAT_Lane1_Ctrl_Tfh2


title: Gene expression IDH1 wild-type 2619


title: CTCTCTACTTAAAG_Lane1_Ctrl_Tfh1


title: Gene expression IDH1 wild-type 3591


title: CoVi16_4_S_6_9P_TCR


title: HighSaltRP_WT_5min [ks11]


title: Gene expression IDH1 mutant 4122


title: AGGCAGAA_SM_Ctrl3

value: SMARTA Cd4-CreERT2+ Bcl6+/+ CD45.1/2


title: HighSaltRP_WT_15min [ks12]

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 15 min


title: CoVi10_4_0_0_5P_TCR


title: Gene expression IDH1 mutant 4167


title: 4166-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 4166


title: StRP_RRFKD_60min [ks10]


title: 4166-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 4166


title: CGTACTAG_SM_Ctrl2


title: Gene expression IDH1 mutant 1730


title: CoVi01_4_0_0_5P_TCR


title: StRP_RRFKD_15min [ks9]


title: Gene expression IDH1 mutant 3797


title: Gene expression IDH1 wild-type 4143


title: 2475-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 2475


title: CoVi17_4_MS_24_9P_Gex

description: Single-cell RNA-seq with 10x Genomics 5' paired-end


title: TAAGGCGA_SM_Ctrl1


title: CAGAGAGG_SM_Bcl6KO5

value: SMARTA Cd4-CreERT2+ Bcl6fl/fl CD45.1/2


title: StRP_RRFKD_5min [ks8]

value: 37 C in arabinose, 37 in glucose for 10 min, 37 in glucose for 5 min


title: Gene expression IDH1 mutant 4235


title: CoVi04_4_0_0_8P_TCR


title: 2165-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 2165


title: 3921-BS_IDH1 mutant

description:
Bisulfite converted sample
Methylation IDH1 mutant 3921


title: CTCTCTAC_SM_Bcl6KO4


title: StRP_WT_60min [ks7]

value: wild type


title: CoVi16_4_S_6_9P_Gex


title: CoVi16_4_M_6_9P_Gex


title: Healthy-s115-3

description:
Pompe_vs_healthy-expression_matrix.csv
healthy-s115

value: engineered skeletal muscle

value: 2 weeks of 3D differentiation culture

value: wildtype


title: 2165-OxBS_IDH1 mutant

description:
Oxidative bisulfite converted sample
Methylation IDH1 mutant 2165

value: glioma

value: mutant


title: Gene expression IDH1 mutant 3734


title: TAGGCATG_SM_Bcl6KO3


title: CoVi10_4_0_0_5P_Gex


title: Gene expression IDH1 mutant 4238


title: StRP_WT_5min [ks5]


title: Non-inoculated-Rep3

city: Bellaterra

first: Blanca

last: San Segundo

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

institute: Center for Research in Agricultural Genomics (CRAG)

data_processing:
Raw reads were checked for quality by using FastQC v0.11.3
Trimming and removal of adapters involved using Trimmomatic v0.33 (minimum quality score 35, minimum length 25).
The obtained reads were mapped against the Oryza sativa Japonica (IRGSP-1.0) by using STAR (v2.4.0j)
Alignment files were filtered to remove reads with mapping quality (MAPQ) <30. FeatureCounts (v1.4.5-p1)
Statistical analysis of read counts was performed with R, with the HTSFilter package to remove low-expressed genes and the edge R package
Genome_build: IRGSP-1.0
Supplementary_files_format_and_content: FPKM

organism: Oryza sativa

source_name: Wildtype Rice (cv. Loto)

growth_protocol: Non-inoculated and F-mosseae-inoculated transplantes seedlings were grown at the greenhouse under a 14h/10h day/night cycle, 28ºC/25ºC and 60% humidity

extract_protocol:
Total RNA was extracted with the Maxwell 16 LEV Plant RNA Kit (Promega) following manufacturer's instructions.
Indexed libraries prepared from 1ug purified RNA with TruSeq Stranded mRNA Sample Prep Kit (Illumina). Samples pooled; each index-tagged sample present in equimolar amounts (final concentration of pooled samples at 2nm). Pooled samples subjected to cluster generation and sequencing using Illumina Hseq 2500. 2x100 paired-ennd at final concentration of 8pmol.

treatment_protocol: Rice Loto seeds were dehusked, surface-sterilized twice with 5% sodium hypochlorite for 15 min, and washed extensively with sterile water. Seeds were germinated on petri dishes with sterile water for 7 days and then transplanted to 150ml-cones (20.5 cm; 2 plants/cone) containing a mix of 63.3% quartz sand (0.3-0.8 mm), 31.6% soil (turface and vermiculite 2:1), and 5% of granular inoculum of Funneliformis mosseae. No inoculum was added to the substrate for the non-inoculated, control plants.

value: leaf

tag: rice cultivar

value: Loto (japonica)


title: Gene expression IDH1 mutant 3690


title: CoVi04_4_0_0_8P_Gex


title: TCCTGAGC_SM_Bcl6KO1


title: GGACTCCT_SM_Bcl6KO2


title: Non-inoculated-Rep2


title: ZNF598-null replicate 2 for Ribo-seq

city: Schlieren

first: Ramona

last: Weber

address: Wagistrasse 12

department: Institute for Regenerative Medicine

institute: University of Zurich

description:
small RNA
ZNF598_2

data_processing:
Library strategy: Ribo-Seq
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translation efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimited file for translation efficiency analysis

growth_protocol: 6.4x10^6 cells of HEK293T WT or ZNF598-null cells were plated on 15 cm dishes 24 hrs before harvesting.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) and a library prepared using the TruSeq RNA Sample Prep Kit (Illumina). For Ribo-seq, the original procedure of Ingolia et al (2012) Nature Protocols was followed with modifications from Calviello et al (2016) Nature Methods.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: CoVi17_4_MS_24_9P_CITE

description: Single-cell RNA-seq with 10x Genomics 5' v1


title: CoVi01_4_0_0_5P_Gex


title: Non-inoculated-Rep1


title: Gene expression IDH1 mutant 4166


title: CoVi16_4_S_6_9P_CITE


title: StRP_WT_15min [ks6]

value: monosome fraction

value: mRNA:ribosome footprints


title: Infantile Pompe-untreated - B

description:
Pompe_vs_healthy-expression_matrix.csv
disease-ip2


title: ZNF598-null replicate 1 for Ribo-seq

description:
small RNA
ZNF598_1


title: Wild-type, control replicate 2 for Ribo-seq

description:
small RNA
WT_2


title: CoVi16_4_M_6_9P_CITE

value: Blood


title: Wild-type, control replicate 1 for Ribo-seq

description:
small RNA
WT_1


title: ATAC-seq - ABa 200 minutes #2

city: Vienna

first: Jingkui

last: Wang

address: Campus-Vienna-Biocenter 1

institute: Research Institute of Molecular Pathology (IMP)

description: ATAC-Seq 25k cells, sorted (ABa) 200' (green)

data_processing:
For ChIP-seq, the single-end raw reads of ChIP-seq dataset were mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). Uniquely mapped reads were retained and duplicated reads were marked and discarded using SAMtools (v0.1.18). For visualization, the coverage tracks (i.e. bigWig files) were generated from bam files using kent-ucsc (v2.79). Sharp peaks were identified with macs2 (v2.1.0) against the pooled control samples with default parameters.
For ATAC-seq, the paired-end raw reads of ATAC-seq data were trimmed with Cutadapt (v1.18) and mapped to the C. elegans genome (ce11) with bowtie2 (v2.2.4). For all samples, multi-mapped reads were filtered with SAMtools (v0.1.20) and duplicate reads were marked and discarded with Picard-tools (v2.18.27; Broad Institute). For visualization, the normalized coverage tracks (i.e. bigWig files) were generated from bam files using with R packages GenomicRanges (v1.38.0) and rtracklayer (v1.46.0) with paired-end option.
Genome_build: ce11
Supplementary_files_format_and_content: *.bw files: bigWig Track format of read density coverage in reads per million

source_name: Embryo (ABa) - 200 minutes

extract_protocol:
ChIP assays were performed as previously described in (Askjaer et al., 2014) with minor modifications. ATAC-seq libraries were prepared as described in (Corces et al., 2017) with minor modifications.
ChIP-seq: NEBNext® Ultra II DNA Library Prep Kit. ATAC-seq: Nextera DNA Library Prep Kit

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]

tag: developmental stage

value: Embryo - 200 minutes

value: ABa


title: Gene expression IDH1 mutant 2475


title: CoVi10_4_0_0_5P_CITE

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+


title: ATAC-seq - ABp 350 minutes #2

description: ATAC-Seq 25k cells, sorted (ABp) 350' (black)

source_name: Embryo (ABp) - 350 minutes

value: Embryo - 350 minutes

value: ABp


title: CoVi04_4_0_0_8P_CITE


title: ZNF598-null replicate 1 for RNA-seq

description:
messenger RNA
ZNF598_1

data_processing:
Illumina software used for basecalling.
Adapters removed with Flexbar, ribosomal-derived reads were removed using Bowtie2
Remaining reads were then mapped on hg19 using Tophat2
Ribo-seq reads were analyzed for three-nucleotide periodicity using the RiboTaper
Read count analysis was done with an R/Bioconductor package QuasR
Differential gene expression analysis with an R/Bioconductor package edgeR
Translation efficiency (TE) was estimated using the statistical framework and analysis as implemented in the RiboDiff program
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file for readcounts; tab-delimited file for differential expression analysis; tab-delimited file for translation efficiency analysis


title: Tax1BP1 wildtype 2 [miRNA]

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: GeneChip® miRNA 3.0 arrays (Affymetrix) were hybridized with 500 ng labelled microRNA, Hybridisation time was 18 hours.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: UnsupportedGeneChip® miRNA 3.0 Array CDF Files
meta-probeset file: miRNA 3.0 Annotations, Unsupported, CSV format from Affymetrix

source_name: Tax1BP1 wildtype

label_protocol: miRNA was labeled with the Affymetrix FlashTag Biotin HSR RNA Labeling Kit

growth_protocol: Mice were housed under 12 h day/night cycles, were fed standard rodent chow and had access to drinking water ad libitum.

extract_protocol: miRNA was extracted with the miRNeasy Mini Kit from Qiagen

tag: strain background

value: Tax1BP1 wildtype

tag: age

value: 12 weeks

tag: Sex

value: male

value: liver


title: Tax1BP1 wildtype 3 [miRNA]

tag: genotype/variation


title: Tax1BP1 wildtype 1 [miRNA]


title: ATAC-seq - ABa 90 minutes #2

description: ATAC-Seq 25k cells, sorted (ABa) 90' (green)

source_name: Embryo (ABa) - 90 minutes

value: Embryo - 90 minutes


title: Pooled & sorted from AGED lungs ivCD90- CD8a+ CD44hi CD69+ D^b-NP tetramer (PE+ & APC+) T cells

first: Jie

last: Sun

state: MN

address: 200 1st St SW

department: medicine, immunology

institute: mayo clinic

description: single cell RNA library

data_processing:
Paired-end sequencing was performed using an Illumina HiSeq 2500 in rapid-run mode.
CellRanger software package (10x Genomics) were used to align and quantify sequencing data from 10x Genomics.
All scRNA-seq analyses were performed in R  using the package Seurat (version 3.0; Butler, 2018)
https://satijalab.org/seurat/v3.2/pbmc3k_tutorial.html
Genome_build: mm10
Supplementary_files_format_and_content: h5

source_name: Lung parenchymal CD8+ T cells

extract_protocol:
Pooled & sorted from YOUNG or AGED lungs ivCD90- CD8a+ CD44hi CD69+ D^b-NP tetramer (PE+ & APC+) T cells from influenza virus infected mice (60 d.p.i.) were loaded on the Chromium Controller (10x Genomics).
Single-cell libraries were prepared using the Chromium Single Cell 3’ Reagent kit (10x Genomics)
All scRNA-seq analyses were performed in R using the Seurat package (version 3.0) {Butler, 2018 #903}. Paired-end RNA-seq reads were aligned to the mouse mm10 genome

treatment_protocol: sorted into 4 degree C RPMI media containing 50% FCS

value: Lung

tag: cell markers

tag: infection

value: Influenza A/PR8/34 (60 d.p.i.)


title: ZNF598-null replicate 2 for RNA-seq

description:
messenger RNA
ZNF598_2

tag: genotype


title: Gene expression IDH1 mutant 2165

value: glioma

tag: idh1 status

value: mutant


title: Tax1BP1 knock-out 3 [miRNA]

source_name: Tax1BP1 knock-out

value: Tax1BP1 knock-out

tag: tissue


title: Wild-type, control replicate 1 for RNA-seq

description:
messenger RNA
WT_1

value: wild type


title: ATAC-seq - ABp 200 minutes #2

description: ATAC-Seq 25k cells, sorted (ABp) 200' (black)

source_name: Embryo (ABp) - 200 minutes

tag: strain

value: lucIs39[tbx-37p(1,87kb)::mNeonGreen::2xNLS::tbx-37 3'UTR(20ng); pal-1p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); med-2p::mScarlet-I::2xNLS::tbb-2 3'UTR (100ng); pBluescript(30ng)]


title: Pooled & sorted from YOUNG lungs ivCD90- CD8a+ CD44hi CD69+ D^b-NP tetramer (PE+ & APC+) T cells

description: single cell RNA library


title: Tax1BP1 knock-out 2 [miRNA]


title: ATAC-seq - ABp 90 minutes #2

description: ATAC-Seq 25k cells, sorted (ABp) 90' (black)

source_name: Embryo (ABp) - 90 minutes


title: Wild-type, control replicate 2 for RNA-seq

description:
messenger RNA
WT_2


title: DN_m5

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
RRBS FASTQ files were aligned to the in silico bisulfite converted genome mm9 using Bismark with the Bowtie2 option.  Binary Alignment Map BAM files were parsed to derive DNA methylation calls that were collapsed to the CpG level using custom R scripts that made use of the ‘Rsamtools’ and ‘data.table’ packages available upon request  Data were summarized for CpGs that were covered at 10x in all samples and CpGs that were covered at 10x by all groups
Genome_build: mm10
Supplementary_files_format_and_content: Count matrix of methylaed and unmethylated reads for each CpG covered by a minimum of 10 reads within each group.  For each CpG there is the chromosome location and for each sample there are three columns of data containing the sample name followed by the following extensions: ".meth", % of reads methylated; ".u", number of reads unmethylated; ".m", number of reads methylated.

source_name: pooled inguinal, brachial, axillary, cervical, and popliteal lymph nodes

growth_protocol: BM cells were cultured in RPMI supplemented with 10% FBS, 2 mM L-glutamine, 1 mM sodium pyruvate, 100 U penicillin-streptomycin, 0.05 mM 2-ME, and 20% of Flt3L containing supernatant, secreted by an SP2/0 transfected cell line for the indicated number of days.

extract_protocol:
Genomic DNA was isolated by phenol-chloroform extraction followed by ethanol precipitation.
Two aliquots of DNA were separately digested with either TaqI or MspI restriction enzymes over night and subsequently pooled for all downstream processing.  Digested DNA was end-repaired, A-tailed, and adapters containing methylated cytosines ligated on using the KAPA HyperPrep kit according to the manufacturers instructions.  Adapter-ligated DNA was bisulfite converted over using the EpiTech Bisulfite kit Qiagen, Inc.  Bisulfite treated libraries were PCR amplified using indexed primers and the HiFi HotStart Uracil+ polymerase KAPA Biosystems.

value: CD4-CD8-TCR-ab+ T cells


title: ATAC-seq - ABa 350 minutes #2

description: ATAC-Seq 15k cells, sorted (ABa) 350' (green)

source_name: Embryo (ABa) - 350 minutes

value: ABa


title: CoVi01_4_0_0_5P_CITE

value: Blood

value: Memory CD4 T cells, helper enriched:CD3+ CD4+ CD45RA- CD154+ CD69+