title: Albumin-derived HCC without CLC_rep1

description: HCC in an Alb-AID mouse at 90 weeks age

source_name: HCC without CLC, Albumin-derived, replicate 1


title: Input DNA ChIP-Seq P14 replicate 2

status: Public on Feb 18 2020

type: SRA

city: Vassilika Vouton, Herakleion

first: Iannis

last: Talianidis

state: Crete

address: 100 N. Plastira Str

department: Institute of Molecular Biology and Biotechnology

country: Greece

institute: Foundation for Research and Technology - Hellas

library_source: genomic

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer as well as standard Illumina base callers (bcl2fastq).
The RNA-Seq FASTQ files were mapped on the UCSC mm9 reference genome using tophat2 , with default settings and using additional transcript annotation data for the mm9 genome from Illumina iGenomes (http://cufflinks.cbcb.umd.edu/igenomes.html). The ChIP-Seq FASTQ files were also mapped to the mm9 genome using bwa  with standard parameters. The resulting BAM files were visualized in the UCSC Genome Browser using bedtools  and tools provided by the UCSC Genome Browser toolkit. Prior to any alignment or further analysis, the quality all the FASTQ files and the reads contained therein was inspected with the FastQC package.
The raw bam files were summarized to an exon read counts table and the exon read counts were filtered for artifacts as follows: if an annotated gene had up to 5 exons, read presence was required in at least 2 of the exons, else if an annotated gene had more than 5 exons, then read presence was required in at least 0.2x⌈E⌉ exons, where ⌈.⌉ is the ceiling mathematical function. After exon filtering, the final read counts for each gene model were calculated as the sums of their exon reads, creating a gene counts table where each row corresponded to an Ensembl gene model and each column corresponded to an RNA-Seq sample. The gene counts table was normalized using the Bioconductor package DESeq after removing genes that had zero counts over all samples. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500, ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp, iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis using the Bioconductor package DESeq. Differentially expressed genes were identified with an FDR threshold of 0.05 and a fold change threshold of -1 and 1 (log2) scale for up and down regulated genes respectively. All the analyses and reporting  were performed within the Bioconductor package metaseqR.  For the transcription factor data (CEBPα, HNF4α), the two biological replicates for each developmental stage and their respective DNA input samples were subjected to peak calling using MACS 1.4  with the default settings for mouse genome. Prior to peak calling and in order to compensate for differences in library sizes between ChIP and Input DNA sequencing samples, the total number of reads of each sample was equalized by uniformly downsampling reads relatively to the sample with the lower number of reads. The putative binding sites returned by MACS were further filtered for artifacts by i) imposing an additional MACS FDR threshold of 0.1%, ii) excluding peaks demonstrating a fold enrichment less than 1 in log2 scale (where fold enrichment is the ratio of reads under a peak area in the ChIP sample to the respective number of reads in the Input DNA sample).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene for RNA-Seq data. BED files with peak coordinates for ChIP-Seq data. BigWig signal files for ChIP-Seq data.

molecule: genomic DNA

organism: Mus musculus

source_name: Input DNA ChIP-Seq P14

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) or High Fat Diet (34% crude Fat, 23% crude Protein, 5% crude fiber by Mucedola s.r.l.) and water ad libitum. All animal experiments were approved by the Prefecture of Attica and were performed in accordance with the respective national and European Union regulations. All the experiments were performed in randomly chosen age-matched male mice. No blinding was used in this study.

extract_protocol:
RNA preparation: Total RNA was prepared by homogenizing liver pieces in 10 volumes of Trizol reagent followed by the addition of 2 volumes of chlorophorm and centrifugation at 12000 g for 15 minutes. The aqueous phases were precipitated with isopropanol. Following resuspension in water RNAs were subjected to additional precipitation with ethanol. The RNA samples were digested with 10 units of DNase I for 10 min at 37 0C, followed by purification with phenol/chlorophorm extraction and ethanol precipitation. Chromatin immunoprecipitation: Liver tissue was minced to small pieces in PBS and after addition of formaldehyde to a 1% final concentration immediately was subjected to 10 strokes of dounce homogenization. Cross-linking was continued for 10 min and stopped by the addition of glycine at 0.125 M final concentration. Cross-linked cells were treated with a buffer containing 50 mM HEPES pH 7.5, 0.14 M NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40 and 0.25% Triton-X100, for 10 minutes and then with a buffer containing 0.2 M NaCl, 1 mM EDTA, 0.5 mM EGTA and 10 mM Tris-HCl pH 8.0 for 5 minutes. The nuclei were resuspended up to 4 ml with sonication buffer containing 10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate and 0.5% N-lauroylsarcosine and sonicated for 12 minutes in Covaris Sonicator instrument. After sonication, samples were supplemented with 400 μl of 10% Triton X-100 and centrifuged for 10 minutes at 20.000 rcf. After centrifugation, the extracted chromatin was incubated overnight with Dynabeads Protein G, that were prebound by 10 ug of the respective antibodies. The beads were washed six times with a buffer containing 50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, and 0.7% Na-deoxycholate, and then once with a buffer containing 20 mM Tris-HCl pH 7.6 and 150 mM NaCl. Immunoprecipitated chromatin was eluted from the beads and reverse crosslinked by overnight incubation with a buffer containing 50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1 % SDS, at 65 0C. Following incubation, samples were diluted by addition of one volume of TE. RNAs and proteins were removed by incubation with 20 ug/ml RNAse A for 30 minutes at 37 C, followed by incubation with 20 ug/ml Proteinase-K for 2 hours at 55 0C. DNA was extracted by phenol/chlorophorm and precipitated with ethanol. About 10 ng of the immunoprecipitated DNA and input DNA was used for library preparation.
Libraries were prepared using TruSeq or NEBNext Adaptors, depending on whether less or more than 6 indexes were included. In all cases, 25 μl of immunoprecipitated DNA was purified using the MinElute columns (Qiagen, 28604) and eluted with 10 ul elution buffer. The concentration of the eluted DNA was measured in Qubit using the dsDNA HS Assay Kit (Invitrogen Q32851). Subsequently, ten ng of ChIP or input DNA were subject to end repair, in a mix containing T4 DNA polymerase (NEB M0203L), Klenow fragment (NEB M0210L), T4 DNA PNK (NEB M0201L) and dNTPs in T4 DNA Ligase Buffer (NEB, B02025) at 20 °C for 30 min. Following end repair, samples were purified using the Agentcourt AMPURE XP system (Agentcourt A63881) and subject to A addition by incubation with dATP and Klenow 3’-->5’ exo- 37 °C for 30 min. Another AMPURE XP purification was performed and then Truseq or NEBNext adaptors were ligated using Quick Ligase in Quick Ligase Buffer. Following adaptor ligation, samples were incubated with 1.5 ul USER enzyme at 37 °C for 15 minutes, to cleave the adaptor hairpin loop. Purification and size selection was performed again by AMPURE XP and PCR amplification was performed using Truseq or NEBnext Primers in Kapa Hifi Hotstart mix. A final purification was performed and libraries were ready for Bioanalyzer assessment and sequencing.

treatment_protocol: The mice were not treated.

tag: strain

value: F1 mice (C57Bl6/CBA)

tag: age

value: 14 days postnatal

tag: genotype

value: Wild type

tag: tissue

value: liver


title: Wild type RNA-Seq replicate 2

library_source: transcriptomic

molecule: total RNA

source_name: Wild type RNA-Seq

value: 60 days postnatal


title: DM11.DNMT3B-amp.BRAF-OIS.Rep2

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

country: United Kingdom

institute: University of Glasgow

description:
FPKM_Matrix.csv
DNMT3B-BRAF_vs_vector-vector.gene_exp.diff

data_processing:
Paired-end reads were aligned to the human genome (hg19) using a splicing-aware aligner (TopHat2) (Kim et al., 2013)
Only unique reads were retained. Reference splice junctions were provided by a reference transcriptome (Ensembl build 73) and novel splicing junctions defined by the detection of reads that spanned exons not in the reference annotation.
True read abundance at each transcript isoform was assessed using HTSeq (Python) before determination of differential expression using CuffDiff, from which differential expression and splicing can be derived (Trapnell et al., 2013). Significance was determined using an FDR corrected p-value of <0.05. Heatmaps were created in R using the ggplots package.
Genome_build: hg19
Supplementary_files_format_and_content: CuffDiff results files and FPKM matrix

organism: Homo sapiens

growth_protocol: Human fetal lung fibroblasts (IMR-90) were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 10units/mL Penicillin G and 10μg/ml streptomycin. Cells were cultured in 10cm plates in a humidified atmosphere with 3% O2 and 5% CO2. Passaging of cells was performed at 70-80% confluency. Culture media were aspirated, and the cells lavaged twice with sterile phosphate-buffered saline to remove remaining traces of culture media. Trypsinisation was then performed with 1mL of 1% trypsin in phosphate-buffered EDTA solution for 3 minutes at 37°C. With cell detachment confirmed by visual inspection with a microscope, the trypsin solution was neutralised by the addition of fresh culture media (supplemented with FBS) to the plate. Cells were then resuspended in culture media, passaged to fresh plates, and returned to the incubator.

extract_protocol:
RNA was extracted from adherent cells using the RNeasy Mini Kit according to the manufacturer’s protocol. In summary, cell pellets were lysed on ice into buffer RLT supplemented with β-mercaptoethanol. Cell lysates were then homogenised by centrifugation in QiaShredder columns. RNA isolation was then performed using RNeasy mini kit columns, with residual DNA removed by on-column treatment with DNaseI. Following wash steps, RNA was eluted into RNase-free distilled water, and stored at -80°C prior to subsequent analysis.
Prior to sequencing, RNA quantification was performed using the Qubit RNA HS assay kit, and qualitative assessment performed using the Agilent RNA ScreenTape assay according to the manufacturer’s instructions. RNA-sequencing was performed in the sequencing facility at the Beatson Institute for Cancer Research, Glasgow. RNA was prepared for sequencing using the TruSeq RNA sample preparation kit. RNA is first purified, fragmented and reverse transcribed to produce cDNA. Following the removal of any remaining RNA, single stranded cDNA is converted to double stranded cDNA. Blunt-end DNA fragments are then generated. The subsequent addition of an “A” base to blunt ends prepares them for ligation to the sequencing adapters, which possess a “T” base overhang at the 3’ end, thus providing a complementary overhang for adapter ligation. Adapters possess sequencing primer hybridisation sites for single, paired-end and multiplex reads. PCR is then employed to selectively enrich for those DNA fragments in possession of an adapter molecule on both ends (12 cycles only to prevent skewed representation in the library) and then libraries validated using the Agilent DNA 1000 kit. Libraries were then sequenced using the Illumina GAIIX sequencer at the Beatson Institute for Cancer Research, Glasgow.

treatment_protocol: 12x106 HEK-293T cells were seeded in 25 mL of culture medium to TC175 flasks 20 hours prior to transfection. Cells were approximately 70% confluent for transfection. Immediately prior to transfection, 13mL of culture medium was aspirated from flasks, and the cells returned to the incubator. Lipofectamine 2000 was selected as a transfection agent for all lentivirus production. 120μL of transfection agent were added dropwise to 1.5mL of sterile DMEM in a 15mL centrifuge tube, gently agitated and incubated for five minutes at room temperature. Concurrently, packaging plasmids (5μg plpVSVG and 8μg psPAX2) were combined with 20μg of vector genome in 1.5mL of sterile DMEM in a separate 15mL centrifuge tube. Thereafter the DNA and transfection reagent solutions were combined, gently agitated and incubated for 20 minutes at room temperature. The transfection solution was then added to the prepared HEK-293T flasks to yield a total final transfection volume of 15mL. Following transfection, HEK-293T cells were returned to the incubator for six hours, following which the transfection solution was aspirated, and a fresh 15mL of culture medium added to the flask. For all transfections, a separate green fluorescent protein (GFP) control transfection was performed in parallel to confirm transfection efficiency. After a period of twenty hours following transfection, GFP controls were examined to confirm transfection efficiency. Lentiviral supernatant was then aspirated from transfected HEK-293T cells, reserved and stored at 4°C. A further 15mL of culture medium was added to the HEK-293T cells and returned to the incubator for a further twenty hours. The second lentiviral supernatant fraction was then combined with the first, centrifuged at 3000RPM in a table-top centrifuge, and filtered through a 0.45μM low-protein binding PVDF filter prior to concentration. Filtered viral supernatants were transferred to sterile 38.5mL polypropylene centrifuge tubes (Beckman 326823) and weights equalised by the addition of sterile PBS. Ultracentrifugation was performed at 47,000 x g in an SW-28 Beckman- Coulter ultracentrifuge for two hours at 10°C. Following centrifugation, the supernatant was discarded by gentle inversion, and the viral pellet resuspended in 100μL of sterile PBS overnight at 4°C, prior to being aliquoted and stored at -80°C. The multiplicity of infection (MOI) for lentiviral preparations was calculated empirically by seeding cells to a 6-well plate twenty-four hours prior to transduction. Culture medium was then aspirated from each well, replaced with 1mL of fresh culture medium supplemented with polybrene at a final concentration of 8μg/mL, and the cells returned to the incubator for four hours prior to transduction. Concentrated lentivirus was then added to each well at 0, 1, 2, 4, 8 and 16 μL/mL, and returned to the incubator for sixteen hours. Following transduction, the infection medium was removed from each well, and replenished with 2mL of fresh culture medium supplemented with the appropriate drug selection as determined by the construct design. The minimum volume of lentiviral construct required to yield 100% cell survival following drug-selection was then employed for all subsequent experiments. All experiments involving lentivirus were performed in their entirety under drug selection.

tag: cell type

value: Human Fetal Lung Fibroblasts

tag: passages

value: Ectopically expressed DNMT3B / BRAF OIS


title: Input DNA ChIP-Seq e15.5 replicate 2

source_name: Input DNA ChIP-Seq e15.5

value: 15.5 days embryonic


title: Input DNA ChIP-Seq e18.5 replicate 2

source_name: Input DNA ChIP-Seq e18.5

value: 18.5 days embryonic


title: Input DNA ChIP-Seq P0.5 replicate 2

source_name: Input DNA ChIP-Seq P0.5

value: 0.5 days postnatal


title: PolII ChIP-Seq P14 replicate 1

source_name: PolII ChIP-Seq P14

tag: chip antibody

value: RNA-Pol-II

tag: chip antibody vendor

value: Euromedex

tag: chip antibody cat. #

tag: chip antibody lot #


title: PolII ChIP-Seq P14 replicate 2


title: PolII ChIP-Seq e15.5 replicate 1

source_name: PolII ChIP-Seq e15.5


title: HNF4a ChIP-Seq P60 replicate 2

source_name: HNF4a ChIP-Seq P60

value: Santa Cruz Biotech/Aviva


title: PolII ChIP-Seq e15.5 replicate 2


title: CEBPa ChIP-Seq P60 replicate 1

source_name: CEBPa ChIP-Seq P60

value: C/EBPa

value: Santa Cruz Biotech


title: CEBPa ChIP-Seq P60 replicate 2


title: HNF4a ChIP-Seq e15.5 replicate 1

source_name: HNF4a ChIP-Seq e15.5


title: CEBPa ChIP-Seq P0.5 replicate 2

source_name: CEBPa ChIP-Seq P0.5


title: HNF4a ChIP-Seq P60 replicate 1


title: Input DNA ChIP-Seq P60 replicate 2

source_name: Input DNA ChIP-Seq P60


title: CEBPa ChIP-Seq e18.5 replicate 2

source_name: CEBPa ChIP-Seq e18.5


title: CEBPa ChIP-Seq e18.5 replicate 1


title: CEBPa ChIP-Seq e15.5 replicate 1

source_name: CEBPa ChIP-Seq e15.5


title: CEBPa ChIP-Seq e15.5 replicate 2


title: CEBPa ChIP-Seq P0.5 replicate 1


title: 201148310012_R09C01

status: Public on Feb 19 2020

type: genomic

city: Langston

first: Yonathan

last: Tilahun

state: OK

address: 100 Success Dr.

department: Extension

country: USA

institute: Langston University

description: Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping Beadchips (Illumina).

hyb_protocol: Third party preparation conducted at the Oklahoma Medical Research Foundation Core Genomics Laboratory.

data_processing:
Genomic DNA extracted from Bronopol preserved goat milk somatic cells was genotyped using InfiniumGoatIGGC_conf_60K Genotyping BeadChips (Illumina).
Image data was analyzed using Genome Studio and further analysis was conducted using PLINK, R, Qlik, and GoldenHelix SNP &Variation Suite

label: Cy3, Cy5

organism: Capra hircus

source_name: Milk Somatic Cells

extract_protocol: Norgen Biotek Corp. Milk DNA Preservation and Isolation Kit was used to extract genomic DNA from Bronopol preserved goat milk somatic cells.

treatment_protocol: Goat milk obtained from different sources and different locations throughout the United States were preserved by Bronopol tablet placement in the milk before shipment and downstream procedures.

tag: Sex

value: Female

value: Milk Somatic Cells


title: TSRS Differentiated

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Convert BAM files to FASTQ files using picard-toolds-1.108, SamToFastq.jar
Trimming of adapter and poor quality reads with trim_galore_v0.3.3
Align to genome and get methylation calls with bsmap-2.74
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file containing information for each sample: chrBase, chr, base, strand, coverage, FreqC (methylation), FreqT

source_name: Trophoblast Stem Cell line

growth_protocol: Trophoblast cells were cultured at 37°C under 5% CO2 in air and maintained in RPMI 1640 culture medium supplemented with 20% fetal bovine serum, 1mM sodium pyruvate, 50 mg/mL penicillin/streptomycin, 5.5x10-5 M β-mercaptoethanol, 25 ng/mL bFGF, and 1 mg/mL heparin with 70% of the medium being preconditioned by incubation with embryonic fibroblasts for 48 h

extract_protocol:
Genomic DNA was extracted from tissues and cell lines using DNeasy Blood & Tissue Kit (Qiagen) as per manufacturer protocols
Reduced representation bisulfite sequencing (RRBS) libraries were prepared according to previously published prototols using gel-free technique (Boyle, P. Genome Biol., 2012).  Briefly, DNA was digested with MspI restriction enzyme, followed by size selection, gap filling and 3'-A-tailing.  Ligation of NEBNext methylated adaptors was performed, followed by bisulfite conversion and index PCR amplificaton.

treatment_protocol: Cell lines were differentiatiated by the removal of bFGF, heparin, embryonic fibroblast pre-condition, and the addition of retinoic acid (5uM)

value: LacZ transgene

tag: cell line

value: TSRS

tag: time

value: day 4 of differentiation


title: TSRS Undifferentiated

value: day 0


title: Placenta Rep2

source_name: Embryonic placenta

value: whole placenta


title: Placenta Rep4


title: TSG28 Undifferentiated


title: Placenta Rep1


title: TSG28 Differentiated


title: Placenta Rep3


title: HNF4a ChIP-Seq e15.5 replicate 2

value: F1 mice (C57Bl6/CBA)

value: Wild type

value: liver


title: Embryo Rep4

source_name: Embryonic embryo

value: whole embryo


title: Embryo Rep3


title: Embryo Rep2


title: Embryo Rep1


title: LHSR12-1 7-day old Col-0 seedlings recover 12 hours after long heat stress

city: Beijing

first: li

last: kuan

address: zhongguancun

country: China

institute: Tsinghua University

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome with Bowtie 2 using default settings, with all duplicates removed by Picard tools. The total mapped reads (non-strand R-loops) were divided into forward (wR-loops,representing an R-loop formation containing single-strand DNA on the Watson strand and an DNA:RNA hybrid on the Crick strand) and reverse reads(cR-loops) by using samtools.
DESeq2 was used to analyze R-loop differences between samples.The FDR (false discovery rate) method was used to calculate adjusted p value (q value), and the q values and log2FC values were used to determine significant difference. MACS2 was used to identify peaks with default parameters.
For visualization, the aligned reads files (BAM) were converted to normalized coverage files(bigWig) with 1 bp bins using bamCoverage from deepTools. Normalization was performed using bamCoverage from deepTools, with read coverage normalized to 1× sequencing depth (also known as Reads Per Genomic Content) with a re-normalization by shuffled peaks (total R-loop peaks were shuffled randomly, and the 95% mean of R-loop signal from each sample on shuffled peaks was used as denominator) to eliminate the disturbances from abnormally high value regions. Snapshots of the data were constructed using the Integrative Genomics Viewer(IGV).
Genome_build: TAIR10
Supplementary_files_format_and_content: Input_Watson: Watson strand of input DNA; Input_Crick: Crick strand of input DNA

organism: Arabidopsis thaliana

source_name: Wild type

extract_protocol:
Nuclei were isolated from Arabidopsis plants, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments .
The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

tag: ecotype

value: Columbia

value: seedlings

tag: sample type

value: DNA:RNA hybird


title: pDC + CpG-A. Rep3

type: RNA

city: Campinas

first: Renata

last: Sesti-Costa

state: SP

address: Rua Carlos Chagas 480

country: Brazil

institute: UNICAMP

description: G3 = group 3

hyb_protocol: RNA amplification and hibridization was performed according to Affymetrix standard protocol

scan_protocol: not provided

data_processing: Data were processed and normalized using RMA (robust multichip average) and analyzed with Gene Pattern software (Brad Institute)

label: biotin

source_name: pDC stimulated with CpG-A - replicate 3

extract_protocol: RNA was extracted from cells using RNeasy microkit (QIAGEN)

treatment_protocol: pDCs were treated with LIF (10ng/ml) for 1h followed or not of CpG-B or A stimulation for additional 19-23h. Total treatment of LIF was 20-24h.

value: Bone marrow

value: pDC


title: pDC + CpG-A+ LIF. Rep3

description: G3 = group 3

source_name: pDC stimulated with CpG-A followed treatment with LIF - replicate 3

label_protocol: RNA amplification and hibridization was performed according to Affymetrix standard protocol


title: pDC + CpG-B. Rep3

description: G3 = group 3

source_name: pDC stimulated with CpG-B - replicate 3


title: pDC + CpG-A+ LIF. Rep2

description: G2 = group 2

source_name: pDC stimulated with CpG-A followed treatment with LIF - replicate 2


title: pDC + CpG-A. Rep2

description: G2 = group 2

source_name: pDC stimulated with CpG-A - replicate 2


title: vy4beta_cells_control2

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

description: naïve Vγ4TCRβ+  T cells

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Kallisto (version 0.44) with parameters -b 100 --single -l 125 -s 13
Transcript abundances were summarized to gene-level estimates in  R (version 3.4.4) using the tximport Bioconductor package (version 1.8) and  the makeTxDbFromGFF package using a GTF annotation file from Ensembl (release 93).
Data were normalized using the trimmed mean of log expression values   approach in NOISeq (version 2.22.1)
Samples 7 (vy4_cells_control_plus_eae2) and 18 (vy4beta_cells_control_plus_eae3) were outliers and removed from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Due to different analyses carried out, two different normalisation files are provided. One that comprises only naive cells from each cell type "CONTROL_Normalised_gene_counts_naive_conv_vs_naive_hybrid.txt" and the other that comprises all samples "EXPERIMENTAL_Normalised_gene_counts_naive_vs_EAE.txt". They are tab-delimited text files which include normalised gene-based read count data provided as a matrix table.

source_name: Vγ4 T cell

growth_protocol: T cells were purified from LNs by magnetic separation using a Pan T Cell Isolation Kit (Miltenyi Biotec) and labeled with anti-TCRβ (clone H57-597, 0.1 μg/106 cells, eBioscience), anti-TCRδ (clone GL3, 0.1 µg/106 cells, eBioscience), and anti-Vγ4 (clone UC3-1OA6, 0.1 μg/106 cells, BioLegend). Cells were then flow-purified as TCRδ+Vγ4+TCRβ+ or TCRδ+Vγ4+TCRβ– populations from the lymph nodes of naive mice or mice with EAE.

extract_protocol:
Clontech NucleoSpin® RNA XS kit was used to extract RNA
RNAseq was performed on total RNA by normalizing the input mass to cell number according to cell type. For TCRδ+Vγ4+TCRβ– cells, input was normalized to 30,000 cells where possible (2 samples fell below this input target, reaching totals of 12,687 and 21,772 cells). For TCRδ+Vγ4+TCRβ+ cells, input was normalized to 5,000 cells where possible (3 samples fell below this input target, reaching totals of 2,036, 3,649, and 4,577 cells). cDNA was amplified using a SMARTer Ultra Low Input RNA Kit for Illumina Sequencing (Clontech) and sequenced at a target depth of 30 x 106 single-end (1 x 50 bp) reads per sample using a HiSeq 3000 System (Illumina).

treatment_protocol: Experimental protocol for EAE: Active EAE was induced by injecting mice subcutaneously with 100 μg of MOG35–55 peptide (GenScript) emulsified in CFA containing 4 mg/ml (0.4 mg/mouse) of heat-killed M. tuberculosis (Chondrex). Mice were further injected intraperitoneally with 250 ng of pertussis toxin (Kaketsuken) on d 0 and 2. Lymph nodes were isolated from these mice at day 3 post induction of EAE.

value: Lymph node

value: wild type

value: V<gamma>4 T cell


title: pDC + CpG-B + LIF. Rep1

description: G1 = group 1

source_name: pDC stimulated with CpG-B followed treatment with LIF - replicate 1


title: vy4beta_cells_control_plus_eae4

description: Vγ4TCRβ+ T cells post EAE


title: vy4beta_cells_control4

description: naïve Vγ4TCRβ+  T cells


title: vy4beta_cells_control_plus_eae5

description: Vγ4TCRβ+ T cells post EAE


title: vy4beta_cells_control5

description: naïve Vγ4TCRβ+  T cells


title: vy4beta_cells_control3

description: naïve Vγ4TCRβ+  T cells


title: vy4beta_cells_control_plus_eae1

description: Vγ4TCRβ+ T cells post EAE


title: vy4beta_cells_control_plus_eae2

description: Vγ4TCRβ+ T cells post EAE


title: pDC + CpG-B + LIF. Rep2

description: G2 = group 2

source_name: pDC stimulated with CpG-B followed treatment with LIF - replicate 2


title: pDC + CpG-B + LIF. Rep3

description: G3 = group 3

source_name: pDC stimulated with CpG-B followed treatment with LIF - replicate 3


title: vy4beta_cells_control_plus_eae3

description: Vγ4TCRβ+ T cells post EAE


title: pDC + CpG-A. Rep1

description: G1 = group 1

source_name: pDC stimulated with CpG-A - replicate 1


title: pDC + LIF. Rep3

description: G3 = group 3

source_name: pDC treated with LIF - replicate 3


title: pDC + CpG-A+ LIF. Rep1

description: G1 = group 1

source_name: pDC stimulated with CpG-A followed treatment with LIF - replicate 1


title: pDC + LIF. Rep2

description: G2 = group 2

source_name: pDC treated with LIF - replicate 2


title: pDC + medium. Rep3

description: G3 = group 3

source_name: pDC without treatment - replicate 3


title: pDC + LIF. Rep1

description: G1 = group 1

source_name: pDC treated with LIF - replicate 1


title: vy4_cells_control_plus_eae5

description: Vγ4TCRβ– T cells post EAE


title: pDC + medium. Rep1

description: G1 = group 1

source_name: pDC without treatment - replicate 1


title: pDC + CpG-B. Rep1

description: G1 = group 1

source_name: pDC stimulated with CpG-B - replicate 1


title: pDC + CpG-B. Rep2

description: G2 = group 2

source_name: pDC stimulated with CpG-B - replicate 2


title: vy4_cells_control_plus_eae4

description: Vγ4TCRβ– T cells post EAE


title: vy4beta_cells_control1

description: naïve Vγ4TCRβ+  T cells


title: vy4_cells_control_plus_eae2

description: Vγ4TCRβ– T cells post EAE


title: vy4_cells_control_plus_eae3

description: Vγ4TCRβ– T cells post EAE


title: vy4_cells_control_plus_eae1

description: Vγ4TCRβ– T cells post EAE


title: vy4_cells_control5

description: naïve Vγ4TCRβ–  T cells


title: vy4_cells_control4

description: naïve Vγ4TCRβ–  T cells


title: vy4_cells_control3

description: naïve Vγ4TCRβ–  T cells


title: vy4_cells_control2

description: naïve Vγ4TCRβ–  T cells


title: NM ProQ FLAG  -crosslink replicate 2

city: Würzburg

first: Thorsten

last: Bischler

address: Josef-Schneider-Straße 2 / D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

description: background control sample

data_processing:
Quality trimming: FASTX 0.0.13 fastq_quality_trimmer, Phred cut-off of 20
Adapter trimming using cutadapt (Martin, 2011) version 1.7.1 (R1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC, R2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT), discard empty reads
Filtering of reads without mate via cmpfastq (http://compbio.brc.iop.kcl.ac.uk/software/cmpfastq.php)
Collapsing of identical reads and conversion to FASTA format using FastUniq (Xu et al. 2012)
Read mapping using segemehl version 0.2.0 with minimum accuracy 80% (READemption 0.3.7, Förstner et al., 2014)
Coverage calculation based on uniquely mapped reads (READemption 0.3.7, Förstner et al., 2014)
Calculation of size factors by applying the DESeq normalization method (Anders et al., 2010) to non-enriched nucleotide positions from coverage files (for details see associated publication)
Final coverage calculation during peak calling via PEAKachu (https://github.com/tbischler/PEAKachu, manuscript in preparation) based on previously calculated size factors
Genome_build: Neisseria meningitidis 8013 (Assembly acc.: GCF_000026965.1, Sequence ID: NC_017501.1 )
Supplementary_files_format_and_content: wiggle

organism: Neisseria meningitidis 8013

source_name: Neisseria meninigitidis 8013 ProQ::3xFLAG cells

growth_protocol: Neisseria meninigitidis strain 8013 containing a proQ::3xflag allele grown as solid culture overnight was harvested and a starter culture was inoculated to a final optical density (OD600nm)  of 1.0 in 5 ml GCB-liquid medium supplemented with  Kellogg’s supplement I and II  (GCBL++) in 50ml Falcon-tubes. After one hour the starter culture was used to inoculate GCBL++ medium to a final OD600nm of 0.15. Bacteria were grown in 100 ml Falcon-tubes at 37 °C at 220 rpm without added CO2 until an OD600 of 2.0 was reached.

extract_protocol:
Bacteria were lysed and the FLAG-tagged proteins was immunoprecipitated using a monoclonal anti-FLAG antibody. The samples were treated with benzonase nuclease, calf intestine phophorylase, and polynucleotide kinase in the presence of radioactive gamma-ATP. Samples were separated with SDS-PAGE and followed by transfer to nitrocellulose membranes. Radioactively labelled RNA-protein complexes were eluted from membranes and treated with Proteinase K. RNA was purified with phenol:chloroform extraction and ethanol precipitation.
Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit according to the manufacturer’s instructions.
Purified RNA was used as input for library preparation using the NEB Next Small RNA Library kit according to the manufacturer’s instructions.

treatment_protocol: When the cultures reached an OD600 of 2.0, half of each culture was irradiated with UV light (254 nm, 800 mJ/cm2) while the other half was left untreated.

tag: clip antibody

value: M2 anti-FLAG monoclonal antibody attached to superparamagnetic iron impregnated agarose beads (Sigma-Aldrich, M8823)

tag: fraction

value: Unspecifically-bound RNA


title: NM ProQ FLAG  -crosslink replicate 1

description: background control sample

tag: strain


title: NM8013 wt R3

data_processing:
Demutliplexing via bcl2fastq v2.20.0.422
Fastq quality and adapter trimming using cutadapt (Martin, 2011) version 1.16 (Command line parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Size filtering: discard read pairs with at least one read shorter than 12 nt (READemption 0.4.5, Förstner et al., 2014)
Read mapping using segemehl version 0.2.0 with minimum accuracy 95% (READemption 0.4.5, Förstner et al., 2014)
Coverage calculation based on all aligned reads (full-length); Normalization: coverage-tnoar_min_normalized (counts divided by total number of aligned reads and multiplied by minimum over all libraries) (READemption 0.4.5, Förstner et al., 2014)
Genome_build: Neisseria meningitidis 8013 (Assembly acc.: GCF_000026965.1, Sequence ID: NC_017501.1 )
Supplementary_files_format_and_content: wiggle

source_name: Neisseria meninigitidis 8013 wt

growth_protocol: Neisseria meninigitidis strains 8013 wild-type and proQ deletion grown on solid media overnight were harvested and starter cultures were inoculated to a final optical density (OD600nm)  of 1.0 in 5 ml GCB-liquid medium supplemented with  Kellogg’s supplement I and II  (GCBL++) in 50ml Falcon-tubes. After one hour the starter cultures were used to inoculate GCBL++ medium to a final OD600nm of 0.15. Bacteria were grown in 50 ml Falcon-tubes at 37 °C at 220 rpm without added CO2 until an OD600nm of 2.0 was reached.

extract_protocol:
Total RNA extraction with the hot phenol method. cDNA libraries of RNA-seq-samples were constructed by Vertis Biotechnology AG, Munich, Germany. To deplete ribosomal transcripts, RNA-seq samples were treated with the Ribo-Zero “Bacteria” kit (Illumina) followed by RNA fragmentation and adapter ligation. cDNA libraries of RNA-seq samples were pooled on an Illumina NextSeq 500 high‐output flow cell and sequenced in single-read mode (1x76 cycles).
cDNA libraries of RNA-seq-samples were constructed by Vertis Biotechnology AG, Munich, Germany. To deplete ribosomal transcripts, RNA-seq samples were treated with the Ribo-Zero “Bacteria” kit (Illumina) followed by RNA fragmentation and adapter ligation.

treatment_protocol: When the cultures reached an OD600nm of 2.0, bacteria were snapfrozen inliquid nitrogen prior to total RNA extraction with the hot phenol method. Wild-type and proQ deletion samples were treated equally.


title: NM ProQ FLAG  +crosslink replicate 2

description: signal sample

value: ProQ-bound RNA


title: NM ProQ FLAG  +crosslink replicate 1

description: signal sample


title: NM8013 ΔproQ R3

source_name: Neisseria meninigitidis 8013 ProQ::Cm

value: proQ-


title: NM8013 wt R1


title: NM8013 ΔproQ R1


title: NM8013 wt R2


title: NM8013 ΔproQ R2


title: 4016-T2-D0

city: Davis

first: Samuel

middle: Taler

last: Westreich

state: CA

address: 1 Shields Ave

department: Genome Center

institute: University of California, Davis

description: ribodepleted

data_processing:
Paired-end alignment with PEAR software
Cleanup & low-quality sequence removal with Trimmomatic
Removal of ribosomal sequences with SortMeRNA
Annotation with DIAMOND against RefSeq Bacteria database (release 102, 22 December 2015)
Aggregation by genus with SAMSA2 pipeline script
Normalization with R and DESeq2 package
Genome_build: NCBI RefSeq Bacteria, release 102, 22 December 2015
Supplementary_files_format_and_content: Processed data files contain annotation results against RefSeq bacterial complete database for either best organism match (top 1) or best function match (top 1) per read.  Results are normalized across all samples, done using the DESeq package.

organism: feces metagenome

source_name: Human feces

extract_protocol:
Total RNA was extracted using Qiagen's RNeasy Micro kit, with RNA concentration and integrity verified by BioAnalyzer
Ribodepletion was performed using Illumina Ribo-Zero Gold (Epidemiology) kit, then cDNA libraries were prepared for PE100 sequencing

treatment_protocol: Feces were preserved in RNAlater, then frozen at -20 degrees C until transport on ice to -80 C freezer.

tag: subject id

value: feces

tag: bmo dose


title: 4016-T3-D11

description: ribodepleted

tag: tissue


title: 4016-T2-D11

description: ribodepleted


title: 4009-T3-D11

description: ribodepleted


title: 4008-T3-D11

description: ribodepleted


title: 4009-T2-D11

description: ribodepleted


title: 4009-T2-D0

description: ribodepleted


title: 4008-T2-D11

description: ribodepleted


title: CTRL-7d-2 7-day old Col-0 seedlings grown under normal condition

source_name: Wild type


title: 4008-T2-D0

description: ribodepleted


title: vy4_cells_control1

description: naïve Vγ4TCRβ–  T cells

source_name: Vγ4 T cell

tag: genotype

tag: cell type


title: 4016-T1-D0

description: ribodepleted


title: 4006-T3-D11

description: ribodepleted


title: 4009-T1-D0

description: ribodepleted


title: 4008-T1-D0

description: ribodepleted


title: 4005-T2-D0

description: ribodepleted


title: 4006-T2-D0

description: ribodepleted


title: 4003-T3-D11

description: ribodepleted


title: 4006-T2-D11

description: ribodepleted


title: 4003-T2-D11

description: ribodepleted


title: 4003-T1-D0

description: ribodepleted


title: hFSiPS1_PD03(100nM_2d)_5%FBS_1W_rep2

city: Cheongju

first: Yong-Ou

last: Kim

state: Chungchung buk do

address: Osongsangmyeong 2ro

country: South Korea

institute: Korea National Institute of Health

description:
2019_D12_S20_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_5%FBS(1W)_2

data_processing:
fastq files were aligned to human reference genome hg19 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: human hg19

growth_protocol: 1x10^6 cells/well were plated in 35 mm tissue culture dishes and placed in a 5% CO2 37 °C incubator for 22 hours

extract_protocol:
RNA was isolated using the Maxwell RSC RNA FFPE kit with the automated Maxwell RSC Instrument (Promega) according to the manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded mRNA Prep Kit, according to the manufacturer’s instructions.

treatment_protocol: Cells were cultured in KSR and E8 media for more than 3 weeks and differentiated with 5% FBS for 1, 2 3 weeks.

value: human pluripotent stem cells

tag: treatment

value: differentiated with 5% FBS for 1 W


title: hFSiPS1_PD03(100nM_2d)_5%FBS_2W_rep1

description:
2019_D17_S25_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_5%FBS(2W)_1

value: differentiated with 5% FBS for 2 W


title: hFSiPS1_PD03(100nM_2d)_rep2

description:
2019_D6_S53_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_2

value: untreated


title: hFSiPS1_PD03(100nM_2d)_rep1

description:
2019_D5_S52_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_1


title: 4006-T1-D0

description: ribodepleted


title: 4005-T3-D11

description: ribodepleted


title: 4005-T2-D11

description: ribodepleted


title: 4003-T2-D0

description: ribodepleted


title: 4005-T1-D0

description: ribodepleted


title: hFSiPS1_DMSO_rep2

description:
2019_D4_S51_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
hFSiPS1_DMSO_2


title: hFSiPS1_con_5%FBS_2W_rep2

description:
2019_D14_S22_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
Con_5%FBS(2W)_2


title: hFSiPS1_DMSO_5%FBS_2W_rep1

description:
2019_D15_S23_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
DMSO_5%FBS(2W)_1


title: hFSiPS1_DMSO_5%FBS_1W_rep2

description:
2019_D10_S18_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
DMSO_5%FBS(1W)_2


title: hFSiPS1_PD03(100nM_2d)_5%FBS_2W_rep2

description:
2019_D18_S26_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_5%FBS(2W)_2


title: hFSiPS1_con_5%FBS_1W_rep2

description:
2019_D8_S55_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
Con_5%FBS(1W)_2


title: hFSiPS1_con_5%FBS_1W_rep1

description:
2019_D7_S54_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
Con_5%FBS(1W)_1


title: hFSiPS1_con_rep2

description:
2019_D2_S49_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
hFSiPS1_Con_2


title: hFSiPS1_con_rep1

description:
2019_D1_S48_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
hFSiPS1_Con_1


title: hFSiPS1_DMSO_5%FBS_1W_rep1

description:
2019_D9_S56_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
DMSO_5%FBS(1W)_1


title: hFSiPS1_DMSO_5%FBS_2W_rep2

description:
2019_D16_S24_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
DMSO_5%FBS(2W)_2


title: hFSiPS1_DMSO_rep1

description:
2019_D3_S50_L002
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
hFSiPS1_DMSO_1


title: hFSiPS1_PD03(100nM_2d)_5%FBS_1W_rep1

description:
2019_D11_S19_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
PD03(2d)_5%FBS(1W)_1


title: hFSiPS1_con_5%FBS_2W_rep1

description:
2019_D13_S21_L001
processed data file: RNA-seq_FPKM (PD03_5%FBS).csv
Con_5%FBS(2W)_1


title: Human colon cancer cell line HCT116 was transfected with a control non-targeting siRNA, biological rep 1

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: Expression data for human colon cancer cell line HCT116 transfected with a control non-targeting siRNA to cells for 36 hours.

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using Hisat2, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: human genome GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

growth_protocol: The human colon cancer cell lines HCT116 were cultured in both DMEM medium supplemented with 10% fetal bovine serum, 100 units/m of penicillin and streptomycin. Cultures were incubated at 37°C in a humidified incubator at 5% CO2.

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: Cells were grown in DMEM medium (with 10% serum), and was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting LINC00152 for 36 hours.

value: colon cancer cell line

tag: agent

value: control siRNA(100nM)


title: Human colon cancer cell line HCT116 was transfected with LINC00152 siRNA, biological rep 1

description: Expression data for human colon cancer cell line HCT116 transfected with siRNA targeting LINC000152 to cells for 36 hours.

value: LINC00152 siRNA(100nM)


title: Human colon cancer cell line HCT116 was transfected with LINC00152 siRNA, biological rep 2

description: Expression data for human colon cancer cell line HCT116 transfected with siRNA targeting LINC00152 to cells for 36 hours.


title: patient 21005 9 mo post tx 3mo post Tac w/d

city: New York

first: Miguel

last: Fribourg

state: NY

address: 1 Gustave Levy Pl

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

description:
21005v10
mRNA

hyb_protocol: We performed the microarray analysis with the Affymetrix HT HG-U133+ PM array (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Arrays were scanned.

data_processing:
Quality Assessment/Quality control:
1) Probe level diagnostics. Probe-level models were created samples were screened for relative log expression (RLE) within -0.1 and 0.1 in median measurement as well as for Normalized Unscaled Standard Error (NUSE) within 0.95 and 1.05 (no samples failed these tests). R Packages (affy 1.60.0, simpleaffy 2.62.0, arrayQualityMetics 3.42.0, affyQCReport 1.64.0, affy PLM 1.62.0).
2) The arrays were background adjusted using sequence information GC robust Multi-array Average (GCRMA) background adjustment. R package (gcrma 2.28.0).

source_name: PBMC

label_protocol: Biotin

extract_protocol: We extracted total RNA of CTOT-09 minimum of 107 PBMCs samples collected in Paxgene tubes using miRNeasy Mini Kit (Qiagen, Hilden, Germany). Total RNA concentration and integrity were assessed using a Nanodrop spectrophotometer ND-1000 (Thermo Scientific, Waltham, MA, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), respectively.

value: PBMC

tag: tacrolimus withdrawal

value: Withdrawal Stable (WS)

tag: time point

value: 9 mo post tx, 3mo post Tac w/d

tag: patient id


title: patient 21005 6 mo post tx pre Tac w/d

description:
21005v06
mRNA

value: 6 mo post tx, pre Tac w/d


title: patient 21003 9 mo post tx 3mo post Tac w/d

description:
21003v10
mRNA

value: Withdrawal Rejection (WR)


title: patient 21007 9 mo post tx 3mo post Tac w/d

description:
21007v10
mRNA


title: patient 4004 6 mo post tx pre Tac w/d

description:
4004v06
mRNA


title: patient 5004 9 mo post tx 3mo post Tac w/d

description:
5004v10
mRNA


title: patient 5004 6 mo post tx pre Tac w/d

description:
5004v06
mRNA


title: patient 15002 9 mo post tx 3mo post Tac w/d

description:
15002v10
mRNA


title: patient 5003 9 mo post tx 3mo post Tac w/d

description:
5003v10
mRNA


title: patient 15004 6 mo post tx pre Tac w/d

description:
15004v06
mRNA


title: patient 15003 9 mo post tx 3mo post Tac w/d

description:
15003v10
mRNA


title: patient 15004 9 mo post tx 3mo post Tac w/d

description:
15004v10
mRNA


title: patient 21003 6 mo post tx pre Tac w/d

description:
21003v06
mRNA


title: patient 4008 9 mo post tx 3mo post Tac w/d

description:
4008v10
mRNA


title: patient 21001 9 mo post tx 3mo post Tac w/d

description:
21001v10
mRNA


title: patient 23003 6 mo post tx pre Tac w/d

description:
23003v06
mRNA

value: No withdrawal (NW)


title: patient 15003 6 mo post tx pre Tac w/d

description:
15003v06
mRNA


title: patient 5003 6 mo post tx pre Tac w/d

description:
5003v06
mRNA


title: patient 5006 9 mo post tx 3mo post Tac w/d

description:
5006v10
mRNA


title: patient 15002 6 mo post tx pre Tac w/d

description:
15002v06
mRNA


title: patient 4005 6 mo post tx pre Tac w/d

description:
4005v06
mRNA


title: patient 4005 9 mo post tx 3mo post Tac w/d

description:
4005v10
mRNA


title: patient 21007 6 mo post tx pre Tac w/d

description:
21007v06
mRNA


title: patient 21001 6 mo post tx pre Tac w/d

description:
21001v06
mRNA


title: patient 5002 6 mo post tx pre Tac w/d

description:
5002v06
mRNA


title: patient 4008 6 mo post tx pre Tac w/d

description:
4008v06
mRNA


title: patient 23003 9 mo post tx 3mo post Tac w/d

description:
23003v10
mRNA


title: Input DNA ChIP-Seq P60 replicate 1

source_name: Input DNA ChIP-Seq P60

value: F1 mice (C57Bl6/CBA)

tag: age

value: 60 days postnatal

value: Wild type

value: liver


title: Input DNA ChIP-Seq e18.5 replicate 1

source_name: Input DNA ChIP-Seq e18.5

value: 18.5 days embryonic


title: patient 5006 6 mo post tx pre Tac w/d

description:
5006v06
mRNA


title: PAI-1 KO; BBN, biological rep1

city: Los Angeles

first: Hideki

last: Furuya

address: 110 N. George Burns Road, Davis 2025

department: Surgery

institute: Cedars Sinai Medical Center

description: Gene expression data from mouse bladder cancer tissue

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

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

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Power Tools (APT). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis.

source_name: Bladder cancer from PAI-1 KO mice

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

growth_protocol: Mice were maintained under controlled conditions of humidity (50 ± 10%), light (12-h light-dark cycle) and temperature (23 ± 2°C).

extract_protocol: RNA was extracted from frozen tissues using RNeasy Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: PAI-1 KO mice and wild-type C57BL/6 wild type (WT) mice at 6 to 8 weeks of age were treated with 0.05% BBN in drinking water continuously for 20 weeks.

value: bladder

value: PAI-1 KO

value: BBN treatment


title: Input DNA ChIP-Seq P0.5 replicate 1

source_name: Input DNA ChIP-Seq P0.5

value: 0.5 days postnatal


title: PAI-1 KO; control, biological rep1

description: Gene expression data from mouse bladder normal tissue

source_name: Normal bladder from PAI-1 KO mice

value: no treatment


title: Input DNA ChIP-Seq e15.5 replicate 1

source_name: Input DNA ChIP-Seq e15.5

value: 15.5 days embryonic


title: patient 5002 9 mo post tx 3mo post Tac w/d

description:
5002v10
mRNA

value: PBMC


title: Wild type; control, biological rep1

source_name: Normal bladder from wild type mice

value: WT


title: patient 4004 9 mo post tx 3mo post Tac w/d

description:
4004v10
mRNA

value: 9 mo post tx, 3mo post Tac w/d


title: Wild type; BBN, biological rep2

source_name: Bladder cancer from wild type mice


title: PAI-1 KO; control, biological rep2


title: Wild type; control, biological rep2


title: patient 1001 9 mo post tx 3mo post Tac w/d

description:
1001v10
mRNA


title: donor 2_GalNAcβ1-4Gal_no LPS, moDCs

city: Amsterdam

first: Anouk

last: Zaal

address: Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

data_processing:
library strategy: RNA-Seq (CAGE)
Trimming reads for quality using Sickle --> trimmed fastQ files
read and sequence allignment using STAR 2.5.4a to create SAM files
SAMtools 1.3.0 was used to generate BAM files from the SAM files
Feature counts (R package Subread 1.26.1, R 3.4.0) was used to quantify aligned reads. Multimapping and multi-overlag genes were excluded as decribed in Subread user guide.
R package EdgeR (version 3.18.1) was used to adjust for libery size and trimmed mean of M-values (TMM) Normalization. Gnes were filtered and kept if expression was greater than 1 count per million (CPM) in at least 3 samples.
R package EdgeR (version 3.18.1) was used to build a generalized linear model (GLM) to identify the significant differentially expressed genes
Genome_build: Ensemble human genome GRCh38.p10 release 90
Supplementary_files_format_and_content: txt format file with normalized counts created with EdgeR. The content includes sample names, genes and normalized counts for every read.

molecule: polyA RNA

source_name: monocyte-derived dendritic cells

growth_protocol: Monocyte-derirved dendritic cells were generated by culturing isolated monocytes for 4 days with IL-4 and GM-CSF.

extract_protocol:
Dendritic cells were harvested and washed with ice-cold PBS after 4 h of dendrimer stimulation, and pooled to obtain sufficient amounts of RNA. Total RNA was extracted with a standard TRIzol isolation protocol (Thermo Fisher Scientific, cat#15596018).
To prepare the mRNA library, 2 μg RNA per sample was used. The library was synthesized using the TruSeq® Stranded mRNA Sample preparation kit (Illumina , cat# RS-122-9004), according to manufacturer’s LS protocol.

treatment_protocol: Stimulation for 4 h with plate-bound control, αGalNAc or GalNAcβ1-4Gal glycodendrimers in the absence or presence of LPS

tag: dendrimer

tag: additional stimulus

value: no

tag: donor

value: donor 2

value: monocyte-derived dendritic cells


title: donor 2_GalNAcβ1-4Gal_LPS, moDCs

value: LPS


title: donor 3_GalNAcβ1-4Gal_LPS, moDCs

value: donor 3


title: patient 4006 6 mo post tx pre Tac w/d

description:
4006v06
mRNA

value: No withdrawal (NW)

value: 6 mo post tx, pre Tac w/d


title: donor 1_GalNAcβ1-4Gal_LPS, moDCs

value: donor 1


title: patient 5007 9 mo post tx 3mo post Tac w/d

description:
5007v10
mRNA


title: Wild type; BBN, biological rep1

value: bladder


title: PAI-1 KO; BBN, biological rep2

value: PAI-1 KO


title: Input DNA ChIP-Seq P14 replicate 1

source_name: Input DNA ChIP-Seq P14

value: F1 mice (C57Bl6/CBA)

value: 14 days postnatal

value: Wild type

value: liver


title: patient 1001 6 mo post tx pre Tac w/d

description:
1001v06
mRNA

value: PBMC


title: donor 1_GalNAcβ1-4Gal_no LPS, moDCs


title: donor 2_αGalNAc_LPS, moDCs

value: αGalNAc


title: donor 3_αGalNAc_no LPS, moDCs


title: donor 3_control_no LPS, moDCs

value: control


title: donor 1_αGalNAc_LPS, moDCs


title: donor 1_αGalNAc_no LPS, moDCs

value: no


title: donor 2_control_LPS, moDCs

value: donor 2


title: donor 2_αGalNAc_no LPS, moDCs

value: monocyte-derived dendritic cells


title: donor 1_control_no LPS, moDCs


title: patient 5007 6 mo post tx pre Tac w/d

description:
5007v06
mRNA


title: donor 1_control_LPS, moDCs

value: LPS


title: hFmiPS2_E8LN_rep2

description:
TN1510R0122_GCCAAT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_10W_LN

value: human pluripotent stem cells

value: untreated


title: hFmiPS2_E8VN_rep1

description:
TN1510R0118_TTAGGC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_1W_VN


title: hFmiPS2_KSR_rep2

description:
TN1510R0120_ACAGTG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_10W_STO


title: hFmiPS2_E8LN_rep1

description:
TN1510R0119_TGACCA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_1W_LN


title: hFmiPS2_E8VN_rep2

description:
TN1510R0121_ATTCCT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_10W_VN


title: donor 3_GalNAcβ1-4Gal_no LPS, moDCs

value: donor 3


title: hFSiPS1_E8LN_rep2

description:
TN1510R0116_ATCACG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_10W_LN


title: hFSiPS1_E8LN_rep1

description:
TN1510R0113_GAGTGG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_1W_LN


title: hFSiPS1_E8VN_rep2

description:
TN1510R0115_ATTCCT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_7W_VN


title: hFSiPS1_E8VN_rep1

description:
TN1510R0112_CGTACG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_1W_VN


title: hFmiPS2_KSR_rep1

description:
TN1510R0117_CGATGT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFmiPS2_1W_STO


title: hFSiPS1_KSR_rep1

description:
TN1510R0111_GTTTCG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_1W_STO


title: H9_E8LN_rep2

description:
TN1510R0110_GTGGCC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_10W_LN

value: human embryonic stem cells


title: H9_E8LN_rep1

description:
TN1510R0107_CCGTCC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_1W_LN


title: donor 3_αGalNAc_LPS, moDCs


title: H9_E8VN_rep1

description:
TN1510R0106_ATGTCA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_1W_VN


title: H9_KSR_rep2

description:
TN1510R0108_GTCCGC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_10W_STO


title: SNUhES31_E8LN_rep2

description:
TN1510R0104_AGTCAA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_10W_LN


title: SNUhES31_E8LN_rep1

description:
TN1510R0101_TAGCTT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_1W_LN


title: H9_KSR_rep1

description:
TN1510R0105_AGTTCC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_1W_STO


title: donor 2_control_no LPS, moDCs


title: SNUhES31_E8VN_rep2

description:
TN1510R0103_CTTGTA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_10W_VN


title: SNUhES31_KSR_rep1

description:
TN1510R0099_ACTTGA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_1W_STO


title: donor 3_control_LPS, moDCs


title: hFSiPS1_E8LN_5%FBS_3W_rep1

description:
12_1_CGTACG_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
12-1_E8-LN_5%FBS_3W

value: differentiated with 5% FBS for 3 W


title: hFSiPS1_KSR_rep2

description:
TN1510R0114_ACTGAT
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
hFSiPS1_10W_STO


title: hFSiPS1_E8LN_5%FBS_2W_rep2

description:
11_2_GTTTCG_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
11-2_E8-LN_5%FBS_2W

value: differentiated with 5% FBS for 2 W


title: hFSiPS1_E8LN_5%FBS_1W_rep1

description:
10_2_CAGATC_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
10-2_E8-LN_5%FBS_1W

value: differentiated with 5% FBS for 1 W


title: hFSiPS1_E8VN_5%FBS_3W_rep2

description:
08_2_ACTGAT_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
08-2_E8-VN_5%FBS_3W


title: hFSiPS1_E8LN_5%FBS_2W_rep1

description:
11_1_ACTTGA_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
11-1_E8-LN_5%FBS_2W


title: hFSiPS1_E8VN_5%FBS_1W_rep2

description:
06_2_AGTTCC_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
06-2_E8-VN_5%FBS_1W


title: hFSiPS1_E8VN_5%FBS_1W_rep1

description:
06_1_GGCTAC_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
06-1_E8-VN_5%FBS_1W


title: hFSiPS1_E8VN_undiff_rep1

description:
05_1_CGATGT_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
05-1_E8-VN_Undiff


title: SNUhES31_E8VN_rep1

description:
TN1510R0100_GATCAG
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_1W_VN


title: hFSiPS1_KSR_5%FBS_3W_rep2

description:
04_2_GTGGCC_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
04-2_KSR-STO_5%FBS_3W


title: hFSiPS1_E8VN_undiff_rep2

description:
05_2_TGACCA_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
05-2_E8-VN_Undiff


title: hFSiPS1_E8VN_5%FBS_2W_rep1

description:
07_1_ATGTCA_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
07-1_E8-VN_5%FBS_2W


title: hFSiPS1_E8VN_5%FBS_2W_rep2

description:
07_2_GTCCGC_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
07-2_E8-VN_5%FBS_2W


title: hFSiPS1_KSR_5%FBS_2W_rep1

description:
03_1_CTTGTA_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
03-1_KSR-STO_5%FBS_2W


title: hFSiPS1_KSR_5%FBS_2W_rep2

description:
03_2_CCGTCC_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
03-2_KSR-STO_5%FBS_2W


title: hFSiPS1_KSR_undiff_rep2

description:
01_2_ACAGTG_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
01-2_KSR-STO_Undiff


title: H9_E8VN_rep2

description:
TN1510R0109_GTGAAA
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
H9_10W_VN


title: hFSiPS1_KSR_5%FBS_1W_rep1

description:
02_1_GATCAG_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
02-1_KSR-STO_5%FBS_1W


title: SNUhES31_KSR_rep2

description:
TN1510R0102_GGCTAC
processed data file: RNA-seq_FPKM (KSR E8VN E8LN).csv
SNUhES31_10W_STO


title: hFSiPS1_E8LN_5%FBS_3W_rep2

description:
12_2_ATTCCT_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
12-2_E8-LN_5%FBS_3W


title: hFSiPS1_E8LN_undiff_rep2

description:
09_2_GCCAAT_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
09-2_E8-LN_Undiff


title: hFSiPS1_E8LN_undiff_rep1

description:
09_1_TTAGGC_L005
processed data file: RNA-seq_FPKM (5%FBS).csv
09-1_E8-LN_Undiff


title: MM.1S 30 nM carfilzomib 16 h mRNA

city: San Francisco

first: Hector

middle: Han-Li

last: Huang

state: CALIFORNIA

address: 185 Berry St, Ste 290/Rm 2410

department: Laboratory Medicine

institute: University of California San Francisco

description: MM.1S 30cfz 16h

data_processing:
Alignment: four libraries from timecourse study were aligned with Bowtie v0.12.8 allowing for up to two mismatches.  Aligned rRNA and tRNA reads were discarded.  Remaining transcripts were aligned to known canonical transcripts to human genome draft GRCh37/hg19 .  All other libraries were aligned with HISAT v2.1.0.
Compression: The mapped reads were converted from sequence alignment map format to binary alignment map format using Samtools (v1.3.1 for timecourse samples and v0.1.19 for all others).
Assembly and Expression: transcriptome assembled and abundance quantified for four libraries from timecourse study by in-house C++ scripts, which assign and count unique reads mapping to canonical hg19 transcripts. Only uniquely mapping reads were used for analysis.  All other binary alignment mapped reads were quantified for gene-level expression with HTSeq-0.7.2
Differential Expression: Differential gene expression analysis for single timepoint response study was performed in R with DESeq2
Alternative splicing analysis: For all mapped reads, except for the timecourse study, alternative splicing events were quantified through JuncBASE v1.2-beta using default parameters.  Intron-exon junction database was created from hg19 annotations.  T-test was used to compare number of inclusion and exclusion reads and p-values were adjusted with Benjamini-Hochberg correction.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: "delink_c2g_fw5rv_xpr.txt" in-house C++ scripts output with UCSC Gene ID, raw reads, and normalized RPKM.  Conversion tables available from UCSC through the kgXref function were used to convert UCSC gene ID to HUGO gene nomenclature and to UniProt accession number for further analysis
Supplementary_files_format_and_content: "juncbase_tables…tsv" JuncBASE alternative splicing output with gene symbols, Known annotated or Novel splice site, splicing event type, chromosome number, strand, junction coordinates, percent spliced in (PSI) value for each sample replicate, comparison sample set medians, the difference in percent spliced in between the medians of two comparison sets, statistical T-test p-value, and B-H corrected p-value.  Each JuncBASE file compares two conditions and is associated with six samples from the two conditions (exccept "AMO1_all_constructs_DMSO_vs_AMO1_all_constructs_15cfz" which pools 24 samples from AMO1_parent, WT, SD, and SA for both DMSO and 15 nM cfz").  Set1_med and Set2_med are median PSI for samples in each condition.  Extraneous columns for other conditions not associated with the JuncBASE file were processed together and left in the table, but do not participate in the comparison.
Supplementary_files_format_and_content: "deseq2_counts.csv" DESEQ2 output tables with Gene Symbol, log2(fold change) for each gene between two comparing conditions, the standard error for the log2 change and the statistical p-value for that comparison and the multiple comparison adjusted p-value.

source_name: MM.1S myeloma cell line

growth_protocol: Timecourse MM.1S cultures were grown in RPMI-1640, 10% FBS, 1% Pencillin-Streptomycin.  Single time point MM.1S and AMO-1 cultures were used for concurrent global proteomics and phosphoproteomics analysis and grown in SILAC media with dialyzed FBS, 1% pencillin streptomycin and supplemented with either Lysine and Arginine (for drug treated samples) or Lys8 and Arg10 (for isotopically heavy labeled protein DMSO) samples.  AMO-1 SRSF1 samples were engineered to overexpress either wildtype SRSF1 (WT) or phosphomimetic (SD) or phosphodead (SA) RS domain mutants and were grown in RPMI-1640, 10% FBS, 1% Penicillin-Streptomycin.  All cells were passaged every 2-3 days and disposed after 50 passages.

extract_protocol:
Total RNA was extracted by standard RNA extraction kit (RNeasy, Qiagen) and cleaned up with RNA clean & concentrator columns (Zymo).  For all except the timecourse samples, polyA-mRNA was enriched from total RNA with polyA-binding magnetic bead protocol (NEB).
RNA libraries were prepared for sequencing using standard Illumina protocols and Hyper Prep RNA sequencing kit (Kapa, with RiboErase for timecourse samples to remove abundant rRNA).  Protocol aimed at generating 200-300 bp fragments.  Reverse-transcribed cDNA was ligated to TruSeq barcode adapters for Illumina platform.  200-400 bp cDNA libraries were selected by PAGE extraction and purification, or AMPure bead size selection in the case of SRSF1 overexpression samples.  Four samples were multiplexed in a single lane for sequencing for the timecourse samples, seven samples were multiplexed for the single timepoint samples, and 9 samples were multiplexed for the SRSF1 overexpression samples.

treatment_protocol: Timecourse MM.1S cultures were treated with 30 nM carfilzomib and harvested after 0, 8, 16, or 24 h treatment in a single biological replicate.  Single timepoint cultures were harvested after 24 h of drug (or DMSO) treatment) in 3 biological replicates.  AMO-1 SRSF1 expressing cultures were also treated with either 15 nM carfilzomib or DMSO for 24 h and harvested in 3 biological replicates.

tag: cell line

tag: experiment

value: timecourse gene expression

tag: timepoint

tag: drug

value: 30 nM carfilzomib


title: MM.1S 30 nM carfilzomib 08 h mRNA

description: MM.1S 30cfz 08h

value: 8 h


title: MM.1S 30 nM carfilzomib 00 h mRNA

description: MM.1S 30cfz 00h

value: 0 h (untreated)


title: Whole blood, D, O, sample_48

city: Bialystok

first: Magdalena

last: Paczkowska-Abdulsalam

address: M. Sklodowskiej-Curie 24A

country: Poland

institute: Medical University of Bialystok

description: rnaseq.txt

data_processing:
Illumina BaseSpace Onsite version 2.0 was used for base-calling.
The reads were aligned against Homo sapiens reference genome (Ensembl GRCh37 release) with STAR version 2.5.1b using the 2-pass alignment mode.
The number of reads aligned within each gene was counted using HTSeq tool version 0.5.4p3.
The counts were normalized using TMM normalization methods of the edgeR R/Bioconductor (R version 3.2.0, Bioconductor version 3.1).
Genome_build: Ensembl GRCh37 release
Supplementary_files_format_and_content: Tab-delimited text file with TPM values for each sample

source_name: Whole blood

extract_protocol:
PAXgene Blood RNA, PreAnalytix/Qiagen
TruSeq Stranded mRNA, Illumina

value: Whole blood

tag: metabolic health (h - healthy, d - disease)

value: D

tag: bmi (o - obese, l - lean)

value: O


title: Whole blood, D, L, sample_47

description: rnaseq.txt

tag: tissue

value: L


title: Whole blood, D, O, sample_44

description: rnaseq.txt


title: MM.1S 30 nM carfilzomib 24 h mRNA

description: MM.1S 30cfz 24h


title: Whole blood, H, O, sample_43

description: rnaseq.txt

value: H


title: Whole blood, D, O, sample_35

description: rnaseq.txt


title: Whole blood, H, L, sample_32

description: rnaseq.txt


title: Whole blood, H, O, sample_33

description: rnaseq.txt


title: Whole blood, D, L, sample_34

description: rnaseq.txt


title: hFSiPS1_KSR_undiff_rep1

description:
01_1_ATCACG_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
01-1_KSR-STO_Undiff

tag: cell type


title: Whole blood, H, O, sample_29

description: rnaseq.txt


title: Whole blood, H, L, sample_36

description: rnaseq.txt


title: Whole blood, H, O, sample_39

description: rnaseq.txt


title: Whole blood, H, O, sample_25

description: rnaseq.txt


title: hFSiPS1_KSR_5%FBS_1W_rep2

description:
02_2_TAGCTT_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
02-2_KSR-STO_5%FBS_1W

tag: treatment


title: Whole blood, H, O, sample_28

description: rnaseq.txt


title: Whole blood, H, L, sample_42

description: rnaseq.txt


title: Whole blood, D, O, sample_22

description: rnaseq.txt


title: Whole blood, D, O, sample_21

description: rnaseq.txt


title: Whole blood, D, L, sample_19

description: rnaseq.txt


title: hFSiPS1_E8VN_5%FBS_3W_rep1

description:
08_1_GAGTGG_L002
processed data file: RNA-seq_FPKM (5%FBS).csv
08-1_E8-VN_5%FBS_3W


title: Whole blood, D, L, sample_24

description: rnaseq.txt


title: Whole blood, D, L, sample_18

description: rnaseq.txt


title: Whole blood, H, L, sample_17

description: rnaseq.txt


title: Whole blood, D, L, sample_46

description: rnaseq.txt


title: hFSiPS1_KSR_5%FBS_3W_rep1

description:
04_1_GTGAAA_L001
processed data file: RNA-seq_FPKM (5%FBS).csv
04-1_KSR-STO_5%FBS_3W


title: Whole blood, H, L, sample_10

description: rnaseq.txt


title: Whole blood, H, L, sample_15

description: rnaseq.txt


title: Whole blood, H, O, sample_9

description: rnaseq.txt


title: Whole blood, D, O, sample_7

description: rnaseq.txt


title: Whole blood, D, O, sample_6

description: rnaseq.txt


title: Whole blood, D, L, sample_8

description: rnaseq.txt


title: Whole blood, H, O, sample_1

description: rnaseq.txt


title: Whole blood, H, L, sample_4

description: rnaseq.txt


title: Whole blood, D, L, sample_5

description: rnaseq.txt


title: HepG2-SC: Scrambled(Control)

city: Incheon

first: Hanhee

last: Jo

address: Academiro 119

institute: Incheon university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

source_name: HepG2 cell line

growth_protocol: HepG2 cells were maintained using RPMI media supplemented with 10% Fetal Bovine Serum(GE healthcare lifescience, chicago, IL, USA) and 1% Penicillin Streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

tag: origin

value: liver

tag: histopathology

value: Hepatocellular carcinoma


title: HepG2-CDK4-6-KD: siCDK4 and siCDK6 transfected


title: HepG2-CTL: DMSO treated


title: HepG2-PD: PD-0332991 treated


title: 002-B_RNA_Gillies_CICPT_175-49180182

city: Tampa

first: Mehdi

last: Damaghi

state: Fl

address: 12906 magnolia dr

institute: Moffitt Cancer Center

data_processing:
Sequence read quality control was conducted by FastQC version 0.11.8 program (Ubuntu OS). The quality of reads were assessed by different parameters.
Trimmomatic 0.39 program was used to trim low quality sequence reads and in order to obtain high quality reads. (ubuntu OS)
Trimmed sequence reads quality assessd after trimming to ensure about trimmed sequence read quality by FastQC version 0.11.8
Clean reads were aligned to the human reference genome (GRCh37) using HISAT2 version 2.1.0 (ubuntu OS)
Read count values for the aligned sequences of genes were computed to represent the expression values of genes using HTSeq version 11.1 (ubuntu OS)
Genome_build: GRCh37
Supplementary_files_format_and_content: Prcessed data files contain raw counts for refseq gene ids in a .txt file in Tab Separated Format

growth_protocol: Normal pH MCF7 cells were grown in DMEM/F12 media with 25 mM Hepes added to it and pH adjusted to 7.4. Acid-adapted MCF7 cells were grwon in acidic media (DMEM/F12 with 25mM HEPES, pH 6.5) for at least 3 month.

extract_protocol:
RNA was extracted from cell pellets using the Trizol reagent following the manufacturer’s protocol.  The RNA was then cleaned up using a Qiagen RNEasy Mini column with a single modification.  After adding RLT, 1225 ul of 100% ethanol was added to the lysate (as opposed to 250 ul), and two subsequent column binding steps were performed.  This ensure that small RNAs were retained during the cleanup. The RNA samples were NanoDrop and Qubit quantitated, and were checked for quality on the Agilent TapeStation with an RNA ScreenTape.
Starting with 100 ng of input, total RNA-seq libraries were prepared using the NuGen Encore Complete RNA-Seq Library system according to the manufacturer’s protocol.  Final libraries were quantitated using the Kapa Library Quantification Kit and prepared for sequencing on a mid-output NextSeq 500 sequencing run.

tag: phenotype

value: Acid adapted MCF7 cell line


title: 003-B_RNA_Gillies_CICPT_175-49177173

value: Non Acid adapted MCF7 cell line


title: piRNA_Day_7_Chondro_donor#2_replicate#1

city: Davos Platz

first: Martin

middle: J

last: Stoddart

address: Clavadelerstrasse 8

country: Switzerland

institute: AO Research Institute Davos

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_34

data_processing:
Illumina NextSeq 500 raw sequencing read datathat passed the Illumina chastity filter were used for the following analysis. Trimmed reads (with 5’,3’-adaptor bases removed) were aligned to the piRBase, which is a manually curated resource of piRNAs. The maximum mismatch <= 2 reads are kept. The alignment statistical analysis was applied to retain the valid sequences for piRNA expression profiling and differential expression analysis. Hierarchical clustering, scatter plots and classification analysis were performed for the differentially expressed piRNAin R or Perl environment for statistical computing and graphics.
Raw data files in FASTQ format were generated by the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted.
After Illumina quality control, the sequencing reads were 5', 3'-adaptor trimmed, filtered for >=15 nt by cutadapt software, and aligned to piRBase (a manually curated resource of piRNAs) using NovoAlign software (v2.07.11) [3].The maximum mismatch <= 2 reads to the piRBase were kept.
After passing the Solexa CHASTITY filtering and 3'-adapter filter, the 3'-adapter trimmed reads were formatted into a non-redundant FASTA file where the copy number and sequence were recorded for each unique read. A bar graph is used to show the sequence read length distribution.
The piRNAs, which total number of sequence reads larger than five, were kept for normalization. The piRNA expression levels were measured and normalized as tag counts per million of total aligned piRNA reads (TPM/CPM). When comparing two groups of profile differences (such as disease versus control) use the normalized tag number of piRNAs, including the tag count of each sample, the "fold change" (i.e. the ratio of the group averages) between the groups for each piRNA is computed. piRNAs having fold changes >= 1.5 or fold changes <= 0.67 are selected as the differentially expressed piRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file with known expression (Reads Count)

source_name: Human mesenchymal stromal cells from bone marrow (vertebra)

growth_protocol: MSCs were seeded at an initial cell density of 3x10^3 cells/cm2 and grown until passage 2 in α-MEM with 10% MSC-qualified FBS, 100 U/mL penicillin, 100 μg/mL streptomycin and 5 ng/ml basic Fibroblast Growth Factor. Cultures were maintained at 37°C/5% CO2, and the medium was refreshed every second day.

extract_protocol:
Total RNA was isolated from day 0 2D and 3D samples collected in TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.
Total RNA of each sample was used to prepare the piRNA-sequencing library, which included the following steps: 1) 3'-adapter ligation; 2) 5'-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~142-153bp PCR amplified fragments (corresponding to ~24-35 nt small RNAs). The libraries are qualified and quantified using Agilent BioAnalyzer2100. The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq follow the manufacturer’s instructions.

treatment_protocol: At passage 3, cells were seeded for the induction of osteogenic or chondrogenic differentiation. For osteogenic differentiation, cells were seeded at a density of 1.5x10^4 cells/cm2 in 6-well plates. After cell attachment the medium was changed: control (CRL) samples were kept in DMEM 1g/l glucose (Gibco), 10% heat inactivated FBS (Gibco), 100 U/mL penicillin and 100 μg/mL streptomycin (Gibco). Osteogenic differentiation was induced by the addition of 50 µg/mL ascorbic acid 2-phosphate, 5 mM β-glycerol phosphate and 10 nM dexamethasone (all from Sigma-Aldrich) to the control medium. Samples were prepared in triplicate for each donor and each condition.   For chondrogenic differentiation, cells were seeded into pellet culture, using 2x10^5 cells/pellet. Cell were directly seeded into either control (CRL) or chondrogenic medium. Control medium was composed by DMEM 4.5 g/l glucose, 100 U/mL penicillin, 100 μg/mL streptomycin, 1% ITS+, and 1% NEAA. Chondrogenic medium was with the addition of 50 µg/mL ascorbic acid 2-phosphate, 100 nM dexamethasone, and 10 ng/ml TGF-β1 (Fitzgerald Industries). The medium was refreshed every second day to ensure to keep stable levels of differentiation factors in the media and samples were collected at day 7 for RNA isolation.

value: 80 years

tag: Sex

value: Male

tag: cell status

value: Chondrogenic differentiation in pellet (day 7)


title: piRNA_Day_7_Chondro_donor#2_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_35

tag: age


title: piRNA_Day_7_Chondro_donor#1_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_17

value: 59 years


title: piRNA_Day_7_Chondro_donor#1_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_16


title: piRNA_Day_7_CRL_pellet_donor#3_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_49

value: 55 years

value: Female

value: Pellet culture control (day 7)


title: piRNA_Day_7_CRL_pellet_donor#2_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_32


title: Whole blood, D, O, sample_13

description: rnaseq.txt


title: piRNA_Day_7_CRL_pellet_donor#2_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_33


title: piRNA_Day_7_Chondro_donor#3_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_53


title: piRNA_Day_7_CRL_pellet_donor#3_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_51


title: piRNA_Day_7_CRL_pellet_donor#1_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_13


title: 004-B_RNA_Gillies_CICPT_175-49186162


title: piRNA_Day_7_Osteo_donor#3_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_46

value: Osteogenic differentiation in monolayer (day 7)


title: piRNA_Day_7_CRL_monolayer_donor#3_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_45

value: Monolayer culture control (day 7)


title: piRNA_Day_7_Osteo_donor#2_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_29


title: piRNA_Day_7_Osteo_donor#1_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_11


title: piRNA_Day_7_Osteo_donor#2_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_28


title: piRNA_Day_7_Osteo_donor#1_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_12


title: piRNA_Day_7_Osteo_donor#3_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_47


title: piRNA_Day_7_Chondro_donor#3_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_52


title: 001-B_RNA_Gillies_CICPT_175-49181183


title: piRNA_Day_7_CRL_monolayer_donor#3_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_44


title: piRNA_Day_7_CRL_monolayer_donor#2_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_25


title: piRNA_Day_7_CRL_monolayer_donor#2_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_26


title: piRNA_Day_7_CRL_monolayer_donor#1_replicate#1

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_8


title: piRNA_Day_7_CRL_monolayer_donor#1_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_9


title: Whole blood, H, L, sample_11

description: rnaseq.txt

value: Whole blood


title: miRNA_Day_7_Chondro_donor#3_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_52

data_processing:
Raw sequencing data generated from Illumina NextSeq 500 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis, we determine whether the results can be used for subsequent data analysis. If so, the expression profiling, differentially expressed miRNA are calculated. The novel miRNA are also predicted.  Hierarchical Clustering, miRNA Target analysis, Target Gene Ontology (GO), Target Pathway Analysis, scatter plots and volcano plots are performed for the differentially expressed miRNA in R or Python environment for statistical computing and graphics.
Raw data files in FASTQ format were generated from the Illumina sequencer. To examine the sequencing quality, the quality score plot of each sample was plotted.
After quality control, the reads were 3’-adaptor trimmed and filtered ≤15 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with bowtie software.
The expression level (Reads count) of miRNA were calculated using mirdeep2.
Differentially expressed miRNAs analyses were performed with R package edgeR. Fold change (cutoff 1.5), p-value ( 0.05) and CPM ( 1 mean in one group) were used for filtering differentially expressed miRNAs.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file with known expression (Reads Count)

extract_protocol:
Total RNA was isolated with TRIreagent following manufacturer's instructions. Briefly, 100 µl of 1-Bromo-3-chloropropane (Sigma-Aldrich, St. Louis, MO, USA) were added to TRIreagent, mixed thoroughly and the samples were centrifuged at 12000 g for 15 min at 4°C. The recovered aqueous phase was mixed with 500 µl of 2-propanol (Sigma-Aldrich) and precipitation of RNA was carried out overnight at -20°C for enhanced recovery of small RNA species. RNA pellet was then washed with 75% EtOH (Sigma-Aldrich) and resuspended in 20 µl of DEPC-treated H2O. Total RNA concentration was measured with NanoDrop 1000 (Thermo Fisher) and purity was assessed by evaluation of the A260/280 and A260/230 ratios.
Total RNA of each sample was used to prepare the miRNA sequencing library, which included the following steps: 1) 3’-adaptor ligation; 2) 5’-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of 135~155 bp PCR amplified fragments (corresponding to 15~35 nt small RNAs). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer’s instructions. Agilent 2100 Bioanalyzer was used for assessment of the quality of sequencing library. Library concentration was determined by qPCR method.


title: miRNA_Day_7_Chondro_donor#3_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_53


title: miRNA_Day_7_Chondro_donor#2_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_35


title: miRNA_Day_7_Chondro_donor#2_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_34


title: miRNA_Day_7_Chondro_donor#1_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_16


title: piRNA_Day_7_CRL_pellet_donor#1_replicate#2

description:
All_Differentially_Expressed_piRNA.xlsx
sample name:
Sample_15


title: miRNA_Day_7_Chondro_donor#1_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_17


title: miRNA_Day_7_CRL_pellet_donor#2_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_33


title: miRNA_Day_7_CRL_pellet_donor#3_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_49


title: miRNA_Day_7_CRL_pellet_donor#2_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_32


title: miRNA_Day_7_CRL_pellet_donor#3_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_51


title: miRNA_Day_7_CRL_pellet_donor#1_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_15


title: miRNA_Day_7_CRL_pellet_donor#1_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_13


title: patient 4006 9 mo post tx 3mo post Tac w/d

description:
4006v10
mRNA

value: PBMC

tag: tacrolimus withdrawal

value: No withdrawal (NW)

tag: time point

value: 9 mo post tx, 3mo post Tac w/d

tag: patient id


title: miRNA_Day_7_Osteo_donor#3_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_47

tag: donor


title: miRNA_Day_7_Osteo_donor#3_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_46


title: miRNA_Day_7_Osteo_donor#2_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_29


title: miRNA_Day_7_Osteo_donor#2_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_28


title: miRNA_Day_7_Osteo_donor#1_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_11


title: miRNA_Day_7_CRL_monolayer_donor#3_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_45


title: miRNA_Day_7_CRL_monolayer_donor#2_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_26


title: miRNA_Day_7_CRL_monolayer_donor#2_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_25


title: T1D Subject. 3

city: Naples

first: Mario

last: Galgani

address: via S. Pansini, 5

country: Italy

institute: IEOS Istituto per l'endocrinologia e l'oncologia sperimentale

data_processing:
Raw data were processed by Bcl2Fastq 2.0.2 version of the Illumina pipeline for both format conversion and de-multiplexing and lower quality bases and adapters were removed by ERNE and Cutadapt software.
On average 30M of reads were produced per sample (min 29.1M, max 32.5M). Reads were then deduplicated based on unique molecular identifier (UMI) composed of 8 random bases for unambiguous identification of unique library molecules.
Reads were aligned on reference GRCh38 genome/transcriptome with STAR.
Full-length transcripts representing multiple spliced variants for each gene locus were assembled and quantified by Stringtie and RNA-Seq data was preprocessed by counting the overlap of reads with genes through htseq-count.
DESeq2 was used to perform comparisons between expression levels of genes and transcripts. Normalization was performed using the median-of-ratios method.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

source_name: TR3-56 cells

extract_protocol:
TR3-56 cells were flow sorted, a cell suspension was prepared and RNA was extracted using the RNeasy Micro Kit from QIAGEN, according to manufacturer’s instructions. RNA samples were then quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA).
Libraries were prepared by the ‘Ovation SoLo RNA-seq Library Preparation kit’ (NuGEN, San Carlos, CA), following the manufacturer’s instructions and checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA).
Libraries were then processed and sequenced on single-end 1x75 mode on NextsSeq500 (Illumina, San Diego, CA) following the manufacturer’s instructions.

tag: subject ethnicity

value: Caucasian

tag: subject status

value: T1D Subject

value: Flow sorted TR3-56 cells


title: miRNA_Day_7_CRL_monolayer_donor#1_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_9


title: miRNA_Day_7_Osteo_donor#1_replicate#2

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_12


title: T1D Subject. 2


title: Healthy Subject.3

value: Healthy Subject


title: T1D Subject. 1


title: Healthy Subject.2


title: miRNA_Day_7_CRL_monolayer_donor#1_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_8


title: WTN_rep3

first: Menno

last: de Winther

address: Meibergdreef 9

department: Medical Biochemistry

institute: Academic Medical Center University of Amsterdam

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Reads were aligned to the mouse genome mm10 by STAR 2.5.2b
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.3.1
Raw tag counts per gene were counted using HOMER2’s analyzeRepeats.pl script
Genome_build: mm10
Supplementary_files_format_and_content: matrix of read counts per gene

source_name: Bone marrow-derived macrophages

extract_protocol:
RNA was extracted uisng the Qiagen RNAeasy mini kit
Libraries were constructed using the KAPA HyperPrep mRNA kit

tag: genotype

value: WT

value: Naive


title: WTN_rep2


title: WTN_rep1


title: KON_rep3

value: KO


title: KON_rep2


title: KON_rep1


title: Stem4

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

description: Replicates of mouse DG Stem cells

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Genome_build: GRCm38p4
Supplementary_files_format_and_content: TSV Counts tables generated using Subread FeatureCounts, Unfiltered

source_name: Mouse Dente Gyrus

extract_protocol:
Cells were resuspended in PBS without calcium/magnesium and filtered through a 35µm nylon filter before staining with the following antibodies: O4-APC (1:100, R&D FAB1326A), O1-eFluor660 (1:100, Thermo Fisher/eBioscience, Pittsburgh, PA, 5065082), GLAST-PE (1:50, Miltenyi Biotec, Bergisch Gladbach, Germany, 130-098-804), CD45-APC (1:100, BD Biosciences, Franklin Lakes, NJ, 561018), CD31-APC (1:100, BD Biosciences, Franklin Lakes, NJ, 561814). Cells were incubated with antibodies on ice for 30 minutes. During the last 10 minutes of staining, Hoechst dye (1:10,000, Thermo Fisher, Pittsburgh, PA, 33342) was added for live/dead discrimination. All cells were washed twice following staining and immediately sorted as stem, progenitor, or astrocyte populations based on fluorescent markers with the FACSAria III (BD Biosciences, Franklin Lakes, NJ). CD31, CD45, O1, and O4 negative live cells were designated as stem cells if double positive for GLAST and GFP, progenitors if only GFP positive, and astrocytes if only GLAST positive. For cells in the limited cell number study, 50 cells were sorted into 96 well format plate for downstream lcRNA-seq library generation.
The Clontech SMARTer v4 kit (Takara Bio USA, Inc., Mountain View, CA) was used for direct global preamplification in FACS-derived murine DG cell types prior to library generation at triplicate with the Nextera XT DNA Library Prep kit (Illumina, Inc., San Diego, CA).
Low Input RNA-Seq

value: Stem Cell


title: Stem3

description: Replicates of mouse DG Stem cells


title: Stem1

description: Replicates of mouse DG Stem cells


title: Stem2

description: Replicates of mouse DG Stem cells


title: miRNA_Day_7_CRL_monolayer_donor#3_replicate#1

description:
All_Differentially_Expressed_miRNA.xlsx
sample name:
Sample_44

value: 55 years


title: Progenitor4

description: Replicates of mouse DG Progenitor cells

value: Progenitor


title: Progenitor2

description: Replicates of mouse DG Progenitor cells


title: Progenitor1

description: Replicates of mouse DG Progenitor cells


title: Astrocyte2

description: Replicates of mouse DG Astrocyte cells

value: Astrocyte


title: Astrocyte4

description: Replicates of mouse DG Astrocyte cells


title: Tumor4

city: SOUTH SAN FRANCISCO

first: Kobe

last: Yuen

state: California

address: 1 DNA WAY

department: Oncology Biomarker Development

institute: Genentech

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq". Expression data processed with "cellranger count" using a custom reference package of 30,727 genes from RefSeq gene models
Genome_build: hg38
Supplementary_files_format_and_content: Cellranger version 3.0.3

source_name: renal tumor

growth_protocol: procured matched blood and tumor samples were used. No further cell culture was performed.

extract_protocol:
fresh samples containing at least 1 million cells were thawed for 1 minute at 37°C and washed twice with RPMI complete media (RPMI containing 10% fetal bovine serum with 2 mM L-glutamine and Pen/Strep). Samples with >50% red blood cells were treated with RBC Lysis buffer for 3 minutes at RT to remove red blood cells and then washed one more time with RPMI complete media. The cell density and viability of the single-cell suspension were then determined by Vi-CELL XR cell counter (Beckman Coulter, Pasadena, CA). All of the samples had >80% viable cells. Sample processing for single-cell RNA-seq was done using Chromium Single Cell 3’ Library and Gel bead kit v2 following the manufacturer’s user guide (10x Genomics)
The total cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~ 6,000 cells per sample. cDNAs and libraries were prepared following the manufacturer’s user guide (10x Genomics). cDNA amplification and indexed libraries were prepared using 12 and 14 cycles of PCR, respectively.

treatment_protocol: No treatment was performed.

tag: patient

value: male

value: renal tumor


title: Tumor3

tag: tissue


title: Tumor2

value: female


title: Tumor1


title: Blood3

source_name: Blood

value: Blood


title: Blood2


title: Blood1


title: Blood4


title: 4-month-old_leaf 3

city: Kusatsu, Shiga

first: Midori

last: Tabara

address: 1-1-1, Noji-Higashi

country: Japan

institute: Ritsumeikan University

data_processing:
Illumina Casava ver.1.8.2 software was used for base calling.
Sequenced reads were mapped to the petunia genome using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19 (Trapnell et al., 2009). Since the genome of Petunia hybrida was amphidiploid of Petunia axillaris and Petunia inflata, genome data was prepared to merge these genome datasets (P. axillaris, v1.0.1; P. inflata, v1.6.2; Sol Genomic Network https://solgenomics.net/).
The number of fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cuffnorm ver. 2.2.1 (Trapnell et al., 2010).
Genome_build: P. axillaris, v1.0.1; P. inflata, v1.6.2; Sol Genomic Network https://solgenomics.net/
Supplementary_files_format_and_content: FPKM

organism: Petunia x hybrida

extract_protocol:
Total RNAs were extracted by using the Trizol reagent following the manufacturer’s protocol (Thermo Fisher Scientific, MA).
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

tag: cultivar

value: Rondo Rose-star

value: leaf


title: 2-month-old_leaf 3


title: 4-month-old_leaf 2


title: 2-month-old_leaf 2


title: 2-month-old_leaf 1