title: Th17_miR29WT_1.1

city: San Francisco

first: Robin

last: Kageyama

state: California

address: 513 Parnassus Ave

institute: University of California San Francisco

data_processing:
Samples were split using the fastx_barcode_splitter
Linker sequences were removed using cutadapt: GTGTCTTTACACAGCTACGGCGTCG
Linker dimer reads were discarded and one uniquely aligning read with a given di-nucleotide randomer in the 3' RNA linker was kept for further analysis to remove PCR duplicates
Samples were aligned to the genome using bowtie2: bowtie2 -x mm10  -q --trim3 2 --phred33 --time -p 4 -
Genome_build: mm10
Supplementary_files_format_and_content: bw

source_name: CD4+ T cells

extract_protocol: Cells were lysed by resuspension in PXL buffer without SDS. Cell debris was pelleted and lysate was treated with magnetically bound AGO2 antibody (Wako). Beads were treated to an on bead ligation of radiolabeled 3' linker RNA. RNA was removed from beads and run on a size selecting SDS-PAGE gel, and AGO2-RNA complexes were selected. RNA gel extracted and treated with proteinase K, and treated with a 5' linker before reverse transription and used for cDNA amplification.

treatment_protocol: Four hours before harvest cells were re-plated in fresh medium (resting) or re-stimulated with PMA/Ionomycin (stimulated). Cells were crosslinked with 800 mJ high energy (254 nM) UV light


title: Genomic DNA.Sample 39

status: Public on Aug 12 2019

type: genomic

city: Toronto

first: Cynthia

last: Hawkins

address: 686 Bay Street

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium® HumanMethylation450 BeadChip using standard Illumina protocol

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

data_processing:
Raw data was processed  with minfi package, with Noob (normal-exponential out-of-band) normalisation and  probes with a SNP at or near the CpG, plus those on the X and Y chromosomes were removed. All bioinformatics was completed using R studio.
Noob-normalized average beta in processed data file.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Glioma Tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using the Qiagen QIAamp DNA FFPE Tissue Kit under manufacturer specification.

tag: tissue

value: pediatric low-grade glioma


title: Liver_Control_Rep 2

type: RNA

city: Columbia

first: Diego

last: Altomare

state: SC

address: 715 Sumter Street, Room 617

department: Department of Drug Discovery and Biomedical Sciences

country: USA

institute: University of South Carolina

description: Gene expression of liver from LDLR knockout mice transplanted with bone marrow cells isolated from wild type mice

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >11.5 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then immersed in acetonitrile and dried immediately by slowly removing the slide.

scan_protocol: Slides were scanned immediately after washing on an Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green at 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software  10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid 028005_D_F_20130207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Data was uploaded into Genespring version 11.5.1 where it was log2 transformed, quantile normalized and base line transformed using the median of all samples. Data was filted by flags in a way that at least 75% of the samples in any of the experimental groups had DETECTED flags. Then, differentially expressed genes were determined.

molecule: total RNA

organism: Mus musculus

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from wild type mice, Replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with a NanoDrop 2000c Spectrophotometer.

growth_protocol: Seven week-old female LDLR−/− mice were obtained from Jackson Laboratories (Bar Harbor, Maine). All mice were kept under specific pathogen-free conditions in a temperature controlled environment at the University of South Carolina according to National Institutes of Health (NIH) guidelines. Animal care and experiments were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of South Carolina

extract_protocol: Total RNAs were isolated from liver tissue using RNeasy Mini kit (Qiagen, Germantown, MD) following the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with an Agilent 2100 Bioanalyzer.

treatment_protocol: 8 week-old female LDLR−/− mice on C57BL/6J background were lethally irradiated  and reconstituted with a wild type (TTP+/+) or TTP knockout (TTP−/−) bone marrow cells. Four weeks after bone marrow transplantation, the mice started to be fed a Western diet for 12 weeks.

tag: genotype/variation

value: LDLR knockout

value: Liver

tag: gender

value: female

tag: age

value: 24 weeks of age


title: 904 IL4

type: SRA

city: Grand Rapids

first: Sonia

last: George

state: MI

address: 333 Bostwick Ave

institute: Van Andel Research Institute

library_source: transcriptomic

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Following sequencing, paired-end fastq files were aligned to the GRCm38 primary assembly with STAR v2.5
Alignments (bam files) were converted to feature counts using HTSeq v0.6.0 referenced against the ENSEMBLE annotation of mm10: GRCm38.95.chr.gtf counting against the feature “exon”, grouped by “gene_id”, and using the strand parameter “reverse” (supplemental material). This set included exon locations for 54,752 genomic entities including pseudogenes, lncRNAs, and 21,949 protein coding genes. The resulting gene_id counts were normalized using edgeR (TMM) and tested for significant differential expression with Limma and Voom in R (v3.3.1)
Prior to statistical testing, genes without more than 0.1 counts per million (CPM) in at least 3 samples were excluded (giving 24,227 genes). Three contrasts were made comparing each pairwise combination of LPS, IL-4, and PBS treatment groups for differential gene expression. A significance threshold of FDR = 0.05 was used with a secondary abs(log2FC) > 1 filter was used to define the highest magnitude changes.
After the PBS group was excluded from further analysis an additional minimum average expression filter of log2CPM > 0 in either the LPS or IL-4 groups was imposed. Expression values (log2CPM) for each sample are included as supplemental data. Some expression data was later converted to FPKM or z-scores for later visualization and comparison.  Z-scores were calculated based on the mean and standard deviation of the IL-4 treatment group only.
Gene ontology enrichment analysis was done using String v.111.0 {Szklarczyk:2015cn} against a background of the 15,938 minimally expressed genes. Genes set enrichment (GSEA, Broad, V3.0) [ https://doi.org/10.1073/pnas.0506580102] was also used to identify affected pathways with both unranked (log2CPM) and preranked (FDR) analysis. Included as supplemental figure are the highest results based on the unranked GSEA. Grouping of enriched biological pathways was done using the Cytoscape (V3.7.1) with the add-on Autoannotate [PMID: 27830058] and c5.bp.v6.2.symbols.gmt. Finally, a subset of biological process gene sets were downloaded from Amigo2 (v2.5.12) for Fig. 6e.
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel file with raw counts and statistical analysis

source_name: brain-striatum

extract_protocol:
Total RNA was extracted from brain homogenates from the ipsilateral striatum from control, LPS and IL-4 injected mice using the QIAshredder and RNeasy micro kit with on-column DNAse treatment, (QIAGEN) according to manufacturer’s protocol. The samples used for RNA-seq were from the biochemistry cohort of animals, separate from the set of mice used for immunohistochemistry and confocal analysis. Quality was assessed by Bioanalyzer (Agilent Technologies) and samples with an RIN >8 were used for library construction.
Libraries were prepared by the Van Andel Genomics Core from 500 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboseErase (v1.16) (Kapa Biosystems). RNA was sheared to 300-400 bp. Prior to PCR amplification, cDNA fragments were ligated to Bioo Scientific NEXTflex dual adapters (Bioo Scientific). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer using an SP 100 cycle kit (Illumina Inc).

value: ipsilateral striatum

value: 10-14 weeks old

tag: treatment

value: AAV over expression, neural graft, inflammatory injection

tag: injected with

tag: strain


title: 50 hpf asb2b mutant hearts

city: Bad Nauheim

first: Ryuichi

last: Fukuda

state: Select...

address: Ludwigstrasse 43

country: Germany

institute: Max Planck Institute for Heart and Lung Research

hyb_protocol: For the hybridisation the Agilent Gene Expression Hybridisation Kit (Agilent Technologies)  is used following the manufacture's protocol. For example, 600 ng cRNA is hybridised on a  8x60K microarray at 65  C for 17 h using Agilent`s recommended hybridisation chamber and  oven. Finally the microarray is washed once with the Agilent Gene Expression Wash Bu er 1  for one minute at ambient temperature followed by a second wash with preheated (37  C)  Gene Expression Wash Bu er 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent  Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and  5 micron for HD Microarray formats, generating a 20 bit TIFF  le respectively.

data_processing: Data of all samples are quantile normalised using the ranked median quantiles according to  Bolstad et al. \A comparison of normalisation methods for high density oligonucleotide array  data based on variance and bias, Bioinformatics (19), 2003, Oxford Univ Press. Briefly, the mean signal of each target is ranked relative to all other targets.

organism: Danio rerio

source_name: 50 hpf zebrafish hearts

label_protocol: The Low Input QuickAmp Labeling Kit (Agilent Technologies) is used for generation of    uorescent cRNA (complementary RNA) following the manufacture's protocol. For 1st strand  synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer)  is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled  with cyanine 3-CTP is performed.

extract_protocol: Qiagen RNA extraction kit

value: heart

tag: genotype

value: asb2b mutant

tag: developmental stage

value: 50 hpf


title: Liver_Control_Rep 3

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from wild type mice, Replicate 3


title: Liver_Control_Rep 4

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from wild type mice, Replicate 4


title: Liver_Control_Rep 1

source_name: Liver from LDLR knockout mice transplanted with bone marrow cells isolated from wild type mice, Replicate 1


title: Th17_miR29KO_1.1


title: Genomic DNA.Sample 38


title: ZNF763 ChIPexo

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

library_source: genomic

data_processing:
Reads were mapped to the human genome (hg19) using Bowtie2 (v2.2.1) in sensitive mode (bowtie2 -p 6 --sensitive-local -x $index -U $reads). For ChIPexo –very-sensitive-local was used.
For ChIP-seq, reads with mapping quality lower than 10 were removed from the analysis.
Peaks were called using MACS v1.4 with default parameters. For ChIP-exo, the “--keep-dup all” was added.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *_peaks.bed: Bed files as output by MACS.

source_name: transduced 293T cell line

growth_protocol: Human embryonic kidney-derived 293T cells were maintained in Dulbecco's modified Eagle's complete medium supplemented with 10% fetal bovine serum, 0.29 mg/ml L-glutamine, and 100 U/ml penicillin-streptomycin at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Chromatin was prepared by resuspending 3x10e7 293T cells in 6 mL of PBS, adding 375 µL of methanol-free formaldehyde (16% - 1% final) and incubating for 10 min on a rotating wheel, quenching with Tris pH 8.0 (250 mM final) for 10 min on a rotating wheel, rinsing with PBS twice and freezing the pellet at -80°C. Nuclear extraction was performed as follows: fixed cell pellets were thawed on ice and resuspended in 1.5 mL of LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP40, 0.25% Tx100) and incubated for 10 min at 4°C on a rotating wheel. The mixture was centrifuged at 1,700g at 4°C, the supernatant removed, the pellet resuspended in 1 mL LB2 buffer (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) and incubated for 10 min at 4°C on a rotating wheel. The same procedure was repeated 2 more times, replacing LB2 with SDS shearing buffer (10 mM Tris pH 8.0, EDTA 1 mM, SDS 0.15%) and the pellet was finally resuspended in 1 mL of this last buffer. Every buffer was prechilled and contained a protease inhibitor cocktail (cOmplete ULTRA Tablets EDTA-free, Roche). The suspension was transferred to a milliTUBE 1 ml AFA Fiber (part #520130) and processed in batch of 24 on an E220 focused-ultrasonicator from Covaris Inc. (Woburn, Massachusetts, USA) with the following settings: 20 min at 5% duty cycle, 140W, 200 cycles. The lysate was transferred to a 1.5 mL Eppendorf, centrifuged at 10,000g for 5 min to clear insoluble material – the supernatant was either frozen at -80°C or used right away for chromatin immunoprecipitation. Quality control was performed on a Bioanalyzer 2100 (Agilent) to verify that most fragments were between 200 and 600 bp. Chromatin immunoprecipitation was performed using anti-HA.11 antibody (clone 16B12, Covance), 15 µg per IP, and Protein G Dynabeads (ThermoFisher).
NextSeq v2 (with Illumina protocol #15048776).

treatment_protocol: Transduced cell lines were selected using puromycin (1 ug/mL) for 7 days and induced using doxycycline (1 ug/mL) for a few days before fixation with formaldehyde (1% for 10 min).

tag: host cell line

value: HEK 293T

tag: transduced kzfp

tag: chip antibody

value: Anti-HA (clone 16B12, Covance)


title: Th2_B6_NoRestim


title: 910 IL4


title: Genomic DNA.Sample 37


title: ZNF729 ChIPexo


title: ZNF724P ChIPexo


title: Th2_B6_6hrStim


title: Th2_B6_2hrStim


title: ZNF578 ChIPexo


title: Genomic DNA.Sample 35


title: 1001 IL4


title: 930 IL4


title: Th2_miR29WT_4.3


title: 1110 LPS

value: LPS


title: Genomic DNA.Sample 34


title: ZNF546 ChIPexo


title: Th2_miR29WT_4.2


title: Genomic DNA.Sample 33


title: 1130 LPS


title: ZNF446 ChIPexo


title: Th2_miR29WT_4.1


title: 1101 LPS


title: Genomic DNA.Sample 36


title: ZNF426 ChIPexo


title: Genomic DNA.Sample 32


title: 703 LPS


title: ZNF416 ChIPexo


title: Genomic DNA.Sample 31


title: Th2_miR29KO_4.3


title: Genomic DNA.Sample 30


title: ZNF34 ChIPexo


title: ZNF577 ChIPexo


title: Genomic DNA.Sample 29


title: Th2_miR29KO_4.2


title: ZNF251 ChIPexo


title: 1103 LPS


title: Th2_miR29KO_4.1


title: Th2_miR29WT_3.1


title: ZNF138 ChIPexo


title: 604 PBS

value: PBS


title: Genomic DNA.Sample 28


title: 630 PBS


title: Th2_miR29WT_2.3


title: ZNF195 ChIPexo


title: Genomic DNA.Sample 27


title: Th2_miR29WT_2.2


title: 1010 PBS


title: 1004 PBS


title: Genomic DNA.Sample 26


title: Th2_miR29WT_2.1


title: Genomic DNA.Sample 25


title: ZKSCAN4 ChIPexo


title: Th2_miR29KO_2.3


title: Genomic DNA.Sample 24


title: RPFA0002_24_1G_BY_FAA4-GFP_to_BY

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

institute: University of Minnesota

data_processing:
Base calls were made on instrument using Illumina Real Time Analysis RTA 2.4.11
Basecalls were converted to Fastq using bcl2fastq v2.20.0.422
Reads were trimmed using trimmomatic version 0.38; using parameters ILLUMINACLIP:Trimmomatic-0.38/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Gene expression was quanitified using kalisto 0.44.0 using parameters kallisto quant -i Saccharomyces_cerevisiae.R64-1-1.cdna.all.kallistoIndex -t 28 --single -l 200 -s 30 --rf-stranded -b 100
Genome_build: sacCer3
Supplementary_files_format_and_content: We combined expression quantifications ("estimated counts" from the kalisto output ) from all samples into one tab-separated file. Sample are in columns and genes are in rows

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: yeast culture

growth_protocol: Yeast cultures were grown in YNB in 1mL of medium in a 2mL deep weel plate. To an average optical density (OD600) of 0.37

extract_protocol:
The plate was centrifuged for 3 min at 2,100g, the supernatant was removed, and each cell pellet was resuspended in 1 ml of H2O and transferred to a 1.5 ml centrifuge tube.  After centrifugation for 2 min at 16,000g, the supernatant was removed and the cell pellet was flash frozen by immersion of the tube in liquid nitrogen and stored at -80. Total RNA was isolated from cell pellets in 5 batches, with each batch containing a sample of each of the 5 strains, using the ZR Fungal/Bacterial RNA mini-prep kit, including the DNase I on-column digestion step (Zymo Research). Cell pellets chosen for RNA isolation had the most uniform OD600 reading across strains, with an average OD600=0.37 (range of 0.34 to 0.40). Each cell pellet was resuspended in lysis buffer and transferred to screw-capped tubes containing glass beads and the cells were broken open using a mini-beadbeater (Biospec Products) in 5 cycles of 2 min bead beating followed by 2 min at -80℃. The total RNA was eluted in 50 ul of DNAse/RNAse free water. Poly-A RNA was extracted from 550 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
PolyA RNA was used as input into the NEB Ultra II Directional RNA library kit for Illumina (NEB E7760) in two batches. NEBNext Multiplex Oligos for Illumina (Dual Index Primers Set1) were used to amplify and barcode the libraries using the following cycling conditions: Initial Denaturation at 98℃ for 30s and 10 cycles of: 98℃ for 10 sec and 65℃ for 75 sec, followed by a 65℃ extension for 5 min. The amplified DNA was quantified using Qubit DNA HS. Sample concentrations ranged from 47-102 ng/ul. An equal concentration of each of the 25 barcoded libraries was pooled and the average fragment size of the library was determined using a Agilent High Sensitivity chip. High-output sequencing was performed on an Illumina NextSeq 550 at the University of Minnesota Genomics Core.


title: RPFA0002_23_2B_BY_OAF1_L63S


title: RPFA0002_25_4D_BY_RGT2_V539I


title: Genomic DNA.Sample 23


title: Genomic DNA.Sample 22


title: ZFP28 ChIPexo


title: RPFA0002_22_2F_BY_OAF1_L63S


title: Th2_miR29KO_2.1


title: R1_EpiSC 1.15_H3K4me3

city: La Jolla

first: Daria

last: Merkurjev

state: CA

address: 9500 Gilman Drive, Mail Code 0648

department: Medicine

institute: UCSD

description:
AGTCAA
EpiSC-15_S14_L002

data_processing:
Reads were aligned to the hg18 human genome with bowtie2 (–very-sensitive option) and tophat. One mismatch was allowed.
Artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data
Read counts were calculated with HOMER 3.9 considering only exonic regions of human RefSeq genes
The bedGraph and bigwig files were generated by using Homer v3.9, which the total tags are normalized to 1.00e+07.
Genome_build: hg18 and mm9
Supplementary_files_format_and_content: bedGraph

source_name: R1 EpiSC 1.15 subline

growth_protocol: hiPSC/hESC lines and sublines were cultured on a feeder layer of gamma-irradiated mouse embryonic fibroblasts (MEFs), and maintained in hESC media made with knockout (KO) Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 10% Plasmanate from Talecris Biotherapeutics; 10% Knockout serum replacement (KOSR) from Gibco; 20 mM GlutaMax, 20 mM nonessential amino acids (NEAA) and 20 mM Pen/Strep from Invitrogen; and, 20 ng/µL FGF from Millipore. Mouse ESCs were prepared in feeder free condition with DMEM-KO supplemented with 15% ESC qualified-fetal bovine serum, 2 mM nonessential amino acids, glutamx, penicillin/streptomycin, 2-mercaptoethanol and 1000u/ml LIF.

extract_protocol:
Cells were fixed with 2mM disuccinimidyl glutarate (DSG) for 45 mins and 1% formaldehyde for 10mins, and followed by glycine for 5 mins. Chromatin DNA was sheared to 200–500 bp average in size by sonication and chromatin was immunoprecipitated with antibodies. Protein A/G beads Sigma were added and incubated overnight at 4°C. After washing and elution, the protein–DNA complex was reverse-crosslinked by heating at 65°C, and immunoprecipitated DNA was purified by using QIAquick Spin column.
ChIP-seq libraries were prepared using the KAPA Library Preparation Kit (KK8201)

treatment_protocol: No particular treatments were applied.

tag: cell line

value: R1 EpiSC subline

tag: chip antibody used for chip or oligonucletides used for chirp (chromatin isolation by rna purification)

value: H3K4me3 (Millipore, 07-473)


title: Sample NTC replicate 1

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description: CRISPR NTC in HEL cells replicate 1

data_processing:
Sequencing was performed using an Illumina HiSeq 2000 in Rapid Run mode and  employed a paired-end, 50 base read length (PE50) sequencing strategy.
RNA-seq reads were aligned to the UCSC hg19 assembly using Tophat2 and counted for gene associations against the UCSC genes database with HTSeq
All data was combined and normalized using a CPM method from the R/Bioconductor package, edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each Sample.

source_name: cell line

extract_protocol:
RNA was extracted from cell cultures every two weeks during the exponential growth phase; RNA was isolated from 0.5-1.0×106 cells. Total RNA was prepared using RNeasy Mini Kit with DNase I (Qiagen). RNA concentration and quality (A260/A280) was measured using a NanoDrop 1000 Spectrophotometer (Thermo Scientific)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CRISPR NTC in HEL cells


title: Th2_miR29WT_1.1


title: ZNF160 ChIPexo


title: Th2_miR29KO_1.1


title: RPFA0002_20_4G_BY_RGT2_V539I


title: Genomic DNA.Sample 21

value: pediatric low-grade glioma


title: Genomic DNA.Sample 20


title: RPFA0002_21_1E_BY_FAA4-GFP_to_BY


title: R1_EpiSC 1.14_H3K4me3

description:
CTTGTA
EpiSC-14_S13_L002

source_name: R1 EpiSC 1.14 subline


title: N-KO-3

city: New York

first: Igor

last: Dolgalev

state: New York

address: 550 1st Ave

institute: NYU Grossman School of Medicine

description:
N.counts.raw.txt.gz
N.counts.normalized.txt.gz

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.

source_name: N-KO

extract_protocol:
RNeasy Micro Kit - QIAGEN
SMART-Seq v4 Ultra Low Input RNA Kit - Clontech

value: Spop(D/D)

value: bone marrow

tag: cell type

value: Neutrophil (Ly6G+)

value: 4-12 weeks


title: Genomic DNA.Sample 19


title: Th2_miR29KO_2.2


title: N-KO-2


title: R1_EpiSC 1.11_H3K4me3

description:
ATTCCT
EpiSC-11_S10_L002

source_name: R1 EpiSC 1.11 subline


title: Genomic DNA.Sample 70


title: Genomic DNA.Sample 18


title: RPFA0002_19_5F_BY_rgt2KanMX_to_BY


title: ZKSCAN7 ChIPexo


title: RPFA0002_18_5C_BY_rgt2KanMX_to_BY


title: R1_EpiSC 1.12_H3K4me3

description:
ACAGTG
EpiSC-12_S11_L002

source_name: R1 EpiSC 1.12 subline


title: N-KO-1


title: RPFA0002_17_4F_BY_RGT2_V539I


title: R1_EpiSC 1.10_H3K4me3

description:
ACTGAT
EpiSC-10_S9_L002

source_name: R1 EpiSC 1.10 subline


title: Genomic DNA.Sample 17


title: RPFA0002_16_3D_BY_OLE1_FAR_RM


title: R1_EpiSC 1.9_H3K4me3

description:
GAGTGG
EpiSC-9_S8_L002

source_name: R1 EpiSC 1.9 subline


title: R1_EpiSC 1.13_H3K4me3

description:
GGCTAC
EpiSC-13_S12_L002

source_name: R1 EpiSC 1.13 subline


title: N-WT-1

source_name: N-WT


title: Genomic DNA.Sample 16

source_name: Glioma Tissue


title: RPFA0002_15_3E_BY_OLE1_FAR_RM


title: Genomic DNA.Sample 15


title: R1_EpiSC 1.8_H3K4me3

description:
CGTACG
EpiSC-8_S7_L002

source_name: R1 EpiSC 1.8 subline


title: RPFA0002_14_3C_BY_OLE1_FAR_RM


title: R1_EpiSC 1.7_H3K4me3

description:
GTTTCG
EpiSC-7_S6_L002

source_name: R1 EpiSC 1.7 subline


title: LSK-KO-2

description:
LSK.counts.raw.txt.gz
LSK.counts.normalized.txt.gz

source_name: LSK-KO


title: LSK-KO-1

value: LSK


title: R1_EpiSC 1.5_H3K4me3

description:
GTGGCC
EpiSC-5_S5_L002

source_name: R1 EpiSC 1.5 subline


title: Genomic DNA.Sample 13


title: RPFA0002_13_4C_BY_RGT2_V539I


title: LSK-WT-2

source_name: LSK-WT


title: LSK-WT-1


title: N-WT-2


title: R1_EpiSC 1.1_H3K4me3

description:
GATCAG
EpiSC-1_S2_L002

source_name: R1 EpiSC 1.1 subline


title: Genomic DNA.Sample 12


title: RPFA0002_12_5A_BY_rgt2KanMX_to_BY

source_name: yeast culture


title: RPFA0002_11_2D_BY_OAF1_L63S


title: R1_EpiSC 1.2_H3K4me3

description:
TAGCTT
EpiSC-2_S3_L002

source_name: R1 EpiSC 1.2 subline


title: ZNF746_Ti ChIP-seq

source_name: transduced 293T cell line


title: Genomic DNA.Sample 11


title: 293Tctrl_Ti ChIP-seq


title: RPFA0002_10_1A_BY_FAA4-GFP_to_BY


title: Genomic DNA.Sample 10


title: Genomic DNA.Sample 9


title: R1_EpiSC_H3K4me3

description:
CTTGTA
mEPiSC_S12_L007

source_name: R1 EpiSC line

value: R1 EpiSC line


title: RPFA0002_9_2A_BY_OAF1_L63S


title: 293Tctrl ChIP-seq


title: Genomic DNA.Sample 14


title: RPFA0002_8_2E_BY_OAF1_L63S


title: R1_mESC_2.13_H3K4me3

description:
CAGATC
mESC_SC_2_13_S6_L004

source_name: R1 mESC 2.13 subline

value: R1 mESC subline


title: Genomic DNA.Sample 8


title: Genomic DNA.Sample 7


title: RPFA0002_7_3F_BY_OLE1_FAR_RM


title: R1_EpiSC 1.4_H3K4me3

description:
ATGTCA
EpiSC-4_S4_L002

source_name: R1 EpiSC 1.4 subline


title: R1_mESC_2.10_H3K4me3

description:
ACAGTG
mESC_SC_2_10_S5_L004

source_name: R1 mESC 2.10 subline


title: R1_mESC_1.7_H3K4me3

description:
AGTTCC
mESC_SC_1_7_S14_L007

source_name: R1 mESC 1.7 subline


title: ZNF597 ChIP-seq


title: ZNF20 ChIP-seq


title: RPFA0002_5_5E_BY_rgt2KanMX_to_BY


title: Genomic DNA.Sample 6


title: R1_mESC_1.4_H3K4me3

description:
AGTCAA
mESC_SC_1_4_S13_L007

source_name: R1 mESC 1.4 subline


title: ZNF215 ChIP-seq


title: RPFA0002_6_3G_BY_OLE1_FAR_RM


title: ZKSCAN8 ChIP-seq


title: WT

description:
counts.raw.csv
counts.normalized.csv

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Counts were filtered and normalized with Seurat R package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (CSV), normalized counts (CSV), gene-barcode matrix (HDF5)

extract_protocol:
RNeasy Micro Kit - QIAGEN
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)


title: ZNF213 ChIP-seq


title: R1_mESC_H3K4me3

description:
ACTTGA
mESC-parent_S1_L002

source_name: R1 mESC line

value: R1 mESC line


title: KO

description:
counts.raw.csv
counts.normalized.csv


title: Genomic DNA.Sample 5

source_name: Glioma Tissue


title: RPFA0002_4_1D_BY_FAA4-GFP_to_BY


title: Genomic DNA.Sample 4


title: ZNF256 ChIP-seq


title: RPFA0002_3_4B_BY_RGT2_V539I


title: DKO

description:
counts.raw.csv
counts.normalized.csv

source_name: LSK-DKO


title: Genomic DNA.Sample 3


title: LN229/EGFRvIII+erlotinib input

status: Public on Aug 11 2019

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 5bp bin in the genome
Genome_build: hg19

source_name: brain

growth_protocol: LN229 glioma cells were maintained in 10% FBS/DMEM

extract_protocol:
LN229 cells were cross-linked with formaldehyde to a final concentration of 1%. ChIP samples were prepared as described previously [(Buschbeck et al. The histone variant macroH2A is an epigenetic regulator of key developmental genes. Nat Struct Mol Biol 16, 1074-1079 (2009)].Immunoprecipitations were performed using 1μg anti- macroH2A1 antibody (07-219, Millipore) or the relevant non-specific IgG (Santa Cruz).
ChIP-seq libraries generation were performed according to standard protocols using BioScientific’s DNA Sample Kit.

treatment_protocol: LN229 cells with stable expression of EGFRvIII were treated with vehicle (0.1% DMSO), erlotinib (10 μM) or Roscovitine (20 μM) for 16 h.

value: stable expression of EGFRvIII

value: glioblastoma

value: brain

tag: antibody

value: input

value: 10 uM erlotinib


title: RPFA0002_2_1F_BY_FAA4-GFP_to_BY


title: LN229/EGFRvIII+vehicle IP

value: anti-macroH2A1 antibody (07-219, Millipore)

value: 0.1% DMSO


title: LN229/EGFRvIII+erlotinib IP


title: ZNF746 ChIP-seq

value: HEK 293T

value: Anti-HA (clone 16B12, Covance)


title: 22RV1 CC115 1

city: Philadelphia

first: Emanuela

last: Dylgjeri

state: Pennsylvania

address: 233 S 10th St

department: Cancer Biology

institute: Thomas Jefferson University

data_processing:
alignment to hg19 with STAR v2.5.2a
Generate count table using featureCounts Version 1.5.0-p3
Differential expression using DESeq2_1.14.1
Genome_build: hg19
Supplementary_files_format_and_content: Count matrix

source_name: 22RV1 Cell Line

growth_protocol: 22RV1 cells were cultured in hormone proficient media .

extract_protocol:
RNA Seq was prepared according to manufacturesrs instructions ( RNAeasy Mini kit, Qiagen)
RNA-Seq libraries were constructed using TruSeq Stranded Total RNA Library Prep Gold kit (protocol# 15031048 Rev E)

treatment_protocol: Cells were treated with 1uM CC-115 or control as indicated for 24 hours.

tag: dna-pk inhibition


title: Genomic DNA.Sample 2

tag: tissue

value: pediatric low-grade glioma


title: Genomic DNA.Sample 1


title: LN229/EGFRvIII+roscovitine input

tag: genotype/variation

value: 20 uM roscovitine


title: 22RV1 Control 3

value: control, none


title: LN229/EGFRvIII+roscovitine IP


title: LN229/EGFRvIII+vehicle input


title: C4-2 CC-223+ Enza Rep3

growth_protocol: C4-2 cells were cultured in hormone proficient media .

treatment_protocol: Cells were treated with 1uM NU7441, 1uM CC-115, 1uM CC-223, 1uM Enzalutamide (Enza) or the combination as indicated for 24 hours.

value: C4-2 prostate cancer cells

tag: ar antagonist

value: 24hr Enza 1uM

tag: tork inhibitor


title: 22RV1 CC115 2


title: C4-2 CC-223+ Enza Rep1


title: 22RV1 Control 2


title: C4-2 CC-115+ Enza Rep3


title: C4-2 CC-115+ Enza Rep1


title: C4-2 CC-223+ Enza Rep2


title: C4-2 NU7441+ Enza Rep2


title: C4-2 CC-115+ Enza Rep2


title: 22RV1 Control 1


title: C4-2 Enza Rep1

source_name: C4-2 Enza


title: C4-2 NU7441+ Enza Rep3


title: C4-2 CC-223 Rep1


title: C4-2 NU7441+ Enza Rep1


title: C4-2 CC-115 Rep2


title: C4-2 NU7441 Rep3


title: C4-2 NU7441 Rep2


title: C4-2 NU7441 Rep1


title: C4-2 Enza Rep3


title: C4-2 CC-115 Rep1


title: C4-2 Enza Rep2


title: C4-2 Ctrl Rep3

source_name: C4-2 Ctrl


title: C4-2 CC-223 Rep2


title: HAP1 SMUG1 KO rep2

city: Lørenskog

first: Hilde

middle: Loge

last: Nilsen

state: Lørenskog

address: Sykehusveien 25

department: Akershus University Hospital

country: Norway

institute: University of Oslo

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_KO1_b

data_processing:
Basecalls performed using RTA v2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38.p7 whole genome and to the control RNA sequences using STAR aligner
Read counts per gene (Encode release 84) were determined with htseq-count
The gene count matrix was normalized with voom, using normalization factors computed with the TMM method from the reads aligning to the control RNAs
Limma package was used on normalized matrix for gene expression analysis
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: [RNA-Seq_AllGenes_KOandP.txt]  tab-separated text files with count-matrix (combined output from htseq-count). Ensemble ID in column 1, all other columns are experimental read counts.

source_name: HAP1 cell line

growth_protocol: HAP1 Parental and SMUG1-KO cells (Horizon) were maintained in culture as predominantly diploid cells in Iscove's modified Dulbecco's medium (IMDM, Life Technologies) containing 10% (vol/vol) FBS and 1x Penicillin/Streptomycin.

extract_protocol:
RNeasy kit (Qiagen) or with Trizol (Invitrogen). RNA was treated with DNase I.
Lexogen SENSE Total RNA-Seq Library Prep Kit (RNA-seq) and Illumina TruSeq Nano DNA LT library Prep kit (3'RACE)

tag: cell line source

value: near-haploid cell line derived from Male Chronic Myelogenous Leukemia (CML) cell line KBM-7

tag: passage

value: SMUG1 KO


title: C4-2 CC-115 Rep3


title: HAP1 SMUG1 WT rep3

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_P1_c

value: SMUG1 WT


title: C4-2 Ctrl Rep2


title: HAP1 SMUG1 WT rep2

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_P1_b


title: HAP1 SMUG1 KO rep1

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_KO1_a


title: C4-2 CC-223 Rep3


title: C4-2 Ctrl Rep1


title: HAP1 SMUG1 KO rep3

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_KO1_c


title: Castrated 1

city: Tallahassee

first: gang

last: wang

state: Florida

address: 319 Stadium Dr

department: The Center for Genomics and Personalized Medicine

institute: Florida State University

description: Gene expression data from Tibialis Anterior of Castrated Mouse

hyb_protocol: Following fragmentation, 5.5 ug of single stranded cDNA was hybridized for 16 hr at 45 degrees C on GeneChip Mouse Gene 2.0 ST Arrays.  The staining and washing of the arrays were conducted using an Affymetrix Fluidics 450 Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Command Console Sofware and GeneChip Scanner 3000 7G according to manufacturer's instructions.

data_processing: Raw data files were imported into Partek's Genomic Software.  The Robust Microarray Average method was used for data processing which included background correctio, quantile normalization, and median polish corrections.  Signals for probes were Log2 transformed to create data sets closer to the normal distruibution.

label: biotin

source_name: Tibialis Anterior from Refed Mouse

label_protocol: 300 ng of total RNA was labeled according to the Whole Transcript Sense Target Labeling Assay protocol using Affymetrix's GeneChip WT PLUS Reagent kit (cat. #902281)

growth_protocol: Mice were bred and housed in a temperature (25 degree C) and light controlled environment (12hr:12hr light:dark) on corn cob bedding.  Mice were provided rodent chow (irradiated PicoLab 5053; LabDiet, St. Louis, MO) and water ad libitum.  Mice were subjected to a sham or castration surgery at 11 weeks of age and allowed to recover for 7 weeks until sacrifice.

extract_protocol: Tibialis Anterior muscle samples (~25 mg) were homogenized in Tri Reagent (Zymo, Irvine, CA).  Total RNA was then extracted using Zymo Direct-zol RNA Miniprep kit with on column DNase treatment according to manufacturer's instructions (cat. #R2051).   Samples were eluted from the columns with 25 ul of water.

treatment_protocol: Mice were subjected to a sham or castration surgery at 11 weeks of age.  Mice recovered for 7 weeks, at which point they were were fasted beginning at 1800 hr.  The next morning (~0800 hr), mice were allowed to refeed for 30 minutes.  Following the refeeding, all mice were fasted for an additional 4 hr until sacrifice.  At sacrifice, all mice were anesthetized with isoflurane, and the tibialis anterior muscle was extracted and flash frozen in liquid nitrogen, and stored at -80 degree C until analysis.

value: Tibialis Anterior

tag: strain

tag: gender

value: Male

tag: age

value: 18 weeks

tag: diet

value: refed


title: Castrated 3


title: HAP1 SMUG1 WT rep1

description:
RNA-Seq
RNA-Seq_AllGenes.txt
HAP1_P1_a

tag: genotype


title: Sham 1

description: Gene expression data from Tibialis Anterior of Sham Mouse

source_name: Tibialis Anterior from Fasted Mouse

value: fasted


title: Sham 2


title: ABHD5-KD-2(T)

city: Chongqing

first: Hongming

last: Miao

state: Chongqing

address: Gaotanyan Street NO.30

department: Department of Biochemistry and Molecular Biology

institute: Third Military Medical University (Army Medical University)

description: ABHD5-KD RAW cell-primed CT-26 cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.7.3.1 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: ABHD5-KD RAW cell-primed CT-26 cells

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: The control,ABHD5-silenced Raw264.7 macrophages or those macrophage-primed CT-26 cells were subjected to gene expression microarray analysis.

value: CT-26 cells


title: ABHD5-KD-1(T)

description: ABHD5-KD RAW cell-primed CT-26 cells


title: Castrated 2


title: Sham 3


title: Ctrl-2(T)

description: RAW cell-primed CT-26 cells

source_name: RAW cell-primed CT-26 cells

value: control


title: ABHD5-KD-2

description: RAW264.7 cells transfected with a ABHD5 shRNA (ABHD5-KD)

value: RAW264.7 cells


title: ABHD5-KD-3(T)

description: ABHD5-KD RAW cell-primed CT-26 cells


title: Ctrl-3(T)

description: RAW cell-primed CT-26 cells


title: N2_6h_Clone13

city: Jena

first: Martin

last: Hölzer

state: Thuringia

address: Leutragraben 1

department: Faculty of Mathematics and Informatics

institute: University of Jena

data_processing:
Reference sequence and annotation of the closely related microbat Myotis lucifugus were downloaded from Ensembl (Myoluc2.0, release 86).
We quality trimmed with a Q20 threshold and a window size of length 4 using Prinseq v0.20.3. Reads shorter 15nt were discarded.
We used SortMeRNA (v2.1) to detect and remove ribosomal RNAs.
The quality-controlled and rRNA-depleted reads were mapped to the concatenated reference genomes of M. lucifugus and RVFV using STAR (v2.5.2) with an adjusted --outFilterScoreMinOverLread and -outFilterMatchNminOverLread of 0.4.
We used featureCounts (v1.5.0) to quantify the mapped reads based on the Ensembl annotation (originally release 86) of M. lucifugus comprising 25,849 genes (19,728 coding for proteins). Reads were counted strand-specific on exon level and accumulated per gene ID to obtain one count per gene. Only uniquely mapped reads were used in the differential gene expression analysis and further evaluations.
The read counts were passed to DESeq2 (v1.16.1) to call significantly (adjusted p <= 0.05) differentially expressed genes and to calculate fold changes between the different time points and conditions.
To reduce the amount of low expressed genes/false positive hits, the DESeq2 results were filtered by calculating TPM values as shown in https://www.ncbi.nlm.nih.gov/pubmed/20022975.
Genome_build: Myoluc2.0
Supplementary_files_format_and_content: tab-delimited text files include gene id, chromosome position, orientation, length, and unique raw read counts obtained by featureCounts for each sample

organism: Myotis daubentonii

source_name: 6h_Clone13, kidney

growth_protocol: Immortalized kidney cells from Myotis Daubentonii (MyDauNi) were maintained in DMEM (4,5 g/L) supplemented with 200 µM L-Alanine, 225 µM L-Aspartic acid, 933 µM Glycin, 510 µM L-Glutamic acid, 217 µM L-Proline, 292 µg/L L-glutamine, 184 µM Hypoxanthine, 0,1 mg/L Biotin, 44 mM NaHCO3, 10 % FBS, 10 U/L Penicillin, and 10 µg/L Streptomycin.

extract_protocol:
The medium was removed and the cells washed once in PBS. Total RNA were extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions. The samples from each treatment were pooled and the amount of RNA determined using a Nanodrop. The quality and integrity of the respective RNA were deterimend using a Agilent 2100 Bioanalyzer. The samples were then stored at -80°C
RNA libraries were prepared for sequencing using the Illumina Ribo-Zero rRNA Removal Kit for human/mouse/rat

treatment_protocol: 3×10^5 MyDauNi cells/well were seeded in a 12-well plate and then incubated 24 h at 37°C, 5% CO2. The following day four wells were mock treated, four wells were treated with 1000 U/ml pan-species interferon-alpha (B/D) and the remaining four wells were infected with RVFV Clone 13 (MOI 5). At 6 and 24 h post-infection samples were taken.

tag: treatment

value: RVFV-clone 13 infection, MOI5

tag: time

value: 6h poi

value: kidney


title: Ctrl-3

description: RAW264.7 cells transfected with PLKO

source_name: RAW264.7 cells transfected with PLKO

tag: cell line


title: ABHD5-KD-3

source_name: RAW264.7 cells transfected with a ABHD5 shRNA (ABHD5-KD)


title: Ctrl-1(T)

description: RAW cell-primed CT-26 cells


title: ABHD5-KD-1


title: N1_6h_Clone13


title: N2_24h_IFN

source_name: 24h_IFN, kidney

value: IFN-alpha (1000 U/ml)

value: 24h after treatment


title: N2_6h_IFN

source_name: 6h_IFN, kidney

value: 6h after treatment


title: Ctrl-2

description: RAW264.7 cells transfected with PLKO


title: N2_24h_Clone13

source_name: 24h_Clone13, kidney

value: 24h poi


title: N3_6h_Clone13


title: N1_6h_IFN


title: N3_6h_IFN


title: Ctrl-1

description: RAW264.7 cells transfected with PLKO


title: N3_24h_mock

source_name: 24h_mock, kidney


title: N1_24h_mock


title: N3_6h_mock

source_name: 6h_mock, kidney


title: N3_24h_Clone13


title: N1_24h_Clone13


title: N3_24h_IFN


title: N1_6h_mock


title: Liver, HS-2

city: lanzhou

first: jinqiang

last: quan

address: No. 1 Yingmen Village, Anning District

department: College of Animal Science & Technology

institute: Gansu Agricultural University

data_processing:
Reads obtained from the sequencing machines included raw reads containing adapters or low quality bases which would affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered according to the following rules: 1) Removing reads containing adapters; 2) Removing reads consisting of all A bases; 3) Removing reads containing more than 10% of unknown nucleotides (N); 4) Removing low quality reads containing more than 50% of low quality (Q-value≤20) bases
Short reads alignment tool Bowtie2 (2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads were then removed. The remaining reads were further used in assembly and analysis of transcriptome.
The rRNA removed reads of each sample were then mapped to reference genome by TopHat2 (version 2.1.1), respectively. The alignment parameters were as follows: 1) Maximum read mismatch is 2 2) Disables the coverage based search for junctions 3) The distance between mate-pair reads is 50bp 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80bp
After aligned with reference genome, unmapped reads (or mapped very poorly) were then re-aligned with Bowtie2, the enriched unmapped reads were split into smaller segments which were then used to find potential splice sites. The section and the section position of these short segments were predicted as well. A set of splice sites was built with initial unmapped reads by TopHat2 without relying on the known genes annotation. Not only be used for identifying expressed genes and their quantitative expression, the sequence alignment will also be helpful to find alternative splicing and new transcripts.
Genome_build: Oncorhynchus mykiss Omyk_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
After total RNA was mixed, rRNAs were removed to retain mRNAs and ncRNAs. The enriched mRNAs and ncRNAs were fragmented into short fragments by using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP (dUTP instead of dTTP) and buffer. Next, the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to Illumina sequencing adapters.

treatment_protocol: Fish with a mean weight 200 ± 5.5 g were transferred into a 6000 L aerated water tank and were cultured at 18 °C for seven days. Prior to the experiment, the fish were randomly divided into two groups in 500 L water tanks, and allowed to acclimate for another seven days. To simulate temperature conditions in natural environment, the water temperature in the heat stress groups was increased from 18 °C to 24 °C at a constant rate of 1 °C per 24 h using a temperature control system. After anesthetizing with a lethal dose of MS-222 (Sigma Aldrich Co., St. Louis, USA), the liver were harvested from twelve female fishes from both the 18 °C control group and the 24 °C heat stress group. Tissues were immediately flash frozen in liquid nitrogen and stored at −80 °C for gene expression profiling analysis.

tag: stress

value: liver

value: 150 day


title: Leucocarpa_130DAF

city: Rende

first: Fabrizio

last: Carbone

state: CS

address: C.da Li Rocchi Vermicelli

country: Italy

institute: Council for Agricultural Research and Economics (CREA)

data_processing:
Pre-processing was based on miRExpress software to merge the identical reads into a unique read, to count each unique read and to remove full and partial adaptor sequences. Sequences below 18 bp and above 32 bp were also discarded.
In order to identify known miRNAs in olive, the remaining unique sequences were aligned against known Viridiplantae miRNA (miRBase database version 21.0)  by using miRExpress software.
To identify putative novel miRNAs, sequences that no matched the miRBase database were aligned with genome sequence of the olive tree (Olea europaea L. cv Farga) using the SOAP 2.0 software. The secondary structures of the matched sequences were analyzed by the Mireap software in order to identify new candidate miRNAs, followed by the prediction of secondary structures by Mfold program.
The frequency of both known and putative novel miRNA read count was normalized as transcript per million (TPM) and normalization of miRNA expression levels among four libraries was carried out.
miRNA target identification was carried out by alignment with the olive drupe transcripts obtained through an Illumina RNA-seq approach (Iaria et al., 2016 Frontiers in Plant Science 6, 1246) by Bowtie program. Moreover, enrichment analysis  were performed by using KOBAS-3.0 software.
Genome_build: Reference genome of Olea europaea - WGS Sequence Set: FKYM01000000 /  Reference transcriptome of Olea europaea - SRA accession numbers: SRR1574719, SRR1574772, SRR1573503, SRR1574328
Supplementary_files_format_and_content: FASTA file of filtered data. FASTA headers report sample name, progressive number of filtered reads and count of identical reads in the same sample

organism: Olea europaea

source_name: Drupes of 20-year-old plants randomly collected at 130 DAF

growth_protocol: Drupes were collected from 20-year-old plants, clonally propagated and belonging to the olive germplasm collection of the CREA – Research Centre for Olive, Citrus and Tree Fruit , in Rende (Cosenza, Calabria, Italy). Olive trees were grown using the same field conditions and were located at latitude 39°22′55′′N, longitude 16°14′15′′ E and altitude 210 m asl.

extract_protocol:
Total RNA was extracted from the epi-mesocarp tissues of drupes collected together, using the RNeasy Plant Mini kit (Qiagen) according to the manufacturer’s instructions. Each RNA sample was subjected to DNase digestion (Dnase I, Roche) to remove any DNA contamination and pooled equally.
Library preparation and sequencing was carried out by Technology Services of the Institute of Applied Genomics (IGA, Udine, Italy). Workflow starts with isolated total RNA. Upon the quality control of the starting material libraries are generated and size is selected in a range that maximizes the number of relevant reads. Sequencing is performed on HiSeq2500 in a 50 bp single-read mode.

treatment_protocol: no treatment

tag: developmental stage

value: drupe


title: Liver, HS-1


title: HAP1 SMUG1 KO clone 2

description:
RNA-seq (3'RACE)
TERC-RACE-pileupdata_KoandP.txt
KO2

data_processing:
Basecalls performed using RTA v2
Sequenced reads were mapped to TERC gene sequence (UCSC gene ID uc003ffr.2) using bowtie2
Filtering of the reads  with unsigned value of SAM field 9 was identical and > 0 and SAM field 9 had opposite signs for the read pair
Read coverage was calculated using bedtools
For polyA analysis, 3' adapter sequences and the 5' part of the reads (up to 8 nt downstream the end of TERC) were trimmed by using cutadapt and filtered for keeping at least one adenine and at most 25% other nucleotides.
Genome_build: TERC gene sequence (UCSC gene ID uc003ffr.2)
Supplementary_files_format_and_content: [TERC-RACE-pileupdata_KOandP.txt]  RPM-normalized read-depth, columns are: TERC sequence ID ("Seq); start and sto-position for region ("Start", "End);normalised read depth in region (Depth (RPM)", Sample ID ("Sample") and Group ID ("Group)

value: near-haploid cell line derived from Male Chronic Myelogenous Leukemia (CML) cell line KBM-7

value: SMUG1 KO


title: N1_24h_IFN


title: N2_6h_mock


title: Leucocarpa_100DAF

department: Research Centre for Olive, Citrus and Tree Fruit

source_name: Drupes of 20-year-old plants randomly collected at 100 DAF


title: N2_24h_mock


title: HAP1 SMUG1 KO clone 1

description:
RNA-seq (3'RACE)
TERC-RACE-pileupdata_KoandP.txt
KO1


title: MDSCs, EGCG_1

city: Hangzhou

first: Ping

last: Xu

state: Zhejiang

address: 866 Yuhangtang Rd

department: Department of Tea Science

institute: Zhejiang University

data_processing:
bcl2fastq 1.8.4 used for basecalling.
Raw reads were quality checked with FastQC, and then mapped to GRCm38 using STAR 2.6.0c with default settings
Gene counts were generated using featureCounts 1.6.2 with mouse GTF files from ENSEMBL (version 91).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include gene counts for each sample

source_name: spleen-sorted MDSCs

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BALB/c mice were injected with 1×10^6 4T1 cells, and mice were sacrificed on the 21st day and we sorted MDSCs from spleens. MDSCs were then treated with either control medium or 5 ug/mL EGCG for 6h.

value: BALB/c

tag: tumor type

value: 4T1 breast cancer cell model

value: spleen

tag: cell type

value: spleen-sorted MDSCs

value: EGCG


title: MDSCs, EGCG_2

tag: tissue


title: MDSCs, Control_2

value: control


title: Liver, CG-2


title: Liver, HS-3


title: MDSCs, Control_1


title: Cassanese_130DAF


title: HAP1 SMUG1 WT clone 2

description:
RNA-seq (3'RACE)
TERC-RACE-pileupdata_KoandP.txt
P2

source_name: HAP1 cell line

value: SMUG1 WT


title: nasRNAseq Hl-60 ActD-treated

status: Public on Aug 10 2019

city: Singapore

first: Vladimir

last: Espinosa Angarica

state: Singapore

address: 14 Medical Drive, #12-01

department: Cancer Science Institute

country: Singapore

institute: National University of Singapore

description: Nascent RNA from HL60 cells ActD-treated

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trim_galore, Cutadapt and FastQC, and mapped to the GRCh38 human reference genome (release 88) using STAR v2.5.2b with parameters (--sjdbOverhang 150 --runThreadN 16 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate Unsorted --quantMode TranscriptomeSAM --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFtagExonParentGene gene_id --alignWindowsPerReadNmax 10000 --alignTranscriptsPerWindowNmax 100) and other default parameters set by the program
The ChIP-seq (or RIP-seq) and IgG control mapped reads were processed with HOMER for assessing the statistical significance of ChIP-seq (or RIP-seq) peaks. The peak size was set to 500bp (or 100bp for RIP-seq), and adjacent peaks within regions of 1000bp are stitched together, and the ChIP signal vs IgG control peaks were filtered over regions of size 1000bp, using a Poisson p-value threshold of 1×10-3, and a Poisson tag threshold of 32, with a peak fold change between ChIP signal vs IgG control of 4.
Genome_build: GRCh38, release 88

growth_protocol: HL-60 were A49:B56 in DMEM supplemented with 10%FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
Nascent RNA capture was performed using Click-iT® Nascent RNA Capture Kit according to the manufacturer’s instructions with minor modifications.
RIP-seq libraries:H2A.Z-; acH2A.Z-; TIP60-; and IgG-interacting RNA was immunoprecipitated by the respective antibodies. RNA was reverse transcribed into ds-cDNA before sequencing library preparation using Illumina ChIP-Seq sample preparation kit (cat# IP-102-1001) following manufacturer's instruction.
ChIP-seq libraries: Cells were crosslinked with 1% formaldehyde for 10 min at 37°C. Pellets of 1M cells were used for immunoprecipitation as previously described (7) and lysed for 10 minutes on ice and chromatin fragmented using a Branson 250 digital sonifier. Each ChIP was performed with 4ug of antibody, incubated overnight at 4°C. A 50/50 slurry of protein A and protein G Dynabeads was used to capture enriched chromatin, which was then washed before reverse-crosslinking and proteinase K digestion at 65C. AMPure XP beads were used to clean up and isolate ChIP DNA for subsequent library construction. The following antibodies were used for ChIP: H2A.Z (Abcam ab4174, lot GR3176820-1), acH2A.Z (Abcam ab18262, lot GR306397-1), and IgG (ab171870).

treatment_protocol: HL-60 cells were treated with 100 μM of 5,6-Dichlorobenzimidazole 1-β–D-ribofuranoside (DRB) (Sigma Aldrich) and 0.8 μM of Actinomycin D (Sigma Aldrich) as indicated at each time point.

value: ActD-treated

tag: antibody


title: HAP1 SMUG1 WT clone 1

description:
RNA-seq (3'RACE)
TERC-RACE-pileupdata_KoandP.txt
P1


title: Cassanese_100DAF


title: Liver, CG-3


title: nasRNAseq Hl-60

description: Nascent RNA


title: nasRNAseq Hl-60 DRB-treated

description: Nascent RNA from HL60 cells DRB-treated

value: DRB-treated


title: RIPseq HL-60 IgG rabbit

description: RNA IP with IgG rabbit

value: IgG rabbit


title: RIPseq HL-60 IgG goat

description: RNA IP with IgG goat

value: IgG goat


title: RIPseq HL-60 IgG sheep

description: RNA IP with IgG sheep

value: IgG sheep


title: RIPseq HL-60 Tip60

description: RNA IP with Tip60 antibody


title: nasRNAseq Hl-60 DMSO-treated

description: Nascent RNA from HL60 cells DMSO-treated

value: DMSO-treated


title: RNAseq Hl-60

description: Total RNA


title: ChIPseq HL-60 DRB-treated input

description: Input DNA

value: input


title: RIPseq HL-60a acH2A.Z

description: RNA IP with acH2A.Z antibody


title: ChIPseq HL-60 DRB-treated IgG

description: Genomic DNA IP with IgG

value: IgG


title: RIPseq HL-60 H2A.Z

description: RNA IP with H2A.Z antibody


title: ChIPseq HL-60 ActD-treated input

description: Input DNA


title: ChIPseq HL-60 ActD-treated acH2A.Z

description: Genomic DNA IP with acH2A.Z antibody


title: Liver, CG-1

value: liver

value: 150 day


title: ChIPseq HL-60 DMSO-treated input

description: Input DNA


title: ChIPseq HL-60 ActD-treated IgG

description: Genomic DNA IP with IgG


title: ChIPseq HL-60 DMSO-treated acH2A.Z

description: Genomic DNA IP with acH2A.Z antibody


title: ChIPseq HL-60 DMSO-treated IgG

description: Genomic DNA IP with IgG


title: ChIPseq HL-60 ActD-treated H2A.Z

description: Genomic DNA IP with H2A.Z antibody


title: ChIPseq HL-60 DRB-treated acH2A.Z

description: Genomic DNA IP with acH2A.Z antibody


title: ChIPseq HL-60 DRB-treated H2A.Z

description: Genomic DNA IP with H2A.Z antibody


title: ChIPseq HL-60 DMSO-treated H2A.Z

description: Genomic DNA IP with H2A.Z antibody


title: ChIPseq HL-60 siNTC H2A.Z

description: Genomic DNA IP with H2A.Z antibody

value: siNTC


title: Lung, KO3_4

city: Rochester

first: Jared

last: Mereness

address: 204 Robert B. Goergen Hall, Department of Biomedical Engineering, Box 270168

department: Biomedical Engineering

institute: University of Rochester

description: Pool: Col6a1-/- animals 3+4

data_processing:
Approximately 35 million reads were generated for each sample. Sequences were aligned to the mouse reference genome GRCm38.p5 using STAR (version 2.5.2b) implemented in R (version 3.4.1). Count estimation was performed using subread (version 1.5.0p3) as implemented in R. Differential expression of genes was assessed using DESeq2 with default parameters and lfcshrink to perform Log2 transformation of the data (release 3.8, Bioconductor.org).
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, Unique   "-s 2 -t exon -g gene_name"
DIFFERENTIAL EXP - DESeq2_1.16.1 1 with lfcShrink
Genome_build: GRCm38.p5 + Gencode-M12 Annotation
Supplementary_files_format_and_content: .txt file contain DESeq2 normalized counts and results of DESeq2 differential expression analysis

source_name: Whole Perfused Lung Tissue

extract_protocol:
To isolate total RNA, frozen tissue from right lung lobes was homogenized in 1ml of TRIzol reagent (Invitrogen, 15596026) with a Tissue Tearor homogenizer (Biospec, 985370) on ice, for 3 minutes.  For each sample, 200µl of chloroform was added, and the sample was vortexed for 15 seconds.  Samples were then centrifuged at 12,000g for 15 minutes at 4°C.  The top, aqueous layer was collected, and RNA was precipitated by adding 500µl isopropanol.  Samples were incubated at room-temperature for 15 minutes, and then centrifuged at 12,000g for 10 minutes.  The supernatant was removed, and the RNA pellet was washed with 500µl of 75% ethanol.  Samples were mixed by vortexing for 10 seconds, and centrifuged at 10,000g for 5 minutes at 4°C.  The supernatant was removed, and the wash step was repeated once more.  The ethanol supernatant was removed after the second wash, and samples were allowed to air-dry for 10 minutes.  The RNA was then dissolved in 100µl of RNAse/DNAse-free water.  Isolated RNA was repurified and rendered DNA-free by an on-column DNase I treatment according to the Agilent MiniPrep protocol (Agilent Technologies, Santa Clara, CA).  RNA quantity was measured using ultraviolet absorbance, and quality was assessed using an Agilent 2100 Bioanalyzer. Only samples with an RNA concentration >100ng/μl and an RNA integrity number (RIN) >8 were used for RNA-Seq.
In attempt to reduce the effects of biological variation, total RNA from two animals of the same genotype was pooled to generate each cDNA library. Each animal contributed to a single pool, with 6 total Col6a1-/- mice and 6 WT C57BL/6 mice contributing to 3 samples for each group.  Next, cDNA libraries (n = 3 for Col6a1-/-, n=3 for wild-type) were generated, and high-throughput sequencing was completed by the University of Rochester Genomics Research Center using an Illumina HiSeq 2500 high-throughput DNA sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were euthanized at 6 weeks of age by CO2 narcosis and cervical dislocation.   The thoracic cavity was opened, and the descending aorta was cut prior to perfusion of the lung vasculature with 1ml cold PBS via the right ventricle.  A suture was tied around the right main stem bronchus to prevent agarose inflation.  The right lung lobes were removed, snap-frozen in liquid nitrogen, and stored in -80°C for RNA and protein extraction.

value: 6 weeks

value: Lung


title: ChIPseq HL-60 siNTC acH2A.Z

description: Genomic DNA IP with acH2A.Z antibody


title: ChIPseq HL-60 siMyc acH2A.Z

description: Genomic DNA IP with acH2A.Z antibody

value: siMyc


title: Lung, KO1_2

description: Pool: Col6a1-/- animals 1+2


title: Lung, KO5_6

description: Pool: Col6a1-/- animals5+6


title: ChIPseq HL-60 siMyc H2A.Z

description: Genomic DNA IP with H2A.Z antibody


title: Lung, WT1_2

description: Pool: WT animals1+2

value: wildtype


title: Lung, WT5_6

description: Pool: WT animals 5+6


title: Lung, WT3_4

description: Pool: WT animals 3+4


title: BFR2_X9b2

city: Amherst

first: Alexander

last: Suvorov

state: MA

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

data_processing:
Reads were mapped to the reference rat genome (rn5) using TopHat 2 aligner.
Aligned reads were used for assembly of novel transcripts and differential expression of novel and reference transcripts with Cuffdiff 2.1.1.
Genome_build: rn5
Supplementary_files_format_and_content: XLSX file showing Log2(FPKM) for control and exposed condition and Log2 of their FPKM ratio for each transcript, as well as transcript coordinates and gene names.

organism: Rattus norvegicus

source_name: testis

growth_protocol: Seven-week old timed-pregnant female (150-200 g) Wistar rats were obtained from Charles River Laboratories (Kingston, NY, USA) on 6th day after vaginal plaque detection and housed in a temperature (23±2◦C), and humidity (40±10%) controlled environment, with a 12-h light/dark cycle, and food and water available ad libitum.

extract_protocol:
Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen).
Samples of RNA isolated from testis samples with integrity values > 9 were used for library preparation. RS-122-2101-TruSeq® Stranded mRNA LT – SetA kit (Illumina, San-Diego, CA) was used to isolate intact poly(A)+ RNA from 4 µg of total RNA and construct strand-specific libraries with multiplexing indexes. The quality and purity of the libraries was assessed by The Agilent 2200 TapeStation system,  and the concentration of the libraries was measured by real time PCR with primers for P5 and P7 flow cell oligo sequences using KAPA Library Quantification Kit (KR0405, Kapa Biosystems, Boston, MA) in a 384-well plate on a CFX384 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA).

treatment_protocol: The dams were assigned to one of two treatment groups (n=7 per group) based on weight match, and were exposed to tocopherol stripped corn oil (MP Biomedicals, Solon, OH) or 1 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) in tocopherol stripped corn oil daily from pregnancy day 8 through postpartum day 21; the females were fed 0.2 µl/gram body weight from the tip of a pipette, resulting in exposure of 0.2 mg/kg body weight/day.

value: Vehicle

value: Wistar

value: testis

value: postnatal day 120


title: BFR2_X14-2


title: BFR2_X12-1


title: LPS3cells bulk RNA-seq

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

data_processing:
QC with FASTQC
Trimming with TrimGalore v0.4.5
Alignment with HiSat v2.1
Counting with FeatureCounts
Supplementary_files_format_and_content: Raw count file

source_name: brain

extract_protocol:
RNA isolation with Rneasy Plus Micro Kit (Qiagen)
Quant Seq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen) and Chromium Single Cell 3’ v2 kit from 10x Genomics

treatment_protocol: I.p. PBS or LPS injection, 1mg/kg for 3 hours

value: brain

tag: sampletype

value: Microglia cells

tag: sequencing protocol

value: 3’ Quantseq

tag: tissue type

value: fresh

value: LPS


title: LPS1nuc bulk RNA-seq

value: Microglia nuclei


title: PBS1nuc bulk RNA-seq

value: PBS


title: LPS3nuc bulk RNA-seq


title: PBS3nuc bulk RNA-seq


title: LPS2nuc bulk RNA-seq


title: LPS2cells bulk RNA-seq


title: PBSnuclei scRNA-seq

data_processing:
Cell ranger with default settings
genome build: M.Musculus (GRCm38.91)
Supplementary_files_format_and_content: Raw count file

value: 10x Genomics


title: LPScells scRNA-seq


title: LPSnuclei scRNA-seq


title: PBScells scRNA-seq


title: BFR2_C2-2

value: 0.2 mg/kg BDE-47

tag: strain


title: BFR2_C3-1


title: BFR2_C4-2


title: FReP 2-4

city: Los Angeles

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

description: After fibromodulin reprogramming

data_processing:
Illuminata RTA2 is used for basecalling and bcl2fastq v.18.1.14 is used for demultiplex.
Tophat-Cufflink package through Galaxy platform
Genome_build: hg38
Supplementary_files_format_and_content: Cufflink output files

source_name: Human newborn foreskin BJ cell after fibromodulin reprogramming

extract_protocol:
RNA was extracted using Rneasy® Mini Kit with Dnase treatment (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Confluence BJ cells were treated with DMEM + 0.4 mg/ml fibromodulin in a serum-free condition for 21 days. Medium was changed daily. After the 21-day fibromodulin reprogramming, the yield FReP cells were collected by either scratching or ReLeSR reagent.

value: newborn

value: foreskin

value: BJ


title: BFR2_C7b1


title: LPS1cells bulk RNA-seq


title: PBScells bulk RNA-seq


title: PBS2nuc bulk RNA-seq


title: BFR2_X13-1


title: FReP 2-3

description: After fibromodulin reprogramming


title: ABHD5-KO-3

city: Phoenix

first: Tobias

last: Jakobi

state: Arizona

address: 475 N. 5th Street

department: Internal Medicine

institute: University of Arizona

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 STAR v2.6.1d.
Quantification performed via cufflink 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: *_STARmapping.cxb files include abundance data.

source_name: Left ventricle

extract_protocol:
RNA samples are prepared following the TRIzol™ Reagent protocol of Invitrogen as described in the reagent manual (Invitrogen, 15596026).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

tag: type of deletion

value: Cardiac-specific ABHD5 deletion

value: heart


title: ABHD5-KO + AAV9-NT-3

description: expressing FLAG-HDAC4-NT using AAV9 gene transfer

value: ABHD5-KO + AAV9-NT


title: ABHD5-KO + AAV9-NT-1


title: ABHD5-KO + AAV9-NT-2


title: BFR2_C5-2

value: Wistar

value: testis

tag: age


title: ABHD5-KO-2


title: FReP 2-2

description: After fibromodulin reprogramming


title: FReP 1-3

description: After fibromodulin reprogramming


title: PBS2cells bulk RNA-seq

value: brain

tag: treatment


title: Ctrl-2

value: Control

value: Cardiac-specific Cre expression


title: exp_lfm10

first: Fuming

last: Li

state: PA

address: 421 Curie Blvd

institute: University of Pennsylvania

data_processing:
Standard Illumina Casava pipeline for basecalling, demuliplexing and adapter trimming to yield fastq files by Novogene Corporation.
raw data (*.fastq.gz) was aligned to the transcriptome using salmon, and summarized to gene level with tximport
Genome_build: gencode M19 (built on GRCm38)
Supplementary_files_format_and_content: un-normalized read counts per sample per gene

extract_protocol:
Total RNA was isolated from snap frozen tissue samples using RNeasy Mini Kit (Qiagen), followed by standard QC pipeline by Novogene Corporation.
250~300 bp insert cDNA library, eukaryotic mRNA non-directional library was built using standard Illumina kits and protocols.

treatment_protocol: 24-week old WT and hepatic FBP1-deficient mice were saced following approvied protocols, and livers were sanpfrozen in liqiud nitrogene ultil use.

tag: strain background

value: Liver


title: ABHD5-KO-1


title: FReP Batch 1- Sample 1 (FRep 1-1)

description: After fibromodulin reprogramming


title: Ctrl-3


title: AS3: AS, biological rep3

city: 重庆

first: Bi

last: xianjin

address: gaotaoyan

institute: tmmu

description: Gene expression data from mouse aortic smooth muscle cells

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Affymetrix Mouse Gene 1.0ST Array  in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA (Robust Multi-chip Average ) method.

source_name: mouse aortic smooth muscle cells from AS mice

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

extract_protocol: Total RNA was extracted and purified using miRNeasy Micro Kit and RNase-Free Dnase Set.

treatment_protocol: AAS mouse model was conducted by creating a 5/6 nephrectomy CKD mouse model in ApoE-/- mice, then which were fed by high fat diet for 12 weeks. ApoE-/- mice which were fed with high fat diet or normal diet for 12 weeks were AS group or ND group.

value: mouse aortic smooth muscle cells


title: PBS1cells bulk RNA-seq

value: Microglia cells

value: 3’ Quantseq

value: fresh


title: AS1: AS, biological rep1


title: FReP 1-2

description: After fibromodulin reprogramming


title: exp_lfm08


title: exp_lfm09


title: AAS3: AAS, biological rep3

source_name: mouse aortic smooth muscle cells from AAS mice


title: Ctrl-1


title: AAS1: AAS, biological rep1


title: BFR2_X8b2

value: Vehicle

value: postnatal day 120


title: ND3: ND, biological rep3

source_name: mouse aortic smooth muscle cells from ND mice


title: exp_lfm07


title: ND2: ND, biological rep2


title: T09_12h_miRNA_rep3

city: Xiamen

first: Jun

last: Yang

address: 1799 Jimei Road, Xiamen, 361021 PR China

institute: Chinese Academy of Sciences

data_processing:
Raw reads were cleaned up by trimming adapter sequences, removing poly-N containing reads (⩾5% of nucleotides in each read) and filtering low quality reads (Q-score⩽20 for⩾50% of nucleotides in each read) using an in-house Perl script.
Reads smaller than 18 nt or longer than 30 nt in length were removed.
Sequence tags originating from non-coding RNAs (rRNA, scRNA, snoRNA, snRNA and tRNA) deposited in Rfam 10.1 database were also excluded.
The remaining reads were used to detect known microRNAs and novel microRNAs predicted by comparing with known microRNAs from miRBase 21.0.
The expression level of all microRNAs were normalized by dividing the absolute read count with the total read count of the sample and multiplying the result by 1,000,000.
The differentially expressed microRNAs were defined with |log2 (fold change)| > 1 and p-value < 0.05.
Genome_build: reference sequence use for reads alignment
Supplementary_files_format_and_content: tab-delimited text files include expression values for each Sample

organism: Euplotes vannus

source_name: single cell organism, ciliate protist

growth_protocol: Clonal cultures were established and maintained in Oshima’s artificial seawater at 25℃ under cool white fluorescent light (16 h light: 8 h dark) at a light intensity of ~40 μmol photons m^-2 s^-1

extract_protocol:
About 5 × 10^4 cells were collected on each treatment and homogenized in TRIzol Reagent, and RNA was extracted according to the manufacturer's protocol. Ethanol precipitation instead of RNA binding column was used in this isolation, which enables us to analyze both mRNA and microRNA from one sample.
Small RNA libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) from 1.5 μg total RNA.

treatment_protocol: We conducted transcriptomic and microRNAomic analyses after 0, 1 and 12 hours of 15 mg/L AgNPs treatment.

value: whole organism


title: ND1: ND, biological rep1


title: exp_lfm06


title: T08_12h_miRNA_rep2


title: T07_12h_miRNA_rep1


title: con_lfm05

source_name: wild type_liver

value: wild type


title: AAS2: AAS, biological rep2


title: GI LP2

city: Columbus

first: Ramaswamy

last: Bhuvaneswari

state: OH

address: 320 W 10th Ave

department: Internal Medicine, Division of Medical Oncology

institute: The Ohio State University's Wexner Medical Center

description:
O
GI, Luminal Progenitor 2

hyb_protocol: As per GeneChip Hybridization, wash and stain kit Cat. No. 900720.

scan_protocol: Used GeneChip 3000 7G scanner and GeneChip Command Console software.

data_processing:
Transcriptome Analysis Console
RMA

source_name: Mouse mammary gland

label_protocol: Affymetrix proprietary terminal DNA labeling, followed by biotinylation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions, followed by DNase treatment. GeneChip WT-Pico kit was used for cDNA prep according to manufacturer's instructions.

treatment_protocol: Single cell suspension of the mammary glands was enriched for lineage-negative (Lin−) epithelial cells using EasySepTM Mouse Epithelial Cell Enrichment kit (Stem Cell Technology) excluding the Lin+ cells, specifically hematopoietic (biotinylated CD45 and TER119), endothelial (biotinylated CD31), and immune (biotinylated BP-1) cells. The negatively selected cell population was enriched for luminal epithelium (LE) and mammary stem cell (MaSC)-enriched/basal epithelium (MaSC-enriched). For FACS analysis, Lin− populations were labeled with CD24-PE, CD29-FITC (BD Pharminogen), and CD61-APC (Invitrogen) while their respective isotypes (Thermo Fisher, eBioscience) were used as negative controls. Cell suspensions were incubated with the appropriate antibodies for 30 min on ice. Cells were resuspended in FACS buffer (1 mM EDTA, 1% HI-FBS, and 25 mM HEPES, pH 7.0 in 1× phosphate-buffered saline) and sorted on a FACS BD LSR II Flow Cytometer (BD Biosciences).

value: FVB/N

value: Wild type

value: Mammary luminal progenitor cells

tag: mammary gland involution

value: Gradual


title: AS2: AS, biological rep2


title: con_lfm04

city: Philadelphia


title: AI LP2

description:
K
AI, Luminal Progenitor 2

value: Abrupt


title: AI LP1

description:
P
AI, Luminal Progenitor 1


title: T06_1h_miRNA_rep3


title: con_lfm03


title: GI LP1

description:
I
GI, Luminal Progenitor 1


title: T04_1h_miRNA_rep1


title: T03_0h_miRNA_rep3


title: con_lfm01


title: con_lfm02


title: 4_24h_mock_1_25uM_RBV

city: Bochum

first: Daniel

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

institute: Ruhr University Bochum

data_processing:
RNA libraries were run on Illumina NovaSeq6000, basecalling was performed using Real-Time Analysis (RTA) v3.3.3
bcl files were converted to fastq files with bcl2fastq v2.20.0.422
Quality of fastq files was checked with CLC Genomics Workbench 11.0.1
mapping of fastq files to homo sapiens (hg 38) sequence and calculation of Reads Per Kilobase of exon per Megabase of library size (RPKM) was performed using CLC Genomics Workbench 11.0.1 (Mismatch cost = 2; Insertion cost = 3; Deletion cost = 3; Length fraction = 0.8; Similarity fraction = 0.8)
Genome_build: hg38

source_name: surrounding tissue from partial liver resection after recurrent hepatic metastasis

growth_protocol: Primary human hepatocytes (PHH) were isolated from liver specimens, plated at a density of 1.3×10e6 on collagen-coated 6-well dishes, and kept in hepatocyte culture medium (Williams´ medium E)

extract_protocol:
Total RNA from primary cells was extracted using a NucleoSpin RNA kit (Macherey-Nagel, Ref 740955.250) according to the manufacturer’s instructions. RNA quality was checked on an Agilent Bioanalyzer.
Libraries were prepared according to manufacturer's instructions accompanying the NEBNext Ultra II Directional RNA Library Prep Kit (#E7765S/L)

treatment_protocol: Virus stock of HEVcc intracellular p6_G1634R was produced in HepG2 in DMEM complete with freeze and thaw cycles in DMEM complete. The virus was filtered through a 0.45 μm filter to remove all potential leftover cell debris. Afterwards virus was used for inoculation of the primary cells at an MOI of 1 and diluted – if necessary – in DMEM complete for the human primary cells (PHH). As a control 25 μM ribavirin was used.

tag: gender

value: male

tag: cells

value: primary human hepatocytes

tag: inoculation

value: control

value: ribavirin 25 µM

tag: time point of rna extraction post inoculation


title: 4_48h_mock_1_25uM_RBV


title: 4_7d_mock_1_25uM_RBV


title: 4_4h_mock_1_25uM_RBV

value: 4 h


title: 3_7d_mock_untreated

value: PBS


title: 4_12h_mock_1_25uM_RBV


title: 4_8h_mock_1_25uM_RBV

value: 8 h


title: T02_0h_miRNA_rep2

tag: tissue


title: 3_48h_mock_untreated


title: 3_24h_mock_untreated


title: T01_0h_miRNA_rep1


title: Donor2frozen scRNA-seq

data_processing:
Cell ranger with default settings
Supplementary_files_format_and_content: Raw count file

value: brain

value: NeuN-Olig2- nuclei

value: 10x Genomics

value: frozen


title: 3_12h_mock_untreated


title: 3_8h_mock_untreated


title: T09_12h_RNA_rep3

data_processing:
Raw reads were cleaned up by trimming adapter sequences, removing poly-N containing reads (⩾5% of nucleotides in each read) and filtering low quality reads (Q-score⩽20 for⩾50% of nucleotides in each read) using an in-house Perl script.
Transcriptome assembly was performed using Trinity (min_kmer_cov=2, and all other parameters set default).
Differentially expressed genes were estimated using edgeR (V3.6),Genes with |log2 (fold change)| > 1 and FDR < 0.01 were defined as differentially expressed genes.
Genome_build: reference sequence use for reads alignment
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
About 5 × 10^4 cells were collected on each treatment and homogenized in TRIzol Reagent, and RNA was extracted according to the manufacturer's protocol. Ethanol precipitation instead of RNA binding column was used in this isolation, which enables us to analyze both mRNA and microRNA from one sample.
A total of 3 μg RNA per sample was used to generate a paired-end RNA-seq library using NEBNext®UltraTM RNA Library Prep Kit, following the manufacturer’s instructions.

value: whole organism


title: 3_4h_mock_untreated


title: T05_1h_miRNA_rep2


title: 2_7d_MOI_1_25uM_RBV

value: HEV genotype 3 p6 (Kernow C-1) G1634R MOI = 1


title: 2_24h_MOI_1_25uM_RBV


title: 2_48h_MOI_1_25uM_RBV


title: Donor2cells scRNA-seq

value: Microglia cells

value: fresh


title: T07_12h_RNA_rep1


title: 2_8h_MOI_1_25uM_RBV


title: Donor1cells scRNA-seq


title: 2_4h_MOI_1_25uM_RBV


title: T08_12h_RNA_rep2


title: 1_7d_MOI_1_untreated


title: Donor1frozen scRNA-seq


title: Donor1nuclei scRNA-seq

value: Microglia nuclei


title: G2_PC_2

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from GENERGY BIO company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of GENERGY BIO.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina X ten was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: mouse embryonic stem cells


title: 2_12h_MOI_1_25uM_RBV

value: male


title: Donor2nuclei scRNA-seq

tag: sampletype

tag: sequencing protocol


title: T04_1h_RNA_rep1


title: T06_1h_RNA_rep3


title: T03_0h_RNA_rep3


title: 1_12h_MOI_1_untreated

value: primary human hepatocytes


title: C6orf203 wild-type cells

city: Stockholm

first: Shreekara

last: Gopalakrishna

state: Solna

address: Solnavägen 9

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Adaptor sequences were trimmed using the FASTX-Toolkit
Trimmed reads mapping to nuclear-encoded rRNA were discarded
The remaining reads were mapped sequentially to mitochondrial rRNA (mt-rRNA); mitochondrial tRNA (mt-tRNA); and mitochondrial mRNA (mt-mRNA) using bowtie version 1, with parameters -v 2 --best (i.e. maximum two mismatches, report best match)
When calculating the expression levels of mitochondrial genes, to normalise for different library sizes, counts for a given library were expressed as reads per million (RPM) mapped in the positive-sense orientation to nuclear-encoded mRNA in that library
Regions of coding sequence (CDS) that overlap (ATP8/ATP6 and ND4L/ND4) were excluded due to ambiguous CDS assignment
Mitochondrial ribosome-protected fragments (mtRPFs) with 5' ends mapping within 15 nt of the start codon or 45 nt of the stop codon were excluded
The reference genome assembly used for read mapping was from GenBank, accession number: GQ472310.1
Genome_build: GQ472310.1
Supplementary_files_format_and_content: Tab-delimited text file including normalized counts per gene as Ensemble Gene ID for each sample

source_name: Human Embryonic Kidney_Flp-In™ 293 T-REx

growth_protocol: Flp-In T-Rex human embryonic kidney 293T (HEK293T, Invitrogen) cells (wildtype and C6orf203 KO) were cultured in DMEM (Dulbecco´s modified eagle medium) supplemented with 10% (v/v) tetracycline-free fetal bovine serum (FBS), 2 mM GlutaMax (Gibco), 1x Penicillin/Streptomycin (Gibco), 50 μg/ml uridine, 100 μg/ml Zeocin (Invitrogen) and 10 μg/ml blasticidin (Gibco) at 37°C under 5% CO2 humidified atmosphere

extract_protocol:
200 μl aliquots of cell lysates were treated with 7.5 μl RNase 1 (100 units/μl) at 28°C. The reaction was layered onto a 10–30% sucrose gradient as described above for ‘Analysis of mitochondrial ribosome integrity’. Subsequently, all fractions containing mitochondrial monosomes, ascertained by western blotting, were pooled and digested with proteinase K (200 μg/ml) for 30 min at 42°C. RPFs were recovered by extracting twice with pre-warmed (65°C) acidic phenol:chloroform and once with chloroform (1:1, v/v, buffered with 10 mM Tris pH 7.5, 0.1 mM EDTA) followed by ethanol precipitation
RPFs (1 μg) were separated on 15% denaturing polyacrylamide gels and RNA species migrating between 10 and 50 nt were harvested. RNA was eluted from the gel slices and ethanol precipitated. The RNA samples from above were heated at 80°C for 2 min, cooled and the 3’ phosphate group removed using T4 polynucleotide kinase (New England Biolabs) for 2 hr at 37°C in a 20 μl reaction. The RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated in a 20 μl reaction overnight at 14°C to a preadenylated 3’-adaptor using T4 RNA Ligase 2 (New England Biolabs). RNA was precipitated, loaded into a 15% denaturing polyacrylamide gel and ligated RNA fragments migrating between 10 and 50 nt were excised. The RNA was eluted, precipitated, resuspended as above, and 5’ phosphorylated using T4 PNK in the presence of 1 mM ATP for 2 hr at 37°C. RNA was concentrated by ethanol precipitation, resuspended in 10 mM Tris-HCl (pH 7.5) and ligated to a 5’ RNA adaptor overnight at 14°C using T4 RNA Ligase (New England Biolabs). The fully adapted RNAs were recovered by ethanol precipitation, dissolved in 6 μl 10 mM Tris-HCl (pH 7.5), and ligated product annealed to an RT primer for 5 min at 65°C. The RNA was subsequently reverse transcribed for 50 min at 55°C in using SuperScript III according to manufacturer’s instructions, followed by heat inactivation for 5 min at 85°C. Standard PCR reactions were used to prepare amplicons using forward primer RP1 and RPIX as reverse primer, where X is primer number (1-24). PCR reactions were loaded onto 10% non-denaturing polyacrylamide-TBE gels and products of ~150 bp were excised from the gel and eluted. These amplicon libraries were ethanol precipitated and resuspended in 15 μl 10 mM Tris-HCl (pH 7.5)
Ribosomal RNA was depleted from MitoRibo-Seq samples at the library amplicon stage; 12 µL of the relevant MitoRibo-Seq library was mixed with 4 µL of 4 × hybridization buffer (200 mM HEPES pH 7.5 and 2 M NaCl) and denatured at 98°C for 2 min. DNA was re-annealed for 5 hr at 68°C prior to addition of 2 µL of 10 × DSN master buffer and 2 µL of DSN (four units, Evrogen). Digestion was allowed to proceed for 25 min at 68°C, before addition of 20 µL 10 mM EDTA and incubation for a further 5 min at 68°C. DNA was recovered by a single extraction with phenol–chloroform (1:1, vol/vol) followed by ethanol precipitation and resuspended in 4 µL 10 mM Tris–HCl pH 7.5. The treated amplicon library was subjected to another round of PCR (as above) and the resulting library subjected to a second round of DSN treatment.

treatment_protocol: Generation of HEK293T knockout cell line for C6orf203 was performed using CRISPR/Cas9 system. Briefly, guide RNAs (gRNAs) designed to generate an out-of-frame deletion in exon 1 were cloned into pSpCas9(BB)-2A-Puro (pX459) V2.0 vector. C6orf203 targeting pX459 vectors were transfected to cells using Lipofectamine 3000 according to the manufacturer’s instructions. After 48 h of puromycin (1.5 μg/ml) selection, cells were serially diluted to plate single cells in each well of a 96-well plate. Resultant clones were screened by PCR and Western blotting. Loss of C6orf203 in selected clones was confirmed by Sanger sequencing

tag: genotype

value: Wildtype


title: C6orf203 KO cells


title: G1_PD_2

value: 1 µM PD0325901/serum


title: 1_8h_MOI_1_untreated

source_name: surrounding, healthy tissue from partial liver resection after recurrent hepatic metastasis


title: G1_PD_1


title: sRNA apical spikelets

city: Bhubaneswar

first: Birendra

middle: Prasad

last: Shaw

state: Odisha

address: Nalco Square, Besides Kalinga Hospital

country: India

institute: Institute of Life Sciences

data_processing:
The sRNA raw reads were subjected to bioinformatics analysis using Fastx Toolkit by which the read quality and length below 17 were trimmed. The filtered reads were mapped on the rice genome using SHRiMP package.
Quantification of the known miRNAs was done using miRDeep2 software, which generated normalized counts utilizing information on the mapped data and known precursors.
The unique reads were searched for the known sequences in the miRBase 22.1 for the identification of the known miRNAs.
The sRNA sequences were then mapped on rice genome for the identification of possible novel miRNAs and their precursors.
The basic criteria described in literature were followed for putative miRNA prediction, including the length of the precursors, formation of hairpin, MFEI value of the precursors, and others.
Genome_build: NCBI Build 4.0, Rfam
Supplementary_files_format_and_content: Excel sheet of known and novel miRNAs and the related information on their ientification

organism: Oryza sativa

source_name: Spikelets

growth_protocol: Seeds of Oryza sativa cv. Mahalaxmi were germinated on nursery bed and transplanted in field. Pesticides and fertilizers were applied as per the requirement

extract_protocol:
Total RNA was extracted from the individual spikelet samples using Plant RNA purification reagent (Invitrogen). The quality of the RNA was checked for integrity on bioanalyzer, and only the RNA preparation with RNA integrity (RIN) greater than 7.0 was considered for the downstream application.
Ion Total-Seq Kit v2.0 (Thermo Fisher) was used for enrichment of the sRNA population in the individual RNA preparation, ligation of barcoded adapters to sRNAs and conversion of the sRNAs to cDNAs.
The cDNA libraries of sRNAs prepared was verified for size distribution using Agilent 2100 Bioanalyzer. The individual libraries were diluted to 100 pM and pooled in equimolar concentrations for clonal amplification and sequencing. The clonal amplification was done on ion sphere particles (ISs) by emulsion PCR. ISPs positive templates were loaded on Ion PI chip kit (Thermo Fisher) after denaturing and sequencing was on the Ion Proton System

treatment_protocol: The indiviual plants were tagged on the days of anthesis. The spikelets were sampled from the apical and basal regions of the panicle on the 6th days after fertilization

tag: cultivar

value: Mahalaxmi

tag: location on panicle

value: Apical spikelets

value: Spikelets

tag: maturity

value: 6th days after fertilization


title: T01_0h_RNA_rep1


title: sRNA basal spikelets

value: Basal spikelets


title: T05_1h_RNA_rep2


title: 1_24h_MOI_1_untreated

value: PBS


title: G2_PC_1


title: T02_0h_RNA_rep2


title: TDP43siRNAplusATP_2

status: Public on Aug 09 2019

city: Boulder

first: Thomas

last: LaRocca

state: CO

address: 1725 Pleasant St

institute: University of Colorado Boulder

data_processing:
Adapters trimmed using Trimmomatic.
Reads aligned with Tophat2, followed by remapping of unaligned reads with Bowtie2.
Repetitive element transcripts aligned using Repenrich algorithim.
Differential expression analyzed with Deseq2.
Genome_build: rn6
Supplementary_files_format_and_content: Raw gene and repetitive element counts for each sample.

source_name: TDP-43 siRNA and ATP-treated RNA-seq

growth_protocol: Primary astrocytes were harvested from neonatal pups and purified using standard protocols. Cells were grown in DMEM/F12, subcultured at 90% confluency, and transfected and/or treated at 70% confluency.

extract_protocol:
RNA for polyA RNA-seq extracted using Trizol and Zymo spin columns. IP lysates purified using J2 antibody-bound immunoprecipitation beads, and total RNA extracted with Trizol.
PolyA libraries were prepared according to Illumina's instructions using the TruSeq kit, and total RNA libraries for immunoprecipitated samples were prepared using the V2 Scriptseq kit (Epicenter).

treatment_protocol: siRNA treatments using Lipofectamine 3000 according to manufacturer's instructions.

tag: strain

value: Sprague-Dawley

value: Primary rat astrocytes

tag: passages

value: TDP-43 siRNAplusATP

tag: ip antibody


title: TDP43siRNA_J2ip3

source_name: IP TDP-43 siRNA-treated immunoprecipitated RNA-seq

tag: treatment

value: TDP-43 siRNA

value: J2 antibody


title: TDP43siRNAplusATP_3


title: TDP43siRNAplusATP_1


title: TDP43siRNA_J2ip1


title: TDP43siRNA_input3

source_name: IP TDP-43 siRNA-treated input RNA-seq


title: NT-Empty

city: Seoul

first: Sung Hoon

last: Choi

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Yonsei Liver Center

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to hg19 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human HCC cell lines (Hep3B)

growth_protocol: Hep3B (KCLB88064, Korean Cell line Bank) cells were cultured at 37°C with 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Grand Island, NY) supplemented with 10% fetal bovine serum (FBS; Gibco, CA, USA)

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

treatment_protocol: Cells were transfected with respective siRNAs and pcDNA3.1 expression vector using Fugene HD transfection agent (Promega, Madison, WI, USA) according to the manufacturer’s instructions. After transfection, the cells were incubated at normal conditions (21% O2) for 6 h, then replaced with fresh culture medium.

value: Fugene treatment


title: siTERT

value: siTERT transfection


title: HKR3

value: pcDNA3.1-HKR3 transfection


title: LNCAP_DMSO_INPUT

city: CHICAGO

first: Rajita

last: Vatapalli

state: IL

address: 303 E SUPERIOR, 6-250

institute: Northwestern University

description: LNCaP treated with DMSO vehicle for 8 days

data_processing:
Sequence reads were aligned to the Human Reference Genome (assembly hg19) using Burrows-Wheeler Alignment (BWA) Tool Version 0.6.1
Peak identification, overlapping, subtraction and feature annotation of enriched regions were performed using Hypergeometric Optimization of Motif EnRichment suite (HOMER)
Genome_build: hg19
Supplementary_files_format_and_content: BED graphs

source_name: LNCaP

growth_protocol: LNCaP and PC3 were routinely grown in RPMI media with 10% FBS and 1% Pen-strep.

extract_protocol:
Cells were fixed with formaldehyde and lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Barcoded sequencing libraries were generated using KAPA Library Preparation Kits (Kapa Biosystems) according to the manufacturer’s protocol. Libraries were quantified using a qPCR-based quantification (Kapa Biosystems).

treatment_protocol: Cells were treated with either DMSO vehicle or 1uM EPZ004777.

value: LNCaP

value: Prostate cell line

tag: chip antibody

value: DMSO


title: PC3_DMSO_INPUT

description: PC3 treated with DMSO vehicle for 8 days


title: LNCAP_EPZ_INPUT

description: LNCaP treated with 1uM EPZ004777 for 8 days


title: PC3_EPZ_INPUT

description: PC3 treated with 1uM EPZ004777 for 8 days


title: PC3_DMSO_H3K79ME2


title: LNCAP_DMSO_H3K79ME2


title: PC3_EPZ_H3K79ME2


title: 1_4h_MOI_1_untreated

tag: gender

value: male

tag: cells

value: primary human hepatocytes

value: HEV genotype 3 p6 (Kernow C-1) G1634R MOI = 1

value: 4 h


title: TDP43siRNA_input2


title: LNCAP_EPZ_H3K79ME2


title: TDP43siRNA_J2ip2


title: TDP43siRNA_input1


title: 1_48h_MOI_1_untreated

tag: inoculation

tag: time point of rna extraction post inoculation


title: TDP43siRNA_3

source_name: TDP-43 siRNA-treated RNA-seq


title: TDP43siRNA_2


title: TDP43siRNA_1


title: NegativeControl_3

source_name: Control (scrambled) siRNA-treated RNA-seq

value: scrambled (control) siRNA