title: Input-2

city: London

first: Stephen

middle: James

last: Renaud

state: Ontario

address: 1151 Richmond St

department: Anatomy and Cell Biology

country: Canada

institute: Western University

data_processing:
Basecalling was done in BaseSpace.
Raw reads were trimmed.
BigWig coverage tracks were generated from the aligned reads using deepTools2. A sliding window approach implemented in the csaw R/Bioconductor package was used to identify regions enriched in AcH3. Windows were filtered out if the fold enrichment was below log2(3) compared to background. Filtered windows less than 100 bp apart were merged and a maximum region size of 5000 bp was permitted, conferring a total of 49 648 regions.
Differential binding analysis of count data within these regions using DESeq2 R/Bioconductor package, and used the independent hypothesis weighting R/Bioconductor package to weight P-values and adjust for multiple testing.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: merged.csaw.tol100.max5000.bed: Bed file contains coordinates of regions enriched for AcH3.

source_name: Placenta

extract_protocol:
The cells were fixed and then lysed, followed by sonication. The sonicated DNA was incubated in AcH3 antibody overnight and was pulled down using agarose beads.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: The cells were treated with 8 bromo cyclic AMP to differentiate to syncytiotrophoblast.

value: BeWo trophoblast cells

value: Cytotrophoblast + Syncytiotrophoblast

tag: chip antibody


title: hot  treated 6 hr replicate 4 [H4-6hr_S27_L003]

status: Public on Aug 11 2021

type: SRA

city: Brisbane

first: Peter

middle: A

last: Crisp

state: QLD

address: John Hines Building (62), The University of Queensland

department: School of Agriculture and Food Science

country: Australia

institute: The University of Queensland

library_source: transcriptomic

data_processing:
bcl2fastq2 Conversion Software v2.20 was used to convert bcl to fastq files and remove adapter sequences
Quality control was performed with FastQC v.0.11.2. Adapters were removed using scythe v.0.991 with flags -p 0.01 for the prior and reads were quality trimmed with sickle v.1.33 with flags -q 20 (quality threshold) -l 20 (minimum read length after trimming). The trimmed and quality filtered reads were aligned to the rice reference genome Os-Nipponbare-Reference-IRGSP-1.0 from the MSU Rice Genome Annotation Project Database v7 (http://rice.plantbiology.msu.edu/) using the subjunc aligner v1.5.0-p1 with -u and -H flags to report only reads with a single unambiguous best mapping location, -P 3 for phred+33 encoding (Liao et al., 2013). Reads were then sorted, indexed and compressed using samtools v1.1-26-g29b0367 (Li et al., 2009) and strand-specific bigwig files were generated using bedtools genomecov v2.16.1 (Quinlan and Hall, 2010) and the UCSC utility bedGraphToBigWig for viewing in IGV (Robinson et al., 2011). Summary statistics for each sample are provided in Supplementary Dataset S1: Summary of transcriptomic datasets.
For standard differential gene expression testing, the number of reads mapping per IRGSP-1.0 gene loci was summarised using featureCounts v1.5.0-p1(Liao et al., 2014) with flags -P and -c to discard read pairs mapping to different chromosomes and the -s flag set to 2 for strand specificity for a strand specific library, multimapping reads and multioverlapping reads were not counted. Reads were summarised to parent IRGSP-1.0 gene loci rather than individual splice variants by summarising to the genomic coordinates defined by the feature "gene" in the IRGSP-1.0.gff reference (last modified 7/2/2012 ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/all.dir/all.gff3). Only loci with an abundance of at least 1 CPM (approximately 5 reads) in at least 4 samples were retained. Statistical testing for relative gene expression was performed in R following the “edgeR-limma-voom” approach (https://www.bioconductor.org/help/workflows/RNAseq123/); using, edgeR v.3.4.2(McCarthy et al., 2012; Robinson and Oshlack, 2010; Robinson et al., 2010; Robinson and Smyth, 2007, 2008), and voom in the limma package 3.20.1(Law et al., 2014; Smyth, 2005, 2004).
Genome_build: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary_files_format_and_content: Gene expression counts were normalised using limma-voom and are provided as a normalised counts per million per gene locus matrix.

molecule: total RNA

organism: Oryza sativa

source_name: hot  treated 6 hr_leaf tissue

growth_protocol: Rice (Oryza sativa) cultivar IR64 plants were grown hydroponically in a glasshouse facility at the Research School of Biology, Australian National University between October and December 2015. Seeds were initially incubated at 40-42°C for two days before soaking in water for eight hours, placed on wet Whatman filter papers in Petri dishes and kept in the dark at 30°C for five days. The germinated seedlings were then transferred to trays of vermiculite and placed in temperature-controlled glasshouses (30°C day and 25°C night) under natural sunlight and photoperiod with photosynthetically active radiation (PAR) between 400 and 1200 µmol m-2 s-1.   When the third leaf had emerged, seedlings were transplanted from vermiculite to a hydroponic system. Individual plants were placed within PVC tubes with a 3.7 cm diameter and 13 cm height. Tubes were then suspended at the top of 20 L capacity hydroponic tanks (12 tanks in total), with each tank holding a maximum of 20 plants. Each tank was filled with hydroponic solution (Table S1) (Hubbart et al., 2007). The nutrient solution was replaced weekly and sulphuric acid or sodium hydroxide were used to adjust the pH to between 5-6, with pH monitored using a portable pH meter (Rowe Scientific Pty. Ltd., NSW, Australia). The hydroponic solution was aerated continuously using Infinity AP-950 air pumps (Kong’s Pty. Ltd., Ingleburn, Australia). After two weeks of hydroponic growth at 30/25°C, the most recently fully-expanded leaves were labelled as pre-existing (PE) leaves. Following labelling, four tanks were randomly chosen and shifted to an adjacent glasshouse room set to 25°C day and 20°C night (25/20°C), and four tanks to a room set at 40°C day and 35°C night (40/35°C) temperature regime, while four tanks were retained at 30/25°C as controls. Newly-developed (ND) leaves that emerged in each thermal regime were labelled, with all measurements reported on ND leaves being made 21-days after T transfer. For all experiments, four separate leaves from separate plants, one from each hydroponic tank (pot replicates) per T treatment were sampled.

extract_protocol:
For each time point and temperature treatment, approximately 8 cm of middle leaf section (less than 100 mg) were sampled by immediately freezing leaf material in liquid N2 and storing at -80°C until RNA extraction. Total RNA was extracted using the RNeasy plant mini protocol (Qiagen, Doncaster, VIC, AU) and treated with DNase I (Qiagen, Doncaster, VIC, AU) to remove any contaminating DNA.
RNAseq libraries were prepared using the Illumina Stranded Total RNAseq kit with RiboZero rRNA depletion as per the manufacturer's guidelines (Illumina). Libraries were pooled and sequenced on a HiSeq1500 for 61 cycles in single end mode at the Centre for AgriBioscience, LaTrobe University, Melbourne, Australia.

treatment_protocol: To quantify transcript abundance following changes in thermal regimes, the labelled pre-existing (PE) leaves were harvested 2, 6 and 24 h after the shifting of the plants 3 h into the day period so that all sample points were collected during the day.

tag: cultivar

tag: treatment teperature

value: hot

tag: timepoint

tag: tissue

value: leaf tissue


title: Lin-  eCLIP for IGF2BP3 rep5

city: Los Angeles

first: Dinesh

last: Rao

address: 650 Charles E Young Dr S

department: Pathology & Lab Medicine

country: USA

institute: UCLA

description:
technical rep
bm_linms_jd132e

data_processing:
Library strategy: eCLIP-Seq
mapping to mm10 with STAR (v 2.5.3a)
repeatmasking with bowtie2
peak calling - CLIPper with default parameters
differential expression with DESeq2 on all genes with non-zero counts
Genome_build: mm10

organism: Mus musculus

source_name: Lin- cells

growth_protocol: Lin- cells were obtained by harvesting the BM from mice, lysing in red blood cell lysis buffer, and staining with a cocktail of biotinylated antibodies for lineage depletion by MACS (Miltenyi). Lin- cells were spin-infected with the MSCV-MLL-flag-Af4 retroviral supernatant four times at 30°C for 45 minutes in the presence of polybrene. Cells were selected with 400 μg/ml of G418 for 7 days.

extract_protocol:
CD11b+ cells were obtained by harvesting the splenic tumors from the WT/MLL-Af4 or I3/MLL-Af4 mice, lysing in red blood cell lysis buffer, and staining with a CD11b biotinylated antibody for positive selection by MACS (Miltenyi). RNA from both cell types was collected using QIAzol Lysis Reagent and purified using the miRNeasy Mini Kit (217004; Qiagen). The Agilent 2100 Bioanalyzer using RNA pico chip was utilized to quality check total RNA. The Nugen Universal plus mRNA-Seq Kit was used to generate strand-specific RNA-seq libraries. Samples were subjected to poly(A) RNA selection, RNA fragmentation and double-stranded cDNA generation using a mixture of random and oligo(dT) priming. The cDNA samples were then subjected to end repair to generate blunt ends, adapter ligation, strand selection, and PCR amplification to generate the final library. To mulitplex samples in one sequencing lane, different index adapters were used. Single-end, strand-specific RNA sequencing was performed on the Illumina HiSeq3000 system for the Lin- and CD11b+ samples, resulting in 15-20 million reads per sample, at the the UCLA Technology Center for Genomics & Bioinformatics.
Nugen Universal plus mRNA-Seq Kit (RNA-seq) and Eclipse BioInnovations Inc eCLIP kit (eCLIP)

tag: cell type

value: Lin- cells

tag: eclip antibody

value: MBL IGF2BP3 antibody (RN009P)

tag: treatment

value: no treatment


title: hif2aKO_normoxia_rep2

city: Oxford

first: Adrian

middle: L

last: Harris

address: John Radcliffe Hospital

department: Department of Medical Oncology

country: United Kingdom

institute: University of Oxford

data_processing:
Cutadapt was used to trim low quality sequences
STAR was used to align the reads to genome and counts per gene was calculated using featurecounts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix containing raw gene counts for 786-0 cells upon knockout of HIF2α & upon treatment with PT2385 (drug) in normoxia

organism: Homo sapiens

source_name: 786-0 cells

growth_protocol: cells were grown in DMEM 5mM glucose supplemented with 10% FBS

extract_protocol:
RNA was extracted using Tri-Reagent following the manufacturer´s instructions
libraries were prepared using Illumina’s instructions

treatment_protocol: 786-0 WT and 786-0 KO cells were cultured under normoxia (21% O2) for 48h. 786-0 WT cells were additionally treated with 10uM PT2385 for 48h.

tag: cell line

value: clear cell renal cell carcinoma

tag: genotype

value: hif2a KO


title: Lin- size-matched input rep4

value: input


title: hif2aKO_normoxia_rep1


title: Input-1

library_source: genomic

molecule: genomic DNA


title: Input-3


title: Lin-  eCLIP for IGF2BP3 rep4

description:
technical rep
bm_linms_jd131e


title: hot  treated 24 hr replicate 1 [H1-24hr_S19_L002]

source_name: hot  treated 24 hr_leaf tissue


title: Diff-3

value: Syncytiotrophoblast

value: AcH3 (Sigma-Aldrich catalog 06-599)


title: normoxia_control_rep3

value: WT


title: hot  treated 6 hr replicate 2 [H2-6hr_S21_L003]


title: Lin- size-matched input rep3


title: Lin- size-matched input rep5


title: hot  treated 2 hr replicate 4 [H4-2hr_S26_L003]

source_name: hot  treated 2 hr_leaf tissue


title: Diff-2


title: hot  treated 2 hr replicate 3 [H3-2hr_S23_L003]


title: Diff-1


title: hot  treated 24 hr replicate 3 [H3-24hr_S25_L003]


title: Lin-  eCLIP for IGF2BP3 rep3

description:
biological rep
bm_linms_jd123e


title: normoxia_control_rep1


title: CTRL-3

value: Cytotrophoblast


title: Lin- size-matched input rep2


title: Lin-  eCLIP for IGF2BP3 rep2

description:
biological rep
bm_linms_jd122e


title: hot  treated 2 hr replicate 2 [H2-2hr_S20_L002]


title: Reactor 5 under Aerobic conditions

city: Hayward

first: Fatemeh

last: Shirazi

state: CA

address: 26229 Eden Landing Rd.

institute: Microvi Biotech Inc.

data_processing:
Cutadapt [version 1.10] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (version 0.10.1 ) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used bowtie2 [version 2.2.0] to map reads to the genome of https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/203/895/GCF_000203895.1_ASM20389v1.
Trancripts for each sample were assembled independently using StringTie version 1.3 and then all the assemblies were merged to create a StringTie merged gtf to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
Profiling of the mRNAs expression were performed using StringTie software version 1.3
StringTie [version 1.3] was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [version date 2016/09/29].
Genome_build: GCF_000203895.1_ASM20389v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Paracoccus denitrificans

source_name: Bacterial Cell

growth_protocol: Cells were grown in Terrific Broth media under Aerobic conditions. After growth, the cells were harvested and used for Chromium reduction experiment with minimal media and 1000 ug/L Cr (VI).

extract_protocol:
QIAGEN RNeasy Mini Kit was used for purification of total RNA from bacteria. Bacterial cells were disrupted and homogenized by bead-milling in a guanidine-thiocyanate–containing lysis buffer. After addition of ethanol, the sample was loaded onto an RNeasy Mini spin column. Total RNA binds to the RNeasy silica-membrane, contaminants were efficiently washed away, and high-quality RNA was eluted in RNase-free water.
For Total RNA sequencing service, RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Ribosomal RNA was removed, followed by fragmentation with divalent cation buffers in elevated temperature. The sequencing library was prepared following Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: Samples taken after exposure to Cr(VI) and immediately preserved with RNAprotect Bacteria Reagent

value: Exposed to Cr(VI) under aerobic conditions for 5 hours


title: hot treated 2 hr replicate 1 [H1-2hr_S17_L002]

source_name: hot treated 2 hr_leaf tissue


title: Lin- size-matched input rep1


title: CTRL-2


title: cold treated 6 hr replicate 4 [C4-6hr_S39_L004]

source_name: cold treated 6 hr_leaf tissue

value: cold


title: Acetate and CATPB treated sample 2 [PBO-6]

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to hg19 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

source_name: HEK293_Acetate and CATPB

growth_protocol: human GPR43 expressing cells were maintained in DMEM supplemented with 10% FBS and 2ug/ml puromycin.

extract_protocol:
RNA-seq : Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
RNA-seq : TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
RNA-seq : The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: The relevant reagents were treated with the cells for 90min.

tag: genotype/variation

value: expressing GPR43

value: Acetate and CATPB


title: CTRL-1

value: BeWo trophoblast cells


title: Lin-  eCLIP for IGF2BP3 rep1

description:
biological rep
bm_linms_jd121e


title: cold treated 6 hr replicate 3 [C3-6hr_S36_L004]


title: normoxia_control_rep2


title: Acetate and CATPB treated sample 1 [PBO-5]


title: cold treated 6 hr replicate 2 [C2-6hr_S33_L004]


title: cold treated 6 hr replicate 1 [C1-6hr_S30_L003]


title: CD11b+  size-matched input rep4

source_name: CD11b+ cells

value: CD11b+ cells


title: Acetate treated sample 2 [PBO-4]

value: Acetate


title: CD11b+  eCLIP for IGF2BP3 rep4

description:
technical rep
bm_cd11b_jd136e


title: Acetate treated sample 1 [PBO-3]


title: Reactor 1 under Anoxic conditions

value: Exposed to Cr(VI) with Nitrate for 5 hours


title: DMSO treated sample 2 [PBO-2]

value: DMSO


title: cold treated 24 hr replicate 3 [C3-24hr_S37_L004]

source_name: cold treated 24 hr_leaf tissue

value: leaf tissue


title: cold treated 24 hr replicate 4 [C4-24hr_S40_L004]


title: cold treated 2 hr replicate 4 [C4-2hr_S38_L004]

source_name: cold treated 2 hr_leaf tissue


title: cold treated 24 hr replicate 2 [C2-24hr_S34_L004]


title: URSA patients replicate5

type: RNA

city: Guangzhou

first: Meilan

last: Liu

address: Yanjiang Weat Road 107

department: Obstetrics and Gynecology

country: China

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: lncRNA and mRNA expression in Peripheral blood of URSA patients

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Peripheral blood of URSA patients

label_protocol: LncRNA and mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Total RNA was isolated from peripheral blood of URSA patients and healthy controls using TRIzol reagent. RNA integrity was assessed by standard denaturing agarose gel electrophoresis. The RNA samples were labeled, purified and amplified. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

treatment_protocol: 5 mL of heparinized venous blood from 5 URSA patients and 5 healthy controls were collected from the Department of Obstetrics and Gynecology of SunYat-Sen Memorial Hospital in China from Jan 2017 to Sep 2017. All samples were immediately frozen in liquid nitrogen before RNA isolation.

value: Peripheral blood

tag: disease state

value: URSA


title: DMSO treated sample 1 [PBO-1]


title: CD11b+  eCLIP for IGF2BP3 rep3

description:
technical rep
bm_cd11b_jd135e

value: MBL IGF2BP3 antibody (RN009P)

value: no treatment


title: URSA patients replicate3


title: CD11b+  size-matched input rep3

value: input


title: URSA patients replicate4


title: 12-0884 Peripheral Retina

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
RNA-seq data was aligned to the hg38 reference genome using GSNAP (v.   ) with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v.  ). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: cxb

source_name: Peripheral Retina

extract_protocol:
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).

tag: age

tag: Sex

value: F

value: early


title: URSA patients replicate1


title: cold treated 2 hr replicate 3 [C3-2hr_S35_L004]


title: normal controls replicate5

description: lncRNA and mRNA expression in Peripheral blood of normal controls

source_name: Peripheral blood of normal controls

value: healthy


title: normal controls replicate3


title: cold treated 24 hr replicate 1 [C1-24hr_S31_L004]

value: cold


title: CD11b+  size-matched input rep2


title: URSA patients replicate2


title: 12-0094 Macula Retina

source_name: Macula Retina

value: geographic atrophy


title: normal controls replicate4


title: Leiotrametes sp., aspen rep2

city: Marseille

first: Marie-Noëlle

last: Rosso

address: 163 avenue de Luminy

department: Biodiversity and Biotechnology of Fungi - BBF

country: France

institute: INRAE - Aix Marseille University

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the  genome of Leiotrametes sp. BRFM1775, available via Mycocosm JGI portal, using TopHat2 (Kim et al. 2013. Genome Biol. 14(4):R36) with only unique mapping allowed.
Read counts were determined by HTSeq (Anders S, Pyl PT, Huber W. 2015. Bioinformatics. 31(2):166-169)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5; Love MI, Huber W, Anders S. 2014. Genome Biol. 15:550)
The mean normalized read counts for each gene were calcuated from the normalized read counts of three replicates for each growth condition, except for cellulose and wheat straw for which only two replicates were considered.
The mean normalized counts of CAZyme coding genes were log2 converted and retrieved
Supplementary_files_format_and_content: The Excel file includes the mean normalized log2 read count values for each CAZyme coding gene in each growth condition

organism: Cubamyces sp. BRFM 1775

source_name: mycelium

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.( g.l-1), 1 mm Wiley-milled aspen (15 g.l-1 )

extract_protocol:
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HiSeq 2500 JGI platform generating paired end reads of 150bp each.

treatment_protocol: Mycelium and remaining solid substrate were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.

tag: strain

tag: substrate

value: aspen

tag: time

value: day 3


title: CD11b+  eCLIP for IGF2BP3 rep1

description:
biological rep
bm_cd11b_jd125e

value: CD11b+ cells


title: CD11b+  eCLIP for IGF2BP3 rep2

description:
biological rep
bm_cd11b_jd126e


title: 11-2253 Peripheral Retina


title: cold treated 2 hr replicate 2 [C2-2hr_S32_L004]


title: MYC-KI rep2

city: Shanghai

first: Jing

address: Huashan Road 1954

institute: Shanghai Jiao Tong University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Stomach

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Stomach

value: 12-week old


title: Leiotrametes sp., aspen rep3


title: 11-2253 Macula Retina


title: Trametes ljubarskyi, aspen rep1

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the  genome of Trametes ljubarskyi BRFM1659, available via Mycocosm JGI portal, using TopHat2 (Kim et al. 2013. Genome Biol. 14(4):R36) with only unique mapping allowed.
Read counts were determined by HTSeq (Anders S, Pyl PT, Huber W. 2015. Bioinformatics. 31(2):166-169)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5; Love MI, Huber W, Anders S. 2014. Genome Biol. 15:550)
The mean normalized read counts for each gene were calcuated from the normalized read counts of three replicates for each growth condition, except for pine wood for which only two replicates were considered.
The mean normalized counts of CAZyme coding genes were log2 converted and retrieved
Supplementary_files_format_and_content: The Excel file includes the mean normalized log2 read count values for each CAZyme coding gene in each growth condition

organism: Pilatotrama ljubarskyi

extract_protocol:
Total RNA was extracted from 100 mg tissue ground with FastPrep Lysis Matrix A (MP Biomedicals) in 1 ml TRIZOL (Ambion). Nucleic acids were precipitated with isopropanol, resuspended in water and treated with RNase-Free DNase I (QIAGEN). Total RNA was precipitated with LiCl and resuspended in DEPC-treated water. RNA quantity and quality were determined using the Experion RNA StdSens kit (QIAGEN).
Double stranded cDNAs were synthesized from Poly A RNA and fragmented (200-300bp) before construction of the sequencing libraries (Kapa Library Amplification Kit ; Kapa Biosystems).
Illumina HiSeq 2000 JGI platform generating paired end reads of 150bp each.


title: CD11b+  size-matched input rep1


title: 12-0884 Macula Retina


title: 11-2104 Peripheral Retina

value: M


title: MYC-KI rep1


title: Leiotrametes sp., pine rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted pine wood fragments < 2 mm (15 g.l-1)

value: pine


title: 12-0094 Peripheral Retina


title: Trametes ljubarskyi, pine rep1


title: WT rep1

value: wild type


title: 11-2033 Peripheral Retina


title: 11-2104 Macula Retina


title: Trametes ljubarskyi, wheat straw rep3

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and sifted wheat straw fragments < 2 mm (15 g.l-1)

value: wheat straw


title: Leiotrametes sp., wheat straw rep2


title: Trametes ljubarskyi, aspen rep3


title: cold treated 2 hr replicate 1 [C1-2hr_S29_L003]

value: leaf tissue


title: normal controls replicate2

value: Peripheral blood


title: Trametes ljubarskyi, wheat straw rep1


title: Ascl1 overexpression #2

city: University Park

first: Gong

last: Chen

state: Pennsylvania

address: Life Science bldg

department: Biology

institute: Penn State University

description: retroviral expression of Ascl1 replicate#2

data_processing:
FastQC (v. 0.11.3)
BWA alignment (v. 0.7.17-r1188)
DESeq2 (v. 1.16.1)
DESeq2 (v. 1.16.1) normalization
R console
Genome_build: hg38
Supplementary_files_format_and_content: txt

source_name: U251 cells

extract_protocol:
NucleoSpin RNA-isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: U251 cells

value: Ascl1 overexpression

tag: time point

value: 6 days post retroviral infection


title: Leiotrametes sp., aspen rep1


title: Leiotrametes sp., cellulose rep3

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (2.5 g.l-1), ground and Avicel (15 g.l-1)

value: avicel


title: 11-1732 Peripheral Retina

value: early


title: Leiotrametes sp., pine rep1


title: 11-1732 Macula Retina


title: Trametes ljubarskyi, cellulose rep2


title: Neurog2 overexpression #2

description: retroviral expression of Neurog2 replicate#2

value: Neurog2 overexpression


title: WT rep2


title: 11-2033 Macula Retina

value: F


title: Ascl1 overexpression #3

description: retroviral expression of Ascl1 replicate#3


title: normal controls replicate1

value: healthy


title: Trametes ljubarskyi, cellulose rep1

value: day 3


title: Leiotrametes sp., pine rep3


title: Trametes ljubarskyi, wheat straw rep2


title: Trametes ljubarskyi, pine rep2


title: Neurog2 overexpression #1

description: retroviral expression of Neurog2 replicate#1


title: SmallRNAseq.testis.unox.rep1

city: Rochester

first: Xin

last: Li

state: NY

address: 602 Elmwood Drive

institute: University of Rochester

description: Unoxidized, rep1

data_processing:
Analyses were performed using piPipes v1.4. All data from RNA sequencing were analyzed using the latest chicken genome release galGal6 (GCA_000001635.7). Generally, one mismatch is allowed for genome mapping.
The small RNA adapter was trimmed
The expression tpm (transcripts per million) value was quantified using the Salmon software for RNAseq
For small RNA-seq analysis, uniquely mapping reads excluding rRNA and miRNA  between 26 nt and 32 nt were selected for further analysis.
Genome_build: Gallus gallus: galGal6 (GCA_000002315.5)
Supplementary_files_format_and_content: RNAseq quantification results are .sf files output by Salmon software and small RNA processed data files are the unique genome alignment results in BED2 format (https://github.com/bowhan/piPipes/wiki/nomenclature)

organism: Gallus gallus

source_name: testis

growth_protocol: Animals mice were maintained and used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester. Chickens were used according to guidelines for animal care of the NIH and the University Committee on Animal Resources at the University of Rochester.

extract_protocol:
Total RNAs were extracted using mirVana miRNA Isolation Kit (ThermoFisher, AM1560).
1,RNA-seq: libraries were constructed following the TruSeq RNA sample preparation protocol..  2, Small RNA-seq: Testes and kidney  samples were lysed and treated with sodium periodate for library constrution. The 3'-adapter is TGGAATTCTCGGGTGCCAAGG and was trimmed in the raw data.

treatment_protocol: Chicken kidney and testis samples were used for high-throughput sequencing

tag: oxidation

value: Unoxidized

value: 12 weeks


title: Neurog2 overexpression #3

description: retroviral expression of Neurog2 replicate#3


title: Trametes ljubarskyi, aspen rep2

value: aspen


title: SmallRNAseq.CILIIP.unox.kidney.rep1

description: Unoxidized, rep1

source_name: kidney

value: adult


title: SmallRNAseq.CILIIP.ox.kidney.rep1

description: Oxidized, rep1

value: Oxidized


title: Trametes ljubarskyi, maltose rep2

growth_protocol: Culture for 3 days at 30°C in a rotary shaker at 120 rpm in 250-ml Erlenmeyer flasks containing 100 ml of  diammonium tartrate (1.84 g.l-1); KH2PO4 (0.2 g.l-1); CaCl2 (0.01 g.l-1); MgSO4.7H2O (0.5 g.l-1); Fe-SO4.7H2O (0.074 g.l-1); ZnSO4.7H2O (0.077 g.l-1); MnSO4.H2O (0.035 g.l-1); CuSO4.5H2O (0.007 g.l-1); yeast extract (0.5 g.l-1); thiamin (0.002 g.l-1); maltose (20 g.l-1)

value: maltose


title: GFP overexpression #2

description: retroviral expression of GFP replicate#2

value: GFP overexpression


title: Leiotrametes sp., maltose rep1


title: GFP overexpression #1

description: retroviral expression of GFP replicate#1


title: SmallRNA.CIWIIP.ox.rep1

description: Oxidized, rep1


title: Leiotrametes sp., wheat straw rep1

value: wheat straw


title: SmallRNA.CILIIP.unox.rep1

description: Unoxidized, rep1


title: Trametes ljubarskyi, cellulose rep3


title: Artolenzites elegans, aspen rep2

data_processing:
Raw fastq file reads were filtered and trimmed using the JGI QC pipeline.
QCed reads from each library were aligned to the  genome Artolenzites elegans BRFM 1663, available via Mycocosm JGI portal, using TopHat2 (Kim et al. 2013. Genome Biol. 14(4):R36) with only unique mapping allowed.
Read counts were determined by HTSeq (Anders S, Pyl PT, Huber W. 2015. Bioinformatics. 31(2):166-169)
Read counts were normalized using ddsNorm from the DESeq Bioconductor package (version 1.5; Love MI, Huber W, Anders S. 2014. Genome Biol. 15:550)
The mean normalized read counts for each gene were calcuated from the normalized read counts of three replicates for each growth condition, except for wheat-straw for which only two replicates were considered.
The mean normalized counts of CAZyme coding genes were log2 converted and retrieved
Supplementary_files_format_and_content: The Excel file includes the  mean normalized log2 read count values for each CAZyme coding gene in each growth condition

organism: Trametes elegans

value: BRFM 1663


title: SmallRNA.CILIIP.ox.rep1

description: Oxidized, rep1


title: RWPE-1_m6A_rep2

city: San Antonio

first: Kexin

last: Xu

state: Texas

address: 7703 Floyd Curl, MC 8257

department: Molecular Medicine

institute: UT Health Science Center at San Antonio

description: MeRIP-Seq

data_processing:
Library strategy: MeRIP-seq
Basecalls performed using Illuminal CASAVA software.
Cutadapt was used to remove the first 9 bases and N’s on both ends of reads. Reads with minimum of 25 bases were kept. Reads were aligned to human genome (hg19) using STAR. Duplicated reads were marked and removed by Picard. The bam files were transformed into bed12 format by bedtools, and then shifted to 200nt by a custom script and transformed back to bed6 format. Macs2 bdgopt sub-command was used to normalize each sample to a 10 million total reads.
MeTDiff was used to call m6A enriched peaks by combining both replicates with default parameters, and a custom script was used to merge all the peaks in LNCaP and RWPE to generate a reference peak set, on which the differential m6A enrichment analysis was based.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig file

growth_protocol: The human prostate epithelial cell line RWPE-1 (ATCC; CRL-11609) were cultured with Keratinoyte serum free medium supplemented with 0.05 mg/mL bovine pituitary extract (BPE), 5 ng/mL human recombinant epidermal growth factors (EGF), 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. The human prostate adenocarcinoma cell line LNCaP was cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C. All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara-Clontech, 634413), according to the manufacturer’s instructions.

tag: antibody


title: RWPE-1_m6A_rep1

description: MeRIP-Seq


title: In vitro 28.1-Y.pestis

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

country: Israel

institute: Israel Institute For Biological Research

description:
mRNA after depletion with riboZiro rRNA removal kit (Gram negative bacteria).
OA001

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
Reads were mapped  to the reference genome Mouse: UCSC/mm10 using STAR(2.5.2b) and featureCounts(v1.5.0-p3)
Reads were mapped  to the reference genome Yersinia pestis CO92 (NC_003143,NC_003131, NC_003132, NC_003134) using bowtie2 (2.2.0) and htseq-count 0.6.1
Supplementary_files_format_and_content: Matrix table with raw read counts for every gene and every sample

organism: Yersinia pestis

source_name: Bacteria grown in LB  at 28°C

growth_protocol: Yersinia pestis Kimberly53 strain were used for intranasal infection. Bacterial cultures were grown at 28◦C overnight in HIB (BD, MD USA), supplemented with 0.2% (+) xylose and 2.5 mM CaCl2 (Sigma-Aldrich). The bacteria were used for intranasal infection of mice (OF1 strain).

extract_protocol:
One, 24 and 48 hours post infection, mice were sacrificed, lungs were removed and used for RNA extraction. RNA was also extracted from bacteria grown in culture (at 28° and 37° C) and naive mice, as control. Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen). In order to enrich the mRNA bacteria grown in culture (In vitro) we used riboZiro rRNA removal kit for depletion of rRNA, in each sample and ribozero gold rRNA depletion for dual RNA samples (mouse and Y. pestis).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice (OF1)  were infected intranasally with 800,000 cfu/mouse (~1500 LD50).

value: Grown in calture at 28degreeC


title: RNAseq of Arabidopsis: ddm1cmt2_rep3

city: Stockholm

first: Cheng

last: Zhao

state: Stockholm

address: H9 Klinisk vetenskap,171 77 Stockholm

department: Clinical Science

country: Sweden

institute: Karolinska institute

data_processing:
For RNA-seq data, low-quality sequences and adaptors were trimmed using Trimmomatic. Clean reads were mapped to the reference genome by TopHat with the parameter "-g 1". The total number of reads mapping to each gene was calculated with the htseq-count script in HTSeq with the parameter “--nonunique all”, to minimize over-estimation of TE expression caused by overlapping genes; read counts for each TE were calculated by htseq-count with parameters "--nonunique all  -m intersection-strict" based on the TE-only annotation. Genes and TEs with a normalized expression level of at least one count per million mapped reads (CPM) in three or more libraries were considered as expressed. Principle component analysis (PCA) based on the transcript levels of the expressed protein-coding genes and TEs was performed using the prcomp function in R software with default settings. Differentially expressed TEs with at least a 2-fold change in expression and an FDR < 0.05 were identified by the R package edgeR using the trimmed mean of M-values (TMM) method.
For methylation data, low-quality sequences and adapters were trimmed using Trimmomatic with parameters “LEADING: 3 SLIDINGWINDOW: 4: 30 MINLEN: 36”, and clean reads were mapped to the A. thaliana TAIR 10 genome using Bisulfite Sequence Mapping Program (BSMAP) with parameters “-v 2 -S 1” which allowing 2 mismatches. The methratio.py script from BSMAP with parameters “-r -z -p -m 1” was used to extract the methylation ratio from mapping results; only mapped reads after deduplication were considered for subsequent analyses.
For ChIP-seq data analysis, around 15.2 million raw paired-end reads were obtained for each sample and subsequently cleaned by Trimmomatic. Clean reads were mapped to the reference genome by Bowtie2 using the parameter "--very-sensitive --no-unal --no-mixed --no-discordant -k 2". Subsequently, uniquely mapped reads were selected and marked as duplicates using the Picard tool followed by using the SAMtools “rmdup” command. Coverage of deduplicated reads was normalized to 1 × sequencing depth by bamCoverage in deepTools with parameters "--normalizeUsing RPGC --exactScaling -bs 10".
Identification of non-reference TE insertions with TSDs (Target Site Duplications) was conducted using SPLITREADER with some modifications.
Genome_build: TAIR10
Supplementary_files_format_and_content: methylation wig files, RNA-seq coverage bedgGraph, ChIP-seq BigWig files

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis seeds were plated on 1/2 Murashige and Skoog (MS) medium with 0.6% agar and 1.5% sucrose and stratified for 7 days at 4℃ in darkness before being transferred to the growth chamber (16 h light/8 h dark, 22℃)

extract_protocol:
Total RNA was extracted from two-week-old seedlings using the RNeasy Plant Mini kit (Takara)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: two-week-seedling

value: seedling


title: Ascl1 overexpression #1

description: retroviral expression of Ascl1 replicate#1

value: U251 cells

value: Ascl1 overexpression

value: 6 days post retroviral infection


title: Leiotrametes sp., cellulose rep2

value: avicel


title: Trametes ljubarskyi, maltose rep3

value: day 3


title: SmallRNAseq.malekidney.unox.rep2

description: Unoxidized, rep2

value: Unoxidized


title: Leiotrametes sp., cellulose rep1


title: RNAseq of Arabidopsis: ddm1cmt2_rep2


title: LNCaP_m6A_rep1

description: MeRIP-Seq

source_name: LNCaP

value: LNCaP


title: RNAseq of Arabidopsis: ddm1cmt2_rep1


title: Leiotrametes sp., maltose rep3


title: SmallRNA.CIWIIP.unox.rep1

description: Unoxidized, rep1

value: 12 weeks


title: RNAseq.kidney.rep1

value: adult


title: Leiotrametes sp., maltose rep2


title: Artolenzites elegans, pine rep1

value: pine


title: In vitro 37.2-Y.pestis

description:
mRNA after depletion with riboZiro rRNA removal kit (Gram negative bacteria).
OA0010

source_name: Bacteria grown in LB  at 37°C

value: Grown in calture at 37degreeC


title: GFP overexpression #3

description: retroviral expression of GFP replicate#3

value: GFP overexpression


title: Trametes ljubarskyi, maltose rep1

value: maltose


title: In vitro 37.1-Y.pestis

description:
mRNA after depletion with riboZiro rRNA removal kit (Gram negative bacteria).
OA002


title: SmallRNAseq.malekidney.ox.rep2

description: Oxidized, rep2

value: Oxidized


title: Artolenzites elegans, aspen rep3

value: BRFM 1663

value: aspen


title: LNCaP_m6A_rep2

description: MeRIP-Seq


title: Artolenzites elegans, aspen rep1


title: CHIPseq of Arabidopsis: WT_Input_rep1

growth_protocol: Arabidopsis seeds were plated on 1/2 Murashige and Skoog (MS) medium with 1.2% agar and 1.5% sucrose and stratified for 7 days at 4℃ in darkness before being transferred to the growth chamber (16 h light/8 h dark, 22℃)

extract_protocol:
Protein-DNA complexes were isolated with anti-Flag antibodies (Sigma, F3165). ChIP-DNA was extracted with phenol:chloroform:isoamyl alcohol (25:24:1), precipitated with 2-propanol, and resuspended in TE buffer.
Seedlings were cross-linked with 1% formaldehyde, and ChIP-seq was performed with anti-Flag antibodies (Sigma, F3165). Library preparation and sequencing were performed by the PSC Genomics Core Facility using standard Illumina protocols.

value: input

value: two-week-seedling

value: seedling


title: SmallRNAseq.malekidney.unox.rep3

description: Unoxidized, rep3


title: Artolenzites elegans, wheat straw rep1

value: wheat straw


title: In vitro 28.2-Y.pestis

description:
mRNA after depletion with riboZiro rRNA removal kit (Gram negative bacteria).
OA007

value: Grown in calture at 28degreeC


title: shMETTL3_vector_rep2

data_processing:
Basecalls were performed using Illumina Casava software.
Reads were aligned to hg19 genome assembly using STAR 2.5.2b. Refseq transcripts were supplied in GTF format file.
featureCounts package was used to count the uniquely mapped reads in union mode.
Differentially expressed genes were detected by DESeq2 with FDR thresold 0.05
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

growth_protocol: The human prostate adenocarcinoma cell line LNCaP was cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C. All cell lines were routinely tested for mycoplasma contamination.

extract_protocol:
Total RNA was extracted by TRIzol™ Reagent (Thermo Fisher, 15596018)
RNA library was prepared by KAPA Stranded mRNA- Seq Kit (96rxn, KK8421), according to the manufacturer’s instructions.

treatment_protocol: LNCaP cell line was established by transducing with lenti-virus containing shControl, shMETTL3 , shMETTL3-resistant METTL3 wildtype and shMETTL3-resistant METTL3 catalytically dead mutant. Cells were selected with 1ug/ml puromycin and cultured with RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin. Cells were grown in a 5% CO2 cell culture incubator at 37 °C.

tag: transfection

value: Cells were infected with METTL3 shRNAs


title: SmallRNAseq.femalekidney.unox.rep3

description: Unoxidized, rep3

value: Unoxidized


title: CHIPseq of Arabidopsis: NRPD_WT_rep1

value: NRPD

tag: tissue


title: LNCaP_input

description: MeRIP-Seq

value: LNCaP


title: RWPE-1_input

description: MeRIP-Seq


title: SmallRNAseq.femalekidney.unox.rep2

description: Unoxidized, rep2

value: adult


title: CHIPseq of Arabidopsis: NRPD_ddm1_rep2


title: SmallRNAseq.malekidney.ox.rep3

description: Oxidized, rep3


title: SmallRNAseq.femalekidney.unox.rep1

description: Unoxidized, rep1


title: Artolenzites elegans, pine rep2

value: pine

value: day 3


title: Artolenzites elegans, pine rep3


title: CHIPseq of Arabidopsis: WT_Input_rep2


title: CHIPseq of Arabidopsis: NRPD_ddm1_rep1


title: shMETTL3_WT_rep2

value: Cells were infected with METTL3 shRNAs and shRNA-resistant METTL3 wild-type


title: Artolenzites elegans, wheat straw rep3


title: shCtrl_vector_rep2

value: Cells were infected with control shRNAs


title: CHIPseq of Arabidopsis: ddm1_Input_rep2


title: SmallRNAseq.femalekidney.ox.rep2

description: Oxidized, rep2

value: Oxidized


title: Artolenzites elegans, wheat straw rep2

value: BRFM 1663


title: SmallRNAseq.malekidney.unox.rep1

description: Unoxidized, rep1


title: shMETTL3_WT_rep1


title: SmallRNAseq.malekidney.ox.rep1

description: Oxidized, rep1


title: Artolenzites elegans, maltose rep2

value: maltose


title: shMETTL3_MT_rep2

value: Cells were infected with METTL3 shRNAs and shRNA-resistant METTL3 mutant


title: CHIPseq of Arabidopsis: NRPD_WT_rep2

value: two-week-seedling


title: ATAC - RII Cux1mid 2

status: Public on Aug 10 2021

city: Chicago

first: Stephanie

middle: N

last: Konecki

state: IL

address: 625 W Madison, Apt 1904

institute: The University of Chicago

data_processing:
RNA-seq reads were aligned to mm10 using STAR, mapping quality <30 were removed. Differental gene expression analysis was done using DESeq2
ATAC-seq reads were aligned to mm10 using BWA, mapping quality <30 were removed. Peaks were called with MACS2, DiffBind was used for differential accessibility
ChIP-seq and CUT&RUN reads were mapped to hg19 using BWA, mapping quality <30 were removed. Peaks were called with MACS2 and analyzed by IDR
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNA-seq files contain DESeq2 results for gene ID and CPM;  ATAC-seq, ChIP-seq, and CUT&RUN samples have bed files attached

source_name: RII basophlic erythroblasts

extract_protocol:
RNA was isolated using Trizol. ATAC-seq was iscolated using MinElute kit.  ChIP and CUT&RUN samples  were generated from iscolated nuceli using a CUX1 specific antibody
libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: RII basophlic erythroblasts


title: ATAC - RII Cux1mid 1


title: ATAC - RII Cux1low 2


title: ATAC - MEP Cux1low 1

source_name: Megakaryocyte erythrocyte progenitors

value: Megakaryocyte erythrocyte progenitors


title: ATAC - RII Renilla 2

value: Renilla


title: ATAC - RII Renilla 1


title: ATAC - MEP Cux1low 2


title: RNA - RII Cux1mid 1


title: shCtrl_vector_rep1


title: Artolenzites elegans, cellulose rep2

value: avicel


title: CHIPseq of Arabidopsis: ddm1_Input_rep1

value: input

value: seedling


title: shMETTL3_vector_rep1

value: LNCaP

value: Cells were infected with METTL3 shRNAs


title: shMETTL3_MT_rep1


title: SmallRNAseq.femalekidney.ox.rep1

description: Oxidized, rep1

value: adult


title: Artolenzites elegans, maltose rep1

value: day 3


title: Artolenzites elegans, maltose rep3


title: SmallRNAseq.femalekidney.ox.rep3

description: Oxidized, rep3


title: Artolenzites elegans, cellulose rep1


title: RNA - MEP Cux1mid 2


title: ATAC - RII Cux1low 1


title: ATAC - MEP Renilla 1


title: ATAC - MEP Cux1mid 1


title: RNA - MEP Cux1mid 1


title: ATAC - MEP Cux1mid 2


title: RNA - RII Cux1mid 2


title: ATAC - MEP Renilla 2


title: RNA - MEP Cux1low 1


title: BLA17_VCX_LPS_IN_F

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

description:
input
2018-9024

data_processing:
Aligned to moouse genome (mm10) using STAR spliced read aligner
Count reads using HT-seq and using mm10 RefSeq as reference
Normalization (TMM), quantitation and differential expression analysis using Bioconductor packages
FPKM values
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

source_name: VCX

extract_protocol:
After homogenization RNA was purified from (i) cleared lysate as the input, and (ii) astrocyte-specific ribosome-associated RNA precipitated via a hemagglutinin (HA) tag with anti-HA (Biolegend cat #901514, lot #B224726). LPS samples were compared to PBS samples. PFC samples were compared to VCX samples. Input and IP samples underwent DNA depletion and RNA purification with the RNeasy Micro Plus kit (Qiagen). Integrity of the eluted RNA was analyzed by a 2100 Bioanalyzer (Agilent).
Sequencing libraries were prepared using Illumina TruSeq RNA sample prep kit following manufacturer's protocol.  After library preparation, amplified double-stranded cDNA was fragmented into 125 bp (Covaris-S2, Woburn, MA) DNA fragments, which were (200 ng) end-repaired to generate blunt ends with 5’- phosphates and 3’- hydroxyls and adapters ligated.

treatment_protocol: Mice were injected i.p. with PBS or LPS (5 mg/kg). 1, 2 and 14 days after the injection PFC and VCX were homogenized.

value: LPS

value: F

tag: brain area

value: VCX

tag: rna-sample type

tag: days after injection

value: 14 days


title: BLA9_VCX_PBS_IN_F

description:
input
2018-9024

tag: treatment

value: PBS


title: BLA10_VCX_PBS_IN_F

description:
input
2018-9024


title: BLA4_VCX_LPS_IN_F

description:
input
2018-9024


title: Artolenzites elegans, cellulose rep3

value: BRFM 1663


title: BLA25_PFC_LPS_IN_F

description:
input
2018-9024

source_name: PFC

value: PFC


title: RNA - RII Cux1low 2

tag: genotype

value: RII basophlic erythroblasts


title: RNA - RII Renilla 1


title: RNA - RII Renilla 2


title: BLA32_PFC_PBS_IN_M

description:
input
2018-9024

value: M


title: BLA24_PFC_PBS_IN_F

description:
input
2018-9024


title: RNA - RII Cux1low 1


title: BLA30_VCX_PBS_IN_M

description:
input
2018-9024


title: BLA6_VCX_LPS_IP_M

description:
IP
2018-9024

value: IP


title: BLA1_VCX_LPS_IP_F

description:
IP
2018-9024


title: RNA - MEP Renilla 1

value: Renilla

value: Megakaryocyte erythrocyte progenitors


title: BLA29_VCX_PBS_IP_F

description:
IP
2018-9024


title: BLA16_VCX_LPS_IP_M

description:
IP
2018-9024


title: RNA - MEP Cux1low 2


title: BLA5_VCX_PBS_IP_M

description:
IP
2018-9024


title: BLA11_VCX_LPS_IN_M

description:
input
2018-9024

value: input


title: BLA26_VCX_PBS_IN_M

description:
input
2018-9024


title: BLA31_PFC_LPS_IN_M

description:
input
2018-9024


title: BLA3_PFC_LPS_IN_M

description:
input
2018-9024


title: RNA - MEP Renilla 2


title: BLA13_VCX_LPS_IN_M

description:
input
2018-9024


title: BLA28_VCX_LPS_IP_F

description:
IP
2018-9024


title: BLA15_PFC_LPS_IP_M

description:
IP
2018-9024


title: BLA21_PFC_LPS_IP_F

description:
IP
2018-9024


title: BLA20_PFC_PBS_IP_M

description:
IP
2018-9024


title: BLA8_PFC_PBS_IN_M

description:
input
2018-9024


title: BLA22_PFC_LPS_IN_F

description:
input
2018-9024


title: BLA2_PFC_LPS_IP_M

description:
IP
2018-9024


title: BLA18_PFC_PBS_IN_F

description:
input
2018-9024


title: BLA23_PFC_PBS_IP_M

description:
IP
2018-9024


title: BLA19_PFC_LPS_IP_F

description:
IP
2018-9024


title: BL17_V_inp_LPS

description:
input
2016-9262

value: 2 days


title: BLA12_VCX_PBS_IP_M

description:
IP
2018-9024


title: BL29_V_inp_LPS

description:
input
2016-9262


title: BL31_V_inp_PBS

description:
input
2016-9262


title: BLA14_PFC_PBS_IP_F

description:
IP
2018-9024


title: BLA27_PFC_PBS_IP_F

description:
IP
2018-9024


title: BL27_V_inp_PBS

description:
input
2016-9262


title: BL7_V_inp_PBS

description:
input
2016-9262


title: BL34_P_inp_LPS

description:
input
2016-9262


title: BL21_V_inp_PBS

description:
input
2016-9262


title: BL42_V_inp_LPS

description:
input
2016-9262


title: BL1_P_inp_LPS

description:
input
2016-9262


title: BL2_P_inp_PBS

description:
input
2016-9262


title: BL38_V_IP_LPS

description:
IP
2016-9262


title: BL12_P_inp_PBS

description:
input
2016-9262


title: BL3_P_inp_LPS

description:
input
2016-9262


title: BL19_V_IP_LPS

description:
IP
2016-9262


title: BL14_V_IP_PBS

description:
IP
2016-9262


title: BL24_V_IP_LPS

description:
IP
2016-9262


title: BL23_V_IP_PBS

description:
IP
2016-9262


title: BLA7_VCX_PBS_IP_F

description:
IP
2018-9024


title: BL41_P_IP_LPS

description:
IP
2016-9262


title: BL9_P_IP_LPS

description:
IP
2016-9262


title: BL20_P_inp_LPS

description:
input
2016-9262


title: BL32_V_IP_PBS

description:
IP
2016-9262


title: BL11_V_IP_LPS

description:
IP
2016-9262


title: BL8_V_IP_PBS

description:
IP
2016-9262


title: BL18_P_IP_LPS

description:
IP
2016-9262


title: BL16_P_inp_PBS

description:
input
2016-9262


title: BL10_P_inp_PBS

description:
input
2016-9262


title: BL6_P_IP_PBS

description:
IP
2016-9262


title: BL30_P_IP_PBS

description:
IP
2016-9262


title: B31_VCX_LPS_IN_F

description:
input
2017-9270

value: 1 day


title: BL28_P_IP_PBS

description:
IP
2016-9262


title: BL13_P_IP_PBS

description:
IP
2016-9262


title: B22_VCX_LPS_IN_M

description:
input
2017-9270


title: B19_VCX_LPS_IN_F

description:
input
2017-9270


title: B11_VCX_PBS_IN_M

description:
input
2017-9270


title: B5_VCX_PBS_IN_M

description:
input
2017-9270


title: B6_VCX_LPS_IN_M

description:
input
2017-9270


title: B2_VCX_PBS_IN_F

description:
input
2017-9270


title: B12_VCX_PBS_IN_F

description:
input
2017-9270


title: B30_PFC_LPS_IN_F

description:
input
2017-9270


title: B28_PFC_LPS_IN_M

description:
input
2017-9270


title: B26_PFC_PBS_IN_M

description:
input
2017-9270


title: B18_VCX_LPS_IP_F

description:
IP
2017-9270


title: B29_PFC_LPS_IN_M

description:
input
2017-9270


title: B24_PFC_PBS_IN_M

description:
input
2017-9270


title: B9_PFC_PBS_IN_F

description:
input
2017-9270


title: B15_VCX_LPS_IP_M

description:
IP
2017-9270


title: B20_VCX_LPS_IP_M

description:
IP
2017-9270


title: B32_PFC_LPS_IN_F

description:
input
2017-9270


title: B17_VCX_PBS_IP_F

description:
IP
2017-9270


title: B23_VCX_PBS_IP_M

description:
IP
2017-9270


title: RNA-GCN-3opt

city: Dallas

first: xueliang

last: lyu

address: 6001 Forest Park Road

department: Physiology

institute: UT Southwestern Medical Center

data_processing:
Sequenced reads were trimmed for adaptor sequence by our in-house scripts.
Clean reads were then mapped to reference sequences using bowtie2 and RPKM values were calculated by cufflinks with parameters --min-intron-length 4 --max-intron-length 5000 --library-type fr-firststrand --multi-read-correct --upper-quartile-norm
Genome_build: All of the ribosome profiling and accompanying mRNA-seq clean reads were mapped to coding sequence (CDS) regions of N. crassa genes.
Supplementary_files_format_and_content: For both of ribosome profiling and accompanying mRNA-seq, tab-delimited text files including RPKM values were generated by cufflinks for each sample.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: For both of ribosome profiling and the accompanying mRNA-seq, fresh conidia (one week post inoculation on slants) of Δcpc-3 and wild-type strains were cultured in plates with 50 ml growth medium (1 × Vogel’s, 2% glucose) at room temperate for two days. The cultures were cut into small discs with a diameter of 1 cm and then were transferred into flasks with the same medium and grown with orbital shaking (200 rpm) under constant light for 12 h.

extract_protocol:
For both of ribosome profiling and the accompanying mRNA-seq, the ribosome protected fragments (RPFs) and total RNAs were extracted according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).
For both of ribosome profiling and the accompanying mRNA-seq, libraries were prepared for sequencing according to ARTseq Ribosome Profiling Kit(Catalog Number: RPYSC12116).

treatment_protocol: For both of ribosome profiling and the accompanying mRNA-seq, CHX (final concentration of 0.1 mg/ml) was only added into the cell lysis buffer.

tag: host strain

tag: reporter expressed in host strain

value: mycelia

tag: molecule

value: mRNA


title: B21_PFC_PBS_IN_F

description:
input
2017-9270

tag: Sex

tag: strain


title: B3_PFC_LPS_IP_F

description:
IP
2017-9270

value: LPS


title: RNA-GCN-1wt


title: RNA-GCN-1opt


title: RNA-GCN-3wt


title: B1_VCX_PBS_IP_F

description:
IP
2017-9270

value: F


title: B27_VCX_PBS_IP_M

description:
IP
2017-9270

value: VCX


title: RNA-WT-3opt

value: WT


title: B14_PFC_PBS_IP_M

description:
IP
2017-9270

value: PBS


title: B13_PFC_LPS_IP_F

description:
IP
2017-9270


title: B7_PFC_LPS_IP_M

description:
IP
2017-9270


title: B4_PFC_LPS_IP_M

description:
IP
2017-9270


title: RNA-WT-3wt


title: B10_PFC_PBS_IP_M

description:
IP
2017-9270


title: RNA-WT-1opt


title: A_LPS_69

description:
whole tissue
2016-9065

value: whole tissue


title: A_LPS_68

description:
whole tissue
2016-9065

value: PFC


title: A_LPS_71

description:
whole tissue
2016-9065


title: Ribo-CPC3-3opt_3

value: ribosome protected fragments


title: Ribo-CPC3-3opt_2


title: A_LPS_67

description:
whole tissue
2016-9065


title: B16_VCX_LPS_IP_F

description:
IP
2017-9270


title: RNA-WT-1wt


title: FLSs, Trauma patient 4 N8

first: Jingnan

last: Wang

state: Guangdong

address: Zhongshan 2nd Road

institute: Department of Rheumatology and Immunology, The First Affiliated Hospital, Sun  Yat-sen University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Firstly, assembling the slides into an slide holder. Then,placing assembled slide holders into scanner carousel.Following verify scan settings for one-color scans, clicking Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Fibroblast-like synoviocytes

label_protocol: Label procdures followed the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) standard protocol.

extract_protocol: Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.

value: synovial tissues

value: Fibroblast-like synoviocytes

tag: disease state

value: control


title: B8_PFC_PBS_IP_F

description:
IP
2017-9270

value: IP


title: A_LPS_65

description:
whole tissue
2016-9065


title: A_LPS_62

description:
whole tissue
2016-9065


title: B25_PFC_PBS_IP_F

description:
IP
2017-9270


title: Ribo-CPC3-1opt_2


title: Ribo-CPC3-1opt_1


title: A_LPS_63

description:
whole tissue
2016-9065


title: Ribo-CPC3-1opt_3


title: FLSs, Trauma patient 3 N14


title: FLSs, RA patient 5 R9

value: rheumatoid arthritis


title: Ribo-CPC3-3opt_1


title: A_LPS_70

description:
whole tissue
2016-9065


title: FLSs, Trauma patient 5 N9


title: HL-1 cell line_MuRF1 KD_non-stretched_rep5

city: Indianapolis

first: Monte

middle: S

last: Willis

address: 635 Barnhill Street Drive

institute: University of Indiana School of Medicine

description:
Sample 17
17-5-b2

data_processing:
Kallisto (v0.44.0) count abundance over GENCODE ‘comprehensive gene annotation’ (Release M18) with 50x bootstrap
tximport (v1.6.0) read count input
DESeq2 (v1.18.1) read count normalization and differential expression analysis
R (v3.4.4) for all other analyses
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: TSV, raw and normalized counts

source_name: HL-1 cell line_MuRF1 KD_non-stretched

growth_protocol: The cardiomyocyte-derived HL-1 cell line was obtained from Dr. Claycomb and maintained in complete Claycomb media containing 10% serum (Cat. #51800C, Sigma-Aldrich®; St. Louis, MO) as previously described by Dr. Claycomb. Cells were split and cultured to ~90% confluency in 6-well BioFlex® culture plates (Flexcell International Corporation, Hillsborough, NC) coated with 0.02% gelatin (wt/vol) and 0.5% fibronectin (vol/vol) for ∼30 min and grown in complete Claycomb media containing 10% serum and supplemented 1% penicillin-streptomycin. Media was changed to serum-free Dulbecco’s modified Eagle’s medium (DMEM) supplemented 1% penicillin-streptomycin.

extract_protocol:
Total RNA was extracted from HL-1 cells immediately harvested after 60 minutes stretch (or no stretch) using TRIZOL® Reagent, according to the manufacturer’s instructions.
A KAPA Stranded mRNA-Seq kit (Cat.# KK8420, KAPA Biosystems, Wilmington, MA) was used to capture poly(A) mRNA and construct a stranded mRNA-seq library, according to the manufacturer’s instructions.

treatment_protocol: HL-1 cells were transduced with 30 MOI adenoviruses expressing shRNA-MuRF1 or shRNAscramble control (custom made by Vector Biolabs, Philadelphia, PA) to transiently knock down MuRF1. Forty-eight hours later, HL-1 cells in 6-well BioFlex® culture plates were stretched at 15% uniaxial stretch at 1 Hz for 60 min in a computer-regulated Flexcell® FX-5000™ Compression System (Flexcell International Corporation, Hillsborough, NC), with parallel non-stretched cells (0 min stretch) used as a control.

tag: cell line

value: cardiomyocyte-derived HL-1 cell line

tag: transduction

value: MuRF1 KD

value: non-stretched (0 min stretch)

tag: replicate


title: HL-1 cell line_control_non-stretched_rep3

description:
Sample 21
21-1-a3

source_name: HL-1 cell line_control_non-stretched


title: HL-1 cell line_MuRF1 KD_non-stretched_rep6

description:
Sample 18
18-5-b3


title: HL-1 cell line_control_non-stretched_rep2

description:
Sample 20
20-1-a2


title: HL-1 cell line_control_non-stretched_rep4

description:
Sample 22
22-1-b1


title: Ribo-CPC3-3wt_3

value: mycelia


title: HL-1 cell line_MuRF1 KD_non-stretched_rep4

description:
Sample 16
16-5-b1


title: HL-1 cell line_control_non-stretched_rep5

description:
Sample 23
23-1-b2


title: HL-1 cell line_control_non-stretched_rep1

description:
Sample 19
19-1-a1


title: FLSs, Trauma patient 2 N12


title: Ribo-CPC3-3wt_2


title: FLSs, RA patient 2 R20


title: FLSs, Trauma patient 1 N10


title: FLSs, RA patient 4 R8


title: FLSs, RA patient 3 R21


title: HL-1 cell line_control_cyclic stretch_rep3

description:
Sample 9
9-4-a3

source_name: HL-1 cell line_control_cyclic stretch

value: cyclic stretch (15% biaxial stretch at 1 Hz for 60 min)


title: Ribo-CPC3-1wt_4


title: Ribo-CPC3-1wt_3


title: Cmm inoculated 6dpi

city: Athens

first: Stamatis

last: Rigas

state: Attiki

address: Iera Odos 75

department: Biotechnology

country: Greece

institute: Agricultural University of Athens

data_processing:
Raw reads were filtered into clean reads and aligned to the Tomato genome (GCF_000188115.3_SL2.50_ncbi_20180905)
RNA-seq data were analyzed using the SOAPnuke (version v.1.5.2) with parameters ‘‘-l 15 -q 0.4 -n 0.1’’ and the HISAT2 pipeline (version 2.0.4) with parameters ‘‘--phred33 --sensitive --no-discordant --no-mixed -I 1 -X 1000’’
Clean reads were mapped to reference with Bowtie2 (version v2.2.5).
Gene expression level was calculated with RSEM with default parameters.
Analysis of differential gene expression was performed with DEseq2 with parameters ‘‘Fold Change ≥ 2.00 and Adjusted Pvalue ≤ 0.05’’
Genome_build: Tomato genome reference (GCF_000188115.3_SL2.50_ncbi_20180905)
Supplementary_files_format_and_content: Excel files with gene expression values and log2FoldChange between samples as generated by DEseq2

organism: Solanum lycopersicum

source_name: Solanum lycopersicum 1cm stem section

growth_protocol: Tomato (Solanum lycopersicum) Ekstasis F1 hybrid seeds (Nirit seeds Ltd., Moshav Hadar Am, Israel),  were planted in plastic pots containing a natural turf mixture (Potgrond P, Agrohoum SA, Greece), and grown at 22°C in a Fitotron (Weiss Gallenkamp, Loughborough, UK) growth chamber under a long day photoperiod with 16 h of light and 8 h of darkness per day and 100 μmol m–2 s–1 light intensity. Cmm bacteria were grown for 36hrs at 26oC in a rotating shaker, in YPDNM medium containing 1% Yeast extract, 2% Peptone, 2% D-Glucose, 1% NaCl and 10mM MgCl2.

extract_protocol:
1 cm sections of the stems above the inoculation site from mock treated and Cmm infected tomato seedlings were collected at 6 and 12 days post inoculation (dpi) for RNA-Seq analysis. Total RNA was extracted using the Direct-zol RNA Miniprep (Zymo research, Irvine CA, USA) kit with an on-column DNase treatment according to the manufacturer’s instructions.
RNA-seq libraries were generated using the TruSeq Low Input kit according to the manufacturer’s instructions (Illumina).
Sequencing was performed on BGISEQ-500 platform instrument at BGI (Beijing Genomics Institute) in three biological replicates for each sample.

treatment_protocol: Bacteria were pelleted by centrifugation at 1200g for 10 min, washed, and diluted to a titer of 108 cfu/mL in Dilution buffer (10 mM MgCl2, 10mM Tris-HCl pH:6.8). Bacterial suspensions or dilution buffer were injected into the stem region between the cotyledons of 2 week-old plants with a syringe fitted with a 30-gauge needle.

value: tomato stem

tag: accession

value: EKSTASIS F1 hybrid

value: Cmm inoculated

tag: time point


title: HL-1 cell line_control_cyclic stretch_rep4

description:
Sample 10
10-4-b1


title: HL-1 cell line_MuRF1 KD_non-stretched_rep2

description:
Sample 14
14-5-a2


title: Ribo-CPC3-1wt_2

tag: tissue


title: mock treated 12dpi

value: mock treated


title: HL-1 cell line_control_cyclic stretch_rep5

description:
Sample 11
11-4-b2


title: HL-1 cell line_control_cyclic stretch_rep2

description:
Sample 8
8-4-a2


title: Ribo-CPC3-1wt_1


title: mock treated 6dpi


title: HL-1 cell line_control_cyclic stretch_rep1

description:
Sample 7
7-4-a1


title: HL-1 cell line_MuRF1 KD_non-stretched_rep1

description:
Sample 13
13-5-a1


title: Cut&Tag_WTC11 iPSCs - H3K4me3_rep1

city: SAN FRANCISCO

first: Yin

last: Shen

state: CALIFORNIA

address: 513 Parnassus Ave

department: Department of Neurology

institute: UCSF

data_processing:
Library strategy: CUT&Tag
Sequencing reads were mapped to hg38 using bowtie2 with the following options: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Picard Tools was used to remove blacklisted regions and duplicate reads
SEACR (Meers et al. 2019) was used to call peaks on merged replicates.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig file was generated with bamCoverage --binSize=1
Supplementary_files_format_and_content: Peaks called by MACS2

source_name: human iPSCs

growth_protocol: WTC11 iPS cells were cultured on Matrigel-coated (Corning, 354277) plates with Essential 8™ Medium (Life Technologies, A1517001). WTC11 iPSCs were passaged using Accutase (STEMCELL Technologies, 07922) and 10 μM ROCK inhibitor Y-27632 (STEMCELL Technologies, 72302).

extract_protocol:
Cells were washed with PBS and nuclei were extracted prior to library construction.
CUT&Tag libraries were prepaed according to the published protocol (Kaya-Okur, H.S. et al. 2019).

tag: cell type

value: WTC11 iPSCs

tag: antibody


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep4

description:
Sample 4
4-8-b1

source_name: HL-1 cell line_MuRF1 KD_cyclic stretch


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep6

description:
Sample 6
6-8-b3


title: FLSs, RA patient 1 R11


title: HL-1 cell line_control_non-stretched_rep6

description:
Sample 24
24-1-b3


title: Ribo-CPC3-3wt_1


title: Cmm inoculated 12dpi


title: OFLX_ rep2

first: ren

last: zehui

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Sequenced reads  filgered to find singal sequence
Sequenced reads were trimmed for adaptor sequence
mapped to whole genome using bowtie2
analysis insertion site with python program
Genome_build: GCF_000006765.1_ASM676v1_genomic
Supplementary_files_format_and_content: Matrix table with raw UMI counts for every insertion site and every sample

organism: Pseudomonas aeruginosa PAO1

source_name: bacteria

growth_protocol: A glycerol stock of pooled P. aeruginosa CTAGE library was thawed on ice and 1:1000 diluted into 100 mL LB medium.

extract_protocol: The genomic DNA of each sample was extracted by the Ezup column bacteria genomic DNA purification kit (Sangon, Shanghai, China).

treatment_protocol: The cells were treated for ~16h in the absence or in the presence of antibiotics (8 μg/mL imipenem, 1 μg/mL ceftazidime, and 1 μg/mL ofloxacin).

value: treated with oflx


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep3

description:
Sample 3
3-8-a3


title: Ribo-WT-3opt_1

value: WT

value: ribosome protected fragments


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep2

description:
Sample 2
2-8-a2


title: Ribo-WT-3opt_2


title: Ribo-WT-1opt_2


title: tg(sox10:GFP)

city: Easton

first: Ezra

last: Lencer

address: 746 High Street

department: Department of Biology

institute: Lafayette College

description: trunk tg(sox10:GFP) cells from 20-24hpf zebrafish

data_processing:
cellranger v3.2
seurat v3.2.2
Genome_build: GRCz11
Supplementary_files_format_and_content: features, barcodes, counts matrix for scRNAseq
Supplementary_files_format_and_content: Cluster assignments

organism: Danio rerio

source_name: zebrafish trunk tg(sox10:GFP) positive cells

extract_protocol: tg(sox10:GFP) cells were isolated by FACS from dissociated trunks of 20-24hpf zebrafish and submitted to 10x Sequencing

value: trunk neural crest cells

tag: developmental stage

value: 24 hpf


title: HL-1 cell line_control_cyclic stretch_rep6

description:
Sample 12
12-4-b3

value: control

tag: treatment


title: IMP_ rep1

value: treated with imp


title: CUT&RUN - CUX1

data_processing:
Library strategy: CUT&RUN
RNA-seq reads were aligned to mm10 using STAR, mapping quality <30 were removed. Differental gene expression analysis was done using DESeq2
ATAC-seq reads were aligned to mm10 using BWA, mapping quality <30 were removed. Peaks were called with MACS2, DiffBind was used for differential accessibility
ChIP-seq and CUT&RUN reads were mapped to hg19 using BWA, mapping quality <30 were removed. Peaks were called with MACS2 and analyzed by IDR
Genome_build: mm10, hg19
Supplementary_files_format_and_content: RNA-seq files contain DESeq2 results for gene ID and CPM;  ATAC-seq, ChIP-seq, and CUT&RUN samples have bed files attached

source_name: D7 erythroid differentated erythroblasts

tag: genotype

value: human CD34 cells 7 days after erythroid differentation


title: IMP_ rep2


title: CUT&RUN - CUX2


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep1

description:
Sample 1
1-8-a1

value: cardiomyocyte-derived HL-1 cell line

value: MuRF1 KD


title: ChIP-seq CUX1 2

source_name: K562 cell line

tag: chip antibody


title: OFLX_ rep1


title: Ribo-WT-1opt_1

tag: host strain

tag: reporter expressed in host strain

value: mycelia


title: HL-1 cell line_MuRF1 KD_cyclic stretch_rep5

description:
Sample 5
5-8-b2

value: cyclic stretch (15% biaxial stretch at 1 Hz for 60 min)


title: Ribo-WT-3wt_2

tag: molecule


title: CAZ_ rep1

value: treated with caz


title: ChIP-seq CUX1 1


title: CAZ_ rep2


title: RA FLSs, R37-NC

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software,version 1.8 ) used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Cutadapt software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Pertea M et al.,Nature methods,2008
Genome_build: hg18
Supplementary_files_format_and_content: FPKM values for each Sample, gene-level and transcript-level

source_name: rheumatoid fibroblast-like synoviocytes

extract_protocol:
The RNA of  rheumatoid fibroblast-like synoviocytes was harvested using Trizol reagent. KAPA Stranded RNA-Seq Library Prep Kit(Illumina) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: NC


title: Cut&Tag_WTC11 iPSCs - H3K4me3_rep2

value: WTC11 iPSCs


title: Ribo-WT-3wt_1


title: HL-1 cell line_MuRF1 KD_non-stretched_rep3

description:
Sample 15
15-5-a3

value: non-stretched (0 min stretch)


title: CUT&RUN - CUX3


title: RA FLSs, R22-si

value: siLINK-A


title: Base_ rep2

value: untreated


title: RA FLSs, R22-NC


title: Ribo-WT-1wt_2

value: WT

value: ribosome protected fragments


title: Base_ rep1


title: RA FLSs, R37-si


title: Ribo-WT-1wt_1


title: MDA-MB-231_Ribociclib&D 4476_rep3

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

institute: Dana-Farber Cancer Institute

data_processing:
Basecalling performed using bcl2fastq v2.18
Raw sequencing reads were quality trimmed and aligned to reference human genome hg38 using HISAT2 (2.0.4) package
The transcript abundances for each sample was estimated with StringTie (1.3.4). All transcriptomes from each samples were merged to reconstruct a comprehensive transcriptome and subjected to StringTie and Ballgown to estimate the expression levels of all transcripts.
The FPKM value for mRNA expression levels were calculated with Ballgown.
Genome_build: hg38
Supplementary_files_format_and_content: xlsx format containing gene abundance measurements

source_name: Triple negative breast cancer cell line

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% heat inactivated FBS and 1% Penicillin-Streptomycin

extract_protocol:
For RNA-seq, total RNA was purified using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen)
Libraries were prepared using Illumina TruSeq mRNA sample preparation kits from 500 ng of purified total RNA

treatment_protocol: MDA-MB-231 cells were cultured in 10 cm cell culture dishes and treated with DMSO, Ribociclib (1uM), and Ribociclib (1uM) & D 4476 (25uM) for 48 hours before collection of total RNA.

value: Ribociclib&D 4476


title: PAO1_LE_library


title: MDA-MB-231_Ribociclib_rep1

value: Ribociclib


title: MDA-MB-231_Ribociclib&D 4476_rep1


title: MDA-MB-231_Ribociclib&D 4476_rep2


title: primary hepatocytes, butyric acid treatment, replicate 1

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

data_processing:
Sequencing reads that contained adapters and/or had low quality, aligned to rRNA were filtered off before mapping.
The tool Salmon (version 1.2.1) was used to map the cleaned reads to the GRCm38.p6 mouse genome assembly-based transcriptome sequences as annotated by the GENCODE consortium (release M25). Salmon parameters used: -i ./salmon_index_M25  --libType A --seqBias --numBiasSamples 10000000 --gcBias --biasSpeedSamp 5 --validateMappings --numGibbsSamples 100
The Salmon-obtained transcript abundance estimates and lengths were imported in R using the package tximport (version 1.16.1) to estimate gene level counts.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (gene level counts were calculated from the Salmon-obtained transcript abundance estimates; TxImport.GeneLevel.counts.GEO.txt)
Supplementary_files_format_and_content: R-object (txi.counts.annotated.GEO.Rdata; exported tximport object) containing gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was not transformed nor scaled (i.e. countsFromAbundance = "no"), and can be used for subsequent analysis in edgeR or DESeq2.
Supplementary_files_format_and_content: R object (txi.lengthScaledTPM.annotated.GEO.Rdata; exported tximport object) containing scaled gene level counts estimated from the Salmon-obtained transcript abundance estimates. Note: count data was scaled using library size and transcript gene length (i.e. countsFromAbundance = "lengthScaledTPM"), and these scaled counts can be used for subsequent analysis in limma (voom function).

source_name: primary mouse hepatocytes, treated with butyric acid (bOHB; 5mM) for 6 hrs

growth_protocol: Primary mouse adipocytes (isolation and differentiation of stromal vascular fraction): Inguinal white adipose tissue from 3-4 C57Bl/6 male mice was collected and placed in Dulbecco’s modified eagle’s medium (DMEM; Lonza) supplemented with 1% Penicillin/Streptomycin (PS) and 1% bovine serum albumin (BSA; Sigma-Aldrich). Material was minced finely with scissors and digested in collagenase-containing medium (DMEM with 3.2 mM CaCl2, 1.5 mg/ml collagenase type II (C6885, Sigma-Aldrich), 10% FBS, 0.5% BSA, and 15 mM HEPES) for 1 h at 37°C, with occasional vortexing. Cells were filtered through a 100-μm cell strainer (Falcon). Subsequently, the cell suspension was centrifuged at 1600 rpm for 10 min and the pellet was resuspended in erythrocyte lysis buffer (155 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA). Upon incubation for 2 min at room temperature, cells were centrifuged at 1200 rpm for 5 min and the pelleted cells were resuspended in DMEM containing 10% fetal bovine serum (FBS) and 1% PS (DMEM/FBS/PS) and plated. Upon confluence, the cells were differentiated according to the protocol as described previously [PMID: 22569073 and 23150577]. Briefly, confluent SVFs were plated in 1:1 surface ratio, and differentiation was induced 2 days afterwards by switching to a differentiation induction cocktail (DMEM/FBS/PS, 0.5 mM isobutylmethylxanthine, 1 μM dexamethasone, 7 μg/ml insulin and 1 µM rosiglitazone) for 3 days. Subsequently, cells were maintained in DMEM/FBS/PS, and 7 μg/ml insulin for 3-6 days and switched to DMEM/FBS/PS for 3 days. Average rate of differentiation was at least 80% as determined by eye. Primary mouse macrophages (isolation and differentiation of bone marrow derived monocytes): Bone marrow cells were isolated from femurs of C57Bl/6 male mice following standard protocol and differentiated into macrophages (bone marrow-derived macrophages, BMDMs) in 6-8 days in DMEM/FBS/PS supplemented with 20% L929-conditioned medium (L929). After 6-8 days, non-adherent cells were removed, and adherent cells were washed and plated in 12-well plates in DMEM/FBS/PS + 10% L929. After 24 hours, medium was switched to 2% L929 in DMEM/FBS/PS overnight. Cells were treated the following day. Primary skeletal myotubes (isolation and differentiation of skeletal myocytes): Myoblasts from hindlimb muscle of WT-C57Bl/6 male mice were isolated as previously described [PMID: 29879622]. In brief, the muscles were excised, washed in 1× PBS, minced thoroughly, and digested using 1.5 mL collagenase digestion buffer (500 U/ml or 4 mg/mL collagenase type II (C6885, Sigma-Aldrich), 1.5 U/ml or 5 mg/mL Dispase II (D4693, Sigma-Aldrich), and 2.5 mM CaCl2 in 1× PBS) at 37°C water bath for 1 h in a 50 ml tube, agitating the tube every 5 min. After digestion, the cell suspension containing small pieces of muscle tissue was diluted in proliferation medium (PM: Ham's F-10 Nutrient Mix (#31550023, Thermo Fisher Scientific) supplemented with 20% fetal calf serum, 10% HS, 0.5% sterile filtered chicken embryo extract (#092850145, MP Biomedicals), 2.5 ng/ml basic fibroblast growth factor (#PHG0367, Thermo Fisher Scientific), 1% gentamycin, and 1% PS), and the suspension was seeded onto matrigel-coated (0.9 mg/ml, #354234, Corning) T150 flasks at 20% surface coverage. Cells were grown in 5% CO2 incubator at 37°C. Confluence was reached latest after 5 d in culture, upon which cells were trypsinized (0.25% trypsin), filtered with 70 µm filters, centrifuged at 300 g for 5 min, and then seeded on an uncoated T150 flask for 45 min to get rid of fibroblasts. Subsequently, myoblasts were seeded in PM at 150.000 cells/mL onto matrigel-coated 12-well plates cells. Upon reaching confluence, differentiation was induced by switching to differentiation medium (DM: Ham's F-10 Nutrient Mix supplemented with 5% horse serum (HS) and 1% PS). DM was replaced every other day. Myotubes fully differentiated by Day 5 of differentiation in DM. The medium was renewed every other day. Primary mouse hepatocytes (isolation and culturing of hepatocytes): Primary hepatocytes were isolated from C57BL/6NHsd male mice via collagenase perfusion. Cells were plated onto collagen (0.9 mg/ml) coated 24-well plates at 200,000 cells/well in Williams E medium (PAN Biotech), substituted with 10% FBS, 100 nM dexamethasone and penicillin/streptomycin and maintained at 37 °C in an atmosphere with 5% CO2. After four hours of attachment, cells were washed with phosphate buffer saline (PBS) and allowed to rest in dexamethasone-free medium overnight before treatment.

extract_protocol:
Total RNA from all cell culture samples was extracted using TRIzol reagent (Thermo Fisher Scientific) and purified using the Qiagen RNeasy Mini kit (Qiagen) according to manufacturer’s instructions. RNA concentration was measured with a Nanodrop 1000 spectrometer and RNA integrity was determined using an Agilent 2100 Bioanalyzer with RNA 6000 microchips (Agilent Technologies).
Library construction and RNA sequencing on BGISEQ-500 were conducted at Beijing Genomics Institute (BGI) for pair-end 150bp runs. At BGI, Genomic DNA was removed with two digestions using Amplification grade DNAse I (Invitrogen). The RNA was sheared and reverse transcribed using random primers to obtain cDNA, which was used for library construction. The library quality was determined by using Bioanalyzer 2100 (Agilent Technologies). Then, the library was used for sequencing with the sequencing platform BGISEQ-500 (BGI).

treatment_protocol: Primary cells were treated for 6h with 5 mM βOHB or Butyrate, with PBS as control. Adipocytes and Macrophages were treated in DMEM/FCS/PS. Myotubes were treated in DM. Hepatocytes were treated in Williams E medium. Cells were washed with PBS once and stored in -80 °C until RNA was isolated.

tag: strain

value: primary hepatocytes

value: 5 mM NaB [butyric acid sodium salt]

tag: exposure time

value: 6 hrs


title: MDA-MB-231_DMSO_rep1

tag: cell line

value: DMSO


title: primary hepatocytes, bOHB treatment, replicate 3

source_name: primary mouse hepatocytes, treated with β-hydroxybutyric acid (bOHB; 5mM) for 6 hrs

value: 5 mM bOHB [(R)-(–)-3-Hydroxybutyric acid sodium salt]


title: MDA-MB-231_Ribociclib_rep2


title: MDA-MB-231_DMSO_rep2


title: WTC11 iPSCs - ATAC_rep1

data_processing:
All libaries were processed using the ENCODE ATAC-seq pipeline (v1.8.0) using default settings
Briefly, reads were mapped to bowtie2, duplicates removed by picard and peaks were called by MACS2
Genome_build: hg38
Supplementary_files_format_and_content: Optimal IDR peak called using MACS2
Supplementary_files_format_and_content: bigwig file was generated with bamCoverage --binSize=1 and merged with UCSC bigWigMerge

extract_protocol:
Cells were harvested, washed with ice cold PBS containing protease inhibitor and nuclei were extracted prior to library construction.
The standard ATAC-seq protocol was used, with the transposase reaction carried out for 30 minutes at 37C. 8-10 cycles of amplification were performed and dual size selection was performed with SPRIselect beads.


title: MDA-MB-231_Ribociclib_rep3


title: primary hepatocytes, bOHB treatment, replicate 1


title: primary hepatocytes, butyric acid treatment, replicate 3


title: primary hepatocytes, bOHB treatment, replicate 2


title: Adult Brain, TADA_UAS-Dam-acj6_x_ato sample 1

city: LEUVEN

first: Stein

last: Aerts

address: Herestraat 49, bus 602

department: Center for Brain & Disease Research

country: Belgium

institute: KULeuven/VIB

description: final_peak_file_for_UAS-Dam-acj6_x_atonal-Gal4_1rep_FDR_0.01_with_peak_height_and_highest_associated_FDR.gff

data_processing:
Library strategy: DamID-seq
The 10X samples were each processed (alignment, barcode assignment and UMI counting) with Cell Ranger ATAC (version 1.2.0) count pipeline.
For the ATAC samples the raw reads were first filtered and scanned for adapters using fastq‐mcf from the ea‐utils package. Read quality was then checked using FastQC. The reads were mapped to the Drosophila genome (dm6) using STAR. The outputted BAM file from STAR was then indexedand sorted using SAMtools. Using genomeCoverageBed from BedTools, the BAM file was converted to a BedGraph file. For fast, visualization in the IGV GenomeBrowser, the BedGraph file was further processed to a BigWig file using bedGraphtoBigWig.
Cut&Tag samples were processed similarly to ATAC-seq samples
TaDa sequencing data were mapped back to release 6.03 of the Drosophila genome using a previously described pipelines ( Marshall and Brand, 2015). Peaks were called and mapped to genes using a custom Perl program (available at https://github.com/tonysouthall/Peak_calling_DamID)
Genome_build: dm6 (dmel_r6.16_FB2017_03)
Supplementary_files_format_and_content: gff, narrowPeak, bigWig

organism: Drosophila melanogaster

source_name: Adult Brain

extract_protocol:
Flies were allowed to lay eggs for 2 days at 18˚C in fly food vials. Vials containing those eggs were kept at 18˚C (restrictive temperature) until adult flies eclosed. They were then kept at 18˚C for 3-7 days before being transferred to 29˚C (permissive temperature) for 24 hours. For the Dam-Mef2 experiments in R16A06, a minimum of 90 brains were dissected per replicate, for the Dam-Mef2 experiments in R74G01 cells, 40 brains were dissected, and for the Dam-acj6 in atonal cells, a minimum of 30 brains. 2 biological replicates were performed for each experiment. The DamID protocol is based on (Marshall et al., 2016) with the following changes: After the overnight DpnI digestion , 0.5 µl of DpnI was added for an extra 1 hour incubation and MyTaq™ HS DNA Polymerase was used for the PCR amplification (instead of Advantage 2 cDNA Polymerase).
Targeted DamID

value: Brain

value: Adult

tag: age

value: 4-8 day


title: Adult Brain, TADA_UAS-Dam_x_ato sample 1


title: WTC11 iPSCs - ATAC_rep2


title: Adult Brain, TADA_UAS-Dam_x_R74G01 sample 1

description: final_peak_file_for_UAS-Dam-Mef2_x_R74G01-Gal4_2rep_FDR_0.01_with_peak_height_and_highest_assoiciated_FDR.gff


title: HS lin-29 trial 2

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

description: Samples prepared 1hr after heat shock induction

data_processing:
Bcl2fastq v2.18 was used to convert the bcl files to fastq files.
We aligned to ce10 reference genome using STAR, version 2.5.2b.
We counted number of reads mapped to genes using htseq, version 0.6.1p1.
Differential gene expression analysis was performed using DESeq2, version 1.12.3  with the cutoff of 0.05 on False Discovery Rate (FDR). R version 3.3.2 (2016-10- 31) was used, and  Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation, we used  UCSC's ce10.
Genome_build: ce10
Supplementary_files_format_and_content: count

organism: Caenorhabditis elegans

source_name: C. elegans synchronized population

growth_protocol: C. elegans animals were cultured using standard methods (Brenner, 1974). L1-stage syncrhonized populations were grown at 20C on NGM plates and fed with E. coli OP50

extract_protocol:
Pellets of 50-100 µl of frozen worms were suspended in 600 µl of DEPC water and homogenized with a gentleMAC dissociator (miltenyibiotec). RNA preparations were performed with Quick-RNA™ MiniPrep kit (Zymo Research) according to manufacturer's protocol.
RNA-seq libraries are constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina from NEB.

treatment_protocol: Populations in the L3 stage (28 hours post feeding) were induced by heat shock exposure of 30 minutes at 37°C and returned to growing temperature for one hour before sample preparation

tag: Stage

value: L3-stage larvae

value: whole body


title: primary hepatocytes, butyric acid treatment, replicate 2


title: RA FLSs, R11-NC

city: Guangzhou

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes

value: NC


title: PAO1_RE_library

value: untreated


title: HS lin-29 trial 3


title: RA FLSs, R11-si

value: siLINK-A


title: Adult Brain, TADA_UAS-Dam-Mef2_x_R74G01 sample 2


title: Adult Brain, TADA_UAS-Dam_x_R74G01 sample 2


title: primary hepatocytes, control treatment, replicate 3

source_name: primary mouse hepatocytes, treated with vehicle (PBS) for 6 hrs

value: control (PBS)


title: HS lin-29 trial 1


title: primary hepatocytes, control treatment, replicate 2


title: Adult Brain, TADA_UAS-Dam-Mef2_x_R74G01 sample 1


title: HS control trial 2


title: ΔH3.3B; ΔH3.3A round 2 sample7

city: Umeå

first: Henrik

last: Lindehell

address: Umeå universitet

department: Department of Molecular Biology

institute: Umeå University

data_processing:
Adaptor sequence was trimmed from the sequenced reads, and masked for low-complexity or low-quality sequence, then mapped to BDGP6 whole genome using Star v2.5.3 (DOBIN et al. 2013) with default settings.
Read counts were obtained with featureCounts v1.5.1 with default settings
Genome_build: BDGP6
Supplementary_files_format_and_content: Raw count table in tab delimited .txt format

source_name: Male 3rd Instar larvae brain

extract_protocol:
For each sample, five male third instar larvae brains were homogenized and RNA was purified using the Directzol microprep kit (Zymo research) and the standard protocol with on column DNase treatment was used.
Total-RNA libraries were synthesised using the Ovation RNA-Seq system for Drosophila (NuGEN). Standard protocol procedure with integrated DNase treatment was used to make the sequencing libraries. Fragmentation was performed using a Covaris E220 Focused-ultrasonicator with the recommended settings for 200 base pair target length.

value: 3rd instar larvae

value: brain

tag: Sex

value: male

value: delta-H3.3B; delta-H3.3A


title: ΔH3.3B; ΔH3.3A round 2 sample6


title: HS control trial 1


title: ΔH3.3B; ΔH3.3A round 2 sample4


title: primary skeletal myotubes, butyric acid treatment, replicate 2

source_name: primary mouse skeletal myotubes, treated with butyric acid (bOHB; 5mM) for 6 hrs

value: primary skeletal myotubes

value: 5 mM NaB [butyric acid sodium salt]

value: 6 hrs


title: HS control trial 3


title: MDA-MB-231_DMSO_rep3

value: DMSO


title: ΔH3.3B; ΔH3.3A round 2 sample8


title: primary skeletal myotubes, butyric acid treatment, replicate 3


title: primary skeletal myotubes, bOHB treatment, replicate 2

source_name: primary mouse skeletal myotubes, treated with β-hydroxybutyric acid (bOHB; 5mM) for 6 hrs

value: 5 mM bOHB [(R)-(–)-3-Hydroxybutyric acid sodium salt]


title: Adult Brain, TADA_UAS-Dam_x_R16A06 sample2

description: final_peak_file_for_UAS-Dam-Mef2_x_R16A06-Gal4_2rep_FDR_0.01_with_peak_height_and_highest_associated_FDR.gff

value: Brain

value: Adult

value: 4-8 day


title: Adult Brain, TADA_UAS-Mef2-Dam_x_R16A06 sample1