title: 8h control group_1

city: Shanghai

first: Hongru

last: Lin

state: Shanghai

address: Siping road 1239

department: life and science technology

institute: Tongji university

description: 8h control group

data_processing:
Illumina Casava1.8 software used for basecalling.
HISAT2 (2.05) and stringtie (1.33)
filtering RNA-seq data with the following cut-off: a two-fold change in expression level and a false discovery rate analog of p < 0.05.
DESeq2 was used for differential expression analysis.
Assembly: c.elegans

organism: Caenorhabditis elegans

growth_protocol: L1 stage c.elegans cultured on ngm medium with OP50

extract_protocol:
RNA was extracted from nematodes using standard extraction methods, and RNA samples were then subjected to strict quality control, mainly by the Agilent 2100 bioanalyzer: precise detection of RNA integrity
Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA was synthesized in the M-MuLV reverse transcriptase system, and then the RNA strand was degraded by RNaseH, and dNTPs were used as the DNA polymerase I system. The starting material is used to synthesize the second strand of cDNA. The purified double-stranded cDNA is end-repaired, A-tailed, and connected to a sequencing adapter. The 250-300 bp cDNA is screened with AMPure XP beads, amplified by PCR, and the PCR product is purified again with AMPure XP beads to finally obtain a library.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: Induction of Aβ expression by transwarming

tag: induction

tag: developmental stage


title: E13.5 FlashTag collected at P7 IL05_Pool5

status: Public on Apr 20 2022

type: SRA

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

library_source: transcriptomic

data_processing:
Reads were aligned with STAR aligner
The count matrix were generated with HTSeq
cells expressing less <2000 genes or >12% of mitochondrial RNAs were excluded
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: RPM normalized matrix

molecule: total RNA

organism: Mus musculus

source_name: Neurons

extract_protocol:
SMART-Seq v4 3’ DE Kit
Single cells were collected into tubes and the library was constructed with Nextera XT library prep kit according to manufacturers

tag: strain

tag: genotype

value: WT

tag: age


title: Aβ induction for 8h_2

country: China

description: Aβ induction for 8h


title: WT PBS neuutrophil

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

country: USA

institute: Virginia Tech

data_processing:
Cellranger
Genome_build: mm10
Supplementary_files_format_and_content: matrix table

molecule: polyA RNA

source_name: neutrophil

growth_protocol: Murine bone marrow neutrophils were purified by the percoll gradient method, and cultured in complete RPMI medium (10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin) supplemented with 100 ng/ml G-CSF.

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
ingle-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.

treatment_protocol: Cultured bone marrow neutrophils from WT and TRAM knockout mice were treated with PBS or 1mM 4-PBA for 24 h.

tag: cell type

value: BM derived

tag: treatment

value: PBS


title: Aβ induction for 8h_1

description: Aβ induction for 8h


title: AERD_03_TK198s1

city: Vienna

first: Christine

last: Bangert

address: Waehringer Guertel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
The raw sequencing reads were aligned to the reference genome GRCh38 and demultiplexed using Cell Ranger 3.0.2
The resulting count-matrices were then imported into R for further analysis using the Seurat package v3
Cells were filtered based on their number of unique reads, number of expressed features and the percentage of mitochondrial reads present to ensure cell quality .
Samples were normalized with Seurat’s NormalizeData function using log normalisation.
Genome_build: GRCh38
Supplementary_files_format_and_content: individual gene expression matrix per patient, in .csv format containing log-normalized cell-counts

organism: Homo sapiens

source_name: nasal polyps

extract_protocol:
Biopsies were taken during endoscopy and kept in phosphate buffered saline (PBS) on ice until further processing.
The partial nasal biopsy was enzymatically digested for one hour at 37°C using RPMI-1640 medium (Thermo Fisher Scientific, Waltham, Massachusetts, USA) supplemented with 2.8 mg/ml Collagenase IV Thermo Fisher Scientific) and 0.03 mg/ml DNAse (Merck, Burlington, Massachusetts, USA). Single cell suspension was obtained by passing the tissue through a 70 µm cell strainer (BD, Franklin Lakes, New Jersey, USA) and washing it twice with RPMI-1640 medium supplemented with 20% foetal bovine serum (FBS, Thermo Fisher Scientific). Thereafter cells were blocked with 10% mouse serum (Thermo Fisher Scientific) in MACS buffer (Miltenyi Biotec, Bergisch Gladbach, Germany) on ice for 5 minutes. Preparing cell suspensions for FACS sorting, cells were stained with anti-human CD15 FITC (clone W6D3, Biolegend), anti-human CD94 PE (clone DX22, Biolegend), anti-human CD14 APC (clone HCD14, Biolegend), anti-human HLA-DR BV421 (clone L243, Biolegend), anti-human CD45 PE-CF594 (clone HI30, BD BioSciences), anti-human CD11c PE-Cy7 (clone 3.9, Biolegend), anti-human CD20 APC-Cy7 (clone 2H7, Biolegend) and anti-human CD3 BV605 (clone SK7, Biolegend) with an incubation period of 30 minutes on ice under light protection. Cells were then subjected to FACS sorting (FACSAria III, BD Biosciences, Franklin Lakes, NJ) for enrichment of CD45+ leukocyte subsets to obtain comparable numbers between all samples allowing for comparison of small cell populations. Up to 18,000 sort-purified cells from each sample were suspended in reverse transcription reagents, along with gel beads, and then segregated into aqueous nanoliter-scale gel bead-in-emulsions. After gel bead-in-emulsions reverse transcription, single-cell droplets were broken, and the single-strand cDNA was isolated and amplified. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated followed by post-ligation amplification. The sequencing-ready libraries were sequenced by the Biomedical Sequencing Facility at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, using the Illumina HiSeq 3000/4000 platform and the 75 bp paired-end configuration.

treatment_protocol: Prior to polyp biopsy, patients received local anasthetics and decongestants.

tag: Sex

value: F

tag: 10x chromium chemistry version

tag: condition

value: CRSwNP


title: PF_D2

city: Shenyang

first: Jingyu

last: Yue

address: Dongling Road

institute: Shenyang Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary_files_format_and_content: expression profiles

organism: Fragaria hybrid cultivar

growth_protocol: The pink-flowered strawberry cultivar 'Sijihong' was used in this study released by Shenyang Agricultural University in China with red flowers, and fifty plants was planted in the open ground for sampling.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: Petals of three developmental stages with obviously different color (‘L’, ‘Z’ and ‘D’) were selected for miRNAsanalysis and three biological repetitions were set for each treatment.

tag: cultivar

value: Pink-flowered strawberry 'Sijihong', interspecific hybrid from Fragaria x Potentilla

value: D

tag: tissue

value: flower; petal

tag: molecule subtype

value: Small RNA


title: PF_D3


title: E13.5 FlashTag collected at P7 IL05_Pool4


title: E13.5 FlashTag collected at P7 IL05_Pool3


title: WT high dose LPS neutrophil

value: High dose LPS


title: E13.5 FlashTag collected at P7 IL06_Pool4


title: 24h control group_3

description: 24h control group


title: Wrinkly Fried Egg Rep 3

city: Christchurch

first: Heather

last: Hendrickson

department: Biological Sciences

country: New Zealand

institute: University of Cantebury

data_processing:
reads were aligned to the Acanthamoeba reference genome (Acanthamoeba castellanii strain NEFF GCA_000313135.1) using HiSat2
unused reads were then aligned to the bacterial reference genome (Pseudomonas fluorescens SBW25 GCA_000009225.1) using Bowtie2
Sequence reads were assigned to genomic features using featureCounts
Differential expression using GLM and count normalisation was calculated with edgeR, Counts were normalised by library size (counts per million, CPM) with log2 transformation.
Assembly: GCA_000313135.1, GCA_000009225.1
Supplementary files format and content: tab-delimited text files include CPM values per sample

organism: Pseudomonas fluorescens

source_name: Bacteria

growth_protocol: Individual colonies of bacterial strains pre-cultured on LB agar were homogenised in LB broth and spread in single lines across PM agar plates using a 1ul transfer loop. Plates were allowed to dry before applying 2 ul of suspension containing ~103 Acanthamoeba cysts µl-1 at one end of the bacterial line. Plates were incubated at 28˚C for up to 1 week and the interaction zone was collected once the amoeba had formed a visible clearing. Pseudomonas fluorescens SBW25 strains were collected with Acanthamoeba from the bacteria-protozoa interaction zone and alone from the opposite end of the culture line with a transfer loop and immediately homogenised in RNA shield (n=4

extract_protocol:
Total RNA was extracted from bacterial and amoebae cells using the Quick-RNA MiniPrep Kit (Zymo Research, USA)
Preparations were dried in GenTegra RNA tubes according to manufacturer’s instructions (Gentegra, USA) and sent to the Microbial Genome Sequencing (MiGS, USA) Center for Illumina Stranded RNA library preparation with RiboZero Plus rRNA depletion and sequencing on the NextSeq 550 platform.

value: SBW25 WFE


title: 33L

city: guangzhou

first: peng

last: wang

address: 1838 North Guangzhou Avenue

institute: Southern Medical University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the CPM value for circRNA and transcript level were calculated with R package Ballgown (v2.6.0)
To evaluate the expression of circRNA after RNA-seq, the junction site was identified by STAR software, then the backsplice junction reads were calculated by CICexplorer2. circRNAs were annotated through blasting the sequence in circBase
Genome_build: mm10
Supplementary_files_format_and_content: counts

source_name: Renal tubules

extract_protocol:
1 day after Ischemic-reperfusion-injury, the renal tubules from control mice, mild injury (20min-ischemia) or severe injury (40-min ischemia) (n=3 in each group) were isolated. Total RNA were extracted from these isolated tubules by TRIzol reagent.
For the preparation of RNA-seq library, total RNA (3μg) from each sample were treated with the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Vazyme Biotech, Nanjing, China) to erase ribosomal RNA but retained mRNA and non-coding RNA (ncRNA). Purified RNA was digested with RNase R (Epicenter) followed by purification with TRIzol (Invitrogen). RNA-seq libraries were constructed using the KAPA Stranded RNA-Seq Library Prep Kit (Roche) and subjected to deep sequencing with an Illumina HiSeq 4000 (Aksomics).

value: 8 weeks

value: Severe IRI


title: 8h control group_2

description: 8h control group


title: PF_Z3

value: Z


title: 70R

value: Mild IRI


title: 31R


title: 24h control group_2

description: 24h control group


title: E13.5 FlashTag collected at P7 IL05_Pool2


title: 63L


title: PF_Z2


title: 34L


title: 24h control group_1

description: 24h control group


title: E13.5 FlashTag collected at P7 IL05_Pool1


title: PF_Z1


title: E13.5 FlashTag collected at P7 IL04_Pool5


title: PF_D1


title: Aβ induction for 24h_2

description: Aβ induction for 24h


title: E13.5 FlashTag collected at P7 IL04_Pool4


title: Aβ induction for 24h_3

description: Aβ induction for 24h


title: PF_L3

value: L


title: PF_L2


title: 62L


title: 45L

value: Control


title: E13.5 FlashTag collected at P7 IL04_Pool3

value: WT


title: PF_L1


title: Aβ induction for 24h_1

description: Aβ induction for 24h


title: 44L


title: Alb-Cre; Pak4 flox/flox, rep 3

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Liver tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

value: Liver

value: 10 weeks

value: Hepatocyte-specific Pak4 KO


title: 43L


title: Alb-Cre; Pak4 flox/flox, rep 2


title: SKD3

city: Pittsburgh

first: Shivendra

middle: V

last: Singh

state: PA

address: 5117 Centre Avenue UPMC HCC Research Pavilion Suite 2.32A

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
STAR v2.6.1d was used to count the read numbers mapped of each gene. The fragments per kilobase per million mapped (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: FPKM represents summary of gene expression level analysis by FPKM; DEG represents differential gene expression analysis

source_name: breast cancer cells

growth_protocol: MCF-10A and SK-BR-3 cells were plated in 10-cm dish at a density of 1×106 cells/dish and incubated overnight for attachment.

extract_protocol:
The cells were harvested by trypsin treatment and total RNA was extracted using the RNeasy mini kit (Qiagen, Germantown, MD).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were treated with DMSO (final concentration- 0.07%) or 20 µM of DATS for 16 hours prior to RNA isolation and RNA-Seq analysis. Samples were prepared three times independently.

tag: cell line name

value: Cells were treated with 20 µM of DATS for 16 hours.


title: SKD2


title: E13.5 FlashTag collected at P7 IL04_Pool1


title: E13.5 FlashTag collected at P7 IL03_Pool5


title: eif4a2_eCLIP_IP_rep2

city: New York

first: Jianlong

last: Wang

state: NY

department: Department of Medicine

institute: Columbia University Irving Medical Center

description:
eif4a2 eCLIP IP rep2
eif4A2_peak_norm_compressed_FC2.bed

data_processing:
Adapters were trimmed (cutadapt v1.18), and reads less than 18 bp were discarded using parameters -m 18 -a NNNNNNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -g ACGCTCTTCCGATCT -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT for round 1 and parameters -m 18 -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT for round 2.
Mapping reads were then performed against mouse elements in RepBase with STAR (v2.6.1b). Repeat mapping reads were segregated, and all others were then mapped against the mouse mm9 genome with STAR (v2.6.1b).
PCR duplicates were removed from uniquely mapping reads to get usable reads. Multiple in-line barcodes were merged for usable reads, followed by peak identification with the clipper software (v0.2.0, https://pypi.org/project/clipper/) using parameters -s mm9 --bonferroni --superlocal --threshold-method binomial --save-pickle on read 2 only. In addition, only peaks with fold change > 2 were kept.
Genome_build: mm9
Supplementary_files_format_and_content: bed files - tab-delimited files containing peaks for RNA-binding proteins.

source_name: Embryonic stem cells

growth_protocol: Feeder-free murine ESCs were grown on 0.1% gelatin-coated tissue culture plates in ESC medium containing high-glucose DMEM, 15% fetal bovine serum (FBS), 100 μM nonessential amino acids, 1% nucleoside mix, 2 mM L-Glutamine, 50 U/mL Penicillin/Streptomycin, 0.1 mM 2-mercaptoethanol, and homemade recombinant leukemia inhibitory factor (LIF) tested for efficient self-renewal maintenance, at 37℃.

extract_protocol:
eCLIP-seq was performed as previously described (Van Nostrand et al., 2016) by using an anti-eIF4A2 antibody (Abcam, ab31218).
Two biological replicates were performed for Input and eIF4A2 eCLIPed RNA. Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufactory protocol, and paired-end 50 bp-length reads were produced.

treatment_protocol: Feeder-free murine ESCs were UV crosslinked at 400 mJ/cm2 with 254 nm radiation before the cell collection.

tag: cell line

value: mESC J1

tag: antibody


title: Pak4 flox/flox, rep 2


title: Pak4 flox/flox, rep 3


title: eif4a2_eCLIP_IP_rep1

description:
eif4a2 eCLIP IP rep1
eif4A2_peak_norm_compressed_FC2.bed


title: SKC3

value: Cells were treated with vehicle (DMSO) for 16 hours.


title: eif4a2_eCLIP_input_rep2

description:
eif4a2 eCLIP input rep2
eif4A2_peak_norm_compressed_FC2.bed


title: Alb-Cre; Pak4 flox/flox, rep 1


title: E13.5 FlashTag collected at P7 IL03_Pool2


title: SKC1


title: E13.5 FlashTag collected at P7 IL03_Pool1


title: Pak4 flox/flox, rep 1


title: E13.5 FlashTag collected at P7 IL03_Pool3


title: eif4a2_eCLIP_input_rep1

description:
eif4a2 eCLIP input rep1
eif4A2_peak_norm_compressed_FC2.bed


title: SKC2


title: E13.5 FlashTag collected at P7 IL04_Pool2


title: 10AD3

source_name: normal epithelial cells


title: SKD1


title: E13.5 FlashTag collected at P7 IL02_Pool5


title: E13.5 FlashTag collected at P7 IL02_Pool4


title: T7_CT14_rep3

city: Bethesda

first: Samer

last: Hattar

state: MD

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

data_processing:
RNAseq reads were mapped to the mouse genome (mm10) using STAR aligner (v2.4.2a)
Aligned reads were counted using HTSeq-count (v0.9.1) with parameters --mode=union --stranded=no --idattr=gene_name, and the mm10 GTF annotation
Assembly: mm10
Supplementary files format and content: htseq-count output .txt files for each sample with feature counts mapped to gene_name

source_name: Perihabenular nucleus

extract_protocol:
Mice housed under T24 or T7 cycles were kept in darkness for 1 day prior to dissection to negate any acute effects of light. Brains were isolated and placed ventral side up on an ice-cold coronal slice brain matrix (Kent Scientific). A 1mm coronal slice of the brain was sectioned using ice-cold razor blades positioned caudal to the optic chiasm. PHb tissue was collected, immediately placed in ice-cold Qiazol lysis reagent (Qiagen) and stored at -80 C. Bilateral PHb tissue samples were pooled from 4 mice per replicate with a total of 4 replicates per condition. RNA isolation was performed with the Qiagen RNEasy Lipid Tissue Mini kit following manufacturer instructions. cDNA was prepared from total RNA using the Ovation RNASeq System V2 (Tecan) and end-repaired using the NEBNext End Repair Module (New England Biolabs).
RNA-Seq libraries were prepared from end-repaired cDNA with the TruSeq Stranded RNA Kit (Illumina). Libraries were pooled in an equimolar ratio prior to sequencing on an Illumina NovaSeq 6000 to a minimum depth of 128 million 150-bp paired-end reads per library.

value: Brain

tag: light cycle treatment

tag: circadian time


title: E13.5 FlashTag collected at P7 IL03_Pool4


title: T7_CT2_rep3


title: E13.5 FlashTag collected at P7 IL02_Pool3


title: T7_CT2_rep1


title: 10AD2


title: T7_CT14_rep4


title: T7_CT2_rep4


title: 10AC3


title: 10AD1


title: T7_CT2_rep2


title: pancreatic cancer tissue 6

type: RNA

city: Xi'an

first: Shibin

last: Qu

state: Shaanxi

address: 127 West Changle Road

department: Department of Hepatobiliary Surgery

institute: Xijing Hospital

description: lncRNA and mRNA expression in pancreatic cancer tissue 6

hyb_protocol: The labeled cRNAs were hybridized onto the LncRNA+mRNA Human Gene Expression Microarray V4.0, 4x180K

scan_protocol: The hybridized arrays were washed, fixed, and scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software  was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using theGeneSpring  GX . Differentially expressed lncRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed lncRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable lncRNAs expression pattern among samples.

source_name: pancreatic cancer tissue

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA, The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: tissue samples were obtained from  pancreatic ductal adenocarcinoma  patients. This study was approved by the institutional Ethics Review Board of the Xijing Hospital

extract_protocol: Total RNA was isolated from six PDAC and paired adjacent normal tissues using Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s protocol.

treatment_protocol: Each sample was snap-forzen in liquid nitrogen immediately after surgery resection, then stored at -130℃ until further use.

tag: gender

value: female

value: pancreatic cancer


title: E13.5 FlashTag collected at P7 IL09_Pool1

tag: strain


title: E13.5 FlashTag collected at P7 IL01_Pool5

tag: genotype


title: E13.5 FlashTag collected at P7 IL02_Pool2

tag: age


title: pancreatic cancer tissue 5

description: lncRNA and mRNA expression in pancreatic cancer tissue 5


title: pancreatic cancer tissue 4

description: lncRNA and mRNA expression in pancreatic cancer tissue 4


title: OC cells_Ovc316_resistant

city: Vejle

first: Silvia

middle: Regina

last: Rogatto

address: Beriderbakken 4

department: Clinical Genetics

country: Denmark

institute: Vejle Hospital

data_processing:
Data quality control was performed using FastQC and MultiQC
Reads were aligned using STAR (v.2.7.6a), and the gene read count was performed with HTSeq-count using the Ensembl human genome assembly GRCh38, release 99.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The cell lines were cultured in RPMI medium (Sigma Aldrich, Saint Louis, USA) (cell lines IGROV1, OVCAR3, and OVCAR4) or Dulbecco’s modified Eagle medium (DMEM, Sigma Aldrich) (OVCAR5, OVCAR8, and Ovc316), as recommended. The media were supplemented with 10% FBS (Biological Industries) and 1% antibiotic-antimycotic (Thermo Fisher).

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen, Valencia, CA, USA) according to the manufacturer's recommendations. The RNA purity and quantity were measured with a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, USA), and the integrity was assessed with RNA screen tape on a 2200 TapeStation (Agilent, Santa Clara, USA).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina, San Diego, California, USA) according to the manufacturer’s protocol.

treatment_protocol: Not applicable

tag: cell type

value: ovarian cancer cell line

tag: phenotype

value: carboplatin-resistant


title: pancreatic cancer tissue 3

description: lncRNA and mRNA expression in pancreatic cancer tissue 3


title: 10AC2

tag: treatment


title: E13.5 FlashTag collected at P7 IL02_Pool1


title: E13.5 FlashTag collected at P7 IL01_Pool4


title: OC cells_OVCAR-8_resistant


title: T7_CT14_rep1


title: E13.5 FlashTag collected at P7 IL01_Pool2


title: T24_CT2_rep3


title: 10AC1


title: pancreatic cancer tissue 2

description: lncRNA and mRNA expression in pancreatic cancer tissue 2


title: OC cells_OVCAR-3-R1_resistant

treatment_protocol: To establish resistant cell lines, the baseline schedule consisted of four days treatment with 1 µM of carboplatin in the culture media followed by three recovery days in media without carboplatin. For cell lines tolerating this treatment well, the concentration was increased gradually (1-5-10-15 µM) when the cells reached a high confluency. For cell lines not tolerating the treatment well, the recovery was extended, and the low dose was maintained.


title: normal pancreatic tissue 4

description: lncRNA and mRNA expression in normal pancreatic tissue 4

source_name: adjacent normal pancreatic tissue

value: normal pancreatic


title: T24_CT2_rep1


title: OC cells_OVCAR-5_sensitive

value: carboplatin-sensisitive


title: GckPVT 4 input

city: Lausanne

first: Sophie

last: Croizier

state: Vaud

address: Building Genopode-Quartier Sorge

department: Center for integrative genomics

institute: University of Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Genome_build: Mus musculus.GRCm38.92
Supplementary_files_format_and_content: raw gene counts for every gene in every sample

source_name: cells not expressing glucokinase

extract_protocol: RNA-seq libraries were prepared using 10 ng of total RNA and Ovation® RNA-Seq System V2 kit (Tecan; Männedorf, Switzerland). 100ng of cDNA was then taken into the TruSeq DNA Nano kit (Illumina; San Diego, California, USA).

value: Paraventricular Thalamus

tag: source

value: input


title: T24_CT2_rep4


title: E13.5 FlashTag collected at P7 IL01_Pool3


title: OC cells_OVCAR-5-R1_resistant


title: normal pancreatic tissue 1

description: lncRNA and mRNA expression in normal pancreatic tissue 1


title: GckPVT 3 input


title: T24_CT2_rep2


title: normal pancreatic tissue 6

description: lncRNA and mRNA expression in normal pancreatic tissue 6


title: E13.5 FlashTag collected at P7 IL01_Pool1


title: OC cells_OVCAR-3_sensitive


title: T24_CT14_rep4


title: GckPVT 4 output

source_name: glucokinase-expressing cells

value: output


title: OC cells_IGROV-1-R1_resistant


title: hMSNs-1mM-Ch1h-r3

city: Raleigh

first: Ryan

middle: W

last: Tam

state: North Carolina

address: 840 Main Campus Drive, Building Partners II, Room 3700

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
Qiagen CLC Workbench version 21.0.5 software "Trim Reads" tool was used for Reads Trimming of Illumina Universal adapters
Qiagen CLC Workbench version 21.0.5 software "RNA-seq Analysis" tool was used for Reads Mapping
Qiagen CLC Workbench version 21.0.5 software "Differential Expression for RNA-seq" tool was used for Differential Expression Analysis
Genome_build: hg38_v99
Supplementary_files_format_and_content: comma separated value files of gene symbols, chromosome location and region, expression value, transcripts per million (TPM), reads Per Kilobase of transcript per Million mapped reads (RPKM), exon read counts, ensemble gene ids, gene length, biotype, unique gene reads, total gene reads, number of transcripts annotated, number of uniquely identified transcripts, exon length, unique exon reads, total exon reads, ratio of unique to total exon reads, unique exon-exon reads, total exon-exon reads, unique intron reads, total intron reads, and ratio of intron to total gene reads.

growth_protocol: hMSNs were obtained following previously described protocols (Arber et al., 2015). Feeder-independent cell lines were H9 and H1 hESCs (WA09 and WA01; WiCell).  Cells were maintained in 6-well tissue culture dishes (Greiner Bio-One) coated with 0.5 µg/mL reduced growth factor Matrigel solution (Corning) in E8 medium (Stemcell Technologies) and passaged using standard protocols. Cells were grown to ~75-80% confluency prior to differentiation. On Day 0 of differentiation, E8 medium was removed, cells were washed with 1X PBS (Gibco) and media switched to DMEM-F12/Neurobasal media (2:1)(Gibco) supplemented with N2 (Gibco) and B27 minus Vitamin A (Gibco) (together referred to as N2B27). From Day 0 to 4, cultures were supplemented with SB431542 (10 µM in 95% EtOH; Selleck Chemicals), LDN-193189 (100 nM in DMSO; BioVision) and dorsomorphin (200 nM; BioVision). Media was changed every day. From Day 5 to 8, cultures were supplemented with just LDN-193189 and dorsomorphin. Media was changed every day. On Day 9, cultures were washed with 1X PBS, and media switched to N2B27 supplemented with activin A (25 ng/ml in 4 mM HCl; R&D). Cells were then lifted using cell scrapers (Greiner Bio-One), triturated 1X with a 5 mL serological pipette and replated onto Matrigel-coated 6-well plates at a 1:2 or 1:3 dilution. Half-media was changed the next day and then every other day afterwards. On Day 18, cultures were passaged using 0.5 mM EDTA for 2 minutes at 37 °C and 10-15X trituration using P1000 mechanical pipette then replated onto Poly-L-Ornithine (15 µg/mL in Water; Sigma) and Laminin (5 µg/mL in PBS; Corning) coated 24-well plates (Greiner Bio-One) at a 1:2 dilution. Half-media was changed the next day and then every other day afterwards. From Day 20 to 24, media was switched to N2B27 with Vitamin A (Gibco). On Day 25 to analysis, BDNF and GDNF (10 ng/ml in 0.1% BSA (w/v); Peprotech) were added to aid neuronal maturation and survival (referred to as Maturation Medium). Cells are repassaged again after 10-14 days to maintain neuron attachment. Cells were maintained in a humid incubator at 37 °C with 5 % CO2.

extract_protocol:
hMSNs were washed 1X in PBS. Total RNA was isolated using Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol. RNA samples were collected in 2mL RNAse-free tubes and chilled on ice throughout the procedure. cDNA synthesis was performed using 1000 ng of total RNA and the iScript Reverse Transcription Kit (BIO-RAD) according to the manufacturer’s protocol. qPCR reactions were performed using SsoAdvanced™ Universal SYBR® Green Supermix (BIO-RAD) on a BIORAD 384-well machine (CXF384) with custom designed using Primer3
RNA libraries were prepared for sequencing using standard Illumina protocols through Azenta and UNC HTSF

treatment_protocol: Three replicates were 1 uM and 1 mM Dopamine treated Acutely for 1 hour and extracted at 1 hour or 24 hours later and Chronically for 1 hour over 5 days and extracted at 1 hour and 24 hours later.

value: Chronic 1h 1mM

value: H9 hPSC-derived medium spiny neurons (MSNs)

tag: source cell line


title: normal pancreatic tissue 3

description: lncRNA and mRNA expression in normal pancreatic tissue 3


title: T24_CT14_rep3


title: hMSNs-1mM-Ch24h-r1

value: Chronic 24h 1mM


title: T24_CT14_rep1


title: normal pancreatic tissue 5

description: lncRNA and mRNA expression in normal pancreatic tissue 5


title: OC cells_OVCAR-4_sensitive


title: GckPVT 2 input


title: OC cells_IGROV-1_sensitive


title: hMSNs-1mM-Ch24h-r3


title: ILC2 Knockout

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

data_processing:
The reads were aligned to the mouse transcriptome (GRCm38) and expression calculated using the 10X Cellranger (v3.0.2) wrapper for the STAR aligner (Spliced Transcripts Alignment to a Reference, Alexander Dobin)
Separate libraries were generated using FACS-sorted tumor cells (each consist of 2500 tumor CD45-EpCAM+ epithelial cells, 500 tumor CD45+CD11b+Ly6C+Ly6G-M-MDSCs, and 5000 CD45+ total immune cells) from ILC2-deficient (Roraf/fIl7rCre/+) and Cre control (Rora+/+Il7rCre/+) Apc1322T/+ mice, and then combined using Cell Ranger
Assembly: GRCm38
Supplementary files format and content: Cloupe file

source_name: Tumor cells

extract_protocol:
FACS purified cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40) to obtain nuclei extract
10X Single cell library preparation was performed using the 10X Genomics technology platform. The 10X Genomics Chromium Single Cell 3’ v3 protocol was followed to obtain 3’ libraries for subsequent sequencing

value: Tumor cells


title: hMSNs-1mM-Ch24h-r2


title: normal pancreatic tissue 2

description: lncRNA and mRNA expression in normal pancreatic tissue 2


title: Cre control


title: GckPVT 1 input


title: OC cells_OVCAR-3-R2_resistant


title: abl_Atuveciclib_rep2

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

data_processing:
Read alignment was conducted using HISAT2 v2.2.1, and relative transcript abundances and differentially expressed genes were determined using the Partek Genomics Suite (v6.6) with default settings. The reads count in exon regions was used to estimate the gene expression level.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM

source_name: prostate

growth_protocol: LNCaP-abl cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
Total RNA was isolated using an RNeasy Mini kit (QIAGEN).
mRNA was enriched using the NEBNext Poly (A) mRNA Magnetic Isolation Module. After two rounds of this process, the mRNA was recovered for library generation, which was performed with the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina following the manufacturer’s instructions. The cDNA molecules were amplified by 8 cycles of PCR. Non-size-selected libraries were then sequenced using an Illumina Novaseq 6000 instrument.

treatment_protocol: Cells were treated with 1 uM Atuveciclib for 24hr.

value: prostate cancer cells

value: Atuveciclib

value: LNCaP-abl


title: GckPVT 3 output


title: GckPVT 2 output


title: T24_CT14_rep2

value: Brain


title: hMSNs-1mM-Ac24h-r3

value: Acute 24h 1mM


title: hMSNs-1mM-Ac24h-r2


title: Large_intestine_high_R2

city: Amsterdam

first: Jacco

last: van Rheenen

state: Noord holland

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Demultiplexing of sequencing reads was performed with Illumina bcl2fastq.
Adapters were trimmed with Skewer.
Trimmed raw reads were aligned to genome mm10 using START.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file for raw gene counts for each sample across all genes.
Supplementary_files_format_and_content: tab-delimited text file for normalized counts (median-of-ratios method - DESeq2) for each sample across all genes.

source_name: Intestine

extract_protocol:
Small and large intestinal crypts were treated with TrypLE supplemented with DNaseI and Y-27632. Dissociated cells were filtrated, resuspended and incubated with antibodies in PBS. Dead cells were eliminated and Lgr5+ cells were sorted by positive staining for Epcam and endogenous Lgr5-GFP signal. RNA was isolated using RNeasy Micro Kit (Qiagen) with 270 pg or more of RNA.
RNA libraries were prepared for sequencing using SMART-Seq Stranded Kit (Takara) and sequenced as paired end (2x100bp) using NovaSeq 6000.

value: Large intestine

value: Post natal 8-20 weeks

value: Untreated


title: Large_intestine_high_R3


title: hMSNs-1mM-Ch1h-r2


title: GckPVT 1 output


title: Large_intestine_mid_R3


title: pancreatic cancer tissue 1

description: lncRNA and mRNA expression in pancreatic cancer tissue 1

value: female

value: pancreatic cancer


title: abl_vehicle_rep1

value: vehicle


title: 36574 c-Maf KO - mouse ILC2

first: Tania

last: Wyss

address: Rue du Bugnon 25A

institute: SIB Swiss Institute of Bioinformatics

description:
36574KO
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv

data_processing:
Base calling, fastq file generation and demultiplexing were performed using Illumina RTA v.1.18.66.3 and Illumina pipeline v.2.19.1.
To remove adapter sequences and trim low-quality bases, raw sequencing reads were scanned using AdapterRemoval v.2.1.7 with parameters --trimns and –trimqualities. Reads were aligned against the mouse GRCm38.95 reference genome using STAR v.2.6.0c. Using samtools v.1.8, we converted sequence alignment map files to bam files and merged the aligned reads spread across 3 lanes of each sample into a single bam file per sample. Numbers of reads per gene were summarized using the htseq-count function of the HTSeq package v.0.9.1.
Genome_build: Mus musculus GRCm38.95
Supplementary_files_format_and_content: Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv: Comma-separated values file containing raw counts per gene (in rows) per sample (in columns), as output by htseq-count. The first column contains the mouse Ensembl ID of each gene, the second column contains the symbol of each gene, and columns 3 to 12 contain counts per gene per sample. Genotype information (WT or KO) is contained in column names.

source_name: ILC2 isolated from lungs

growth_protocol: WT or c-Maf KO mice were cohoused and littermate were used in all experiments.

extract_protocol:
Whole RNA was extracted using the RNeasy Plus Micro Kit according to manufacturer’s instructions.
Illumina TruSeq Stranded total RNA library prep kit.

treatment_protocol: mILC2s (lin-CD90.2+ST2+/-KLRG1+/-) were isolated from the lungs and sorted on a FACSAria (Becton Dickinson) at the Flow Cytometry Facility of the University of Lausanne. ILC2s were collected in RNA later buffer.

value: c-Maf KO


title: abl_Atuveciclib_rep1


title: abl_vehicle_rep3


title: abl_Atuveciclib_rep3


title: hMSNs-1mM-Ac1h-r1

value: Acute 1h 1mM


title: Large_intestine_mid_R2


title: hMSNs-1mM-Ac24h-r1


title: 36576 c-Maf KO - mouse ILC2

description:
36576KO
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: 36573 c-Maf KO - mouse ILC2

description:
36573KO
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: Large_intestine_high_R1


title: hMSNs-1mM-Ch1h-r1

value: Chronic 1h 1mM


title: hMSNs-water-agonist-r1

source_name: hMSNs-water-agonist

value: Water Ctrl

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: hMSNs-1mM-Ac1h-r3


title: Large_intestine_low_R2


title: Large_intestine_mid_R1


title: 36487 c-Maf KO - mouse ILC2

description:
36487KO
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: hMSNs-1mM-Ac1h-r2


title: hMSNs-quin-cgs-r3

source_name: hMSNs-quin-cgs

value: Quinpirole CGS21680


title: Large_intestine_low_R3


title: hMSNs-quin-cgs-r2


title: 36137 WT - mouse ILC2

description:
36137WT
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv

value: WT


title: hMSNs-1mM-PBS-r3

value: PBS 1mM


title: hMSNs-water-agonist-r3


title: abl_vehicle_rep2

value: prostate cancer cells

value: LNCaP-abl


title: Small_intestine_high_R3

value: Small intestine


title: hMSNs-1mM-PBS-r1


title: hMSNs-quin-cgs-r1


title: 36486 c-Maf KO - mouse ILC2

description:
36486KO
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: 35995 WT - mouse ILC2

description:
35995WT
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: Large_intestine_low_R1

value: Large intestine


title: ovary tissue_PCOS-MV_2

city: HengYang

first: Lan'e

last: Huang

state: Hunan

address: 28 Changsheng Xi Lu, Hengyang City, Hunan Province, China

department: Department of Histology and Embryology

institute: University of South China

data_processing:
Raw data (raw reads) of fastq format were firstly processed by removing reads containing adapter, reads containing ploy-N and low quality reads.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5.1b). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: Rattus norvegicus
Supplementary_files_format_and_content: Matrix table with gene FPKM for every gene and every sample

organism: Rattus norvegicus

source_name: ovary

extract_protocol:
Ovaries were removed, flash frozen on liquid nitrogen then stored at -80°, and RNA was harvested using Trizol reagent.  NEBNext® UltraTM   RNA Library Prep Kit (NEB, USA)  was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: ovary

value: post natal week 15

value: wild type

value: treated with letrozole for 30 days，then treated with mogroside V for 30 days


title: hMSNs-water-agonist-r2


title: Small_intestine_high_R1

value: Post natal 8-20 weeks

value: Untreated


title: 35987 WT - mouse ILC2

description:
35987WT
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: Small_intestine_high_R2


title: ovary tissue_PCOS-MV_1


title: hMSNs-1mM-PBS-r2


title: ovary tissue_PCOS-MV_4


title: 35547 WT - mouse ILC2

description:
35547WT
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: 35549 WT - mouse ILC2

description:
35549WT
Trabanelli_MafKO_ILC2_Mmu_htseq_counts.csv


title: Dnmt2_4HF

city: Nice

first: Minoo

last: Rassoulzadegan

address: parc Valrose

department: Institut de Biologie Valrose: iBV

country: France

institute: Nice Sophia Antipolis

data_processing:
FastQC was used to do some quality control checks on the raw sequence data. RNA-seq reads adapters removed by cutadapt. Based on the FastQC results, trimming of bad-quality reads was performed using Trimmomatic version 0.36 (10 nucleotides were cropped from the 5' end of each read, and trimmed bases with Phred score lower than 20 from heading and trailing of each read and the trimmed reads with a size less than 30 bp were removed). Then transcript quantification performed using Salmon and imported into tximport for downstream analysis. High enriched transcripts visualized to show difference of expression in HFD/ND and Dnmt2-/- samples.
HOMER version 4.9 was used for peak finding and generating bedGraph files to visualization of alignment. The bedGraphs were cross-sample normalized in order to make visualization of different samples comparable. The alignment files are visualized using IGV
Statistically significant peaks of expression identified using HOMER (10000 size of region used for local filtering, 4-fold over local region, Poisson p-value over local region < 0.0001, false discovery rate (FDR) rate threshold < 0.001). Peak annotation was performed using Homer annotate_peaks. Annotated positions for different regions promoter-TSS, exons, introns and others was on the basis of mm10 transcripts. Enrichment analysis of region associated genes was also performed using Enrichr significantly over-represented by associated gene sets. Percent of significant peaks that were located in each genomic region was also measured.
Genome_build: mm10
Supplementary_files_format_and_content: files include bedgraph files for each Sample and peak annotation files from HOMER ...

source_name: Sperm

extract_protocol:
RNA from purified sperm (centrifugation) was extracted using TRIzol reagent. The quality of the RNA preparations was verified by spectrometry on an Agilent Bioanalyzer 2100 apparatus. Microinjection into fertilized eggs was performed according to established transgenesis methods. RNA solutions were adjusted to a concentration of 1 µg/ml, and 1-2 pl were microinjected into the male pronuclei of fertilized eggs isolated after normal ovulation and mating to a Balb/c strain. Synthetic miRNA was prepared in a filtered microinjection buffer (10 mM Tris, pH 7.4; 0.1 mM EDTA) at a concentration of 3,000,000-5,000,000 molecules/pl.
After digestion of DNase, 10-100 ng of RNA were prepared and sent to Eurofins for high-throughput sequencing on Illumina Hiseq 2500 or Illumina MiSeq.
Libraries of all samples corresponding to DNA-associated RNA and free-RNA molecules were generated

treatment_protocol: Four lines of mice were maintained: C57BL/6, B6/D2, Balb/c and Dnmt2-/- (Charles River, Wilmington, Ma, USA). After weaning, 4-week-old males were divided into two groups. One group was maintained on a normal diet (ND), and the other was fed a western diet containing 17% casein, 0.3% DL-methionine, 34% sucrose, 14.5% cornstarch, 0.2% cholesterol, 5% cellulose, 7% CM 205B, 1% vit200 and 21% or 35% butter (Diet Western 1635, Safe, Augy; France).

value: 6-8 month-old

value: Sperm

value: free-RNA


title: hMSNs-cgs21680-10uM-r3

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: ovary tissue_PCOS_4

value: treated with letrozole for 30 days


title: Small_intestine_mid_R2


title: Dnmt2_3HF


title: Small_intestine_mid_R1


title: Small_intestine_mid_R3


title: Dnmt2_3HD

value: DNA-associated RNA


title: hMSNs-quinpirole-50uM-r2

value: Quinpirole 50uM


title: ovary tissue_PCOS_3


title: ovary tissue_PCOS-MV_3


title: ovary tissue_PCOS_2


title: Dnmt2_2NF

value: 6 -8 month-old


title: hMSNs-quinpirole-50uM-r1


title: Small_intestine_low_R2

value: Small intestine


title: ovary tissue_Control_4

value: untreated


title: Small_intestine_low_R3


title: hMSNs-cgs21680-10uM-r2


title: hMSNs-skf82958-50uM-r2


title: ovary tissue_PCOS_1

value: Sprague Dawley


title: Dnmt2_2ND


title: ovary tissue_Control_3

value: ovary


title: Dnmt2_1ND


title: Small_intestine_low_R1


title: D3 VPA_4 [mPCLS072D3VPA_D3_VPAWME_S39]

city: Brussels

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
Trimming FastQ files (polyA, rRNA, adaptors)
Mapping using STAR
Assembly using StringTie
Genome_build: mm10
Supplementary_files_format_and_content: raw gene counts for every gene and every sample

source_name: Precision-cut liver slice

growth_protocol: 250µm thick and 3 mm diameter mouse precision-cut liver slices (PCLS) from healthy male Balb/c mice were made using a Leica VT1200S vibrating blade microtome. Using a P1000 pipet with cut tip, PCLS were transferred into a 24-well plate, pre-filled with cold supplemented WME medium. After slicing and punching was finished, PCLS were refreshed with pre-heated WME medium (Gibco, supplemented with 1% Ultraglutamine I and 1% Penicillin-Streptomycin and cultured on an orbital shaker at a speed of 80 rpm. PCLS were cultured at 37°C , and refreshed 4 hours after production and every 24 hours. Culture medium contained no VPA (CTR, 'REG') or 2.5 mM VPA ('VPA'). PCLS were collected on day 3.

extract_protocol:
PCLS were collected for RNA analysis. Total RNA was extracted with TRIzol Reagent (Thermofisher) according to the manufacturer's manual
RNA libraries were prepared for sequencing using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen, Greenland, USA) for Illumina according to supplier protocol.

value: Balb/c

tag: model

value: Precision-cut liver slice

value: 2.5 mM VPA

tag: culture time

value: 3 days


title: hMSNs-skf82958-50uM-r3


title: Dnmt2_4HD

tag: tissue

tag: molecule subtype


title: Dnmt2_1NF


title: hMSNs-cgs21680-10uM-r1


title: hMSNs-quinpirole-50uM-r3


title: D3 VPA_3 [mPCLS071D3VPA_D3_VPAWME_S34]


title: hMSNs-skf82958-50uM-r1


title: hMSNs-1mM-ChAACtrl-r3

value: Chronic AA Ctrl 1mM


title: F1N_RNA_6

value: 6-8 month-old


title: ovary tissue_Control_1

value: post natal week 15

value: wild type


title: ovary tissue_Control_2


title: hMSNs-1mM-ChAACtrl-r2

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: F1F_RNA_8

value: Sperm

value: free-RNA


title: D3 VPA_1 [mPCLS073D3VPA_D3_VPAWME_S43]


title: 33_2

city: Shihezi

first: li

middle: guo

last: zhi

state: xinjiang

address: Xiangyang Street

department: College of Life Sciences

institute: Shihezi University

description: G. uralensis underground parts CK

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp (https://github.com/OpenGene/fastp) with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml) software. The mapped reads of
each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2/DEGseq/EdgeRwith Q value ≤ 0.05, DEGs with |log2FC|>1 and Q value <= 0.05(DESeq2 or EdgeR) /Q value <= 0.001(DEGseq) were considered to be significantly different expressed genes). In addition, functional-enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferroni-corrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do).
All the alternative splice events that occurred in our sample were identified by using recently releases program rMATS(http：//rnaseq-mats.sourceforge.net/index.html). Only the isoforms that were similar to the reference or comprised novel splice junctions were considered, and the splicing differences were detected as exon inclusion, exclusion, alternative 5', 3', and intron retention events.
Genome_build: http://ngs-data-archive.psc.riken.jp/Gur-genome/index.pl
Supplementary_files_format_and_content: The results of expression quantification are expressed in TPM, and the homogenisation process of TPM results in consistent total expression across samples.

organism: Glycyrrhiza uralensis

source_name: underground parts

extract_protocol:
Total RNA was extracted from the tissue using Plant RNA Purification Reagent for plant tissue according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥8.0, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The G. uralensis seedlings were grown hydroponically for 1 week and then subjected to a simulated drought treatment (MS nutrient solution containing polyethylene glycol 6000 at 100 g·L-1) for 0, 2, 6, 12, and 24 hours. The 0 h sample served as the control group.

value: root

value: seedlings of 60days

value: distilled water


title: F0N_RNA_3


title: hMSNs-1mM-ChAACtrl-r1


title: D3 CTR_3 [mPCLS071D3REG_D3_REGWME_S31]


title: F0F_RNA_5


title: 31_2

description: G. uralensis underground parts CK


title: 32_2

description: G. uralensis underground parts CK


title: D3 CTR_2 [mPCLS074D3REG_D3_REGWME_S46]


title: F1N_D_RNA_6

value: DNA-associated RNA


title: hMSNs-1mM-Ch5D-r3

value: Chronic 5D 1h 1mM


title: D3 CTR_1 [mPCLS072D3REG_D3_REGWME_S36]


title: 12_2

description: G. uralensis underground parts drought stress 24h

value: polyethylene glycol 6000 at 100 g.L-1 for 24h


title: D3 VPA_2 [mPCLS074D3VPA_D3_VPAWME_S48]

value: Balb/c


title: hMSNs-1mM-Ch5D-r2


title: 11_2


title: hMSNs-1mM-Ch4D-r3

value: Chronic 4D 1h 1mM


title: 10_2


title: F0N_D_RNA_3

value: 6 -8 month-old


title: totalRNA_Con_rep2

description:
Con rep2 for total RNA
RiboSeq_eif4a2_totalrna.txt

data_processing:
Library strategy: Ribo-seq
Ribo-seq data reads were firstly adapter trimmed using FASTX-Tookit (v0.0.14; http://hannonlab.cshl.edu/fastx_toolkit) with the parameter -a AGATCGGAAGAGCACACGTCT.
Ribosomal RNA and transfer RNA reads were removed using Bowtie (v1.2.3).
The remained reads are aligned to the mouse mm9 genome using TopHat (v2.1.1). The matched total RNA-seq data were also processed with the same processing procedure.
These aligned bam files were sorted by name with the parameter –n, and counted by HTSeq (v0.11.2).
All read counts are normalized using the TMM method using edgeR (v3.26.8).
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

source_name: Embryonic stem cells

extract_protocol:
Ribosome profiling was performed according to the manufacturer's instructions. Total RNA and RPF libraries were prepared using the TruSeq Ribo Profile (Mammalian) Kit (Illumina, RPHMR12126) according to the manufacturer’s reference guide (document #15066016 v01) with Ribo-Zero Gold Kit (H/M/R) (Illumina, MRZG126).
Two biological replicates were performed for total RNA and RPF RNA of control shRNA- and eIF4A2 shRNA-infected ESCs. Massively parallel sequencing was performed with the Illumina HiSeq2500 according to the manufactory protocol, and single-end 50 bp-length reads were produced. For RPF samples, each sample was sequenced four times  to increase the sequencing depth.

treatment_protocol: Ribosome profiling was performed using ESCs infected with control shRNAs (shNT, shGFP) or eIF4A2 shRNAs. ESCs were infected with control shRNAs (shNT, shGFP) or eIF4A2 shRNAs (sheIF4A2-2, sheIF4A2-3) (day 0). After 3 days of 1 μg/mL puromycin selection, on day 4.5, the ESCs were cultured in fresh serum/LIF ESC medium supplemented with 0.1 mg/mL cycloheximide for 1 min, followed with ice-cold PBS supplemented with 0.1 mg/mL cycloheximide wash before the cell lysis.

tag: cell line

value: mESC J1

tag: transfection

value: control shRNA


title: F0F_D_RNA_5

value: 6-8 month-old


title: 9_2

description: G. uralensis underground parts drought stress 12h

value: polyethylene glycol 6000 at 100 g.L-1 for 12h


title: miR-125b-Gata1s-FLC+Arid3a-FLAG [ATAC-seq]

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

library_source: genomic

data_processing:
Raw reads were trimmed and filtered using Skewer v0.2.2.
Clean reads were aligned to mm10 using BWA v0.7.12-r1039 with the parameters -T 25 -k 18.
Mitochondrial reads were removed prior to subsequent analysis.
Normalized bigWig files were generated using bamCoverage from deepTools v3.0.2.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized (RPM) bigWig tracks

molecule: genomic DNA

source_name: fetal liver cells

extract_protocol:
We performed ATAC-seq as previously described (Buenrostro et al., Curr Protoc Mol Biol 2015, Buenrostro et al., Nat Methods 2013). 48 hours post-induction, 50K cells were sorted and processed via the Illumina Tagment DNA Enzyme and Buffer Kit (20034197).
Illumina libraries were constructed from the transposed DNA as previously described (Buenrostro et al., Curr Protoc Mol Biol 2015, Buenrostro et al., Nat Methods 2013), and sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).

value: Doxycycline 1μg/mL for 48h

tag: developmental stage

value: Arid3a-FLAG (doxycycline inducible)


title: hMSNs-1mM-Ch4D-r2

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: Smad3_miR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN

data_processing:
library strategy: CUT&RUN
Raw reads were processed using Trimmomatic v0.39 to remove adapter sequences. Parameters: -phred33 ILLUMINACLIP:Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25.
Kseq (Zhu et al., Genome Biol 2019) was to trim reads containing ≤6 bp of adapter sequence, which are not effectively handled by Trimmomatic.
Trimmed reads were aligned to murine reference genome mm10 using bowtie v2.3.5.1
Aligned reads were sorted and indexed using Samtools v1.3.1.
Normalized bigWig files were generated using bamCoverage from deepTools v3.5.1.
Genome_build: mm10
Supplementary_files_format_and_content: Raw pileups as bigWig tracks for each sample

extract_protocol:
We performed CUT&RUN as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018). On day 2 post-induction, 0.2 million cells were sorted and incubated  with the following antibodies: rabbit anti-DRIL-1 (abcam), rabbit anti-GATA1 (Abcam), rabbit anti-SMAD2 and anti-SMAD3 (Cell Signalling) and rabbit anti-IgG (Diagenode).  pAG/MNase nuclease (Addgene 123461) was produced and purified as previously described, after removal of the HA tag.
Illumina libraries were constructed from the cleaved DNA as previously described (Meers et al., eLife 2019; Skene et al., Nat Protoc 2018), and sequenced by Novogene Company, Ltd. on an Illumina NovaSeq platform (150 bp paired-end reads).


title: IgG_miR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN


title: hMSNs-1mM-Ch4D-r1


title: totalRNA_Con_rep1

description:
Con rep1 for total RNA
RiboSeq_eif4a2_totalrna.txt


title: Smad2_miR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN


title: 8_2

description: G. uralensis underground parts drought stress_12h


title: hMSNs-1mM-Ch3D-r3

value: Chronic 3D 1h 1mM


title: Gata1_miR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN


title: hMSNs-1mM-Ch5D-r1


title: eif4a2_totalRNA_KD_rep2

description:
eif4a2 KD rep2 for total RNA
RiboSeq_eif4a2_totalrna.txt

value: eIF4A2 shRNA


title: hMSNs-1mM-Ch3D-r2


title: F1F_D_RNA_8

value: Sperm


title: eif4a2_totalRNA_KD_rep1

description:
eif4a2 KD rep1 for total RNA
RiboSeq_eif4a2_totalrna.txt


title: 5_2

description: G. uralensis underground parts drought stress 6h

value: root

value: seedlings of 60days

value: polyethylene glycol 6000 at 100 g.L-1 for 6h


title: FLAG_CUT&RUNmiR-125b-Gata1s-FLC+Arid3a-FLAG_CUT&RUN


title: hMSNs-1mM-Ch2D-r3

value: Chronic 2D 1h 1mM


title: RPF_Con_rep2

description:
Con rep2 for ribosome protected fragments
RiboSeq_eif4a2_rpfgene.txt


title: miR-125b-Gata1s-FLC+LUC_R1 [RNA-seq]

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
hisat 2 (v2.0.5.) was used to mapp to the reference genome (--dta --phred33)
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

extract_protocol:
Quick-RNA Miniprep (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LUC (doxycyline inducible)


title: 4_2


title: 3_2

description: G. uralensis underground parts drought stress 2h

value: polyethylene glycol 6000 at 100 g.L-1 for 2h


title: hMSNs-1mM-Ch3D-r1


title: eif4a2_RPF_KD_rep1

description:
eif4a2 KD rep1 for ribosome protected fragments
RiboSeq_eif4a2_rpfgene.txt


title: miR-125b-Gata1s-FLC+LUC_R2 [RNA-seq]


title: miR-125b-Gata1s-FLC+Arid3a-FLAG_R3 [RNA-seq]

value: Arid3a-FLAG (doxycyline inducible)


title: miR-125b-Gata1s-FLC+LUC_R3 [RNA-seq]


title: 6_2


title: eif4a2_RPF_KD_rep2

description:
eif4a2 KD rep2 for ribosome protected fragments
RiboSeq_eif4a2_rpfgene.txt

value: mESC J1


title: hMSNs-1mM-Ch2D-r2


title: 2_2


title: 7_2


title: hMSNs-1uM-Ch24h-r3

value: Chronic 24h 1uM


title: hMSNs-1mM-Ch2D-r1


title: 1_2


title: miR-125b-Gata1s-FLC+Arid3a-FLAG_R2 [RNA-seq]


title: rnaseq_Con_rep2

description:
eif4a2 Con rep2
RNAseq_4a2.txt

data_processing:
RNAseq reads were aligned to the mouse mm9 genome using Bowtie2 (v2.3.4.3)
Aligned bam files were sorted by samtools (v1.9) using the parameter -n
HTSeq software (v0.11.2) was used to count reads for each gene using parameters -r name -f bam
Read counts were normalized with the trimmed mean of M-values (TMM) method for differential expression analysis using edgeR (v3.26.8)
Genome_build: mm9
Supplementary_files_format_and_content: txt files - tab-delimited files containing TMM values for genes in each sample.

extract_protocol:
RNA was extracted with the Rneasy Plus kit (Qiagen, #74136) according to the manufacturer's instructions.
For ESCs, 1 µg total RNA from each sample was taken for the preparation of PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq platform. Single-end 100 bp-length reads were produced.

treatment_protocol: Feeder-free murine ESCs were infected with control shRNAs (shLuc, shEV) or eIF4A2 shRNAs (sheIF4A2-2, sheIF4A2-3) (day 0). After 3 days of 1 μg/mL puromycin selection, the cells were collected on day 4.5.

value: mESC CCE

value: control shRNA


title: RPF_Con_rep1

description:
Con rep1 for ribosome protected fragments
RiboSeq_eif4a2_rpfgene.txt


title: 33_1

description: G. uralensis aboveground parts CK

source_name: aboveground parts

value: stems and leaves

value: distilled water


title: miR-125b-Gata1s-FLC+Arid3a-FLAG_R1 [RNA-seq]

value: Doxycycline 1μg/mL for 48h


title: hMSNs-1uM-Ch24h-r2

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: rnaseq_Con_rep1

description:
eif4a2 Con rep1
RNAseq_4a2.txt


title: hMSNs-1uM-Ch24h-r1


title: R4B: TRT 6D CAF

city: Philadelphia

first: Andres

last: Blanco

address: 380 S. University Avenue, Hill Pavillion Room 414

department: Biomedical Sciences

institute: University of Pennsylvania

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Indices of the reference genome were built using STAR.
Paired-end clean reads were aligned to the reference genome using STAR (v2.5), using the Maximal Mappable Prefix (MMP) method.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene, and FPKM of each gene was calculated based on the length of the gene and reads count mapped to the gene.
Differential expression analysis between conditions (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3).
Initial DESeq2 p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR).
Genome_build: mm10
Supplementary_files_format_and_content: Normalized FPKM values of all mouse genes as identified by Ensembl stable gene ID.

source_name: MMTV-PyMT; Dll1 mcherry+

extract_protocol:
Tumors were removed and digested with collagenase and hyaluronidase. Tumors were treated with PDGFRa antibody to detect cancer fibroblats. RNA was harvested using Purelink RNA Mini Kit cat#12183018A and 1 ug of total RNA was used for the construction of sequencing libraries.
DNase treatment was applied to RNA samples using DNase I, RNase-free (ThermoFisher, Massachusetts, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HS D1000 ScreenTape (Agilent Technologies Inc., California, USA).

value: with targetd radiation at day 6

value: primary mouse breast cancer-associated fibroblasts


title: 32_1

description: G. uralensis aboveground parts CK


title: 31_1

description: G. uralensis aboveground parts CK


title: hMSNs-1uM-Ch1h-r2

value: Chronic 1h 1uM


title: eif4a2_rnaseq_KD_rep2

description:
eif4a2 KD rep2
RNAseq_4a2.txt

value: eIF4A2 shRNA


title: hMSNs-1uM-Ch1h-r3


title: eif4a2_rnaseq_KD_rep1

description:
eif4a2 KD rep1
RNAseq_4a2.txt


title: R4A: TRT 6D CAF


title: 12_1

description: G. uralensis aboveground parts drought stress 24h

value: seedlings of 60days

value: polyethylene glycol 6000 at 100 g.L-1 for 24h


title: R3B: TRT 6D CTRL CAF

value: no radiation


title: 11_1


title: hMSNs-1uM-Ac24h-r3

value: Acute 24h 1uM


title: 10_1


title: R14B: TRT-30d Tumor Mch+ 2

extract_protocol:
Tumors were removed and digested with collagenase and hyaluronidase. Tumor cells were sorted with CD45, CD31 and TER119 antibodies to isolate tumor cell enriched population. Based on mcherry (Dll1 expression), mcherry (Dll1)+ cells were further sorted from epithelial enriched population. RNA was harvested using Purelink RNA Mini Kit cat#12183018A and 1 ug of total RNA was used for the construction of sequencing libraries.
DNase treatment was applied to RNA samples using DNase I, RNase-free (ThermoFisher, Massachusetts, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 40 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HS D1000 ScreenTape (Agilent Technologies Inc., California, USA).

value: with targetd radiation

value: primary mouse breast cancer


title: R3A: TRT 6D CTRL CAF


title: R14A: TRT-30d Tumor Mch+ 1


title: hMSNs-1uM-Ac24h-r2


title: 9_1

description: G. uralensis aboveground parts drought stress 12h

value: polyethylene glycol 6000 at 100 g.L-1 for 12h


title: hMSNs-1uM-Ac24h-r1


title: 8_1


title: hMSNs-1uM-Ac1h-r3

value: Acute 1h 1uM


title: 7_1


title: hMSNs-1uM-Ch1h-r1


title: R11A: Control Tumor Mch+ 1


title: Gata1s-FLC+miR-ctrl_Day13WD_R3

value: Day 13, Dox withdrawal on day 10

value: miR-ctrl


title: 6_1

description: G. uralensis aboveground parts drought stress 6h

value: stems and leaves

value: polyethylene glycol 6000 at 100 g.L-1 for 6h


title: hMSNs-1uM-Ac1h-r2

value: H9 hPSC-derived medium spiny neurons (MSNs)


title: C57BL/6J male metformin (1000 mg/kg) 1

city: Gifu

first: Hiroshi

last: Takemori

state: Gifu

address: Yanagido 1-1

department: Chemistry and Biomolecular Science

country: Japan

institute: Gifu University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with FGeneSpring software (TOMY digital biotechnology, Tokyo, Japan).

source_name: C57BL/6J male ileum metformin 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: ileal RNA is purified by Fast Gene RNA Premium kit

treatment_protocol: Mice were orally treated with metformin (1000 mg/kg)

value: male


title: C57BL/6J male control 2

source_name: C57BL/6J male ileum RNA Control 2


title: hMSNs-1uM-Ac1h-r1

extract_protocol:
hMSNs were washed 1X in PBS. Total RNA was isolated using Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s protocol. RNA samples were collected in 2mL RNAse-free tubes and chilled on ice throughout the procedure. cDNA synthesis was performed using 1000 ng of total RNA and the iScript Reverse Transcription Kit (BIO-RAD) according to the manufacturer’s protocol. qPCR reactions were performed using SsoAdvanced™ Universal SYBR® Green Supermix (BIO-RAD) on a BIORAD 384-well machine (CXF384) with custom designed using Primer3
RNA libraries were prepared for sequencing using standard Illumina protocols through Azenta and UNC HTSF


title: C57BL/6J male control 1

source_name: C57BL/6J male ileum RNA Control 1


title: C57BL/6J male metformin (1000 mg/kg) 2

source_name: C57BL/6J male ileum metformin 2


title: Gata1s-FLC+miR-ctrl_Day13WD_R2


title: 4_1


title: 5_1


title: hMSNs-1uM-PBS-r3

value: PBS 1uM


title: R11B: Control tumor  Mch+ 2


title: hMSNs-1uM-PBS-r2


title: Gata1s-FLC+miR-ctrl_Day13_R3

value: Doxycycline 1ug/mL for 13 days


title: NTX301, day4, rep3

city: Daejeon

first: Byungho

last: Lim

address: 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea

institute: KRICT

description: Gene expression data from drug treated AML cells

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

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

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: NTX-301 treatment

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

growth_protocol: MV4-11 leukimia cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) in a CO2 incubator.

extract_protocol: Total RNA was extracted by using RNeasy mini kit (Qiagen).

treatment_protocol: During 48 and 96h, DMSO, NTX-301 (60nM), and DAC (60nM) were treated to 5x105 MV4-11 cells plated on 6-well plates in triplicates.

tag: disease

value: AML

tag: time point


title: hMSNs-1uM-PBS-r1

data_processing:
Qiagen CLC Workbench version 21.0.5 software "Trim Reads" tool was used for Reads Trimming of Illumina Universal adapters
Qiagen CLC Workbench version 21.0.5 software "RNA-seq Analysis" tool was used for Reads Mapping
Qiagen CLC Workbench version 21.0.5 software "Differential Expression for RNA-seq" tool was used for Differential Expression Analysis
Genome_build: hg38_v99
Supplementary_files_format_and_content: comma separated value files of gene symbols, chromosome location and region, expression value, transcripts per million (TPM), reads Per Kilobase of transcript per Million mapped reads (RPKM), exon read counts, ensemble gene ids, gene length, biotype, unique gene reads, total gene reads, number of transcripts annotated, number of uniquely identified transcripts, exon length, unique exon reads, total exon reads, ratio of unique to total exon reads, unique exon-exon reads, total exon-exon reads, unique intron reads, total intron reads, and ratio of intron to total gene reads.


title: NTX301, day4, rep1


title: NTX301, day4, rep2


title: DAC, day4, rep3

source_name: DAC treatment


title: 2_1

description: G. uralensis aboveground parts drought stress 2h

value: seedlings of 60days

value: polyethylene glycol 6000 at 100 g.L-1 for 2h


title: 1_1


title: Gata1s-FLC+miR-ctrl_Day13_R1

tag: strain


title: DAC, day4, rep2


title: Gata1s-FLC+miR-125b_Day13WD_R2


title: DAC, day4, rep1


title: 3_1


title: AT3_GAMB_Sp_V

city: Boston

first: Flaminia

last: Catteruccia

state: MA

address: 655 huntington ave

institute: Harvard University

data_processing:
Alignment: hisat2/2.0.5. Parameters: -q -x --threads 4
Mapping quality filter: samtools/1.3.1. Parameters: view -bS -q 30
Sort mapped reads: samtools/1.3.1. Parameter: sort
Read count: htseq/0.9.1. Parameters: --stranded=no  --mode=union --quiet  -a 30
Assembly: Anopheles gambiae PEST AgamP4.12; Anopheles albimanus STECLA AalbS2.4
Supplementary files format and content: Processed data files format: Plain text file.  Content: Read counts

organism: Anopheles gambiae

source_name: Anopheles gambiae Virgin spermatheca rep A 24 hr

extract_protocol:
Total RNA was extracted with TRI reagent (Thermo Fisher Scientific, MA) from pools of 10–12  tissues following the manufacturer’s instructions. RNA was treated with TURBO DNase (Thermo Fisher Scientific, MA), and purified with Qiagen RNeasy MinElute Cleanup Kit.
Illumina TruSeq Stranded mRNA kit

value: spermatheca

tag: Sex

value: Female

tag: mating status

value: Virgin

tag: replicate

value: A

value: 24 hr post-mating or time-matching virgins


title: DT3_GAMB_Sp_V

source_name: Anopheles gambiae Virgin spermatheca rep D 24 hr

value: D


title: BT3_GAMB_Sp_V

source_name: Anopheles gambiae Virgin spermatheca rep B 24 hr

value: B


title: CT3_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep C 24 hr

value: Mated

value: C


title: DMSO, day4, rep3

source_name: DMSO treatment


title: DT3_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep D 24 hr


title: Gata1s-FLC+miR-125b_Day13_R2


title: Gata1s-FLC+miR-ctrl_Day13WD_R1

value: Day 13, Dox withdrawal on day 10

value: miR-ctrl


title: BT3_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep B 24 hr


title: DMSO, day4, rep1


title: DMSO, day4, rep2


title: NTX301, day2, rep3


title: Gata1s-FLC+miR-125b_Day13_R3


title: Gata1s-FLC+miR-ctrl_Day13_R2


title: Gata1s-FLC+miR-125b_Day13_R1


title: Gata1s-FLC+miR-125b_Day13WD_R3


title: NTX301, day2, rep2


title: Gata1s-FLC+miR-ctrl_Day10_R3

value: Doxycycline 1ug/mL for 10 days


title: NTX301, day2, rep1


title: Gata1s-FLC+miR-125b_Day13WD_R1


title: DAC, day2, rep3


title: DT1_GAMB_Sp_V

source_name: Anopheles gambiae Virgin spermatheca rep D 3 hr

value: 3 hr post-mating or time-matching virgins


title: AT1_GAMB_Sp_V

source_name: Anopheles gambiae Virgin spermatheca rep A 3 hr


title: Gata1s-FLC+miR-ctrl_Day10_R1


title: BT1_GAMB_Sp_V

source_name: Anopheles gambiae Virgin spermatheca rep B 3 hr


title: DAC, day2, rep2


title: AT1_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep A 3 hr


title: Gata1s-FLC+miR-ctrl_Day10_R2


title: Gata1s-FLC+miR-125b_Day10_R2


title: DT3_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 24 hr


title: BT1_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep B 3 hr


title: DMSO, day2, rep3


title: CT3_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 24 hr


title: Gata1s-FLC+miR-125b_Day10_R1


title: DAC, day2, rep1


title: Gata1s-FLC+miR-125b_Day10_R3


title: Gata1s-FLC+miR-ctrl_Day2_R1

value: Doxycycline 1ug/mL for 48h


title: DT1_GAMB_Sp_M

source_name: Anopheles gambiae Mated spermatheca rep D 3 hr


title: DMSO, day0, rep3

value: AML


title: DMSO, day0, rep1


title: DMSO, day2, rep1


title: MOLM13_NTX301, day2, rep3 (NTX-301 dataset)

data_processing:
Sequencing reads were processed using FastQC for quality check
Trimmomatic 0.38 for trimming
HISAT2 for mapping
StringTie for transcript assembly and quantification
Genome_build: hg19
Supplementary_files_format_and_content: normalized expression value text file

source_name: MOLM-13 leukemia cell line

growth_protocol: Leukimia cells (HL-60 and MOLM-13) were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS) in a CO2 incubator.

extract_protocol:
Total RNA was extracted by using RNeasy mini kit (Qiagen).
TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E

treatment_protocol: During 48h, DMSO, NTX-301, and DAC (30nM for HL-60, 15nM for MOLM-13) were treated to 5x105  cells plated on 6-well plates in triplicates.

tag: cell type


title: MOLM13_NTX301, day2, rep2 (NTX-301 dataset)


title: Nfix_mHypoA_25K

city: Cold Spring Harbor

first: Melody

last: Wu

address: 1 Bungtown Rd

institute: Cold Spring Harbor Laboratory

description: 25,000 cells

data_processing:
Library strategy: CUT&RUN
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700.
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called using MACS2 callpeak (q < 0.05). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent normalized genomic coverage. narrowPeak files represent genomic binding events.

source_name: mHypoA cells

growth_protocol: Cells were maintained in standard DMEM medium supplemented with 10% FBS and Pen-Strep then harvested using trypsin.

extract_protocol:
Tissue was homogenized 15x with a loose pestle in a glass homogenizer containing Homogenization Medium (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X Roche EDTA-free protease inhibitor cocktail, pH 7.8). 0.3% IGEPAL CA-630 was added, and the tissue was further dounced 5x with a tight pestle. After douncing, the homogenate was filtered through a 40 µm strainer and mixed 1:1 with 50% OptiPrep solution (Millipore Sigma) prepared in Dilution Buffer (150 mM KCl, 30 mM MgCl2, 120 mM Tricine-KOH, pH 7.8). The homogenate was underlaid with 5 ml of 30% and 40% OptiPrep solution, respectively, and centrifuged at 10,000xg for 18 min at 4°C in an ultracentrifuge. ~2 ml of nuclei solution were removed from the 30 - 40% OptiPrep. interface by direct tube puncture. Following nuclei isolation, 0.4% IGEPAL CA-630 was added to improve binding to concanavalin A magnetic beads.
Takara SMARTer ThruPlex DNA-seq Kit

value: Cell line


title: CT3_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 24 hr


title: BT3_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 24 hr


title: WT FLCs_R2

description:
sgL_shL2.gz
WT FLCs_readcount_genename

source_name: FLCs

tag: treatment

value: sgLuc

value: shLuc


title: DMSO, day2, rep2


title: BCD-T3_RBv_Gamb

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [BCD] combined 24 hr

value: Male

value: [BCD] combined


title: BT3_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 24 hr

value: Female


title: MOLM13_DAC, day2, rep1 (NTX-301 dataset)


title: Gata1s-FLC+miR-125b_Day2_R2


title: Gata1s-FLC+miR-ctrl_Day2_R3


title: Gata1s-FLC+miR-ctrl_Day2_R2


title: Gata1s-FLC+miR-125b_Day2_R1


title: Gata1s-FLC+miR-125b_Day2_R3


title: MOLM13_NTX301, day2, rep1 (NTX-301 dataset)


title: DMSO, day0, rep2

source_name: DMSO treatment


title: MOLM13_DAC, day2, rep3 (NTX-301 dataset)


title: DT1_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 3 hr

value: Virgin


title: MOLM13_DAC, day2, rep2 (NTX-301 dataset)


title: CT1_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 3 hr


title: MOLM13_DMSO, day2, rep2 (NTX-301 dataset)


title: BCD-T3_RBm_Gamb

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [BCD] combined 24 hr

value: 24 hr post-mating or time-matching virgins


title: Gata1s-FLCs+miR-125b_R3

description:
m125_015.gz
Knockdown.genes.readcount.annot

value: Doxycycline 1μg/mL for 10 days


title: MOLM13_DMSO, day2, rep3 (NTX-301 dataset)


title: Control_3

city: Zheng Zhou

first: Geyi

last: Zhang

address: No. 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
RNA was extracted by the Trizol and assayed for RNA integrity and total amount with 2100 bioanalyzer(Agilent, CA, USA).
Library construction will be performed using RAP treatment for 24 hours and control RNA samples(n=3), and then sequenced on Illumina HiSeq 6000(Illumina, CA, USA).
Differential expression analysis was performed using the DESeq2 R package (1.20.0) for 2 groups.
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of differentially expressed genes(DEGs) was implemented by the clusterProfiler R package (3.8.1).
Protein-protein interaction (PPI) network analyses with Cytoscape software(3.9.0).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: umbilical cord

growth_protocol: HUVEC were added in six-well plates and cultured using DMEM containing 10% fetal bovine serum in a 37%, 5% CO2 incubator.

extract_protocol:
RNA was extracted by Trizol,NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® was used  for the construction of sequencing libraries.
Library construction will be performed using RAP treatment for  24 hours and control RNA samples, and then sequenced on Illumina HiSeq 6000

treatment_protocol: Every replicate was RAP treated for 24 hours.

value: HUVEC

value: untreated


title: BT1_RBV_GAMB

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 3 hr

value: B


title: WT FLCs_R3

description:
sgL_shL3.gz
WT FLCs_readcount_genename


title: Gata1s-FLC+shArid3a_R3

description:
shA_027.gz
Knockdown.genes.readcount.annot


title: WT FLCs_R1

description:
sgL_shL1.gz
WT FLCs_readcount_genename


title: HL60_NTX301, day2, rep2 (NTX-301 dataset)

source_name: HL-60 leukemia cell line


title: CT1_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep C 3 hr

value: Mated

value: C


title: Gata1s-FLCs+miR-125b_R1

description:
m125_013.gz
Knockdown.genes.readcount.annot


title: RAP_3

value: RAP


title: MOLM13_DMSO, day2, rep1 (NTX-301 dataset)


title: HL60_NTX301, day2, rep3 (NTX-301 dataset)


title: BCD-T1_RBv_Gamb

source_name: Anopheles gambiae Virgin Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [BCD] combined 3 hr

value: 3 hr post-mating or time-matching virgins


title: Control_1


title: Control_2


title: BT1_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep B 3 hr


title: Gata1s-FLC+sh-ctrl_R3

description:
Ctrl_021.gz
Knockdown.genes.readcount.annot

value: sh-ctrl


title: Gata1s-FLCs+miR-125b_R2

description:
m125_014.gz
Knockdown.genes.readcount.annot


title: RAP_2


title: Gata1s-FLC+sh-ctrl_R2

description:
Ctrl_020.gz
Knockdown.genes.readcount.annot


title: DT1_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 3 hr

value: D


title: Gata1s-FLC+shArid3a_R1

description:
shA_025.gz
Knockdown.genes.readcount.annot


title: HL60_DAC, day2, rep2 (NTX-301 dataset)

value: AML


title: HL60_DAC, day2, rep1 (NTX-301 dataset)


title: HL60_NTX301, day2, rep1 (NTX-301 dataset)


title: HL60_DAC, day2, rep3 (NTX-301 dataset)


title: BCD-T1_RBm_Gamb

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep [BCD] combined 3 hr


title: RAP_1


title: Gata1s-FLC+sh-ctrl_R1

description:
Ctrl_019.gz
Knockdown.genes.readcount.annot


title: B-T3_MAG-V_Gamb

source_name: Anopheles gambiae Virgin Male accessor glands rep B 24 hr

value: Male accessor glands


title: Gata1s-FLC+Arid3a_R2

description:
FLC_023
FLCs.overexpression.genes.readcount.annot

value: Doxycycline 1μg/mL for 48h


title: D-T3_MAG-V_Gamb

source_name: Anopheles gambiae Virgin Male accessor glands rep D 24 hr

value: Male


title: HL60_DMSO, day2, rep3 (NTX-301 dataset)


title: D-T3_MAG-M_Gamb

source_name: Anopheles gambiae Mated Male accessor glands rep D 24 hr


title: Gata1s-FLC+Arid3a_R1

description:
FLC_022
FLCs.overexpression.genes.readcount.annot


title: AR-positive CRPC_vehicle_OCT1

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

institute: Tokyo Metropolitan Institute of Gerontology

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files that summarized significant peak regions (P-value < 1.0xE-4)

source_name: AR-positive CRPC cells

growth_protocol:
For culturing organoids, PDXs were minced and digested in growth factor reduced, phenol red-free, ldEV-free Matrigel and cultured in advanced DMEM/F-12 media containing 1% penicillin-streptomycin, 2 mM Glutamax, 1 nM DHT, 1.25 mM N-acetylcysteine, 50 ng/ml EGF, 500 nM A83-01, 10 mM, nicotinamide, 10 μM SB202190, 2% B27, 100 ng/ml noggin, 10 ng/ml FGF10, 5 ng/ml FGF2, 1 μM prostaglandin E2 and 10% R-spondin 1 conditioned media. 10 μM Y-27632 dihydrochloride.
For 2D-culture, PDXs were minced and cultured in DMEM media containing 1% penicillin-streptomycin, 0.5ug/ml fungizone, 0.1mg gentamicin, 25mM HEPES buffer, 10% fetal calf serum, 225U/ml Collagenase Type 1, 25U/ml Hyaluronidase then cultured in advanced DMEM/F-12 media containing 1% penicillin-streptomycin, 2 mM Glutamax, 1 nM DHT, 1.25 mM N-acetylcysteine, 50 ng/ml EGF, 500 nM A83-01, 10 mM, nicotinamide, 10 μM SB202190, 2% B27, 100 ng/ml noggin, 10 ng/ml FGF10, 5 ng/ml FGF2, 1 μM prostaglandin E2 and 10% R-spondin 1 conditioned media. 10 μM Y-27632 dihydrochloride.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).
300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.
Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN).
The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: We treated cells with 10 µM OCT1-PI-polyamide (PI) for 48 h or vehicle (water). All cells were treated with 10 nM dehydrotestosterone（DHT) for 24 hours before collecting cells.

value: AR-positive CRPC cells

tag: culture

value: 2D cultured from PDX

value: DHT 10 nM for 24 h + vehicle  for 48 h

tag: chip antibody

value: OCT1 (abcam 15112)


title: C-T3_MAG-V_Gamb

source_name: Anopheles gambiae Virgin Male accessor glands rep C 24 hr

value: Virgin

value: 24 hr post-mating or time-matching virgins


title: HL60_DMSO, day2, rep1 (NTX-301 dataset)


title: AR-positive CRPC_vehicle_AR

value: AR (Santacruz H280)


title: B-T3_MAG-M_Gamb

source_name: Anopheles gambiae Mated Male accessor glands rep B 24 hr

value: Mated

value: B


title: Gata1s-FLC+LUC_R3

description:
FLC_018
FLCs.overexpression.genes.readcount.annot

value: LUC


title: ABL_pMed1_siCon_FP_inhibition_40min_ChIPSeq

data_processing:
ChIP-seq reads were aligned to the hg19 and mm10 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19 and mm10

source_name: prostate

extract_protocol:
cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300 nM FP for indicated time.

value: prostate cancer cells

tag: passages

value: LNCaP-abl

value: pMED1 (Yenzyme, Custom antibody)


title: HL60_DMSO, day2, rep2 (NTX-301 dataset)

value: AML


title: AR-positive CRPC_PI_input

value: DHT 10 nM for 24 h + PI for 48 h


title: Gata1s-FLC+LUC_R2

description:
FLC_017
FLCs.overexpression.genes.readcount.annot

value: Doxycycline 1μg/mL for 48h


title: DT3_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep D 24 hr

value: Head

value: Female

value: D


title: AR-positive CRPC_PI_OCT1

value: AR-positive CRPC cells

value: 2D cultured from PDX


title: Gata1s-FLC+Arid3a_R3

description:
FLC_024
FLCs.overexpression.genes.readcount.annot


title: ABL_pMed1_siCon_FP_inhibition_20min_ChIPSeq


title: ABL_pMed1_siCon_FP_inhibition_30min_ChIPSeq


title: Gata1s-FLC+LUC_R1

description:
FLC_016
FLCs.overexpression.genes.readcount.annot


title: CT3_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep C 24 hr

value: Virgin

value: C


title: ABL_pMed1_siCon_FP_inhibition_10min_ChIPSeq


title: AR-positive CRPC_AR

value: DHT 10 nM for 24h

value: AR (Santacruz H280)


title: ABL_pMed1_siCon_FP_inhibition_0min_ChIPSeq


title: osbzip47dsRNAI#14 rep2

city: Bangalore

first: Usha

last: Vijayraghavan

state: Karnataka

address: New biological Science building

department: Microbiology and cell biology

country: India

institute: Indian Institute of Science

data_processing:
Illumina Hiseq. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oryzastaiva (RAPDB) whole genome using STAR 2.5.3a with optimzed parameters
Trimed Mean of M-values (TMM) of each gene is calculated using the edgeR software (3.82.0).
Genome_build: RAPDB
Supplementary_files_format_and_content: tab-delimited excel file include TMM values for every sample
Supplementary_files_format_and_content: tab-delimited excel file with raw gene counts for every gene and every sample

organism: Oryza sativa Japonica Group

source_name: Inflorescence

extract_protocol:
Total RNA was extracted using Trizol reagent.
1 ug of total RNA for the construction of sequencing libraries using RNA depletion-based NEB next UltraII RNA kit

tag: cultivar

value: Inflorescence

tag: length

tag: genotype

value: osbzip47 dsRNAi#14


title: AR-positive CRPC_PI_AR