title: N2 SW480 colon adenocarcinoma cells transfected with Stealth Negative Control Medium GC siRNAs


title: ATACseq_day2_6

status: Public on Mar 04 2020

type: SRA

city: Stanford

first: Zhana

last: Duren

state: CA

address: 318 Campus Drive

country: USA

institute: Stanford university

description: Retinoic-acid induction

library_source: genomic

data_processing:
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using SRAR.
RNA-seq: Fregments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using RSEM.
ATAC-seq: Reads are mapped to mm9 by ATAC-seq pipeline described in https://www.encodeproject.org/atac-seq/.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include openess values for each Sample on union peaks

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic stem cell

growth_protocol: mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini kit.
RNA-seq library were constructed using the NEBNext Ultra RNA Library Prep kit for Illumina. ATAC-seq library were constructed using Tn5 transposase, followed by PCR amplification.

treatment_protocol: EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for up to 20 days, with the medium being changed daily.

tag: cell line

tag: time point


title: ATACseq_day4_3

description: Retinoic-acid induction


title: ATACseq_day4_5

description: Retinoic-acid induction


title: ATACseq_day4_6

description: Retinoic-acid induction


title: N1 SW480 colon adenocarcinoma cells transfected with Stealth Negative Control Medium GC siRNAs

type: RNA

city: Budapest

first: Wichmann

last: Barna

address: Szentkirály

country: Hungary

institute: SOTE

description: Whole transcriptome expression data from SW480 colon adenocarcinoma cells

hyb_protocol: For sscDNA synthesis 15 µg cRNA was used and 5.5 µg fragmented and labeled sscDNA sample was hybridized to HTA 2.0 microarrays (Affymetrix) for 16 hours at 45°C with 60 rpm rotation in the Hybridization Oven (Affymetrix).

scan_protocol: Scanning was performed with GeneChip Scanner 3000 (Affymetrix).

data_processing: The data were preprocessed by the function SST-RMA- by Gene Expression Console

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SW480 colon adenocarcinoma cells

label_protocol: standard Affymetrix protocol

extract_protocol: 100 ng input total RNA samples were applied as staring material according to the manufacturer instructions

tag: treatment

value: SW480 colon adenocarcinoma cells transfected with Stealth Negative Control Medium GC siRNAS


title: ATACseq_day4_2

description: Retinoic-acid induction


title: ATACseq_day4_1

description: Retinoic-acid induction


title: ATACseq_day4_4

description: Retinoic-acid induction


title: ATACseq_day2_4

description: Retinoic-acid induction


title: ATACseq_day2_5

description: Retinoic-acid induction


title: Foot shock [SH_A3_S2]

city: Seattle

first: Koichi

last: Hashikawa

state: WA

address: 1959 NE Pacific St. HSB J135

institute: University of Washington

library_source: transcriptomic

data_processing:
Nextseq v2.5 following standard illumina protocols.
fastq files were aligned to mouse genome using Cell ranger pipeline (v2, 10x genomics)
Genome_build: mm10
Supplementary_files_format_and_content: barcode.tsv, genes.tsv and matrix.mtx to generate genexcells matrix. Txt files showing non-doublets barcodes.

source_name: habenula

extract_protocol:
Immediately after the shock session, mice were deeply anesthetized with intraperitoneal injection of 0.2 mL of stock solution containing sodium pentobarbital (39 mg/mL) and phenytoin sodium (5mg/mL) and transcardially perfused with ice-old NMDG-aCSF containing inhibitor cocktails which was used throughout procedures unless noted. NMDG-aCSF: 96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ ascorbate, 3 mM Na+ pyruvate, 0.6 mM glutathione-ethyl-ester, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4; pH 7.35-7.40, 300-305 mOsm, oxygenated with 95% O2 and 5% CO2. Inhibitor cocktails: 500 nM TTX, 10 uM APV, 10 uM DNQX, 5 µM actinomycin, 37.7 µM anysomycin. Mice in the control group were removed directly from the home cage. Brains were extracted and coronal sections containing the habenula were prepared at 300 µm using a vibratome (Leica, VT1200). Slices including the habenula (3-4 slices/animal) were recovered in a chamber for 30 min on ice. Habenula samples were then punched (0.75 mm diameter, EMS) from 4 animals/group (6-8 punches/animal) were pooled and enzymatically digested with 1 mg/mL pronase (Roche) for 45 min at room temperature, followed by mechanical trituration with fire-polished glass capillaries (tip diameter 200-300 µm) and filtered through strainers (pore size 40 µm) to remove cellular aggregates. Dead and dying cells in the cell suspension were then removed using a dead cell removal kit (Miltenyi Biotec). After centrifugation, cell concentration was manually counted using a hemocytometer and final cell concentration was adjusted to 1,000 cells/µL.
cDNA libraries were constructed following manufacture's instruction (Chronium Single Cell 3' Reagents Kits V2 User Guide, 10x Genomics). Briefly, ~17,000 dissociated cells were mixed with reverse transcription mix and loaded into the chip. The mRNAs of single cells were captured by barcoded beads using a Chromium controller. Reverse transcribed cDNAs were then PCR amplified, fragmented, and ligated with adaptors followed by sample index PCR.  cDNA libraries were sequenced on an Illumina Nextseq 500 (v2.5) and the alignment of raw sequencing reads to the mouse genome was conducted using the 10x Genomics Cell Ranger pipeline (V2) to obtain cell by gene matrices for subsequent downstream analysis.

treatment_protocol: Shock (n=4) and Control (n=4) groups were handled 5 min/day for 7 days. Mice in the Shock group were habituated to the shock chamber (Med Associates Inc.) 10 min/day for 7 days prior to the behavior experiment. On the shock day, mice in the Shock group received 30 foot-shocks (0.3 mA, 1 s duration, mean inter shock intervals: 116 s) in 60 min.

tag: strain

tag: tissue

value: habenula


title: ATACseq_day20_4

description: Retinoic-acid induction


title: ATACseq_day0_4

description: Retinoic-acid induction


title: ATACseq_day0_5

description: Retinoic-acid induction


title: ATACseq_day0_6

description: Retinoic-acid induction


title: ATACseq_day0_7

description: Retinoic-acid induction


title: ATACseq_day0_3

description: Retinoic-acid induction


title: ATACseq_day2_1

description: Retinoic-acid induction


title: ATACseq_day0_2

description: Retinoic-acid induction


title: ATACseq_day0_1

description: Retinoic-acid induction


title: ATACseq_day2_3

description: Retinoic-acid induction


title: ATACseq_day2_2

description: Retinoic-acid induction


title: p8 NSC diff NC D8

city: Guangzhou

first: Lining

last: Liang

address: 190,Kaiyuan Ave.

country: China

institute: Guangzhou Institute of Biomedicine and Health,Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

source_name: NSC

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: passages


title: p8 NSC diff Damgo D8


title: p8 NSC diff Naloxone D8


title: p8 NSC diff Naloxone D4


title: p8 NSC diff Naloxone D2


title: p8 NSC diff Damgo D2


title: p8 NSC diff Damgo D4


title: p8 NSC diff NC D2


title: p8 NSC NC


title: p8 NSC Damgo


title: p8 NSC diff NC D4


title: p13 NSC


title: p8 NSC


title: p8 NSC Naloxone


title: testis, GRTH Knock-In 5

city: Bethesda

first: Raghuveer

last: Kavarthapu

state: MD

address: 10 Center Dr, Bldg 10, Room 1E3340

department: NICHD

institute: National Institutes of Health (NIH)

data_processing:
PartekFlow software was used for read QA/QC report
The sequenced reads were trimmed to remove the adapters
STAR method was used to align the RNA-seq reads with mouse mm10 reference genome
The quantification of transcriptome abundance was performed using Partek E/M algorithm in PartekFlow software.
Differentially expressed genes (DEGs) between WT and KI gentotypes were generated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with counts from each sample

source_name: testis

growth_protocol: Mice were housed in pathogen-free, temperature- and light-controlled conditions (22 oC), with an alternating light–dark cycle with 14 h of light and 10 h of darkness.

extract_protocol:
Total RNA was prepared using Qiagen RNeasy mini kit
RNA-Seq library was constructed from mRNA according to a standard protocol provided by Illumina

value: testis

tag: cell type

value: germ cells

tag: genotype

value: GRTH Knock-In


title: testis, GRTH Knock-In 3


title: testis, GRTH Knock-In 4


title: testis, Wild Type 5

value: WT


title: testis, Wild Type 4


title: testis, GRTH Knock-In 2


title: testis, GRTH Knock-In 1


title: RNAseq_day20_2

description: Retinoic-acid induction

molecule: polyA RNA


title: testis, Wild Type 2


title: testis, Wild Type 1


title: Wild-type erythrocytes [WT_485]

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

department: Epigenetics and Development Division

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Illumina software was used for instrument control (HSCS version 2.2.38), basecalling and quality control (RTA version 1.18.61) and fastq file generation and de-multiplexing (CASAVA version 1.8.2).
Short reads were mapped using the subread alignment algorithm from the Rsubread package (version 1.18.0, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.18.0) using the in-built mm10 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Wild-type erythrocytes

extract_protocol:
Red blood cells were obtained from cardiac puncture, mixed with 100µl Aster Jandl citrate-based anticoagulant and subsequently diluted in 2 ml of phosphate buffer saline (PBS) with 2mM EDTA. This suspension was layered with 1.5 ml Ficoll-paque PLUS (GE Healthcare) and centrifuged at 400g for 30 minutes at room temperature with minimal acceleration and brake. The red blood cell containing pellet was washed twice with PBS 2mM EDTA and lysed for RNA extraction with Qiagen RNA extraction kit.  The purity of each sample was checked by flow cytometry to assess the relative contamination of Ter199+ RBC with CD41+ platelets, CD45+ lymphocytes and DRAQ5+ (Thermo Fisher Scientific) nucleated cells. RBC suspensions used for RNAseq were > 99.8% pure.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA v2 sample preparation kit, HiSeq PE Cluster Kit v4-cBot-HS and HiSeq SBS Kit v4).

tag: strain background

value: BalB/c

value: purified erythrocyte

tag: genotype/variation

tag: batch


title: RNAseq_day20_3

description: Retinoic-acid induction


title: Nxf1 mutant erythrocytes [Nxf1_482]

source_name: Nxf1 mutant erythrocytes


title: testis, Wild Type 3


title: Nxf1 mutant erythrocytes [Nxf1_486]


title: Wild-type erythrocytes [WT_476]


title: RNAseq_day20_4

description: Retinoic-acid induction


title: Nxf1 mutant erythrocytes [Nxf1_477]


title: Tmbim1-KO1

city: Wuhan

first: yanfang

last: su

state: Hubei

address: No. 169, EastLakeRoad, Wuchang, Wuhan

department: Zhongnan hospital

institute: Wuhan University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃.

scan_protocol: GeneChips were scanned using the Scanner 7G.

data_processing: The data were analyzed with R/Bioconductor. RMA analysis was employed to normalize and evaluate the gene expression. The differentially expressed genes (DEGs) were obtained by limma R package with the standard that fold > 1.5 & P < 0.05. RMA analysis was employed to evaluate the gene expression

source_name: Tmbim1-KO_aortic binding surgery_heart

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400ng total RNA

growth_protocol: The mice were exposed to a 12-h light/dark cycle with controlled temperature and humidity. Food and water were provided ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Mice were treated with aortic binding surgery for 2 weeks, the hearts were dissected and immediately put in RNA latter reagent.

value: Tmbim1 KO

tag: treated with

value: aortic binding surgery for 2 weeks

value: heart


title: Tmbim1-KO2


title: Tmbim1-KO3


title: Flox3

source_name: wild type_aortic binding surgery_heart

value: Flox; wild type


title: Flox2


title: RNAseq_day20_1

description: Retinoic-acid induction


title: Control vs. 200 ppm GABA in drinking water Rat 1

city: seoul

first: keuntae

last: Park

address: 5FL, D-dong, Beopwon-ro 9 gil, Songpa-gu

country: South Korea

institute: Milaebioresource

description:
cont vs. G200 1_1
Normal rat, 5 weeks, male, kidney tissue.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.
The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity.

organism: Rattus norvegicus

source_name: SD male rat, control

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Five-week-old male SD rats were randomly divided into two groups (n=3/group) and fed control diet (Harlan Diet 2018S, Madison Laboratories, WI, USA) or moderate environment condition in specific pathogen zone.

extract_protocol: Non-tumor kidney region was isolated from each rat kidney tissue. Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: GABA was supplied via water containing 200 ppm.

value: Sprague-Dawley

tag: Sex

value: male

value: kidney tissue (non-tumor region)

value: control

source_name: SD male rat, GABA

value: 200 ppm GABA in drinking water


title: RNAseq_day4_3

description: Retinoic-acid induction


title: Flox1


title: RNAseq_day4_2

description: Retinoic-acid induction


title: RNAseq_day2_1

description: Retinoic-acid induction


title: RNAseq_day2_2

description: Retinoic-acid induction


title: RNAseq_day2_3

description: Retinoic-acid induction


title: RNAseq_day0_7

description: Retinoic-acid induction


title: RNAseq_day0_4

description: Retinoic-acid induction


title: RNAseq_day0_6

description: Retinoic-acid induction


title: RNAseq_day0_2

description: Retinoic-acid induction


title: RNAseq_day0_5

description: Retinoic-acid induction


title: RNAseq_day0_3

description: Retinoic-acid induction


title: RNAseq_day0_1

description: Retinoic-acid induction


title: p8 NSC diff NC D2

data_processing:
Base calling performed using CASAVA version 1.4
Reads were filtered by using perl trim_galore v 0.3.7 with the following parameters: -q 20 –paired -a AGATCGGAAGAGC –a2 GATCGGAAGAGC --phred33 --gzip --rrbs --keep --fastqc --fastqc_args --threads 2 FastqFile -o OutFile.
BS-seq reads were aligned with the mouse reference genome (mm10) using bismark version 0.9.0 with the following configurations: -pe -N 1 --bowtie2 --path_to_bowtie Bowtie2Path --bam --samtools_path SamtoolsPath –o OutFile <genome_folder> -1 fastq1 -2 fastq2.
Methylation calling was obtained using bismark version 0.9.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-separated values: chr, position of C, directon of read/alignment, number of reads support the site's methylation,number of reads do not support the site's methylation, type of methylation C，C and downstream bases, p value, q value.

source_name: p8 NSCs differentiated without naloxone

extract_protocol:
Around 3×106 cells were harvested by 0.25 % trypsin digestion. DNA was extracted according to the instructions of Wizard® Genomic DNA Purification Kit (Promega A1125). Purity of DNA was determined by K5500 spectrophotometer, DNA quantification was performed using Qubit® 3.0 Fluorometer.
DNA was digested by MspI followed by end-repaired. The 3’end of the end-repaired, phosphorylated fragments were tailed with dA, and the single A overhangs were ligated by the methylated adaptors. Library fragments of 40~220 bp were band isolated from 2% agarose gel, converted by bisulfite treatment, and amplified by PCR. The RRBS library was sequenced on an Illumina HiSeq2500 Analyzer platform  paired-end 50 bp reads.

value: neural stem cells

value: NSCs (neural stem cells)


title: p8 NSC pro NC

source_name: p8 NSCs cultured without naloxone


title: Control vs. 200 ppm GABA in drinking water Rat 2

description:
cont vs. G200 2_2
Normal rat, 5 weeks, male, kidney tissue.


title: Control vs. 200 ppm GABA in drinking water Rat 3

description:
cont vs. G200 3_3
Normal rat, 5 weeks, male, kidney tissue.


title: RNAseq_day4_1

description: Retinoic-acid induction


title: 33 rep 1

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

description: biological replicate 1

data_processing:
MiSeq Real-Time analysis (RTA), version v1.18.54
The quality filtered sequencing reads from different time points were aligned against the YerA41 assembly scaffolds and against the Y. ruckeri PB-H2 (LN681231.1) reference sequence using Bowtie2 aligner.
The reads aligning over each gene were counted using the HTSeq.
Supplementary_files_format_and_content: Text files (tab-delimited) presenting the gene expression matrix for bacterial and phage genenomes separetely

organism: Yersinia ruckeri

source_name: liquid culture

growth_protocol: RNA extractions were carried out from three separate infection experiments. In the first experiment, the RS41 bacteria were grown for 16 h at RT and subsequently diluted 1:20 in fresh LB to a total volume of 20 ml and when the OD600 of the culture reached 0.7, duplicate 1 ml samples were withdrawn to represent 0 min uninfected samples, then 9 ml of the culture was infected with 1 ml of phage YerA41 stock (5×1010 pfu/ml) to achieve a MOI of ca. 50. Duplicate 1 ml aliquots were withdrawn at 5, 15, and 30 min postinfection. In the second experiment, the RS41 bacteria were grown for 16 h at RT and subsequently diluted 1:20 in fresh LB to a total volume of 20 ml and when the OD600 of the culture reached 0.7, 8.5 ml of the culture was infected with 1.5 ml of phage YerA41 stock to achieve a MOI of 10. One ml aliquots were withdrawn at 33, 45, 63, 75 and 92 min postinfection in one replicate each. In the third experiment, three biological replicates were grown for 16 h at RT and diluted 1:20 in 10 ml. When the cultures reached OD600 of 0.6, one ml aliquots were withdrawn from each culture, these representing the uninfected 0 min samples in triplicate. Then, to 5.3 ml of culture 0.7 ml of phage stock was added to reach a MOI of 50, mixed for 3 min followed by 3 min standing and 3 min centrifugation at 4500xg at 22°C. The supernatant was replaced with 6 ml fresh medium and triplicate 1 ml samples, one from each tube, were withdrawn at 15, 30 and 60 minutes postinfection.

extract_protocol:
In all experiments, total RNA was isolated from the samples using the SV Total RNA Isolation System (Promega, USA) and the quality assessment was performed using LabChip (PerkinElmer, USA).
The rRNA was removed using Ribo-ZeroTM rRNA Removal Kit for Gram-negative Bacteria (Epicentre, USA). The sequencing library was prepared using the ScriptSeq-v2 RNA-Seq Library Preparation Kit (Epicentre, USA). Paired-end sequencing was performed on MiSeq (Illumina, USA) with the read length of 150 nucleotides.

tag: time point post infection

tag: condition

value: infected with bacteriophage YerA41


title: 30 rep 1

description: biological replicate 1


title: 60_A rep 1

description: biological replicate 1


title: 60_B rep 2

description: biological replicate 2


title: 75 rep 1

description: biological replicate 1


title: 60_C rep 3

description: biological replicate 3


title: 45 rep 1

description: biological replicate 1


title: 92 rep 1

description: biological replicate 1


title: p8 NSC diff Naloxone D2

source_name: p8 NSCs differentiated with naloxone


title: 15_C rep 3

description: biological replicate 3


title: 30_A rep 1

description: biological replicate 1


title: 15 rep 1

description: biological replicate 1


title: 15_A rep 1

description: biological replicate 1


title: p8 NSC pro Naloxone

source_name: p8 NSCs cultured with naloxone


title: 5 rep 1

description: biological replicate 1


title: 15_B rep 2

description: biological replicate 2


title: 63 rep 1

description: biological replicate 1


title: 0_C rep 3

description: biological replicate 3

value: 2 (Negative control)


title: 0 rep 4

description: biological replicate 4

value: 3 (Negative control)


title: 30_C rep 2

description: biological replicate 2


title: 0_B rep 2

description: biological replicate 2

value: 1 (Negative control)


title: 0_A rep 1

description: biological replicate 1

value: 0 (Negative control)


title: KNSR36

city: Illkirch

first: Kenny

last: Schumacher

address: 1, rue Laurent Fries

department: Department of Developmental Bioliogy and Stem Cells

country: France

institute: IGBMC

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for total RNA samples RNA-seq analysis was performed on total RNA extracts
totalRNA-Med1417

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Genome_build: sacCer3

organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

growth_protocol: S. cerevisiae cells were grown until midlog phase in YPD medium from OD595 = 0.1 to OD595 = 0.6 at 30°C with constant shaking (Optical Density), The S. pombe cells were grown until midlog phase in YPD medium from OD595 = 0.1 to OD595 = 0.8 at 32°C

extract_protocol:
Cells were mixed in a defined ratio (1 S. cerevisiae : 3 S. pombe) RNA was extracted RiboPure Yeast Kit, Ambion, AM1926
Total RNA-Seq  and newly-synthesized RNA-seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 10 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: After reaching midlog phase S.cerevisiae are treated with auxin (3-indole acetic acid, 3-IAA) or DMSO (carrier) for 30 min, followed by a 6 min treatment with 4-thiouracil to label newly synthesized RNAs

value: OsTIR1 MED14-IAA7 MED17-IAA7

value: 500 μM auxin (30 min)

value: (GZY380) MATalpha ade2<delta>::hisG his3<delta>200 leu2<delta>0 lys2<delta>0met15<delta>0 trp1<delta>63 ura3<delta>0 his3::pGPD1-OsTIR1-HIS3 MED14-3HA-IAA7-URA3 MED17-3V5-IAA7-kanMX6


title: KNSR40

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for newly-synthesized RNA samples RNA-seq analysis was performed on 4tU labelled RNA (newly synthesized RNA) purified of total RNA extracts
newly synthesized RNA-Med1417


title: KNSR39


title: KNSR35


title: KNSR37

value: DMSO (30 min)


title: KNSR34


title: KNSR33


title: KNSR32

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for newly-synthesized RNA samples RNA-seq analysis was performed on 4tU labelled RNA (newly synthesized RNA) purified of total RNA extracts
Sua7-newly synthesized RNA

extract_protocol:
Cells were mixed in a defined ratio (1 S. cerevisiae : 3 S. pombe) RNA was extracted RiboPure Yeast Kit, Ambion, AM1926
Total RNA-Seq libraries were generated from 800 (Total RNA ) or 300 (newly-synthesized RNA) ng of RNA using TruSeq Stranded Total RNA Library Prep Gold kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA) with modifications. Briefly, ribosomal RNA was removed using biotinylated target-specific oligos, riboPOOL targeting S. cerevisiae ribosomal RNA (siTOOLs Biotech, Planegg/Martinsried, DE) combined with Dynabeads MyOne Streptavidin C1 (Thermo Fisher) according to manufacturer's instructions. Following purification on Agencourt RNAClean XP (Beckman-Coulter, Villepinte, France) with a 1.8X ratio, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: OsTIR1 SUA7-IAA7

value: (GZY364) MATalpha ade2<delta>::hisG his3<delta>200 leu2<delta>0 lys2<delta>0met15<delta>0 trp1<delta>63 ura3<delta>0 his3::pGPD1-OsTIR1-HIS3 SUA7-3V5-IAA7-kanMX6


title: KNSR30


title: KNSR31


title: KNSR29


title: KNSR28

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for total RNA samples RNA-seq analysis was performed on total RNA extracts
Sua7-totalRNA


title: KNSR38


title: KNSR27


title: KNSR26


title: KNSR25


title: KNSR23

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for newly-synthesized RNA samples RNA-seq analysis was performed on 4tU labelled RNA (newly synthesized RNA) purified of total RNA extracts
newly-synthesized RNA
nsRNA-Med14-Med17

extract_protocol:
Cells were mixed in a defined ratio (1 S. cerevisiae : 3 S. pombe) RNA was extracted RiboPure Yeast Kit, Ambion, AM1926
Total RNA-Seq libraries were generated from 1000 ng of total RNA using TruSeq Stranded Total RNA LT Sample Prep Kit with Ribo-Zero Gold (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, cytoplasmic and mitochondrial ribosomal RNA (rRNA) was removed using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. Following purification, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 10 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: After reaching midlog phase S.cerevisiae are treated with 500 μM auxin (3-indole acetic acid, 3-IAA) or DMSO (carrier) for 30 min, followed by a 6 min treatment with 5 mM 4-thiouracil to label newly synthesized RNAs

value: OsTIR1 MED14-IAA7

value: (GZY219) MATalpha ade2<delta>::hisG his3<delta>200 leu2<delta>0 lys2<delta>0met15<delta>0 trp1<delta>63 ura3<delta>0 his3::pGPD1-OsTIR1-HIS3 MED14-3V5-IAA7-kanMX6


title: KNSR24


title: KNSR16

value: OsTIR1 MED17-IAA7

value: (GZY269) MATalpha ade2<delta>::hisG his3<delta>200 leu2<delta>0 lys2<delta>0met15<delta>0 trp1<delta>63 ura3<delta>0 his3::pGPD1-OsTIR1-HIS3 MED14-3V5-IAA7-kanMX6


title: KNSR13


title: KNSR15


title: KNSR14


title: KNSR11


title: 131_Wapl-KO

city: Vienna

first: Kikuë

last: Tachibana

state: --- Select a state ---

address: Dr.-Bohr-Gasse 3

country: Austria

institute: IMBA

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.

source_name: oocyte

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.

value: oocyte

value: Wapl-KO


title: KNSR8

description:
after treatment RNA were labelled for 6 min with 5mM 4tU, for total RNA samples RNA-seq analysis was performed on total RNA extracts
totalRNA-Med14-Med17


title: 129_Wapl-KO


title: KNSR7


title: KNSR6


title: 128_Wapl-KO


title: 127_Wapl-KO


title: KNSR5


title: 126_Wapl-KO


title: HESC_sicontrol_2

city: Xiamen

first: Wenbo

last: Deng

state: Fujian

address: Xiang'an Road

department: School of Medicine

institute: Xiamen University

description:
HESC_sicontrol_2
exp_X3_sicontrol

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hg19 whole genome using HISAT2 with default parameters
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: HG19
Supplementary_files_format_and_content: abundance measurements

growth_protocol: Cells were seeded 70% confluence  at the present of decidual cocktail (E2,P4, cAMP) and cultured with DMEM/F-12 containing 10% CS-FBS.

extract_protocol:
Decidualized stromal cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4003 ATCC cell line

value: endometrial cell line

tag: status

value: decidualized

tag: tissue source

value: human uterus


title: 4003_normal_expression

source_name: ATCC cell line 4003

growth_protocol: Cells were seeded 70% confluence and cultured with DMEM/F-12 containing 10% CS-FBS.

extract_protocol:
Stromal cells were harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: undecidualized

value: Uterus


title: HESC_sisox4_2

description:
HESC_sisox4_2
exp_X3_sisox4


title: HESC_sicontrol_1

description:
HESC_sicontrol_1
exp_X2_sicontrol


title: HESC_sisox4_1

description:
HESC_sisox4_1
exp_X2_sisox4


title: KNSR4

value: 500 μM auxin (30 min)


title: KNSR9


title: KNSR3


title: KNSR2


title: 130_Wapl-KO


title: 125_Wapl-KO


title: 123_Wapl-KO


title: 124_Wapl-KO


title: KNSR1


title: MDA-MB-231 sg1_rep4

first: linbin

last: Yang

address: yanjiangxilu 107

institute: Sun Yet-sen University

description: CCDC25 knockout MDA-MB-231 transfected with NET-DNA

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

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

source_name: MDA-MB-231 sg1_rep4

label_protocol: The total RNA from each sample was linearly amplified and labeled with Cy3-UTP. 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.

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: 5 x 105 MDA-MB-231 with or without CCDC25 knockout were trasfected with 0.5 ug NET-DNA and cultured in a humidified incubator with 5% CO2 for 24 hours with DMEM medium supplemented with 10% heat-inactivated fetal bovine serum

tag: tumor cells


title: MDA-MB-231 ctrl1_rep4

description: Control MDA-MB-231transfected with NET-DNA

source_name: MDA-MB-231 ctrl1_rep4


title: Wild-type erythrocytes [WT_481]

value: BalB/c

value: purified erythrocyte


title: 122_Wapl-KO


title: 121_Wapl-KO


title: 20160831_20160831-ASM14_01_11

city: New Haven

first: Jose

middle: Luis

last: Gomez

state: CT

address: 300 Cedar Street

department: Pulmonary, Critical Care and Sleep Medicine

institute: Yale University

description: MicroRNA

hyb_protocol: Purified total RNA was processed using the Nanostring nCounter v3.0a array.

scan_protocol: Arrays were scanned using the Nanostring scanner.

data_processing: Nanostring nCounter arrays were normalized using the top 100 genes without background substraction using the generic mean in the nSolver Analysis Software v3.

source_name: Sputum

extract_protocol: RNA was quantified using nanodrop and agilent bioanalyzer.

treatment_protocol: Sputum samples were processed using a standardized protocol to solubilize mucus plugs using DTT. Cell pellets were processed and RNA  was extracted using Norgen kit.

value: Sputum

tag: age

value: F

tag: disease status

value: Asthma


title: 20160831_20160831-ASM14_01_07

description: MicroRNA

label_protocol: Purified total RNA was processed using the Nanostring nCounter v3.0a array.

tag: tissue


title: MDA-MB-231 sg1_rep3

source_name: MDA-MB-231 sg1_rep3


title: 119_Wapl-KO

tag: strain


title: 116_Wapl-KO


title: 118_Wapl-KO


title: 20160831_20160831-ASM14_01_01

description: MicroRNA


title: MDA-MB-231 ctrl1_rep3

description: Control MDA-MB-231 transfected with NET-DNA

source_name: MDA-MB-231 ctrl1_rep3


title: 115_Wapl-KO


title: 114_Wapl-KO


title: 117_Wapl-KO


title: 20160819_20160819-ASM12_01_09

description: MicroRNA


title: 112_Wapl-KO


title: 113_Wapl-KO


title: 20160820_20160820-ASM13_01_06

description: MicroRNA

value: M


title: 111_Wapl-KO


title: 20160820_20160820-ASM13_01_02

description: MicroRNA


title: 20160819_20160819-ASM12_01_12

description: MicroRNA


title: 20160819_20160819-ASM12_01_10

description: MicroRNA


title: 20160819_20160819-ASM12_01_08

description: MicroRNA


title: 120_Wapl-KO


title: 110_Wapl-KO


title: MDA-MB-231 sg1_rep2

source_name: MDA-MB-231 sg1_rep2


title: MDA-MB-231 ctrl1_rep2

source_name: MDA-MB-231 ctrl1_rep2


title: 20160819_20160819-ASM12_01_04

description: MicroRNA


title: MDA-MB-231 ctrl1_rep1

source_name: MDA-MB-231 ctrl1_rep1


title: MDA-MB-231 sg1_rep1

source_name: MDA-MB-231 sg1_rep1


title: 108_Wapl-KO


title: 104_Wapl-KO


title: 105_Wapl-KO


title: 109_Wapl-KO


title: 106_Wapl-KO


title: 20160819_20160819-ASM12_01_01

description: MicroRNA


title: 20160818_20160818-ASM11_01_11

description: MicroRNA

value: Control


title: 103_Wapl-KO


title: 20160818_20160818-ASM11_01_12

description: MicroRNA


title: 20160819_20160819-ASM12_01_02

description: MicroRNA


title: 107_Wapl-KO


title: 102_Wapl-KO


title: 20160818_20160818-ASM11_01_09

description: MicroRNA


title: 20160819_20160819-ASM12_01_07

description: MicroRNA


title: 99_Wapl-KO


title: 20160818_20160818-ASM11_01_10

description: MicroRNA


title: 98_Wapl-KO


title: 101_Wapl-KO


title: 100_Wapl-KO


title: 20160818_20160818-ASM11_01_04

description: MicroRNA


title: 20160819_20160819-ASM12_01_03

description: MicroRNA


title: 97_Wapl-KO


title: 20160818_20160818-ASM11_01_05

description: MicroRNA


title: 20160818_20160818-ASM11_01_07

description: MicroRNA


title: 20160818_20160818-ASM11_01_03

description: MicroRNA


title: 20160818_20160818-ASM11_01_02

description: MicroRNA


title: 96_Wapl-KO


title: 20160818_20160818-ASM11_01_01

description: MicroRNA


title: 20160818_20160818-ASM11_01_08

description: MicroRNA


title: 95_Wapl-Control

value: Wapl-Control


title: 20160813_20160813-ASM10_01_12

description: MicroRNA


title: 93_Wapl-Control

value: oocyte


title: 94_Wapl-Control


title: 92_Wapl-Control


title: 89_Wapl-Control


title: 20160813_20160813-ASM10_01_11

description: MicroRNA


title: 90_Wapl-Control


title: 20160831_20160831-ASM14_01_09

description: MicroRNA


title: 20160813_20160813-ASM10_01_10

description: MicroRNA


title: 87_Wapl-Control


title: 88_Wapl-Control


title: 20160813_20160813-ASM10_01_09

description: MicroRNA


title: 20160813_20160813-ASM10_01_08

description: MicroRNA


title: 85_Wapl-Control


title: 84_Wapl-Control


title: 20160813_20160813-ASM10_01_03

description: MicroRNA


title: 20160813_20160813-ASM10_01_04

description: MicroRNA


title: 20160809_20160809-ASM9_01_11

description: MicroRNA


title: 20160809_20160809-ASM9_01_10

description: MicroRNA


title: 20160813_20160813-ASM10_01_05

description: MicroRNA


title: 20160809_20160809-ASM9_01_09

description: MicroRNA


title: 83_Wapl-Control


title: 91_Wapl-Control


title: 20160809_20160809-ASM9_01_08

description: MicroRNA


title: 82_Wapl-Control


title: 86_Wapl-Control


title: 81_Wapl-Control


title: 20160813_20160813-ASM10_01_07

description: MicroRNA


title: 79_Wapl-Control


title: 80_Wapl-Control


title: PV-2

city: Calgary

first: Steven

last: Greenway

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

data_processing:
Raw FASTQ files were generated using Illumina NextSeq Control software (version 2.02). To process and analyze RRBS data several tools were used. FASTQC and TrimGalore were used to perform initial quality checks and initial processing of reads with RRBS settings respectively.
Ensemble GRCh37 was used as reference genome. Cleaned reads were mapped to reference genome using Bismark software (genome prep script). Bismark was used for aligning bisulfite sequencing data as well as for making methylation calls. Alignments that mapped uniquely were kept for analysis and that mapped to multiple regions were discarded. For all samples on an average, 70-75% mappeing efficincy was achieved.
Next, we extracted single CpG information from all the samples to determine methylation status using Bismark methylation extraction script. The position of every single C was written into a new output file depending upon on its context (CpG, CHG, CHH where H is A, T or C). For each refernce cytosine seqeunced, we computed the percentage of reads in which cytosines was methylated (remained a C after bisulfite treatment) out of total reads covering that position. This percent methylated value represents the percentage of molecules that were methylated at each cytosine position.
Genome_build: GRCh37
Supplementary_files_format_and_content: bedGraph

source_name: pulmonary valve

extract_protocol:
Genomic DNA was isolated from biological replicates of frozen non-diseased human cardiac tissues (n=29)  using the QIAGEN DNeasy Blood & Tissue Kit according to the instructions provided by the manufacturer
Typically, 1 µg of DNA was used to make an reduced representation bisulfite sequencing  (RRBS) library.  Genomic DNA was digested with methyl sensitive MspI enzyme which cut at every CCGG regardless of methylation status. Following enzymatic digestion, DNA end repiar and A-tailing were conducted by adding Klenow fragment and dNTP mixture. Next, DNA was then ligated to indexed TrueSeq adapters (Illumina) according to manufacturer's protocol. Adapted ligated DNA fragments were then size selected for the desired input fragments (150-250bps) and (250-350bps) with AMPure XP beads (Beckman Coulter). Bisulfite conversion of size selected libraries was then performed by using Epimark Bisulfite Conversion kit (New Englands Biolabs) using manufacturer's instructions. Final libraries from RRBS were generated by PCR amplification and pooled libraries were quantified using Qubit fluorometer. DNA libraries were then sequenced on Illumina NextSeq 500 machine generating 75 bp single end reads and base calling was performed  using standard Ilumina base calling software.

value: heart

value: healthy control


title: AV-2

source_name: aortic valve


title: AV-1


title: 78_Wapl-Control


title: AV-3


title: PV-3


title: PV-1


title: TV-3

source_name: tricuspid valve


title: TV-2


title: 20160809_20160809-ASM9_01_03

description: MicroRNA


title: 77_Wapl-Control


title: 20160809_20160809-ASM9_01_07

description: MicroRNA


title: MV-3

source_name: mitral valve


title: 20160809_20160809-ASM9_01_05

description: MicroRNA


title: 20160809_20160809-ASM9_01_06

description: MicroRNA


title: 20160809_20160809-ASM9_01_12

description: MicroRNA


title: TV-1


title: MV-2


title: MV-1


title: 76_Wapl-Control


title: 20160809_20160809-ASM9_01_01

description: MicroRNA


title: 75_Wapl-Control


title: PA-2

source_name: pulmonary artery


title: 20160808_20160808-ASM8_01_12

description: MicroRNA


title: PA-1


title: 20160808_20160808-ASM8_01_10

description: MicroRNA


title: 74_Wapl-Control


title: AOR-3

source_name: aorta


title: 73_Wapl-Control

source_name: oocyte


title: AOR-1


title: AOR-2


title: 20160809_20160809-ASM9_01_02

description: MicroRNA


title: 20160808_20160808-ASM8_01_08

description: MicroRNA


title: RA-1

source_name: right atrium


title: RA-2


title: 71_Scc1-KO


title: 70_Scc1-KO


title: 20160808_20160808-ASM8_01_07

description: MicroRNA


title: 20160808_20160808-ASM8_01_06

description: MicroRNA


title: 20160808_20160808-ASM8_01_05

description: MicroRNA


title: 69_Scc1-KO


title: 20160808_20160808-ASM8_01_03

description: MicroRNA


title: RV-1

source_name: right ventricle


title: RV-2


title: LA-3

source_name: left atrium


title: 68_Scc1-KO


title: RV-3


title: 20160807_20160807-ASM7_01_12

description: MicroRNA

source_name: Sputum


title: LV-3

source_name: left ventricle


title: LA-1


title: RA-3


title: LV-2


title: 20160807_20160807-ASM7_01_10

description: MicroRNA


title: 72_Scc1-KO


title: LV-1


title: 66_Scc1-KO


title: 67_Scc1-KO


title: LA-2


title: 65_Scc1-KO


title: 64_Scc1-KO


title: 62_Scc1-KO


title: 63_Scc1-KO


title: 20160807_20160807-ASM7_01_07

description: MicroRNA


title: 20160807_20160807-ASM7_01_08

description: MicroRNA


title: 20160807_20160807-ASM7_01_04

description: MicroRNA


title: 20160807_20160807-ASM7_01_06

description: MicroRNA


title: HCT116 control rep 1

first: Yuelin

middle: Jack

last: Zhu

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization within lumi package in R

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: HCT116 cells were cultured in DMEM/F12 with 10% Horse serum, at 37oC, 5%CO2.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Stable knock down of circ-MDM2 was made in HCT116 using siRNAs. Allstars negative siRNAs was used as control in HCT116 cells.

tag: treatment


title: HCT116 sicirc-MDM2 rep 1


title: HCT116 sicirc-MDM2 rep 2


title: 20160807_20160807-ASM7_01_03

description: MicroRNA


title: 20160807_20160807-ASM7_01_05

description: MicroRNA


title: Su_R5 [TA1795]

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

data_processing:
Reads were mapped with TopHat 2.0. Only uniquely mapping reads were allowed.
The mapped reads were then assembled into transcripts with Cufflinks 2.0 and the UCSC RefSeq gene model.
Gene expression (FPKM) was quantile normalized using the R statistical system.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: FPKM

growth_protocol: 4 week old mice were shaved and euthanized as untreated mice or included in the UVB treatment protocol

extract_protocol:
Total RNA from frozen (-80C) skin and tumors were extracted using the Ambion miRVANA RNA extraction kit
Illumina TruSeq RNA Sample Preparation Kit

treatment_protocol: Dorsal skin from control mice was collected and flash frozen in liquid nitrogen and stored at -80C, while SCC tissues were harvested from euthanized mice chronically treated with UVR (2.5 kJ/m2, 3x a week) and flash frozen in liquid nitrogen and stored at -80C

value: 4 weeks

value: Untreated - skin

tag: tissue type

value: skin


title: Su_R6 [TA1796]

tag: strain background


title: Su_R2 [WT1788]

source_name: WT-Untreated

tag: genotype/variation

value: Wild-type


title: LM3R [TA1466]

value: >35 weeks

value: Chronic UVR (2.5 kJ/m2, 3x a week) - SCC

value: cutaneous squamous cell carcinoma


title: LM6R [TA1417]


title: Su_R1 [WT1790]


title: LM5R [TA1413]


title: 20160807_20160807-ASM7_01_02

description: MicroRNA


title: HCT116 control rep 2


title: Su_R4 [TA1782]


title: wild type Platelets [WT_212]

description:
212_D2DRCACXX_ACAGTG_L006
This is duplicated sample record of GSM1969532 for the convenient retrieval of the complete raw data from SRA

data_processing:
Illumina software was used for instrument control (HSCS version 2.0.12.0), basecalling and quality control (RTA version 1.17.21.3) and fastq file generation and de-multiplexing (CASAVA version 1.8.2).
Short reads were mapped using the subread alignment algorithm from the Rsubread package (version 1.18.0, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using the featureCounts function (Liao et al. Bioinformatics, 2014) from the Rsubread package (version 1.18.0) using the in-built mm10 annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: wild type Platelets

extract_protocol:
Platelets were purified as previously described (Josefsson et al. (2011) J Exp Med 208, 2017-2031) from individual males. The purity of each platelet suspension was assessed by flow cytometry and suspensions for which more than 98% of total events were CD41+ platelets were pooled together. RNA extraction and purification was performed with a Norgen RNA purification kit.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA v2 sample preparation kit, TruSeq PE Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3).

value: BalB/c

value: wild type

tag: cell type

value: purified platelets

tag: batch


title: 61_Scc1-KO

tag: genotype


title: LM4R [TA1412]


title: wild type Platelets [WT_208]

description:
208_D2DRCACXX_TTAGGC_L006
This is duplicated sample record of GSM1969531 for the convenient retrieval of the complete raw data from SRA


title: LM1R [WT1402]

source_name: WT-UVB


title: 60_Scc1-KO


title: 20160807_20160807-ASM7_01_09

description: MicroRNA

value: Sputum

tag: Sex

value: F

value: Asthma


title: 59_Scc1-KO


title: LM2R [WT1481]


title: Su_R3 [WT1789]


title: wild type Platelets [WT_204]

description:
204_D2DRCACXX_ATCACG_L006
This is duplicated sample record of GSM1969530 for the convenient retrieval of the complete raw data from SRA


title: 57_Scc1-KO


title: 58_Scc1-KO


title: Nxf1-mutant lymphocytes [Nxf1_176]

data_processing:
Illumina software was used for instrument control (HSCS version 1.5.15.1), basecalling and quality control (RTA version 1.13.48) and fastq file generation and de-multiplexing (CASAVA version 1.8.2).
Short reads were mapped using the subread alignment algorithm from the Subread package (version 1.2.2, Liao et al. Nucleic Acids Research, 2013) with default parameters.
Gene-level counts were obtained using featureCounts (v1.3.5-p5) (Liao et al. Bioinformatics, 2014).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene.

source_name: Nxf1-mutant lymphocytes

extract_protocol:
For Naïve CD8 T cell isolation, splenocyte suspensions were submitted to red blood cell lysis, stained first with biotinylated CD8 antibodies and then labelled with anti-Biotin microbeads. CD8+ T cells were magnetically enriched by positive selection on MACS separation columns, stained with fluorescently-labelled antibodies before being FACS-sorted as CD8+ CD44low CD62L+. Sorted Naïve T cells were fractionated with Norgen cytoplasmic and nuclear fractionation RNA purification kit. Only cytoplasmic fractions were used for subsequent RNAseq.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSeq RNA v2 sample preparation kit, TruSeq SR Cluster Kit v3-cBot-HS and TruSeq SBS Kit v3).

value: sorted Naive CD8T cells

tag: cell subtype

value: CD8+ CD44low CD62L+ Naive CD8 T cells


title: 20160805_20160805-ASM6_01_09

description: MicroRNA


title: 20160805_20160805-ASM6_01_11

description: MicroRNA


title: 56_Scc1-KO

value: oocyte


title: 20160805_20160805-ASM6_01_08

description: MicroRNA

value: M

value: Control


title: Nxf1-mutant Platelets [Nxf1_206]

source_name: Nxf1-mutant Platelets


title: Nxf1-mutant Platelets [Nxf1_213]


title: Wild-type lymphocytes [WT_190]

source_name: Wild-type lymphocytes


title: 52_Scc1-KO


title: Nxf1-mutant Platelets [Nxf1_209]


title: 51_Scc1-KO


title: Wild-type lymphocytes [WT_182]


title: 20160805_20160805-ASM6_01_10

description: MicroRNA


title: 55_Scc1-KO


title: Nxf1-mutant lymphocytes [Nxf1_192]


title: Nxf1-mutant lymphocytes [Nxf1_184]


title: 54_Scc1-KO


title: PROseq_MEF_preC_25HS_BR1

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
library strategy: PRO-seq
Adapters were removed using cutadapt (Marcel, 2011), and UMIs (where applicable) trmmed with fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were trimmed and filtered, and complement reads were generated using fastx (http://hannonlab.cshl.edu/fastx_toolkit/).
The reads were aligned to combined mm10-dm3 genome using Bowtie2 (Langmead et al., 2009)
Reads that uniquely mapped to hg19 were processed to bed, bedgraph and bigWig files. The number of uniquely mapping reads to Drosophila genome (whole-genome invariant spike-in) was used for sample normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized and replicate combined bigWig files. Since PRO-seq reports positions of transcription complexes strand-specifically, the plus strand and minus strand are given in separate bigWig files.

growth_protocol: Mouse embryonic fibroblasts were maintained in 37C in a humidified 5% CO2 athmosphere and cultured in Dulbecco's modified medium (Gibco), containing10% fetal calf serum, 2mM L-glutamate, 100 ug/ml streptomycin, and 100 U/ml penicillin.

extract_protocol:
After treatments, the cells were harvested by centrifugation, washed with PBS, and permeabilized. Run-on reactions were performed with biotinylated nucleotides as described by Kwak H, Fuda NJ, Core LJ, Lis JT. Precise maps of RNA polymerase reveal how promoters direct initiation and pausing. Science 2013 Feb 22;339(6122):950-3. The run-on reaction was conducted in the presence ofpermeabilized S2 cells, which provides an invariant whole-genome spike-in control between samples
Libraries were generated using TruSeq small-RNA adaptors, universal molecular indexing (UMI) barcodes (where applicable) and the 5' adaptor sequences are indicated for each individual raw data.

treatment_protocol: Heat shocks were instantly induced by adding prewarmed media from parallelly cultured cells, and placing the cells in 42C incubator. Recoveries were conducted by placing the cells into 37C incubators.

value: Mouse embryonic fibroblasts (MEF)

tag: preconditioning

value: 1h at 42C + 48h Recovery (pC)

tag: heat shock (additional to preconditioning)

value: 25 minutes at 42C

tag: 3' umi

value: yes (7nt)

tag: 5' adapter sequence

value: ATCTCGTATGCCGTCTTCTGCTTG

tag: molecule subtype

value: nascent RNA


title: Wild-type lymphocytes [WT_174]

value: BalB/c


title: 20160805_20160805-ASM6_01_06

description: MicroRNA

tag: age

tag: disease status


title: 53_Scc1-KO

tag: tissue

tag: strain


title: PROseq_MEF_preC_40HS_BR2

value: 40 minutes at 42C


title: 49_Scc1-KO


title: PROseq_MEF_preC_40HS_BR1


title: PROseq_MEF_preC_0HS_BR1b

value: no additional stress applied

value: yes (8nt)

value: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC


title: PROseq_MEF_preC_25HS_BR2


title: PROseq_MEF_60HS_4hRec_BR2

value: 1h at 42C + 4h Recovery

value: no


title: 20160805_20160805-ASM6_01_02

description: MicroRNA

value: Sputum

value: Asthma


title: 20160805_20160805-ASM6_01_05

description: MicroRNA

value: F


title: 48_Scc1-KO

value: oocyte


title: PROseq_MEF_preC_12HS_BR2

value: Mouse embryonic fibroblasts (MEF)

value: 12.5 minutes at 42C


title: PROseq_MEF_preC_12HS_BR1

value: 1h at 42C + 48h Recovery (pC)


title: PROseq_MEF_60HS_4hRec_BR1b


title: 20160807_20160807-ASM7_01_01

description: MicroRNA

value: M


title: 20160805_20160805-ASM6_01_12

description: MicroRNA


title: 47_Scc1-KO


title: PROseq_MEF_60HS_4hRec_BR1a


title: 20160804_20160804-ASM5_01_12

description: MicroRNA

value: Control


title: PROseq_MEF_uC_40HS_BR1

value: none (uC)

value: yes (7nt)

value: ATCTCGTATGCCGTCTTCTGCTTG

value: nascent RNA


title: 20160805_20160805-ASM6_01_04

description: MicroRNA


title: 46_Scc1-KO


title: 50_Scc1-KO


title: 20160803_20160803-ASM4_01_12

description: MicroRNA


title: PROseq_MEF_uC_25HS_BR2

value: 25 minutes at 42C


title: PROseq_MEF_uC_0HS_BR2

value: no heat stress applied

value: yes (8nt)

value: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC


title: 20160805_20160805-ASM6_01_01

description: MicroRNA

value: Sputum


title: PROseq_MEF_preC_0HS_BR1a

value: no additional stress applied

value: no


title: PROseq_MEF_uC_25HS_BR1


title: 43_Scc1-KO

value: oocyte


title: PROseq_MEF_uC_40HS_BR2

value: Mouse embryonic fibroblasts (MEF)

value: 40 minutes at 42C


title: PROseq_MEF_uC_60HS_BR1

value: 60 minutes at 42C


title: PROseq_MEF_uC_60HS_BR2


title: PROseq_MEF_preC_0HS_BR2

value: 1h at 42C + 48h Recovery (pC)


title: HA_RIP_IP_Rep3

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

description:
HA-IP-3
45_S45

data_processing:
Illumina Casava 1.8 software was used for basecalling and demultiplexing.
Reads were pre-processed with trimmomatic, trimming bases having quality lower than Q30 and removing sequencing adapters. Remaining reads were aligned to the human genome hg38 assembly with bowtie2.
CPMs were computed on a per-gene basis with the samtools idxstats program and the Gencode v27 annotation.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each gene and sample

source_name: HEK293 cells

growth_protocol: HEK-293 cells were cultured in DMEM with 10% FBS, 100 U/ml penicillin–streptomycin and 0.01 mM l-glutamine (all media ingredients were obtained from Gibco® Thermo Fisher scientific, Waltham, MA USA). Cultures were maintained at 37°C in a 5% CO2 incubator.

extract_protocol:
Cell extracts were resuspended in NT2 buffer [50mM Tris HCl pH=7.5, 150mM NaCl, 1mM MgCl2, 0.05% NP40, 1 U/ml Ribolock (Fermentas, Glen Burnie, MD, USA), 2mM DTT, 30mM EDTA supplemented with a protease inhibitor cocktail (P8340, Sigma,
RNA libraries were prepared for sequencing using standard Illumina protocols: the Illumina TruSeq Targeted RNA Custom Panel Kit was used with 500 ng of total or polysomal RNA.

treatment_protocol: 1.5 × 10^6 HEK cells were seeded into two 10-cm Petri dishes for total and polysomal RNA extractions and were transiently transfected using Lipofectamine2000 (Invitrogen, Thermo Fisher scientific, Waltham, MA USA) with 2µg of pCMV6-HIS-HA-RBMX and with the mock empty vector as control.

value: RBMX overexpressed


title: 44_Scc1-KO


title: 45_Scc1-KO


title: PROseq_MEF_uC_0HS_BR1

value: none (uC)


title: 20160803_20160803-ASM4_01_10

description: MicroRNA

value: F

value: Asthma


title: RBMX_RIP_IP_Rep2

description:
RBMX-IP-2
47_S47


title: 20160803_20160803-ASM4_01_07

description: MicroRNA


title: RBMX_RIP_IP_Rep1

description:
RBMX-IP-1
46_S46


title: HA_RIP_IP_Rep2

description:
HA-IP-2
44_S44


title: 20160804_20160804-ASM5_01_02

description: MicroRNA


title: RBMX_RIP_INPUT_Rep2

description:
RBMX-INPUT-2
41_S41


title: HA_RIP_IP_Rep1

description:
HA-IP-1
43_S43


title: RBMX_RIP_INPUT_Rep3

description:
RBMX-INPUT-3
42_S42


title: 41_Scc1-KO


title: RBMX_RIP_INPUT_Rep1

description:
RBMX-INPUT-1
40_S40


title: HA_RIP_INPUT_Rep3

description:
HA-INPUT-3
39_S39


title: 40_Scc1-KO


title: 38_Scc1-KO


title: 20160803_20160803-ASM4_01_05

description: MicroRNA

value: M

value: Control


title: HA_RIP_INPUT_Rep1

description:
HA-INPUT-1
37_S37


title: HA_RIP_INPUT_Rep2

description:
HA-INPUT-2
38_S38


title: 39_Scc1-KO


title: RBMX_KD_POL_Rep3

description:
polysomal RNA
siRNA-POLY-3
34_S34

extract_protocol:
Once the 80% confluence was reached, cells were incubated for 3–4 min with 10 µg/ml cycloheximide at 37°C  to block translational elongation. Cells were washed with PBS + 10 µg/ml cycloheximide and scraped directly on the plate with 300 µl lysis buffer (10 mM NaCl, 10 mM MgCl2, 10 mM Tris-HCl, pH 7.5, 1% Triton X-100, 1% sodium deoxycholate, 0.2 U/µl RNase inhibitor [Fermentas  Burlington, CA], 10 µg/ml cycloheximide, 5 U/mL Dnase I [New England Biolabs, Hitchin, UK] and 1 mM DTT) and transferred to a tube. Nuclei and cellular debris were removed by centrifugation for 5 min at 13,000 g at 4°C. The polysome-containing lysate was stored at -80 °C or directly layered onto a linear sucrose gradient (15–50% sucrose (w/v), in 30 mM Tris–HCl at pH 7.5, 100 mM NaCl, 10 mM MgCl2) and centrifuged in a SW41Ti rotor (Beckman Coulter, Indianapolis, IN) at 4 °C for 100 min at 180,000 g. Ultracentrifugation allows the polysome separation according to the sedimentation coefficient of macromolecules. After ultracentrifugation, gradients can be fractionated and mRNAs in active translation, corresponding to polysome containing fractions, separated from untranslated mRNAs. Fractions of 1 mL volume were collected with continuous monitoring absorbance at 254 nm. Total RNA was obtained by pooling together a fixed amount (20%) of  each collected fraction. To extract RNA,  polysomal and total fractions were  treated directly with 0.1 mg/ml proteinase K (Euroclone,  Italy) for 2 h at 37°C. After phenol–chloroform extraction and isopropanol precipitation, polysomal RNA was resuspended in 30 µl of RNAse-free water. Both total RNA and polysome RNA were analyzed on an Agilent Bioanalyzer to assess RNA integrity and quantified using the QBit.
RNA libraries were prepared for sequencing using standard Illumina protocols: the Illumina TruSeq Targeted RNA Custom Panel Kit was used with 500 ng of total or polysomal RNA.

treatment_protocol: 1.5 × 10^6 HEK cells were seeded into two 10-cm Petri dishes for total and polysomal RNA extractions and were transiently transfected using Lipofectamine2000 (Invitrogen, Thermo Fisher scientific, Waltham, MA USA) with 25nM of each of the two RBMX siRNA or with the scramble siRNA as control.

value: RBMX knock-down


title: RBMX_KD_POL_Rep5

description:
polysomal RNA
siRNA-POLY-5
36_S36


title: 20160803_20160803-ASM4_01_01

description: MicroRNA


title: 20160803_20160803-ASM4_01_09

description: MicroRNA


title: RBMX_RIP_IP_Rep3

description:
RBMX-IP-3
48_S48


title: 42_Scc1-KO


title: 20160803_20160803-ASM4_01_08

description: MicroRNA


title: 37_Scc1-Control


title: 20160803_20160803-ASM4_01_04

description: MicroRNA


title: RBMX_KD_TOT_Rep5

description:
siRNA-TOT-5
31_S31


title: RBMX_KD_TOT_Rep3

description:
siRNA-TOT-3
29_S29


title: 33_Scc1-Control


title: 20160803_20160803-ASM4_01_02

description: MicroRNA


title: RBMX_KD_POL_Rep4

description:
polysomal RNA
siRNA-POLY-4
35_S35


title: 20160803_20160803-ASM4_01_06

description: MicroRNA


title: 36_Scc1-Control


title: RBMX_KD_POL_Rep2

description:
polysomal RNA
siRNA-POLY-3
33_S33


title: 32_Scc1-Control


title: RBMX_KD_POL_Rep1

description:
polysomal RNA
siRNA-POLY-2
32_S32


title: 35_Scc1-Control


title: Guy11-0h-1

city: Nanjing

first: Ying

last: Li

department: College of Plant protection

institute: Nanjing Agricultural University

data_processing:
Isolation of Poly (A) mRNA from total RNA and construction of cDNA libraries were preformed according to Dong et al. (Dong et al., 2015). Finally, the cDNA libraries were loaded onto the flow cell channels of an Illumina HiSeqTM 4000 platform for paired-end 151 bp x 2 sequencing at the Beijing Genomics Institute (BGI), Shenzhen, China (Zhang et al., 2013).
After discarding low-quality raw reads (contain the connectors and discarded the reads whose content had more than 5% unknown bases.), the clean reads from each library were assembled to M. oryzae. Gene expression levels were measured in the RNA-Seq analysis as reads per kb of exon model per million mapped reads (RPKM) (Mortazavi et al., 2008).
Differentially expressed genes and their corresponding P-values were determined using the DEG. Fold changes (Log2 Ratio) were estimated according to the normalized gene expression level in each sample. We used the absolute value of Log2Ratio>1, p-values<0.001, q-value<0.001 as the threshold to judge differentially expressed genes.
Genome_build: novel_coding_transcript.gtf
Supplementary_files_format_and_content: transcript.fpkm

organism: Pyricularia oryzae

extract_protocol:
The samples of the inoculated rice leaves with conidial suspensions were immediately frozen in liquid nitrogen, total RNA was extracted using an Invitrogen kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: Magnaporthe oryzae and rice leaves mixed sample

value: wild type

tag: timepoint

value: Conidia were inoculated onto rice leaves for 0 h


title: rgs7-24h-3

tag: strain background

tag: genotype/variation

value: {deleta}Morgs7 mutants

value: Conidia were inoculated onto rice leaves for 24 h


title: WT_POL_Rep4

description:
polysomal RNA
CTRL-POLY-4
25_S25


title: 34_Scc1-Control

value: oocyte


title: 20160729_20160729-ASM2_01_03

description: MicroRNA

value: Sputum


title: WT_POL_Rep2

description:
polysomal RNA
CTRL-POLY-2
23_S23


title: 20160727_20160727-ASM1_01_04

description: MicroRNA


title: WT_POL_Rep5

description:
polysomal RNA
CTRL-POLY-5
26_S26


title: RBMX_KD_TOT_Rep1

description:
siRNA-TOT-1
27_S27


title: WT_POL_Rep3

description:
polysomal RNA
CTRL-POLY-3
24_S24


title: 29_Scc1-Control


title: RBMX_KD_TOT_Rep2

description:
siRNA-TOT-2
28_S28


title: 31_Scc1-Control


title: rgs7-24h-1


title: 20160730_20160730-ASM3_01_02

description: MicroRNA


title: WT_TOT_Rep5

description:
CRTL-TOT-5
21_S21


title: rgs7-4h-2

value: Conidia were inoculated onto rice leaves for 4 h


title: WT_TOT_Rep4

description:
CRTL-TOT-4
20_S20


title: rgs7-24h-2


title: 30_Scc1-Control


title: WT_TOT_Rep3

description:
CRTL-TOT-3
19_S19


title: RBMX_KD_TOT_Rep4

description:
siRNA-TOT-4
30_S30


title: WT_TOT_Rep1

description:
CRTL-TOT-1
17_S17


title: WT_POL_Rep1

description:
polysomal RNA
CTRL-POLY-1
22_S22


title: rgs7-4h-3


title: 28_Scc1-Control


title: WT_TOT_Rep2

description:
CRTL-TOT-2
18_S18


title: 25_Scc1-Control


title: 27_Scc1-Control


title: 26_Scc1-Control


title: rgs7-4h-1


title: PBS treatment, PAEC line 4 [PBS_1p5_4]

city: Cambridge

first: Wei

address: Hills Road

department: Medicine

country: United Kingdom

institute: University of Cambridge

description: Gene expression data from PAEC treated with PBS for 1.5 hours

hyb_protocol: Plate arrays were processed on the GeneTitan instrument (Affymetrix) using the GeneTitan Hybridization, Wash and Stain kit (Affymetrix). Samples were hybridized to the array, washed, stained and scanned using the array specific parameters provided by Affymetrix.

scan_protocol: Automated protocol from the GeneTitan, according to the automated settings provided for the array

data_processing: The processing of the data was carried out in R, using the package Oligo and the normalisation method used is RMA (Robust Multichip Analysis), the comparisonbs are done using the limma package

source_name: pulmonary artery endothelial cells

label_protocol: 100 ng total RNA was amplified along with inline PolyA spike in control RNA, using the WT PLUS amplification kit (Affymetrix). Successfully amplified samples were labelled using the GeneChip WT terminal labelling kit (Affymetrix) Using the in line hybridization controls.

growth_protocol: PAECs were seeded in 6-well plates and grown in EGM-2 with 10% FBS to 90% confluency. Cells were then put into EGM-2 with 0.1% FBS for 16-18 hours before the treatments applied.

extract_protocol: Using RNeasy Mini Kit from Qiagen following manufacturer's instruction

treatment_protocol: All ligands (at a final growth factor domain concentration of 0.3 ng/ml ) were added to the serum-starved cells. The 6-well plates were returned into CO2 incubator at 37 C for 1.5 hours before cells were harvested for RNA extraction.

value: male

tag: agent


title: rgs7-1h-2

value: Conidia were inoculated onto rice leaves for 1 h


title: 24_Scc1-Control

tag: genotype


title: rgs7-1h-1


title: rgs7-1h-3


title: 23_Scc1-Control


title: rgs7-0h-3


title: rgs7-0h-2


title: 22_Scc1-Control


title: PBS treatment, PAEC line 3 [PBS_1p5_3]

tag: Sex


title: 21_Scc1-Control


title: PBS treatment, PAEC line 2 [PBS_1p5_2]


title: pro-BMP10 treatment, PAEC line 4 [pB10_1p5_4]

description: Gene expression data from PAEC treated with pro-BMP10 for 1.5 hours

value: PBS


title: pro-BMP9 treatment, PAEC line 2 [pB9G1_1p5_2]

description: Gene expression data from PAEC treated with pro-BMP9 for 1.5 hours


title: pro-BMP10 treatment, PAEC line 2 [pB10_1p5_2]


title: pro-BMP9 treatment, PAEC line 4 [pB9G1_1p5_4]


title: 19_Scc1-Control


title: 20_Scc1-Control


title: TSA

city: Fukui-shi

first: Fumito

last: Kanada

address: 3-9-1 Bunkyo

country: Japan

institute: Fukui univercity

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 45° for 5 minutes centrifuge at max speed for 1 minute. • Transfer 130μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0002

scan_protocol: Gene ChIP Scanner 3000 7G System

data_processing:
Data were processed using R. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
RaGene-2_0-st.pgf
RaGene-2_0-st.mps

source_name: Day4 lens, galactose, 0.8mM TSA added

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: The lens removed from the culture medium was ground with a biosmasher until it fell apart. Then treat the sample with TRIZOL, cDNA synthesis and amplification was performed

value: Sprague Dawley

value: 6 week old

value: lens

value: wild-type


title: rgs7-0h-1


title: pro-BMP9 treatment, PAEC line 3 [pB9G1_1p5_3]


title: rgs4-24h-3

value: {deleta}Morgs4 mutants


title: rgs4-24h-2


title: PBS treatment, PAEC line 1 [PBS_1p5_1]


title: pro-BMP10 treatment, PAEC line 1 [pB10_1p5_1]


title: pro-BMP9 treatment, PAEC line 1 [pB9G1_1p5_1]


title: 18_Scc1-Control


title: KU55933

source_name: Day4 lens, galactose, 10mM KU55933 added


title: GW843682X

source_name: Day4 lens, galactose, 1mM GW843682X added


title: pro-BMP10 treatment, PAEC line 3 [pB10_1p5_3]


title: rgs4-24h-1


title: 17_Scc1-Control

source_name: oocyte


title: rgs4-4h-3


title: 16_Scc1-Control


title: C646

source_name: Day4 lens, galactose, 40mM C646 added


title: rgs4-4h-2


title: 15_Scc1-Control


title: rgs4-4h-1


title: 14_Scc1-Control


title: rgs4-1h-3


title: 13_Scc1-Control


title: B.subtilis_t = 60_rep3

city: Amsterdam

first: Bhagyashree

last: Swarge

state: North Holland

address: Science park 908

country: Netherlands

institute: Swammerdam institute of life sciences, University of Amsterdam

hyb_protocol: Each hybridization mixture comprised 1.1 μg Test (Cy3) and 1.1 μg Reference (Cy5), a common reference pool of all samples. Microarrays were with the NimbleGen Hybridization System (Roche NimbleGen).

scan_protocol: Scanning was performed by NimbleScan v2.6 (Roche NimbleGen).

data_processing: For the raw data Log2 ratios were calculated for each feature and gene expression values were calculated using the median polish algorithm

organism: Bacillus subtilis

source_name: Bacillus subtilis wild type

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Purified spores were heat activated (HA) (70°C for 30 min) prior to germination. The spores were suspended at 4.5* 10˄10 spores/ml in MOPS liquid minimal medium (pH 7.4) supplemented with a mixture of AGFK (10mM L-asparagine, 10mM D-glucose, 1mM D-fructose, 1mM KCl) and 10mM L-alanine. Throughout the spore revival, samples were drawn at regular time intervals for further analysis

extract_protocol: Total RNA was extracted using the RNeasy MinElute Cleanup kit from Qiagen and DNA was removed by Turbo DNA-free kit (Ambion Inc., Applied Biosystems, USA). The purity and quantity of isolated RNA were checked spectrophotometrically on a NanoDrop spectrophotometer (ND-1000, Isogen Life Science, NL).

tag: development phase

value: burst


title: B.subtilis_t = 60_rep1

value: phase dark spore


title: rgs4-1h-2

value: Magnaporthe oryzae and rice leaves mixed sample


title: B.subtilis_t = 60_rep2


title: 12_Scc1-Control

extract_protocol:
snHi-C protocol according to Flyamer et al., 2017
The library preparation was done by the VBCF NGS unit (vbcf.ac.at) following the standard DNA sample preparation protocol.


title: B.subtilis_t = 150_rep2


title: B.subtilis_t = 30_rep3


title: B.subtilis_t = 330_rep1

value: vegetative cell


title: Galactose

source_name: Day4 lens, galactose, inhibitor free addition


title: B.subtilis_t = 30_rep4


title: rgs4-1h-1


title: rgs4-0h-3

value: Conidia were inoculated onto rice leaves for 0 h


title: Ctrl

source_name: Day4 lens, without galactose


title: 11_Scc1-Control


title: B.subtilis_t = 15_rep2


title: 10_Scc1-Control


title: B.subtilis_t = 15_rep1


title: B.subtilis_t = 30_rep2


title: 9_Scc1-Control


title: rgs4-0h-2


title: B.subtilis_t = 0_rep3


title: B.subtilis_t = 150_rep1


title: rgs4-0h-1


title: 8_Scc1-Control


title: rgs3-24h-3

value: {deleta}Morgs3 mutants

value: Conidia were inoculated onto rice leaves for 24 h


title: 7_Scc1-Control

value: oocyte


title: B.subtilis_t = 0_rep1


title: rgs3-24h-2


title: 6_Scc1-Control


title: rgs3-24h-1


title: C. lari 46°C Replicate 1

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
FastQ quality trimming: cut-off value of 20 (FastX package 0.0.13)
Fastq to fasta conversion (FastX package 0.0.13)
PolyA clipping  (READemption 0.3.4)
Size filtering: discarding reads shorter than 12 nt (READemption 0.3.4)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Coverage calculation and normalisation (READemption 0.3.4)
Genome_build: NC_012039.1, NC_012040.1
Supplementary_files_format_and_content: wiggle

organism: Campylobacter lari

source_name: bacteria

growth_protocol: Bacterial cultures were grown in Brucella Boullion under microaerobic conditions until treatment

extract_protocol:
Total RNA was extracted using a hot phenol/lysozyme method
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The RNA samples were poly(A)-tailed by using poly(A) polymerase. The 5'PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR- amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics, Essex, UK) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina (San Diego, CA).

treatment_protocol: bacterial cultures were cultivated for 30 min at indicated temperatures before RNA extraction

tag: treatment

value: Heat shock 46°C


title: B.subtilis_t = 0_rep2


title: C. lari 37°C Replicate 2

value: control at 37°C


title: C. lari 37°C Replicate 1


title: 5_Scc1-Control


title: rgs3-4h-3

value: Conidia were inoculated onto rice leaves for 4 h


title: B.subtilis_t = -15_rep2

value: phase bright spore


title: B.subtilis_t = -15_rep3


title: rgs3-4h-2


title: B.subtilis_t = -15_rep1


title: C. lari 46°C Replicate 2


title: C. coli 46°C Replicate 1

organism: Campylobacter coli


title: 3_Scc1-Control


title: 4_Scc1-Control


title: C. coli 37°C Replicate 2


title: C. coli 46°C Replicate 2


title: C. coli 37°C Replicate 1


title: rgs3-1h-3

value: Conidia were inoculated onto rice leaves for 1 h


title: B.subtilis_t = 330_rep3


title: B.subtilis_t = 330_rep2


title: rgs3-4h-1


title: B.subtilis_t = -30_rep3


title: 1_Scc1-Control


title: Tbr1 Layer 5 Homozygous (Tbr1f/f::Rbp4cre::tdTomato)

city: San Francisco

first: Siavash

last: Fazel Darbandi

address: 1550 4th Street

department: Psychiatry

institute: University of California San Francisco

data_processing:
The alignment, UMI counting, barcode counting, and read quality  metrics were generated using cellranger 2.0.1 with default paramters, lane 1 and 2 for each sample were processed together.
Cells with greater than 30% of mitochondrial genes were removed. Cells with fewer than 500 or more than 10,000 unique-molecular-identifier (UMI) counts were removed. Cells with fewer than 500 or more than 3,000 genes were removed. Genes which occurred in less than 0.01% of cells were removed. There were a remaining 17,396 cells and 14,933 genes.
The raw data from the identified neuronal clusters was retained and filtered again based on the distribution of UMI counts ( < 4000) and the number of genes per cell (> 500 & <1700). Mitochondrial genes, ribosomal genes, pseudogenes, genes that did not occur in 1% of neuronal cells, and genes with a variation below  the median variation across all genes were removed. There were a remaining 7,174 genes and 11943 cells, 11070  of which were used in DEX analysis.
Genome_build: mm10
Supplementary_files_format_and_content: raw gene bc matrices

source_name: P5 Medial Prefrontal Cortex

extract_protocol:
Cells were dissociated using papain dissociation kit and FACS purified using endogenous tdTomato.
scRNA-seq libraries were generated using 10X Genomics single cell RNA-seq kit following manufacturer’s protocol. Libraries were sequenced on Illumina HiSeq 4000 using PE100 strategy.

tag: developmental stage

value: Postnatal Day 5 (P5)


title: PHBA4_R [root, RNA-Seq]

first: Chen

last: Jishuang

state: Jiangsu

address: NO.30 Puzhu Road(S)

department: College of Biotechnology and Pharmaceutical Engineering

institute: Nanjing Tech University

data_processing:
The clean reads were assembled using Trinity (version 2.4.0) with min_kmer_cov set to 5 and other parameters to default values.
All possible open reading frames within the assembled transcripts were extracted using TransDecoder (https://github.com/TransDecoder). Transcripts lacking a likely CDS were discarded and all predicted CDS sequences were translated into protein sequences and clustered by CD-HIT (version 4.6.6) with 95 % global sequence identity. Only the unique transcript with CDS sequence was designated as a unigene.The longest sequence in each cluster was transferred to the final data set.
The translated protein sequences of all ORFs were annotated by performing BLAST searches against the NCBI non-redundant protein database (NR), Swiss-Prot, Gene Ontology (GO), Kyoto Encyclopedia of Unigenes and Genomes (KEGG), eggNOG and protein family (PFAM) databases with e-value threshold set to 1e-5
processed data files format and content: FPKM

organism: Populus x canadensis

source_name: the roots samples with treatment uner para-hydroxybenzoic acid concentration of 4 mML-1

growth_protocol: Cuttings with a length of approximately 20 cm and a diameter of approximately 2 cm were collected from the middle and lower parts of 1-year-old healthy branches of Populus × euramericana “Neva.” Subsequently, the cuttings were planted in conical flasks under water culture and controlled conditions (25°C during daytime and 20°C during the night, 12-h photoperiod) in a light incubator. Following the appearance of roots, the cuttings were transferred to half-strength Hoagland’s nutrient solution.

extract_protocol:
All samples were frozen in liquid nitrogen and stored at –80°C. Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s instructions. DNase I (TaKaRa, Dalian, China) was used to treat RNA samples to avoid genomic DNA contamination. The quantity and purity of the total RNA was measured with a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) (RIN number >7.0). Equal parts of RNA samples for the same treatment were mixed for transcriptome sequencing and sRNA sequencing. Subsequently, the total mixed RNA sample for leaves was prepared for degradome sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treatment was carried out on 60-day water-cultured plants, which were treated with pHBA solutions in different concentrations (0, 2, 4mML-1) for three days. Subsequently, the roots were sampled under pHBA concentrations of 0 mML-1(L1), 2 mML-1 (L2) and 4 mML-1(L4).

value: root


title: PHBA0_R [root, miRNA-Seq]

data_processing:
Illumina bcl2fastq v1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then detected miRNA using miRDeep2 v2_0_0_8; mapper.pl with parameters -d -c -i -j -l 18 -m,miRDeep2.pl with default parameter
miRNA expression were calcuated using quantifier.pl from miRDeep2 v2_0_0_8 with parameters, then differential analysis using R package Ballgown
Genome_build: NCBI Aradu1.0 and Araip1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: the roots samples without treatment under para-hydroxybenzoic acid


title: PHBA4_R [root, miRNA-Seq]

source_name: the roots samples with treatment under para-hydroxybenzoic acid concentration of 4 mML-1


title: rgs3-0h-3


title: PHBA2_L [leaf, miRNA-Seq]

source_name: the leaves samples with treatment under para-hydroxybenzoic acid concentration of 2 mML-1

treatment_protocol: Treatment was carried out on 90-day water-cultured plants, which were treated with pHBA solutions in different concentrations (0, 2, 4, or 8 mML-1) for three days. Subsequently, the leaves were sampled under pHBA concentrations of 0 mML-1(L1), 2 mML-1 (L2), 4 mML-1(L4), and 8 mML-1(L8).

value: leaf


title: PHBA0_L [leaf, miRNA-Seq]

source_name: the leaves samples without treatment under para-hydroxybenzoic acid


title: 2_Scc1-Control

data_processing:
Base calling was performed by VBCF NGS unit
Mapping: iterative mapping (see Imakaev et al, 2012) using bwa
Read filtering was performed as in Flyamer et al., 2017:
Summary of filtering: If two reads map to the same strand, and each side of the read is within 500 bp of any side of the other read, we retain only one copy of the read. We separate the genome into 500 bp bins. If any two bins are interacting more than once, only one interaction is counted. Since each region is only present in the single cell up to 4 times (in oocytes), we eliminated all 500 bp bins that form more than 8 unique interactions with other bins.
Filtered reads were then binned at different resolutions (we provide 4 resolutions) using read start as a read position and stored in the Cool file format. No normalization was applied to the data.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of whole-genome locus interaction frequencies binned at 1kb, 10kb, 40kb, and 100kb resolutions stored in the Cool file format.


title: B.subtilis_t = -30_rep2


title: Wildtype (Rbp4cre::tdTomato)


title: rgs3-0h-2


title: PHBA2_R [root, miRNA-Seq]

source_name: the roots samples with treatment under para-hydroxybenzoic acid concentration of 2 mML-1


title: B.subtilis_t = -30_rep1


title: rgs3-1h-1


title: PHBA2_R [root, RNA-Seq]

source_name: the roots samples with treatment uner para-hydroxybenzoic acid concentration of 2 mML-1


title: PHBA8_L [leaf, RNA-Seq]

source_name: the leaves samples with treatment under para-hydroxybenzoic acid concentration of 8 mML-1


title: PHBA0_R [root, RNA-Seq]


title: PHBA8_L [leaf, miRNA-Seq]

value: para-hydroxybenzoic acid concentration of 8 mML-1


title: rgs3-1h-2


title: Day 0 miR-206 xOP replicate A

city: Boulder

first: Jennifer

last: Kugel

address: 3415 Colorado Ave

institute: University of Colorado Boulder

data_processing:
Library strategy: miRNA pulldown
Read quality was assessed using FastQC.
Reads were mapped to the mm10 genome using Bowtie2 (version 2.3.2) in the -D 5 -R 1 -N 0 -L 25 -i S,1,2.00 alignment mode plus trimming 10 bps of the 3' end where read quality decreased.
Meta-analyses and per-gene quantificatin of mapped reads were performed using the suite of tools available in HOMER and in Bedtools (v2.26.0). Tag directories in HOMER were created from the sam files generated by Bowtie2. To allow visualization of the mapped reads in the UCSC Genome Browser, bedGraph files were generated using the makeUCSCfile command in HOMER.
The bedtools intersect command in Bedtools was used to identify RefSeq genes that contained a miR-206 6mer seed (5'-CCTTAC-3') in their 3'UTR. The tag directories created in HOMER were converted to bed files using the tagDir2bed command in HOMER. The bedtools coverage command in Bedtools was used to count RNA sequence tags across 3'UTRs of genes that contained a miR-206 6mer seed.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files generated using the default makeUCSCfile command in HOMER

source_name: myoblast

growth_protocol: C2C12 myoblast cells were cultured in 5% CO2 at 37°C and maintained at ~70% confluency in DMEM supplemented with 20% FBS, 1% penicillin-streptomycin, 1% sodium pyruvate, and 1% L-glutamate (growth media). Differentiation was induced by culturing cells in differentiation media (DMEM supplemented with 5% horse serum, 1% penicillin-streptomycin, 1% sodium pyruvate, and 1% L-glutamate).

extract_protocol:
Cyotplasmic extracts were made, miR-206-containing complexes were captured usign a biotinylated DNA oligo antisense to miR-206, and complexes were purified on neutravidin beads. After extensive washing, the crosslinks were reversed, and mRNAs that co-purified were prepared for sequencing.
Libraries were prepared using a custom 3' end protocol. Libraries were sequenced on an Illumina HiSEQ 4000

treatment_protocol: After 48 hours in growth media, cells were either crosslinked and harvested (undifferentiated/Day 0) or switched to differentiation media for 96 hours before crosslinking and harvesting (Day 4 differentiated). For each condition in duplicate, cells were crosslinked with 1% formaldehyde for 10 minutes prior to harvest for miR-206 pulldown.

tag: cell line

tag: dna antisense oligo tag

value: undifferentiated(UN)/Day 0


title: PHBA4_L [leaf, miRNA-Seq]

source_name: the leaves samples with treatment under para-hydroxybenzoic acid concentration of 4 mML-1


title: Day 0 miR-206 xOP replicate B


title: Tbr1 Layer 5 Heterozygous (Tbr1f/+::Rbp4cre::tdTomato)


title: Day 4 miR-206 xOP replicate B

value: Day 4 differentiated (D4DM)/Day 4


title: PHBA4_L [leaf, RNA-Seq]

value: para-hydroxybenzoic acid concentration of 4 mML-1


title: hMSCs nSi rep 1

city: Bryan

first: Irtisha

last: Singh

state: TX

address: 8447 Riverside Pkwy Medical Research and Education Building II

institute: Texas A&M Health Science Center

description: rpkm.txt

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all samples

source_name: Mesenchymal stem cells

growth_protocol: Two-Dimensional seeded hMSC cells were cultured in normal media conditions until 65% confluency, then exposed to 50 μg/mL Laponite XLG nanosilicates for 48 h. Cells were then cultured in osteocondictive media for 21 days. Control cells were cultured in osteocondictive media for 21 days in absence of nanosilicates.

extract_protocol:
At the end of 21 days of culture, total RNA was extracted (High Pure RNA Isolation, Roche Life Sciences), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: hMSCs (2500 cell/cm2) were exposed to nanosilicates (50 μg/mL)

tag: cell type

value: Bone marrow derived mesenchymal stem cells

value: nSi treatment


title: rgs1-24h-2

value: Magnaporthe oryzae and rice leaves mixed sample

value: {deleta}Morgs1 mutants


title: PHBA0_L [leaf, RNA-Seq]


title: T-DM1-refractory NCI-N87 tumor

city: Tsukuba

first: Hiroki

last: Irie

state: Ibaraki

address: Okubo 3

institute: Taiho Pharmaceutical Co., Ltd.

data_processing:
Basecalls performed using bcl2fastq2 v2.20.
Sequenced read were mapped to both human GRCh38 and mouse GRCm38, using STAR 2.7.0e software, with gene annotation files from Illumina iGenomes.
Mouse-derived reads were removed from the fastq files using R package XenofilteR version 1.6.
The filtered reads were mapped to the human transcriptome and estimated read counts were calculated using RSEM v1.2.28 software.
Gene expression fold changes and p-values were calculated using R package edgeR version 3.26.8.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file includes read counts and FPKM values for each sample, and fold changes and p-values.

source_name: mouse xenograft

growth_protocol: The cells were cultured in a CO2 incubator set at 37°C, 5% CO2, and passaged once a week or twice a week. The cell suspension was implanted subcutaneously in the vicinity of the right hindmost rib of nude mice.

extract_protocol:
Total RNA was extracted from the NCI-N87 tumor using NucleoSpin®RNA
Libraries were prepared accroding to TruSeq Standaded mRNA Reference Gide v00.

treatment_protocol: T-DM1 was administered into the nude mice bearing NCI-N87 tumor once every three weeks for 18 weeks.

value: xenograft tumor


title: rgs3-0h-1

value: {deleta}Morgs3 mutants

value: Conidia were inoculated onto rice leaves for 0 h


title: Day 4 miR-206 xOP replicate A


title: hMSCs nSi rep 2

description: rpkm.txt


title: PHBA2_L [leaf, RNA-Seq]

value: para-hydroxybenzoic acid concentration of 2 mML-1


title: No-treatment NCI-N87 tumor

value: no treatment


title: rgs1-24h-3

value: Conidia were inoculated onto rice leaves for 24 h


title: ATACseq_day10_3

city: Stanford

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

description: Retinoic-acid induction

data_processing:
RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using SRAR.
RNA-seq: Fregments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using RSEM.
ATAC-seq: Reads are mapped to mm9 by ATAC-seq pipeline described in https://www.encodeproject.org/atac-seq/.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include openess values for each Sample on union peaks

source_name: mouse embryonic stem cell

growth_protocol: mESC cells R1 were grown in mESC medium supplemented with 15% Knockout Serum Replacement and 1,000 U/ml of LIF. mESCs were differentiated using the handing drop method for 48 hours. Then, embryoid bodies (EBs) were collected for further treatment.

extract_protocol:
Total RNA were extracted using Qiagen RNeasy mini kit.
RNA-seq library were constructed using the NEBNext Ultra RNA Library Prep kit for Illumina. ATAC-seq library were constructed using Tn5 transposase, followed by PCR amplification.

treatment_protocol: EBs were placed in the well of a 6-well ultra-low attachment plate with fresh differentiation medium containing 0.5 mM retinoic acid (RA) for up to 20 days, with the medium being changed daily.

tag: time point


title: rgs1-4h-3

value: Conidia were inoculated onto rice leaves for 4 h


title: rgs1-24h-1


title: hMSCs rep  2

description: rpkm.txt

value: Control


title: hMSCs rep 1

description: rpkm.txt


title: ATACseq_day10_4

description: Retinoic-acid induction


title: PC3-siKHDRBS3-rep2

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

description:
growth condition: RPMI1640+FBS
Sample8

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.5.2).
The number of fragments in each known gene from GENCODE (version 25) was enumerated using STAR QuantMode (GeneCounts) function.
The normalized fragment count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq2) for all the samples.

growth_protocol: Early passages of PC3 cells (obtained from ATCC) were grown in RPMI1640 medium supplemented with 7% serum.

extract_protocol:
PC3 cells treated with siRNAs for 8-10hrs in vitro and RNA harvested 48-72hrs after transfection by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell cultures (~75% confluence) were transfected with siRNAs at 20nM for 8-10 hrs in Opti-MEM, then cultured in normal medium for 48-72 hrs before RNA isolation.

value: Prostate cancer cell line

tag: sirna treatment

tag: ar status

value: AR-


title: PC3-siES+KHD-rep2

description:
growth condition: RPMI1640+FBS
Sample11

value: siESRP1 + siKHDRBS3


title: ATACseq_day10_2

description: Retinoic-acid induction


title: PC3-siKHDRBS3-rep1

description:
growth condition: RPMI1640+FBS
Sample7


title: PC3-siKHDRBS3-rep3

description:
growth condition: RPMI1640+FBS
Sample9


title: PC3-siESRP1-rep2

description:
growth condition: RPMI1640+FBS
Sample5


title: RNAseq_day10_5

description: Retinoic-acid induction


title: rgs1-4h-2


title: PC3-siESRP1-rep3

description:
growth condition: RPMI1640+FBS
Sample6


title: ATACseq_day10_1

description: Retinoic-acid induction


title: rgs1-1h-2

value: Conidia were inoculated onto rice leaves for 1 h


title: PC3-siESRP1-rep1

description:
growth condition: RPMI1640+FBS
Sample4


title: rgs1-4h-1


title: rgs1-1h-3


title: PC3-siES+KHD-rep1

description:
growth condition: RPMI1640+FBS
Sample10


title: PC3-siNC-rep3

description:
growth condition: RPMI1640+FBS
Sample3

value: negative control


title: PC3-siES+KHD-rep3

description:
growth condition: RPMI1640+FBS
Sample12


title: rgs1-1h-1


title: RNAseq_day10_4

description: Retinoic-acid induction


title: RNAseq_day10_3

description: Retinoic-acid induction


title: RNAseq_day10_2

description: Retinoic-acid induction


title: RNAseq_day10_1

description: Retinoic-acid induction