title: MEFs- Chrysin treated - replica 4

city: Downers Grove

first: Prasanth

last: Puthanveetil

address: 555, 31st Street

department: Pharmacology

institute: Midwestern University

description:
Media+ Chrysin - 50 µM
Sample 12- C4

data_processing:
Rosalind™ RNA-seq Methods
This was provided by our service provider - Omegabioservices, GA, USA.  Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Mus musculus genome build mm9 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5. Read Distribution percentages,identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC6. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library7. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library8, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro9, NCBI10, MSigDB11,12, REACTOME13, WikiPathways14. Enrichment was calculated relative to a set of background genes relevant for the experiment. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER15.
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA). Reads were trimmed using cutadapt1. Quality scores were assessed using FastQC2. Reads were aligned to the Mus musculus genome build mm9 using STAR3. Individual sample reads were quantified using HTseq4 and normalized via Relative Log Expression (RLE) using DESeq2 R library5. Read Distribution percentages,identity heatmaps, and sample MDS plots were generated as part of the QC step using RSeQC6. DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction. Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library7. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library8, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro9, NCBI10, MSigDB11,12, REACTOME13, WikiPathways14. Enrichment was calculated relative to a set of background genes relevant for the experiment. Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER15.
The references as provided by the service provider (Omega bioservices) are as follows;  1.       Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10–12 (2011).  2.       Andrews, S. FastQC: a quality control tool for high throughput sequence data. (2010).  3.       Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).  4.       Anders, S., Pyl, P. T. & Huber, W. HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).  5.       Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).  6.       Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184–2185 (2012).  7.       Hennig, C. Cran-package fpc. https://cran.r-project.org/web/packages/fpc/index.html  8.       Alexa A, Rahnenfuhrer J. topGO: Enrichment Analysis for Gene Ontology. R package version 1.38.1 (2019).  9.       Mitchell, A. et al. InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research 47, D351–D360 (2019).  10.    Geer, LY. et al. The NCBI BioSystems database. Nucleic Acids Research 38, D492–D496 (2009).  11.    Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. PNAS 43, 15545-15550 (2005).  12.    Liberzon, A. et al. Molecular signatures database (MSigDB) 3.0. Bioinformatics 43, 1739-1740 (2011).  13.    Fabregat, A. et al. The Reactome Pathway Knowledgebase. Nucleic Acids Research 46, D649-D655 (2018).  14.    Slenter, D. et al. WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research. Nucleic Acids Research 46, D661-D667 (2017).  15.   Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell. 38, 576-589 (2010).
Supplementary_files_format_and_content: R087ONBOW19_normalizedExpression with fold calculation based on raw data- Puthanveetil.xlsx
Genome_build: mm9
Supplementary_files_format_and_content: Expressed as Log 2

source_name: Mouse Embryonic Fibroblasts

growth_protocol: MEFs were plated in T75 flasks and passaged upto 5th, beyond which the growth and proliferation is retarded.

extract_protocol:
mRNA wwas isolated using PureLink™ RNA Mini Kit from Thermofisher (Cat# 12183018A) as prescribed by the protocol and RiboLock RNase Inhibitor (40 U/µL)-Cat # EO0381 added to preserve the samples
RNA sequencing libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc., San Diego, CA, USA) according to the manufacturer`s protocol
Stranded mRNA(TruSeq Stranded mRNA Library Prep Kit)

treatment_protocol: Treatments with control media, or Apigenin 50 µM or Chrysin 50 µM were treated for 24 hours

value: Chrysin - 50 microM

value: Embryonic

tag: time point

value: Treated for 24 hours


title: Input_HIV_rep2

status: Public on Aug 09 2021

type: SRA

city: La jolla

first: Qiong

last: Zhang

state: California

address: 9500 Gilman Dr.

department: Pediatrics

country: USA

institute: UCSD

library_source: transcriptomic

data_processing:
Library strategy: m6Am-exo-seq
Fastqc was used to perform quality control on sequencing data.
cutadapt was applied to remove adapters and trim reads.
The pre-processed reads were aligned to human genome (built on Release 31 (GRCh38.p12) gencode) by STAR
MACS2(q value: 0.05, call-summit mode) was used based on its paired IP/input data.
To generate the peak distribution across chromosome region, including intron, CDS, intergenic region) and across gene region (3’UTR, 5’UTR and CDS) RSeQC and Guitar Plot were applied. The gene annotation used here is from GENCODE. For further m6Am peak analysis, we extracted common peaks whose summit is in the 5’UTR region.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: bigwig
Supplementary_files_format_and_content: m6Am genes with decreased peak density.xlsx
Supplementary_files_format_and_content: peak distribution.xls

molecule: polyA RNA

organism: Homo sapiens

source_name: Jurkat cells

growth_protocol: Jurkat cells were cultured in RPMI containing 10% fetal bovine serum (FBS) and 50 µM β-mercaptoethanol (Sigma).

extract_protocol:
Total RNA was extracted using TRIzol. About 100mg RNA were then used to isolate poly(A) RNA using two rounds of oligo25 Dynabeads capture.
For one sample, 100 μg poly(A) RNA was fragmented in fragmenting buffer at 70°C for 15min. Fragmentation is stopped by the addition of EDTA to a final concentration of 70 mM. mRNA is purified  with the RNA Clean and Concentrator 5 kit (Zymo Research). Uncapped and fragmented transcripts are phosphorylated by treating the mRNA with 200 U of T4 PNK (NEB) in T4 ligase buffer for 1:30 h at  37°C. Then, 20 U of Terminator 5'-Phosphate-Dependent Exonuclease (Lucigen) is added with 1X Exonuclease buffer A. Samples are treated for 3 h at 30°C to remove phosphorylated (ie. uncapped and sheared) transcripts. The RNA enriched for 5'-capped transcripts is purified with the RNA clean and concentrator 5 kit (Zymo Research). 30 U of Cap-Clip (CellScript) are added and incubated for 2 h at 37°C in CAP-CLIP buffer to remove the cap. RNA is again purified with the RNA clean and Concentrator 5 kit. 10% of the treated RNA is saved as input, the rest is diluted and incubated with 5 μg of anti-m6A antibody (abcam, ab151230) at 4 °C for 2 h. 100 μl protein G magnetic beads were added to pull down the m6A immunoprecipitation complex. After wash for three times, the bound RNA was eluted in 100 μl elution buffer and purified using RNA clean and concentrator-5 kit. Final libraries amplified and were subjected to paired-end sequencing in the HT sequencing IGM Genomics core, UCSD.

treatment_protocol: 100 million control or PCIF1 KO Jurkat cells were mock treated or infected with HIV LAI strain at an MOI of 4 for 3 days.

tag: cell line

value: T cell line

tag: genotype

value: control

tag: agent

value: HIV


title: AAb_6267

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

data_processing:
Quality control performed with fastqc and trimmomatic.
Reads mapped to human genome reference using Bowtie2.
Gene expression quantified with RSEM.
A multi-dimensional scaling (MDS) plot was used to detect outlier samples before differential gene expression analysis.
Empirical Bayes techniques were implemented using limma voom in R to identify differentially expressed genes between donor groups.
Network analysis and functional enrichment were performed using Ingenuity Pathway Analysis (IPA) software.
Genome_build: hg38
Supplementary_files_format_and_content: RNAseq-counts.xlsx: Excel table containing raw counts for all genes in all samples.
Supplementary_files_format_and_content: AAb-ND_core_analysis.xls: Results of IPA (pathway) analysis on differentially expressed genes in Aab vs ND
Supplementary_files_format_and_content: AAb-T1D_core_analysis.xls: Results of IPA (pathway) analysis on differentially expressed genes in Aab vs T1D

source_name: laser microdissected islets

extract_protocol:
PicoPure RNA extraction kit (Thermofisher Scientific, cat# 12204-01) with genomic DNA removal using recombinant DNAse1 (Worthington Biochemical Corporation, cat# LS006361)
Agilent 2100 Bioanalyzer (Picotape, Agilent Technologies)
A sample of 6 ng RNA was used to extract mRNA with 15μl of NEBNext Magnetic Oligo d(T) and fragmented in NEBNext First Strand Synthesis Buffer by heating at 94°C for 8 minutes in a 96-well plate. First strand cDNA synthesis was performed using reverse transcriptase and random primers. Synthesis of double-stranded (ds) cDNA was performed using the second strand master mix provided in the kit. The resulting ds cDNA was end-repaired, dA-tailed, and ligated with NEBNext adaptors. The library was enriched by PCR amplification and purified by Agencourt AMPure beads (Beckman Coulter). Barcoded libraries were sized on the Bioanalyzer and quantitated by QUBIT. The library's functionality was validated by quantitative reverse transcription PCR (qRT-PCR), using the KAPA library quantification kit (Kapa Biosystems).

tag: tissue

value: laser microdissected islets

tag: disease state

value: non-diabetic islet autoantibody-positive individuals

tag: biorep


title: TAM 276

city: Madrid

first: Rafael

last: Samaniego

address: Calle Dr Esquerdo 46

country: Spain

institute: Fundación para la Investigación Biomédica del Hospital Gregorio Marañón

data_processing:
DNBseq platform
Low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) were filtered to get the clean reads. Sequences were mapped to GRCh38 genome using  Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene ID and FPKM values for each sample

molecule: total RNA

source_name: Macrophages isolated from human melanoma

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from three healthy donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal calf serum (FCS).

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA purification kit from Macherey-Nagel
RNA libraries were prepared for sequencing using standard BGI protocols

tag: cell type

value: Tumor Associated Macrophages CD14+

value: Skin melanoma


title: Input_PCIF1 KO_rep1

value: PCIF1 KO


title: MEFs- Chrysin treated - replica 3

description:
Media+ Chrysin - 50 µM
Sample 11- C3

organism: Mus musculus

tag: developmental stage


title: HH_GN2

city: Jinan

first: Huawei

last: Li

address: North Industry Road

country: China

institute: Crop Research Institute, Shandong Academy of Agricultural Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
A cDNA library constructed by technology from the pooled RNA  was sequenced run with Illumina sequence platform. Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT package.
The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes from Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
Genome_build: Triticum aestivum release36_Ensembl
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Triticum aestivum

source_name: grains

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA is purified from total RNA(5ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing ( 2 x 150 bp) on an Illumina Hiseq 4000 at the (LC Sceiences,USA) following the vendor’s recommended protocol.

value: grain filling stage

value: grains

tag: treatment

value: Take off half of the head of wheat


title: Input_control_rep1


title: MEFs- Chrysin treated - replica 2

description:
Media+ Chrysin - 50 µM
Sample 10- C2


title: MEFs- Apigenin treated - replica 4

description:
Media+ Apigenin - 50 µM
Sample 8 - B4

value: Apigenin - 50 microM


title: Input_control_rep2


title: 4OHT_3

city: Southampton

first: Yihua

last: Wang

address: University Road

country: United Kingdom

institute: University of Southampton

data_processing:
Quality control of RNA-seq raw paired data was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) and MultiQC
Trim Galore (https://github.com/FelixKrueger/TrimGalore) was used to trim adapters, reads with low quality (< 30), and short length (< 50 bp).
RNA-seq reads were mapped to Human genome Ensembl GRCh38 using Hisat2 (version 2.1.0) with default code
read counts of each gene were summarized using featureCounts (version 1.6.5)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MRC5 cells

growth_protocol: MRC5 lung fibroblasts were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% foetal bovine serum (FBS), 50 units/ml penicillin, 50μg/ml streptomycin, 2mM L-glutamine, 1mM sodium pyruvate and 1x non-essential amino acids (DMEM/FBS) (all from Life Technologies).

extract_protocol:
A total amount of 3 μg RNA per sample was used as input material for library construction. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, Ipswich, Massachusetts, USA) following manufacturer’s instruction
Libraries were pooled in equimolar and sequenced using the paired-end strategy (2 × 150) on the Illumina NovaSeq 6000 platform following the standard protocols

treatment_protocol: MRC5 lung fibroblasts were treated with conditioned media collected from control or 4-OHT-treated ATIIER:KRASV12 cells for 24 hours.

value: MRC5 cells

value: fibroblasts

value: Treated (4-OHT group)


title: CK_GN3

value: Normal growing plants


title: CK_LF1

source_name: flag leaf

value: leaf


title: MEFs- Apigenin treated - replica 3

description:
Media+ Apigenin - 50 µM
Sample 7 - B3

value: Embryonic

value: Treated for 24 hours


title: MEFs- Chrysin treated - replica 1

description:
Media+ Chrysin - 50 µM
Sample 9 - C1

value: Chrysin - 50 microM


title: MCF-7_control RAC1_ChIPSeq rep2

city: Miami

first: Jun

last: Sun

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

description:
RAC1_ChIPSeq rep2
MCF-7_control

library_source: genomic

data_processing:
Base calling using Illumina BCL2fastq v2.19.0.316
Trimmed fastq files with cutadapt v.1.18  --a AGATCGGAAGAGCACACGTC -m 30
Aligned to the hg19 genome assembly using bowtie2 2.2.6 with the default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: bw file was generated by deeptools 3.1.1 that was normalized to CPM.

molecule: genomic DNA

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured with 5% FBS in IMEM. MDA-MB-231 cells were cultured with 10% FBS in DMEM.

extract_protocol:
Cells were fixed in 1% formaldehyde for 15 min at RT. Sonicated nuclear lysates were used in immunoprecipitation with a target antibody.
Libraries were prepared using NEBNext UltraII DNA library Kit for Illumina (E7645).

treatment_protocol: MCF-7 cells were switched to IMEM containing 5% charcoal-treated FBS for 3 days before treating the cells for 45 min with 10 nM E2, 50 µM EHT 1864 or combination.

value: Breast cancer cell line

tag: chip antibody

value: Rac1 (Millipore, 05-389)

value: control


title: 4OHT_2


title: CK_GN2


title: CK_LF2


title: MCF-7_E2-EHT ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MCF-7_E2-EHT

value: ER (Santa Cruz, sc543)


title: MCF-7_EHT ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MCF-7_EHT


title: 4OHT_1


title: MCF-7_E2 ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MCF-7_E2

value: 10 nM E2


title: MCF-7_E2-EHT ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MCF-7_E2-EHT


title: CH_GN3

value: grain filling stage

value: Shade the heads and remove all the leaves of wheat


title: HH_GN1

value: grains

value: Take off half of the head of wheat


title: CK_LF3


title: MEFs- Apigenin treated - replica 1

description:
Media+ Apigenin - 50 µM
Sample 5 - B1

value: Apigenin - 50 microM


title: Control_1

value: MRC5 cells

value: fibroblasts

value: Control group


title: CH_GN2


title: MCF-7_control ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MCF-7_control


title: MEFs-untreated - replica 2

description:
Control media
Sample 2- A2

value: Untreated


title: MCF-7_EHT ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MCF-7_EHT


title: MCF-7_control RAC1_ChIPSeq rep1

description:
RAC1_ChIPSeq rep1
MCF-7_control


title: MEFs- Apigenin treated - replica 2

description:
Media+ Apigenin - 50 µM
Sample 6 - B2

value: Embryonic


title: MEFs-untreated - replica 1

description:
Control media
Sample 1- A1

value: Treated for 24 hours


title: Bab RNA_30pg

status: Public on Aug 08 2021

type: RNA

city: San Antonio

first: Elizabeth

last: Gould

state: Texas

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center San Antonio

description:
Positive control
RNA

data_processing:
The GE Flex Six Fast PCR+Melt v1 program was used to collect the cycle threshold (CT) values
CT values were converted to mRNA levels using 2^(25-CT)

label: Eva Green

organism: Papio anubis

source_name: Cerebellum slice

label_protocol:
Single-cell qRT-PCR was carried out using Cells DirectTM one-step RT-PCR kit (cat #11753–100, Invitrogen)
Target genes were amplified using a BioMark HB MX/HX system with 1X SsoFast Eva-Green supermix with low ROX (cat #PN172-5211, Bio-Rad, Hercules, CA) and 1X DNA binding dye sample loading reagent (cat #PN 100-3738, Fluidigm).

extract_protocol: Cells were collected after electrophysiological recordings

value: Tissue

tag: physiology


title: MouUni RNA

description:
Negative control
RNA


title: NTC

description:
Negative control
No template

organism: synthetic construct


title: MEFs-untreated - replica 3

description:
Control media
Sample 3- A3


title: 6-19_2

description:
Spiking
Spiking

value: Oligodendrocyte

value: Spiking


title: 6-18_5

description:
Spiking
Spiking


title: 6-18_4

description:
Spiking
Spiking


title: MEFs-untreated - replica 4

description:
Control media
Sample 4- A4


title: CK_GN1

value: Normal growing plants


title: Control_2


title: 6-18_2

description:
Non-spiking
Non-spiking

value: Non-spiking


title: 6-18_1

description:
Non-spiking
Non-spiking


title: MCF-7_E2 ER_ChIPSeq rep2

description:
ER_ChIPSeq rep2
MCF-7_E2

value: Breast cancer cell line

value: ER (Santa Cruz, sc543)

value: 10 nM E2


title: Control_3


title: CH_GN1

value: grain filling stage

value: grains

value: Shade the heads and remove all the leaves of wheat


title: RB281

city: New York

first: Weijia

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads of the COVID-19 biopsy sample with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using STAR alignment algorithm. After filtering reads mapped to contamination database, the reads that were uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: kidney

extract_protocol:
RNA was extracted from frozen kidney biopsy tissue using a Qiagen miRNeasy Mini Kit (217004) and eluted in water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease


title: Sample 30 (s30)_T2 ∆cebR rep C

city: Liège

first: Sinaeda

last: Anderssen

address: Allée du six aout

country: Belgium

institute: Université de Liège

data_processing:
Basecalling : Real-Time Analysis v2.11.3 (integrated in Nextseq Control Software (NCS))
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic with parameters: LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 CROP:100 MINLEN:30
Read mapping on reference genome with Bowtie2 (v2.3.5.1) with standard parameters
Mapped reads are counted for each feature (transcript) with FeatureCounts (v1.6.4)
Genome_build: GCF_000091305.1_ASM9130v1
Supplementary_files_format_and_content: Matrix table with raw transcript counts for every gene and every sample

organism: Streptomyces scabiei

source_name: Mycelium pellet from liquid culture

growth_protocol: Pre-culture in liquid ISP2 (50 mL in 250-mL erlenmeyer flasks with 10 mL glass beads) inoculated with 4*10^7 spores, incubated for 24 hours at 28°C shaking at 180rpm. Washing twice in TDM or ISP2 and put in culture at 16 mg(wet biomass)/mL (see medium conditions in the Samples section) with the same culture parameters and in 100-mL erlenmeyers flasks containing 5 mL glass beads and 25 mL of medium

extract_protocol:
Total RNA were harvested using the RiboPure™ Bacteria RNA Purification Kit (Invitrogen)
Library preparation was carried out in combination with Ribosomal RNA depletion using the Ovation Complete Prokariotic RNAseq kit (NuGEN)
RNA-Seq (NextSeq® 500 System (Illumina) HM 2X75 bp read length with 7 million reads per library)

treatment_protocol: Centrifugation of 2.5-mL samples (5 minutes, 3500xg, room temperature) and removal of the supernatant + flash freezing in liquid nitrogen and freezing at -70°C until extraction

tag: strain

value: 87-22 - {delta}cebR mutant

tag: culture medium

value: International Streptomyces Project 2

tag: inducer

value: Not applicable

tag: incubation time (hours)


title: Sample 28 (s28)_T2 ∆cebR rep A


title: Sample 23 (s23)_T1 ∆cebR rep B


title: Bab RNA_300pg

description:
Positive control
RNA


title: 6-21_1

description:
Spiking
Spiking


title: Sample 29 (s29)_T2 ∆cebR rep B


title: Sample 27 (s27)_T2 WT rep C

value: 87-22 (Wild-type)


title: 6-18_3

description:
Non-spiking
Non-spiking


title: Sample 21 (s21)_T1 WT rep C


title: Sample 26 (s26)_T2 WT rep B


title: 6-19_1

description:
Spiking
Spiking


title: MCF-7_control ER_ChIPSeq rep1

description:
ER_ChIPSeq rep1
MCF-7_control

value: control


title: Sample 22 (s22)_T1 ∆cebR rep A


title: Sample 25 (s25)_T2 WT rep A


title: Sample 18 (s18)_T2 Cellotriose rep C

value: Thaxtomin-defined medium maltose (0.5%)

value: Cellotriose (2.5 mM)


title: Sample 17 (s17)_T2 Cellotriose rep B


title: Sample 16 (s16)_T2 Cellotriose rep A


title: Sample 20 (s20)_T1 WT rep B


title: Sample 10 (s10)_T1 Cellotriose rep A


title: Sample 13 (s13)_T2 Cellobiose rep A

value: Cellobiose (2.5 mM)


title: Sample 24 (s24)_T1 ∆cebR rep C


title: Sample 6 (s6)_T0 Cellotriose rep C


title: Sample 14 (s14)_T2 Cellobiose rep B


title: Sample 9 (s9)_T1 Cellobiose rep C


title: Sample 19 (s19)_T1 WT rep A


title: Sample 15 (s15)_T2 Cellobiose rep C


title: Sample 8 (s8)_T1 Cellobiose rep B


title: Sample 7 (s7)_T1 Cellobiose rep A


title: Sample 11 (s11)_T1 Cellotriose rep B


title: Sample 5 (s5)_T0 Cellotriose rep B


title: Sample 3 (s3)_T0 Cellobiose rep C


title: Sample 4 (s4)_T0 Cellotriose rep A


title: Sample 2 (s2)_T0 Cellobiose rep B


title: Sample 1 (s1)_T0 Cellobiose rep A


title: A549_IPT ChIP-Seq

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

country: South Korea

institute: KAIST

description:
A549 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (Welgene, Republic of Korea).
apporiate antibodies.Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.

data_processing:
Raw reads were mapped to the reference mouse human (hg19) genome assembly using Bowtie allowing two-mismatches for only unique alignment; -v 2 -m 1 -best --strata. To avoid clonal artifacts introduced in the library amplification steps, duplicated mapped reads were further discarded using SAMtools (http://samtools.sourceforge.net).HOMER suite (http://homer.salk.edu/homer/) was used for overall analysis. Details were described in the experimental procedues of this study.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Lysates were prepared from upto 10 millon single cell dissociates. Sonicated nuclei with Bioruptor were further proceeded to ChIP assay with a apporiate antibodies. Libraries were prepared according to Illumina's instructions of TruSeq ChIP Sample Prep kit.
The Libraries were prepared using the TruSeq ChIP-Seq preparation kit (Illumina).

treatment_protocol: DMSO or 10 µM of GSK-J4, and siNT or siKDM6B were treated for 24hr.

value: Lung adenocarcinoma

tag: antibody


title: Sample 12 (s12)_T1 Cellotriose rep C


title: A549_DMSO_K27me3 ChIP-Seq

value: DMSO


title: A549_siKDM6B_K27me3 ChIP-Seq


title: A549_siNT_K27me3 ChIP-Seq

value: siNT


title: A549_GSK-J4_K27me3 ChIP-Seq


title: A549_GSK-J4_K4me3 ChIP-Seq


title: H23_siKDM6B_rep1 RNA-Seq

data_processing:
Raw reads were mapped to the reference human (hg19) genome assembly with Tophat, and rpkm values were calculated with Cufflink
Genome_build: hg19
Supplementary_files_format_and_content: none

growth_protocol: HCC827, H23 and A549 were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (Welgene, Republic of Korea).

extract_protocol:
Total RNAs were isolated using RNeasy mini kits (Qiagen, Valencia, CA).
The Libraries were prepared using the TruSeq stranded mRNA sample preparation kit (Illumina).


title: H23_siNT_rep1 RNA-Seq


title: A549_siNT_rep1 RNA-Seq


title: H23_siKDM6B_rep2 RNA-Seq


title: A549_siKDM6B_rep2 RNA-Seq


title: A549 DMSO rep2

description: A549 DMSO rep2

data_processing:
Raw reads were mapped to the reference human (hg19) genome assembly with Tophat, and rpkm values were calculated with Cufflink
Genome_build: Hg19
Supplementary_files_format_and_content: RPKM

treatment_protocol: DMSO or 10 µM of GSK-J4 is treated for 24h.

tag: cell line


title: H23_siNT_rep2 RNA-Seq


title: A549_siKDM6B_rep1 RNA-Seq


title: H23 GSK-J4 rep2

description: H23 GSK-J4 rep2


title: A549 GSK-J4 rep1

description: A549 GSK-J4 rep1


title: HCC827 GSK-J4 rep2

description: HCC827 GSK-J4 rep2


title: Lamtor1 knockdown RAW264.7 cells

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 1650 ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Images were quantified using Agilent Feature Extraction Software (v 10.7.3.1).

source_name: Lamtor1 knockdown RAW264.7 cells

label_protocol: 200 ng of total RNAs were independently reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence to generate cDNAs and AffinityScript, RTase, which were then subjected to in vitro transcription using T7 RNA polymerase to label the cRNAs with Cy3-CTP (Amersham Pharmacia Biotech, Piscataway, NJ) using a Low input Quick-Amp Labeling Kit (Agilent Technologies).

growth_protocol: RAW 264.7 cells were purchased from ATCC. They were culture in Dulbecco’s modified Eagle medium (DMEM, #08458-45, Nacalai Tesque, Japan) supplemented with 10% fetal bovine serum and final 100 ug/ml of penicillin and streptomycin.

extract_protocol: Total RNA from Lamtor1 knockdown and control RAW264.7 cells was extracted using the RNeasy Mini kit (#74104; QIAGEN, Hilden, Germany).

treatment_protocol: After 2 times of passages, the RAW 264.7 cells were infected with a commercial lentiviral vector expressing shRNA that targets Lamtor1 (sc-108727-V, Santa Cruz Biotechnology, TX, USA). The lentiviral vector was the mixture of two vectors targeting mouse Lamtor1 mRNA. Two days after the vector infection, cells underwent limited dilution.

value: RAW264.7 cells

tag: genotype

value: Lamtor1 knockdown


title: H23 DMSO rep1

description: H23 DMSO rep1

tag: agent


title: A549_DMSO_K4me3 ChIP-Seq


title: A549 GSK-J4 rep2

description: A549 GSK-J4 rep2


title: A549 DMSO rep1

description: A549 DMSO rep1


title: H23 GSK-J4 rep1

description: H23 GSK-J4 rep1


title: A549_siNT_rep2 RNA-Seq


title: HCC827 GSK-J4 rep1

description: HCC827 GSK-J4 rep1


title: control RAW264.7 cells

source_name: control RAW264.7 cells


title: HCC827 DMSO rep2

description: HCC827 DMSO rep2


title: F3_CRMBPool_S22_

city: New Haven

first: Mathieu

middle: F

last: Bakhoum

state: CT

address: 300 George St.

department: Ophthalmology

institute: Yale University

description: CUT&RUNPeaks.txt

data_processing:
Library strategy: CUT&RUN
Raw reads (FASTQ) were aligned to the human reference genome (Ch38) using STAR on Partek Flow software, version 8.0. Aligned reads were mapped to transcripts (Ensembl Transcripts release 102) using Partek’s modified expectation-maximization (EM) algorithm for transcript quantification, with strict paired-end compatibility. Gene counts were normalized per sample to generate fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Raw reads (FASTQ) were aligned to the human reference genome (Ch38), using STAR on Partek Flow software, version 10.0 (Partek). Genomic peaks were called using MACS2 with the following parameters (BAM, cutoff q-value 0.05, no down-sampling).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

growth_protocol: Melanoma cells were grown in RPMI-1640 media (Gibco) supplemented with 10% fetal bovine serum (FBS, Sigma). Cell culture media were supplemented with 1% penicillin/streptomycin and cells were maintained at 37 °C and 5% CO2.

extract_protocol:
Total RNA was the extracted using the QIAShredder and the RNeasy extraction kit (Qiagen) and sequenced on NovaSeq (Illumina) to generate 150 bp pair-end reads. CUT&RUN were prepared using the CUTANA kit (EpiCypher, 14-1048)
RNA libraries were prepared for sequencing using standard Illumina protocols, CUT&RUN Library preparation was performed using the NEBNext Ultra II Library Prep Kit for Illumina (New England BioLabs, E7103S)

treatment_protocol: Cells were grown under regular conditions until they reached approximately 80% confluence. Culture media (RPMI) containing the following compounds dissolved in DMSO (Fisher BioReagents), or an equal volume of DMSO, were added to the cells; 50 μM PRT (PRT4165, Sigma-Aldrich), 1 μM UMK57 (Aobious) and 0.5 μM reversine (Cayman Chemical). For experiments with treatment extending beyond 2 hours, culture media were supplemented with 10% FBS and replenished after the first 24 hours, with the applicable compound.

value: Uveal melanoma cells

tag: cut&run antibody


title: H23 DMSO rep2

description: H23 DMSO rep2


title: F6_CRMBPool_S46_

description: CUT&RUNPeaks.txt


title: HCC827 DMSO rep1

description: HCC827 DMSO rep1


title: ddm1_total_NanoPare_2

city: San Francisco

first: Stefan

last: Oberlin

address: 505 Parnassus Ave

department: Department of Microbiology and Immunology

institute: University of California, San Francisco

description:
mRNA 5'-end sequencing
end_feature.rpm.csv
consensus_features.bed

data_processing:
nanoPARE Analysis Tools
Read trimming - Cutadapt
Read mapping - STAR
5p-end calssifcation and quantification - EndGraph
Genome_build: TAIR10
Supplementary_files_format_and_content: TPM

organism: Arabidopsis thaliana

source_name: inflorescence

extract_protocol:
RNA was extracted with the standard TRIzol method.
NanoPARE and SMART-seq2 mRNA library preparation was performed as previously reported. cDNA was tagmented using the Illumina Nextera DNA library preparation kit, purified using the Zymo 5× DNAClean and Concentrator kit (ZymoResearch) and eluted with nuclease-free water. For final enrichment PCR, the purified reaction was split and amplified either with Tn5.1/TSO enrichment oligonucleotide or Tn5.2/TSO enrichment oligonucleotide primer sets. PCR reaction products with Tn5.1/TSO enrichment oligonucleotide and Tn5.2/TSO enrichment oligonucleotide primer sets were pooled and purified using AMPureXP DNA beads.

tag: tissue

value: inflorescence

tag: rna isolation

value: TRIzol

tag: library preparation

value: NanoPARE


title: ddm1_total_NanoPare_1


title: F4_CRMBPool_S30_

description: CUT&RUNPeaks.txt

tag: cell type


title: F2_CRMBPool_S14_

description: CUT&RUNPeaks.txt


title: col0_total_NanoPare_1

value: wildtype (col0)


title: ddm1_total_SMARTseq_2

description:
mRNA-seq
gene_TPM_SMARTseq2.csv
consensus_features.bed


title: E6_CRMBPool_S45_

description: CUT&RUNPeaks.txt


title: E5_CRMBPool_S37_

description: CUT&RUNPeaks.txt


title: col0_total_NanoPare_2


title: F1_CRMBPool_S6_

description: CUT&RUNPeaks.txt

value: IgG


title: E2_CRMBPool_S13_

description: CUT&RUNPeaks.txt


title: ddm1_total_SMARTseq_1


title: col0_total_SMARTseq_1


title: B6_CRMBPool_S42_

description: CUT&RUNPeaks.txt


title: col0_total_SMARTseq_2


title: E3_CRMBPool_S21_

description: CUT&RUNPeaks.txt


title: E1_CRMBPool_S5_

description: CUT&RUNPeaks.txt


title: 35S.GFP-EVD-GUS.Col-0 sRNA-seq

description:
sRNA
normalized_counts_sRNA.csv

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimming of reads with bbduk v. 37.66.
Mapping to the Arabidopsis thaliana genome (TAIR10) with STAR v. 020201.
Read counting with Rsubread 1.26.1.
Read normalization with DEseq2.
P-site occupancies estimation of RIBO-seq data using RiboProfiling.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized_counts_sRNA.csv: Comma-separated text file of log2 normalized read counts.
Supplementary_files_format_and_content: RiboSeq_transcript_counts.csv: Comma-separated text file of P-site counts per codon position along all coding sequences.

extract_protocol:
RNA was extracted with the standard TRIzol method or with the TRaPR isolation method.
Libraries were prepared with TRIzol or TRaPR isolated RNA with the TRUseq or Lexogen sRNA library preparation kits or with a custom library preparation protocol.

tag: overexpression

value: GFP-EVD-GUS

value: Lexogen small RNA kit


title: F5_CRMBPool_S38_

description: CUT&RUNPeaks.txt


title: 35S.GFP-EVD-GUS.rdr6 sRNA-seq

description:
sRNA
normalized_counts_sRNA.csv


title: 35S.EVD.rdr6 sRNA-seq

description:
sRNA
normalized_counts_sRNA.csv

value: EVD


title: B5_CRMBPool_S34_

description: CUT&RUNPeaks.txt


title: 35S.EVD.Col-0 sRNA-seq

description:
sRNA
normalized_counts_sRNA.csv


title: B3_CRMBPool_S18_

description: CUT&RUNPeaks.txt


title: B2_CRMBPool_S10_

description: CUT&RUNPeaks.txt


title: 35S.GFP-EVD-GUS.rdr6 RIBO-seq

description:
Ribosome protected fragments
RiboSeq_transcript_counts.csv

data_processing:
Library strategy: Ribo-seq
Illumina Casava1.8 software used for basecalling.
Trimming of reads with bbduk v. 37.66.
Mapping to the Arabidopsis thaliana genome (TAIR10) with STAR v. 020201.
Read counting with Rsubread 1.26.1.
Read normalization with DEseq2.
P-site occupancies estimation of RIBO-seq data using RiboProfiling.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized_counts_sRNA.csv: Comma-separated text file of log2 normalized read counts.
Supplementary_files_format_and_content: RiboSeq_transcript_counts.csv: Comma-separated text file of P-site counts per codon position along all coding sequences.


title: E4_CRMBPool_S29_

description: CUT&RUNPeaks.txt


title: 35S.EVD.rdr6 RIBO-seq


title: B1_CRMBPool_S2_

description: CUT&RUNPeaks.txt


title: 35S.EVD.Col-0 RIBO-seq


title: A6_CRMBPool_S41_

description: CUT&RUNPeaks.txt


title: Acini-cKO-3

city: Daejeon

first: Jinhyuk

last: Choi

address: 291, Daehak-ro, Yuseong-gu

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (using fastx_trimmer), then mapped to mm10 whole genome using Bowtie2.
Read count extraction and normalization were performed using edgeR.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw counts.

source_name: primary acinar cells

growth_protocol: Primary acinar cells were maintained in Waymouth's media supplemented with 2.5 % FBS, 1% Penicillin-Streptomycin mixture (PS), 0.25 mg/ml of trypsin inhibitor, and 25 ng/ml of recombinant human Epidermal Growth Factor (EGF).

extract_protocol:
Total RNA was harvested using Trizol reagent (Invitrogen).
500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#015.96) standard protocols.

value: ERRgamma -/-

value: Pancreas

value: primary acinar cells


title: Acini-CON-3

value: wild type


title: A5_CRMBPool_S33_

description: CUT&RUNPeaks.txt


title: Acini-CON-1


title: B4_CRMBPool_S26_

description: CUT&RUNPeaks.txt


title: A3_CRMBPool_S17_

description: CUT&RUNPeaks.txt


title: Acini-CON-2


title: A4_CRMBPool_S25_

description: CUT&RUNPeaks.txt


title: NS3.IP

city: wuxi

first: Siyu

last: Liu

address: Street of River Deans, Binhu District, Wuxi City

institute: Jiangnan University Affiliated Hospital

data_processing:
[m6A]  Briefly, Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (HG19)  by Hisat2 software (v2.0.4).
[m6A]  Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts. GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes.
[Input]  Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
[Input]  Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Genome_build: UCSC HG19
Supplementary_files_format_and_content: Methylated_RNA_sites.mRNA.xlsx
Supplementary_files_format_and_content: mRNA Expression Profiling.xlsx

source_name: tissue

extract_protocol:
Total RNA was isolated using trizol.Total RNA (1 μg) was used for removing the rRNAs using NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA)  following the manufacturer's instructions
[m6A]  m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer’s instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA).
[m6A]  The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.
[Input]  RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions.
[Input]  Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

value: normal skin

tag: rip antibody

value: anti-m6A antibody


title: NS2.IP


title: NS3.input


title: negative lymph node-scRNA

city: Nanjing

first: kun

last: xu

address: guangzhou road 300

institute: Department of Oncology, The First Affiliated Hospital of Nanjing Medical University

data_processing:
Quality control
scRNA-seq reads were aligned to the GRCh38 genome assembly using STAR version 2.6.1a
aligned bam files were dealing with Featurecounts Version 1.6.2 to get UMI counts of each cell
Genome_build: GRCh38
Supplementary_files_format_and_content: expression matrix file using RNA raw count

source_name: negative lymph node

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.
Single cell suspension was then loaded onto a microfluidic chip (part of Singleron GEXSCOPETM Single Cell RNAseq Kit, Singleron Biotechnologies) and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron Biotechnologies).

tag: treatment

value: untreated

tag: tnm stage

tag: molecular typing

value: luminal B


title: NS2.input


title: 35S.GFP-EVD-GUS.Col-0 RIBO-seq


title: NS1.input


title: NS1.IP


title: positive lymph node-scRNA

source_name: positive lymph node


title: Acini-cKO-2

tag: strain


title: primary breast cancer-scRNA

source_name: primary breast cancer


title: Acini-cKO-1


title: HS2.input

value: hypertrophic scar


title: HS3.IP


title: Hela MeRIP-Seq reanalysis siCTL

city: HOUSTON

first: Ruoyu

address: 6431 Fannin St

institute: UTHealth McGovern Medical School

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
hg19
bigWig
MINT-Seq, TT-Seq, MeRIP-Seq,RNA-Seq, ChIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: Hela cell

growth_protocol: MCF7 cells were incubated in DMEM media supplemented with 10% Fetal Bovine Serum (FBS, GenDEPOT) in 37°C CO2 incubator. . In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours. To induce the estrogen signaling pathway, 100 nM 17-?-estradiol (E2) were added to the cells for an hour.

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.  M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.  M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: Cells were labeled in media for 15 min with 700 ?M 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: Human cervical cancer cells


title: HS3.input


title: pro-BMP9 treatment, PAEC line 4

city: Cambridge

first: Wei

address: Hills Road

department: Medicine

institute: University of Cambridge

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 comparisons were performed using the limma package

label: biotin

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: RNeasy Mini Kit from Qiagen following manufacturer's instruction

treatment_protocol: All ligands (at a final concentration of 0.4 ng/ml growth factor concentration) were added to the serum-starved cells. The 6-well plates were returned into CO2 incubator at 37 ºC for 5 hours before cells were harvested for RNA extraction.

tag: Sex

value: male

tag: age

value: pro-BMP9, containing 0.4 ng/ml of final growth factor domain


title: PBS treatment, PAEC line 4

value: PBS


title: pro-BMP9 treatment, PAEC line 3


title: 5-13_3

description:
Negative control
HEK

data_processing: The GE Flex Six Fast PCR+Melt v1 program was used to collect the cycle threshold (CT) values

source_name: Culture

value: HEK

tag: physiology


title: pro-BMP9 treatment, PAEC line 2


title: 5-13_2

description:
Negative control
HEK


title: PBS treatment, PAEC line 3


title: pro-BMP9 treatment, PAEC line 1


title: UniRNA

description:
Positive control
UniRNA

source_name: mouse tissue


title: PBS treatment, PAEC line 2


title: 5-13_1

description:
Negative control
HEK


title: NTC

description:
No template control
NTC


title: HS1.input


title: HS1.IP


title: 8-27_8

description:
Neuron
Neuron

value: Neuron


title: 8-27_9

description:
Neuron
Neuron


title: 8-27_6

description:
Neuron
Neuron


title: UniRNA2

description:
Positive control
UniRNA


title: HS2.IP


title: Hela TT-Seq reanalysis siCTL


title: PBS treatment, PAEC line 1


title: Hela MINT-Seq reanalysis siCTL


title: Hela RNA-Seq reanalysis siCTL


title: K562 MeRIP-Seq reanalysis rep1

source_name: K562 cell

value: immortalized myelogenous leukemia cell line


title: GA9hr_c

city: Shatin

first: Ho Man Holly

last: Tang

address: Science Centre South Block

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Illumina CASAVA v1.8 software was used for base calling
LncRNA-Seq reads were aligned to Homo sapiens (human) reference genome GRCh38 (hg38).  Bowtie2 v2.2.8 software was used to build index of reference genome, and Paired-end clean reads of LncRNA-Seq were aligned to the reference genome using HISAT2 (Langmead, B.et al., Nat Methods. 2012 Mar 4;9(4):357-9) v2.0.4. HISAT2 was run with ‘--rna-strandness RF’. DEG analysis was done using Cuffdiff.
Raw data files were filtered with GATK standard filter method and other parameters ( cluster： 3；WindowSize: 35; QD < 2.0 or FS > 60.0 or MQ < 40.0 or SOR > 4.0 or MQRankSum < - 12.5 or ReadPosRankSum Ø -8.0 or DP < 10)
We have a quantitative analysis of mRNA and the screening lncRNA by cuffdiff software(http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/index.html)to get the FPKM information of mRNA and lncRNA of every sample.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: Text files include FPKM values for each of 15 samples, of all transcripts, mRNA transcripts, lncRNA transcripts and TUCP transcripts (as indicated in the processed data file names).

source_name: HeLa_gallic acid for 9 hours

growth_protocol: HeLa cells were cultured in DMEM/F-12 (Dulbecco’s Modified Eagle medium: Nutrient Mixture F-12) media, supplemented with 10% fetal bovine serum (FBS), 2mM GlutaMAX, 100 U/mL penicillin, and 100 μg/mL streptomycin (Thermo Fisher Scientific, Carlsbad, CA, USA). The cells were maintained in optimal culture condition, at 37 degree Celsius (°C) under an atmosphere of 5% CO2. They were seeded on culture dishes for 24 hours to achieve 50–60% confluence, before subjected to experiment.

extract_protocol:
The total RNA in these corresponding conditions was harvested using TRIzol Reagent (Thermo Fisher Scientific, Carlsbad, CA, USA). The total RNA was isolated and purified using the Direct-zol™ RNA MiniPrep (Qiagen, Irvine, CA, USA) with the standard protocol as described by the manufacturer.
The RNA was first subjected to the Ribosomal RNA depletion, which was performed with Ribo-zero Magnetic Gold Kit (Illumina Inc., San Diego, CA). Samples were randomly primed and fragmented based on manufacturer’s recommendation (NEBNext® Ultra™ II Directional RNA Library Prep Kit, Illumina). The first strand was synthesized with the Protoscript II Reverse Transcriptase with a longer extension period (30 minutes for 42°C). All remaining steps for library construction were performed according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Gallic acid was diluted into the cell culture medium to achieve the working concentration of 50 µg/mL, immediately before being applied to HeLa cells. The cells were then incubated with gallic acid for 0 hour (GA0hr, untreated), 2 hours (GA2hr), 4 hours (GA4hr), 6 hours (GA6hr), and 9 hours (GA9hr), before collected for RNA sequencing.

tag: cell line

value: HeLa

value: human cervical cancer cells

value: gallic acid for 9 hours


title: GA9hr_b


title: 8-27_3

description:
Neuron
Neuron

source_name: Cerebellum slice


title: GA9hr_a


title: 8-27_2

description:
Neuron
Neuron


title: Hela MeRIP-Seq


title: GA6hr_b

source_name: HeLa_gallic acid for 6 hours

value: gallic acid for 6 hours


title: GA6hr_c


title: 8-27_1

description:
Neuron
Neuron


title: 8-12_1

description:
Myelinating
Myelinating

value: Oligodendrocyte

value: Myelinating


title: 6-13_2

description:
Myelinating
Myelinating


title: Hela MINT-Seq


title: 5-29_1

description:
Myelinating
Myelinating


title: 5-15_1

description:
Myelinating
Myelinating


title: K562 MINT-Seq reanalysis rep1


title: 8-27_5

description:
Neuron
Neuron


title: GA4hr_c

source_name: HeLa_gallic acid for 4 hours

value: gallic acid for 4 hours


title: K562 MeRIP-Seq


title: K562 RNA-Seq reanalysis rep1


title: 8-1_1

description:
Pre-myelinating
Pre-myelinating

value: Pre-myelinating


title: Hela RNA-Seq


title: 8-27_10

description:
Neuron
Neuron


title: K562 RNA-Seq


title: GA6hr_a


title: GA4hr_a


title: K562 TT-Seq reanalysis rep1


title: K562 TT-Seq


title: 8-1_2

description:
Myelinating
Myelinating


title: GA2hr_b

source_name: HeLa_gallic acid for 2 hours

value: gallic acid for 2 hours


title: Hela TT-Seq


title: 5-4_1

description:
OPC
OPC

value: OPC


title: 5-14_1

description:
Myelinating
Myelinating


title: 8-13_2

description:
OPC
OPC


title: 8-27_7

description:
Neuron
Neuron


title: 5-28_2

description:
OPC
OPC


title: 5-21_1

description:
OPC
OPC


title: 8-26_2

description:
OPC
OPC


title: 8-27_4

description:
Neuron
Neuron


title: MCF7 E2 siMETTL314 YTHDC1 ChIP-Seq rep1

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
hg19
bed
MINT-Seq, TT-Seq, MeRIP-Seq,RNA-Seq, ChIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: MCF7 cell

growth_protocol:
MCF7 cells were incubated in DMEM media supplemented with 10% Fetal Bovine Serum (FBS, GenDEPOT) in 37°C CO2 incubator.
MCF7 cells were incubated in DMEM media supplemented with 10% Fetal Bovine Serum (FBS, GenDEPOT) in 37°C CO2 incubator. . In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours. To induce the estrogen signaling pathway, 100 nM 17-?-estradiol (E2) were added to the cells for an hour.

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin were isolated with specific antibody.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.  M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol:
In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH or E2 were added to the cells for an hour.
Cells were labeled in media for 15 min with 700 ?M 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: human breast cancer cell line

value: E2 60 mins,siMETTL3/14

tag: antibody


title: GA0hr_b

value: untreated


title: GA4hr_b


title: MCF7 E2 mClover-YTHDC1 W377A/W428A ChIP-Seq

value: E2 60 mins

value: GFP, Abcam,Ab290


title: GA0hr_a


title: GA2hr_a


title: 5-3_3

description:
Myelinating
Myelinating


title: GA2hr_c


title: 6-13_1

description:
Spiking
Spiking

value: Spiking


title: 8-13_1

description:
Spiking
Spiking


title: 5-14_2

description:
Pre-myelinating
Pre-myelinating


title: MCF7 E2 mClover-YTHDC1 WT ChIP-Seq


title: 5-3_2

description:
Pre-myelinating
Pre-myelinating


title: 8-26_1

description:
Spiking
Spiking


title: K562 MINT-Seq

value: immortalized myelogenous leukemia cell line


title: MCF7 E2 siCTL YTHDC1 ChIP-Seq rep2

value: E2 60 mins, siCTL


title: GA0hr_c

value: HeLa

value: human cervical cancer cells


title: 8-15_1

description:
Spiking
Spiking


title: MCF7 E2 siMETTL314 YTHDC1 ChIP-Seq rep2


title: MCF7 E2 siCTL YTHDC1 ChIP-Seq rep1

value: E2 60 mins,siCTL


title: MCF7-YTHDC1-HaloTag PROTAC3 8h polyA RNA-Seq

value: E2 60 mins, PROTAC3 8h


title: 5-22 _1

description:
Spiking
Spiking

value: Oligodendrocyte


title: SK-EPI-siNC-3

city: Tianjin

first: He

state: Tianjin

address: Tianjin 300060

department: Public Laboratory

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Reads mapping to the reference genome: Hisat2 v2.0.5
Quantification of gene expression level: featureCounts v1.5.0-p3
Differential expression analysis: DESeq2 R package (1.16.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM value for each sample

source_name: SK-BR-3 cell line

growth_protocol: Human breast cancer cell lines SK-BR-3 were purchased from American Type Culture Collection (ATCC, Manassas, VA, USA). The epirubicin-resistant cell lines (SK/EPI) were established based  SK-BR-3 cells by long-time multistage induction using an increasing concentration of epirubicin.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer’s instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H - ). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: For knockdown of BCRP, cells were treated with siNC or siBCRP siRNAs using Lipofectamine RNAiMax for 48 h, then the RNA was isolated by Trozol reagent.

value: breast cancer

value: breast

tag: knock down

value: siNC


title: 5-3_4

description:
Spiking
Spiking

extract_protocol: Cells were collected after electrophysiological recordings


title: 8-23_2

description:
Spiking
Spiking


title: 5-28_1

description:
OPC
OPC

value: OPC


title: 8-13_4

description:
OPC
OPC


title: 8-12_2

description:
Pre-myelinating
Pre-myelinating

value: Pre-myelinating


title: MCF7-YTHDC1-HaloTag DMSO polyA RNA-Seq

value: human breast cancer cell line

value: E2 60 mins, DMSO


title: 8-13_3

description:
Spiking
Spiking


title: SK-EPI-3


title: MCF7 E2 siMETTL314 MeRIP-Seq IP

value: E2 60 mins, siMETTL3/14

value: anti-m6A antibodies (202003, SYSY)


title: 8-23_1

description:
OPC
OPC


title: 5-3_1

description:
Spiking
Spiking

value: Spiking


title: MCF7 E2 YTHDC1 ChIP-Seq rep2

value: E2 60 mins


title: 5-16_1

description:
Spiking
Spiking


title: 3/1 #5

description: Neuron

source_name: Brainstem slice

value: Neuron


title: 2/28 #3

description: Myelinating

value: Myelinating


title: 3/4 #1

description: Neuron


title: 2/28 #2

description: Myelinating


title: 3/6 #1

description: Myelinating


title: SK-BR-3-1


title: MCF7-YTHDC1-HaloTag PROTAC3 24h polyA RNA-Seq

value: E2 60 mins, PROTAC3 24h


title: SK-EPI-siBCRP-1

value: siBCRP


title: 3/1 #2

description: Myelinating


title: A2_CRMBPool_S9_

description: CUT&RUNPeaks.txt

value: Uveal melanoma cells

tag: cut&run antibody


title: MCF7 E2 siCTL MeRIP-Seq Input

value: E2 60 mins, siCTL


title: SK-EPI-siBCRP-3

value: breast cancer

tag: tissue


title: 4/10 #1

description: Myelinating

value: Oligodendrocyte


title: 5-22 _2

description:
Spiking
Spiking


title: SK-EPI-siNC-1

value: breast

value: siNC


title: SK-EPI-siBCRP-2


title: SK-EPI-2


title: 2/20 #2

description: Myelinating


title: MCF7 E2 siMETTL314 TT-Seq batch2

value: E2 60 mins, 4sU 15 mins,siMETTL3/14


title: MCF7 E2 siMETTL314 MeRIP-Seq Input

value: human breast cancer cell line


title: SK-EPI-siNC-2


title: MCF7 E2 siCTL MeRIP-Seq IP


title: SK-BR-3-3


title: SK-BR-3-2


title: 3/1 #3

description: Myelinating


title: MCF7 EtOH siCTL TT-Seq batch2

value: EtOH 60 mins, 4sU 15 mins,siCTL


title: 104-25

data_processing:
Raw reads (FASTQ) were aligned to the human reference genome (Ch38) using STAR on Partek Flow software, version 8.0. Aligned reads were mapped to transcripts (Ensembl Transcripts release 102) using Partek’s modified expectation-maximization (EM) algorithm for transcript quantification, with strict paired-end compatibility. Gene counts were normalized per sample to generate fragments Per Kilobase of transcript per Million mapped reads (FPKM) values.
Raw reads (FASTQ) were aligned to the human reference genome (Ch38), using STAR on Partek Flow software, version 10.0 (Partek). Genomic peaks were called using MACS2 with the following parameters (BAM, cutoff q-value 0.05, no down-sampling).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with normalized counts for every gene and every sample

value: DMSO


title: 104-15

value: PRT + UMK57


title: 104-29


title: 104-14


title: A1_CRMBPool_S1_

description: CUT&RUNPeaks.txt

value: IgG


title: 104-30


title: MCF7 E2 siCTL TT-Seq batch2

value: E2 60 mins, 4sU 15 mins,siCTL


title: SK-EPI-1


title: 104-28


title: 104-26


title: 104-13


title: 104-27


title: 3/5 #1

description: Pre-myelinating

value: Pre-myelinating


title: 2/21 #1

description: Myelinating

value: Myelinating


title: K3-2

description: Pre-myelinating


title: MCF7 siYTHDC1 E2 H3K27ac ChIP-Seq

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
MINT-Seq, TT-Seq, MeRIP-Seq,RNA-Seq, ChIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

growth_protocol: MCF7 cells were incubated in DMEM media supplemented with 10% Fetal Bovine Serum (FBS, GenDEPOT) in 37°C CO2 incubator.

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin were isolated with ER-a antibody.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.100 nM 17-β-estradiol (E2)  were added to the cells for an hour.

value: E2 60 mins,siYTHDC1


title: 104-11

value: PRT


title: 104-12

value: Uveal melanoma cells


title: MCF7-YTHDC1-HaloTag PROTAC3 E2 PRO-Seq

value: E2 60 mins,PROTAC3 24h


title: 3/27 #1

description: Pre-myelinating


title: 4/8 #2

description: Pre-myelinating


title: 104-10


title: 104-06

value: Reversine


title: K2-5

description: Pre-myelinating

value: Oligodendrocyte


title: MCF7 E2 YTHDC1 ChIP-Seq

value: E2 60 mins


title: 3/1 #4

description: Pre-myelinating


title: 104-05


title: 104-03


title: 104-04


title: MCF7-YTHDC1-HaloTag WT E2 PRO-Seq


title: MCF7 siCTL E2 H3K27ac ChIP-Seq

extract_protocol:
Lysates were clarified from sonicated nuclei and biotin-labelled DNA were isolated with C1 beads
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

value: E2 60 mins,siCTL


title: 3/20 #2

description: Pre-myelinating


title: 104-01


title: S_2546_26


title: S_2546_27


title: MCF7-YTHDC1-HaloTag PROTAC3 E2 TT-Seq

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.  M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH were added to the cells for an hour. Cells were labeled in media for 15 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: E2 60 mins,PROTAC3 24 hour

tag: molecule subtype

value: nuclear RNA


title: 4/7#4

description: Spiking

value: Spiking


title: S_2546_29

value: DMSO


title: PR2_2541


title: PR1_2541


title: K3-1

description: Spiking


title: MCF7-YTHDC1-HaloTag WT E2 TT-Seq

value: human breast cancer cell line

value: E2 60 mins,Vehice


title: 104-02


title: MCF7 E2 siCTL BRD4-2 ChIP-Seq

data_processing:
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
Genome build: hg19
MINT-Seq, TT-Seq, MeRIP-Seq,RNA-Seq, ChIP-Seq raw data were de-multiplexed by bcl2fastq (v2.20), and quality-controlled with fastqc.
All clean-reads were mapped to human reference genome hg19 by STAR v2.7.0, with parameters of –-genomeSAindexNbases 14 –outFilterMultimapNmax 10 –outFilterMismatchNmax 10.   Duplicated reads were further removed, and only unique aligned reads will be considered for later visualization and quantification.
For gene/mRNA quantification, hg19 RefSeq gene annotation coordinates were used. And HOMER tool-sets were used to calculate the FPKM value of individual repeat elements, based on repeat mask annotation.
The unique aligned reads were further converted to bigwig format with a fragment length of 75 on IGV browser.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and chromatin were isolated with BRD4 antibody.
DNA libraries were prepared using NEB Next Ultra II DNA library prep kit for illumina according to manufactorer's instructions

value: BRD4,Active Motif,#91302


title: MCF7 E2 siYTHDC1 BRD4-2 ChIP-Seq


title: S_2546_28


title: DM2_2541


title: K1-4

description: Spiking


title: DM1_2541


title: K2-3

description: Spiking


title: MCF7 E2 siYTHDC1 BRD4-1 ChIP-Seq


title: K2-1

description: Spiking


title: S_2538_19


title: K1-2

description: Spiking


title: S_2538_23


title: MCF7 E2 siCTL BRD4-1 ChIP-Seq


title: S_2538_22


title: MCF7 E2 siCTL ER-a ChIP-Seq

value: Era,Santa Cruz,sc-543


title: PR1_2520


title: DM1_2520


title: S_2538_20


title: MCF7 EtOH siCTL ER-a ChIP-Seq

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH were added to the cells for an hour.

value: EtOH 60 mins,siCTL


title: DM2_2520


title: MCF7 E2 MeRIP-Seq

molecule: nuclear RNA

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), M6A methylated RNA was immunoprecipitated by anti-m6A antibodies (202003, SYSY).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions


title: 4/7 #1

description: Spiking


title: PR1_2592

extract_protocol:
Total RNA was the extracted using the QIAShredder and the RNeasy extraction kit (Qiagen) and sequenced on NovaSeq (Illumina) to generate 150 bp pair-end reads. CUT&RUN were prepared using the CUTANA kit (EpiCypher, 14-1048)
RNA libraries were prepared for sequencing using standard Illumina protocols, CUT&RUN Library preparation was performed using the NEBNext Ultra II Library Prep Kit for Illumina (New England BioLabs, E7103S)


title: 4/7 #2

description: Spiking


title: MCF7 E2 RNA-Seq


title: DM2_2592


title: K1-1

description: Spiking


title: PR3_2520


title: MCF7 E2 siYTHDC1 GRO-Seq

extract_protocol:
RNA was extracted using TRIzol (Life Technologies).The fragmented brU labeled RNAs were purified using an anti-brdU antibody from Santa Cruz (sc-32323 ac).
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions

value: E2 60 mins,siYTHDC1


title: TGFWNT3a6

city: Kraków

first: Przemysław

last: Błyszczuk

address: Wielicka 265

country: Poland

institute: Jagiellonian University

description:
TGFWNT3a6
Significant-DEGs_TGFvsTGF+WNT3a.txt

data_processing:
add
Genome_build: GRch38
Supplementary_files_format_and_content: Significant-DEG

source_name: cardiac fibroblasts

extract_protocol:
RNA libraries were prepared for sequencing using standard Illumina protocols
Libraries were run with Illumina, strand-specific RNA-Seq with PolyA selection and Illumina NovaSeq 2x150 bp sequencing

treatment_protocol: After 72h of stimulation cardiac fibroblats RNAs was harvested using Trizol reagent. Illumina, strand-specific RNA-Seq with PolyA selection and Illumina NovaSeq 2x150 bp sequencing, 10M read pairs.

value: fetal human cardiac cell line


title: DM1_2592

value: Uveal melanoma cells


title: 3/26 #2

description: Spiking


title: TGFWNT5a1

description:
TGFWNT5a1
Significant-DEGs_TGFvsTGF+WNT5a.txt


title: MCF7 E2 siCTL GRO-Seq


title: K3-3

description: OPC

value: OPC


title: K3-4

description: OPC


title: 3/26 #1

description: Spiking


title: TGFWNT5a6

description:
TGFWNT5a6
Significant-DEGs_TGFvsTGF+WNT5a.txt


title: 4/5 #1

description: Spiking


title: Sudan+MT-1

city: 南京

first: 春华

last: 邢

state: 江苏

address: 江苏省南京市玄武区孝陵卫街道

institute: 南京农业大学

data_processing:
isolation and purify mRNA from total RNA
synthesis the first strand cDNA and synthesis the second strand cDNA
Purify the double-stranded cDNA with 1.8X  AMPure XP beads
cDNA were end repaired and added A base to the 3’ end and cDNA were ligated adaptors
Purify  and the adaptor purificated library with AMPure XP beads

source_name: mouse oocyte

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: germinal vesicle (GV)

tag: condition

value: Sudan I-exposed + melatonin rescue


title: MCF7 EtOH siCTL GRO-Seq

tag: cell type


title: TGFWNT5a2

description:
TGFWNT5a2
Significant-DEGs_TGFvsTGF+WNT5a.txt


title: Sudan+MT-2

address: 江苏省南京市玄武区孝陵卫街道


title: PR2_2592

value: PRT


title: TGFWNT3a3

description:
TGFWNT3a3
Significant-DEGs_TGFvsTGF+WNT3a.txt


title: MCF7 E2 siCTL TT-Seq

extract_protocol:
RNA was extracted using TRIzol (Life Technologies), 4sU-labeled RNA was exctracted according to Duffy et al., Mol Cell, 2015.
RNA libraries were prepared using NEB Next Ultra II RNA library prep kit for illumina according to manufactorer's instructions

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.100 nM 17-β-estradiol (E2)  were added to the cells for an hour. Cells were labeled in media for 5  min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: E2 60 mins, 4sU 5 mins,siCTL


title: Sudan-2

address: 江苏省南京市玄武区孝陵卫街道

value: Sudan I-exposed


title: K2-4

description: OPC

value: Oligodendrocyte


title: MCF7 E2 siYTHDC1 TT-Seq

value: E2 60 mins, 4sU 5 mins,siYTHDC1


title: MCF7 E2 MINT-Seq rep2

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.100 nM 17-β-estradiol (E2)  were added to the cells for an hour. Cells were labeled in media for 15 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: E2 60 mins, 4sU 15 mins

value: anti-m6A antibodies (202003, SYSY)


title: K2-2

description: OPC


title: Sudan-1

address: 江苏省南京市玄武区孝陵卫街道


title: TGFWNT3a5

description:
TGFWNT3a5
Significant-DEGs_TGFvsTGF+WNT3a.txt


title: K1-5

description: OPC


title: TGF5

description:
TGF5
Significant-DEGsCTRVSTGF.txt.
Significant-DEGs_TGFvsTGF+WNT3a.txt
Significant-DEGs_TGFvsTGF+WNT5a.txt

value: TGF


title: TGF4

description:
TGF4
Significant-DEGsCTRVSTGF.txt.
Significant-DEGs_TGFvsTGF+WNT3a.txt
Significant-DEGs_TGFvsTGF+WNT5a.txt


title: Control-2

address: 江苏省南京市玄武区孝陵卫街道

value: control


title: TGF2

description:
TGF2
Significant-DEGsCTRVSTGF.txt.
Significant-DEGs_TGFvsTGF+WNT3a.txt
Significant-DEGs_TGFvsTGF+WNT5a.txt


title: K1-3

description: OPC


title: MCF7 EtOH TT-Seq rep2

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH were added to the cells for an hour.  Cells were labeled in media for 15 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: human breast cancer cell line

value: EtOH 60 mins, 4sU 15 mins


title: Control-1

address: 江苏省南京市玄武区孝陵卫街道


title: MCF7 EtOH siCTL TT-Seq

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.EtOH were added to the cells for an hour.  Cells were labeled in media for 5  min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.

value: EtOH 60 mins, 4sU 5 mins,siCTL


title: CTR3

description:
CTR3
Significant-DEGsCTRVSTGF.txt.

value: fetal human cardiac cell line

value: untreated


title: CTR4

description:
CTR4
Significant-DEGsCTRVSTGF.txt.


title: MCF7 E2 MINT-Seq rep1


title: T2DM-6MON-3

city: Qingdao

first: Bin

last: Zhang

state: Shandong

address: Yanerdao Road 5

institute: Shangdong Eye Institue

description:
T2DM mouse
post treatment 24 weeks
Expression_Gene.xlsx

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8. Sequence quality was examined using the FastQC software. The trimmed reads were aligned to reference genome using Hisat2. The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with Ballgown.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Expression_Gene.xlsx: Excel file includes FPKM values for each Sample.

source_name: Lacrimal gland

extract_protocol:
The LG samples from type 2 diabetic mice or vehicles were collected with Trizol reagent. The mRNA was enriched by NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), and the produced RNA was used for construction library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: high fat diet + STZ

value: lacrimal gland

value: 24 weeks


title: MCF7 EtOH MINT-Seq rep2


title: CON-6MON-2

description:
Counterpart
Expression_Gene.xlsx


title: T2DM-6MON-1


title: CTR2

description:
CTR2
Significant-DEGsCTRVSTGF.txt.


title: T2DM-6MON-2


title: positive lymph node-scATAC

data_processing:
The scATAC-seq data analysis was processed by “cellranger ATAC 1.2.0”. The reference genome was GRCh38. For the downstream analysis, SnapATAC was used to convert the data format based on fragments data.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw MEX format for called peaks (barcode, mtx file, peak file ) and fragment file

source_name: positive lymph node

extract_protocol:
The concentration of single-cell suspension was adjusted to 1×105 cells/mL in PBS.  Cell suspension was transferred to 2-ml tube and centrifuged (300rcf,5 min) to remove supernatant. Then added lysis buffer (Tris-HCl (pH 7.4): 10 mM, NaCl: 10mM, MgCl2: 3mM, Tween-20: 0.1%, Nonidet P40 Substitute: 0.1%, Digitonin: 0.01%, BSA: 1%, right amount nuclease-free waster) to pellet and mixed. Incubated the mixture on ice (3~5min). After that, added wash buffer (Tris-HCl (pH 7.4): 10mM, NaCl: 10mM, MgCl2: 3mM, Tween-20: 0.1%, BSA: 1%, right amount nuclease-free waster) to the mixture, mixed and centrifuged (500 rcf, 5min). The supernatant was removed, and resuspended the pellet by diluted nuclei buffer (10x Genomics, 2000153/2000207). After nuclei concentration was determined by Countess II FL Automated Cell Counter, the resulting nuclei solution was used for library construction immediately.
The scATAC libraries were constructed according to the user guide of Chromium Next GEM Single Cell ATAC Reagent Kits v1.1.
scATAC-seq

value: luminal B


title: MCF7 E2 TT-Seq rep2


title: CON-6MON-3

description:
Counterpart
Expression_Gene.xlsx


title: 4/8 #1

city: San Antonio

first: Elizabeth

description: OPC

value: OPC


title: 4/7 #3

description: OPC


title: 4/5 #2

description: OPC


title: 3/20 #1

description: OPC


title: negative lymph node-scATAC

source_name: negative lymph node


title: MCF7 E2 TT-Seq rep1

treatment_protocol: In order to deprive hormone signaling in MCF7 cells, the cells were incubated in phenol red-free DMEM with 10% Charcoal-stripped fetal bovine serum (CS-FBS, Omega Scientific Inc) for 72 hours.100 nM 17-β-estradiol (E2)  were added to the cells for an hour.  Cells were labeled in media for 15 min with 700 μM 4-thiouridine (4sU, Sigma-Aldrich) and harvested through centrifugation for 1 min at 1,000g.


title: INEN-0008

status: Public on Aug 07 2021

city: Madrid

first: Marta

last: Roche-Molina

address: C/Maiquez 7

department: Servicio de Oncologia Medica

institute: LAOT

description:
CP-1070-Spain-134553-FFPE-Roi
150225_UNC12-SN629_0404_AC5HDYACXX_ACTTGA_L003

data_processing:
Read mapping performed with MapSplice v 2.2.1
Transcript cuantification was obtained with RSEM v1.3.0
Normalization was performed by upper quartile normalization (Quartile=75)
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with quantile normalized gene counts for every gene and every sample

source_name: Breast tumor sample

extract_protocol:
mRNA was extracted using High Pure FFPET RNA Isolation Kit in accordance with the protocol provided by the manufacturer. Quality control was performed with Agilent Bioanalyser.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Breast tumor sample

tag: subtype

value: Basal


title: HVDH-0003

description:
CP-1068-Spain-13B9644-A1-FFPE-Roi
150225_UNC12-SN629_0404_AC5HDYACXX_CCGTCC_L002


title: MCF7 EtOH TT-Seq rep1


title: HVDH-0005

description:
CP-1069-Spain-13B20483-A1-FFPE-Roi
150225_UNC12-SN629_0404_AC5HDYACXX_CAGATC_L002


title: CON-6MON-1

description:
Counterpart
Expression_Gene.xlsx


title: HCSC-0011

description:
CP-1065-Spain-12B4899-FFPE-Roi
150204_UNC11-SN627_0396_AC5J3LACXX_AGTTCC_L008


title: HUGM-0041

description:
CP-954-Spain-13B0015028A1-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_GGCTAC_L002


title: MCF7 EtOH MINT-Seq rep1


title: HUGM-0045

description:
CP-955-Spain-13B0017271-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_CTTGTA_L002


title: HUGM-0031

description:
CP-1066-Spain-10B0028107-FFPE-Roi
150225_UNC12-SN629_0404_AC5HDYACXX_ACAGTG_L001


title: HCSC-0021

description:
CP-957-Spain-13B9793-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_AGTTCC_L003


title: INEN-0003

description:
CP-959-Spain-284234-2-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_CCGTCC_L004

value: LumB


title: HUGM-0032

description:
CP-952-Spain-13B0014842-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_GATCAG_L001


title: 2/28 #1

address: 7703 Floyd Curl Dr

institute: University of Texas Health Science Center San Antonio

description: OPC

value: Oligodendrocyte


title: HCSC-0010

description:
CP-1064-Spain-11B3955-FFPE-ROi
150204_UNC11-SN627_0396_AC5J3LACXX_AGTCAA_L008


title: HUGM-0034

description:
CP-953-Spain-13B0015025-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_TAGCTT_L001


title: 2/20 #1

description: OPC


title: HUGM-0052

description:
CP-946-Spain-13B0001681-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_TTAGGC_L006


title: HCSC-0017

description:
CP-956-Spain-13B7563-1-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_AGTCAA_L003


title: HUGM-0026

description:
CP-947-Spain-13B0005258A1-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_TGACCA_L006


title: HVDH-0002

description:
CP-1067-Spain-13M1298-FFPE-Roi
150225_UNC12-SN629_0404_AC5HDYACXX_ATGTCA_L001


title: INEN-0002

description:
CP-958-Spain-283942-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_ATGTCA_L004


title: HUGM-0018

description:
CP-937-Spain-12B0018136-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_TAGCTT_L001


title: HUGM-0015

description:
CP-936-Spain-12B0017538-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_GATCAG_L001


title: HUGM-0027

description:
CP-949-Spain-13B0008549-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_GCCAAT_L007


title: HUGM-0048

description:
CP-938-Spain-12B0022767-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_GGCTAC_L002


title: HVDH-0004

description:
CP-943-Spain-13-106709-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_CCGTCC_L004


title: HUGM-0028

description:
CP-950-Spain-13B0011726-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_CAGATC_L008


title: HCSC-0020

description:
CP-945-Spain-13B00009485-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_CGATGT_L005


title: HCSC-0013

description:
CP-941-Spain-12B17225-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_AGTTCC_L003


title: HUGM-0022

description:
CP-939-Spain-12B0024177-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_CTTGTA_L002


title: HCSC-0007

description:
CP-930-Spain-11B7857-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_TTAGGC_L006


title: HCSC-0014

description:
CP-931-Spain-12-1758-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_TGACCA_L006


title: HUGM-0009

description:
CP-926-Spain-11B0024113-3-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_ATGTCA_L004


title: HUGM-0011

description:
CP-934-Spain-12B0003907-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_CAGATC_L008


title: HUGM-0001

description:
CP-924-Spain-11B0018461-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_AGTCAA_L003


title: HCSC-0003

description:
CP-932-Spain-12B0001018-E07-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_ACAGTG_L007


title: INEN-0009

description:
CP-914-Spain-290911-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_TTAGGC_L006


title: HUGM-0037

description:
CP-935-Spain-12B0011259-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_ACTTGA_L008


title: HUGM-0047

description:
CP-915-Spain-10B0022870-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_TGACCA_L006


title: HUGM-0050

description:
CP-920-Spain-11B0007386-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_GATCAG_L001


title: INEN-0007

description:
CP-960-Spain-286274-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_ATCACG_L005


title: HCSC-0008

description:
CP-917-Spain-10B22363-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_GCCAAT_L007


title: HUGM-0019

description:
CP-940-Spain-12B0025291-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_AGTCAA_L003


title: HUGM-0038

description:
CP-922-Spain-11B0016939-C09-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_GGCTAC_L002


title: INEN-0006

description:
CP-913-Spain-285011-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_CGATGT_L005


title: HCSC-0022

description:
CP-961-Spain-13B0004511-FFPE-R0i
140703_UNC9-SN296_0425_AC4TR2ACXX_CGATGT_L005


title: HCSC-0004

description:
CP-929-Spain-11B17783-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_CGATGT_L005


title: HUGM-0044

description:
CP-921-Spain-11B0010205-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_TAGCTT_L001


title: HUGM-0029

description:
CP-916-Spain-10B0028649-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_ACAGTG_L007


title: INEN-0012

description:
CP-850-Spain-292952--FFPE-R0i
140324_UNC13-SN749_0335_AC3LP4ACXX_CGATGT_L006


title: HUGM-0042

description:
CP-925-Spain-11B0019861-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_AGTTCC_L003


title: INEN-0010

description:
CP-848-Spain-292226-FFPE-R0i
140324_UNC13-SN749_0335_AC3LP4ACXX_ATCACG_L005


title: HVDH-0001

description:
CP-942-Spain-13-102488-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_ATGTCA_L004


title: INEN-0023

description:
Spain-7-319019_0
150916_UNC17-D00216_0344_AC6P3BANXX_CAGATC_L002


title: INEN-0024

description:
Spain-48-CTC-1583-A
150916_UNC17-D00216_0344_AC6P3BANXX_ATTCCT_L001


title: INEN-0022

description:
Spain-8-320118_0
150916_UNC17-D00216_0344_AC6P3BANXX_ACTTGA_L003


title: HUGM-0036

description:
CP-918-Spain-11B0000541-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_CAGATC_L008


title: INEN-0020

description:
Spain-50-LAS-1470A
151005_UNC18-D00493_0265_AC7JERANXX_TAGCTT_L002


title: HUGM-0008

description:
CP-927-Spain-11B0025545-A06-FFPE-R0i
140626_UNC15-SN850_0373_BC4J8DACXX_CCGTCC_L004


title: INEN-0014

description:
Spain-2-297768_0
150825_UNC15-SN850_0412_BC7L2HACXX_CGATGT_L002


title: HVDH-0012

description:
Spain-40-15B5949
150911_UNC17-D00216_0343_AC7ABBANXX_CCGTCC_L006


title: INEN-0004

description:
CP-912-Spain-42494-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_ATCACG_L005


title: HCSC-0023

description:
CP-849-Spain-13B07957-FFPE-R0i
140324_UNC13-SN749_0335_AC3LP4ACXX_TGACCA_L005


title: HVDH-0007

description:
Spain-14-14-101736
150825_UNC15-SN850_0411_AC7E3PACXX_AGTTCC_L004


title: HUGM-0030

description:
CP-951-Spain-13B0013608-FFPE-R0i
140703_UNC15-SN850_0375_BC4V6RACXX_ACTTGA_L008


title: HUGM-0058

description:
Spain-27-14B0027947
150825_UNC15-SN850_0412_BC7L2HACXX_TTAGGC_L006


title: HUGM-0054

description:
Spain-30-14B13442A2
150825_UNC15-SN850_0412_BC7L2HACXX_GCCAAT_L008


title: INEN-0015

description:
Spain-1-296785_0
150825_UNC15-SN850_0411_AC7E3PACXX_ATCACG_L005


title: HUGM-0056

description:
Spain-25-14B0023311
150825_UNC15-SN850_0412_BC7L2HACXX_ATCACG_L005

value: Normal


title: HUGM-0053

description:
Spain-20-14B0009265A1
150825_UNC15-SN850_0412_BC7L2HACXX_GTTTCG_L003


title: HUGM-0051

description:
CP-919-Spain-11B0004587-FFPE-R0i
140624_UNC12-SN629_0375_AC4K57ACXX_ACTTGA_L008


title: HSCP-0002

description:
Spain-41-27768-19-14B0014171
150825_UNC15-SN850_0412_BC7L2HACXX_GTCCGC_L001


title: HLPR-004

description:
Spain-46-B14-09292
150911_UNC17-D00216_0343_AC7ABBANXX_GAGTGG_L008


title: HSCP-0001

description:
Spain-16-14B0000831B1
150825_UNC15-SN850_0411_AC7E3PACXX_CCGTCC_L008


title: HVDH-0008

description:
Spain-15-14-102050
150825_UNC15-SN850_0411_AC7E3PACXX_ATGTCA_L008


title: HLPR-001

description:
Spain-43-B14-01682_A2
150911_UNC17-D00216_0343_AC7ABBANXX_GTGGCC_L007


title: HVDH-0006

description:
Spain-13-14-100177
150825_UNC15-SN850_0411_AC7E3PACXX_AGTCAA_L007


title: HUGM-0060

description:
Spain-26-14B0027481
150825_UNC15-SN850_0412_BC7L2HACXX_CGATGT_L006


title: INEN-0021

description:
Spain-5-306311_0
150916_UNC17-D00216_0344_AC6P3BANXX_ACAGTG_L002


title: HUGM-0061

description:
Spain-33-15B000054A2
150911_UNC17-D00216_0343_AC7ABBANXX_GATCAG_L002


title: HUGM-0063

description:
Spain-34-15B0002149
150911_UNC17-D00216_0343_AC7ABBANXX_TAGCTT_L002


title: INEN-0017

description:
Spain-4-305532_0
150911_UNC17-D00216_0343_AC7ABBANXX_TGACCA_L005


title: INEN-0016

description:
Spain-3-304915_0
150825_UNC15-SN850_0412_BC7L2HACXX_TTAGGC_L008


title: HVDH-0011

description:
Spain-29-14B12926A1
150825_UNC15-SN850_0412_BC7L2HACXX_ACAGTG_L007


title: HUGM-0002

description:
Spain-10-11B0015859
150825_UNC15-SN850_0411_AC7E3PACXX_TAGCTT_L005


title: INEN-0005

description:
CP-851-Spain-43768-FFPE-R0i
140324_UNC13-SN749_0335_AC3LP4ACXX_TTAGGC_L006


title: HCSC-0032

description:
Spain-21-14B0009733
150825_UNC15-SN850_0412_BC7L2HACXX_CGTACG_L003


title: HCSC-0031

description:
Spain-19-14B0008157
150911_UNC17-D00216_0343_AC7ABBANXX_GTGGCC_L004


title: HUGM-0057

description:
Spain-23-14B0020849
150825_UNC15-SN850_0412_BC7L2HACXX_ACTGAT_L004


title: HUGM-0059

description:
Spain-28-14B0028490
150825_UNC15-SN850_0412_BC7L2HACXX_TGACCA_L007


title: HUGM-0055

description:
Spain-24-14B0023220
150825_UNC15-SN850_0412_BC7L2HACXX_ATTCCT_L005


title: HLPR-003

description:
Spain-45-B14-02712
150911_UNC17-D00216_0343_AC7ABBANXX_CGTACG_L008


title: HCSC-0025

description:
Spain-32-14B807
150911_UNC17-D00216_0343_AC7ABBANXX_ACTTGA_L001


title: HLPR-005

description:
Spain-42-6729B14
150911_UNC17-D00216_0343_AC7ABBANXX_GTGAAA_L006


title: HCSC-0028

description:
Spain-17-14B0002164
150825_UNC15-SN850_0411_AC7E3PACXX_GTCCGC_L007


title: HVDH-0005

hyb_protocol: Follow protocol from Prosigna™ Breast Cancer Prognostic Gene Signature Assay (2015-01 LBL-10010-02). Use 250ng total RNA. Incubate 15h at 65ºC. After that continuue with the sample processing in the prep station (nCounter)

scan_protocol: Follow protocol from Prosigna™ Breast Cancer Prognostic Gene Signature Assay (2015-01 LBL-10010-02) and the user manual form the n Counter analysis sytem (NanoString Technologies-2015-01 MAN-10008-02).

data_processing:
Normalization was performed with Bioconductor package NanostringNorm
Quality control was performed with Bioconductor package NanostringQC
Classification was performed with bioconductor packages ctc and impute
PAM50 classification file

label_protocol: Standard Nanostring protocol

extract_protocol: On average, 5 um-thick sections were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified by a surgical pathologist.

value: Carboplatin and Docetaxel


title: HCSC-0010


title: HUGM-0031


title: HVDH-0002


title: HCSC-0033

description:
Spain-22-14B0013642
150825_UNC15-SN850_0412_BC7L2HACXX_GAGTGG_L004


title: HUGM-0032


title: HCSC-0022


title: INEN-0003


title: INEN-0002


title: HUGM-0034


title: WT_Input_for_RiboSeq_2

city: Guangzhou

first: Haining

address: Zhongshan road 2

institute: The first affiliated hospital of sun yat-sen university

data_processing:
Library strategy: Ribo-seq
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.

source_name: intrahepatic cholangiocarcinoma cell line

growth_protocol: ICC cell lines were  cultrued in RMPI 1640 medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.

extract_protocol:
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.

treatment_protocol: Mettl1 gene knockdown was mediated by short hairpin RNA.

value: wild type


title: HCSC-0026

description:
Spain-18-14B0002337
150825_UNC15-SN850_0412_BC7L2HACXX_GTGAAA_L002


title: WT_RiboSeq_1


title: Knockdown_RiboSeq_2

value: Mettl1 knockdown


title: HUGM-0045


title: INEN-0008