title: Tau_2_PS19(P301S)_PFC_ChIP-Seq

city: Buffalo

first: Zhen

last: Yan

address: 955 Main St

institute: SUNY Buffalo

data_processing:
Purified DNA was used to construct sequencing libraries with 5 ng of DNA (ChIP or input). Libraries were prepared using the Rubicon ThruPLEX DNA-seq Library Prep Reagent Set for Illumina sequencing according to the manufacturer's recommendations. DNA quality was measured with an Advanced Analytical Fragment Analyzer with a high sensitivity chip. 50 bp single end reads per sample were obtained using the HiSeq 2500 platform from Illumina
Supplementary_files_format_and_content: bigWig

source_name: PFC

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with anti-H3K4me3 (ab8580, Abcam, 5 ug/reaction).
Purified DNA was used to construct sequencing libraries with 5 ng of DNA (ChIP or input). Libraries were prepared using the Rubicon ThruPLEX DNA-seq Library Prep Reagent Set for Illumina sequencing according to the manufacturer's recommendations. DNA quality was measured with an Advanced Analytical Fragment Analyzer with a high sensitivity chip. 50 bp single end reads per sample were obtained using the HiSeq 2500 platform from Illumina.

value: PFC

value: Total cell lysate (bulk)

tag: chip antibody

value: H3K4me3 (Abcam ab8580)

value: Vehicle


title: HUVEC_uc003pxg_1_si3

status: Public on Jul 14 2021

type: SRA

city: Suzhou

first: Ping

last: Li

address: 242 Guangji Road，Suzhou ，Jiangsu

country: China

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

library_source: transcriptomic

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Clean reads were obtained after remove of low quality reads and removing reads with 5' linker sequence, reads without 3' linker sequence, reads without the insert tag, reads with poly (A), and reads shorter than 17 nt.
Total clean reads were mapped to the Rat reference genome using the bwa aligner.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM/COUNT values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC

growth_protocol: The HUVECs were cultured in DMEM containing 10% fetal bovine serum, 100 U/ml streptomycin, and 100 U/ml penicillin at 37°C in a humidified 5% CO2 incubator. The cells were washed with phosphate-buffered saline and digested with Trypsin-EDTA Solution. For transfection, HUVECs were seeded at approximately 50% confluence in the wells of a 24-well plate 24 h prior to transfection. The cells were transfected with 100 nm lncRNA si-uc003pxg.1, si-NC using a riboFECTTMCP Transfection Kit.

extract_protocol: NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

treatment_protocol: High-throughput sequencing was performed by RiboBio Co., Ltd.. siRNA (100 nm) was transfected into HUVECs, and RNA was extracted from the cells in the NC and si-uc003pxg.1 groups. The RNA from the HUVEC NC and HUVEC si-uc003pxg.1 groups was selected for high-throughput sequencing with Illumina HiSeqTM 2500 to identify differentially expressed miRNAs. The expression levels were calculated, and the miRNA expression clusters were analyzed for miRNAs that were differentially expressed. miRNA target genes were further predicted, and gene ontology (GO) and KEGG pathway enrichment analyses were performed for the targeted genes.

tag: treatment


title: shKDM4C-3

city: Wuhan

first: hua

middle: xiao

last: jie

state: Hubei

address: Xinhua Road

department: Tongji Medical College

institute: Huazhong University of Science and Technology

data_processing:
Illumina data analysis pipeline was then used for sequence analysis. All samples were allocated to lanes and processed in blinded fashion to keep bias to a minimum
Calculate the expression read count using the Stringtie-1.3.3b software. Then, the gene and transcript FPKM were calculated. In this process we simply filtered the expression:1）Remove genes or transcripts with length less than 100 bp. ;2）If the FPKM of a gene or transcript is less than 0.0001, it is considered to be expressed as 0. Remove genes with a table of 0 in all samples.
Genome_build: Homo_sapiens.GRCh38.dna.toplevel.REF.fa; FASTA file with MSTRG* transcript sequences
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Human Lung cancer cell line

growth_protocol: All the cells were cultured in PRMI-1640 medium containing 10% FBS and 100 μg/mL penicillin and streptomycin in 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen), and concentration was  determined using Nanodrop spectrophotometer (Thermo Scientific). The RNA integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies).
Paired-end libraries sequencing with Illumina HiSeq2500 were prepared with the mRNA-seq sample prep kit (Illumina) according to the manufacturer’s specifications.

treatment_protocol: HEK293T cells were transfected indicated shCtrl or shKDM4C and packaging plasmids pSPAX2 and pMD2G. After 48 h, SPC-A1 cell lines were infected using filtered lentiviral upernatants with the addition of 10 μg/mL Polybrene (Sigma). Stable cell lines were selected with media containing 2 μg/mL puromycin and confirmed by Western blotting.

tag: cell line

tag: cell type

value: Human Lung cancer cell line

tag: genotype


title: Synovial tisssue from Pigmented villonodular synovitis joint [zxs140421A]

city: Beijing

first: Dai

last: Hui

address: Xue Yuan Road 28, Haidian District

institute: Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Peking University

data_processing:
Raw data were cleaned via fastp.
Cleaned reads were aligned to human genome (GRCh38) by hisat2.
Aligned reads were counted by Htseq.
fpkm of 6 samples were produced via DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: raw and fpkm

extract_protocol:
Total cellular RNA of synovial tissues was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).
The sequencing library of each RNA sample was prepared by using Ion Total RNA-Seq Kit v2 according to the protocol provided by manufacturer (Life technologies, USA). Briefly, poly(A)-containing mRNA was purified from 5 ug total RNA with Dynabeads (Life technologies, USA). The mRNA was fragmented using RNaseIII and purified. The fragmented RNA was hybrized and ligated with Ion adaptor. The RNA fragments were reverse- transcribed and amplified to double-stranded cDNA. Then, the amplified cDNA was purified by magnetic bead-based method, and the molar concentration was determined for each cDNA library.

tag: subject status

value: Pigmented villonodular synovitis

tag: tissue

value: Synovial tisssue


title: 24444

type: RNA

city: Dallas

first: Lianghao

last: Ding

state: TX

address: 5323 Harry Hines Blvd

country: USA

institute: UT Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background subtracted and quantile-quantile normalised using MBCB

label: biotin

organism: Mus musculus

source_name: Liver

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

extract_protocol: RNA was extracted with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Bio-rad Experion System.

tag: strain

tag: radiation

value: High-LET

tag: dose

tag: pathology

value: HCC


title: Synovial tisssue from osteoarthritis joint [zxA]

value: osteoarthritis


title: BT145 shHDAC1 Rep3

city: Tempe

first: Christopher

middle: L

last: Plaisier

state: Arizona

department: SBHSE

institute: Arizona State University

data_processing:
Adapter trimming using cutadapt
Alignment using STAR
Counts tabulated using ht-seq-count
Genome_build: GRCh38 V2.7.1a
Supplementary_files_format_and_content: raw counts for all genes across all samples

molecule: polyA RNA

source_name: BT145 GSC

growth_protocol: ihNPCs, hGSCs and mGSCs, were cultured as spheres on non- tissue culture-treated 10cm plates or as adherent cultures on laminin on tissue culture-treated 10cm plates (ThermoFisher Scientific). ihNPCs and hGSCs were grown in DMEM/F12 media, supplemented with B27 and N2 (Invitrogen, ThermoFisher Scientific) in the presence of 20 ng/ml epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) (MilliporeSigma). Primary Human Astrocytes (NHA; ScienCell) were grown in Astrocyte Media (5% FBS, Astrocyte Growth Supplement, 1% penn-strep) on Poly-L Lysine coated plates according to manufacturer recommendations.

extract_protocol:
72 hours post-selection, total RNA was extracted from cells using the PureLink RNA Mini Kit (Ambion) in accordance to the manufacturerÕs instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GSCs, hNPCs and NHAs transduced with either shNT or shHDAC1 shRNAs at a MOI of 3 were selected with 2 _g/mL puromycin 72 hours post-transduction.

value: Brain tumor

tag: disease

value: GBM

value: IV

value: WT

value: Knock-down

tag: replicate


title: Control_2_ (C57BL/6 x C3H) _PFC_ChIP-Seq

state: NY

library_source: genomic

molecule: genomic DNA


title: normal uterine cervical-3

city: beijing

first: chunliang

last: Shang

address: 49 North Garden Rd.,Haidian District Beijing ,P.R.China

institute: peking university third hospital

description: Gene expression in fresh tissues with surgery

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 Ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 Ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arraystar Human microarray V3.0 (Agilent-045997) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash Buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: normal uterine cervical tissues

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Extraction of total RNA from fresh tissues was performed using RNAiso Plus reagent and the total RNA content of each sample was quantified using a NanoDrop ND‑1000.Standard denaturing  agarose gel electrophoresis was performed to evaluate the RNA integrity

treatment_protocol: Samples were selected based on the diagnosis of cervical cancer, determined by at least two pathologists and no patients had received chemotherapy or radiotherapy prior to surgery.

value: normal


title: shKDM4C-2


title: normal uterine cervical-6


title: Col-0_rep2

city: Pohang

first: Ildoo

last: Hwang

state: Kyungbuk

address: 77 Cheongam-Ro, Hyoja-dong, Nam-gu,

department: Department of Life Sciences

country: South Korea

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

organism: Arabidopsis thaliana

source_name: Col-0, cotyledon, replicate 2

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: 7-day-old seedlings were grown under the longday light condition (16h/8h)

extract_protocol: TriZol (Invitrogen) total RNA extraction protocol,

value: cotyledon

tag: age

tag: genotype/variation


title: Control_1_ (C57BL/6 x C3H) _PFC_ChIP-Seq

value: PFC


title: HUVEC_NC1


title: normal uterine cervical-2


title: Tau_1_PS19(P301S)_PFC_ChIP-Seq

value: Total cell lysate (bulk)


title: primary cervical cancer-5

source_name: primary cervical cancer tissues

value: tumor


title: shKDM4C-1


title: primary cervical cancer-3


title: primary cervical cancer-4


title: normal uterine cervical-4


title: normal uterine cervical-5


title: shCtrl-3

value: shCtrl


title: primary cervical cancer-2


title: Tau+WDR5-0103_1_Ps19(P301S)_PFC

data_processing:
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina) then sequencing was carried out with the HiSeq 2500 platform (Illumina)
RNA-seq tags reads were aligned to the mouse RefSeq mRNAs using TopHat2 with default parameters. Alignments with a mapping score <10 were discarded using SAMtools.
Feature Counts was used to generate a matrix of mapped fragments per USCS RefSeq known annotated gene, from which genes annotated by RefSeq as rRNA were discarded.
Analysis for differential gene expression was performed using the edgeR package with the default setting.
Genome_build: mm10
Supplementary_files_format_and_content: counts (tab)

extract_protocol:
RNA extraction from PFC samples of biological duplicates in each group used the RNAeasy Mini kit (Qiagen), coupled to an RNase-free DNase step (Qiagen). The strand-specific RNA sequencing libraries were generated from 1 μg purified RNA using TruSeq stranded total RNA plus Ribo-zero kits (Illumina).
The RNA sequencing libraries was constructed by TruSeq stranded total RNA plus Ribo-zero kits (Illumina). Sequencing was carried out with the HiSeq 2500 platform (Illumina) at the Genomics and Bioinformatics Core of State University of New York at Buffalo.Reads were first trimmed using Cutadapt to remove the 3’ end adapters and trailing sequences, followed by aligning to mouse RefSeq mRNAs using TopHat2 with default parameters.


title: Tau+WDR5-0103_2_Ps19(P301S)_PFC


title: normal uterine cervical-1


title: shCtrl-2

value: Human Lung cancer cell line


title: Synovial tisssue from osteoarthritis joint_9

hyb_protocol: Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: the arrays were scanned by the Agilent Scanner G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies).

source_name: Synovial tissue

label_protocol: Agilent Quick Amp Labeling Kit was used for sample labeling.

extract_protocol: Total cellular RNA of synovial tissues was isolated using a RNeasy Mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. The concentration of each sample was measured by NanoDrop 2000 (Thermo Scientific, USA). The quality was assessed by the Agilent2200 (Agilent, USA).

tag: disease state

value: Synovial


title: S

city: Los Angeles

first: Natalie

middle: Christine

last: Kegulian

state: CA

address: 2250 Alcazar St., CSA 149

department: Center for Craniofacial Molecular Biology

institute: University of Southern California

data_processing:
Raw fastq files were generated by the University of Southern California Molecular Genomics Core.
Fastq files were uploaded to Partek Flow® (© Partek, Inc., St. Louis, MO, USA), where the reads were subjected to pre-alignment QA/QC, bases with poor Phred quality scores were trimmed, and trimmed reads were aligned to the rat rn6 genome using STAR (version 2.5.3a).
Aligned reads were quantified at the gene and transcript levels with Partek E/M, and rn6 annotations (Karolchik D, et al (2004) The UCSC Table Browser data retrieval tool, Nucleic Acids Res (32) (Database issue):D493-496) were added using Ensembl Transcripts release 92.
Features with maximum counts less than or equal to 10 were filtered out in order to reduce noise, and then the data were normalized by the upper-quartile method after adding 1.0 to all counts. Principal component analysis (PCA) identified an outlier (2S, or rat 2, secretory cells). After this outlier was filtered out, gene counts were analyzed for differential expression via ANOVA.
Transcript counts were filtered and normalized by the same methods as gene counts and the same outlier was excluded. Subsequently, the "Detect alt-splicing" feature in Partek Flow was applied to each pair of cell populations (maturation vs. secretory, secretory vs. cervical loop, and maturation vs. cervical loop) separately to assess transcripts for differential expression.
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include processed (i.e., filtered, normalized, etc., as described above) gene and transcript counts, least squares means of genes and transcripts for each cell population, and statistical values (p-values and false discovery rates) in comparing expression between and across populations.
Supplementary_files_format_and_content: *means.txt: Abundance measurements
Supplementary_files_format_and_content: Detect_altsplicing_result_for_all_transcripts*txt: Compares expression for all analyzed transcripts that have alternative splicing (not only significantly different ones, no filters) between the indicated samples
Supplementary_files_format_and_content: ANOVA_result_for_all_genes.txt: Compares expression for all analyzed genes (not only significantly different ones, no filters)

organism: Rattus norvegicus

source_name: Secretory ameloblasts

extract_protocol:
Cervical loop, secretory, and maturation cells were dissected from rat enamel organs as previously described (see references). RNA was extracted from each cell population using the miRNeasy Mini extraction kit (catalogue #217004, Qiagen, Hilden, Germany). Concentrations of extracted RNA were measured using a NanoDrop machine (Thermo Fisher Scientific, Waltham, MA, USA).
cDNA libraries were developed from RNA samples with an RNA Integrity Number (RIN) of at least 7. Sample 1C (rat 1, cervical loop cells) was excluded due to a RIN below 7. Twenty-five million single-ended 75-bp reads were generated per sample. Library construction and RNA-seq were performed by the University of Southern California Molecular Genomics Core.
references: Chavez MG, et al (2014) Isolation and culture of dental epithelial stem cells from the adult mouse incisor, J Vis Exp (87); Lacruz RS, et al (2012) Requirements for ion and solute transport, and pH regulation during enamel maturation, J Cell Physiol 227(4):1776-1785; Wen X, Lacruz RS, & Paine ML (2015) Dental and Cranial Pathologies in Mice Lacking the Cl(-) /H(+) -Exchanger ClC-7, Anat Rec (Hoboken) 298(8):1502-1508.

value: Wistar Hannover

value: Secretory ameloblasts


title: Synovial tisssue from osteoarthritis joint_8


title: M

source_name: Maturation ameloblasts

value: Maturation ameloblasts


title: shCtrl-1


title: primary cervical cancer-1


title: D47WT_3

city: Little Rock

first: Yan

last: Cheng

state: Arkansas

address: 4301 W. Markham St.

department: Internal Medicine

institute: University of Arkansas for Medical Sciences

description: D47 geneexpression

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter the 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%) to get the clean reads.
Then we map those clean reads onto reference genome(hg19), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection.
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample

source_name: Delta47 human myeloma cell line

growth_protocol: Cells were growing in RPMI 1640 medium supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol:
Total RNA from OPM2 cells was extracted via RNeasy Plus Mini Kit (QIAGEN). RNA concentration, RNI value, 28S/18S and the fragment length distribution were detected via Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T ooligoattached magnetic beads. Following purification, theThe first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

tag: crispr editing

tag: overexpressing


title: Synovial tisssue from osteoarthritis joint_7

value: osteoarthritis


title: Synovial tisssue from Pigmented villonodular synovitis joint_3

value: Pigmented villonodular synovitis


title: 23643

value: High-LET

value: Normal


title: Synovial tisssue from Pigmented villonodular synovitis joint_1


title: Control_2_ (C57BL/6 x C3H) _PFC

tag: treatment

value: Vehicle


title: Input_1

first: Gang

last: Zhao

address: sizhisan street 1

institute: huazhong agriculture university

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the Bos taurus genome assembly using BWA version 0.7.12-r1039 (-T25; -k18).
Data were filtered using skewer version 0.1.126.
peaks were called using MACS2 version 2.1.0 with the following setting: Enrichment Fold (1.5), pvalue<=0.005 .
The peaks of IP1 and IP2 were collected together and defined as IP.
Genome_build: Bos taurus (assembly ARS-UCD1.2)
Supplementary_files_format_and_content: peak files

organism: Bos taurus

source_name: BoMac cells

growth_protocol: cultured in Roswell Park Memorial Institute (RPMI) medium supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco, Grand Island, NY, USA).

extract_protocol:
Lysates were clarified from sonicated nuclei and MbovP475-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: BoMac cells infected with M.bovis (MOI=500) for 12 h.

value: lung

value: SV40 plasmid DNA transfected

value: infected with M.bovis

tag: chip antibody


title: D47WT_2

description: D47 geneexpression


title: D47WT_1

description: D47 geneexpression


title: Synovial tisssue from Pigmented villonodular synovitis joint_2


title: IP2_1

tag: cell type

value: Polyconal antibodies against MbovP475 (prepared by ourself)


title: Control_1_ (C57BL/6 x C3H) _PFC

value: PFC

value: Total cell lysate (bulk)

tag: genotype


title: D47KO2_2

description: D47 geneexpression

value: FOXM1 knockout via CRISPR-Cas9


title: Tau_2_PS19(P301S)_PFC


title: IP1_1


title: KD-4

city: Xiamen

first: Lin

last: Zhou

state: Fujian

address: No.422, Siming South Road

department: School of Chemistry and Chemical Engineering

institute: Xiamen University

description: all.genes.expression.annot.txt

data_processing:
1. Filtering of Clean Reads
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
2. Alignment with Ribosome RNA (rRNA)
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
3. Alignment with Reference Genome
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
4 Quantification of Gene Abundance
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software. The FPKM formula is shown as follows: FPKM=10^6*C/NL/10^3. Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Genome_build: mm9 (GRCm38)
Supplementary_files_format_and_content: all.genes.expression.annot.txt: Table document includes raw counts and FPKM values for each sample.

source_name: gastrocnemius

growth_protocol: Tumor cells were subcutaneously injected into the right flank of mice on day 0. BALB/c male and female mice were inoculated with CT26 cells (1.0×10^6/100 μL), while C57BL/6 male mice were inoculated with LLC cells (7×10^5/100 μL). Both BALB/c and C57BL/6 mice showed palpable tumors (about 5 mm in diameter) on day 9 after the inoculation. Both CT26- and LLC-bearing mice were randomly divided into 2 groups (n = 8 per group): one group of mice intraperitoneally injected daily with PBS from day 9 (CAC mice), another group of mice intraperitoneally injected daily with amiloride dissolved in PBS at a dose of 2 mg/kg (AM mice). Furthermore, the Rab27 knock-down tumor cells were subcutaneously injected into the mice following the same procedure (KD mice).

extract_protocol:
On day 30, the mice were sacrificed. Both tumors and gastrocnemius were removed, weighed, and quickly frozen in liquid nitrogen for subsequent analysis.
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Four groups of mice (Nor: normal control mice; CAC: cachexia mice; AM: amiloride-treated mice; KD: mice inoculated with Rab27-knockdown cells).

value: BABL/c

value: gastrocnemius

value: Rab27-KD CT26 injection, un-treated


title: Tau_1_PS19(P301S)_PFC


title: Breast carcinoma 26A

type: genomic

city: Gothenburg

first: Toshima

middle: Z.

last: Parris

address: Medicinaregatan 1G, 6th floor

department: Department of Oncology

country: Sweden

institute: University of Gothenburg

hyb_protocol: Probes annealing and ligation on tumor DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.

scan_protocol: Hybridized probes were captured by streptavidin phycoerythrin conjugates using Fluidics Station 450 and arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: CEL files were processed using the Chromosome Analysis Suite (ChAS; v.3.3.0.139) to produce OSCHP files.

label: Biotin

source_name: Breast carcinoma

label_protocol: Performed according to manufacturer's protocols.

growth_protocol: All samples were formalin-fixed paraffin-embedded (FFPE) tumours.

extract_protocol: Tumor tissues were sectioned and DNA extracted using the AllPrep DNA/RNA FFPE kit (Qiagen). The DNA concentration was determined with the Qubit Fluorometer.

tag: gender

value: Female

tag: tissue type

value: Breast carcinoma


title: D47KO2R_3

description: D47 geneexpression

value: transfected with FOXM1 overexpression vector


title: D47KO2R_2

description: D47 geneexpression


title: Gynecological malignancies 26B

source_name: Gynecological malignancy

value: Gynecological malignancy


title: D47KO2R_1

description: D47 geneexpression


title: KD-3

description: all.genes.expression.annot.txt

tag: strain

tag: tissue


title: D47KO2EV_1

description: D47 geneexpression

value: transfected with empty vector


title: D47KO1_3

description: D47 geneexpression


title: Gynecological malignancies 25B


title: Breast carcinoma 25A


title: C4-2B

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: C4-2B human prostate tumor cell line.

hyb_protocol: Genome scale methylation analyses of NCI-H660 and C4-2B cells were carried out using Infinium MethylationEPIC BeadChip arrays (Illumina) as described previously (PMID: 27717381)

data_processing:
Methylation EPIC BeadChip array data was analyzed using the Minfi Bioconducter package in R. Samples were normalized with the Subset-quantile Within Array Normalization (SWAN) method. Probes with a detection p value of > 0.01 in 50% or more of the samples were removed. Probes with a SNP at the CpG interrogation site or at the single nucleotide extension were removed.
Raw data files are tab-delimited text files. Each file contains 2 columns: The ID (probe ID) and the raw beta values.
Processed files are tab-delimited text files. Each file contains 2 columns: The ID (probe ID) and the normalized beta values.

label: Cy3, Cy5

source_name: C4-2B human prostate tumor cell line.

growth_protocol: Cells were cultured in RPMI-1640 Media (Gibco, Life Technologies) with 10% fetal bovine serum (Atlanta Biologicals).

extract_protocol: Genomic DNA was isolated from prostate tissue samples using the DNeasy Blood & Tissue kit (Qiagen).

tag: Sex

value: male

tag: cell line

value: C4-2B (gift from L. Chung, Cedars-Sinai Medical Center, Los Angeles, CA)

value: prostate cancer


title: T-4

description: all.genes.expression.annot.txt

value: CT26 injection, amiloride-treated


title: D47KO2_1

description: D47 geneexpression


title: D47KO1_1

description: D47 geneexpression


title: WT_3

description: OPM2 geneexpression

source_name: OPM2 human myeloma cell line


title: Hematological malignancies 24B

source_name: Hematological malignancy

value: Hematological malignancy


title: T-3

description: all.genes.expression.annot.txt


title: WT_2

description: OPM2 geneexpression


title: D47KO2EV_2

description: D47 geneexpression


title: KO2_3

description: OPM2 geneexpression


title: Hematological malignancies 23B


title: KO2_2

description: OPM2 geneexpression


title: KO1R_3

description: OPM2 geneexpression


title: KO2_1

description: OPM2 geneexpression


title: T-2

description: all.genes.expression.annot.txt

value: LLC injection, amiloride-treated


title: T-1

description: all.genes.expression.annot.txt


title: Breast carcinoma 23A


title: D47KO2EV_3

description: D47 geneexpression


title: KO1R_2

description: OPM2 geneexpression


title: KO1R_1

description: OPM2 geneexpression


title: KD-2

description: all.genes.expression.annot.txt

value: Rab27-KD LLC injection, un-treated


title: KO1EV_3

description: OPM2 geneexpression


title: CAC-3

description: all.genes.expression.annot.txt

value: CT26 injection, un-treated


title: KO1EV_2

description: OPM2 geneexpression

value: FOXM1 knockout via CRISPR-Cas9


title: D47KO2_3

description: D47 geneexpression


title: Breast carcinoma 22A


title: CAC-2

description: all.genes.expression.annot.txt

value: LLC injection, un-treated


title: KO1EV_1

description: OPM2 geneexpression


title: KO1_3

description: OPM2 geneexpression


title: Malignant melanoma 21B

source_name: Malignant melanoma

value: Malignant melanoma


title: KO1_2

description: OPM2 geneexpression


title: CAC-1

description: all.genes.expression.annot.txt

value: gastrocnemius


title: NCI-H660

description: NCI-H660 human prostate tumor cell line.

scan_protocol: Genome scale methylation analyses of NCI-H660 and C4-2B cells were carried out using Infinium MethylationEPIC BeadChip arrays (Illumina) as described previously (PMID: 27717381)

growth_protocol: Cells were cultured in HITES media (ATCC) supplemented with 5% fetal bovine serum (Atlanta Biologicals).

value: NCI-H660 (ATCC CRL-5813)


title: NOR-4

description: all.genes.expression.annot.txt

value: BABL/c

value: PBS injection, un-treated


title: Breast carcinoma 21A

value: Female

value: Breast carcinoma


title: CAC-4

description: all.genes.expression.annot.txt


title: Breast carcinoma 20A


title: NOR-3

description: all.genes.expression.annot.txt


title: Malignant melanoma 22B


title: MC3T3-E1 Cell Line_treated_rep2

first: Xiuju

last: Wu

address: 650 Charles Young Dr East, CHS A2-237

institute: University of California, Los Angeles

data_processing:
The reads were mapped to the mouse genome (GRCm38) with respect to GENCODE (vM13) annotation using STAR, version 2.5.3a.
Gene counts were generated along the mapping by only using uniquely mapped reads.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen).
Libraries were constructed according to manufacturer's instructions using KAPA DNA HyperPrep Kit (Kapa Biosystems).

treatment_protocol: MC3T3-E1 cells were treated with 10μM SB216763 for 14 days.


title: Mouse pulmonary endothelial cells (EC)_rep1

source_name: Mouse pulmonary endothelial cells


title: Mouse pulmonary endothelial cells (EC)_rep2


title: Mouse pulmonary endothelial cells (EC)_rep3


title: MC3T3-E1 Cell Line_treated_rep1


title: NOR-2

description: all.genes.expression.annot.txt


title: MC3T3-E1 Cell Line_control_rep3

value: control


title: Breast carcinoma 19A


title: MC3T3-E1 Cell Line_control_rep1


title: MC3T3-E1 Cell Line_control_rep2


title: NOR-1

description: all.genes.expression.annot.txt


title: Oral cavity malignancies 18B

source_name: Oral cavity malignancy

value: Oral cavity malignancy


title: KO1_1

description: OPM2 geneexpression


title: KP.3992_000_WT_000_LPS_3h_Rep.2

city: New York

first: Kyung-Hyun

last: Park-Min

email: ParkminK@HSS.EDU, parkmink@gmail.com

address: 535 East 70th Street

institute: Hospital for Special Surgery

data_processing:
Basecalling was performed using bcl2fastq (version bcl2fastq-1.8.4)
Sequenced reads were preprocessed with fastp (with parameters fastp -q 15 -n 10 -l 20)
After preprocessing, sequenced reads were mapped to mm10 whole genome using STAR v2.7.3a (with parameters --outFilterMultimapNmax 1  --outSAMstrandField intronMotif --quantMode GeneCounts), using gencode mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: Matrix tables with raw gene counts, filtered gene counts (min expression cutoff of 5 CPM) and log CPMs from edgeR for every gene and every sample

source_name: Control macropahges stimulated with LPS rep2

growth_protocol: For the generation BMDMs, bone marrow cells were flushed from femurs and tibias of mice and cultured at 37oC, 5% CO2 in complete α-MEM medium (10% heat-inactivated defined FBS (HyClone Fisher), penicillin-streptomycin (Invitrogen), and L-glutamine (Invitrogen)) with 5% L929 cell supernatant as conditioned medium (CM) as a source of M-CSF (Englen et al., 1995) after lysis of RBCs using ACK lysis buffer (Invitrogen). Then, the non-adherent cell population was recovered the next day and cultured for three additional days. Final concentration of M-CSF in our culture was 23.3 ng/ml. Cells that remained in suspension were removed by aspiration and attached cells were washed twice with PBS, then re-plated and cultured with complete α-MEM medium with 20 ng/ml human M-CSF.

extract_protocol:
RNA from the cultures was extracted using a RNeasy Plus Mini Kit (Qiagen) according to the manufacturers instructions.
Libraries were prepared following the manufacturer's procotols for the Illumina TruSeq Stranded mRNA library preparation kit (part # 20020595). Purified mRNA was isolated from total RNA using oligo-dT beads then converted into double stranded cDNA. Fragmented cDNA libraries were individually indexed and properly ligated molecules were PCR enriched to generate final library.

treatment_protocol: Cells were stimulated with or without LPS (10ng/ml) for 3hr

value: LysM cre

value: Bone marrow-derived macrophages

value: WT

value: LPS

value: female


title: Hematological malignancies 20B

value: Hematological malignancy


title: Mouse_control ear

city: Frederick

first: Zhi-Ming

last: Zheng

state: Maryland

department: Center for Cancer Research

institute: National Cancer Institute

data_processing:
Library strategy: Targeted DNA-Seq
Samples were pooled and sequenced on one HiSeq 3000 run.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Reads were aligned to a chimeric mm10+MmuPV1 genome using STAR 2.5.2b with the following parameters: "STAR --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 clip3pAdapterSeq - --runThreadN 32 --outSAMtype BAM Unsorted --chimSegmentMin 20"
Output SAM files were filtered to contain virus sequence
Genome_build: mm10; MmusPV1 (NC_014326; GI:301173443)
Supplementary_files_format_and_content: TXT files containing predicted junctions found by STAR (in junction.out format)

source_name: Uninfected control tissue

growth_protocol: The tissues were observed 6 months for tumor formation after virus innoculation.

extract_protocol:
Mouse tissues were digested with proteinase K at 50°C overnight and the genomic DNA was precipitated with ethanol in the presence of sodium chloride.
One microgram of genomic DNA was fractionated by gel electrophoresis to remove the majority of the episomal viral genomic DNA. The host DNA was recovered and sheared into 300-500 bp long fragments using a Covaris M220 Focused-ultrasonicator (Covaris). The fragmented DNA was end repaired and dA-tailed using the NEBNext Ultra Ligation kit (NEB, #E7445) according to the manufacturer’s instructions. A partially double stranded linker (5’-GTAATACGACTCACTATAGCGCTGCGCTTAAGCGACT-3’, 5'–PO4-GTCGCTTAAGCGCAG-3’-C6) with a 3’ T overhang was ligated to the genomic DNA fragments using the NEB Quick Ligation Kit (NEB, #M220). Virus specific primers (Pr2976/Pr3277/Pr3742) were used to selectively amplify the integration junctions. Two rounds of 20 cycles PCR were conducted to enrich integration junctions in the sequencing libraries using Phusion High-Fidelity PCR Kit (NEB, #E0553).

value: Ear (Control)

tag: infection

value: Uninfected


title: Mouse_Muzzle

source_name: MmuPV1 infected mouse wart

value: Muzzle


title: Mouse_ear

value: Ear


title: KP.3992_000_WT_000_CTRL_0h_Rep.2

source_name: Conrol M0 macrophages rep2

value: MCSF


title: Breast carcinoma 18A


title: Treated_Input_ChIPSeq

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2.
Peaks were called using HOMER tools with the following setting: ChIP-seq peak call  threshold (0.001 FDR, with 4 fold enrichment), treated versus control or vice versa.
Motifs were discovered using HOMER motif analysis function.
Peak annotation was performed to associate peaks with nearest genes using HOMER peak annotation function.
Genome_build: mm10

source_name: MC3T3-E1 Cell Line

growth_protocol: The osteoblast cell line MC3T3 was purchased from ATCC (CRL-2593) and cultured as per the manufacturer's protocol.

extract_protocol:
MC3T3 cell lysates were clarified from sonicated nuclei and ChIPs were performed by using specific antibodies for SMAD1 (Cell Signaling Technology, 9743) and  β-catenin (R&D System, MAB2006).
Libraries were prepared according to manufacturer's instructions using KAPA DNA HyperPrep Kit (Kapa Biosystems).

treatment_protocol: MC3T3 cells were treated with 10μM SB216763 for 14 days.

value: bone/calvaria


title: Control_Input_ChIPSeq


title: KP.3992_000_KO_000_LPS_3h_Rep.2

source_name: MYC deficient  macrophages stimulated with LPS  rep2

value: MYC f/fLysM cre

value: MYC cKO


title: Malignant melanoma 19B

value: Female

value: Malignant melanoma


title: Gynecological malignancies 17B

value: Gynecological malignancy


title: Breast carcinoma 17A

value: Breast carcinoma


title: Control_β-catenin_ChIPSeq


title: Treated_β-catenin_ChIPSeq


title: Malignant melanoma 15B


title: Breast carcinoma 15A


title: Mouse 2_control ear

data_processing:
Samples were pooled and sequenced on one HiSeq 2500 run.
Basecalling was performed by RTA (version 1.18.64).
Demultiplexing and FASTQ generation was performed using bcl2fastq (version 2.17) allowing 1 mismatch.
Reads were filtered with a base call quality >94% of bases with Q30 and and above.
Reads were aligned to the reference genome (mm10 + MmuPV1) using STAR 2.5.1b with the following parameters: "--runThreadN 16 --twopassMode Basic --chimOutType SeparateSAMold --chimSegmentMin 1"
Genome_build: mm10; MmusPV1 (NC_014326; GI:301173443)
Supplementary_files_format_and_content: TXT files containing predicted junctions generated by STAR (in junction.out format)

source_name: MmuPV1 infected control tissue

extract_protocol:
Total RNA from frozen tissues was extracted after homogenization using TriPure Isolation reagent (Roche) and treated with TURBO DNA-free™ Kit (Thermo Fisher Scientific).
cDNA libraries were prepared on ribo-depleted total RNA using Illumina Stranded Total RNA (Illumina, RS-122-2201, San Diego, CA) protocol with TruSeq V4 chemistry and sequenced in the Sequencing Facility of NCI on Illumina HiSeq 2500 with 2×125 nts modality and depth of 100 million reads per sample.

tag: mouse source

value: Mouse 2


title: Mouse 1_control ear

value: Mouse 1


title: HD5

city: Hamburg

first: Ole

last: Pless

state: Hamburg

address: Schnackenburgallee 114

country: Germany

institute: Frauenhofer ITMP

data_processing:
Ensembl human reference genome (GRCh38) with STAR (v.2.4)
Gene counting with featureCounts (v.1.5.1)
Genome_build: Ensembl human reference genome (GRCh38)
Supplementary_files_format_and_content: gene count matrix with all genes on rows and samples on columns

source_name: BCECs

growth_protocol: The hiPSC line WISCi004-B/IMR90-4 was used to differentiate BCECs. a single cell suspension of hiPSCs was prepared with Accutase. The cell suspension was centrifuged at 300 x g for 5 min and cells were seeded in mTeSRTM1 supplemented with 10 µM Y-27632 onto Matrigel-coated 6-well plates. The seeding density was optimized for each hiPSC line. For the differentiation of hiPSCs to BCECs, the neurodevelopmental process in vivo has to be recapitulated in vitro. For brain-capillary endothelial-like cells, a co-differentiation of neural and endothelial cells was initiated by treatment with so-called unconditioned medium. After 2-3 days when optimal cell densities of 2-4x104 cells/cm2 were reached, medium was switched to unconditioned medium in order to initiate co-differentiation of BCECs and neuronal cells (referred to as day 0 of differentiation throughout the manuscript). Unconditioned medium was composed of 78.5% DMEM/F12 , 20% KnockOutTM serum replacement, 1% MEM NEAA, 0.5% L-glutamine, and 0.1 mM β-mercaptoethanol. A daily change of unconditioned medium for 5 days was followed by double feeding at day 6 with endothelial cell (EC) medium supplemented with 20 ng/ml hbFGF  and 10 µM retinoic acid to expand the BCECs. EC medium was composed of Human Endothelial-SFM and, if not stated otherwise, 0.5% B27 Supplement as described recently (Neal et al., 2019). After 48 h without medium change, cells were dissociated with Accutase for 30 min and seeded at a cell density of 1x106 cells/cm2 onto collagen IV/fibronectin-coated transwell insert in EC medium supplemented with 20 ng/mL hFGF and 10 µM RA. This seeding step at day 8 in combination with the collagen IV/fibronectin-coating allows for an efficient purification of BCECs. At day 9, hiPS-BCECs were adapted to EC medium without hFGF and RA (in transwell systems with 200 µl of medium apical and 800 µl basolateral) for 24 h. TEER measurements were performed to evaluate the integrity of the generated in vitro BBB to be used for further applications.

extract_protocol: NEBNext Ultra RNA Library Prep Kit (Illumina)

treatment_protocol: At day 10 of differentiation hipsc-derived BCECs were either mock infected or exposed to SARS-CoV-2. After 24 hours cells were harvested and total RNA was extracted according to the manufacturer’s instructions using the NucleoSpin® RNA Kit (#740955.250, Macherey-Nagel). RNA concentration and quality was determined using a NanoDrop™ 1000 Spectrophotometer (ThermoFisher Scientific) and samples were stored at -80 °C until further use.

value: BCECs


title: HD4


title: Vessel2_39_21


title: Mouse 3_control ear

value: female

value: Mouse 3


title: Mock3

value: Mock


title: Vessel2_654_20


title: Vessel2_37_21


title: Mouse 3_Muzzle


title: KP.3992_000_KO_000_CTRL_0h_Rep.2

source_name: MYC deficient M0 macrophages rep2

value: Bone marrow-derived macrophages


title: Mock2


title: Control_SMAD1_ChIPSeq


title: Thyroid malignancies 13B

source_name: Thyroid malignancy

value: Thyroid malignancy


title: Breast carcinoma 14A

source_name: Breast carcinoma


title: Treated_SMAD1_ChIPSeq


title: Mouse 3_tail

value: Tail


title: Breast carcinoma 13A


title: Mock6


title: Mock5


title: Mock1


title: Mouse 3_ear

value: Ear


title: HD3


title: Malignant melanoma 14B


title: Mock4


title: Oral cavity malignancies 12B

value: Oral cavity malignancy


title: Mouse 2_Muzzle

value: Muzzle


title: HD2


title: Breast carcinoma 12A


title: HD6


title: Mouse 2_tail


title: Sarcoma 11B

source_name: Sarcoma

value: Sarcoma


title: Mouse 2_ear


title: Mouse 1_Muzzle


title: Breast carcinoma 11A

value: Female


title: Mouse 1_tail


title: RNA_TC-797_Pano_rep1_July2020

city: Boston

first: Hitoshi

last: Shiota

state: Massachusetts

address: 77 Avenue Louis Pasteur, NRB rm652

institute: Brigham and Women's Hospital

description:
Total RNA from TC-797 treated with Panobinostat_replicate 1
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls

data_processing:
Reads were trimmed and verified for quality with Trim Galore! (v.0.3.3, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned with STAR (v.2.7.5a) to the human genome (GRCh38 primary assembly) with Gencode (v.34) annotations and to the External RNA Control Consortium (ERCC92) spike-in sequences in a single pass using default settings for gene counting (--quantMode GeneCounts).
Transcripts with < 1 million reads mapped in all samples (73%) were removed before differential expression (DE) analysis.
ERCC-invariant sequences were used with RUVg with k=1 (v.1.18.0) under R 3.6.3. (R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/]) to capture unwanted variation.
The resulting RUVg W_1 weight matrix was incorporated into the DESeq2 (v.1.24) design matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel spreadsheet with counts per gene (raw or normalized)

source_name: TC-797 NUT Carcinoma cell line

growth_protocol: NUT carcinoma (NC) cell lines TC-797 and 10-15 cells were maintained as monolayer cultures in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Hyclone, South Logan, UT), 1% Penicillin Streptomycin (SV30010, Hyclone) and 1X GlutaMAX (35050061, Gibco/Thermo Fisher Scientific, Waltham, MA).

extract_protocol:
RNA was extracted from 1 x 107 cells using TRIzol RNA Isolation Reagent (15596026, Invitrogen) followed by a second purification using RNeasy Plus Mini Kit according to the manufacturer’s instructions (74134, Qiagen, Hilden, Germany).  Genomic DNA was removed by DNase digestion with Turbo DNA-free kit (AM 1907, Fisher Scientific). DNase digestion was repeated twice at 37 ºC for 30 min, and the RNA was cleaned using the Zymo RNA Clean & Concentrator kit according to the manufacturer’s instructions (R1013, Zymo Research). DNA integrity was analyzed on a 2200 TapeStation RNA ScreenTape (Agilent Technologies, Santa Clara, CA) (RIN>7 as intact). ERCC ExFold RNA spike-in mixes (4456739, Invitrogen) were added at 2 µl of 1:100 diluted spike-in per 1000 ng of RNA for normalization of RNA transcript levels. Ribosomal RNA was removed by NEBNext rRNA Depletion Kit (E6350, NEB).
Sequencing libraries were generated using NEBNext Ultra II Directional RNA library kit (E7760S, NEB).

treatment_protocol: TC-797 or 10-15 cells were treated with DMSO, panobinostat (30 nM) or IRBM6 (200 nM) for 4 hours.

value: Panobinostat

tag: replicate


title: RNA_TC-797_Pano_rep2_July2020

description:
Total RNA from TC-797 treated with Panobinostat_replicate 2
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls


title: Hematological malignancies 10B

source_name: Hematological malignancy

value: Hematological malignancy


title: Mouse 1_ear


title: RNA_TC-797_DMSO_rep1_July2020

description:
Total RNA from TC-797 treated with DMSO_replicate 1
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls

value: DMSO


title: HD1


title: Breast carcinoma 09A

value: Breast carcinoma


title: RNA_10-15_DMSO_rep1_July2020

description:
Total RNA from 10-15 treated with DMSO_replicate 1
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls

source_name: 10-15 NUT Carcinoma cell line


title: RNA_10-15_Pano_rep2_July2020

description:
Total RNA from 10-15 treated with Panobinostat_replicate 2
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls


title: Inner medulla DicerAQP2Cre+ rep3

city: Ariano Irpino

first: Fulvio

last: D'Angelo

address: via Camporeale

country: Italy

institute: Biogem

data_processing:
Data quality was checked using FASTQC v0.11.3 (https://github.com/golharam/FastQC).
Data were processed using the iMir tool (https://tools4mirs.org/software/isomirs_identification/imir/) to remove the adapter sequence and reads with at least 15 nucleotides were retained.
Retained reads were mapped to the mouse genome (mm9) to identify miRNAs according to miRBase v.21 (http://www.mirbase.org/) annotations.
miRNA expression normalization was performed using DESeq2 software.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each sample

source_name: Inner medulla

extract_protocol:
Total RNA was extracted from mouse IM with the RNeasy Micro Kit (Qiagen, Milan, Italy, #74004) according to the manufacturer’s protocol.
The library was generated from 1 µg of RNA using a TruSeq small-RNA protocol (Illumina Way, San Diego, CA, USA, #200-0036).

tag: genotype/variation


title: Malignant melanoma 09B

source_name: Malignant melanoma

value: Malignant melanoma


title: Input_H3K27ac_797_Pano_rep2_Nov2020

data_processing:
Reads were trimmed and verified for quality with Trim Galore! (v.0.6.4_dev, https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Trimmed reads were aligned with STAR (v.2.7.5a) to the human genome (GRCh38 primary assembly) using end-to-end alignment (--runMode alignReads --alignIntronMax 1 --alignEndsType EndToEnd).
Alignment files were restricted to named chromosomes (chr1, chr2, …, chrX, chrY). Duplicate reads were filtered out using Picard Tools MarkDuplicates (v.2.23.8).
MACS2 (v.2.2.7.1) was used to identify enrichment peaks in each sample vs its matched input.
Peaks from replicate samples were combined with bedtools2 mergeBed (-d 300) (v2.23.0) to make a superset of peaks per condition.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak for enrichment peaks

growth_protocol: NUT carcinoma (NC) cell line TC-797 cells were maintained as monolayer cultures in DMEM (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Hyclone, South Logan, UT), 1% Penicillin Streptomycin (SV30010, Hyclone) and 1X GlutaMAX (35050061, Gibco/Thermo Fisher Scientific, Waltham, MA).

extract_protocol:
3 x 10^7 cells were used for anti-NUT ChIP and 1 x 10^7 cells were used for anti-H3K27ac ChIP. After the treatment, the cells were trypsinized and crosslinked in 10 ml/1 x 10^7 cells of PBS containing 1% formaldehyde (28908, Thermo Fisher Scientific) for 10 min at room temperature. The formaldehyde solution was quenched by adding 2 M glycine to a final concentration of 125 mM. Crosslinked cells were washed in PBS, and the cell pellet was stored in -80 ºC until use. Chromatin from 1 x 10^7 cells was extracted in 1 ml of buffer I (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40/IGEPAL CA630, 0.25% Triton X-100, 1x cOmplete, EDTA-free Protease Inhibitor Cocktail (11873580001, Millipore Sigma)) for 10 min on ice. The lysate was centrifuged at 1811 x g for 5 min at 4 ºC, and the supernatant was discarded. The pellet was resuspended in 1 ml per 2 x 10^7 cells of buffer II (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, cOmplete EDTA-free Protease Inhibitor Cocktail (Millipore Sigma)) and incubated at room temperature for 10 min with slow, end-over-end rotation. The samples were centrifuged at 1811 x g for 5 min at 4 ºC, and the supernatant was discarded. The pellet was resuspended in 1 m per 2 x 10^7 cells of buffer III (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% sarkosyl, cOmplete, EDTA-free Protease Inhibitor Cocktail (Millipore Sigma)), and transferred to a milliTube 1ml AFA Fiber (520135, Covaris, Woburn, MA), then sheared by a Covaris E220 Focused Ultrasonicator (Covaris). Sheared chromatin was centrifuged at 15,493 x g for 10 min at 4 ºC, and digested with 20 U of benzonase (Sigma-Aldrich, St. Louis, MO) per1 x 10^7 cells. The immunoprecipitation was performed as described (Shiota et al. 2020).
The  library was prepared at Genomics Facility at University of Chicago (Chicago, IL; https://fgf.uchicago.edu/).

treatment_protocol: TC-797 was treated with DMSO or panobinostat (30 nM) for 4 hours.


title: ChIP_H3K27ac_797_Pano_rep2_Nov2020


title: Input_B4N_797_Pano_rep2_Nov2020


title: RNA_10-15_Pano_rep1_July2020

description:
Total RNA from 10-15 treated with Panobinostat_replicate 1
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls


title: Gynecological malignancies 08B

source_name: Gynecological malignancy

value: Gynecological malignancy


title: C

source_name: Cervical loop cells

value: Wistar Hannover

value: Cervical loop cells


title: Inner medulla Control rep3

value: control


title: ChIP_B4N_797_Pano_rep2_Nov2020

value: NUT


title: Breast carcinoma 10A


title: Breast carcinoma 08A


title: Inner medulla Control rep2


title: Input_H3K27ac_797_DMSO_rep2_Nov2020


title: Inner medulla DicerAQP2Cre+ rep2


title: RNA_TC-797_DMSO_rep2_July2020

description:
Total RNA from TC-797 treated with DMSO_replicate 2
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls


title: Input_B4N_797_DMSO_rep2_Nov2020


title: Input_H3K27ac_797_Pano_rep1_Nov2020


title: RNA_10-15_DMSO_rep2_July2020

description:
Total RNA from 10-15 treated with DMSO_replicate 2
RNAseq_July2020_pano_raw_counts.xls
RNAseq_July2020_pano_regularizedLog2.xls


title: Malignant melanoma 07B


title: Input_B4N_797_Pano_rep1_Nov2020


title: ChIP_H3K27ac_797_DMSO_rep2_Nov2020


title: Inner medulla Control rep1


title: ChIP_H3K27ac_797_Pano_rep1_Nov2020


title: Gastrointestinal malignancies 06B

source_name: Gastrointestinal malignancy

value: Gastrointestinal malignancy


title: Input_H3K27ac_797_DMSO_rep1_Nov2020


title: Breast carcinoma 07A


title: Inner medulla DicerAQP2Cre+ rep1


title: ChIP_B4N_797_Pano_rep1_Nov2020


title: ChIP_B4N_797_DMSO_rep2_Nov2020


title: Young/Replicate 6

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
Sequencing was performed on a Illumina HiSeq 2500 with 50 bp single-end runs. Overall quality of the next-generation sequencing data was evaluated automatically and manually with fastQC v0.11.8 (Andrews 2010) and multiQC v1.7 (Ewels et al. 2016 ). Reads from all passing samples were adapter trimmed and quality filtered using cutadapt v2.3 (Martin 2011 ) and filtered for a minimum length of 17nt. Mapping steps were performed with bowtie v1.2.2 (Langmead  et al. 2009) and miRDeep2 v2.0.1.2 (Friedländer et al. 2012 ), whereas reads were mapped first against the genomic reference GRCh38.p12 provided by Ensembl (Zerbino et al. 2018 ) allowing for two mismatches and subsequently miRBase v22.1 (Griffiths-Jones 2004 ), filtered for miRNAs of hsa only, allowing for one mismatch. For a general RNA composition overview, non-miRNA mapped reads were mapped against RNAcentral (Sweeney et al. 2019 ) and then assigned to various RNA species of interest.
Genome_build: GRCm38_p5_mp
Supplementary_files_format_and_content: Microsoft Excel (xlsx)
Supplementary_files_format_and_content: Raw data (raw read counts)
Supplementary_files_format_and_content: Normalized data (reads per million)
Supplementary_files_format_and_content: EdgeR output

source_name: Primary cardiac fibroblasts

growth_protocol: C57BL/6J mice (from Jackson Laboratory) - bred in the animal facility of the Institute of Cellular Biology and Pathology, Bucharest, Romania (specific pathogen free conditions, controlled environment of 12/12 hours light/dark cycle, 21°C, 55% to 60% humidity, with chow and water ad libitum). A cohort of female and male naturally aging mice was established by maintaining the animals in the aforementioned conditions. The animals were sacrificed by heart removal after being anesthetized to surgical level with a cocktail of Ketamine:Xylazine (100:10 mg/kg b.w.). Primary mouse cardiac fibroblasts were isolated as follows: the heart was digested in 0.1% Trypsin and 100 µg/mL Collagenase type I (Sigma) in HBSS (0.137 M NaCl, 5.4 mM KCl, 0.25 mM Na2HPO4, 0.44 mM KH2PO4, 1.3 mM CaCl2, 1 mM MgSO4, 4.2 mM NaHCO3), in a water bath, at 37°C, under constant stirring, in multiple 5-min fractions. The resulting single cell suspension was centrifugated at 400 g for 5 minutes at 4°C. The resulting pellet was resuspended in 10 mL of fibroblast culture medium containing DMEM/F12 supplemented with 10% FBS, 1% Penicillin-Streptomycin-Amphotericin B, 1X L-Glutamine, 10 ng/µL FGF, 10 µg/mL Insulin, divided on two 60 mm × 15 mm Petri dishes and cultured in a humidified atmosphere with 5% CO2 at 37°C. The medium was freshened after the first 24 hours and the next two days. At day 5 we collected the cells for subsequent analyzes.

extract_protocol:
Total RNA was extracted from PBS-washed cell pellets using miRNeasy Mini Kit (Qiagen). The samples were homogenized in 1 mL Qiazol (Qiagen) using a vortex, followed by incubation at room temperature for 5 minutes. Chloroform was added to the lysates followed by cooled centrifugation at 12,000 g for 15 minutes at 4°C. Exactly 650 µL of the upper aqueous phase was mixed with 750 µL ethanol and RNA was precipitated on a miRNeasy mini column followed by automated washing with RPE and RWT buffer in a Qiacube liquid handling robot. Finally, total RNA was eluted in 30 µL nuclease free water. Total RNA integrity was checked using the RNA 6000 Nano Assay (Agilent, CA), as well as spectrophotometric RNA quantification (Nanodrop). All samples showed RIN values between 9.7 and 10.
Equal amounts of total RNA (1 µg) were used for small RNA library preparation using NEBNext small RNA library preparation kit (New England Biolabs, US) according to the manufacture’s declarations. Adapter-ligated libraries were amplified using barcoded Illumina reverse primers in combination with the Illumina forward primer. Libraries were pooled equimolar on the basis of DNA 1000 Bioanalyzer quantification (Agilent, CA) and gel-based size selection was performed on the pooled library to enrich for insert sizes between 18 and 36 base-pairs. Sequencing was performed on Illumina HiSeq 2500 with 50 bp single end read.

value: wild-type

tag: age (months)

tag: age group

value: Young

value: female

tag: passage

tag: time in culture

value: 5 days


title: Breast carcinoma 06A


title: Young/Replicate 5


title: Input_B4N_797_DMSO_rep1_Nov2020

tag: treatment

tag: chip antibody


title: Young/Replicate 4

tag: genotype


title: Malignant melanoma 05B

tag: gender


title: Breast carcinoma 05A

tag: tissue type


title: K562_dMLL_H3_ChIP-seq_2

city: Busan

first: AeRi

last: Kim

address: 2, Busandaehak-ro 63beon-gil, Geumjeong-gu

institute: Pusan national university

data_processing:
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the hg19 canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files.  Peak regions were identified using MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: K562 cells were cultured in RPMI1640 medium containing 10% FBS.

extract_protocol:
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K4me1, H3K27ac and H3) was processed using NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with 1.5 µM NEBNext adaptors. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles). The fragments are purified using NEBNext sample purification beads.

tag: cell type

value: erythroleukemia cells

tag: agent

value: dMLL

value: H3 (Abcam, ab1791)


title: ChIP_H3K27ac_797_DMSO_rep1_Nov2020


title: K562_Con_H3_ChIP-seq_2

value: Con


title: Young/Replicate 3

tag: strain

tag: Sex

value: male


title: K562_dp300_H3_ChIP-seq_2


title: K562_dp300_H3K27ac_ChIP-seq_2

value: H3K27ac (Abcam, ab4729)


title: K562_Con_H3K27ac_ChIP-seq_2


title: Young/Replicate 2


title: K562_dMLL_H3K27ac_ChIP-seq_2


title: ChIP_B4N_797_DMSO_rep1_Nov2020

value: DMSO


title: Thyroid malignancies 04B

value: Female

value: Thyroid malignancy


title: Breast carcinoma 04A

value: Breast carcinoma


title: K562_dp300_H3K4me1_ChIP-seq_2

value: H3K4me1 (Abcam, ab8895)


title: K562_dMLL_H3K4me1_ChIP-seq_2


title: Young/Replicate 1


title: Breast carcinoma 03A


title: CJM-input_L1

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

data_processing:
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Hisat2.
After mapping to transcriptomes, significantly enriched m6A modification sites were detected by using exomePeak (version 2.8.0, an exome-based peak-calling algorithm) with default parameters.
HOMER software (version 4.10) was used to de novo identify consensus motifs from the enriched m6A modification sites.
For differential methylation analysis, peaks overlapping or unique for treated and control samples were detected using exomepeak software and fold changes with adjusted p values were calculated for the hypo- and hypermethylated peaks.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include fold changes and p values
Supplementary_files_format_and_content: raw counts

source_name: conjunctival

extract_protocol:
Total RNA isolation from pterygium and conjunctival was performed using the TRIzol reagent and a Qiagen RNeasy kit, following the manufacturer’s instructions. RNA was reversed using random hexamer priming (Applied Biosystems).
Ribosomal RNA was removed from the products, and the first strand of cDNA was synthesized by SMART. PCR amplification and library purification were used to obtain an ultramicro-RNA methylated m6A library. Bioptic Qsep100 Analyzer was used to conduct quality control over the library.

tag: disease state

value: normal


title: Old/Replicate 5

value: Old


title: Old/Replicate 4

value: wild-type


title: AJM-input_L1


title: Breast carcinoma 24A


title: WT_1

description: OPM2 geneexpression

data_processing:
Firstly, we removed the reads mapped to rRNAs and get rawdata, then we filter the 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%) to get the clean reads.
Then we map those clean reads onto reference genome(hg19), followed with novel gene prediction, SNP & INDEL calling and gene splicing detection.
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include readcount values for each sample

source_name: OPM2 human myeloma cell line

extract_protocol:
Total RNA from OPM2 cells was extracted via RNeasy Plus Mini Kit (QIAGEN). RNA concentration, RNI value, 28S/18S and the fragment length distribution were detected via Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit).
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T ooligoattached magnetic beads. Following purification, theThe first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligoattached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

tag: crispr editing

tag: overexpressing


title: FNR-input_L2

source_name: pterygium

value: pterygium


title: Old/Replicate 6

value: female


title: Malignant melanoma 03B

value: Malignant melanoma


title: CJM-input_L2


title: K562_Con_H3K4me1_ChIP-seq_2

value: erythroleukemia cells


title: 1FNR-input_L2


title: BJM-input_L1


title: Breast carcinoma 01A


title: Old/Replicate 3

value: 5 days


title: Old/Replicate 2


title: D47KO1_2

description: D47 geneexpression

source_name: Delta47 human myeloma cell line

value: FOXM1 knockout via CRISPR-Cas9


title: ENR-input_L1


title: DNR-input_L2


title: DNR-input_L1


title: HE_40 rep1

city: wenzhou zhejiang province china

first: Fugen

last: ShangGuan

address: Nanbaixiang Street, Ouhai District

institute: The First Affiliated Hospital of Wenzhou Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HepG2 cells

extract_protocol:
The CBD (40μM) exposed HepG2 and MHCC97H cells were collected after 24hr and then cells were washed by PBS for 3 times and then lysed by Trizol at 4℃ for 10 minutes . Next, samples were sent to Novogene on dry ice. A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations
RNA libraries were prepared for sequencing using lliumina protocols.

value: CBD exposed for 24hr


title: HE_40 rep2


title: Old/Replicate 1

value: male


title: TC-797_2_IRBM6_200nM_4h_Aug2019

description:
Total RNA from TC-797 treated with IRBM6_replicate 2 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls

tag: cell line

tag: replicate


title: JM-IP-3

description: m6A-IP RNA

tag: meip antibody

value: Abcam, cat. no. ab151230


title: ENR-input_L2


title: HE_0 rep2

value: none treated


title: HE_0 rep1


title: JM-IP-1

description: m6A-IP RNA


title: JM-IP-2

description: m6A-IP RNA


title: NR-IP-3

description: m6A-IP RNA


title: TC-797_1_IRBM6_200nM_4h_Aug2019

description:
Total RNA from TC-797 treated with IRBM6_replicate 1 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls


title: H_40 rep2

source_name: MHCC97H cells


title: 10-15_2_IRBM6_200nM_4h_Aug2019

description:
Total RNA from 10-15 treated with IRBM6_replicate 2 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls


title: NR-IP-2

description: m6A-IP RNA


title: NR-IP-1

description: m6A-IP RNA


title: 10-15_1_IRBM6_200nM_4h_Aug2019

description:
Total RNA from 10-15 treated with IRBM6_replicate 1 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls


title: DU145_SRRM4_1

data_processing:
Sequencing reads were mapped to the hg38 human genome using STAR.v2.7.3a.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.29
Gene level abundance was quantitated from the filtered human alignments in R using the Genomic Alignments Bioconductor package using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.
Genome_build: hg38
Supplementary_files_format_and_content: Processed files are tab-delimited text files. Each file contains 7 columns: Entrez Gene ID, gene symbol, gene name, mRNA size, raw fragment count (by gene), FPM (fragments per million reads mapped) and FPKM (fragments per kilobase per million reads mapped).

source_name: DU145 human prostate tumor cell line transfected with SRRM4 expression vector.

extract_protocol:
Total RNA was isolated from cell lines with RNA STAT-60 (Tel-Test) followed by purification with RNeasy Mini Kit (Qiagen) using the manufacturer’s recommended in solution DNase digestion (Qiagen).
RNA-Seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced on an Illumina NovaSeq S1 100 flowcell generating 50 bp paired end reads.

treatment_protocol: For ectopic expression studies, cells were transfected with Tru ORF Gold expression vectors (OriGene) for SRRM3 (CAT#: RC226066), SRRM4 (CAT#: SC314194) pCMV6-Entry (CAT#: ps100001) or pCMV6-Neo (CAT#: PCMV6NEO) using the TransIT-X2 Transfection Reagent (Mirus Bio) according to manufacturer’s protocols. Cells were seeded 24 hours prior to transfections and total RNA was collected seventy-two hours post-transfection.

value: DU145 (ATCC HTB-81)

value: prostate cancer

tag: transfected with

value: SRRM4 expression vector.


title: DU145_SRRM4_2


title: H_40 rep1


title: H_0 rep2


title: TC-797_2_DMSO_4h_Aug2019

description:
Total RNA from TC-797 treated with DMSO_replicate 2 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls

value: DMSO


title: DU145_CMV_Neo_2

source_name: DU145 human prostate tumor cell line transfected with pCMV6-Neo expression vector.

value: pCMV6-Neo expression vector.


title: DU145_CMV_Neo_1


title: CAD3 RNAseq

city: Suzhou

first: Ping

last: Li

address: 242 Guangji Road，Suzhou ，Jiangsu

institute: The Affiliated Suzhou Hospital of Nanjing Medical University

data_processing:
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), the high quality trimmed reads were aligned to the human reference genome (UCSC hg19).
Then, guided by the Ensembl gtf gene annotation file with hisat2 software (v2.0.4), cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
The LncRNA target genes were predicted based on the nearyby relationship, and GO and KEGG pathway analysis were performed based on these target genes.
Genome_build: Hg19
Supplementary_files_format_and_content: excel format; fpkm

source_name: coronary artery disease 3

growth_protocol: The diagnosis of CAD was based on angiographic evidence of at least one segment of a major coronary artery, including the left anterior descending, left circumflex, and right coronary artery, with ≥ 50% stenosis. During the same period, healthy subjects were screened by medical history, routine blood tests, liver and kidney function, etc. Exclusion criteria: (a) patients with severe primary diseases such as liver, kidney and hematopoietic system; (b) patients with acute infection, trauma or other operations; (c) patients with myocardial infarction, cerebral infarction, cancer and other major diseases; (d) patients with alcoholism and drug addictions; (e) patients older than 85 years and pregnancy patients.

extract_protocol:
Peripheral blood samples (4-6 mL) were collected from CAD patients and healthy subjects using EDTA vacuum anticoagulant blood vessels. After a 30-min incubation at 4°C, the blood samples were centrifuged at 1,500 rpm for 10 min. Then, the plasma was recentrifuged at 12,000 rpm for 10 min to remove debris. Plasma RNA was extracted by TRIzolTM LS Reagent and total RNA (1 μg) was used to lncRNA-Seq high-throughput sequencing.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: tissue

value: plasma

value: coronary artery disease


title: DU145_SRRM3_1

source_name: DU145 human prostate tumor cell line transfected with SRRM3 expression vector.

value: SRRM3 expression vector.


title: KD-1

description: all.genes.expression.annot.txt

data_processing:
1. Filtering of Clean Reads
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters;  2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
2. Alignment with Ribosome RNA (rRNA)
Short reads alignment tool Bowtie2 [2] (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
3. Alignment with Reference Genome
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
4 Quantification of Gene Abundance
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using StringTie software. The FPKM formula is shown as follows: FPKM=10^6*C/NL/10^3. Given FPKM(A) to be the expression of gene A, C to be number of fragments mapped to gene A, N to be total number of fragments that mapped to reference genes, and L to be number of bases on gene A. The FPKM method is able to eliminate the influence of different gene lengths and sequencing data amount on the calculation of gene expression. Therefore, the calculated gene expression can be directly used for comparing the difference of gene expression among samples.
Genome_build: mm9 (GRCm38)
Supplementary_files_format_and_content: all.genes.expression.annot.txt: Table document includes raw counts and FPKM values for each sample.

source_name: gastrocnemius

extract_protocol:
On day 30, the mice were sacrificed. Both tumors and gastrocnemius were removed, weighed, and quickly frozen in liquid nitrogen for subsequent analysis.
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryotic mRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre, Madison, WI, USA). Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcribed into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeq2500 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: gastrocnemius

tag: treatment

value: Rab27-KD LLC injection, un-treated


title: TC-797_1_DMSO_4h_Aug2019

description:
Total RNA from TC-797 treated with DMSO_replicate 1 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls

source_name: TC-797 NUT Carcinoma cell line


title: DU145_SRRM3_2


title: H_0 rep1


title: 10-15_2_DMSO_4h_Aug2019

description:
Total RNA from 10-15 treated with DMSO_replicate 2 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls

source_name: 10-15 NUT Carcinoma cell line


title: DU145_CMV_Entry_1

source_name: DU145 human prostate tumor cell line transfected with pCMV6-Entry expression vector.

value: pCMV6-Entry expression vector.


title: DU145_CMV_Entry_2


title: 10-15_1_DMSO_4h_Aug2019

description:
Total RNA from 10-15 treated with DMSO_replicate 1 performed in August 2019
RNAseq_August2019_IRBM_raw_counts.xls
RNAseq_August2019_IRBM_regularizedLog2.xls


title: C42B_SRRM4_2

source_name: C4-2B human prostate tumor cell line transfected with SRRM4 expression vector.

value: C4-2B (gift from L. Chung, Cedars-Sinai Medical Center, Los Angeles, CA)


title: C42B_CMV_Neo_2

source_name: C4-2B human prostate tumor cell line transfected with pCMV6-Neo expression vector.


title: CAD1 RNAseq

source_name: coronary artery disease 1


title: CAD2 RNAseq

source_name: coronary artery disease 2


title: C42B_SRRM4_1


title: C42B_SRRM3_1

source_name: C4-2B human prostate tumor cell line transfected with SRRM3 expression vector.


title: C42B_CMV_Neo_1


title: CON2 RNAseq

source_name: control 2

value: control


title: C42B_CMV_Entry_2

source_name: C4-2B human prostate tumor cell line transfected with pCMV6-Entry expression vector.


title: AS WT

city: Birmingham

first: Laura

last: Bownes

state: AL

address: 1670 University Blvd, Volker Hall, Volker Hall

institute: UAB

data_processing:
Basecalls performed using bcl2fastq version 2.18.0.12
STAR version 2.7.6.a was used to align the raw reads using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters --library-type fr-firststrand -G -L
Cuffmerge was used to merge samples together using default parameters
Cuffdiff was used to find differentially expressed genes using default parameters
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab delimited Excel file containing FPKM values for each gene in each sample

source_name: Neuroblastoma

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, 30-2601, ATCC) containing 10% fetal bovine serum (FBS, Hyclone, Suwanee, GA), 4 mM L-glutamine (Thermo Fisher Scientific Inc., Waltham, MA), 1 µM non-essential amino acids, and 1 µg/mL penicillin/streptomycin (Gibco, Carlsbad, CA),

extract_protocol:
Total cellular RNA was extracted from AS WT and AS STRAP KO cells using the RNAeasy kit (Qiagen) according to the manufacturer's protocol. UAB Genomics Core performed sample quality control, library preparation, and RNA sequencing. The Agilent 2100 Bioanalyzer was used to assess the total RNA quality, which was followed by two rounds of poly A+ selection and conversion to cDNA
The NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® library generation kit (New England Biolabs) was used per the manufacturer’s instructions. qPCR in a Roche LightCycler 480 with the Kapa Biosystems kit (Kapa Biosystems, Woburn, MA) was used for library quantitation.
The Illumina NextSeq500 was used to perform the sequencing using the latest versions of the sequencing reagents and flow cells with single-end 75 bp reads.

treatment_protocol: Untreated

value: Neuroblastoma

value: SK-N-AS

value: WT


title: CON1 RNAseq

source_name: control 1


title: AS STRAP KO

value: STRAP KO


title: K562_dp300_total RNA seq

data_processing:
Input read ends with poor quality values (quality score 20) were trimmed by Trimmomatic. Trimmed reads were aligned to the human reference genome (hg19, canonical) using RNA STAR. Statistical analysis of Differentially Expressed Genes (DEG) was performed using edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions and qualified by Qubit Fluorometer (RQN > 7)
Ribosomal RNA (rRNA) from extracted RNA was depleted using NEBNext rRNA Depletion Kit (New England Biolabs #E6350L). rRNA-depleted RNA was reversely transcribed using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs #E7765S) as suggested by the manufacturer.

value: erythroleukemia cells

value: p300 HAT domain deletion


title: SETMAR-BS

city: Debrecen

first: Márton

last: Miskei

address: Egyetem tér 1.

department: Department of Molecular Biotechnology and Microbiology

country: Hungary

institute: University of Debrecen

description: paired-end ChIP-seq; reads1 and reads2 in different raw files

data_processing:
241 million reads were sequenced (paired-end) using an Illumina Nextseq 500 machine and the NextSeq® 500/550 Mid Output Kit v2 (Illumina). 97.31% of reads were mapped on the GRCh38 (hg38) human reference genome by Bowtie2 version 2.3.4.1 using default parameters.
Picard was used to remove PCR duplicates from BAM files created by Samtools version 1.10, applying default parameters.
Repetitive segments of the genome were blacklist filtered (according to 05.05.2020, Stanford University, Anshul Kundaje Lab) and BAM files containing 185 million mapped reads were RPKM normalised using deeptools version 3.3.1 applying bamCoverage processing (bin size=100bp; smooth length=300bp).
MACS2 version 2.2.6 was used to identify ChIP peaks from bedGraph files, applying default parameters.
IP and corresponding Input data were processed in parallel. Peaks identified in Input were filtered out from IP samples using Bedtools version 2.29.0
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files from IP and input; txt files contain the processed peaks; SETMAR-BS_peak_set.txt contains annotation (HOMER hg38 genomic annotation).

source_name: HAP1, near-haploid human leukemia cell line

growth_protocol: The HAP1 cell line were maintained in complete Iscove’s Modified Dulbecco’s Medium (IMDM, Sigma) supplemented with 10% heat inactivated Tetracycline free Foetal Bovine Serum (iBiotech), 1% penicillin/ streptomycin (Sigma) at 37 °C with 5% CO2.

extract_protocol:
For ChIP, 2x107 cells were suspended in 1.5ml of ChIP Lysis Buffer (50mM HEPES-KOH pH 7.5, 140mM NaCl, 1mM EDTA pH8, 1% Triton X-100, 0.1% Sodium Deoxycholate, 1% SDS, supplemented with protease inhibitors) and disrupted by Fast prep (speed: 6 m/s; time: 40 sec; 2 cycles; pause time: 120 sec). Chromatin lysates were sonicated in 1.5 ml LowBind  tubes (600 μl sample/tube using Diagenode Bioruptor Plus (2x5 cycles, 30 sec ON/OFF LOW). After sonication, cell debris were pelleted by centrifugation at 16.000 g (at 4°C for 20 minutes). Fragment length distribution of sonicated samples (50 μl) was checked by 1% agarose gel electrophoresis after reverse crosslinking (at 65 °C for 6 hours) and phenol-chloroform extraction.
NGS libraries were prepared by the Nugen Ovation Ultralow System V2 library preparation kit (NuGEN Technologies) following the manufacturer’s instructions.

treatment_protocol: HA-SETMAR-expressing cell line was induced by increasing doxycycline concentrations (0.2 µg/ml, 0.5 µg/ml, 1 µg/ml, 2 µg/ml) 24 hours before the ChIP measurement

value: SETMAR knockout was generated by the CRISPR/Cas9 technology

value: HA-SETMAR-expressing cell line

tag: primer antibody

value: rabbit polyclonal anti-HA tag antibody (Abcam ab9110; 1:4000)

tag: secondary antibody

value: Alexa Fluor 647 goat anti-rabbit IgG (Invitrogen 1:1000, A-21245), and Alexa Fluor® 680 Goat Anti-Mouse IgG (1:1000, ab175775, Abcam)


title: K562_Con_total RNA seq_3

tag: genotype


title: K562_Con_total RNA seq_2


title: K562_Con_total RNA seq_1


title: K562_dMLL_total RNA seq

value: MLL3/4 SET domain deletion


title: PDS_4_rep3

city: Bologna

first: Giovanni

last: Capranico

state: BO

address: Via Selmi 3

department: FABIT

institute: University of Bologna

data_processing:
reads were trimmed using Trimmomatic
Alignment was performed using Hisat2
Transcript quantification with stringtie
Genome_build: hg19
Supplementary_files_format_and_content: Data files contain transript abundance for each gene

source_name: MCF-7 cells

extract_protocol:
rep1 and rep2 of each group were extracted using NucleoSpin RNA kit, rep3 and rep4 using TRI Reagent
NEBNext Ultra Directional RNA library prep

treatment_protocol: PDS samples were treated with pyridostatin 10 microM for 24 hours. All samples were cultured 72h in drug free medium before collection

value: mammary gland, breast

tag: disease

value: adenocarcinoma

value: pyridostatin 10 microM at time 4 (days)


title: C42B_SRRM3_2

value: male

tag: cell type

value: prostate cancer

value: SRRM3 expression vector.


title: PDS_4_rep4


title: GOSH/001 ET [2019-06-05-EPIICAL-23]

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to GRCh38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrices in CSV format containing raw as well as TMM normalized Log2(n+3) CPM summarized reads

growth_protocol: in vivo

extract_protocol:
RNA was extracted from 1 million PBMC using RNeasy Plus Mini Kit from QIAGEN
RNA libraries were prepared for sequencing using the Roche Kapa RNA hyper kit.

tag: donorid

tag: arttreatment

value: ET

tag: age at art start (months)

value: PBMC


title: GOSH/003 LT [2019-06-05-EPIICAL-24]

value: LT


title: SETMAR-BS_input

description: single-end ChIP-seq


title: K562_dMLL_H3_ChIP-Seq

tag: chip antibody

value: H3 (Abcam, ab1791)


title: ICHT/013 ET [2019-06-05-EPIICAL-22]


title: CON3 RNAseq

source_name: control 3

value: plasma

tag: disease state

value: control


title: K562_Con_H3_ChIP-Seq

value: erythroleukemia cells


title: PDS_4_rep2


title: PDS_4_rep1


title: K562_dp300_H3K27ac_ChIP-Seq

value: p300 HAT domain deletion

value: H3K27ac (Abcam, ab4729)


title: C42B_CMV_Entry_1

tag: Sex

value: C4-2B (gift from L. Chung, Cedars-Sinai Medical Center, Los Angeles, CA)

value: pCMV6-Entry expression vector.


title: CT_4_rep4

tag: cell line

value: mammary gland, breast

value: control at time 4 (days)


title: K562_Con_H3K27ac ChIP-Seq


title: K562_dMLL_H3K27ac_ChIP-Seq

value: MLL3/4 SET domain deletion


title: K562_dp300_H3K4me1_ChIP-Seq

value: H3K4me1 (Abcam, ab8895)


title: ICHT/010 ET [2019-06-05-EPIICAL-20]


title: CT_4_rep3

value: adenocarcinoma


title: ICHT/008 LT [2019-06-05-EPIICAL-18]


title: ICHT/005 LT [2019-06-05-EPIICAL-16]


title: K562_dMLL_H3K4me1_ChIP-Seq


title: K562_Con_H3K4me1_ChIP-Seq


title: K562_dp300_H3_ChIP-Seq


title: ICHT/009 ET [2019-06-05-EPIICAL-19]


title: CT_0_rep4

value: control at time 0


title: CT_4_rep2


title: ICHT/004 ET [2019-06-05-EPIICAL-15]

value: ET


title: CT_4_rep1


title: Tumor methylation_CAM20.0152

city: Toronto

first: Yasin

last: Mamatjan

state: Ontario

address: 610 University Ave.

country: Canada

institute: Princess Margaret Cancer Center

hyb_protocol: Samples were fragmented, amplified and hybridized to the Illumina Infinium MethylationEPIC BeadChip as per standard Illumina protocols.

scan_protocol: standard protocol

data_processing:
Normalization and background correction of raw IDAT files was performed using ssNoob in the Bioconductor package minfi (version minfi_1.36.0). Beta values were calculated for each probe across all samples after post-processing.
The 'Matrix processed.txt' contains Normalized Beta using preprocessNoob.
The 'Matrix signal intensities.txt' contains Unmethylated and methylated signal intensities.

label: cy3, cy5

source_name: fresh-frozen human meningioma

label_protocol: 250-500 ng of converted DNA was used as input, and labelled as per standard Illumina protocols.

growth_protocol: not applicable

extract_protocol: Genomic DNA was extracted from fresh-frozen tumor specimens and 250-500ng of bisulfite-treated DNA (EZ DNA Methylation Kit, Zymo, California, USA) per sample was used to obtain genome-wide DNA methylation profiles

treatment_protocol: During sample processing, genomic DNA from each specimen was processed.

value: fresh-frozen human meningioma

tag: molecule subtype

value: bisulfite-treated DNA


title: Tumor methylation_CAM20.0128


title: Tumor methylation_CAM20.0156


title: Tumor methylation_CAM20.0127


title: Tumor methylation_CAM20.0154


title: Tumor methylation_CAM20.0155


title: Tumor methylation_CAM20.0129


title: Tumor methylation_CAM20.0126


title: ICHT/002 LT [2019-06-05-EPIICAL-14]

value: LT

value: PBMC


title: CT_0_rep2


title: Tumor methylation_CAM20.0125


title: ICHT/012 LT [2019-06-05-EPIICAL-21]


title: SW480-shTGM2-1-c

city: Frankfurt am Main

first: Michael

last: Rieger

address: Theodor-Stern-Kai 7

institute: Universitätsklinikum Frankfurt/DKFZ

description: A third generation self-inactivating HIV -1 based lentiviral vector system (lentiviral particles) was used for shRNA transfer into standard culture cell lines.

data_processing:
The resulting FASTQ files were aligned to the hg19 draft of the human genome and counts per gene were estimated using STAR (v. 2.5.3)
Counts per gene were normalized and knock-down gene expression compared to controls using DESeq2 (v. 1.18.1) in R (3.4.4)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with the normalized per gene counts as reads per million (RPM) output from DESeq2 (v. 1.18.1)

source_name: Human colon adenocarcinoma

growth_protocol: SW480 cells were cultured according ATCC recomandations, birefly cells were cultivated in complete growth medium in a75 cm² flask

extract_protocol:
RNA isolation was performed using RNAeasy isolation kit (Quiagen) according to the manufacturer’s instructions. The quality and concentration of libraries were determined by an Agilent 2100 Bioanalyzer and RiboGreen fluorescence on Qubit (Invitrogen).
Library preparation was performed at the DKFZ Core Facilities Genomics and Proteomics Unit (Heidelberg, Germany).
The library was prepared using Illuminas’s TruSeq Stranded Total RNA Library Prep kit and sequenced on an Illumina HiSeq 4000 (San Diego, CA, USA) system using a 100-bp paired-end approach.

value: colon epithelial cells

tag: shRNA

tag: genotype/variation

value: TGM2 knock-down


title: CT_0_rep1

tag: tissue


title: Tumor methylation_CAM20.0122


title: OPBG/014 ET [2019-06-05-EPIICAL-12]


title: Tumor methylation_CAM20.0153


title: ICHT/006 ET [2019-06-05-EPIICAL-17]


title: CT_0_rep3

tag: treatment


title: Tumor methylation_CAM20.0120


title: Tumor methylation_CAM20.0114


title: Tumor methylation_CAM20.0119


title: SW480-shTGM2-1-b


title: Tumor methylation_CAM20.0118


title: Tumor methylation_CAM20.0113


title: Tumor methylation_CAM20.0112


title: SW480-shTGM2-1-a


title: Tumor methylation_CAM20.0108


title: Tumor methylation_CAM20.0124


title: OPBG/013 LT [2019-06-05-EPIICAL-11]


title: Tumor methylation_CAM20.0106


title: Tumor methylation_CAM20.0110


title: Tumor methylation_CAM20.0105


title: OPBG/012 ET [2019-06-05-EPIICAL-10]


title: OPBG/010 ET [2019-06-05-EPIICAL-08]


title: OPBG/011 ET [2019-06-05-EPIICAL-09]


title: SW480-shSCRML-c

value: shSCRMBL

value: scramble control


title: SW480-shTGM2-1-d


title: OPBG/008 ET [2019-06-05-EPIICAL-06]


title: SW480-shSCRML-b


title: OPBG/007 ET [2019-06-05-EPIICAL-05]


title: Tumor methylation_CAM20.0104


title: SW480-shSCRML-a


title: Tumor methylation_CAM20.0109


title: SW480-shSCRML-d


title: Tumor methylation_CAM20.0102


title: Tumor methylation_CAM20.0101


title: OPBG/009 ET [2019-06-05-EPIICAL-07]


title: Tumor methylation_CAM20.0099