title: R628-G-T

city: guangzhou

first: cuicui

last: wang

address: 1 Pan Fu Road

department: rheumatology

institute: Guangzhou First People’s Hospital, The Second Affiliated Hospital of South China University of Technology

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

source_name: rheumatoid fibroblast-like synoviocytes

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

treatment_protocol: Cells were treated with GA (Ginkgolic acid) or SKN (shikonin) or DMSO for 24h and then stimulated with or without TNF-α (10 ng/ml) for 15min.Treatment includes four types: DMSO means that cells were treated with DMSO; D+T means that DMSO treatment and then stimulated with TNF-α; G+T means that GA treatment and then stimulated with TNF-α; S+T means that SKN treatment and then stimulated with TNF-α

tag: disease state

value: rheumatoid arthritis (RA)

tag: individual

value: patient R628

value: synovial tissues

value: rheumatoid fibroblast-like synoviocytes (RA FLSs)

value: G+T


title: R628-S-T

status: Public on Aug 06 2020

type: SRA

state: guangdong

country: China

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: treatment

value: S+T


title: 48hr_4a1_1_Hnf4a_R222

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

library_source: genomic

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
peak finding algorithm MACS (v2.1.0) with the option (-g mm -p 0.00001).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the positions of the peaks that were obtained when normalizing the reads of the ChIP-Seq to the input. The bw files converted from the bedgraph files contain depth of reads.

molecule: genomic DNA

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011).

extract_protocol:
Sonicated DNA from cells was pulled down with antibody.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in iHep cells or MEFs 48 hours after transfection with retroviruses.

value: mouse embryonic fibroblasts

tag: strain

tag: transfection

value: infected with Foxa1, Hnf4alpha

tag: Stage

value: 48hr after transfection

tag: antibody


title: 48hr_4a1_1_input_R222

value: none (input)


title: R628-DMSO

value: DMSO


title: 48hr_4a1_1_Foxa1_R222


title: R3-S-T

value: patient R3


title: Hep_2

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.7.12) with the option (mem -t 6 -M)
Fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using Tigar (v2) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

source_name: hepatocytes obtained from adult mouse livers

growth_protocol: Mouse embryonic fibroblasts (MEFs) were prepared from 13.5 days post coitum embryos. iHep cells were generated and maintained following the previously described protocol (Sekiya and Suzuki, 2011). Hepatocytes were isolated from 10-week-old adult mouse livers by two-step collagenase digestion (Seglen, 1979).

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

treatment_protocol: Retrovirus was produced following standard procedures, following transfection of pGCDNsam retroviral backbones containing the respective cDNAs (available from us via Addgene). Media was changed 8 hours after transfection and viral supernatant collected after another 24 and 48 hours.


title: R3-D-T

value: D+T


title: MEF_2


title: Hep_1

value: hepatocytes obtained from adult mouse livers


title: R3-DMSO


title: MEF_1


title: R2-S-T

value: patient R2


title: iHep_4a3_6

value: infected with Foxa3, Hnf4alpha

value: iHep


title: R2-G-T

value: rheumatoid arthritis (RA)


title: iHep_4a3_5


title: T_HET

city: Toronto

first: Landry

last: Nfonsam

state: Ontario

address: 686 Bay Street

department: Genetics and Genome Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
FASTQ sequence data were generated using bcl2fastq2 v2.17, and quality assessed using FastQC v.0.11.2
Adaptors were trimmed using Trim Galore v. 0.4.0., running Cutadapt v. 1.8. Trim
Trimmed reads were screened for presence of rRNA and mtRNA/DNA sequences using FastQ-Screen v.0.4.3
Read distribution and strandedness of alignments were assessed using RseQC package v. 2.3.7. The distribution of reads across exonic, intronic and intergenic sequences were assessed by the read_distribution.py program, and strandedness confirmed by infer_experiment.py
Raw trimmed reads were aligned to reference genome using Tophat v. 2.0.11
Extraction of raw read counts for genes was achieved using htseq-count v.0.6.1p2(HTSeq
Two-condition differential expression was done with the edgeR R package, v.3.8.6
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample ...

source_name: Embryo Head

extract_protocol:
Two embryo heads from each genotype (wt, het, mut) at E8.5 were dissected in sterile DEPC treated 1X PBS, lysed in 350 µl of buffer RLT (RNeasy Miniprep Kit-Qiagen) using a tissue lyser (TissueLyser II-Qiagen), and total RNA purified from sample lysates using the RNeasy Miniprep Kit (Qiagen) per the manufacturers’ protocol. PolyA+ RNA was isolated from total RNA by oligo-dT selection and stranded paired-end libraries were prepared and sequenced on an Illumina HiSeq 2500 platform at The Centre for Applied Genomics at SickKids.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Prdm15 tm1a+/-


title: R2-DMSO

value: synovial tissues


title: R628-D-T

value: patient R628

value: rheumatoid fibroblast-like synoviocytes (RA FLSs)


title: R2-D-T


title: iHep_4a3_3


title: NRVCM_HectD3_4

city: Kiel

first: Ashraf

middle: Yusuf

last: Rangrez

address: Arnold-Heller Str. 3 (Haus 6)

country: Germany

institute: University Medical Center Kiel

description: Gene expression in HectD3 overexpressed cardiomyocytes

data_processing:
Quality Assessment of Sequencing Library: Agilent 2100 Bioanalyzer was used for assessment of the quality of sequencing library. Library concentration was determined by qPCR method.
Mapping: After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered < 20 bp reads with cutadaptsoftware. The trimmed reads were aligned to reference genome with Hisat 2 software. The fragment statisticalinformation is listed in the table below. In a typical experiment, it is possible to align 40- 90% of the fragmentsto the reference genome. However, this percentage depends on multiple factors, including sample quality, libraryquality and sequencing quality.
Expression: The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through thetranscript abundances estimated with StringTie. The number of identified genes and transcripts per group wascalculated based on the mean of FPKM in group > 0.5.
Principal Component Analysis: Principal Component Analysis (PCA) is a statistic method used in unsupervised analysis to reduce the dimension of large data sets, and it is a useful tool to explore sample classes based on the expression. The following PCA was performed with genes that have the ANOVA p value ≤ 0.05 on FPKM abundance estimations.
Differentially Expressed Gene and Transcript: Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Supplementary_files_format_and_content: Text document containing FPKM values of the processed data.

organism: Rattus norvegicus

source_name: Neonatal rat cardiomyocyte, HectD3 overexpressed, replicate 4

growth_protocol: Isolated cardiomyocytes were cultured in DMEM supplemented with 10% (v/v) FCS, 100 U/ml penicillin and 100 µg/ml streptomycin (Life Technologies), and 2 mmol/L L-glutamine (Life Technologies) for 24 h prior to either LacZ or HectD3 was overexpressed using Adenovirus-mediated overexpression constructs for 72 h.

extract_protocol:
Total RNA was isolated from NRVCMs using QIAzol (Qiagen) according to manufacturer’s instructions
The library preparation procedure included: 1) Fragmentation of the RNA molecules; 2) Reverse transcription to synthesis first strand cDNA; 3) Second strand cDNA synthesis incorporating dUTP; 4) End-repair and A-tailing of the double stranded cDNA; 5) Illumina compatible adapter ligation; 6) PCR amplification and purification for the final RNA-seq library.
The completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distributionbetween 400 - 600 bp, and adapter dimer contamination. The amount was determined by absolutequantification qPCR method. The barcoded libraries were mixed in equal amounts and used for sequencing onthe instrument.

value: Cardiomyocytes

value: HectD3 overexpressed

tag: developmental stage

value: neonatal


title: R_HET


title: 5007_MUT

value: Prdm15 tm1a-/-


title: iHep_4a3_4

value: mouse embryonic fibroblasts


title: 5001_MUT


title: 5003_WT

value: Prdm15 tm1a+/+


title: R3-G-T

value: patient R3

value: G+T


title: iHep_4a1_1_EGS_Foxa1_R164

data_processing:
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using bwa (v0.6.2) with the option (aln -t 6).
peak finding algorithm MACS (v2.1.0) with the option (-g mm -p 0.00001).
The bedgraph files were obtained from the bam files using Bedtools (v2.16.2), then converted into the bw files.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the positions of the peaks that were obtained when normalizing the reads of the ChIP-Seq to the Input. The bw files converted from the bedgraph files contain depth of reads.

treatment_protocol: ChIP-seq experiments were carried out following standard procedures in iHep cells or hepatocytes.

value: infected with Foxa1, Hnf4alpha


title: 3013_WT


title: NRVCM_HectD3_2

source_name: Neonatal rat cardiomyocyte, HectD3 overexpressed, replicate 2


title: iHep_4a3_1


title: iHep_4a2_4

value: infected with Foxa2, Hnf4alpha


title: NRVCM_HectD3_3

source_name: Neonatal rat cardiomyocyte, HectD3 overexpressed, replicate 3


title: iHep_4a3_2

value: infected with Foxa3, Hnf4alpha


title: iHep_4a2_3

value: iHep


title: CR_OGT rep2

city: Bangkok

first: Sudjit

last: Luanpitpong

state: Bangkok

address: Bangkoknoi

department: Research Division

country: Thailand

institute: Mahidol University

data_processing:
Basecalling was performed using CASAVA 1.8
Raw reads filtering conditions are as follows: Remove reads containing adaptors; Remove reads containing N > 10% (N represents base that could not be determined); The Qscore (Quality value) of over 50% bases of the read is <= 5.
Mapping the clean reads to the reference genome hg19 using STAR v2.5
Alignments were parsed using Tophat program and differential expressions were determined through DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Megakaryoblastic MEG-01 cell line

growth_protocol: Cells were cultured in RPMI1640 medium containing 10% FBS and maintained in a humidified atmosphere of 5% CO2 environment at 37 C at the seeding density of 0.1 M cells/mL. Culture densitiy was always kept below 1 M cells/mL.

extract_protocol:
Total RNA was extracted using Total RNA Purification Kit (Gmbiolab)
RNA libraries were prepared for sequencing using NEBNext® Ultra RNA Prep Kit

treatment_protocol: OGT was depleted by CRISPR/Cas9 system using all-in-one lentiviral vector carrying sgRNA against OGT and spCas9.

value: Megakaryoblast

tag: cell line

tag: morphology

value: Myeloblast-like

tag: profile

value: Produced platelet-like particles

value: OGT depletion


title: iHep_4a2_1


title: CR_OGT rep1


title: NRVCM_HectD3_1

source_name: Neonatal rat cardiomyocyte, HectD3 overexpressed, replicate 1


title: NRVCM_Control_4

description: Gene expression in LacZ overexpressed cardiomyocytes to serve as control

source_name: Neonatal rat cardiomyocyte, control, replicate 4

value: Control


title: NRVCM_Control_3

source_name: Neonatal rat cardiomyocyte, control, replicate 3

value: Cardiomyocytes


title: NRVCM_Control_2

source_name: Neonatal rat cardiomyocyte, control, replicate 2


title: WT rep2

value: WT


title: iHep_4a1_6


title: NRVCM_Control_1

source_name: Neonatal rat cardiomyocyte, control, replicate 1

value: neonatal


title: iHep_4a1_5


title: WT rep1


title: iHep_4a1_4


title: KPC7829_untreated

type: RNA

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

institute: University of Ulm

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s protocol. On completion of the fragmentation reaction, 55 µl of 2x Agilent HiRPM hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse GE 4x44Kv2 Microarrays (G4846A) for 17 hours at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C prewarmed GE Wash buffer 2 (Agilent) and 30 seconds with Acetonitril.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray Scanner G2505B (3micron) with the the Agilent Scan Control Version A.8.5.1 .

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent). Further processing (background correction, percentile shift normalization, summarization, log2 transformation, median shift) was done using R and the bioconductor package limma (Ritchie et al., 2015).

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7829, female

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's protocol, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with a NanoPhotometer.

growth_protocol: cells were cultured in Dulbecco’s modified eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin, 1% l-glutamine and 0.1 M β-mercaptoethanol (β-ME)

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoPhotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: cells were treated with recombinant mouse IFN-γ (20 ng/ml, cat. no. 554587, BD Biosciences, Heidelberg, Germany) for 16 h.

tag: tissue of origin

value: pancreatic ductal adenocarcinoma, PDAC

tag: gender

value: female

value: KrasG12D/+, Trp53fl/fl, p48cre/+

value: no treatment


title: KPC7829_IFNγ_16h

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7829, female_IFNγ, 16h

value: IFNγ 20 ng/ml, 16h


title: iHep_4a1_3

value: mouse embryonic fibroblasts

value: infected with Foxa1, Hnf4alpha


title: KPC7742_IIFNγ_16h

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7742, female_IFNγ, 16h


title: KPC7735_IFNγ_16h

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7735, male_IFNγ, 16h

value: male


title: iHep_4a2_2

value: infected with Foxa2, Hnf4alpha

value: iHep


title: KPC7742_untreated

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7742, female


title: iHep_4a1_1

source_name: mouse embryonic fibroblasts


title: iHep_4a1_2


title: 48hr_4a3_2

value: infected with Foxa3, Hnf4alpha

value: 48hr after transfection


title: Ovary_ATACseq_2

city: Bergen

first: Pavla

last: Navratilova

address: Thorm hlensgt. 55

department: Sars International Centre for Marine Molecular Biology

country: Norway

institute: University of Bergen

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence using cutadapt (v1.9.1), and masked for low-complexity or low-quality sequence.
Paired-end reads were mapped using bowtie2 (v2.2.4) with the following parameters: maximum insert size set to  -X 2000 --no-mixed --no-discordant --dovetail.
Alignments were deduplicated (samtools rmdup) and filtered for sufficient alignment quality (samtools view -q 30) and all unpaired or discordant alignments were excluded.
RPKM normalized bigWig tracks for alignments were generated at 20 bp resolution using deeptools v2
Genome_build: od01 (ASM20953v1, https://www.ncbi.nlm.nih.gov/genome/368?genome_assembly_id=28741)
Supplementary_files_format_and_content: BigWig files generated using deeptools v2

organism: Oikopleura dioica

extract_protocol:
ATAC-seq was performed in two replicates according to (Buenrostro et al. 2013). Briefly, a sufficient number of freshly dissected Oikopleura testis, ovaries or batches of hatched embryos were resuspended in Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged for 10 min at 1500 rcf. Nuclei were briefly washed with magnesium buffer (5mM MgCl, 10 mM Tris buffer pH8) and replaced with 25 ul of tagmentase mixture: 10,5 ul H2O, 12,5 ul tagmentase buffer (2x TD, Illumina Cat #FC-121-1030), 2 ul tagmentase (TDE1 Nextera Tn5 Transposase, Illumina Cat #FC-121-1030). The reaction was incubated at 37 for 40 min. Immediately following transposition, fragments were purified using a Qiagen MinElute PCR Purification Kit and 50 ng was amplified using Nextera amplification mix (NPM) in 50 ul - 5 cycles. 5 ul of the reaction was used to determine the number of cycles needed by qPCR (NPM with SybrGold) to ensure sufficient but not excessive amplification. The number of cycles for final amplification varied between 5-6 cycles. Fragment sizes of barcoded libraries were assessed using Bioanalyzer and fragments over 1000 bp were reduced using AMPure beads before pooling and sequencing. Pooled libraries were sequenced in a 2x75bp Paired-End format on HiSeq4000 platform yielding about 50M reads per sample.
Immediately following transposition, fragments were purified using a Qiagen MinElute PCR Purification Kit and 50 ng was amplified using Nextera amplification mix (NPM) in 50 ul - 5 cycles. 5 ul of the reaction was used to determine the number of cycles needed by qPCR (NPM with SybrGold) to ensure sufficient but not excessive amplification. The number of cycles for final amplification varied between 5-6 cycles. Fragment sizes of barcoded libraries were assessed using Bioanalyzer and fragments over 1000 bp were reduced using AMPure beads before pooling and sequencing. Pooled libraries were sequenced in a 2x75bp Paired-End format on HiSeq4000 platform yielding about 50M reads per sample.

value: Ovary


title: KPC7735_untreated

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7735, male


title: Ovary_ATACseq_1


title: Testis_ATACseq_2

value: Testis


title: KPC7612_IFNγ_16h

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7612, male_IFNγ, 16h


title: 48hr_4a2_2


title: 48hr_4a3_1


title: Testis_ATACseq_1


title: 48hr_4a2_1


title: Single-culture 5

city: Berlin

first: Florian

last: Padberg

address: Max-Dohrn-Strasse 8-10

department: Chemicals and Product Safety

institute: German Federal Institute for Risk Assessment (BfR)

description: RNA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Hybridisation was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

scan_protocol: Array scanning was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) according to the manufacturer's instruction (Affymetrix).

data_processing: Raw data were processed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Further analysing was done using Transcriptome Analysis Console (TAC) Software 4.0.

label: biotin

label_protocol: Labelling was performed by the company ATLAS Biolabs GmbH (Friedrichstraße 147, 10117 Berlin, Germany) using standard protocol for Affymetrix Clariom S.

growth_protocol: HepG2 cells were grown in RPMI 1640 (PAN-Biotech, Aidenbach, Germany) with supplements at 37 °C and 5 % CO2 as described previously (Padberg et al. 2019). THP-1 cultivation and the co-culture were performed according to Wewering and co-workers (Wewering et al. 2017). HepG2 cells were seeded at a density of 1.3 x 105 cells per cm2. THP-1 cells were differentiated using 100 nM phorbol-12 myristat-13 acetat (PMA) for 24 h and seeded at a density of 0.65 x 105 cells per cm2.

extract_protocol: RNA was isolated using the NucleoSpin® RNA Kit (Machery-Nagel, Düren, Germany) according to the manufacturer's instructions.

treatment_protocol: HepG2 cells were incubated with or without indirect contact to PMA-differentiated THP-1 cells for 24 h.

value: single culture


title: KPC7598_IFNγ_16h

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7598, male_IFNγ, 16h


title: KPC7612_untreated

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7612, male


title: Single-culture 3


title: Single-culture 4


title: Single-culture 2


title: Tailbud_ATACseq_2

value: Tailbud


title: Co-culture 5

source_name: co-culture of HepG2 and PMA-differentiated THP-1

value: co-culture


title: Tailbud_ATACseq_1


title: 48hr_4a1_2


title: KPC7598_untreated

source_name: cell line derived from pancreatic tumor,  KrasG12D/+, Trp53fl/fl, p48cre/+, #7598, male

value: pancreatic ductal adenocarcinoma, PDAC


title: Co-culture 4


title: 48hr_4a1_1


title: Single-culture 1


title: Y305A TASOR comp H3K9me3 rep1

status: Public on Aug 05 2020

city: Lund

first: Christopher

last: Douse

address: Sölvegatan 17

department: Medicine

country: Sweden

institute: Lund University

data_processing:
Read alignment with bowtie2 (v2.3.4.3) --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
For CUT&RUN, conversion to bedgraph format and normalization was done with bedtools genomecov (v2.27.1; -bg -scale), where the scale factor was 1e4 divided by the number of reads mapping to the yeast spike-in genome (R64-1-1). Peaks were called in SEACR (v1.1; stringent, norm options) for experimental samples against IgG controls. The RUVseq package (v1.20) was used to remove unwanted variation prior to differential binding analysis with edgeR (v3.28.1). TASOR-regulated H3K9me3 peaks were defined as those under a cutoff in the MA plot (log2 fold-change < -1) of KO vs control cells (n=4).
For CUT&Tag, PCR duplicates were removed from bam files (Picard) and coverage tracks generated with bamCoverage (deepTools v3.3.0)
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files with normalized coverage plots
Supplementary_files_format_and_content: bed file listing 393 TASOR-regulated H3K9me3 loci

source_name: HeLa cells

growth_protocol: HeLa and HEK293T cells (ECACC) were grown in IMDM or DMEM plus 10% fetal calf serum (FCS) and penicillin/streptomycin (100 U/mL). Cell lines were routinely tested for mycoplasma contamination using the MycoAlert detection kit (Lonza). Exogenous expression of TASOR variants was done with lentiviral vectors pHRSIN-pSFFV-HA-TASOR-WPRE-pPGK. Lentivirus was generated through the triple transfection of HEK 293T cells with the lentiviral transfer vector plus the two packaging plasmids pCMVΔR8.91 and pMD.G using TransIT-293 transfection reagent (Mirus) as recommended by the manufacturer. Viral supernatant was typically harvested 48 h post-transfection, cell debris removed using a 0.45 µm filter, and TASOR KO HeLa cells transduced by spin infection at 800 g for 1 h.

extract_protocol:
DNA was cleaved by antibody-directed MNase (CUT&RUN) or Tn5-transposase (CUT&Tag) treatment of digitonin-permeabilised cells and purified from the cell supernatant
For CUT&RUN, KAPA Hyperprep kit was used as per instructions. For CUT&Tag, libraries were directly PCR amplified following tagmentation and cleanup. Final cleanup was done with 1.1x KAPA SPRI beads

value: HeLa

value: TASOR KO with expression of Y305A HA-TASOR

value: rabbit anti-H3K9me3 abcam ab8898

tag: protocol

value: CUT&RUN


title: CR IgG TASOR KO rep4

value: Reporter clone with TASOR KO

value: guinea pig anti-rabbit IgG CSB-PA00150E1Gp


title: WT TASOR comp H3K9me3 rep1

value: TASOR KO with expression of WT HA-TASOR


title: Control CT H3K9me3

value: Clone bearing HUSH-repressed GFP transgene reporter

value: CUT&TAG


title: TASOR KO TASOR rep1

value: rabbit anti-TASOR Atlas HPA006735

value: CUT&Tag


title: Control TASOR rep1


title: TASOR KO TASOR rep2


title: Control TASOR rep2


title: CT IgG Control


title: CT IgG TASOR KO


title: CR IgG Control rep3


title: CR IgG Control rep1


title: CR IgG TASOR KO rep3


title: Co-culture 3


title: CR IgG Control rep4


title: Wbec_WT

city: Columbia

first: William

middle: James

last: Becker

state: South Carolina

address: 6439 Garners Ferry Rd.

department: Pathology, Microbiology, and Immunology

country: USA

institute: University of South Carolina School of Medicine

data_processing:
Base call files generated from the Illumina NextSeq 550 were demultiplexed using the cellranger mkfastq command. This pipeline uses bcl2fastq
Single cell feature counts files for each library were generated by running the cellranger count command on the demultiplexed fastq files.
The filtered gene matrices data output from the cellranger count pipeline were loaded into the Seurat package on R studio.
Cell qaulity was measured in Seurat using QC metrics that determined feature, count, and mitochondria read percentage per cell.
Data was scaled, normalized, clustered, and differential expression determined using the Seurat package in R studio.

source_name: colon

extract_protocol:
Single cell suspensions were processed for single-cell RNA by 10X Genomics Chromium Controller and 5' Gene Expression Kit.
Sequencing libraries were generated with 10X Genomics Chromium i7 Indexing Kit.

treatment_protocol: Colons were extracted, cleaned and digested in media contiaing EDTA to disrupt the epithelial layer and then processed through media containing collagenase D, DNAse and Dispase to expose the lamina propria layer which was enriched with a 40/80 Percoll gradient.

value: colon

value: wild-type

value: THC (10mg/kg)


title: Wbec_WV

value: Vehicle Control


title: Control H3K9me3 rep1


title: Hipp_RNA-Seq_Rep3

city: Montreal

first: Jerry

last: Pelletier

state: Quebec

address: McIntyre Medical Sciences Building 3655 promenade Sir-William-Osler

department: Biochemistry

institute: McGill university

data_processing:
Adaptor sequences have been removed from files
UMI's consist of 2 nts at the beginning of each read and 5nts at the end, these were stripped using UMI-tools
ribosomal RNA was removed using bowtie
remaining reads were mapped to the gencode v32 transcriptome using bowtie allowing for 2 mismatches and up to 100 alignments per read.
Genome_build: gencode v32
Supplementary_files_format_and_content: raw count

source_name: HAP1 cells

growth_protocol: Hap1 cells were cultured in IMDM supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin/streptomycin and 2 mM L-glutamine at 37°C and 5% CO2. NIH/3T3 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS), 100U/ml penicillin/streptomycin and 2 mM L-glutamine at 37°C and 5 % CO2.

extract_protocol:
100 ug/ml Cycloheximide (CHX). Cells were scraped in 250 µl of 3x Lysis buffer. Triton X-100 was added to a final concentration of 1 % and vortexed briefly. centrifuged at 4°C for 2 min at full speed on a table top centrifuge. Three hundred microgram of sample was brought up to a volume of 500 ul and supplemented with 5.6 mM CaCl2. The sample was digested with 150 U Micrococcal nuclease (MNase) for 45 min at room temperate (RT), rotating end-over-end. Sucrose gradients were centrifuged at 36,000 rpm for 3h.
Ribo-seq library preparation was performed as described by Glincy and Ingolia using 15 ug of RNA sample (64). The RNA-seq library was prepared using the same protocol as Ribo-seq libraries with the following modifications. Ribosomal RNAs were depleted using the NEB Next rRNA depletion kit from 1 ug total RNA. rRNA-depleted RNA was randomly fragmented using the NEBNext® Magnesium RNA Fragmentation Module and purified using isopropanol precipitation.
Ribosome profiling, mRNA-Seq

treatment_protocol: Cells were treated with 50 nM Hipp for 1h before harvesting

value: HAP1 cells

value: Hippuristanol 50 nM


title: TASOR KO H3K9me3 rep3

value: HeLa


title: TASOR KO H3K9me3 rep1


title: Co-culture 2

value: co-culture


title: Control H3K9me3 rep4

value: rabbit anti-H3K9me3 abcam ab8898


title: Control H3K9me3 rep3

value: CUT&RUN


title: Hipp_RNA-Seq_Rep2


title: DMSO_RNA-Seq_Rep3

value: DMSO


title: Hipp_RNA-Seq_Rep1


title: Co-culture 1


title: DMSO_RNA-Seq_Rep2


title: TASOR KO H3K9me3 rep4

value: Reporter clone with TASOR KO


title: DMSO_RNA-Seq_Rep1


title: Hipp_Ribo-Seq_Rep1


title: DMSO_Ribo-Seq_Rep2


title: C-4

city: Harbin

first: Yang

last: Yang

state: Heilongjiang

address: No. 23 Youzheng Street

institute: Harbin Medcial University

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19
Supplementary_files_format_and_content: The Fastq format file contains the sequence of reads and the sequencing quality of base.

source_name: Bladder_matched normal

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

tag: age(y)

tag: Sex

value: Male

value: Bladder

tag: cause (operation)

value: Bladder para-carcinoma


title: Hipp_Ribo-Seq_Rep2

tag: cell type


title: C-2

value: Female

tag: tissue


title: C-1


title: DMSO_Ribo-Seq_Rep1

tag: treatment


title: C-3


title: Hipp_Ribo-Seq_Rep3


title: DMSO_Ribo-Seq_Rep3


title: S1pr1_DP_4Cseq_rep1

city: Macclesfield

first: Muhammad

middle: Ahmad

last: Maqbool

address: Alderley Park

department: Cancer Research UK Manchester Institut

country: United Kingdom

institute: University of Manchester

description: 4C-seq (DpnII-Csp6I)

data_processing:
Library strategy: 4C-Seq
All sequencing reads were aligned to the mm9 genome assembly using Bowtie2 or TopHat2 (allowing 2 mismatches, keeping uniquely aligned reads only).
For ChIP-seq experiments, all samples were input subtracted and signals were scaled to reads per million so that the same number of units appeared in each experiment after merging of the replicates.
For RNA-seq experiments, reads that aligned to + or - strand were seperated and processed seperately to produce WIG files with strand specific enrichment scores.
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2). Reads were aligned using Bowtie (v1.2.2) with the settings -a -m 1 --best --strata. Mapped reads were filtered and mapped to DpnII restriction fragments, essentially as described in van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nature Methods 910: 969-972.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH, WIG

source_name: CD4+/CD8+ Thymic T Cells (DP)

growth_protocol: Primary DN cells were isolated from thymus of Rag2-/- mice. Primary DP and DN3 cells were sorted from the Thymus of WT C57/Bl6 mice. Naïve CD4+ and CD8+ cells were sorted from Spleen and Lymph nodes of WT C57/Bl6 mice. TH1, TH2 and TH17 cells were generated by in vitro differentiation of Naive CD4+ cells.

extract_protocol:
ChIP DNA was extracted using the Phenol:Chloroform extraction followed by QiaQuick PCR Purification kit using standard protocol. RNA was extracted using TriZol reagent and ethanol precipitation. CapStarr-seq RNA was extracted as described by Vanhille et al. 2015 (Nature Communications). 4C material was extracted as described by Ben Zouari et al. 2020 (Frontiers in Genetics)
ChIP-seq libraries were prepared with Illumina's ChIP Sample Prep Kit according to standard protocol. RNA-seq Libraries were prepared either with ScriptSeq V2 Total RNA Library Prep Kit (EpiCenter, USA) by using manufacturer's recommended protocol. 4C libraries are generated directly during the extraction process.

value: CD4+/CD8+ Thymic T Cells (DP)


title: S1pr1_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)

source_name: CD4+ Naive T Cells (Naïve)

value: CD4+ Naive T Cells (Naive)


title: Runx3_P2_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: S1pr1_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)

source_name: CD4-/CD8-/CD44lo/CD25+ Thymic T Cells (DN3)


title: S1pr1_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: S1pr1_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P2_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)

value: CD4-/CD8-/CD44lo/CD25+ Thymic T Cells (DN3)


title: S1pr1_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P2_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P2_CD8_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)

source_name: CD8+ Naive T Cells

value: CD8+ Naive T Cells


title: Runx3_P2_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P2_CD8_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P2_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: T-3

source_name: Bladder carcinoma

value: Bladder carcinoma


title: T-1


title: T-4


title: Runx3_P2_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: T-2


title: Runx3_P1_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_CD8_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_CD8_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_P1_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_CD8_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E3_CD8_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_CD8_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Cg MMS 1

city: Nutley

first: Erika

last: Shor

state: New Jersey

address: 111 Ideation Way, , CDI

institute: Center for Discovery and Innovation

data_processing:
Raw data was trimmed with fastp version 0.20.0 with the following params: -w 8 --detect_adapter_for_pe-W 4 -M 10 --cut_by_quality3 --length_required 15
Reads were aligned to the transcriptome derived from sacCer3 using STAR version 2.5.1b with default parameters
Read counts for each transcript was measured using featureCounts from subread-1.6.2 package
Differentially expressed genes were determined using DESeq2 and a cut-off of 0.05 on adjusted p-value (corrected for multiple hypotheses testing)
GSEA was performed on normalized gene expression counts, using gene permutations for calculating p-value
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text files with raw expression counts for each sample, Excel file reporting log2ratio(MMS/noMMS)

organism: Nakaseomyces glabratus

source_name: Yeast cells

growth_protocol: YPD 30°C (S. cerevisiae), YPD 37°C (C. glabrata)

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit according to manufacturer instructions
The libraries were made using NEBNext Ultra RNA Library Preparation Kit for polyA selection according to manufacturer instructions

treatment_protocol: 0.1% MMS for 1 hour

tag: strain


title: Cg MMS 3


title: Cg MMS 2


title: Runx3_E2_CD8_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E2_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Cg no MMS 2

value: no MMS control


title: Cg no MMS 1


title: Cg no MMS 3


title: Cellulose rep3

city: Nara

first: Kiwamu

last: Umezawa

department: Applied Biological Chemistry

institute: Kindai University

data_processing:
Basecalls performed using RTA 1.18.61.
Sequenced reads were trimmed and filtered using FaQCs v 1.34 with a minimum phred quality score of 20 and a minimum length of 50 bp.
Clean reads were used to pseudoalign to the filtered models sequences obtained by JGI (https://genome.jgi.doe.gov/ Glotr1_1), using Kallisto v. 0.44.0 (option --bias --rf-stranded -b 100).
Kallisto output was used as input for Sleuth v. 0.29.0 to estimate normalized transcripts per million (TPM).
Genome_build: Reads were aligned to "Glotr1_1.filtered_proteins.FilteredModels1.fa" from the JGI database (https://genome.jgi.doe.gov/ Glotr1_1).
Supplementary_files_format_and_content: The CSV file includes TPM values for each sample normalized with the Sleuth program. Protein IDs refer to the JGI annotation.

organism: Gloeophyllum trabeum

source_name: mycelium

extract_protocol:
Total RNA was isolated from frozen samples using the RNeasy Plant Mini Kit
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit

value: mycelium

tag: culture age

value: 5 days

tag: substrate

value: Cellulose


title: Japanese Cedar rep2

value: Japanese cedar


title: Japanese Cedar rep3


title: Runx3_E1_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Japanese Cedar rep1


title: Runx3_E3_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_CD8_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Cellulose rep2


title: Runx3_E2_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Glucose rep3

value: 3 days

value: Glucose


title: Cellulose rep1


title: Glucose rep2


title: Nfatc1_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Glucose rep1


title: Nfatc1_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Nfatc1_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Nfatc1_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Donor B_S-2HG

city: Cambridge

first: Iosifina

middle: Petrina

last: Foskolou

address: Downing Site

department: Physiology, Development and Neuroscience

institute: Cambridge University

data_processing:
RNA-sequencing: 42-nt sequence reads using Illumina NextSeq 500. Standard Illumina software base-calling and quality-control filtering was applied.
The reads were mapped to the genome using the STAR algorithm with default settings.
Fragment Assignment: Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded. We also require that at least 25 bp overlapping bases in a fragment for read assignment. The gene annotations we used were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene [2].
differential analysis to identify statistically significant differential genes using DESeq2. The DESeq2 model internally corrects for library size using their median- of-ratios method.
Filtering before multiple testing adjustment: After a differential test has been applied to each gene except the ones with zero counts, the p-value of each gene was calculated and needed to be further adjusted to control the number of false positives among all discoveries at a proper level. This procedure is known as multiple testing adjustment. During this process, DESeq2 by default filters out statistical tests (i.e. genes) that have low counts by a statistical technique called independent filtering. It uses the average counts of each gene (i.e. baseMean), across all samples, as its filter criterion, and it omits all genes with average normalized counts below a filtering threshold from multiple testing adjustment. This filtering threshold was automatically determined to maximize detection power (i.e. maximize the number of differential genes detected) at a specified FDR. In the spreadsheet listing the summary of statistics (RNA_stats.xlsx), one can refer to “Genes with low counts” to get an idea of how many genes were omitted in the process of multiple testing adjustment. In spreadsheet “DESeq2_results_allgene.csv”, you can also find these genes with weak signals have valid p-values but “NA” FDRs (i.e. adjusted p-values).
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human lymphocytes

growth_protocol: T-cell isolation was performed with MACS Miltenyi kits (Naïve CD8+ T cells: 130-093-244) following manufacturer’s instructions. T cells were activated with aCD3/CD28 beads (1:1 bead-to-cell ratio) (11132D, Gibco) and IL-2 (30 U/ml) for 4 days. On day 4 after activation the beads were removed. The cells were cultured in RPMI-1640 (Gibco) with 10% heat inactivated FBS (Gibco) and 1% pen/strep (Sigma).

extract_protocol:
On day 12 the cells were collected, centrifuged and lysed with RLT Buffer containing (1:100) β-mercaptoethanol.
Total RNA was isolated from the cells using the Qiagen RNeasy Mini Kit (Qiagen, cat# 74104).
RNA libraries were prepared using Illumina's TruSeq Stranded mRNA Library kit (Cat# 20020594) and sequenced on Illumina NextSeq 500 as paired-end 42-nt reads.

treatment_protocol: S-2HG treatment (H942596, Toronto Research Chemicals) started at day 0 and was at 0.4 mM concentration. Every second day, fresh complete RPMI media containing IL-2 (30 U/ml) and the appropriate amount of S-2HG or vehicle was added.

value: CD8 T cells


title: Donor C_S-2HG


title: Donor B_vehicle

value: Vehicle (water)


title: Donor C_vehicle


title: mir181_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: mir181_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Donor A_vehicle


title: Runx3_E1_CD8_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mir181_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVSLA11

city: Pavia

first: Daisy

last: Sproviero

address: Via Mondino, 2

country: Italy

institute: IRCCS Mondino Foundation

description:
MVSLA11
total RNA

data_processing:
Quality control filter, trimming of adapters, reads mapping against miRNA precursors, is implemented in docker4seq package.
Differential expression analysis was performed with the R package DESeq2, implemented in docker4seq package. We imposed a minimum |Log2FC| of 1 and a FDR lower than 0.1 as thresholds to detect differentially expressed miRNAs.
Differential expression analysis for mRNAs was performed using R package EBSeq
Genome_build: HG19
Supplementary_files_format_and_content: FPKM, TPM

source_name: extracellular vesicles

extract_protocol:
venous blood (5 ml) was collected in sodium citrate tubes. Within 1 h it was centrifuged at 1000 ×g for 15 min to separate plasma, followed by an additional centrifugation at 1600 ×g for 20 min to remove platelets
Small RNA libraries were constructed from the RNA samples using NEBNext® kit (New England Biolabs, USA). Individually-barcoded libraries were mixed. Pools were size selected on Novex 10% TBE gels (Life Technologies, USA) to enrich for miRNAs fraction. Sequencing (75 nts single-end) was performed on Illumina NextSeq500 (Illumina, USA).
Long RNA libraries (mRNAs and lncRNAs) were prepared with the Illumina TruSeq Stranded RNA Library Prep (Illumina, USA). Sequencing (75 nts paired-end) was performed on Illumina NextSeq500 (Illumina, USA). Demultiplexing was done as described for miRNA sequences.

tag: sample type

value: Extracellular vesicles derived from plasma


title: mRNA MVSLA12

description:
MVSLA12
total RNA


title: mRNA MVSLA05B

description:
MVSLA05B
total RNA


title: mir181_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Donor A_S-2HG


title: Lef1_DP_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: Runx3_E1_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mir181_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVSLA04B

description:
MVSLA04B
total RNA


title: mir181_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVSLA10

description:
MVSLA10
total RNA


title: Nfatc1_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: Lef1_DP_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVSLA02B

description:
MVSLA02B
total RNA


title: Lef1_DN3_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVPK11

description:
MVPK11
total RNA


title: Lef1_DN3_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVPK10

description:
MVPK10
total RNA


title: Lef1_CD4_4Cseq_rep2

description: 4C-seq (DpnII-Csp6I)


title: mRNA MVPK8

description:
MVPK8
total RNA


title: mRNA MVPK7

description:
MVPK7
total RNA


title: MC38-WT_3

city: Amsterdam

first: Anouk

last: Zaal

address: Boelelaan 1108

country: Netherlands

institute: Amsterdam UMC

data_processing:
Trimming reads for quality using Sickle --> trimmed FastQ files
Read and sequence alignment using HiSat2 (v2.0.4) to create SAM files
SAMtools (v0.1.19) was used to generate BAM files
FeatureCounts (R package Subread v1.5.0-p3) was used to quantify aligned reads. Multi-overlapping reads were excluded
R package EdgeR (v3.18.1) was used for library size adjustment, trimmed mean of M-values (TMM) normalization and differential expression analysis.
Genome_build: Ensemble Mus Musculus genome build GRCm38.90
Supplementary_files_format_and_content: txt format file with normalized counts created with EdgeR. The content includes sample names, genes and normalized counts for every read

molecule: polyA RNA

source_name: MC38 cancer cell line

growth_protocol: Glycovariant MC38 cancer cell lines were cutured in DMEM suplemented with 10%FCS P/S. Puromycin was added to the cell lines that were modified using CRIPR-Cas9 or CRIPR-dCas-VPR technology. Cultures were split when reaching a confluency of 70-90%.

extract_protocol:
MC38 cell lines (passage 4-9, confluence 70-90%) were harvested with 1% Trypsin EDTA and washed with PBS. Total RNA was extracted with a standard TRIzol isolation protocol (Thermo Fisher Scientific, cat#15596018). Quantity and purity was tested using the Nanodrop-2000 spectrophotometer (Nanodrop Technologies).
The library was synthesized using the TruSeq® Stranded mRNA Sample preparation kit (Illumina , cat# RS-122-9004), according to manufacturer’s LS protocol. The product quality during library generation was analyzed on the Agilent 2100 Bioanalyzer using the DNA 7500 chip (Agilent Technologies, cat# 5067-1506).

treatment_protocol: Cell lines were cultured in the presence of puromycin. Only the MC38-WT cell line was cultured in the absence of puromycin

tag: target gene

tag: technology

value: MC38 cancer cell line

tag: passage


title: mRNA MVPK6

description:
MVPK6
total RNA


title: MC38-WT_2

tag: cell line


title: mRNA MVPK5

description:
MVPK5
total RNA


title: MC38-WT_1


title: mRNA MVPK3

description:
MVPK3
total RNA


title: MC38-MOCK#2_1

value: CRISPR-dCas-VPR

value: gene overexpression


title: MC38-MOCK#2_3


title: MC38-MOCK#2_2


title: mRNA MVFTD9

description:
MVFTD9
total RNA


title: MC38-MOCK#1_3

value: gene knockout


title: mRNA MVFTD6

description:
MVFTD6
total RNA


title: mRNA MVFTD5

description:
MVFTD5
total RNA


title: mRNA MVFTD8

description:
MVFTD8
total RNA


title: MC38-MOCK#1_1


title: mRNA MVFTD7

description:
MVFTD7
total RNA


title: MC38-FUT9_3


title: MC38-MOCK#1_2


title: mRNA MVFTD4

description:
MVFTD4
total RNA


title: MC38-FUT9_2


title: MC38-FUT4_3


title: mRNA MVFTD2

description:
MVFTD2
total RNA


title: Lef1_CD4_4Cseq_rep1

description: 4C-seq (DpnII-Csp6I)

value: CD4+ Naive T Cells (Naive)


title: mRNA MVFTD3

description:
MVFTD3
total RNA


title: MC38-FUT4_2


title: mRNA MVFTD1

description:
MVFTD1
total RNA


title: MC38-FUT9_1


title: MC38-FUT4_1


title: mRNA MVCTRL20

description:
MVCTRL20
total RNA


title: mRNA MVPK2

description:
MVPK2
total RNA


title: mRNA MVPK4

description:
MVPK4
total RNA


title: MC38-DKO_3

value: CMAS and COSMC


title: mRNA MVCTRL19

description:
MVCTRL19
total RNA


title: MC38-DKO_1


title: MC38-DKO_2


title: MC38-COSMC KO_3

value: COSMC


title: mRNA MVCTRL18

description:
MVCTRL18
total RNA


title: mRNA MVCTRL17

description:
MVCTRL17
total RNA


title: MC38-COSMC KO_2


title: mRNA MVCTRL15

description:
MVCTRL15
total RNA


title: mRNA MVCTRL14

description:
MVCTRL14
total RNA


title: MC38-COSMC KO_1


title: mRNA MVAD15

description:
MVAD15
total RNA


title: mRNA MVAD14

description:
MVAD14
total RNA


title: MC38-CMAS KO_2

value: CMAS


title: mRNA MVAD13

description:
MVAD13
total RNA


title: MC38-CMAS KO_1


title: mRNA MVAD12

description:
MVAD12
total RNA


title: mRNA MVAD10

description:
MVAD10
total RNA


title: mRNA MVAD11

description:
MVAD11
total RNA


title: mRNA EXOSLA12

description:
EXOSLA12
total RNA


title: mRNA EXOSLA11

description:
EXOSLA11
total RNA


title: mRNA EXOSLA10

description:
EXOSLA10
total RNA


title: mRNA EXOSLA05B

description:
EXOSLA05B
total RNA


title: mRNA EXOSLA02B

description:
EXOSLA02B
total RNA


title: mRNA EXOPK11

description:
EXOPK11
total RNA


title: mRNA EXOPK8

description:
EXOPK8
total RNA


title: mRNA EXOPK7

description:
EXOPK7
total RNA


title: MC38-CMAS KO_3


title: INS: tdT cells T conditioned medium-2

first: Haiting

last: Ma

state: MA

address: 455 Main Street

institute: Whitehead Institute

data_processing:
Images analysis and base calling was done using the Illumina standard pipeline.
RNA-seq reads were aligned to the hg38 genome assembly using STAR version 2.7.1a with the following configurations: Ensemble 93 transcripte models, and '--sjdbOverhang 100'.
Gene counts were generated with featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts table.

source_name: ES-differentiated beta like cells sorted by INS:tdT

growth_protocol: H1 ES cell were routinely cultured in mTeSR medium in matrigel-coated 6-well plates, and passaged every 3-4 days with versene passaging. Differentiation to beta-like cells were describe in the manuscript.

extract_protocol:
Total RNA extraction were performed with Rneasy-micro plus kit based on Qiagen's instruction.
Libraries were prepared according to instructions accompanying Takara’s SMART-Seq v4 for ultra-low RNA inputs kit (R400752). Briefly, Upto 10 ng of sample was prepared using Takara’s SMART-Seq v4 Ultra Low Input RNA protocol per manufacturer’s guidelines. Briefly, RNA underwent reverse transcription via template switching and amplification, resulting in double stranded cDNA. The amount of cDNA between 100-3000 bp was calculated by Fragment Analyzer and Qubit. 150pg of the sample in range was then added to Illumina’s Nextera XT and processed according to manufacturer’s guidelines. Briefly, the cDNA underwent tagmentation, using Nextera XT’s transposase, and unique dual indexes were added by PCR amplification. Final libraries went through QC with the Fragment Analyzer and qPCR on a Roche Light Cycler 480 II. All libraries were then pooled and sequenced at single-end 40-50 base-pair using the Illumina HiSeq 2500.

treatment_protocol: Samples were treated with RPMI medium supplemented with human serum or activated human T cells conditioned medium.

value: ES derived beta-like cells

tag: cell sorting

value: Sorted based on tdT expression

value: Treated with activated T-cell conditioned medium


title: mRNA EXOPK5

description:
EXOPK5
total RNA


title: mRNA EXOPK6

description:
EXOPK6
total RNA


title: Primary islets, T conditioned medium -2

source_name: Primary pancreatic islet

value: Pancreatic endocrine cells sorted from human pancreatic islets

value: Sorted based on expression of HPi2 positive and absence of HPx1.

tag: sorting antibody

value: A647 conjugated HPi2 antibody:Novus Biologicals  # NBP1-18946AF647. DyLight 488 conjugated HPx1 antibody:Novus Biologicals NBP1-18951G.


title: mRNA EXOPK4

description:
EXOPK4
total RNA


title: mRNA EXOPK3

description:
EXOPK3
total RNA


title: Primary islets CTL-1

value: Human pancreatic islets

value: Not sorted


title: Primary islets CTL-2


title: Primary islets T conditioned medium-1


title: mRNA EXOSLA04B

description:
EXOSLA04B
total RNA

value: Extracellular vesicles derived from plasma


title: mRNA EXOPK2

description:
EXOPK2
total RNA


title: INS:CD19 beta-like cells 1 [HM_081018-1]

source_name: ES-differentiated beta like cells sorted by INS:CD19

value: Sorted based on CD19 expression.

value: CD19 Monoclonal Antibody (HIB19) Affymetrix # 12-0199-42


title: mRNA EXOPK10

description:
EXOPK10
total RNA


title: mRNA EXOAD10

description:
EXOAD10
total RNA


title: INS: tdT cells CTL-2


title: INS: tdT cells T conditioned medium-1


title: INS: tdT cells CTL-1


title: mRNA EXOAD11

description:
EXOAD11
total RNA


title: Undifferentiated ES control [HM_061918-13]

source_name: ES cells

value: H1-ES cells


title: Identification of miR-139-5p target genes in HCT116

city: Chiba

first: Naohiko

last: Seki

state: Chiba

address: 1-8-1, Inohana

department: Functional Genomics

institute: Chiba University

hyb_protocol: Agilent two-color gene expression hyb/wash protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution. Images were quantified using Agilent Feature Extraction software version 11.5.1.1

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log10 of processed Red signal/processed Green signal. Agilent software was used.

source_name: mock

label_protocol: Agilent two-color Low RNA Input Linear Amplification Kit labeling protocol

growth_protocol: Normal cell culture medium RPMI 1640 or DMEM.

extract_protocol: Total RNA was extracted using Trizol following the manufacturer's instructions.

treatment_protocol: microRNA transfection using Lipofectamine RNAiMAX (Invitrogen).

value: colon cancer

tag: transfection

value: no transfection

source_name: miR-139-5p transfected cell line


title: Identification of miR-143-5p target genes in HCT116

source_name: miR-143-5p transfected cell line


title: mRNA EXOAD12

description:
EXOAD12
total RNA


title: Identification of miR-143-3p target genes in HCT116

source_name: miR-143-3p transfected cell line


title: Identification of miR-139-3p target genes in HCT116

source_name: miR-139-3p transfected cell line


title: Identification of miR-30c-5p target genes in PANC-1

value: pancreatic cancer

source_name: miR-30c-5p transfected cell line


title: mRNA EXOAD14

description:
EXOAD14
total RNA


title: mRNA EXOAD13

description:
EXOAD13
total RNA


title: Identification of miR-30a-3p target genes in PANC-1

source_name: miR-30a-3p transfected cell line


title: Identification of miR-30c-2-3p target genes in PANC-1

source_name: miR-30c-2-3p transfected cell line


title: Identification of miR-30a-5p target genes in PANC-1

source_name: miR-30a-5p transfected cell line


title: SAM24158179 IC Donor 1

city: South San Francisco

first: Jason

middle: A

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

data_processing: Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were based on Refseq canonical transcripts mapped to GRCh38. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.

source_name: Characterize the effects of IC activation of monocytes in systemic sclerosis.

extract_protocol: RNA was extracted using Qiagen RNeasy kit as per manufacturer's protocol. Quality control of samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using DS-11 spectrophotometer (DeNovix) and the integrity of RNA was determined by 2100 Bioanalyzer (Agilent Technologies). Approximately few ng of total RNA was used as an input material for the library generation using SMART-seq v4 Ultra Low Input RNA kit (Clontech). Size of the libraries was confirmed using 2200 TapeStation and High Sensitivity D1K screen tape (Agilent Technologies) and their concentration was determined by qPCR based method using Library quantification kit (KAPA). The libraries were multiplexed and then sequenced on Illumina HiSeq 2500 (Illumina) to generate 30M of single end 50 base pair reads.

value: SAM24158179 FC Donor 1 DMSO

tag: stim

value: IC

value: CD14+ monocytes


title: SAM24158190 Unstim Donor 2

value: SAM24158190 Unstim Donor 2

value: Unstim


title: SAM24158181 IC Donor 2

value: SAM24158181 FC Donor 2 DMSO


title: SAM24158183 IC Donor 3

value: SAM24158183 FC Donor 3 DMSO


title: SAM24158193 Unstim Donor 5

value: SAM24158193 Unstim Donor 5


title: SAM24158185 IC Donor 4

value: SAM24158185 FC Donor 4 DMSO


title: INS:CD19 beta-like cells 2 [HM_081018-3]

value: ES derived beta-like cells


title: mRNA EXOCTRL15

description:
EXOCTRL15
total RNA

value: Extracellular vesicles derived from plasma


title: SAM24158173 LPS Donor 3

value: SAM24158173 LPS Donor 3 DMSO

value: LPS


title: SAM24158187 IC Donor 5

value: SAM24158187 FC Donor 5 DMSO


title: mRNA EXOCTRL17

description:
EXOCTRL17
total RNA


title: mRNA EXOCTRL18

description:
EXOCTRL18
total RNA


title: SAM24158177 LPS Donor 5

value: SAM24158177 LPS Donor 5 DMSO


title: mRNA EXOCTRL19

description:
EXOCTRL19
total RNA


title: SAM24158175 LPS Donor 4

value: SAM24158175 LPS Donor 4 DMSO


title: mRNA EXOCTRL20

description:
EXOCTRL20
total RNA


title: mRNA EXOAD15

description:
EXOAD15
total RNA


title: SAM24158189 Unstim Donor 1

value: SAM24158189 Unstim Donor 1


title: mRNA EXOCTRL14

description:
EXOCTRL14
total RNA


title: mRNA EXOFTD1

description:
EXOFTD1
total RNA


title: SAM24158192 Unstim Donor 4

value: SAM24158192 Unstim Donor 4


title: mRNA EXOFTD3

description:
EXOFTD3
total RNA


title: mRNA EXOFTD2

description:
EXOFTD2
total RNA


title: SAM24158169 LPS Donor 1

value: SAM24158169 LPS Donor 1 DMSO


title: SAM24158191 Unstim Donor 3

value: SAM24158191 Unstim Donor 3

value: CD14+ monocytes


title: SAM24158171 LPS Donor 2

value: SAM24158171 LPS Donor 2 DMSO


title: mRNA EXOFTD4

description:
EXOFTD4
total RNA


title: mRNA EXOFTD6

description:
EXOFTD6
total RNA


title: mRNA EXOFTD7

description:
EXOFTD7
total RNA


title: miRNA EXOAD15

description:
EXOAD15
miRNA


title: mRNA EXOFTD9

description:
EXOFTD9
total RNA


title: miRNA_Subject_3400741

city: Chapel Hill

first: Julia

last: Rager

state: NC

address: 135 Dauer Drive, CB 7431

institute: UNC

data_processing:
Standardized samples using log-transformed counts per million standardization
miRNA sequencing data processed in R
The count data was filtered to exclude universally lowly expressed transcripts, and data were normalized by quantiles using algorithms enabled through the DESeq2 processing pipeline.
Normalizing the data by median signal intensity using the DESeq2 package in R
Genome_build: mirBase v20
Supplementary_files_format_and_content: raw counts

source_name: Placenta of infants born at low gestational age

extract_protocol:
Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation.  Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures, including birthweight, were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C untile further analysis. RNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were prepared using the HTG EdgeSeq miRNA Whole Transcriptome Assay, we measured the expression of 2,083 miRNA transcripts in the placenta using next-generation sequencing

value: placenta

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: miRNA_Subject_3400672

tag: tissue


title: miRNA_Subject_3400521


title: miRNA_Subject_3400661


title: miRNA_Subject_3400571


title: miRNA_Subject_3400531


title: miRNA EXOAD10

description:
EXOAD10
miRNA

source_name: extracellular vesicles

tag: sample type


title: miRNA EXOAD11

description:
EXOAD11
miRNA


title: miRNA_Subject_3400401


title: miRNA_Subject_3400371


title: miRNA_Subject_3400362


title: miRNA EXOAD12

description:
EXOAD12
miRNA


title: miRNA EXOAD13

description:
EXOAD13
miRNA


title: miRNA_Subject_3400341


title: miRNA_Subject_3400361


title: miRNA_Subject_3400301


title: mRNA EXOFTD8

description:
EXOFTD8
total RNA


title: miRNA EXOCTRL17

description:
EXOCTRL17
miRNA


title: miRNA_Subject_3400211


title: miRNA_Subject_3400291


title: miRNA EXOCTRL14

description:
EXOCTRL14
miRNA


title: miRNA EXOCTRL15

description:
EXOCTRL15
miRNA


title: miRNA_Subject_3400321


title: mRNA EXOFTD5

description:
EXOFTD5
total RNA


title: miRNA EXOCTRL18

description:
EXOCTRL18
miRNA


title: miRNA_Subject_3400201


title: miRNA EXOAD14

description:
EXOAD14
miRNA


title: miRNA EXOCTRL20

description:
EXOCTRL20
miRNA


title: miRNA EXOFTD2

description:
EXOFTD2
miRNA


title: miRNA EXOFTD1

description:
EXOFTD1
miRNA


title: miRNA_Subject_3301321


title: miRNA EXOFTD3

description:
EXOFTD3
miRNA


title: miRNA_Subject_3301331


title: miRNA EXOFTD4

description:
EXOFTD4
miRNA


title: miRNA EXOFTD6

description:
EXOFTD6
miRNA


title: miRNA EXOFTD5

description:
EXOFTD5
miRNA


title: miRNA_Subject_3301242


title: miRNA_Subject_3301241


title: miRNA_Subject_3301301


title: miRNA_Subject_3301201


title: miRNA EXOFTD7

description:
EXOFTD7
miRNA


title: miRNA_Subject_3301202


title: miRNA EXOFTD8

description:
EXOFTD8
miRNA


title: miRNA EXOCTRL19

description:
EXOCTRL19
miRNA


title: miRNA_Subject_3301191


title: miRNA_Subject_3301021


title: miRNA EXOFTD9

description:
EXOFTD9
miRNA


title: miRNA_Subject_3301011


title: miRNA_Subject_3301001


title: miRNA EXOPK11

description:
EXOPK11
miRNA


title: miRNA_Subject_3300991


title: miRNA EXOPK2

description:
EXOPK2
miRNA


title: miRNA EXOPK10

description:
EXOPK10
miRNA


title: miRNA_Subject_3301081


title: miRNA_Subject_3300911


title: miRNA EXOPK5

description:
EXOPK5
miRNA


title: miRNA_Subject_3300901


title: miRNA_Subject_3300981


title: miRNA EXOPK6

description:
EXOPK6
miRNA


title: miRNA EXOPK4

description:
EXOPK4
miRNA


title: miRNA EXOPK3

description:
EXOPK3
miRNA


title: miRNA EXOPK7

description:
EXOPK7
miRNA


title: miRNA EXOPK8

description:
EXOPK8
miRNA


title: miRNA_Subject_3300761


title: miRNA_Subject_3300841


title: miRNA EXOSLA02B

description:
EXOSLA02B
miRNA


title: miRNA_Subject_3300732


title: miRNA EXOSLA04B

description:
EXOSLA04B
miRNA


title: miRNA_Subject_3300711


title: miRNA EXOSLA05B

description:
EXOSLA05B
miRNA


title: miRNA_Subject_3300641


title: miRNA EXOSLA11

description:
EXOSLA11
miRNA


title: miRNA EXOSLA10

description:
EXOSLA10
miRNA


title: miRNA MVAD11

description:
MVAD11
miRNA


title: miRNA_Subject_3300602


title: miRNA_Subject_3300611


title: miRNA_Subject_3300601


title: miRNA_Subject_3300861


title: miRNA_Subject_3300592


title: miRNA MVAD12

description:
MVAD12
miRNA


title: miRNA EXOSLA12

description:
EXOSLA12
miRNA


title: miRNA_Subject_3300501


title: miRNA_Subject_3300591


title: miRNA MVAD10

description:
MVAD10
miRNA


title: miRNA MVCTRL14

description:
MVCTRL14
miRNA


title: miRNA_Subject_3300721


title: miRNA_Subject_3300411


title: miRNA_Subject_3300381


title: miRNA_Subject_3300371


title: miRNA MVAD13

description:
MVAD13
miRNA


title: miRNA_Subject_3300401


title: miRNA MVAD14

description:
MVAD14
miRNA


title: miRNA MVAD15

description:
MVAD15
miRNA


title: miRNA MVCTRL18

description:
MVCTRL18
miRNA


title: miRNA_Subject_3300361


title: miRNA MVCTRL15

description:
MVCTRL15
miRNA


title: miRNA_Subject_3200721


title: miRNA MVCTRL19

description:
MVCTRL19
miRNA


title: miRNA MVCTRL20

description:
MVCTRL20
miRNA


title: miRNA_Subject_3300531


title: miRNA MVFTD1

description:
MVFTD1
miRNA


title: miRNA MVFTD3

description:
MVFTD3
miRNA


title: miRNA MVFTD2

description:
MVFTD2
miRNA


title: miRNA_Subject_3200651


title: miRNA MVCTRL17

description:
MVCTRL17
miRNA


title: miRNA_Subject_3200611


title: miRNA_Subject_3200612


title: miRNA MVFTD4

description:
MVFTD4
miRNA


title: miRNA MVFTD5

description:
MVFTD5
miRNA


title: miRNA_Subject_3200531


title: miRNA_Subject_3200431


title: miRNA_Subject_3300211


title: miRNA_Subject_3200342


title: miRNA MVFTD7

description:
MVFTD7
miRNA


title: miRNA MVFTD6

description:
MVFTD6
miRNA


title: miRNA_Subject_3200141


title: miRNA_Subject_3200023


title: miRNA_Subject_3101471


title: miRNA MVPK11

description:
MVPK11
miRNA


title: miRNA MVPK2

description:
MVPK2
miRNA


title: miRNA MVFTD8

description:
MVFTD8
miRNA


title: miRNA MVFTD9

description:
MVFTD9
miRNA


title: miRNA MVPK10

description:
MVPK10
miRNA


title: miRNA_Subject_3200022


title: miRNA_Subject_3101411


title: miRNA_Subject_3101401


title: miRNA_Subject_3200021


title: miRNA MVPK3

description:
MVPK3
miRNA


title: miRNA_Subject_3101372


title: miRNA MVPK4

description:
MVPK4
miRNA


title: miRNA MVPK5

description:
MVPK5
miRNA


title: miRNA MVPK6

description:
MVPK6
miRNA


title: miRNA_Subject_3101331


title: miRNA_Subject_3101283


title: miRNA MVPK7

description:
MVPK7
miRNA


title: miRNA_Subject_3101241


title: miRNA MVSLA02B

description:
MVSLA02B
miRNA


title: miRNA MVSLA04B

description:
MVSLA04B
miRNA


title: miRNA MVSLA05B

description:
MVSLA05B
miRNA


title: miRNA_Subject_3101201


title: miRNA MVSLA10

description:
MVSLA10
miRNA


title: miRNA MVSLA12

description:
MVSLA12
miRNA


title: miRNA_Subject_3101181


title: miRNA MVSLA11

description:
MVSLA11
miRNA


title: Pool10

city: Jerusalem

first: Maayan

last: Salton

address: Ein-Kerem Canpus

country: Israel

institute: Hebrew University

data_processing:
Raw reads were quality-trimmed at both ends, then poly-G sequences (NextSeq’s no signal) were removed from the 3' end, then adapter sequences were removed from the 3' end, and finally low-quality reads were filtered out. Trimming was done with cutadapt, version 1.12, using parameters -O 1, --match-read-wildcards, and -m 15. Filtering the remaining reads was done with the fastq_quality_filter program of the FASTX package, version 0.0.14, with parameters -q 20 and -p 80.
Processed reads were aligned with TopHat, version 2.1.1, using parameters -G genes.gtf (gene annotations from Ensembl release 89), -N 10, --read-gap-length 5, --read-edit-dist 15, --segment-length 20, --read-realign-edit-dist 3, --no-coverage-search, and --library-type fr-firststrand.
Raw counts were obtained with htseq-count, version 0.6.0, using -s 'reverse', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA.
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel file with general gene details, columns A to I, and raw counts for the pooled sample at column J. A question mark (?) denotes missing values. Genes with missing counts are due to filtering by gene type (see data processing steps).

source_name: a pool of ten RNA samples from cell free saliva

extract_protocol:
Saliva was kept at -20°C before extraction. Saliva was centrifuged at 4°C for 15 min at 2600 g. RNA was extracted from the supernatant using the NucleoSpin RNA XS Kit (Macherey-Nagel) according to the manufacturer's instructions, with elution in 20 µl. 10 RNA samples were pooled and ethanol precipitation was applied.
Library preparation was done using KAPA stranded mRNA-seq library kit (Roche KK-KK8421) with a modification to the protocol - the RNA library preparation was initiated from the fragmentation step, after which the regular protocol was followed. Library quality control was done using Qubit 4 (Invitrogen) and TapeStation 2200 (Agilent). Library was diluted to 4 nM and sequenced on NextSeq 500, using the NextSeq high output kit v2, 75 cycles (Illumina).

tag: subject

value: healthy women

value: Saliva


title: SEQRS_PUM2_round5

city: Ann Arbor

first: Peter

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

data_processing:
library strategy: SEQRS (in vitro selection, high-throughput sequencing of RNA, and SSLs (sequence specificity landscapes))
Data processing for Bru-seq and BruChase-seq is described in Paulsen et al. (doi: 10.1016/j.ymeth.2013.08.015)
Data processing for SEQRS was performed using custom python scripts to split reads by barcode. 20mers were identified by location in the read using custom python scripts. Lower kmers can be easily calculated from 20mer reads
Genome_build: hg19 for Bru-seq and BruChase-seq
Supplementary_files_format_and_content: read count files contain count of reads over genes or exons where each read is split into fracitonal coverage over the length of the read. 20mer files contain the 20mer variable region extracted from the raw reads

extract_protocol:
Bru-seq and BruChase-seq were conducted as described in Paulsen et al. (doi: 10.1016/j.ymeth.2013.08.015) in HEK293 cells grown in the presence of siPUM1/2 or siNTC.
SEQRS was conducted on PUM1 PUM-HD and PUM2 PUM-HD as described in Campbell et al. (doi: 10.1038/nsmb.2847) with minor modifications including the use of Magnetic Halolink beads.

treatment_protocol: RNAi conditions and siRNA sequences were previously described by Bohn et al. (doi: 10.1093/nar/gkx1120) and include treatment with siRNAs for 48hrs to allow for PUM depletion prior for BrU labeling.

tag: rna-binding protein


title: SEQRS_blank

value: blank (control)


title: miRNA_Subject_3101161


title: miRNA_Subject_3101163


title: SEQRS_PUM2_round4


title: SEQRS_PUM2_round3


title: miRNA_Subject_3101131


title: miRNA MVPK8

description:
MVPK8
miRNA


title: miRNA_Subject_3101341


title: SEQRS_PUM2_round2


title: miRNA_Subject_3101081


title: miRNA_Subject_3101061


title: miRNA_Subject_3101071


title: SEQRS_PUM1_round5


title: SEQRS_PUM2_round1


title: miRNA_Subject_3101096


title: miRNA_Subject_3101232


title: miRNA_Subject_3100991


title: miRNA_Subject_3100981


title: SEQRS_PUM1_round4


title: miRNA_Subject_3101141


title: SEQRS_PUM1_round3


title: SEQRS_PUM1_round2


title: miRNA_Subject_3100971


title: miRNA_Subject_3100891


title: SEQRS_PUM1_round1


title: miRNA_Subject_3100931


title: miRNA_Subject_3100863


title: miRNA_Subject_3100862


title: miRNA_Subject_3101051


title: miRNA_Subject_3100852


title: Contr_Pol2

city: Tampa

first: Elsa

middle: Renee

last: Flores

state: FL

address: 12902 USF Magnolia Drive

department: Department of Molecular Oncology

institute: Moffit Cancer Center

data_processing:
Reads were aligned to the human genome (hg38) using the BWA algorithm
Alignments were extended in silico at their 3’-ends to a length of 200 bp
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of p-value = 1e-7
Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of peaks called for each sample

source_name: Control tumors Pol2 precipitated

growth_protocol: human breast cancer cells MCF10DCIS stably expressing an inducible shDNp63 were injected either in mammary fatpads of nude mice (Control tumors and DNp63-KD tumors)

extract_protocol:
Cells were fixed with 1% formaldehyde.Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Genomic DNA regions of interest were isolated using 4 ug of antibody. Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. An automated system (Apollo 342, Wafergen Biosystems/Takara) was used.

treatment_protocol: mice were fed on control diet (Control tumors) or dox diet (DNp63-KD tumors) after injection; collected tumors after 5 weeks post injection (Control tumors and DNp63-KD tumors)

tag: cell line

value: Human xenograft into nude mice

tag: mice age

value: 6 week old at injection

tag: treatment

value: mice fed on control diet after injection, collected tumors after 5 weeks post injection


title: DNp63_Pol2

source_name: DNp63-KD tumors Pol2 precipitated

value: mice fed on control dox diet after injection, collected tumors after 5 weeks post injection


title: miRNA_Subject_3100861

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: Contr_DNp63

source_name: Control tumors DNp63 precipitated


title: miRNA_Subject_3100851

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)


title: BovinePericytes coculture, Timepoint 96, Replicate 2

city: Lens

first: Maxime

last: Culot

address: Rue Jean Souvraz - SP 18

country: France

institute: Université d'Artois

description: raw B_t96_2

data_processing:
Illumina bcl2fastq2 v2.20 software used for basecalling and demultiplexing.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
PCR duplicates were cleaned using TrueQuant technology (UMI) and in-house GenXPro GmbH script.
Reads were aligned to the human reference genome (hg38) using the bowtie2 2.3.4.1 mapping tool.
Gene count data was normalized to account for differences in sequencing depth. Testing for differential gene expression was performed in the statistical programming platform R using the DeSeq2 R/Bioconductor package.
Genome_build: Genome Reference Consortium Human Build 38 (hg38)
Supplementary_files_format_and_content: Comma-delimited text file include raw counts for each sample

source_name: Hematopoietic stem cell-derived endothelial cells

growth_protocol: The human in vitro BBB model used in this study was modified from the coculture model of Cecchelli et al. (2014). In brief, hematopoietic stem cell-derived ECs were isolated according to the method described in Cecchelli et al. (2014). Vials of frozen ECs (1 x 106 cells) were rapidly thawed and seeded in gelatin-coated (type A from porcine skin) (Sigma-Aldrich) 100-mm Petri dishes (Costar, Corning Incorporated, NY, USA) containing complete medium for ECs i.e. endothelial cell medium (Sigma-Aldrich), supplemented with 5% fetal calf serum (Integro), 1% endothelial cell growth supplement (Sigma-Aldrich) and 0.5% gentamicin (Biochrom AG, Berlin, Germany). Two days after defrosting, around 5.0 x 106 cells were present and ECs were trypsinized with trypsine/ethylenediaminetetraacetic acid (0.05%/0.02% in phosphate buffered saline-calcium and magnesium free (Biochrom AG) and seeded on a semi-permeable Transwell insert (0.4 m, 12-well system, Costar, Corning Incorporated) coated with Matrigel (growth factor reduced BD Matrigel Matrix, BD Biosciences), at a concentration of 16.0 x 104 cells per mL. Cells were cultivated at 37°C in a humified atmosphere at 5% CO2/95% air for a total of 7 days and medium was changed every two days. All sera were heat-inactivated before use.

extract_protocol:
Cell lysates were stored in liquid nitrogen before RNA isolation. Isolation of total RNA from ECs was conducted using the ZR-Duet DNA/RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA) according to manufacturer’s instructions. RNA samples were digested using DNase I and RNA integrity was accessed using automated capillary electrophoresis (RNA pico sensitivity assay, LabChip GX II Touch HT, Perkin Elmer, Villebon-sur-Yvette, France).
Genome-wide gene expression profiling was performed using the MACE-seq method. In general, the procedure follows a modified protocol described in Nold-Petry et al. (2015). In brief, samples with 100 ng of DNase-treated RNA were used for library preparation. Synthesis of cDNA was performed by reverse transcription using oligo (dT) primers following fragmentation of cDNA to an average size of 200 bp using sonification (Bioruptor, Diagenode, Seraing, Belgium). DNA was quantified using a Qubit HS dsDNA assay (Thermo Fisher Scientific). cDNA fragments were ligated to DNA adapters containing TrueQuant unique molecular identifiers included in the kit. Library amplification was done using polymerase chain reaction, purified by solid phase reversible immobilization beads (Agencourt AMPure XP, Beckman Coulter, Brea, CA, USA).

treatment_protocol: Both cocultures were initiated by inserting the Transwell membranes with attached ECs into the pericyte-containing 12-well plates and by changing medium to endothelial cell medium, resulting in a non-contact BBB in vitro model, as no physical interaction exist between the two cell types. Experiments were initiated at different time points (i.e. 0, 24, 48 and 96 hours) starting from t0, as the moment of coculture initiation. Cocultures were cultivated at 37°C in a humified atmosphere and 5% CO2.

tag: culture

value: Coculture with bovine brain pericytes

tag: time of culture after starting coculture

value: 96 hours


title: BovinePericytes coculture, Timepoint 96, Replicate 3

description: raw B_t96_3


title: miRNA_Subject_3100461

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)


title: miRNA_Subject_3100972

tag: tissue

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: miRNA_Subject_3100481


title: miRNA_Subject_3100491


title: miRNA_Subject_3100431


title: miRNA_Subject_3100573


title: BovinePericytes coculture, Timepoint 48, Replicate 2

description: raw B_t48_2

value: 48 hours


title: BovinePericytes coculture, Timepoint 48, Replicate 3

description: raw B_t48_3


title: BovinePericytes coculture, Timepoint 96, Replicate 1

description: raw B_t96_1


title: BovinePericytes coculture, Timepoint 48, Replicate 1

description: raw B_t48_1


title: BovinePericytes coculture, Timepoint 24, Replicate 3

description: raw B_t24_3

value: 24 hours


title: miRNA_Subject_3100421


title: BovinePericytes coculture, Timepoint 24, Replicate 2

description: raw B_t24_2


title: miRNA_Subject_3100381


title: DNp63_DNp63

source_name: DNp63-KD tumors DNp63 precipitated

tag: cell line


title: BovinePericytes coculture, Timepoint 24, Replicate 1

description: raw B_t24_1


title: HumanPericytes coculture, Timepoint 96, Replicate 3

description: raw H_t96_3

value: Coculture with human brain pericytes


title: HumanPericytes coculture, Timepoint 96, Replicate 2

description: raw H_t96_2


title: HumanPericytes coculture, Timepoint 96, Replicate 1

description: raw H_t96_1


title: miRNA_Subject_3100271


title: miRNA_Subject_3100261


title: miRNA_Subject_3100341


title: HumanPericytes coculture, Timepoint 48, Replicate 3

description: raw H_t48_3


title: miRNA_Subject_2302211


title: Solo-culture, Timepoint 96, Replicate 3

description: raw S_t96_3

value: Solo culture


title: miRNA_Subject_2301891


title: HumanPericytes coculture, Timepoint 24, Replicate 3

description: raw H_t24_3


title: miRNA_Subject_3100171


title: HumanPericytes coculture, Timepoint 24, Replicate 2

description: raw H_t24_2


title: Solo-culture, Timepoint 96, Replicate 2

description: raw S_t96_2


title: HumanPericytes coculture, Timepoint 24, Replicate 1

description: raw H_t24_1


title: miRNA_Subject_3100041


title: HumanPericytes coculture, Timepoint 48, Replicate 1

description: raw H_t48_1


title: miRNA_Subject_2301791


title: miRNA_Subject_2301781


title: miRNA_Subject_3100371


title: Solo-culture, Timepoint 48, Replicate 3

description: raw S_t48_3


title: miRNA_Subject_2301751


title: Solo-culture, Timepoint 96, Replicate 1

description: raw S_t96_1


title: miRNA_Subject_3100351


title: Solo-culture, Timepoint 48, Replicate 2

description: raw S_t48_2


title: miRNA_Subject_2301671


title: miRNA_Subject_2301631


title: Solo-culture, Timepoint 48, Replicate 1

description: raw S_t48_1


title: miRNA_Subject_2301592


title: miRNA_Subject_2301591


title: Solo-culture, Timepoint 0, Replicate 3

description: raw S_t0_3

value: 0 hours


title: Solo-culture, Timepoint 0, Replicate 2

description: raw S_t0_2


title: miRNA_Subject_2301542


title: Solo-culture, Timepoint 0, Replicate 1

description: raw S_t0_1


title: miRNA_Subject_2301521


title: miRNA_Subject_2301391


title: miRNA_Subject_2301281


title: miRNA_Subject_2300921


title: miRNA_Subject_2301021


title: miRNA_Subject_2301151


title: miRNA_Subject_2301061


title: miRNA_Subject_2301251


title: miRNA_Subject_2300891


title: miRNA_Subject_2300901


title: miRNA_Subject_2300871


title: HumanPericytes coculture, Timepoint 48, Replicate 2

description: raw H_t48_2


title: miRNA_Subject_2300861


title: MDA_48h_5FU-3

city: Pittsburgh

first: Jian

last: Cui

state: PA

address: E1002 Biomedical Science Tower,  200 Lothrop Street

department: Department of Immunology

institute: University of Pittsburgh

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-3

data_processing:
NextSeq500 75bp PE v2 High Output run, with 27 multiplexed samples per run
The fastq files were generated and trimmed through Basespace with application “FASTQ Generation v1.0.0”.
Differential expression analysis was performed with edgeR and DE genes were selected with a False Discovery Rate (FDR) < 0.05.
Genome_build: hg38, UCSC for Hep G2, and hg19, UCSC  for MDA-MB-231
Supplementary_files_format_and_content: .csv files delimited matrix showing raw counts of refGenes

growth_protocol: Both Hep G2 and MDA-MB-231 cell lines were purchased from ATCC (MA, USA). Cells were cultured in DMEM medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific) at 37 °C with 5% CO2

extract_protocol:
The treated cells were harvested, and the cell pellets were snap frozen with liquid nitrogen and stored at−80°C.Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. After quantified using a NanoDrop Spectrophotometer ND-1000 (Thermo Fisher Scientific), the quality of the total RNA was verified on a Bioanalyzer by Cancer Genome Facility (SA, Australia) ensuring all samples had RINs >7.0. For both cell lines, the sequencing was performed in Ramaciotti Centrefor Genomics (NSW, Australia). The sample preparation for each cell line was TruSeq Stranded mRNA-seq with dual indexed, on the NextSeq500 v2 platform. The parameter was 75bp paired-end High Output.
Total RNA was isolated with PureLink™ RNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol (Rev: 21 May 2012).  Sample preparation were employing TruSeq Stranded mRNA Library Prep Kit (Illumina) with 1μg input total RNA.

treatment_protocol: Drug treatments were designed as follows: pure complete medium,  vehicle control (VC; 0.25% Tween 80 with 10 mM in PBS), 2 mg/ml CKI, or 5FU (150 μg/ml for Hep G2 and 20 μg/ml for MDA-MB-231). Cells were treated with medium only, vehicle control, CKI, and 5Fu are labelled as “untreated”, “CKI”, and “5FU”.

tag: tumor type

value: breast cancer

tag: time


title: MDA_48h_5FU-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-1

tag: treatment


title: MDA_48h_5FU-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-5FU-2


title: miRNA_Subject_2300851

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: miRNA_Subject_2300852

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)


title: MDA_48h_2mg_CKI-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-3

value: 2mg CKI


title: miRNA_Subject_2300741

value: placenta


title: miRNA_Subject_2300701


title: MDA_48h_2mg_CKI-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-1


title: MDA_48h_VC-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-3

value: VC


title: MDA_48h_VC-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-2


title: miRNA_Subject_2300691


title: miRNA_Subject_2300662


title: miRNA_Subject_2301941


title: MDA_48h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-3

value: untreated


title: MDA_48h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-2


title: miRNA_Subject_2300651


title: miRNA_Subject_2300591


title: miRNA_Subject_2300571


title: miRNA_Subject_2300761


title: MDA_24h_5FU-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-2


title: MDA_48h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-UT-1


title: MDA_24h_5FU-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-1


title: miRNA_Subject_2300521


title: miRNA_Subject_2300551


title: miRNA_Subject_2300491


title: MDA_24h_2mg_CKI-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-1


title: MDA_24h_2mg_CKI-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-2


title: MDA_48h_2mg_CKI-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-CKI-2


title: miRNA_Subject_2300522


title: MDA_24h_VC-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-3


title: miRNA_Subject_2300692


title: MDA_48h_VC-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
48h-VC-1


title: miRNA_Subject_2300461


title: MDA_24h_VC-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-2


title: miRNA_Subject_2300661


title: miRNA_Subject_2300441


title: MDA_24h_5FU-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-5FU-3


title: MDA_24h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-3


title: miRNA_Subject_2300431


title: MDA_24h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-2


title: miRNA_Subject_2300601


title: MDA_24h_2mg_CKI-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-CKI-3


title: MDA_24h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-UT-1


title: miRNA_Subject_2200681


title: miRNA_Subject_2200661


title: MDA_0h_untreated-3

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-3


title: miRNA_Subject_2200821


title: MDA_0h_untreated-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-1


title: miRNA_Subject_2200582


title: HEP_48h_5FU-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-3

value: Hep G2

value: liver cancer


title: miRNA_Subject_2200562


title: miRNA_Subject_2200511


title: HEP_48h_5FU-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-2


title: HEP_48h_5FU-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-5FU-1


title: miRNA_Subject_2200421


title: HEP_48h_2mg_CKI-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-3


title: miRNA_Subject_2300481


title: MDA_24h_VC-1

description:
strand-specific RNA-seq
mda_counts_counts.csv
24h-VC-1


title: miRNA_Subject_2200331


title: HEP_48h_2mg_CKI-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-1


title: miRNA_Subject_2200301


title: HEP_48h_VC-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-3


title: HEP_48h_2mg_CKI-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-CKI-2


title: miRNA_Subject_2200221


title: HEP_48h_VC-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-2


title: miRNA_Subject_2200191


title: miRNA_Subject_2200211


title: HEP_48h_VC-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-VC-1


title: miRNA_Subject_2200811


title: MDA_0h_untreated-2

description:
strand-specific RNA-seq
mda_counts_counts.csv
0h-UT-2


title: miRNA_Subject_2200041


title: HEP_48h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-3


title: miRNA_Subject_2200171


title: HEP_48h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-1


title: miRNA_Subject_2101562


title: HEP_48h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
48h-UT-2


title: miRNA_Subject_2101521


title: miRNA_Subject_2101531


title: HEP_24h_5FU-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-1


title: HEP_24h_5FU-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-2


title: miRNA_Subject_2101491


title: HEP_24h_2mg_CKI-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-2


title: miRNA_Subject_2101431


title: HEP_24h_2mg_CKI-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-3


title: miRNA_Subject_2101501


title: HEP_24h_2mg_CKI-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-CKI-1


title: miRNA_Subject_2101391


title: HEP_24h_VC-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-3


title: miRNA_Subject_2101332


title: miRNA_Subject_2101331


title: miRNA_Subject_2101321


title: HEP_24h_VC-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-VC-1


title: miRNA_Subject_2101301


title: HEP_24h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-3


title: HEP_24h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-2


title: miRNA_Subject_2101282


title: HEP_24h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-UT-1


title: HEP_0h_untreated-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-3


title: miRNA_Subject_2101281


title: miRNA_Subject_2101221


title: HEP_24h_5FU-3

description:
strand-specific RNA-seq
hep_counts_counts.csv
24h-5FU-3


title: HEP_0h_untreated-1

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-1


title: HEP_0h_untreated-2

description:
strand-specific RNA-seq
hep_counts_counts.csv
0h-UT-2


title: miRNA_Subject_2101461


title: miRNA_Subject_2101201


title: miRNA_Subject_2101182


title: miRNA_Subject_2101181