title: KO_2_techRep1

description:
HSV skin OT-I.Tgfbr2-/- T cells
Biological replicate 2, technical replicate 1


title: 10_BS_Osdrm1b_T1

status: Public on Jun 24 2021

type: SRA

city: shenzhen

first: yiming

last: yu

state: --- Select a state ---

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology

library_source: genomic

data_processing:
Raw reads were removed adaptors using cutadapt version 1.18.
For BS-Seq, clean reads were mapped to MSU7.0 version reference genome using BSMAP v2.90 allowing 8% mismatches and methylation level was extracted using BSMAP v2.90. For mRNA-Seq, clean reads mapped to MSU7.0 version reference genome using HISAT2 v2.1.0 and quantified using StringTie v1.3.3b. For sRNA-Seq, clean reads were uniquely mapped to MSU7.0 reference genome using Bowtie v1.2.2 by allowing no mismatches.
Genome_build: MSU7.0
Supplementary_files_format_and_content: For BS-Seq, tab-delimited text files include sequencing results at each cytosine sites for each sample. Column 1 is the genomic coordinate of cytosines, and column 2 is methylation levels. For mRNA-Seq, tab-delimited text files include expression values for each sample. Columns 1-6 are the genomic coordinate of genes, column 7 is average coverage, column 8 is FPKM value, and column 9 is TPM value. For sRNA-Seq, tab-delimited text files include sRNA reads information for each sample. Column 1 is chromosome, column 2 is the genomic strand(+/-) the read mapped to, column 3 is the genomic coordinate the read mapped to, and column 4 is the length of the sRNA.

molecule: genomic DNA

organism: Oryza sativa

source_name: Osdrm1b mutant

growth_protocol: The seeds of T0 mutants and callus culture-regenerated wild type were germinated and grown of hormone-free, 1/2 MS medium under 14/10h of light/dark at 28℃/25℃ in the light growth chamber during 14 days. Then the seedlings of homozygous T1 mutants were transplanted to greenhouse and grew in mud under 14/10h of light/dark at 34℃/25℃.

extract_protocol:
For BS-Seq, Genomic DNA was extracted from the mature leaves of 70-day-old wild type and mutant plants using the DNeasy plant mini kit (Qiagen). For mRNA-Seq and sRNA-Seq, total RNA of each genotype was extracted from the mature leaves of 70-day-old wild type and mutant plants using TRIzol reagent (Invitrogen)
The libraries were prepared and sequenced at the GENEWIZ Bioinformatics Institute on an Illumina Hiseq Xten platform.

tag: library strategy

value: Osdrm1b mutant

tag: developmental stage

value: 70-day old

tag: tissue

value: leaves

tag: generation


title: mESC_Rep1

type: RNA

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: Gene expression data from TGFP/+; Foxa2tagRFP/+ mouse ESCs, biological replicate 1

hyb_protocol: According to the Affymetrix expression protocol

data_processing: Expression data were RMA normalized using the oligo package (version 1.48.0)

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: TGFP/+; Foxa2tagRFP/+ mouse ESCs were cultured on mitomycin c-treated mouse embryonic fibroblasts (feeders) in DMEM (Life Technologies, Cat#11965092) supplemented with 15  %  FCS (PAN Biotech) ,  0.1  mM  β-mercaptoethanol (Life Technologies, Cat#31350-10),  2 mM L-glutamine (Life Technologies, Cat#25030081), 1× non-essential amino acid (Sigma, Cat#M7145), 2 mM HEPES (Life Technologies, Cat#15630-056),   and 1000 U/ml leukemia inhibitory factor (LIF; Sigma, Cat#). Every 2-3 days cells were passaged by treatment with 0,05% Trypsin (Life Technologies, Cat#25300054) on new feeders and the medium was changed every day.

extract_protocol: miRNeasy Mini Kit (Qiagen)

treatment_protocol: Before differentiation, Wnt-3a feeders were seeded at a density of ~5 x 104 cells /24-well. TGFP/+; Foxa2tagRFP/+ mouse ESCs (ESCs) were passaged onto gelatine-coated plates for 30 min twice to remove remaining feeders from maintenance cultures. Next, ESCs were transferred to Wnt3a-expressing feeder plate with a seeding density of 2 x 105 cells /24-well. Endoderm differentiation medium (EDM), consisting of 500 ml Advanced DMEM/F-12 (Life Technologies, Cat#12634-10), 500 ml Advanced RPMI 1640 (Life Technologies, Cat#12633-012), 22 ml GlutaMAX (Life Technologies, Cat#12860-01), 200 µl AlbuMAX 100 mg/ml (Life Technologies, Cat#11021-029), 22 ml HEPES 1M, 70 µl Cytidine 150 mg/ml (SIGMA, Cat#C4654), 0,9 ml ß-Mercaptoethanol 50 mM, 12 ml Pen/Strep (10000U/ml) (Life Technologies, Cat#10378016), 1 ml Insulin-Transferrin-Selenium Ethanolamine (Life Technologies, Cat#51500-056) supplemented with 12 ng/ml Act A was used to induce the endoderm differentiation. For mesoderm differentiation, 3 ng/ml Act A and 7.5 ng/ml Bmp4 were added to EDM. The medium was changed every day.

tag: cell line

tag: background strain

tag: differentiation protocol

tag: differentiation stage

value: embryonic stem cell

tag: days of differentiation

tag: facs

value: no


title: 9_BS_Osdrm2_T1

source_name: Osdrm2 mutant

value: Osdrm2 mutant


title: RL lenalidomide - H3K27ac_rep2

city: Toronto

first: Robert

last: Kridel

state: ON

address: 101 College Street, Rm 12-311

country: Canada

institute: Princess Margaret Cancer Centre

data_processing:
The processed reads were then aligned using the BWA aligner (v0.7.15) in single-end mode to hg19 genome.
BAM files across multiple lanes were merged using picard v1.130 MergeSamFiles
Unmapped reads, multi-mapping reads, secondary alignments and PCR duplicates were removed post-alignment using Picard’s MarkDuplicates v1.126 and Bedtools v2.26
Single-end BAM files were used for peak calling using MACS2 v2.1.0. Peak-calling on replicates and pooled data was carried out with the parameters -B –broad –nomodels and –extsize 147 with all others set to default.
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files were generated using MACS2
Supplementary_files_format_and_content: Peaks files were generated using MACS2

organism: Homo sapiens

source_name: RL lenalidomide - H3K27ac

growth_protocol: RL cell line routinely grown at 37°C with 5% CO2 and cultured in RPMI 1640 supplemented with 2mM L-glutamine and 10% FBS (Wisent)

extract_protocol:
ChIP samples were prepared using the SimpleChIP Enzymatic Chromatin IP Kit, based on the manufacturer’s instructions (Cell Signaling, #9003). Briefly, 4 million RL cells were incubated for 48 hours with either DMSO, 10μM lenalidomide, 5μM tazemetostat or combination, followed by cross-linking using 1% formaldehyde. Cells were lysed and chromatin was digested for 20 min using 0.5μl micrococcal nuclease. Nuclei were sonicated
After purification, DNA was used as an input for next-generation sequencing library construction using the SimpleChIP ChIP-seq DNA Library Prep Kit for Illumina (Cell Signaling, #56795) following manufacturer’s protocol and sequenced on a NextSeq SR25 platform (Illumina) after standard library QC.

treatment_protocol: RL cells treated with DMSO, 10μM lenalidomide, 5μM tazemetostat or combination; Two technical replicates of all samples and conditions were prepared. Cells were incubated with drug treatments for 2 days.

value: RL

tag: cell type

value: Diffuse large B-cell lymphoma (DLBCL) cell line

tag: treatment

value: lenalidomide

tag: chip antibody

value: H3K27ac (clone D5E4, Cell Signaling, #8173)


title: myc-h2anc1a-wt-async-x17

city: Rehovot

first: Naama

last: Barkai

address: Herzl St 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

data_processing:
demultiplexing with bcl2fastq
paired end alignment to S288_R64  with bowtie2 (-p8 --local --very-sensitive )
readfiltering based on fragment size (keep 100-170 bp)
genome coverage with bedtools (-pc -d)
Genome_build: GCA_000146045.2
Supplementary_files_format_and_content: *.out.txt file contains genome coverage for all 12,157,105 bases in the yeast genome in one column (chromosomal order 1-16,Mitochondrion)

organism: Saccharomyces cerevisiae

source_name: budding yeast

growth_protocol: yeast cells were grown to saturation overnight in YPD  and then dilute in fresh,pre-warmed YPD and incubated for 6 hours at 30deg before fixation

extract_protocol:
ChIP was carried out as detailed in Gutin et all, Cell reports 2019, with following modifications. Cell pellets (each from 50 ml of cultures at OD600 0.4, 20 ODs total) were thawed on ice and washed in 10 ml 1M sorbitol. After complete liquid removal, pellets were resuspended in 600 ul RIPA buffer (10 mM Tris pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, EDTA-free protease inhibitor cocktail) and transferred to chilled LoBind Eppendorf microcentrifuge tubes containing ~500 ul of 0.5 mm zirconium oxide beads (Next Advance, ZrOB05). Cells were processed for 3 cycles in a Bullet Blender 24 (Next Advance) at level 8 for 1 min, with 1 minute on ice between cycles. Debris and lysate were transferred by piercing a hole in the bottom of the tube, placing a clean chilled tube under and centrifuging at 600xg for 5 seconds at 4C. The upper tube with the Zirconium beads was discarded and the lysate was hard spun at 17,000xg for 10 minutes at 4C. The supernatant containing cleaved solubilized 8xmyc tags was discarded, and the pellet was thoroughly resuspended in 100 ul NP buffer (10 mM Tris pH 7.4, 1 M sorbitol, 50 mM NaCl, 5 mM MgCl2, 1 mM CaCl2, and 0.075% NP-40, freshly supplemented with 1 mM β-mercaptoethanol, 500 μM spermidine, and EDTA-free protease inhibitor cocktail), and SLIM-ChIP protocol was carried continued as in Gutin et al.
SLIM-Chip, as per Gutin et al, Cell Reports 2019

tag: antibody

value: myc

tag: background

value: wt

value: async

tag: sensor

tag: strain

tag: genotype

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-NC-MYC


title: KO_1_techRep2

city: Melbourne

first: Luke

middle: C

last: Gandolfo

state: Victoria

address: 1G Royal Parade Parkville

department: Bioinformatics

country: Australia

institute: WEHI

description:
HSV skin OT-I.Tgfbr2-/- T cells
Biological replicate 1, technical replicate 2

library_source: transcriptomic

data_processing:
FASTQ files were output using standard Illumina protocols and software
Reads were aligned to the mouse genome by Rsubread 2.2.6
Read counts were summarized by Entrez Gene ID using featureCounts and Rsubread's built-in NCBI annotation
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, Symbol, total gene length (total base count of all exons) and the number of reads mapping to that gene

source_name: epidermis

extract_protocol:
Effector OT-I or OT-I/TGFbRII-/- cells were injected into HSV-infected mice and on day 14, skin was harvested from perfused mice and subject to a dispase digestion. This allowed the physical separation of the epidermis from the dermis skin. Epidermal skin was further digested in collagenase,  and the cell suspension was stained for sort purification on OT-I markers. A total of 500 cells were sorted into individual strip tubes containing buffer comprised of dNTPs and BSA.
Libraries were prepared with smartseq-nextera2 kit according to manufacturers instructions

tag: host strain background

tag: transgenic strain

value: HSV Infection d14


title: RL lenalidomide - H3K27ac_rep1


title: KO_1_techRep1

description:
HSV skin OT-I.Tgfbr2-/- T cells
Biological replicate 1, technical replicate 1


title: 8_BS_Osdrm2_T1

tag: library strategy

tag: developmental stage

tag: tissue

tag: generation


title: myc-h2a2b-wt-async-x17

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: RL DMSO - H3K27ac_rep2

source_name: RL DMSO - H3K27ac

tag: cell line

value: DMSO


title: myc-h2anc2b-wt-async-x17


title: myc-h2a2a-wt-async-x17


title: 7_BS_Osdrm1a_T1

source_name: Osdrm1a mutant

value: Osdrm1a mutant


title: RL DMSO - H3K27ac_rep1


title: bulk RNA-seq Outer POD14 Treated [POD14_Faki_Outer_S4_L005]

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

department: Surgery

country: USA

institute: Stanford University

description: bulk RNA-seq Outer POD14 Treated

data_processing:
Fastq files were aligned to the mm10 mouse genome using STAR v2.5.3a.
Counts were extracted from individual bam files using the featureCounts function from the Rsubread library in R.
DESeqDataSet objects were extracted from raw counts matrices using the DESeqDataSetFromMatrix function from the DESeq2 library in R.
genome build: mm10 v3.0.0
processed data files format and content: Counts matrix

source_name: Dorsal wound

extract_protocol:
RNA-seq: For mouse fibroblasts, fibroblasts were isolated from fresh specimens using FACS. RNA extraction was performed using Qiagen miRNeasy kit with on column DAnase treatment per the manufacturer’s recommendations.
RNA-seq: The Clontech Smarter Ultra Low Input RNA kit (Takara Bio) was used to generate cDNA from 150 pg total RNA following the manufacturer’s recommendations. Amplified cDNA was purified using SPRI Ampure Beads (Beckman Coulter) and the quality and quantity was measured using a High Sensitivity DNA chip on the Agilent 2100 Bioanalyzer (Agilent Technologies).  cDNA was sheared to an average length of 300 basepairs using a Covaris S2 ultrasonicator (Covaris) and libraries were generated with the Clontech Low Input Library Prep kit (Takara Bio). The samples were uniquely barcoded, pooled, and sequenced on HiSeq (Illumina).
RNA-seq: The samples were uniquely barcoded, pooled, and sequenced on HiSeq (Illumina).

treatment_protocol: Skin tissue from mouse specimens was minced on ice and digested in DMEM-F12 (GIBCO®) with 0.5mg/ml LiberaseTM (Roche) for 30 minutes at 37º in an orbital shaker. The digests were quenched with quench media (DMEM-F12 with 10% Fetal Bovie Serum (FBS, Sigma)), centrifuged at 300 x G for 5 minutes at 4 deg C, resuspended in quench media, filtered through 100, 70, and 40um cell strainers (Falcon cell strainer, ThermoFisher), centrifuged once more, and resuspended in FACS buffer.

value: Black 6

value: Dorsal wound

value: Splinted excisional wound healing

value: Fibroblasts


title: 6_BS_Oscmt2/cmt3a_T1

source_name: Oscmt2/cmt3a mutant

value: Oscmt2/cmt3a mutant

value: 70-day old

value: leaves


title: myc-h2a1b-wt-async-x17


title: bulk RNA-seq Outer POD14 Treated [POD14_Faki_Outer_S8_L005]

description: bulk RNA-seq Outer POD14 Treated


title: myc-h2a1a-wt-async-x17


title: 5_BS_Oscmt3b_T1

source_name: Oscmt3b mutant

value: Oscmt3b mutant


title: bulk RNA-seq Inner POD14 Treated [POD14_Faki_Inner_S6_L005]

description: bulk RNA-seq Inner POD14 Treated


title: mp clv3 rep2

city: Hefei

first: Zhong

last: Zhao

state: Anhui

address: Huangshan Road 443

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Basecalls performed using CASAVA version 1.7
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 cDNA using BWA with parameters -e 60 -i 15 -q 10 -t 4
Reads Per Kilobase of transcript per Megabase of library size (RPKM) were calculated.
Genome_build: TAIR10
Supplementary_files_format_and_content: spreadsheet include numbers of mapped reads,RPKM values for each Sample as well as log2 RPKM ratios, p-values and FDR for multipairwise comparisons

organism: Arabidopsis thaliana

source_name: plant

growth_protocol: Seeds pretreated with stratification for 2 days at 4°C were transferring the seedlings to the soil in the greenhouse for another 6-weeks (22°C, 16 h/8 h photoperiod).Shoot apices from 6-week inflorescence of Col-0 or mp319 clv3-7 plants were collected and removing older flowers.

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and Total RNA from apices were isolated using the mirVana™ miRNA Isolation Kit (lifetechnology). 10 μg of totalRNA were subject to DNase I treatment and mRNA was purified by Dynabeads® mRNA DIRECT™ Purification Kit(lifetechnology). The strand-specific RNA-seq libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina following the manufacturer's instructions and subjected to Illumina HiseqTM2500 for 2x100bp pair end sequencing.
library source: transcriptomic; library selection: cDNA; instrument model: Illumina HiSeq 2500

value: 6-week adult plant

value: Shoot apices

value: mp clv3


title: bulk RNA-seq Inner POD14 Treated [POD14_Faki_Inner_S4_L006]

description: bulk RNA-seq Inner POD14 Treated


title: 4_BS_Oscmt3a_T1

source_name: Oscmt3a mutant

value: Oscmt3a mutant


title: myc-h2anc1b-wt-async-x17

value: myc

value: wt

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-NC-MYC


title: WT rep2


title: myc-fast2b-wt-async-x18

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: 3_BS_Oscmt2_T1

source_name: Oscmt2 mutant

value: Oscmt2 mutant


title: bulk RNA-seq Outer POD14 Untreated [POD14_Ctrl_Outer_S7_L006]

description: bulk RNA-seq Outer POD14 Untreated

value: Black 6

value: Dorsal wound


title: myc-fast2a-wt-async-x17


title: WT rep1


title: 2_BS_Oscmt2_T1


title: myc-fast1b-wt-async-x18


title: bulk RNA-seq Outer POD14 Untreated [POD14_Ctrl_Outer_S1_L006]

description: bulk RNA-seq Outer POD14 Untreated

value: Splinted excisional wound healing

value: Fibroblasts


title: bulk RNA-seq Inner POD14 Untreated [POD14_Ctrl_Inner_S3_L005]

description: bulk RNA-seq Inner POD14 Untreated


title: ERH_ChIP_rep1

city: Seattle

first: Ryan

middle: Lehman

last: McCarthy

state: WA

address: 1900 9th Ave

department: Pediatrics

institute: University of Washington

description: Sample did not contain Drosophila spike-in chromatin and as such was aligned to hg38 and no normalization to spike-in control was performed.

data_processing:
Samples were demultiplexed (bcl2fastq using BaseSpace) to produce FASTQ files.
For samples with a spike-in control sequenced read were aligned to the human hg38 genome assembly and to the Drosophila melanogaster dm6 genome assembly (to identify reads from the spike in) using STAR (v.2.3.0e)
STAR output files were converted to .bam files using samtools (v.1.1), and then to .bed files using bedtools (v.2.20.1; bamtobed)
BED files were converted to BedGraph files using bedtools (v.2.20.1; genomeCoverageBed) and normalized to the number of millions of reads sequenced.
BedGraphs from samples containing a spike in control were scaled based upon the change between corresponding input and IPs in dm6 to hg38 aligning reads realative to the non-targeting siControl treated samples.
Input subtracted BedGraph files were converted to  bigWig using bedGraphToBigWig (v4)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig

source_name: Human BJ Fibroblast

growth_protocol: Human BJ foreskin fibroblasts were obtained from Stemgent (08-0027) at passage 6 and cultured in Eagle's Minimum Essential Medium (Sigma M2279) supplemented with 10% fetal bovine serum (FBS, Hyclone SH30071) and 2mM L-glutamine (Gibco) at 37°C and 5% CO2

extract_protocol:
Nuclei were isolated and sonicated, lysates were clarified, for H3K9me3 and H3K27me3 ChIP experiments Drosophila spike-in chromatin (Active Motif cat 53083) was added in order to normalize for global changes in histone modification levels during computational analysis, and histone-DNA complexes were isolated with antibody.
Library constructed acording to NEBnext ULTRA II DNA Library Prep Kit for Illumina (#E7645S)

treatment_protocol: Cells were treated with two rounds of transfection with 10nM Silencer Silect siRNAs (Thermo Fisher Scientific) and 2.5 μl Lipofectamine RNAiMAX (Thermo Fisher #13778150), for 3 days per transfection.

value: ERH (Sigma-Millipore - HPA002567, Lot# A41692)


title: 1_BS_Cr_WT_T1

source_name: Wide type

value: Wide type

value: 70-day old

value: leaves


title: myc-fast1a-wt-async-x18


title: bulk RNA-seq Outer POD7 [B6WO2mousefibroblast-GACCTGAA-CTCACCAA_S5_L005]

description: bulk RNA-seq Outer POD7


title: mp clv3 rep1

value: 6-week adult plant

value: Shoot apices


title: AD6

city: Auburn

first: Amarjit

last: Mishra

state: AL

address: 1130 Wire Road, 264 Greene Hall

department: Pathobiology

institute: Auburn University

data_processing:
Illumina HiSeq 2500 was used to process the data
Data Quality Control was done using Fastqc
Data alignment done with STAR aligner
Identification of differential expression of genes by DeSeq2
Genome_build: mm9
Supplementary_files_format_and_content: normalized count

source_name: Lung left lobe

extract_protocol:
Lungs were removed, snap freezed in liquid nitrigen, and RNA was extracted for construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 80 Week old

value: Lung

value: HDM+Dex


title: AD7


title: AD5


title: myc-fast1a-wt-async-x17

value: myc

value: wt

value: async


title: bulk RNA-seq Outer POD7 [B6WO1mousefibroblast-AGTTCAGG-TCTGTTGG_S4_L005]

description: bulk RNA-seq Outer POD7


title: AD4


title: myc-fast1a-wt-async-x14

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-Fast-MYC


title: bulk RNA-seq Inner POD7 [B6WI2mousefibroblast-AATCCGGA-AACTGTAG_S7_L005]

description: bulk RNA-seq Inner POD7

value: Black 6


title: AD3


title: k9ac-fast1a-wt-async-x24

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: bulk RNA-seq Unwounded [B6C2mousefibroblast-CGGCGTGA-ACAGGCGC_S9_L005]

description: bulk RNA-seq Unwounded

source_name: Dorsal unwounded skin

value: Dorsal unwounded skin

value: Splinted excisional wound healing


title: k79m3-fast1b-wt-async-x24


title: WGBS_DM_R24_3

city: Hangzhou

first: Ze-Ting

last: Song

state: Zhejiang

address: No.866 Yuhangtang Road

department: College of Life Science

institute: Zhejiang University

data_processing:
Bisulfite-Seq: Cutadapt and perl scripts in house were used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Bisulfite-Seq: Reads that passed quality control were mapped to reference genome using Bismark. After alignment, reads were further deduplicated using samtool. For each cytosine site (or guanine corresponding to a cytosine on the opposite strand) in the reference genome sequence, the DNA methylation level was determined by the ratio of the number of reads supporting C (methylated) to that of total reads (methylated and unmethylated) using per scripts in house and MethPipe. Differentially methylated regions (DMRs) were calculated by R package-MethylKit with default parameters (100 bp slide windows, 100 bp overlap, p value<0.05)
Genome_build: tair10

source_name: seedlings

extract_protocol: Total DNA was extracted using QIAamp Fast DNA Tissue Kit.The fragmented DNA samples by using sonication were subjected to bisulfite conversion. The Accel-NGS Methyl-Seq DNA Library Kit (Swift, MI,USA) was utilized for attaching adapters to single-stranded DNA fragments.

value: seedlings

value: 22℃ for 5 days,then 35℃ for 5.5 days,and recovery 1 day at 22℃

value: sdg25-1/atx1-7 double-mutant

value: Bisulfite-Seq


title: AD1


title: WGBS_DM_R24_2

value: sdg25-1/atx1-6 double-mutant


title: bulk RNA-seq Unwounded [B6C1mousefibroblast-TAATACAG-GTGAATAT_S8_L005]

description: bulk RNA-seq Unwounded

value: Fibroblasts


title: bulk RNA-seq Inner POD7 [B6WI1mousefibroblast-ATGTAAGT-CATAGAGT_S6_L005]

description: bulk RNA-seq Inner POD7

value: Dorsal wound


title: k79m3-fast1a-wt-async-x24


title: AA6

value: 80 Week old

value: Lung

value: HDM


title: k4m3-fast1b-wt-async-x24

value: wt


title: WGBS_DM_R24_1

value: sdg25-1/atx1-5 double-mutant


title: GC-2 cell line replicate 1

city: MUMBAI

first: PRIYANKA

last: PARTE

state: MAHARASTRA

address: J M STREET

department: GAMETE IMMUNOBIOLOGY

country: India

institute: ICMR-NIRRH

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent Mus musculus Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Data extraction from Images was done using Feature Extraction software  and Normalization of the data was done in GeneSpring GX  : 75th percentile shift  method and gene based analysis was performed.

source_name: GC-2 cell line replicate 1

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: The cells were cultured in DMEM (high glucose) supplemented with 10% FBS 100 U of penicillin/100 µg of streptomycin and maintained at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from Trizol

treatment_protocol: GC-1 and GC-2 cells were harvested at 90% confluency and stored in Trizol at -80°C

value: germ cell line


title: AS11

city: Philadelphia

first: Duancheng

last: Guo

state: PA

address: 333 Cottman AVE

institute: Fox Chase Cancer Center

description: Gene expression data from StromaB RNA-seq

data_processing:
The Cell Ranger Single Cell Software Suite v.2.0.1 (http://support.10xgenomics.com/) by 10x Genomics was used to perform sample de-multiplexing, barcode processing and single-cell 3′ gene counting. In brief, base call files were fastq format were aligned to the mm10 reference genome that used an aligner called STAR with default settings, and aligned reads were filtered for valid cell barcodes and UMI to generate filtered gene-barcode matrices. The pre-processed 10X and DGE matrices were then imported using the Seurat package for the R programming language (version 3.5.4), and the data were filtered to include genes detected in >5 cells, and cells with 500~6000 detected genes and UMI with 1000~30000 and <15% mitochondrial genes. For single-dataset analyses, Log-normalized expression values were obtained by the NormalizeData function, and variable genes were identified using the FindVariableGenes Seurat function, TPM values were obtained from raw UMI counts by normalizing with total UMI counts per cell.
Genome_build: mm10

source_name: Medulloblastoma cells from Patched 1 deficient mice

growth_protocol: Medulloblastoma cells were suspended in NB-B27 culture medium (Neurobasal, 1 mmol/L sodium pyruvate, 2 mmol/L L-glutamine, B27 supplement, and 1% penicillin/streptomycin,all from Invitrogen)

extract_protocol: tumor cells were dissociated enzymatically by papain for 30 mins and then harvested by centrifugation. Single cells were partitioned into Gel Beads in Emulsion (GEMs) in the Chromium Controller instrument with cell lysis and barcoded reverse transcription of RNA, followed by cDNA amplification, shearing, library construction and indexing by PCR amplification. Subsequently, libraries were sequenced by Illumina 2x150 bp sequencing.

treatment_protocol: Flow cytometry to sort primary and recurrent tumor cells, and astrocytes from primary and recurrent tumors

value: Brain tumor

value: Astrocytes

tag: source

value: stroma B

value: Patched 1 deficient


title: AS10

tag: cell type


title: GC-1 cell line replicate2

source_name: GC-1 cell line replicate2


title: GC-1 cell line replicate1

source_name: GC-1 cell line replicate1


title: k4m3-fast1a-wt-async-x24

source_name: budding yeast

tag: treatment

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: AA5


title: WGBS_DM_C24_3

value: seedlings

value: 22℃ for 11.5 days

value: sdg25-1/atx1-4 double-mutant


title: k9ac-fast1b-wt-async-x24


title: AA7


title: GC-2 cell line replicate 2

source_name: GC-2 cell line replicate 2


title: WGBS_DM_C24_2

value: sdg25-1/atx1-3 double-mutant

value: Bisulfite-Seq


title: AS5-2

source_name: Medulloblastoma cells from Patched 1deficient mice


title: AD2

value: 80 Week old

value: HDM+Dex


title: AA4

value: Lung

value: HDM


title: ha-nc1b-wt-async-x20

value: ha

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-NC-MYC


title: AS5-1

description: Gene expression data from StromaA RNA-seq

value: Brain tumor

value: Astrocytes

value: stroma A


title: WGBS_DM_C24_1

value: sdg25-1/atx1-2 double-mutant


title: ha-nc1a-wt-async-x20

value: async


title: AA3


title: WGBS_WT_R24_3

value: seedlings

value: 22℃ for 5 days,then 35℃ for 5.5 days,and recovery 1 day at 22℃

value: wild type


title: ha-nc1a-wt-async-x14


title: AA2


title: WGBS_WT_R24_2


title: AA1


title: AN5

value: Saline


title: ha-h41b-wt-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV, HHF2-GGS-HA-Fast-MYC


title: WGBS_WT_R24_1

value: Bisulfite-Seq


title: WGBS_WT_C24_3

value: 22℃ for 11.5 days


title: AS1

value: Patched 1 deficient


title: AN4

value: 80 Week old

value: Lung


title: Relapsed_3w

description: Gene expression data from Primary Tumor 10x Genomic scRNA-seq

value: Medulloblastoma cells

value: Relapsed Tumor from 3 weeks


title: ha-h41a-wt-async-x20

value: ha

value: wt


title: WGBS_WT_C24_2


title: Primary_Tumor

value: Brain tumor

value: Primary Tumor


title: ha-h2bNC1b-wt-async-x20

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-NC-MYC


title: AN3


title: WGBS_WT_C24_1

value: seedlings


title: ha-h2b2a-wt-async-x20

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC


title: RNA_seq_DM_R24_2

data_processing:
RNA-Seq: Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained. adaptor contamination
RNA-Seq: And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the tair10 genome.The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
RNA-Seq: After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: tair10

extract_protocol:
Total RNA was extracted using Trizol reagent, Illumina TruSeq RNA Sample Preparation v2 (Cat. RS-122-2001,RS-122-2002) was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina (Illumina Hiseq 4000 ) protocols

value: 22℃ for 5 days,then 35℃ for 5.5 days,and recovery 1 day at 22℃

value: sdg25-1/atx1-9 double-mutant

value: RNA-Seq


title: Erlotinib treated sample 3

city: La Jolla

first: Jorge

middle: Silvio

last: Gutkind

state: CALIFORNIA

address: 3855 Health Sciences Drive

department: Moores Cancer Center

institute: UC San Diego

data_processing:
For each sample, paired end sequencing reads were mapped using Bowtie2 version 2.3.4 to GRCh38 reference human genome downloaded from Ensembl.
To compute transcript abundance, uniquely mapped reads were quantified using featureCounts version 1.6.3.
Counts tables were uploaded to the Galaxy web platform and using the public server at usegalaxy.org, EntrezIDs were converted to gene symbols using the annotatemy IDs tool.
Differential gene expression analysis was performed using DESeq2 version 1.18.1, using parametric fit.
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts matrix showing gene-level counts for each sample

source_name: EGFR mutant lung adenocarcinoma cell line

growth_protocol: HCC827 cells were cultured in RPMI 1640 medium, GlutaMAX supplement (#61870-036, Thermo Fisher Scientific, CO), and supplemented with 10% FBS (Sigma-Aldrich Inc., St. Louis, MO), 1x antibiotic/antimycotic solution (Sigma-Aldrich Inc., MO) and 5 μg/ml plasmocinTM prophylactic (InvivoGen, CA).

extract_protocol:
Total RNA was extracted using the Qiagen Rneasy Mini kit, following manufacturers instructions
After the QC procedures, mRNA was enriched using oligo(dT) beads. First, the mRNA was fragmented randomly by adding fragmentation buffer, then the cDNA was synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: HCC827 cells were purchased from ATCC. All cells were incubated at 37°C in 5% CO2 and grown to 60-70% confluence, then treated with DMSO or erlotinib (1 μM) for 24 hrs.

value: erlotinib treated


title: AS4

value: Astrocytes

value: stroma A

value: Patched 1 deficient


title: AN1

value: 80 Week old

value: Lung

value: Saline


title: Erlotinib treated sample 2


title: RNA_seq_DM_R24_1

value: sdg25-1/atx1-8 double-mutant


title: ha-h2b1a-wt-async-x20

value: ha

value: wt


title: YN5

value: 20 Week old


title: Erlotinib treated sample 1


title: RNA_seq_DM_R0_1

value: 22℃ for 5 days,then 35℃ for 5.5 days

value: sdg25-1/atx1-6 double-mutant


title: ha-h2bNC1a-wt-async-x20

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-NC-MYC


title: YN4


title: DMSO treated control sample 3

value: DMSO treated


title: DMSO treated control sample 2


title: AN2


title: ha-h2anc2b-wt-async-x17

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-NC-MYC


title: RNA_seq_DM_C24_2

value: seedlings

value: 22℃ for 11.5 days

value: sdg25-1/atx1-5 double-mutant

value: RNA-Seq


title: ha-h2anc1b-wt-async-x17


title: ha-h2anc2a-wt-async-x17


title: RNA_seq_DM_C24_1

value: sdg25-1/atx1-4 double-mutant


title: YN2

value: Lung


title: YN3

value: Saline


title: RNA_seq_DM_R0_2

value: sdg25-1/atx1-7 double-mutant


title: ha-h2anc1a-wt-async-x17

value: ha


title: YN1


title: DMSO treated control sample 1


title: ha-h2b1b-wt-async-x20

value: wt

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV, HTB2-GGS-HA-Fast-MYC


title: RNA_seq_DM_C0_2

value: 22℃ for 10.5 days

value: sdg25-1/atx1-3 double-mutant


title: RL lenalidomide -  input_DNA_rep1

source_name: RL lenalidomide -  input_DNA

value: RL

value: Diffuse large B-cell lymphoma (DLBCL) cell line

value: lenalidomide

tag: chip antibody

value: negative control rabbit IgG antibody (Cell Signaling, #2729)


title: 17_BS_Oscmt2/cmt3a/drm2_T1

source_name: Oscmt2/cmt3a/drm2 mutant

value: Oscmt2/cmt3a/drm2 mutant

value: 70-day old

value: leaves


title: ha-h2a2b-wt-async-x17

tag: antibody

value: async

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HHT1-GGS-TEV HTA2-GGS-HA-Fast-MYC, bar1


title: RNA_seq_DM_C0_1

value: seedlings

value: sdg25-1/atx1-2 double-mutant

value: RNA-Seq


title: D_FN_2

city: Chengdu

first: Xin

last: Zheng

state: Sichuan

address: No. 14, Section 3, Renmin South Road

institute: Sichuan University

data_processing:
The raw paired-end reads were trimmed, and quality controlled by SeqPrep and Sickle with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software.
The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the fragments per kilobase million (FPKM) method.
Differential expression genes (DEG) analysis was performed using the DESeq2.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with FPKM for every gene and every sample. Means of gene expression level of group DLD-1 co-culture with F. nucleatum (with_FN) and control group (no_FN) are listed.

source_name: Colorectal carcinoma

growth_protocol: Cells were routinely cultured in Dulbecco's modified Eagle medium (DMEM; Thermo Fisher Scientific, Waltham, MA) supplemented with 10% fetal bovine serum (FBS) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA from DLD-1 cultured with or without F. nucleatum were extracted and purified using MiniBest Universal RNA Extraction kit (Takara, Japan) according to the manufacturer’s instruction.
The cDNA library was prepared following the procedures of TruSeqTM RNA sample preparation kit (Illumina, San Diego, CA) using 1μg total RNA

treatment_protocol: Cells were grown to >90% confluency, and then inoculated with F. nucleatum at a multiplicity of infection (MOI) of 10:1, for 24h. Before inoculation, overnight bacterial cultures were back-diluted 1:1000 and grown to mid-exponential phase (~0.5 OD600nm), centrifuged (2 min, 4°C, 12,000 rpm) and resuspended with phosphate buffered saline (PBS).

value: co-cultured with F. nucleatum


title: D_FN_3


title: D_FN_1


title: RNA_seq_WT_R24_2

value: 22℃ for 5 days,then 35℃ for 5.5 days,and recovery 1 day at 22℃

value: wild type


title: ha-h2a2a-wt-async-x17

value: ha

tag: background

value: wt


title: ha-h2a1a-wt-async-x17

tag: sensor


title: DLD1_3

value: treated with PBS


title: ha-h2a1b-wt-async-x17

tag: strain


title: RNA_seq_WT_R24_1

tag: genotype


title: cko sample4

city: Shanghai

first: Chenyang

last: Zhang

address: Middle Fuxing Rd

institute: Fudan University

data_processing:
RNA quantification and qualification: RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer.RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0Flurometer .RNA integrity was assessed using the RNA Nano 6000 Assay Kit of Illumia HiSeq 2500.
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Differential expression analysis: HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: gene ID
Supplementary_files_format_and_content: xls, FPKM.xls is a statistical table of gene expression level, which counts the FPKM value of genes.

source_name: bone marrow

growth_protocol: Bone marrow primary cells were cultured to the third generation in vitro.

extract_protocol:
Total RNA was extracted by Trizol
A total amount of 3 ?g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLVreverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently

treatment_protocol: untreated

tag: cell type / tissue

value: bone progenitors derived from bone marrow

tag: genotype/variation


title: RNA_seq_WT_R0_2

value: 22℃ for 5 days,then 35℃ for 5.5 days

tag: library strategy


title: 36male+ins

description: 38vs36.xls and 44vs36.xls

data_processing:
RNA quantification and qualification: RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer.RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0Flurometer .RNA integrity was assessed using the RNA Nano 6000 Assay Kit of Illumia HiSeq 2500.
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Differential expression analysis: HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.10.1). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: gene ID
Supplementary_files_format_and_content: 38vs36.xls ,44vs38.xls and 44vs36.xls are statistical tables of differencially expressed gene lists.

source_name: femur

growth_protocol: The total RNA was extracted after muscle removal of mouse femur.

extract_protocol:
Total RNA was extracted by Trizol
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo- attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLVreverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently

value: femur

tag: sample type

value: streptozotocin (STZ) induced Type 1 diabetic mouse given daily injections of insulin


title: ha-fast2b-wt-async-x18

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTA2-GGS-TEV HHT1-GGS-HA-Fast-MYC bar1


title: cko sample2


title: RNA_seq_WT_R0_1

tag: tissue


title: ha-fast2a-wt-async-x17


title: RNA_seq_WT_C24_2

value: 22℃ for 11.5 days


title: DLD1_1


title: ha-fast1b-wt-async-x18

value: async


title: control sample4

value: wild type (ctrl)


title: UM-UC-3_DMSO

city: Guangzhou

first: Xu

last: Chen

state: Guangdong

address: 107. W. Yanjiang Road

department: Department of Urology

institute: Sun Yat-sen Memorial Hospital

data_processing:
Base-calling:bcl2fastq2 v2.19.1
Data filtering :in house
Read alignment:hisat2 v2.1.0
transcript assemble:htseq-count v0.6.1
Genome_build: hg19
Supplementary_files_format_and_content: excel files include normalize values for each Sample

source_name: bladder cancer cell line UM-UC-3

growth_protocol: T24 was cultured in RPMI-1640 (Gibco) and UM-UC-3 was cultured in DMEM (Gibco) supplemented with 10% FBS (Biological Industries) and 1% penicillin/streptomycin (Gibco). Cells were grown in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit according to the manufactures’ instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OICR-9429 was  diluted at a stocking solution of 50mM in dimethyl sulfoxide (DMSO, Sigma), and cells were treated for 48h with 140µM of OICR-9429.

tag: inhibitor

value: Negative control


title: RNA_seq_WT_C24_1

value: seedlings


title: ha-fast1a-wt-async-x18


title: 38male+stz

description: 44vs38.xls and 38vs36.xls

value: Type 1 diabete mouse


title: T24_OICR-9429

source_name: bladder cancer cell line T24

tag: cell line


title: control sample3

tag: age


title: RNA_seq_WT_C0_2

value: 22℃ for 10.5 days

value: RNA-Seq


title: DLD1_2


title: cko sample3


title: ha-fast1a-wt-async-x17


title: ha-fast1a-wt-async-x14

value: MATa his3{delta}1 leu2{delta}0 LYS2 met15{delta}0 ura3{delta}0 HTB2-GGS-TEV HHT1-GGS-HA-Fast-MYC


title: T24_DMSO


title: 44male+wt

description: 44vs36.xls and 44vs38.xls

value: Non-diabetic mouse (control)


title: UM-UC-3_OICR-9429


title: RNA_seq_WT_C0_1

value: wild type


title: 33T Organoid

type: genomic

city: Amsterdam

first: Sander

middle: Roeland

last: van Hooff

address: Meibergdreef 9

department: Center for Experimental and Molecular Medicine (CEMM),

country: Netherlands

institute: AUMC

description: SAMPLE 2

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing: Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

source_name: MRT Tumor

label_protocol: Illumina

extract_protocol: Invitek Invisorb Genomic DNA Kit

value: malignant rhabdoid tumor

tag: tissue preparation

value: Frozen

tag: tumor subgroup

value: MRT


title: control sample2

value: bone progenitors derived from bone marrow


title: Cow # 42np

status: Public on Jun 23 2021

first: Rina

last: Meidan

address: Herzl Street POB 12

institute: The Hebrew University of Jerusalem

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome using STAR  v2.4.2a (with the option alignEndsType set to EndToEnd)
Counting proceeded over genes annotated in Ensembl (ARS-UCD1.2) release 95, using htseq-count
Normalization was performed using DESeq2
Genome_build: Bos taurus ARS-UCD1.2
Supplementary_files_format_and_content: Excel file includes the normalized counts, log ratio, p-value and adjusted p-value

organism: Bos indicus

source_name: Corpus Luteum

extract_protocol:
CL tissue were removed,  frozen with liquid nitrogen, and RNA was harvested using Trizol reagent.
Inhouse poly A based RNA seq

tag: status

value: Non-pregnancy


title: Cow # 31np


title: Navie PbT-II mouse CD11a_lo CD49d_lo, biological rep4

city: Nagasaki

first: Katsuyuki

last: Yui

state: Nagasaki

address: 7F, 1-12-4, Sakamoto

country: Japan

institute: Nagasaki University

description: Gene expression from sorted naïve CD11a_lo CD49d_lo PbT-II cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The Affymetric Clariom S microarrays were analyzed with SST-RMA to detect the gene-level differential expression using the Affymetrix Transcriptome Anaylsis Console (TAC) 4.0 Software using default parameters. The significant genes (p<0.05) were ranked by fold-change with a cutoff of 2.

source_name: Navie PbT-II CD11a_lo CD49d_lo

label_protocol: Synthesis of cDNA from the total RNA labeling were performed using GeneChip 3' IVT Pico Kit (Applied Biosystems) according to manufacturer’s instructions

growth_protocol: Mice were adopted transfer 1*10^6 PbT-II CD4 T cells , and then infected with Pcc for 7 days

extract_protocol: Total RNA was prepared from purified T cell subpopulations using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions

treatment_protocol: At D7 of Pcc infection, mice spleen were harvested and Sorted CD45.1 PbT-II cells base on their expression of CD11a and CD49d; Naïve cells were sorted from PbT-II mice

value: spleen

tag: cell type

value: Antigen SP PbT-II


title: Navie PbT-II mouse CD11a_lo CD49d_lo, biological rep1


title: Navie PbT-II mouse CD11a_lo CD49d_lo, biological rep3


title: M0624H3

city: Nutley

first: Erika

last: Shor

state: New Jersey

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack Meridian Health

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 NCBI reference GCF_000002545.3_ASM254v2 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: GCF_000002545.3_ASM254v2
Supplementary_files_format_and_content: Tab-delimited text files with raw expression counts for each sample

organism: Nakaseomyces glabratus

source_name: Yeast cells

growth_protocol: 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 rRNA depletion according to manufacturer instructions

treatment_protocol: 0.06 µg/ml micafungin 24h

tag: treatment

value: 0.06 µg/ml micafungin 24h


title: NT24H1

value: no micafungin control


title: M0624H1


title: Cow # 30np


title: D7 Pcc CD11a_hi CD49d_lo PbT-II, biological rep3

description: Gene expression from sorted CD11a_hi CD49d_lo PbT-II cells 7 days after Pcc infection

source_name: D7 Pcc CD11a_hi CD49d_lo PbT-II


title: D7 Pcc CD11a_hi CD49d_lo PbT-II, biological rep2


title: Cow # 29p

value: Pregnancy


title: Cow # 05np


title: Navie PbT-II mouse CD11a_lo CD49d_lo, biological rep2


title: D7 Pcc CD11a_hi CD49d_hi PbT-II, biological rep2

description: Gene expression from sorted CD11a_hi CD49d_hi PbT-II cells 7 days after Pcc infection

source_name: D7 Pcc CD11a_hi CD49d_hi PbT-II


title: Cow # 22np


title: D7 Pcc CD11a_hi CD49d_hi PbT-II, biological rep3


title: Cow # 27p


title: D7 Pcc CD11a_hi CD49d_hi PbT-II, biological rep1


title: Cow# 19p


title: Cow # 01p


title: Cow# 18p


title: NT24H2


title: D7 Pcc CD11a_hi CD49d_lo PbT-II, biological rep1


title: KO-Saline3

city: Suita city

first: Yumiko

last: Hayashi

address: 3-1 Yamadaoka

institute: Osaka University

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
bcl2fastq2(v2.17.1.14) software used for gerating fastqs
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.4 and SAMtools ver. 1.0.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10

source_name: endothelial cell

extract_protocol:
MC38 tumor-bearing mice were prepared using WT mice and Apelin KO mice. The tumors were recoverd from mice, treated with enzyme, and then stained with CD31 and CD45 antibody. Then, CD31 positive and CD45 negative cells were sorted.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: KO


title: KO-Saline2


title: Cow # 32np

city: Rehovot


title: 33T Tumor

description: SAMPLE 1


title: KO-Saline1


title: Cow # 28p


title: WT-Saline3

value: WT


title: WT-Saline2


title: ESCs-OCT4-WT-24h_ATAC_rep2

city: Edinburgh

first: Abdenour

last: Soufi

address: 5 Little France Drive

department: School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description: Rep2WT24h_FKDL202570735-1a-N703_H7VLMCCX2_L4

data_processing:
The contaminating ME sequences (CTGTCTCTTATACACATCT) were trimmed from the ATAC-seq reads with Cutadapt to prevent multimapping.
The ATAC-seq pair-end reads were mapped to the Mus musculus genome assembly MGSCv37 (mm9) using Bowtie (version 2.3.4.1) and very sensitive parameters.
Duplicated alignments were removed using Picard (https://broadinstitute.github.io/picard/).
ATAC-seq reads (bam files) were normalised for sequencing coverage to 1x genome depth (reads per genome coverage, RPGC) using the bamCoverage tool from DeepTools and a bin size of 10 bp and extendReads parameters.
Reads within the ENCODE blacklist were removed from the analysis.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files showing sequence depth normalized ATAC-seq enrichment

growth_protocol: ZHBTc4.1 ES cells were maintained in GMEM supplemented with 10% FCS, 1 mM glutamine/pyruvate, Non-essential Amino Acids, Penicillin/Streptomycin and 0.05 mM 2-mercaptoethanol on porcine gelatin-coated 6-well plates. Nearly one million cells were seeded and transfected with 2.5 µg plasmid DNA using Lipofectamine 3000 (Thermo Fisher Scientific) diluted in OptiMEM reduced serum medium (Thermo Fisher Scientific) following the protocol recommended by the manufacturer.

extract_protocol:
50,000 of freshly harvested cells were resuspended in ice-cold RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2). The suspension was centrifuged at 500xg for 3 min using a refrigerated centrifuge. The cell pellet was washed once with 50 μl ice-cold PBS and centrifuged at 500xg for 3 min at 4°C. The cell pellet was resuspended in ice-cold Lysis Buffer (48.5 μl RSB buffer supplemented with 0.5 μl of 10% NP-40, 0.5 μl of 10% Tween-20, 0.5 μl of 1% Digitonin) and kept on ice for 3 min. Then, 1 ml of wash buffer (RSB buffer supplemented with 0.1% Tween-20) was added on the lysed cells. Nuclei were pelleted at 500xg for 10 min at 4°C and the supernatant (cytoplasm fraction) was carefully discarded. The nuclei were resuspended in the transposition mix (25 μl of 2X Tagment DNA Buffer (Illumina, #20034197), 16.5 μl of 1X PBS, 0.5 μl 10% of Tween-20, 0.5 μl of 1% Digitonin, 5 μl nuclease-free H2O). Next, 2.5 μl of Tn5 Transposase (Illumina, #20034197) was added to the reaction mix by pipetting up and down 6 times. The reaction was then incubated at 37℃ for 30 minutes on a thermomixer at 1,000 rpm. Finally, the tagmented DNA was isolated using Qiagen MinElute Reaction Cleanup Kit (Qiagen, # 28204) following the manufacturer’s instructions.
ATAC-seq libraries were generated by PCR amplification using custom-made barcodes (Buenrostro et al., 2013). Libraries were amplified with 7-10 cycles using NEBNext High-Fidelity 2X PCR Master Mix (NEB, #M0541S). To remove primer dimers and DNA fragments shorter than 150bp, libraries were purified with SpeedBeads™ beads. 1.8X volume of SpeedBeads™ beads (81 μl beads for 45 μl PCR reaction) was used to clean PCR amplified DNA library. The quality of the DNA libraries was assessed using Agilent HS DNA Screen Tape (Agilent. Santa Clara, CA). The concentration of the DNA libraries was measured by Qubit Fluorometric Quantitation. Equimolar DNA libraries were pooled to a final concentration of 2 nM. The ATAC-seq libraries were sequenced by Novagene (Novogene, UK) on Illumina HiSeq 2500 using pair-ends PE150 in biological duplicates (Illumina, San Diego, CA).

treatment_protocol: For Pou5f1 repression by doxycycline (24 hr post-transfection), 100,000 ZHBTc4.1 ES cells were harvested and cultured for 4 hr before treating with doxycycline (1 µg/ml) and puromycin (2 µg/ml). Cells not treated with doxycycline were used as -Dox control.

value: embryonic stem cells (ESCs)

value: transfected with OCT4-WT

value: Dox-treatment at 24 hours


title: ESCs-OCT4-del79-0h_ATAC_rep2

description: Rep2D790h_FKDL202570735-1a-N706_H7VLMCCX2_L4

value: transfected with OCT4-del79

value: Dox-treatment at 0 hours


title: ESCs-OCT4-del79-24h_ATAC_rep1

description: Rep1D7924h_FKDL202570734-1a-N707_H7VLMCCX2_L7


title: ESCs-OCT4-WT-24h_ATAC_rep1

description: Rep1WT24h_FKDL202570734-1a-N703_H7VLMCCX2_L7


title: ESCs-OCT4-del73-0h_ATAC_rep2

description: Rep2D730h_FKDL202570735-1a-N704_H7VLMCCX2_L4

value: transfected with OCT4-del73


title: ESCs-OCT4-del73-24h_ATAC_rep1

description: Rep1D7324h_FKDL202570734-1a-N705_H7VLMCCX2_L7


title: ESCs-OCT4-del73-0h_ATAC_rep1

description: Rep1D730h_FKDL202570734-1a-N704_H7VLMCCX2_L7


title: ESCs-OCT4-del73-24h_ATAC_rep2

description: Rep2D7324h_FKDL202570735-1a-N705_H7VLMCCX2_L4


title: ESCs-OCT4-WT-0h_ATAC_rep2

description: Rep2WT0h_FKDL202570735-1a-N702_H7VLMCCX2_L4


title: ESCs-OCT4-del79-0h_ATAC_rep1

description: Rep1D790h_FKDL202570734-1a-N706_H7VLMCCX2_L7


title: ESCs-OCT4-del79-24h_ATAC_rep2

description: Rep2D7924h_FKDL202570735-1a-N707_H7VLMCCX2_L4


title: Foxo1flox_rep2

city: Bethesda

first: Chuan

last: Wu

state: MD

address: 10 Center Drive, Building 10, RM 4B17

institute: National Cancer Institute

data_processing:
All analyses were performed in Partek® Flow® software, version 5.0 (Copyright 2016, Partek Inc., St. Louis, MO).
FASTQ files were uploaded into Partek Flow software for processing, aligned using STAR aligner, and quantified to transcriptome (Partek E/M using mm10 – Ensembl Transcripts release 94 as the reference index)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Intestinal epithelial cells

extract_protocol:
Mouse colon was isolated and washed with PBS. The intestinal epithelial cells were purified from the tissues by 2mM EDTA and 2mM DTT incubation.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: 8 week old


title: VilCre Foxo1flox_rep1

value: VilCre/+ Foxo1flox/flox


title: ESCs-OCT4-WT-0h_ATAC_rep1

description: Rep1WT0h_FKDL202570734-1a-N702_H7VLMCCX2_L7


title: VilCre Foxo1flox_rep3


title: VilCre Foxo1flox_rep2


title: Foxo1flox_rep3


title: M0624H2


title: Foxo1flox_rep1


title: P-TEFb input rep1

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

institute: UCL Cancer Institute

description:
protein crosslinked RNA
Background RNA crosslinking for P-TEFb

data_processing:
Fastq files were demultiplexed and aligned using the iCount server. The unique molecular identifiers (UMIs) were registered and experimental barcodes removed before mapping the sequences to mm9 using Bowtie version 0.12.7 (command line: -v 2 -m 1 -a --best --strata.
Reads indicative of PCR duplicates (reads mapping to the same position with the same UMI) and reads aligning to multiple positions in the genome were removed.
Reads were filtered to remove any crosslinks within 50 nt of a repeatMasker-annotated repeat or a short non-coding RNA.
Genome_build: mm9
Supplementary_files_format_and_content: bed files of crosslinks mapping to unqiue positions in the genome filtered for crosslinks mapping to repeat regions or small ncRNAs.

source_name: mESC

growth_protocol: Cells were cultured on  0.1% gelatin-coated surfaces with KO-DMEM medium, 10% FCS, 5% knockout serum replacement, nonessential amino acids, L-glutamine, 2-mercaptoethanol, antibiotics (Invitrogen), and 1000 U/ml of leukaemia inhibitory factor (Abcam).

extract_protocol:
Individual-nucleotide resolution UV crosslinking and immunoprecipitation protocols were based in protocols available at Huppertz et al. Cells were irradiated with 0.2 J/cm2 of UV light in a Strataliker 2400 (Stratagene) with bulbs emitting at 254nm, and 6-10x107 cells  per IP were lysed in 1mL of Lysis buffer. Lysates were syringed with a 27G needle and sonicated for 3x 10s pulses with a Diagenode Picoruptor. Lysates were incubated in a Thermomixer at 37°C and 1100 rpm for three minutes after addition of 200U/mL of DNase Turbo and of 20 U/mL of RNase I. IPs were set up using 5ug of antibody as previously described in the iCLIP protocol. Beads were washed 3x with 900 μl high-salt buffer (50 mM Tris-HCl, pH 7.4; 1 M NaCl; 1 mM EDTA; 1% NP-40; 0.1% SDS; 0.5% sodium deoxycholate and 1M Urea), 2x with 900 μl wash buffer (20 mM Tris-HCl, pH 7.4; 10 mM MgCl2; 0.2% Tween-20) resuspended in 20 μl PNK mix (15 μl water; 4 μl 5x PNK pH 6.5 buffer [350mM Tris-HCl, pH 6.5; 50mM MgCl2 25mM dithiothreitol]; 0.5 μl PNK enzyme; 0.5 μl RNasin [Promega]) and incubated 30 min at 37°C 1100 rpm. Beads were washed 3x with 900 μl high-salt buffer, 2x with 900 μl wash buffer, resuspended in beads in 20 μl ligation mix (9 μl water; 4 μl 4x ligation buffer [200 mM Tris-HCl; 40m mM MgCl2; 40 mM dithiothreitol]; 1 μl RNA ligase [NEB]; 0.5 μl RNasin [Promega]; 1.5 μl pre-adenylated linker L3 [20 μM]; 4 μl PEG400 [81170, Sigma]), ligation was performed over night at 16°C and 1100 rpm. Beads were washed 3x with high-salt buffer, 2x wash buffer and  20% of the beads were incubated with 8 μl of hot PNK mix (0.4 μl PNK [NEB]; 0.8 μl 32P-γ-ATP; 0.8 μl 10x PNK buffer [NEB]; 6 μl water), radiolabelled and non-radiolabelled beads were pooled again and resuspended in 20 μl in NuPAGE loading buffer with reducing agent and run on a 4-12% NuPAGE Bis-Tris gel (Invitrogen) in MOPS buffer according to the manufacturer's instructions. Protein-RNA complexes were transferred to a nitrocellμlose membrane (Hybond, GE Healthcare) washed 2x with 1x PBS and exposed to a Fuji film. Using the auto-radiograph as  a mask RNA-protein complexes  attached to the membrane were isolated and treated with 200 μl PK buffer (100 mM Tris-HCl pH 7.4; 50 mM NaCl; 10 mM EDTA) and 10 μl proteinase K (Roche, 03115828001)  for 20 minutes at 1,100 rpm and 37°C. 200 μl of PK urea buffer (100 mM Tris-HCl pH 7.4; 50 mM NaCl; 10 mM EDTA; 7 M urea) was added and a second incubation was performed for 20 minutes at 37°C and 1100 rpm. Solution was collected and RNA was isolated by phenol:chloroform extraction and ethanol precipitation overnight at -20°C.
RNA pellet was resuspended in 7.25 μl RNA/primer mix (6.25 μl water; 0.5 μll Rclip primer [0.5 uM]; 0.5 μl dNTP mix [10mM]) and transferred in a 0.2 ml tube and incubated at 70°C. Reverse transcription was performed by addition of 2 μl 5x RT buffer; 0.5 μl 0.1M DTT; 0.25 μl Superscript III reverse transcriptase [Invitrogen] and incubation for 20 min at 42°C, 40 min at 50°C and 5 min at 80°C. cDNA was fractionated by running samples on a precast 6% TBE-urea gel at 180 V 40 min and isolating bands at 120-180 nt (high), 85-120 nt (medium) and 70-85 nt (low). Gel slices were submerged and crushed in TE buffer, incubated 1h at 37°C 1100 rpm, flash frozen, and a second incubation was performed 1h at 37°C 1100 rpm. cDNA was isolated by phenol:chloroform extraction and ethanol precipitation overnight at -20°C. cDNA was resuspended in 8 μl ligation mix (6.5 μl water; 0.8 μl 10x CircLigase Buffer II; 0.4 μl 50 mM MnCl2; 0.3 μl; Circligase II [Epicentre])  transferred into a 0.2ml tube and incubated for 1 h at 60°C for circularization. Samples were incubated in 30 μl oligo annealing mix (26 μl water; 3 μl FastDigest Buffer [Fermentas]; 1 μl cut_oligo [10 μM]), the oligo was annealed in a decreasing temperature gradient and circular cDNA re-linearized  by incubating samples with 2 μl BamHI (Fast Fermentas). cDNA was isolated by phenol:chloroform extraction and ethanol precipitation overnight at -20°C and the pellet resuspended in 20 μl of H20. Amplification was performed using 10 μl cDNA; 1 μl primer mix P5/P3 solexa (10 μM each); 20 μl Accuprime Supermix 1 enzyme [Invitrogen], 9 μl H20  and the following PCR programme: 94°C for 2 min, [94°C for 15 sec, 65°C for 30 sec, 68°C for 30 sec]n cycles, 68°C for 3 min, 4°C, with a number of cycles optimized previously. Library integrity was analysed using 8 μl PCR product with 8 μl of 5x TBE loading buffer and loading on a precast 6% TBE gel (Invitrogen). Gel was stained with Sybrgreen I (Invitrogen) and analyse with a gel imager. Library concentration was determined using a KAPA kit according to the manufacturer's instructions.

tag: ip antibody


title: P-TEFb rep3

description: protein crosslinked RNA

value: CDK9 sc-484


title: P-TEFb rep1

description: protein crosslinked RNA


title: Larp7 rep2

description: protein crosslinked RNA


title: P-TEFb rep2

description: protein crosslinked RNA


title: P-TEFb DMSO rep1

description: protein crosslinked RNA

tag: treatment/genotype

value: 0.1% DMSO control 6 hrs


title: Larp7 rep1

description: protein crosslinked RNA

tag: strain


title: WT-Saline1


title: P-TEFb pla-B rep1

description: protein crosslinked RNA

value: 1 uM Pladienolide B for 6 hrs


title: AML_bone marrow, case 60

city: Meldola

first: Giorgia

last: Simonetti

state: FC

address: Via Piero Maroncelli, 40

country: Italy

institute: IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori"

hyb_protocol: Sample hybridization was performed for 16 hours at 45°C according to standard protocol. Washing and staining was performed on Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000.

data_processing: The data were analyzed with Expression Console Software (version 1.4.1, Affymetrix, Thermo Fisher Scientific). Normalization was performed using the Signal Space Transformation-Robust multi-array average method (sst-RMA).

source_name: bone marrow cells

label_protocol: Biotin labeling of ss-cDNA was performed according to standard protocol

growth_protocol: Fresh mononuclear cells were  enriched by Ficoll gradient centrifugation and lysed with RLT buffer (Qiagen), containing a high concentration of guanidine isothiocycanate

extract_protocol: Total RNA was extracted using AllPrep DNA/RNA Mini Kit (Qiagen).

treatment_protocol: None.

tag: percentage of blasts

tag: gender

value: Male

tag: cytogenetic class

value: Normal Karyotype

tag: disease state

value: de novo, AML

value: bone marrow cells


title: AML_bone marrow, case 56

value: Female

value: na, AML


title: AML_bone marrow, case 49

value: Complex Karyotype


title: AML_bone marrow, case 53

value: secondary, AML


title: AML_bone marrow, case 47

value: Other


title: AML_bone marrow, case 57


title: AML_bone marrow, case 34


title: AML_bone marrow, case 48


title: AML_bone marrow, case 37

value: t-AML, AML


title: AML_bone marrow, case 52


title: AML_bone marrow, case 50


title: AML_bone marrow, case 51


title: AML_bone marrow, case 42


title: AML_bone marrow, case 38


title: AML_bone marrow, case 32


title: AML_bone marrow, case 59


title: AML_bone marrow, case 55


title: AML_bone marrow, case 43

value: Monosomy 7


title: AML_bone marrow, case 46


title: AML_bone marrow, case 39


title: AML_bone marrow, case 40


title: AML_bone marrow, case 45


title: AML_bone marrow, case 58


title: AML_bone marrow, case 54


title: AML_bone marrow, case 44


title: AML_bone marrow, case 35


title: AML_bone marrow, case 41


title: AML_bone marrow, case 61


title: AML_bone marrow, case 36


title: AML_bone marrow, case 33

value: MLL-rearranged


title: AML_bone marrow, case 14


title: AML_bone marrow, case 17


title: AML_bone marrow, case 27


title: AML_bone marrow, case 20


title: AML_bone marrow, case 30


title: AML_bone marrow, case 28


title: AML_bone marrow, case 24


title: AML_bone marrow, case 31


title: AML_bone marrow, case 18


title: AML_bone marrow, case 25


title: AML_bone marrow, case 13


title: AML_bone marrow, case 21


title: AML_bone marrow, case 29


title: AML_bone marrow, case 15


title: AML_bone marrow, case 26


title: AML_bone marrow, case 5


title: AML_bone marrow, case 8


title: AML_bone marrow, case 10


title: AML_bone marrow, case 16


title: AML_bone marrow, case 12


title: AML_bone marrow, case 9


title: AML_bone marrow, case 2


title: AML_bone marrow, case 4


title: AML_bone marrow, case 22


title: AML_bone marrow, case 7


title: AML_bone marrow, case 23


title: AML_bone marrow, case 6


title: WT.plus_S5

city: Iwaki

first: Yoshiaki

last: Kanemoto

state: Fukushima

address: kaminodai 57, jyobankamiyunagaya-town

institute: Jyoban Hospital

description:
gene-featureCount-else-int_name.txt
gene-FPKM_name.txt
transcript-featureCount-else-int_name.txt
transcript-FPKM_name.txt

data_processing:
STAR
featureCounts
Cufflinks
DESeq2
clusterProfiler
IGV genome browser
Genome_build: Human (Homo sapience) Genome assembly: GRCh37.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM and peak values for each sample.

source_name: Keratinocyte

growth_protocol: HaCaT WT and VDR KO cells were routinely culutured in DMEM supplemented with 10% fetal bovine serume at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol according to the manufacturer's instructions.
The RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: Three replicates cultured on 6 well-plate were treated with 1,25(OH)2D3 for 8hrs.

value: treated with 1,25(OH)2D3

value: HaCat

tag: genotype/variation

value: WT


title: WT.plus_S6


title: VDR.KO.minus_S8

value: untreated


title: VDR.KO.plus_S11


title: VDR.KO.plus_S12


title: WT.plus_S4


title: AML_bone marrow, case 11


title: AML_bone marrow, case 19


title: VDR.KO.minus_S9


title: VDR.KO.minus_S7


title: WT.minus_S2


title: WT.minus_S3


title: 59C-US-RD5-D3

city: Vancouver

first: Theodore

middle: S

last: Steiner

state: BC

address: Rm. C328 HP East, VGH

department: Medicine/Infectious Diseases

institute: University of British Columbia

description: 5 rounds of ALI damage

data_processing:
The RNA-seq Alignment app v1.1.1 on Basespace Illumina was used to align raw reads using STAR to the hg19 reference genome (abundant reads were filtered out before running STAR)
RnaReadCounter on Basespace Illumina was used to generate the count matrix
DESeq2 v1.1.0 via Basespace Illumina was used for differential expression analysis with the apried-end reads parameter
Differentially expressed genes at a log2FC of =>1 and a BH adjusted p-value of <=0.05 were considered for further analyses
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon

growth_protocol: Cells were grown until fully confluent ( 10 days) on a Transwell insert. Media was removed from the apical side and the cells were differentiated for 7 days (air liquid interface ALI). Following differentiation, media is added to the apical side for 4 hours to induce submergence damage, and flagellin was either added or not, to the basolateral side for 3 hours. Following submergence damage, the apical media was removed and the cells were grown back into ALI to recover from damage. This constitutes one round of damage and was repeated five total times.

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen)
Sample quality control was performed using the Agilent 2100 Bioanalyzer. Qualifying samples were then prepped following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England Biolabs). Sequencing was performed on the Illumina NextSeq2000 with Paired End 61bp × 61bp reads. Sequencing data was demultiplexed using Illumina's bcl2fastq2.

treatment_protocol: Cells were damaged with the addition of apical media, and flagellin was added basolaterally to some wells for 3 hours. Cells were recovered by growth back into ALI and this was repeated five times.

tag: region

value: transverse colon

tag: Sex

value: female

tag: rounds of damage

tag: flic treatment

value: No


title: 75C-FliC-RD1-D3

description: 1 round of ALI damage + FliC

value: ascending colon

value: male

tag: age

value: Yes


title: 59C-FliC-RD5-D3

description: 5 rounds of ALI damage + FliC


title: 75C-FliC-RD5-D3

description: 5 rounds of ALI damage + FliC


title: 75C-US-RD5-D3

description: 5 rounds of ALI damage


title: 59C-FliC-RD1-D3

description: 1 round of ALI damage + FliC


title: 75C-US-RD1-D3

description: 1 round of ALI damage


title: 59C-US-RD1-D3

description: 1 round of ALI damage


title: sh52 1

city: Miami

first: Scott

last: Welford

state: FL

address: 1550 10th Avenue, Pap 503

institute: University of Miami

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

hyb_protocol: Samples were hybridized with GeneChip HTA 2.0 (Affymetrix) and scanned at the Case Western Reserve University Gene Expression Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Transcriptome Analysis Console software from Affymetrix was used.

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown to subconfluence for 5 days after drug selection was completed

extract_protocol: Total RNA was harvested with an RNeasy Kit from Qiagen

tag: shRNA

tag: cell line


title: shGFP 2

source_name: shGFP 2

value: shGFP


title: sh50 2


title: shGFP 1

source_name: shGFP 1


title: AML_bone marrow, case 1

value: Female

value: de novo, AML

tag: cell type

value: bone marrow cells


title: sh50 1


title: WT.minus_S1

tag: treatment


title: 75C-ALI-D7

description: Air liquid interface (ALI) at 7 days


title: TFIIF_ChIPSeq_siSPT6

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.2.7. and normalized to the sample with the spike in control (mm10).
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS-SPT6-AID-C1 and U2OS-WT cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
Cells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay

treatment_protocol: Auxin/siRNA

tag: label

tag: sirna

tag: time point

value: 48H siRNA

tag: antibody

value: Abcam Anti-TFIIF antibody, #ab28179;


title: 75C-Day-10

description: Day 10 (Control)


title: AML_bone marrow, case 3

tag: percentage of blasts

tag: gender

value: Male

value: Other


title: sh52 2


title: TBP_ChIPSeq_siSPT6

value: Abcam Anti-TATA binding protein TBP, #ab818;


title: TFIIF_ChIPSeq_siCTR

value: siCTR


title: H3_ChIPSeq_C1_Auxin

value: Auxin

value: 24H Treatment

value: Abcam anti-Histone H3, #ab1791;


title: 59C-Day-10

description: Day 10 (Control)

value: transverse colon

value: female

value: No


title: VDR.KO.plus_S10

value: treated with 1,25(OH)2D3

value: HaCat


title: Negative control

city: Maebashi, Gunma

first: Navchaa

last: Gombodorj

state: Gunma ken

address: Showa machi 3-39-22

department: Division of Integrated Oncology Research

institute: Gunma University Graduate School of Medicine

description: Control siRNA transfected

data_processing:
Sequenced reads were mapped to hg19 using BWA. Unmapped reads are then mapped to hg19 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr (Nucleic Acids Res. 2015 Apr 30;43(8)).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: EBC-1 cell line

growth_protocol: The human lung squamous cell line EBC-1 was maintained in RPMI1640 medium containing 10% fetal bovine serum (Funakoshi, Inc., Japan) and 100 units/ml penicillin and streptomycin sulfate (Life Technologies, Carlsbad, CA, USA). EBC-1 cells were routinely generated by replating by 1 x 106 cells into 10 cm dish. Cells were cultured in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated by RNeasy mini kit (Qiagen, Hilden, Germany), and the quantity of total RNA was measured by using a NanoDrop equipment (Thermo Fisher Scientific, Waltham, MA, USA). Complementary DNA (cDNA) was synthesized using the cDNA Synthesis kit (Takara, Otsu, Japan). Real-time PCR was performed using SYBR Green PCR Master Mix (Takara) in a StepOnePlus RT-PCR system (Thermo Fisher Scientific). All target genes were normalized to the endogenous reference gene β-actin by using an optimized comparative Ct (2ΔΔCt) value method.
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags.

treatment_protocol: Establishment of RAB11A-suppressed EBC-1 cell lines: RNA interference assays for the target cell lines EBC-1 was performed using an in vitro electroporation protocol after 72 h after plating. RAB11A-specific small interfering RNA (siRNA) #1 (5′-GCAUCCAGGUUGAUGGAAA-3′), siRNA #2 (5′- AGCAAGAGCUUUUGCAGAA-3′), and negative control siRNA were purchased from GeneDesign Inc. (Osaka, Japan). In brief, the cells were suspended in Opti-MEM I (Life Technologies, Carlsbad, CA, USA) without serum at a density of 1 × 107 cells/ml. Six-hundred pmol siRNA was added to the 200 μl cell suspension. Next, the 200 μl cell suspension was transferred to a 2-mm gap cuvette electrode and then subjected to electroporation using an electroporator (CUY21EDIT II; BEX Co., Ltd., Tokyo, Japan). The conditions for electroporation were as follows: one pulse of 125 V with a 10-ms duration and 40-ms interval; followed by five pulses of 10 V with a 50-ms duration and 50-ms interval at 940 μF capacity; and five pulses of 10 V with a 50-ms duration and 50-ms interval at 940 μF capacity with reversed polarity. Total RNA was extracted from EBC-1 transfected with control siRNA and RAB11A specific siRNAs using the RNeasy mini kit (Qiagen, Hilden, Germany).  RAB11A suppression was validated by RT-PCR.  RNA interference assays for the target cell lines EBC-1 was performed using an in vitro electroporation protocol after 72 h after plating. RAB11A-specific small interfering RNA (siRNA) #1 (5′-GCAUCCAGGUUGAUGGAAA-3′), siRNA #2 (5′- AGCAAGAGCUUUUGCAGAA-3′), and negative control siRNA were purchased from GeneDesign Inc. (Osaka, Japan). In brief, the cells were suspended in Opti-MEM I (Life Technologies, Carlsbad, CA, USA) without serum at a density of 1 × 107 cells/ml. Six-hundred pmol siRNA was added to the 200 μl cell suspension. Next, the 200 μl cell suspension was transferred to a 2-mm gap cuvette electrode and then subjected to electroporation using an electroporator (CUY21EDIT II; BEX Co., Ltd., Tokyo, Japan). The conditions for electroporation were as follows: one pulse of 125 V with a 10-ms duration and 40-ms interval; followed by five pulses of 10 V with a 50-ms duration and 50-ms interval at 940 μF capacity; and five pulses of 10 V with a 50-ms duration and 50-ms interval at 940 μF capacity with reversed polarity. Total RNA was extracted from EBC-1 transfected with control siRNA and RAB11A specific siRNAs using the RNeasy mini kit (Qiagen, Hilden, Germany).  RAB11A suppression was validated by RT-PCR.

value: lung squamous cell carcinoma

tag: cell li ne

tag: transfected with

value: Control siRNA


title: RAB11A siRNA 2

description: RAB11A siRNA 2 transfected

value: RAB11A siRNA 2


title: pH2AX_ChIPSeq_C1_Auxin

value: Abcam anti-gammaH2A.X (phospho S139), #ab2893;


title: CSTF2_Input_ChIPSeq_C1

value: 6H Treatment


title: CSTF2_ChIPSeq_C1_Control

value: Bethyl Laboratories anti-CSTF64, #A301-092A;


title: pH2AX_ChIPSeq_C1_Control


title: H3_ChIPSeq_C1_Control


title: RAB11A siRNA 1

description: RAB11A siRNA 1 transfected

value: RAB11A siRNA 1


title: CSTF2_ChIPSeq_C1_Auxin


title: Hepa.ATACseq.H11.Dex

city: Philadelphia

first: Chunjie

last: Jiang

address: 3400 Civic Center Boulevard

department: Institute for Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

description: MergedPeakFile.ATACSeq.txt

data_processing:
none provided by the submitter
Genome_build: hg38

source_name: Hepatocyte

extract_protocol: none provided by the submitter

treatment_protocol:
adipocytes were treated with 1uM dexamethasone for 24h beginning at day 24 for RNA-seq, 6h beginning at day 20 for ChIP-seq,
hepatocytes were treated with 1uM dexamethasone for 24h beginning at day 20 for RNA-seq, 6h beginning at day 20 for ChIP-seq, ATAC-seq and ChIA-PET

value: hiPSC-derived HLCs

tag: chip antibody


title: Hepa.ATACseq.H9.Dex

description: MergedPeakFile.ATACSeq.txt


title: Hepa.ATACseq.H8.Dex

description: MergedPeakFile.ATACSeq.txt


title: TBP_ChIPSeq_siCTR

value: siCTR

value: 48H siRNA

value: Abcam Anti-TATA binding protein TBP, #ab818;


title: Hepa.ATACseq.H2.Dex

description: MergedPeakFile.ATACSeq.txt


title: 59C-ALI-D7

description: Air liquid interface (ALI) at 7 days

tag: region

tag: Sex


title: Hepa.ATACseq.H5.Dex

description: MergedPeakFile.ATACSeq.txt


title: Hepa.ATACseq.H10.Dex

description: MergedPeakFile.ATACSeq.txt

data_processing:
RNA-seq reads were trimmed using fastp v0.19.5 to remove reads with low quality, too short, or too many N. Trimmed reads were then aligned to human reference genome (hg38) using Hisat2 v2.1 with default parameters. Only unique mapped reads extracted by SAMtools v1.9 were considered for downstream analyses. Quantification of gene annotated in GRCh38 v94 from Ensembl database was estimated using StringTie v1.3.4
ChIP-seq raw reads were trimmed using fastp v0.19.5. Trimmed reads were then aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with default parameters. SAMtools v1.9 was used to extract unique mapped reads and remove duplicated reads. Biological replicates from the same individual were pooled together following by peak calling and de novo motif analyses using HOMER v4.9 with default parameters
ATAC-seq raw reads were trimmed using fastp v0.19.5. Next, trimmed reads were aligned to human reference genome (hg38) using Bowtie2 v2.3.0 with parameter --very-sensitive. Reads mapped to mitochondria were ignored. SAMtools v1.9 was applied to extract unique mapped reads and remove duplicated reads. Peak calling was performed using Genrich (https://github.com/jsh58/Genrich#contact)
ChIA-PET paired-end reads were first removed bridge linker and split into 3 category tags: none-linker containing tags, one-end tags and pair-end tags (PETs). Tags longer than 18 bp were used to mapped to human genome (hg38) by Burrows–Wheeler alignment (BWA) (ref). Duplicated PETs are filtered and uniquely non-redundant PETs were classified into inter-chromosomal PETs, intra-chromosomal PETs (two tags distance >=8 kb) and self-ligated PETs (two tags distance <8 kb). Multiple intra-chromosomal PETs whose respective ends were within 1 kb were then clustered together. PET count of each PET cluster represents the interaction strength. Loops with PETs ≥3 were considered for downstream analysis
Genome_build: hg38
Supplementary_files_format_and_content: Normalized abundance measurement was generated using StringTie.Expression profile were extracted using perl script; hic files were generated by ChIAPIPE

growth_protocol:
hASCs were cultured in DMEM medium. Confluent hASCs were then transferred into adipogenic medium for 14 days. Then, cells were further cultured in maintenance medium another 7 days and 1.5%BSA medium for additional 2 days.
hiPSCs were induced differentiation with Definitive Endoderm Kit for 4 days at 30-40% confluence 24 hrs post seeding, then were transferred into RPMI-B27 supplemented with BMP-4 and FGF basic in 5% oxygen/5% CO2 for 5 days, and treated with RPMI-B27 supplemented with recombinant human HGF in 5% oxygen/5% CO2 for 5 days, and were treated with HCM Hepatocyte Culture Medium without EGF and hydrocortisone and supplemented with recombinant human oncostatin M for 5 days in ambient oxygen/5% CO2.

extract_protocol:
Total RNA was extracted by using Qiagen RNeasey Mini kit.
DNA was isolated using phenol/chloroform extraction and NaCl/EtOH precipitated with 20 μg glycogen carrier.
Transposed DNA was purified using a QIAGEN MinElute Reaction Cleanup kit. Transposed fragments were subjected to library preparation following manufacturer protocol
The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)
RNA libraries were prepared for sequencing by Novogene (CA).
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina.
ATAC-seq libraries were sequenced using paired-end, dual-index sequencing on a NextSeq 500 instrument
The H3K4me3 in-situ ChIA-PET was performed according to the previously described protocol (Li et al., 2017)


title: SLAMSeq_Auxin_4sU_4h_R3

description: SLAMSeq_4sU_4h_Auxin_Converted_vs_Total.bw

data_processing:
Fastq files were generated Illumina’s BaseSpace platform and overall sequencing quality was analyzed with the FastQC script.
For ChIP-seq, fastq files were mapped to the human genome (hg19) using Bowtie v2.2.7. and normalized to the sample with the spike in control (mm10).
For 4sU-seq, reads were mapped to hg19 with  Bowtie2,  reads mapping to rRNA,exons and blacklist regions were removed, and then normalized based on read depth.
For SLAM-seq, reads were mapped to hg19 with  Bowtie2. BAM files were normalized based on read depth.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).

growth_protocol: U2OS-SPT6-AID-C1, U2OS-SPT6-AID-C2 and U2OS-WT cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/streptomycin

extract_protocol:
ChIP-seq: Cells were treated with 1% formaldehyde for 5 min at 37°C. After cell lysis, nuclei were re-suspended in RIPA buffer (10 mM Tris/HCl pH 7.5, 150 mM NaCl, 1% NP40, 1% deoxycholic acid (DOC), 0.1% SDS, 1 mM EDTA) and DNA was fragmented to a size <300 bp using Covaris. Chromatin was immunoprecipitated with 15 µg of corresponding antibody for 6 hours. Chromatin was eluted with 1% SDS and crosslinking was reverted overnight. For purification, chloroform/phenol extraction was used.
ChIP-seq: Libraries were prepared according to instructions accompanying the NEBNext Ultra™ II DNA Library Prep Kit for Illumina. Purified DNA was end-repaired, A-tailed, ligated to Illumina adaptors, size-selected (200 bp) and eluted. DNA fragments were amplified by 12 to 17 cycles of PCR and library size was tested with the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using a picogreen assay
RNA-Seq: U2OS cell lysates were spiked 4sU-treated mouse T-cell lysates. Total RNA was isolated using QIAzol and purified with miRNeasy columns and biotinylated. This was followed by  4sU-RNA pulldown pulldown using streptavidin-MyOne beads, followed by purification with RNA minElute columns (Qiagen)
RNA-Seq: 4sU-RNA was used for library preparation with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) and NEBNext Ultra II Directional RNA Library Prep kit. The libraries were amplified with 10-14 PCR cycles depending on the input RNA. The concentration and size distribution of the libraries were determined on a Fragment Analyzer using the NGS Fragment High Sensitivity Analysis Kit (1-6,000 bp; Agilent Technologies). The libraries were sequenced on the NextSeq500 Illumina platform for 75 cycles. Base calling was performed using Illumina’s BaseSpace platform.
3' polyA mRNA-Seq: RNA was isolated using RLT buffer and purified with RNeasy columns and biotinylated. After addition of ERCC spike in (mix1) (Thermo Fisher Scientific),  alkylation of RNA was carried out using 10 mM iodoacetamide (Thermo Fisher Scientific), and the reaction quenched with 1M DTT (Thermo Fisher Scientific). Alkylated RNA was purified with RNA minElute columns (Qiagen).
3' polyA mRNA-Seq: Library preparation was carried out with using QuantSeq kit (Lexogen), and fragments were amplified with 13 PCR cycles.

value: Auxin

value: 3h 4sU


title: SLAMSeq_Auxin_4sU_4h_R2


title: SLAMSeq_Control_4sU_2h_R3

description: SLAMSeq_4sU_2h_Control_Converted_vs_Total.bw

value: 2h 4sU


title: SLAMSeq_Control_4sU_4h_R1

description: SLAMSeq_4sU_4h_Control_Converted_vs_Total.bw


title: Hepa.ATACseq.H3.Dex

description: MergedPeakFile.ATACSeq.txt


title: SLAMSeq_Control_4sU_2h_R2


title: SLAMSeq_Auxin_4sU_2h_R1

description: SLAMSeq_4sU_2h_Auxin_Converted_vs_Total.bw


title: SLAMSeq_Auxin_4sU_2h_R3


title: SLAMSeq_Auxin_4sU_2h_R2


title: SLAMSeq_Control_4sU_2h_R1


title: SLAMSeq_Auxin_4sU_4h_R1


title: SLAMSeq_Control_4sU_4h_R3


title: SLAMSeq_Auxin_4sU_1h_R2

description: SLAMSeq_4sU_1h_Auxin_Converted_vs_Total.bw

value: 1h 4sU


title: SLAMSeq_Auxin_4sU_1h_R3


title: SLAMSeq_Auxin_4sU_1h_R1


title: SLAMSeq_Auxin_4sU_0h_R3

description: SLAMSeq_4sU_0h_Auxin_Converted_vs_Total.bw


title: SLAMSeq_Auxin_4sU_0h_R1


title: SLAMSeq_Control_4sU_1h_R1

description: SLAMSeq_4sU_1h_Control_Converted_vs_Total.bw


title: SLAMSeq_Control_4sU_1h_R3


title: SLAMSeq_Auxin_4sU_0h_R2


title: SLAMSeq_Control_4sU_1h_R2


title: Hepa.ATACseq.H1.Dex

description: MergedPeakFile.ATACSeq.txt


title: SLAMSeq_Control_4sU_0h_R3

description: SLAMSeq_4sU_0h_Control_Converted_vs_Total.bw


title: SLAMSeq_Control_4sU_4h_R2


title: SLAMSeq_Control_4sU_0h_R2


title: SLAMSeq_Control_4sU_0h_R1


title: DRB4sUSeq_30min_Auxin

description: nascent RNA

value: 2.5h DRB, 30min 4sU


title: DRB4sUSeq_20min_Auxin

description: nascent RNA

value: 2.5h DRB, 20min 4sU


title: DRB4sUSeq_20min_Control

description: nascent RNA


title: DRB4sUSeq_30min_Control

description: nascent RNA


title: DRB4sUSeq_10min_Control

description: nascent RNA

value: 2.5h DRB, 10min 4sU


title: DRB4sUSeq_10min_Auxin

description: nascent RNA


title: 4sUSeq_siCTR_R3

description: nascent RNA

value: 15min 4sU


title: 4sUSeq_siCTR_R1

description: nascent RNA


title: 4sUSeq_siSPT6_R1

description: nascent RNA


title: 4sUSeq_siSPT6_R3

description: nascent RNA


title: 4sUSeq_WT_Auxin_R3

description: nascent RNA


title: 4sUSeq_WT_Auxin_R2

description: nascent RNA


title: 4sUSeq_WT_Auxin_R1

description: nascent RNA


title: 4sUSeq_siSPT6_R2

description: nascent RNA


title: 4sUSeq_C2_Auxin_R3

description: nascent RNA


title: 4sUSeq_siCTR_R2

description: nascent RNA


title: 4sUSeq_C2_Auxin_R2

description: nascent RNA


title: 4sUSeq_C1_Auxin_R1

description: nascent RNA


title: 4sUSeq_C2_Control_R3

description: nascent RNA


title: 4sUSeq_C1_Auxin_R2

description: nascent RNA


title: 4sUSeq_C1_Control_R3

description: nascent RNA


title: 4sUSeq_C2_Control_R1

description: nascent RNA


title: 4sUSeq_C1_Auxin_R3

description: nascent RNA


title: POL2_ChIPSeq_C2_control

value: Santa Cruz Biotechnology anti-POL2 (A-10), #sc-17798;


title: pS2POL2_ChIPSeq_C2_auxin

value: Abcam anti-POL2 (phospho S2), #ab5095;


title: 4sUSeq_C1_Control_R2

description: nascent RNA


title: 4sUSeq_C2_Auxin_R1

description: nascent RNA


title: pS2POL2_ChIPSeq_C2_control


title: 4sUSeq_C1_Control_R1

description: nascent RNA


title: ChIPSeq_Input


title: POL2_ChIPSeq_C2_auxin


title: pS2POL2_ChIPSeq_C1_control


title: POL2_ChIPSeq_C1_control


title: SPT6_ChIPSeq_C1_control

value: Novus Biologicals anti-SPT6, #NB100-2582;


title: SPT6_ChIPSeq_C1_auxin


title: SKOV3.ip1 cells, SFRS1_1_n2

city: Sherbrooke

first: Michelle

last: Scott

state: Quebec

address: 3201, rue Jean-Mignault

institute: University of Sherbrooke

data_processing:
The quality of paired-end RNA-seq reads was examined using Fastqc v0.10.1
The reads are trimmed using Trimmomatic v0.38 with the following parameters LEADING:30 TRAILING:30 SLIDINGWINDOW:4:15 MINLEN:50.
Reads retained by the trimming were further trimmed to a fixed length of 50nt
The reads were aligned against human reference genome hg19 (obtained from UCSC genome browser golden path ftp://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/) using Tophat (v2.0.9, Bowtie 2.1.0.0, Samtools 0.1.19.0) with default parameters.
Gene expression level was calculated using CoCo v0.2.1p2 and Ensembl genome GRCh37 release 87
Genome_build: hg19
Supplementary_files_format_and_content: coco.TPM.xlsx contains the gene expression in TPM for all samples

source_name: Human ovarian cancer cell line SKOV3.ip1

growth_protocol: SKOV-3.ip1 cells are cultivated in 50/50 (v/v) mix of DMEM/Ham F12 supplemented with 10% FBS and 0.2mM L-glutamine.

extract_protocol:
RNA was extracted from mock-transfected and siRNA transfected cells 72h post-transfection.
cDNA library produced with TGIRT (thermostable group II reverse transcriptase)  Purified total RNA was ribodepleted by using a RiboZero Gold (Human/Mouse/Rat) kit (Illumina). The resulting ribodepleted RNAs were fragmented with an NEBNext Magnesium RNA Fragmentation Module (New England Biolabs) by incubation at 94°C for 7 minutes and were then treated with T4 polynucleotide kinase (T4PNK; Epicentre) to remove 3’ phosphates or 2’, 3’ cyclic monophosphates.  cDNAs were synthesized via TGIRT template-switching with either 0.5 or 1µM TGIRT-III reverse transcriptase (Ingex, LLC) for 15 min at 60o C, during which a DNA oligonucleotide containing the complement of an Illumina Read 2 sequencing primer-binding site becomes seamlessly linked to the 5’ cDNA end. After reaction cleanup, a 5’ adenylated DNA oligonucleotide containing the complement of an Illumina Read 1 sequencing primer-binding site is then ligated to the 3’ cDNA end with Thermostable 5’ AppDNA / RNA Ligase (New England Biolabs). Properly ligated cDNAs were amplified by PCR (12 cycles) to synthesize the second strand and add Illumina flowcell capture and index sequences. Libraries were size-selected with Ampure XP beads (Beckman-Coulter) and evaluated on an Agilent 2100 Bioanalyzer

treatment_protocol: siRNAs were transfected into cells at 100nM using Invitrogen Lipofectamine 2000. Lipo samples are treated with Lipofectamine without siRNAs.

tag: passage

value: SRSF1 knockdown siRNA_1

tag: genotype

value: SFRS1 depletion


title: 4sUSeq_C2_Control_R2

description: nascent RNA


title: SKOV3.ip1 cells, SFRS1_3_n1

value: SRSF1 knockdown siRNA_3


title: SKOV3.ip1 cells, SFRS1_3_n2


title: SKOV3.ip1 cells, RBM9_1_n4

value: RBFOX2 knockdown siRNA_1

value: RBM9 depletion


title: SKOV3.ip1 cells, RBM9_1_n5


title: SKOV3.ip1 cells, RBM9_2_n4

value: RBFOX2 knockdown siRNA_2


title: SKOV3.ip1 cells, RBM9_2_n5


title: SKOV3.ip1 cells, Lipo_oct_n3

value: Control for hnRNP C Knockdown and hnRNP M siRNA_1

value: control


title: SKOV3.ip1 cells, SFRS1_1_n1


title: SKOV3.ip1 cells, Lipo_oct_n1


title: SKOV3.ip1 cells, Lipo_n5

value: Control for RBFOX2 Knockdown


title: SKOV3.ip1 cells, Lipo_jan_n1

value: Control for hnRNP M knockdown siRNA_3 and SRSF1 knockdown siRNA_3


title: SKOV3.ip1 cells, hnRNPM_3_n1

value: hnRNP M knockdown siRNA_3

value: hnRNPM depletion


title: SKOV3.ip1 cells, hnRNPM_1_n3

value: hnRNP M knockdown siRNA_1