title: csrB mutant 2

city: Urbana

first: Frank

last: Zhao

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v1.8.4 Conversion Software (Illumina)
Sequenced reads were trimmed for adaptor sequence, then mapped to Erwinia amylovora CFBP1430  whole genome using bowtie v0.12.7 with parameters -t --sam -v 2 -B 1 -3 20 --best
The number of reads mapped to CDS of Erwinia amylovora CFBP1430  were counted using bedtools 2.17.0
Normalization and statistical analysis were carried out using the R package DESeq2 as described in Love et al. Genome biology, 2014.
Genome_build: NC_013961
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample (genome or plasmid)

organism: Erwinia amylovora

source_name: ΔcsrB

growth_protocol: Overnight cultures of wild-type and mutant strains grown in LB were harvested and washed twice with hrp-inducing minimal media.

extract_protocol:
Bacterial cells were harvested, and RNA was isolated using Qiagen RNeasy bacteria Mini kit
The stranded RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNA Sample Prep kit'

treatment_protocol: Bacterial cells were adjusted to 2 x 10^8 cfu/ml in 5 mL of hrp-inducing minimal media and incubated for 6 h at 18 °C.

tag: strain background

value: {delta}csrB


title: C57 KO EC VEGF 1 hour, biological rep3

status: Public on Aug 21 2019

type: RNA

city: Uppsala

first: Lena

last: Claesson-Welsh

state: Uppsala

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description: PA317_C57 KO3 V1

hyb_protocol: Clariom™ D Mouse Arrays were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the Clariom™ D Expression Wash, Stain and Scan Manual (P/N 702731 Rev. 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G. The data was run in two batches, which was considered in the normalization step.

data_processing: The raw data was normalized to gene and exon level in the Transcription Analysis Console, version 4.0.1.36, provided by Thermo Fisher (http://www.thermofisher.com), using the Signal Space Transformation-Robust Multi-Array Average (SST-RMA) method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: C57 mouse at postnatal day 7-12

label_protocol: An estimated amount of around 10 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA according to the GeneChip® Pico Reagent Kit User Guide (P/N 703308 Rev. 4, Affymetrix Inc., Santa Clara, CA).

growth_protocol: The isolated ECs were cultured in MV2 medium with supplements in 6-well plates until confluence and then plated in 12-well plates for experiments.

extract_protocol: RNA was isolated immediately by using RNeasy Micro Plus kit (Qiagen). RNA concentration was measured by Nanodrop (ThermoFisher Scientific) and RNA integrity number (RIN) was assessed by Bioanalyzer (Agilent, samples with a RIN>7 were used for microarray).

treatment_protocol: The cells from each mouse were starved for 3 hours in MV2 medium with 0.2% FCS and then either left untreated (basal) or treated with VEGFA (50 ng/mL) for 1 or 3 hours.

tag: strain/background

tag: genotype/variation

value: VEGFR2 Y1212F

tag: age

value: Postnatal day 7-12

tag: cell type

value: Lung endothelial cells

tag: treatment

value: VEGF

tag: time point

value: 1 hour


title: Mlp124499_1

type: SRA

city: Trois-Rivières

first: KarenCristine

last: GonçalvesdosSantos

state: QC

address: 3351 boulevard des Forges

department: Chemistry, biochemistry and physics

country: Canada

institute: Université du Québec à Trois-Rivières

library_source: transcriptomic

data_processing:
Trimming and filtering: Trimmomatic - LEADING:4 TRAILING:4 SLIDINGWINDOW:4:20 MINLEN:20
Alignment: TopHat v2.0.14 and TAIR10 - default options;
Counting: R v.3.2.5, annotation obtained from Ensembl Plants with Genomic Features and overlaps found with GenomicAlignments - summarizeOverlaps for paired-ends in union mode
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: .csv files contain read counts for each gene

organism: Arabidopsis thaliana

source_name: Aerial plant tissue

growth_protocol: Soil-grown; 16hs of light/day; 22ᵒC; harvest 15 days after germination

extract_protocol:
Plant Total RNA Mini Kit (Geneaid) using RB buffer following manufacturer’s protocol, with DNase
NeoPrep Library Prep System (Illumina) with the TruSeq Stranded mRNA Library Prep kit (Illumina) using 100 ng of total RNA

treatment_protocol: Stable transgenic lines

tag: transgenic line

value: Mlp124499-GFP and BAR

tag: ecotype


title: C57 KO EC Control, biological rep3

description: PA317_C57 KO3 C

value: Untreated

value: Control


title: csrB mutant 1

country: USA

tag: genotype


title: 20 SS, nonskin1, replicate A

city: Los Angeles

first: Shawn

middle: J.

last: Cokus

state: CA

address: UCLA, 3000 Terasaki Life Sciences Building, 610 Charles Young Drive East

institute: UCLA

data_processing:
Demultiplexing: single mismatch to expected 7-mers, only keeping PF=1 spots
Adapter, low quality base trimming: CutAdapt 1.8.1 (-m 21 --trim-n --max-n=2 -q 10,10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC), then only keeping reads >=47 nt long and only keeping the first 47 nt of those reads
Alignment: STAR 2.5.3a (to genome and transcriptome, single pass mode with known junctions), retaining multiple locations for non-uniquely aligning reads (see paper or BAMs for parameters)
Quantification: Salmon patched 0.10.2 (--numGibbsSamples=1000 --thinningFactor=25 --useVBOpt --libType=U --fldMean=200 --fldSD=200 --rangeFactorizationBins=4 --minAssignedFrags=1 --seqBias --noBiasLengthThreshold), with 1,000 Gibbs samples per experiment
Statistics: see paper; similar to R Bioconductor Sleuth (with Wasabi as importer), but elaborated and with some DESeq2 features incorporated
Genome_build: Ensembl release 92 top-level reference Zebrafish genome (GRCz11 chr1..25 + MT + 847/120 KN/KZ scaffolds) + PhiX, and associated Ensembl genebuild annotations/models
Supplementary_files_format_and_content: GZIP-TAR-Salmon files: GZIP-compressed TAR archives of Salmon transcript quantification output filesystem trees. Supplementary file: Microsoft Excel workbook in XLSX format, with multiple worksheets, containing a comprehensive collection of analysis input data, intermediate steps, and statistical outputs (see column headers as well as Methods and Supplemental methods of the associated journal publication).

molecule: polyA RNA

organism: Danio rerio

source_name: FACS-isolated nonskin cells from whole embryos

growth_protocol: Zebrafish were maintained in 28.5 C and pH 7.5 fish water. Adults were kept in a 14-hour light / 10-hour dark cycle.

extract_protocol:
Dechorionated embryos were transferred into 1.5 ml tubes and rinsed with Ca2+-free Ringer’s solution for 15 min. During this incubation, yolk was removed by gently pipetting embryos through a 200 µl tip (with the end cut off) three to five times. Yolk-free embryos were transferred into a 35 mm petri dish with 5 ml of 0.25% Trypsin-EDTA. Embryos were incubated at 28.5 °C and homogenized with a 200 µl tip every 10 min until most cells were dissociated (20 to 50 min). 55 µl 100 mM CaCl2 and 550 µl FCS were added to stop digestion. Dissociated cells were transferred into a 15 ml tube and centrifuged at 300 g for 5 min at 15 °C. Cells were rinsed once with 10 ml suspension solution (colorless Leibovitz medium L-15 with 0.3 g/L glutamine, 0.8 mM CaCl2, Pen 50U/ml, Strep 0.05 mg/ml, and 1% FCS). Dissociated cells were resuspended in suspension solution to ~10^7 cells/ml and immediately proceeded to cell sorting at the UCLA Broad Stem Cell Research Center Flow Cytometry Core. BD FACS ARIA II SORP instruments sorted cells, using a 488 nm laser for GFP detection and a 561 nm laser for RFP (dsRed) detection.
Sorted cells in suspension solution were immediately lysed using the Qiagen RNeasy kit. Lysis was completed within two hours of dissociating cells. Total RNA was isolated following the Qiagen RNeasy kit and stored at –80 °C. Quality of all samples was assayed with an Agilent Bioanalyzer, and only samples with RNA Integrity Number > 8 were used for creating sequencing libraries. Poly-A bead-purified RNA-Seq libraries were prepared with the Illumina TruSeq RNA Library Prep Kit.

treatment_protocol: Transgenic embryos without further treatment

tag: strain

value: AB+TU

tag: developmental stage

value: 20 SS

tag: tissue

value: FACS nonskin1

tag: Sex

value: pooled male and female

tag: biomaterial provider

value: Fang Wang (CSUDH)

tag: birth location

value: UCLA


title: Mlp37347_2

value: Mlp37347-GFP and BAR


title: csrA mutant 2

source_name: ΔcsrA

value: {delta}csrA


title: Mlp37347_3


title: 20 SS, nonskin1, replicate B


title: C57 KO EC Control, biological rep4

description: PA317_C57 KO4 C


title: csrB mutant 3

value: {delta}csrB


title: csrA mutant 1


title: C57 KO EC Control, biological rep2

description: PA317_C57 KO2 C

value: VEGFR2 Y1212F


title: 20 SS, all skin, replicate A

source_name: FACS-isolated all skin cells from whole embryos

value: FACS all skin


title: CTD_WT_2

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
alignment: bowtie2 using default settings
expression levels: Gene-level expression measurements for RefSeq genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples. See methods for further details
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file matix containing FPKM values for each transcript

source_name: WT ventral prostates

growth_protocol: FVB Hi-MYC mice, expressing the human c-MYC transgene in prostatic epithelium, were obtained from the National Cancer Institute Mouse Repository at Frederick National Laboratory for Cancer Research5. Upon weaning, male mice heterozygous for the transgene (MYC), together with their wild type littermates (WT), were fed a purified control diet (CTD; Harlan Laboratories, TD.130838) consisting of 10% fat, or a high-fat diet (HFD; Harlan Laboratories, TD. 06414) consisting of 60% fat; ingredients were adjusted on a kcal basis. Food was changed on a weekly basis, and mice were weighed every three weeks, starting at weaning. Animals were kept on a 12-hour light / 12-hour dark cycle, and allowed free access to food and water at the Dana-Farber Cancer Institute (DFCI) Animal Resources Facility. The animal protocol was reviewed and approved by the DFCI Institutial Care and Use Committee (IACUC), and was in accordance with the Animal Welfare Act.

extract_protocol:
Fresh VP tissues from 12-week-old mice were dissociated to form a single cell suspension. RNA from an equal number of cells was extracted using the miRNeasy Micro Kit (#217084, Qiagen) coupled with on-column DNAse treatment (#79254, Qiagen). RNA sample concentration was measured and subjected to quality evaluation, using a Bioanalyzer RNA 6000 Nano kit (#5067-1511, Agilent).
The Dana-Farber Cancer Institute Molecular Biology Core Facilities prepared libraries from 500 ng of purified total RNA, using TruSeq Stranded mRNA sample preparation kits (#RS-122-2101, Illumina) according to the manufacturer’s protocol; finished libraries were quantified by the Qubit dsDNA High-Sensitivity Assay Kit (#32854, Thermo Fisher Scientific), by an Agilent TapeStation 2200 system using D1000 ScreenTape (# 5067-5582, Agilent), and by RT-qPCR using the KAPA library quantification kit (# KK4835, Kapa Biosystems), according to the manufacturers’ protocols; pooled uniquely indexed RNA-seq libraries in equimolar ratios, and sequenced these to a target depth of 40M reads on an Illumina NextSeq500 run with single-end 75bp reads.

tag: cell line

value: ventral prostatic tissues

value: wild type

tag: diet

value: CTD

value: FVB


title: Mlp37347_4


title: csrA mutant 3

tag: strain background


title: WT 2

source_name: wild-type

value: wild-type


title: C57 KO EC VEGF 1 hour, biological rep2

description: PA317_C57 KO2 V1

tag: strain/background

tag: genotype/variation

value: Postnatal day 7-12

value: Lung endothelial cells

value: VEGF

value: 1 hour


title: Sixmonth 3

city: Xinyang

first: Yun

last: Ma

address: Shihe

country: China

institute: Xinyang Normal University

description: mRNA、lncRNA、circRNA

data_processing:
From the raw FASTQ files, adapter was removed using Trim Galore and filtered data were aligned to the Bos taurus reference genome (bosTau7) from UCSC (http://genome.ucsc.edu/) with TopHat2 (version 2.0.14)
Linear transcripts assembly and abundance estimation were performed using CuffLinks analyzed by LC-Bio (Hangzhou, China). The assembled transcripts were mapped to the reference annotation using a program named Cuffcompare in the Cufflinks site to derive novel genes.
The transcript abundances were normalized as the number of uniquely mapped fragments per kilobase of exon per million fragments mapped (FPKM).
Supplementary_files_format_and_content: FPKM

organism: Bubalus bubalis

source_name: sixmonth adipose tissue

growth_protocol: Six adipose samples from Xinyang buffalo of two developmental states (6Month and 30Month old) were collected from Benniu abattoir, a local slaughterhouse of Xinayang, P.R. China. Tissue samples were snap-frozen in liquid nitrogen and stored at –80°C freezer until use.

extract_protocol:
Total RNA was assessed by electrophoresis on a denaturing agarose gel and quantified by NanoDrop spectrophotometer (NanoDrop, USA) and Agilent 2100 Bioanalyzer. The total RNA samples (3 mg) were treated with the epicentre Ribo-ZeroTM Kit to remove rRNA before constructing the RNA-seq libraries.
Then the rRNA depleted RNA samples were fragmented and used to synthesize first- and second-strand complementary DNA (cDNA) with random hexamer primers, dNTPs and DNA Polymerase I. The cDNA fragments were cleaned and concentrated using AMPure XP beads, then the ends were repaired and modified with T4 DNA polymerase Klenow DNA polymerase to add A and adapter at the 3’ end of the DNA fragments. The ligated cDNA products were purified with AMPure XP beads and treated with uracil DNA glycosylase to remove the second-strand cDNA.
Purified first-strand cDNA was subjected to PCR amplification, and the libraries were quality controlled with a Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA) and sequenced by Illumina HiSeq 3000 (LC Sciences, USA) on a 125 bp paired-end run.

value: adipose tissue

tag: age

value: six months


title: Control_3

description: Arabidopsis-GFP

value: GFP and BAR


title: Mlp37347_1

value: Mlp37347-GFP and BAR


title: Sixmonth 2

description: mRNA、lncRNA、circRNA


title: Control_4

description: Arabidopsis-GFP


title: WT 1


title: Sixmonth 1

description: mRNA、lncRNA、circRNA


title: C57 KO EC Control, biological rep1

description: PA317_C57 KO1 C

tag: cell type

tag: treatment

value: Untreated

value: Control


title: C57 KO EC VEGF 1 hour, biological rep1

description: PA317_C57 KO1 V1

value: VEGFR2 Y1212F

tag: time point


title: Control_2

description: Arabidopsis-GFP

tag: transgenic line

tag: ecotype


title: C57 KO EC VEGF 3 hours, biological rep1

description: PA317_C57 KO1 V3

value: 3 hours


title: FVB KO EC VEGF 3 hours, biological rep4

description: PA317_KO5 V3

source_name: FVB mouse at postnatal day 7-12


title: C57 KO EC VEGF 3 hours, biological rep2

description: PA317_C57 KO2 V3


title: Control_1

description: Arabidopsis-GFP


title: C57 WT EC VEGF 3 hours, biological rep5

description: PA317_C57 WT5 V3

value: WT


title: 63-p7: Phf6-KO MPP2 rep2

city: Taipei

first: Yueh-Chwen

last: Hsu

address: No.7, Chung Shan S. Rd.

country: Taiwan

institute: National Taiwan University Hospital

data_processing:
Raw reads were aligned to mouse reference genome mm10 and gene-level expression were quantified by STAR algorithm
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes gene read counts

source_name: bone marrow

extract_protocol:
Mouse bone marrow was harvested from Phf6 wild-type and knockout mice, RBC was lysed and the rest cells were stained with anti-lineage cocktail, anti-Sca-1, anti-cKit, anti-CD150 and anti-CD48.
Libraries were prepared by Nextera XT DNA sample preparation kit (Illumina, CA, USA)

tag: strain

value: bone marrow

tag: genotype

value: Phf6 Knockout

value: 12 weeks


title: lentiGuide-Puro-pDNA-Peak-Library

city: Kansas City

first: Scott

middle: T

last: Younger

state: MO

address: 2401 Gillham Road

institute: Children's Mercy Kansas City

description: plasmid DNA

library_source: genomic

data_processing:
Library strategy: Amplicon sequencing
Read Alignment: 20 bases immediately following 'CACCG' matched to library reference file
Differential Abundance: MAGeCK
Genome_build: N/A
Supplementary_files_format_and_content: TXT files are raw read counts from amplicon sequencing for each sample

molecule: genomic DNA

organism: Expression vector lentiGuide-Puro

source_name: lentiGuide-Puro plasmid DNA

extract_protocol:
Column purification of gDNA
sgRNA libraries were designed to target p53-regulated genes (Gene Library) or p53 binding sites (Peak Library).  Both libraries were cloned into lentiGuide-Puro (Addgene #52963).
Amplicon sequencing - To determine the abundance of individual sgRNAs within the libraries the sgRNA sequences were directly amplified from pDNA/gDNA and the resulting amplicons were sequenced.

tag: tissue

value: lentiGuide-Puro plasmid DNA

tag: library type

value: Peak Library


title: lentiGuide-Puro-pDNA-Gene-Library

description: plasmid DNA

value: Gene Library


title: esg[ts]/+ whole gut. C6706ΔvasK infected. biological rep2

city: Edmonton

first: Edan

last: Foley

state: Alberta

address: 114th St and 87th ave

department: Medical Microbiology and Immunology

institute: University of Alberta

data_processing:
Base calls performed using Cyberduck(FTP)
FASTQC was used to evaluate the quality of raw paired-end sequencing reads. Adaptors and reads of less than 36 base pairs in length were trimmed from the raw reads using Trimmomatic. Reads were aligned to the Drosophila transcriptome- bdgp6 with HISAT2 (version 2.1.0). The resulting BAM files were converted to SAM flies using Samtools (version 1.8).
The converted files were counted using Rsubread (version 1.24.2) and loaded into EdgeR. In EdgeR, genes with counts less than 1 count per million were filtered and libraries were normalized for size. Normalized libraries were used to call genes that were differentially expressed among treatments.
Genome_build: Drosophila transcriptome- bdgp6

organism: Drosophila melanogaster

source_name: Drosophila esg[ts]/+ whole guts 24 hour infection

growth_protocol: Flies were raised on standard cornmeal food at 18C before eclosion. Adult flies were transferred to 29C for 5 days to permit establishment of the adult microbiome. Flies were then mock infected or infected with Vibrio cholerae for 24hours.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
For intestinal progenitor cell RNAseq, library construction and sequencing was performed by the Lunenfeld-Tanenbaum Research Institute. For whole gut RNAseq, library construction and sequencing was performed by Novogene: genome sequencing company.

treatment_protocol: After 24 hours of infection, for intestinal progenitor cell RNAseq a total of 100 guts per sample (virgin female) were and for whole gut RNAseq 10 guts per sample were dissected into Trizol and used for RNA extraction.

value: dissected whole gut

value: w; esgGal4, tubGAL80[ts], UASGFP/+;+/+

tag: infection


title: C57 WT EC VEGF 1 hour, biological rep5

description: PA317_C57 WT5 V1

value: Postnatal day 7-12

value: Lung endothelial cells

value: VEGF

value: 1 hour


title: esg[ts]/+ whole gut. C6706ΔvasK infected. biological rep1


title: C57 WT EC Control, biological rep5

description: PA317_C57 WT5 C

value: Untreated


title: C57 WT EC VEGF 3 hours, biological rep4

description: PA317_C57 WT4 V3


title: esg[ts]/+ whole gut. C6706 infected. biological rep3


title: esg[ts]/+ whole gut. C6706 infected. biological rep2


title: esg[ts]/+ whole gut. C6706ΔvasK infected. biological rep3


title: esg[ts]/+ whole gut. Mock infected. biological rep3

value: mock


title: esg[ts]/+ whole gut. Mock infected. biological rep2


title: C57 WT EC VEGF 1 hour, biological rep3

description: PA317_C57 WT3 V1


title: C57 WT EC VEGF 3 hours, biological rep3

description: PA317_C57 WT3 V3


title: C57 WT EC Control, biological rep3

description: PA317_C57 WT3 C

value: Control


title: C57 WT EC VEGF 3 hours, biological rep2

description: PA317_C57 WT2 V3

value: 3 hours


title: C57 WT EC VEGF 1 hour, biological rep2

description: PA317_C57 WT2 V1

value: WT


title: IgG_ChIP_rep1

city: Beijing

first: Zhang

last: Yi

state: Beijing

address: No.20 Nanxincun, Xiangshan

department: Key Laboratory of Photobiology

institute: Institute of Botany, CAS

description: IgG cpChIP-Seq rep1

data_processing:
Basecalls performed using BGISEQ software set.
ChIP-Seq reads were trimmed using a quality of threshold score <20 with SOAPnuke version 1.5
Reads pairs were mapped to the Arabisopsis thaliana reference genome from TAIR 10 using BWA version 0.7.12 with default parameter settings.
Peak calling was performed with MACS2 version 2.1.1 by using default mode. Peak calling parameters are "callpeak -t Sample.bam -c Control.bam -f BAM -g 1.2e8 -n  -q 0.01 --nomodel".
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files were generated using MACS2 version 2.1.1

source_name: Chloroplast

growth_protocol: Transgenic Arabidopsis seedlings (35S:mTERF5-HA) were grown on MS medium supplied with 80 µmol m-2 s-1 light under a 14-h-light/10-h-dark cycle at 22°C.

extract_protocol:
Chloroplasts were isolated from 10-d-old Arabidopsis Col-0 seedlings, followed by  cross-linking with 1% (v/v) formaldehyde. Cross-linked chloroplasts pellets were suspended with IP buffer [20 mM Tris-HCl (pH 7.6), 150 mM NaCl, 1 mM EDTA, 1% (v/v) Triton X-100, 0.05% (w/v) SDS]. Then, the supernatant of chloroplast extract were sonicated. The supernatant were subsequently incubated HA antibody (abcam, ab9110) or IgG antibody (abmart, B30011)  which both conjugated to ChIP-Grade protein A/G agarose (Thermo scientific, 26161) for  4h. Finally, DNA was isolated from washed agarose beads and "Input" supernatant of chloroplast extract.
DNA libraries were prepared with MGIEasy ChIP Library Prep Kit following the manufacturer’s instruction.

value: Intact chloroplast

tag: cpchip antibody

value: anti-IgG (abmart, B30011, lot 294670)

value: Columbia

tag: molecule subtype

value: genomic DNA of chloroplast


title: IgG_ChIP_rep2

description: IgG cpChIP-Seq rep2


title: C57 WT EC VEGF 1 hour, biological rep4

description: PA317_C57 WT4 V1


title: esg[ts]/+ whole gut. C6706 infected. biological rep1


title: esg[ts]/+ whole gut. Mock infected. biological rep1


title: CIP09

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

description: Gene expression data from primary GBM cells from internal region of GBM tumor

hyb_protocol: Following fragmentation and labelling,5.5 μg ss-cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scan GCS3000.

data_processing: The data were normalized using R software [www.r-project.org] with BioConductor package [www.bioconductor.org] using RMA

organism: Homo sapiens

label_protocol: Labeled and Fragmented ss-cDNA were prepared according to the standard GeneChip WT Plus protocol starting from 10-50 ng of Total RNA

extract_protocol: RNA was isolated from cryopreserved GBM tissues of different tumor regions using Trizol

tag: sample region

value: Internal region

value: Primary Glioblastoma (GBM) Cells

tag: sample code


title: C_input_rep1

description: Input rep1

value: none (input)


title: C57 WT EC VEGF 3 hours, biological rep1

description: PA317_C57 WT1 V3

tag: strain/background


title: C_input_rep2

description: Input rep2


title: C57 WT EC Control, biological rep4

description: PA317_C57 WT4 C

tag: genotype/variation


title: CIP06

description: Gene expression data from primary GBM cells from peripheral region of GBM tumor

value: Periphery region


title: CIP02

source_name: primary GBM cells from peripheral region of GBM tumor


title: CIP10


title: CIP03


title: CIP04

source_name: primary GBM cells from internal region of GBM tumor


title: C57 WT EC VEGF 1 hour, biological rep1

description: PA317_C57 WT1 V1

tag: age

value: Postnatal day 7-12


title: HA_ChIP_rep2

description: mTERF5 cpChIP-Seq rep2

value: anti-HA (abcam, ab9110, lot GR304617-8 )


title: CIP05

tag: cell type


title: CIP01


title: mouse embryo salivary glands TGF-β1 3

city: ChengDu

first: Liu

last: Zhikai

address: People South street

institute: SiChuan University

description: mouse embryo(T13) salivary glands treated with TGF-β1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Clariom S Assay, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

source_name: mouse embryo(T13) salivary glands

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: T13 embryos were collected and harvasted the salivary glands.

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

treatment_protocol: Salivary glands were treated with nothing or TGF-β1 then cultured for 72H. Selected embryos were transferred to a basket, rinsed with PBS and placed in the Trizol solution.

value: mouse embryo(T13) salivary glands


title: C57 WT EC Control, biological rep1

description: PA317_C57 WT1 C

value: Lung endothelial cells

tag: treatment


title: HA_ChIP_rep1

description: mTERF5 cpChIP-Seq rep1


title: mouse embryo salivary glands TGF-β1 1


title: C57 WT EC Control, biological rep2

description: PA317_C57 WT2 C

value: Untreated

tag: time point


title: WT_ST_rep1: wil-type NKG2D stim rep-1

status: Public on Aug 20 2019

city: Milwaukee

first: Robert

last: Burns

state: Wisconsin

address: 8727 W Watertown Plank Rd

institute: Blood Research Institute, Versiti

data_processing:
Samples were demultiplexed using Illumina bcl2fastq.
Read ends with phred base call qualities < 20 were trimmed using Trim Galore v0.4.1 and reads with a mean phred score of >= 20 were retained for analysis.
Reads were aligned to the Ensembl GRCm38 release 88 transcriptome using bowtie2 v2.2.8 and quantified using RSEM v1.3.0
Genome_build: Ensembl GRCm38 release 88
Supplementary_files_format_and_content: comma separated values of raw read counts per gene per sample

source_name: Spleenic IL-2 expanded NK cells

extract_protocol:
Trizol RNA protocol
Illumina TruSeq RNA

value: Spleenic IL-2 expanded NK cells

value: wild-type

value: NKG2D stimulation for 6hr


title: WT_ST_rep2: wil-type NKG2D stim rep-2


title: WT_ST_rep3: wil-type NKG2D stim rep-3


title: WT_nonST_rep3: wild-type unstim rep-3

value: untreated


title: WT_nonST_rep2: wild-type unstim rep-2


title: mouse embryo salivary glands TGF-β1 2


title: KO_ST_rep2: Mirc11-/- NKG2D stim rep-2


title: WT_nonST_rep1: wild-type unstim rep-1


title: KO_nonST_rep3: Mirc11-/- unstim rep-3


title: KO_ST_rep3: Mirc11-/- NKG2D stim rep-3


title: KO_ST_rep1: Mirc11-/- NKG2D stim rep-1


title: mouse embryo salivary glands control 1

description: mouse embryo(T13) salivary glands treated with nothing


title: KO_nonST_rep2: Mirc11-/- unstim rep-2


title: KO_nonST_rep1: Mirc11-/- unstim rep-1


title: WT_nonCHAL_rep2: wild-type unchalenged with listeria rep-1

source_name: Spleen negatively isolated  NK cells

value: Spleen negatively isolated  NK cells

value: Unchalenged with Listeria


title: WT_nonCHAL_rep3: wild-type unchalenged with listeria rep-2


title: WT_CHAL_rep3: wild-type chalenged with listeria rep-3

value: Chalenged with Listeria


title: WT_CHAL_rep2: wild-type chalenged with listeria rep-2


title: KO_nonCHAL_rep4: Mirc11-/- unchalenged with listeria rep-3


title: WT_CHAL_rep1: wild-type chalenged with listeria rep-1


title: KO_nonCHAL_rep3: Mirc11-/- unchalenged with listeria rep-2


title: mouse embryo salivary glands control 3


title: KO_nonCHAL_rep2: Mirc11-/- unchalenged with listeria rep-1


title: KO_CHAL_rep2: Mirc11-/- chalenged with listeria rep-2


title: KO_CHAL_rep3: Mirc11-/- chalenged with listeria rep-3


title: KO_CHAL_rep1: Mirc11-/- chalenged with listeria rep-1


title: Post-fear-extinction, non-ABX-treated sample 4

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with Illumina Casava 1.8.2
Adapter trimming using FLEXBAR (v2.4)
Alignment to mm10 reference genome using STAR version 2.3.0 with default settings
Reads per gene counted using Rsubread R package
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text giving raw number of counts mapped to each gene (identified by Entrez ID) in each sample

source_name: Dissected mPFC

extract_protocol:
Sorted cells were used to prepare RNAseq libraries using the Clontech SMARTer Ultra Low Input RNA Kit V4 (Clontech Laboratories).
Standard Illumina protocols

tag: abx treated

value: No

tag: pre or post fear extinction

value: Post Fear Extinction


title: Post-fear-extinction, non-ABX-treated sample 1

tag: strain


title: Post-fear-extinction, ABX-treated sample 3

value: Yes


title: Post-fear-extinction, ABX-treated sample 2


title: Post-fear-extinction, ABX-treated sample 4


title: Pre-fear-extinction, non-ABX-treated sample 3

value: Pre Fear Extinction


title: Pre-fear-extinction, non-ABX-treated sample 1


title: Post-fear-extinction, ABX-treated sample 1


title: mouse embryo salivary glands control 2


title: Pre-fear-extinction, ABX-treated sample 4


title: WT_nonCHAL_rep4: wild-type unchalenged with listeria rep-3

tag: genotype


title: Pre-fear-extinction, ABX-treated sample 2


title: Pre-fear-extinction, ABX-treated sample 1


title: RNASeq_RawData_T30_Rep3

city: Oslo

first: Philippe

last: Collas

address: PO Box 1112 Blindern

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

data_processing:
ChIP-seq reads were aligned to the mm10 reference genome using bowtie2 version 2.25.0
Duplicate reads were removed using picard MarkDuplicates
ChIP and Input experiments were ensured to have equal read depth for each chromosome individually by downsampling, per chromosome, the deepest sequenced experiment using a home-built python script DownsampleSam
Peak calling was done using Enriched Domain Detector (EDD) version 1.1.15, run 10 times on each sample to optimize BinSize and GapPenalty settings.
LAD with a length less than the estimated EDD technical replicate resolution were reomoved (178 out of a 2942 total LADs, or <1 % of domains )
RNA-seq was processed using the tuxedo protocol
Differential gene expression determined using cuffdiff v2.2.1 against the mouse mm10 reference genome
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: bed files with 4 columns: chromosome, start position, end position, score
Supplementary_files_format_and_content: fpkm_tracking files with 13 columns tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status

source_name: Wild-type C57Bl/6 female mice

growth_protocol: Wild-type C57Bl/6 male mice (Jackson Laboratories) were housed in 12 h light/12 h dark cycles with lights on at 6 am and lights off at 6 pm. Mice were kept off chow for 24 h, refed ad libitum at circadian time CT0 (6 a.m.) and euthanized at CT6, 12, 18, 24 and 30 h (n = 7 mice per CT). Non-synchronized mice (n = 7) were sacrificed at 12:00 on the day prior to food restriction. Livers were collected from all mice, partitioned and snap-frozen in liquid nitrogen

extract_protocol:
RNA-Seq: Total RNA from 3 replicates (i.e. livers from 3 mice at each CT and from NS mice; see above) was extracted from liver pieces using the RNeasy Mini Kit (Qiagen). DNase treatment was performed with RQ1 RNase-Free DNase (M101, Promega). ChiP-Seq: ChIP of LMNB1 was done as described {Rønningen et al 2015 Genome Res 25: 1825-1835}. Snap-frozen liver tissue pieces (40-50 mg) were thawed on ice and minced on ice for 30 sec. Minced tissue was resuspended in PBS with 1 mM PMSF and protease inhibitors, and homogenized by 7-10 strokes in a 2-ml Dounce homogenizer using pestle ‘B’. Samples were centrifuged at 400 g and supernatants discarded. Pellets were resuspended in PBS containing 1% formaldehyde and cross-linking allowed to occur for 10 min at room temperature. Cross-linked samples were sedimented and lysed in RIPA buffer (140 mM NaCl, 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 1% SDS, 0.1% sodium deoxycholate, 1 mM PMSF, protease inhibitors). To generate 200-500 bp DNA fragments, cells were sonicated 4 times 10 min in a Bioruptor (Diagenode). After sedimentation, the supernatant was diluted 10-fold in RIPA and incubated with anti-LMNB1 antibodies (10 µg; Abcam ab16048) coupled to Dynabeads Protein G (Invitrogen) overnight at 4oC. ChIP samples were washed 3 times in ice-cold RIPA. Cross-links were reversed and DNA eluted for 6 h at 68°C in elution buffer (50 mM NaCl, 20 mM Tris-HCl, pH 7.5, 5 mM EDTA, 1% SDS) containing 40 ng/ml proteinase K. DNA was extracted and libraries prepared and sequenced on an Illumina HiSeq2500.
ChIP-seq and RNA-seq sequencing libraries were prepared according to  Illumina protocols for sequencing on a HSeq2500 at the Norwegian Sequencing Center (Oslo University Hospital).

treatment_protocol: Mice were fasted by being kept off chow for 24 h, and refed ad libitum starting at at circadian time CT0 (6 a.m., lights ON)

tag: circadian time

tag: chip-antibody

tag: gender

value: female

tag: tissue

value: wild type


title: RNASeq_RawData_T30_Rep1


title: RNASeq_RawData_T24_Rep1


title: RNASeq_RawData_T18_Rep3


title: Post-fear-extinction, non-ABX-treated sample 3


title: RNASeq_RawData_T18_Rep2


title: RNASeq_RawData_T18_Rep1


title: RNASeq_RawData_T12_Rep2


title: RNASeq_RawData_T12_Rep3


title: RNASeq_RawData_T30_Rep2


title: RNASeq_RawData_T24_Rep2


title: RNASeq_RawData_T12_Rep1


title: Post-fear-extinction, non-ABX-treated sample 2


title: Pre-fear-extinction, non-ABX-treated sample 4


title: Pre-fear-extinction, ABX-treated sample 3


title: RNASeq_RawData_T6_Rep3


title: RNASeq_RawData_T6_Rep2


title: RNASeq_RawData_T6_Rep1


title: RNASeq_RawData_T0_Rep2


title: RNASeq_RawData_T0_Rep3


title: RNASeq_RawData_T0_Rep1


title: RNASeq_RawData_NS_Rep2

value: non-synchronized


title: RNASeq_RawData_NS_Rep3


title: RNASeq_RawData_T24_Rep3


title: RNASeq_RawData_NS_Rep1


title: ChipSeq_RawData_T30_Rep2

value: anti LMNB1 - Abcam rabbit polyclonal Ab16048


title: ChipSeq_RawData_T30_Rep1


title: ChipSeq_RawData_T30_Input


title: ChipSeq_RawData_T24_Input


title: ChipSeq_RawData_T18_Rep1


title: ChipSeq_RawData_T12_Rep2


title: ChipSeq_RawData_T12_Rep1


title: ChipSeq_RawData_T18_Input


title: ChipSeq_RawData_T24_Rep2


title: ChipSeq_RawData_T18_Rep2


title: WT 3

tag: strain background


title: AATt9

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
Adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in  coverage and ≥25% methylation differences between control groups and arsenite groups using the logistic  regression method. DMRs were detected for regions containing ≥3 CpG sites and at least 1  DMC and with ≥20% absolute mean CpG methylation difference by using an eDMR package on  R
TSS distance of DMRs were calculated by using bedtools 2.25.0.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files containing the results of DMRs between CCN vs AAN, CCTn vs AATn and CCTt vs AATt, respectively. The distance of DMRs from the closest gene calculated by bedtools.

source_name: Liver

extract_protocol:
Tissues were lysed in lysis buffer, treated with RNase, and purified with a phenol-chloroform mixture
RRBS libraries were prepared from genomic DNA of liver tissues   according to the protocol reported by Boyle et al (Genome Biol. 2012, 13:R92. doi: 10.1186/gb-2012-13-10-r92). with some modifications. Briefly, 100 ng of genomic DNA was digested with MspI, subjected to gapfilling  and A-tailing, and ligated with TruSeq adaptors included in the TruSeq DNA Sample Prep  Kit (FC-121-1001, Illumina). After DNA size selection and ligation efficiency were checked,  adaptor-ligated DNA was subjected to bisulfite conversion and amplified by PCR. The PCR  products were cleaned-up using Agencourt AMPure XP beads

value: liver

value: 74 weeks

tag: normal or non-tumor or tumor

value: tumor


title: AATt13


title: AATt5


title: AATn9

value: non-tumor


title: AATn13


title: AATn5


title: ChipSeq_RawData_NS_Rep1


title: ChipSeq_RawData_T0_Input


title: ChipSeq_RawData_T6_Input


title: ChipSeq_RawData_T0_Rep1


title: ChipSeq_RawData_NS_Rep2


title: ChipSeq_RawData_T6_Rep2


title: ChipSeq_RawData_T6_Rep1


title: ChipSeq_RawData_T0_Rep2


title: AAN2

value: normal


title: ChipSeq_RawData_NS_Input


title: ChipSeq_RawData_T24_Rep1


title: AAN1


title: AAN4


title: ChipSeq_RawData_T12_Input


title: CCTn15


title: CCTn10


title: sgNegCtrl

first: Kristian

last: Helin

address: 430 East 67 street

institute: MSKCC

data_processing:
Quality assessment and pre-processing of the raw data was performed using the R/Bioconductor library ShortRead v.1.38.0 and the standard R infrastructure.
Mapping using subjunc from the R/Bioconductor library Rsubread v.1.22.3 using default settings of the function subjunc and collected only uniquely mapped reads with the maximum of 3 mismatched bases in the alignment.
The differential abundance of the SRSF1-bound RNA molecules was determined using the functionality of the R/Bioconductor libraries edgeR and limma.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Table with average expression values for all the identified mRNAs and log2 fold changes and p- and q-values between the samples.

source_name: Acute myeloid leukemia cell line

extract_protocol:
The total RNA was extracted using phenol/chloroform method acording to the protocol of the MagnaRIP kit (Millipore,17-700)
Illumina Truseq v2 kit starting with Elute, Prime, Fragment step

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression, UV-crosslinked 6 days after transduction and immunoprecipitated with SRSF1 antibody. The immunoprecipitation and RNA extraction were performed using MagnaRIP kit (Millipore, 17-700) according to manufacturer's instructions

tag: cell line

value: control

tag: antibody

value: SRSF1 antibody

value: monocyte

value: peripheral blood

tag: culture type

value: suspension


title: CCTn8

tag: age


title: 4551_diff

city: Philadelphia

first: Yann

last: Aubert

state: Pennsylvania

address: Biomedical Research Building 421 Curie Blvd

department: Penn Dermatology Research

institute: University of Pennsylvania

data_processing:
basecalls performed using Illumina BaseSpace FASTQ Generation | Version: 1.0.0
reads were aligned to Homo sapiens PAR(pseudo-autosomal regions)-masked hg19 genome build using Illumina BaseSpace RNAseq alignement App  (STAR 2.6.1)
Gene differential expression analysis were perfomed using Illumina BaseSpace RNA-Seq Differential Expression app | Version: 1.0.1 (DESeq2)
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 output

source_name: Normal Human Epidermal Keratinocyte

growth_protocol: Primary epidermal progenitors were isolated from de-identified discarded neonatal human foreskin obtained by Core B of the Penn Skin Biology and Diseases and Resource-based Center. Foreskin was incubated for 12 h at 4°C in 2.4 U/mL dispase II. Sterile forceps were used to separate the underlying dermis. The epidermal sheet was transferred to a 60-mm tissue culture plate, incubated in 0.25% trypsin for 10 min at 37°C, and then neutralized with 1 mL of fetal bovine serum (FBS). Sterile forceps were used to scrape the epidermal sheet against the dish to dissociate cells. The suspension was passed through a 40-µm strainer and then centrifuged at 200g for 5 min. The cell pellet was resuspended in 5 mL keratinocyte medium. Epidermal progenitors were cultured in a 50:50 mix of 1× keratinocyte–SFM supplemented with human recombinant epidermal growth factor and bovine pituitary extract combined with medium 154 supplemented with human keratinocyte growth supplement and 1% 10,000 U/mL penicillin–streptomycin at 37°C.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit following the manufacturer's instructions.
All RNA-seq libraries were prepared using the NEBNext poly(A) mRNA magnetic isolation module followed by NEBNext Ultra Directional RNA library preparation kit for Illumina. Library quality was checked by Agilent BioAnalyzer 2100 and libraries were quantified using the Library Quant Kit for Illumina.

treatment_protocol: Primary human epidermal progenitors were cultured in medium containing 1.22 mM calcium chloride for 48 h and then harvested.

value: Epidermal Keratinocyte

tag: passages

value: 1.22mM CaCl2 48H


title: 4552_undiff

tag: treatment


title: 4552_diff


title: sgPRMT5

tag: genotype/variation

value: PRMT5 knockdown

tag: cell type


title: SE_4715_ControlsiRNA_5242019

data_processing:
basecalls performed using Illumina BaseSpace FASTQ Generation | Version: 1.0.0
reads were aligned to Homo sapiens PAR(pseudo-autosomal regions)-masked hg19 genome build using Illumina BaseSpace RNAseq alignement App  (STAR 2.6.1)
Gene differential expression analysis were perfomed using Illumina BaseSpace RNA-Seq Differential Expression app | Version: 1.0.1 (DESeq2)
Genome_build: hg19
Supplementary_files_format_and_content: DeSeq2 output

treatment_protocol: For siRNA experiments, primary human epidermal progenitors were treated with either siRNAs against LSD1 or a control siRNA at a dose of 500 nM. Cells were harvested 72 hours after transfection.

value: siCTL


title: SE_4729_LSD1siRNA_5242019


title: SE_4559_GSK2uM_D6_312019

treatment_protocol: For 144H (6d) experiments, cells were treated once daily with 2uM GSK-LSD1 (Cayman Chemical, Cat# 16439) at 0, 24, 48, 72, 96, and 120 hours before harvesting at 144 hours.

value: 2uM GSK-LSD1 144H


title: SE_4560_GSK2uM_D6_312019


title: SE_4715_LSD1siRNA_5242019


title: SE_4556_GSK2uM_D6_312019


title: SE_4560_DMSO_D6_312019

value: DMSO 144H


title: SE_4556_DMSO_Day6_312019


title: SE_4559_DMSO_D6_312019


title: 4603_GSKLSD1_02um_062018

treatment_protocol: For 48H (2d) experiments, cells were treated twice with inhibitor (either with 2uM GSK-LSD1, Cayman Chemical, Cat# 16439 or with 100uM 2-PCPA, BPS Bioscience, Cat# 27305) at 0 and 24 hours before harvesting.

value: 2uM GSK-LSD1 48H


title: 4602_GSKLSD1_02um_062018


title: 4601_GSKLSD1_02um_062018


title: 4603_DMSO_062018

value: DMSO 48H


title: 4602_DMSO_062018


title: 4601_DMSO_062018


title: 4603_2PCPA_100um_062018

value: 100uM 2-PCPA 48H


title: 4551_undiff


title: 4602_2PCPA_100um_062018


title: 4602_water_062018

value: water 48H


title: 4603_water_062018


title: SE_4729_ControlsiRNA_5242019


title: 4601_2PCPA_100um_062018


title: DMSO Input 4625

data_processing:
basecalls performed using Illumina BaseSpace FASTQ Generation | Version: 1.0.0
ChIPseq reads were aligned to hg19 human genome assembly using bowtie2-2.1.0 and the following parameters: -N 1, -k 1
Alignment files in SAM format were converted to BAM using samtools-1.1 view with -sB options
Alignment files in BAM format were sorted and indexed using samtools-1.1 and filtered to remove umapped reads (-F 4) and reads with a mapping quality (MAPQ) lower than 10
Alignment files in BAM format were further filtered to remove reads mapping to mitochondrial genes (chrM), Unplaced chromosome (_chrUn) and unlocalized contigs  (_random)
Alignement files in BAM format were used to generate tag directories for each sample using HOMER-v4.6 using the following parameters: -tbp 1, -fragLength given
After visual inspection of individual biological replicates visualization tracks, tag directories form biological replicates were merged using Homer v-4.6 makeTagDirectory script and the following parameters: -tbp 1 -fragLength given
Visualization tracks files in bedGraph format were generated using Homer-v4.9.1 with the following parameters :-fsize 5e7 -fragLength given and by subtracting the corresponding inputs.
For LSD1 ChIPseq, peaks were called on combined biological replicates tag directories using Homer-v4.6 findPeaks.pl script using default parameters and the corresponding inputs:
For H3K4me1/me2 ChIPSeq, peaks were called on biological replicates using filtered BAM files using macs2 version 2.1.1.20160309 and the following parameters: -f BAM -g hs -B --trackline --broad
Genome_build: hg19
Supplementary_files_format_and_content: peak files (.txt, .bed), visualization tracks (.bedGraph)

source_name: DMSO Input

extract_protocol:
ChIP-seq was performed as described previously (Capell et al., 2016; Lin-Shiao et al., 2018). Briefly, keratinocytes cultured in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min, and fixation was quenched with the addition of glycine to 125 mM for an additional 5 min. Cells were harvested by scraping from plates and washed twice in 1× PBS before storage at −80°C. ChIP extracts were sonicated for 15 minutes in a Covaris sonicator. All ChIPs were performed using 500 µg of extract and 2 µg of antibody per sample. Thirty microliters of Protein G Dynabeads was used per ChIP.
Libraries were prepared according to NEBNext Ultra DNA library preparation kit for Illumina instructions.

treatment_protocol: Primary epidermal progenitors were treated with 2mM GSK-LSD1 (Cayman Chemical, Cat# 16439) or vehicle (DMSO) twice, at 0 and 24 hours , before harvesting.

value: Normal Human Epidermal Keratinocyte

tag: chip antibody


title: 4601_water_062018


title: GSK Input 4625

source_name: GSK Input


title: DMSO Input 4624


title: GSK Input 4624


title: GSK H3K4me2 4625

source_name: GSK H3K4me2

value: GSK-LSD1 (2 mM) for 2 days

value: Rabbit polyclonal anti-Histone 3 (dimethyl K4) (Abcam, Cat# ab7766) RRID:ABB_2560996


title: GSK H3K4me2 4624


title: DMSO H3K4me2 4624

source_name: DMSO H3K4me2

value: DMSO


title: DMSO H3K4me2 4625


title: GSK H3K4me1 4624

source_name: GSK H3K4me1

value: Rabbit polyclonal anti-Histone 3 (monomethyl K4) (Abcam, Cat# ab8895) RRID:AB_306847


title: GSK H3K4me1 4625


title: DMSO H3K4me1 4625

source_name: DMSO H3K4me1


title: GSK LSD1 4625

source_name: GSK LSD1

value: Rabbit polyclonal anti-Kdm1a (Abcam, Cat# ab17721) RRID:AB_443964


title: GSK LSD1 4624


title: DMSO H3K4me1 4624


title: DMSO LSD1 4625

source_name: DMSO LSD1


title: DMSO LSD1 4624


title: MED1-chip_VCaP_DHTTHZ1

city: PHILADELPHIA

first: Irfan

last: Asangani

state: PA

address: 421 Curie Bld.

department: Cancer Biology

description: MED1 ChIP DNA

data_processing:
Illumina Nextseq500 reads were demultiplexed using bcl2fastq
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Genome_build: hg19
FPKM values were generated for  each sample
For ChIP-seq data, the bam files were converted to bigwig tracks using bamcoverage from deeptools
For ChIP-seq data, enrichment peaks were computed using MACS2
Supplementary_files_format_and_content: bigwig

source_name: VCaP

growth_protocol: LNCaP, and DU145 prostate cancer cell lines were grown in RPMI 1640 (Gibco, 11875093),  and VCaP prostate cancer cell line was grown in DMEM with Glutamax (Gibco, 21013024). The medium was supplemented with 10% of FBS (HYC, SH30910.03) and 1% of Penicillin  Streptomycin Solution (Invitrogen, 15140122).

extract_protocol: VCaP cells were serum starved, for 72h followed by 12h treatment with 200 nM THZ1 in presence/absence 10 nM DHT. ChIP was performed using iDeal ChIP-seq Kit for Transcription Factors (Diagenode, C01010170) according to manufacturer's protocol. In brief, the cells were crosslinked with 1% formaldehyde in culture medium for 10 min at room temperature. Cross-linking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Chromatin equivalent to 5×106 cells was isolated and incubated with 10 μg antibody overnight at 4 °C (MED1, and AR) (Diagenode). ChIP-seq libraries were prepared from the ChIP-enriched DNA samples using the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012, IP-202-1024) and protocol. In brief, ChIP-enriched DNA (1-10 ng) was converted to blunt-ended fragments. A single A-base was added to fragment ends followed by ligation of Illumina adaptors. The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase. PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina NextSeq 500 Sequencer (75 nucleotide read length).

treatment_protocol:
AR stimulation: Cells were plated in complete media at the required confluency. After 24h cells were washed with DPBS and cultured in RPMI/DMEM without Phenol Red (Invitrogen, 11835030) and 10% charcoal-dextran stripped FBS (Gemini Bio-Products, 100-119) for 72 h. Cells were then stimulated with 10 nM DHT for required time points.
THZ1  treatment: In DHT starvation and stimulation  experiments, cells were treated with CDK7 inhibitor-THZ1 (MedChem Express, HY-80013A/CS-3168) or Enzalutamide (Selleckchem, S1250) 30-45 min before DHT stimulation. Otherwise, the cells were treated with the particular drugs/compounds 24h post seeding. Enzalutamide and DHT was dissolved and aliquoted in DMSO and methanol respectivily.

value: Prostate Cancer

value: VCaP

value: AR stimulation in presence of THZ1 (6h)


title: AR-chip_VCaP_VEH

description: AR ChIP DNA

value: Vehicle control


title: MED1-chip_VCaP_DHT_2

description: MED1 ChIP DNA

value: AR stimulation (6h)


title: AR-chip_VCaP_DHTTHZ1

description: AR ChIP DNA


title: AR-chip_VCaP_DHT

description: AR ChIP DNA


title: VEH_LJN452_rep4

city: San Diego

first: Bin

last: Fang

address: 10675 John Jay Hopkins Dr

department: Discovery Science

institute: Novartis

description: genes.fpkm.table.cuffnorm.txt

data_processing:
BaseCalling was performed using bcl2fastq.gz2 v2.17.1.14
fastq.gz files were aligned o mouse genome by STAR_2.5.1b
Quantification of gene expression was done by cuffquant and cuffnorm in cufflinks package v2.2.1
Differential gene expression was performed using cuffdiff in cufflinks package v2.2.1
Genome_build: GRCm38.84
Supplementary_files_format_and_content: gene expression in rpkm

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded mRNA Library Prep Kit (Cat#FC-122-2103) was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: tropifexor (0.1, 0.3, or 0.9 mg/kg)


title: VEH_LJN452_rep2

description: genes.fpkm.table.cuffnorm.txt


title: VEH_OCA_rep3

description: genes.fpkm.table.cuffnorm.txt

value: OCA (25 mg/kg)


title: VEH_LJN452_rep3

description: genes.fpkm.table.cuffnorm.txt


title: VEH_OCA_rep4

description: genes.fpkm.table.cuffnorm.txt


title: VEH_OCA_rep1

description: genes.fpkm.table.cuffnorm.txt


title: VEH_OCA_rep2

description: genes.fpkm.table.cuffnorm.txt


title: VEH_LJN452_rep1

description: genes.fpkm.table.cuffnorm.txt


title: MED1-chip_VCaP_VEH_2

description: MED1 ChIP DNA


title: LJN452_mid_rep4

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_mid_rep3

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_mid_rep2

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_mid_rep1

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_low_rep4

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_low_rep1

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_low_rep3

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_high_rep4

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_high_rep3

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_high_rep1

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_high_rep2

description: genes.fpkm.table.cuffnorm.txt


title: OCA_rep2

description: genes.fpkm.table.cuffnorm.txt


title: OCA_rep3

description: genes.fpkm.table.cuffnorm.txt


title: OCA_rep1

description: genes.fpkm.table.cuffnorm.txt


title: Normal_control_rep4

description: genes.fpkm.table.cuffnorm.txt

value: low-fat diet (10% kcal) with no fructose or cholesterol


title: Normal_control_rep2

description: genes.fpkm.table.cuffnorm.txt


title: Normal_control_rep3

description: genes.fpkm.table.cuffnorm.txt


title: Normal_control_rep1

description: genes.fpkm.table.cuffnorm.txt


title: LJN452_low_rep2

description: genes.fpkm.table.cuffnorm.txt


title: OCA_rep4

description: genes.fpkm.table.cuffnorm.txt


title: 1_E_CD_41

city: Austin

first: Emma

last: Erickson

state: TX

address: 2500 Speedway MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

data_processing:
Base-calling was performed with BCL2fastq (version 2.17)
Samples were trimmed with FASTX Toolkit (version 0.0.14) and adapter sequences removed with Cutadapt (version 1.8)
Alignment was performed using STAR (version 2.5.0a) against the mouse reference genome (UCSC, mm10)
Duplicate reads were filtered with Picard (version 1.141)
Raw counts were obtained with HTSeq (version 0.6.1p1)
Normalized counts and differential expression results were obtained with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: gff files including raw read counts

source_name: Brain

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was removed and the remaining cells were manually dissociated in Neural Tissue Dissociation Buffer (P) (Miltenyi Biotec). Myelin was removed using a 25% Percoll gradient and microglia were captured using Cd11b microbeads (Miltenyi Biotec). Cells were spun at 1,000 x g and flash frozen in liquid nitrogen.
Tissue isolation described in samples. RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

treatment_protocol: Mice exposed to ethanol vapor 16 hr/day in 4 weekly cycles. Ethanol vapor delivered to mice in Plexiglas chambers at 10 L/min. Ethanol concentrations in the chamber maintained at 15-20mg/L air. Before entering chambers, mice were administered ethanol (1.6g/kg; 8% w/v) and pyrazole (1mmol/kg).

tag: brain region

value: Prefrontal cortex

value: Ethanol

value: Microglia


title: 1_E_TH_41

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was taken as the total homogenate, spun at 1,000 x g and flash frozen in liquid nitrogen
Tissue isolation described in samples. RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

value: Total homogenate


title: 1_E_TH_39


title: 1_E_TH_08


title: 1_E_TH_26


title: 1_E_CD_40


title: 1_E_TH_25


title: 1_E_TH_40


title: 1_E_TH_23


title: 1_E_TH_06


title: 1_E_CD_39


title: 1_E_CD_25


title: 1_E_CD_26


title: THP-1 cells_sgPRMT5

description: 3 biological replicates

data_processing:
Quality assessment and pre-processing of the raw data was performed using the R/Bioconductor library ShortRead v.1.38.0 and the standard R infrastructure.
Mapping using subjunc from the R/Bioconductor library Rsubread v.1.22.3 using default settings of the function subjunc and collected only uniquely mapped reads with the maximum of 3 mismatched bases in the alignment.
We used Cufflinks for transcriptome assembly (minimal isoform fraction threshold assigned to 0.05) and Cuffdiff for differential transcript expression analysis (minimal isoform fraction threshold that was assigned to 0.05)
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Table with FPKM values for all the genes and transcripts in all the samples. Additional columns contain differential splicing analysis.

extract_protocol:
The total RNA was extracted using Qiagen Rneasy kit
Illumina Truseq v2 kit

treatment_protocol: The cells were transduced with the lentiviruses driving the corresponding sgRNA expression and collected for sequencing 6 days post-transduction

value: monocyte

value: peripheral blood

value: suspension

tag: genotype

value: PRMT5 knockdown


title: THP-1 cells_sgNegCtrl

description: 3 biological replicates

value: control


title: 1_E_TH_24


title: MED1-chip_LNCaP_DHTTHZ1

description: MED1 ChIP DNA

data_processing:
Illumina Nextseq500 reads were demultiplexed using bcl2fastq
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
For ChIP-seq data, the bam files were converted to bigwig tracks using bamcoverage from deeptools
For ChIP-seq data, enrichment peaks were computed using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: LNCaP

extract_protocol: VCaP cells were serum starved, for 72h followed by 12h treatment with 200 nM THZ1 in presence/absence 10 nM DHT. ChIP was performed using iDeal ChIP-seq Kit for Transcription Factors (Diagenode, C01010170) according to manufacturer's protocol. In brief, the cells were crosslinked with 1% formaldehyde in culture medium for 10 min at room temperature. Cross-linking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Chromatin equivalent to 5×106 cells was isolated and incubated with 10 micrograms antibody overnight at 4 °C (MED1, and AR) (Diagenode). ChIP-seq libraries were prepared from the ChIP-enriched DNA samples using the TruSeq ChIP Library Preparation Kit (Illumina, IP-202-1012, IP-202-1024) and protocol. In brief, ChIP-enriched DNA (1-10 ng) was converted to blunt-ended fragments. A single A-base was added to fragment ends followed by ligation of Illumina adaptors. The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase. PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina NextSeq 500 Sequencer (75 nucleotide read length).

treatment_protocol:
AR stimulation: Cells were plated in complete media at the required confluency. After 24h cells were washed with DPBS and cultured in RPMI/DMEM without Phenol Red (Invitrogen, 11835030) and 10% charcoal-dextran stripped FBS (Gemini Bio-Products, 100-119) for 72 h. Cells were then stimulated with 10 nM DHT for required time points.
THZ1 and enzalutamide treatment: In DHT starvation and stimulation  experiments, cells were treated with CDK7 inhibitor-THZ1 (MedChem Express, HY-80013A/CS-3168) or Enzalutamide (Selleckchem, S1250) 30-45 min before DHT stimulation. Otherwise, the cells were treated with the particular drugs/compounds 24h post seeding. Enzalutamide and DHT was dissolved and aliquoted in DMSO and methanol respectivily.
MED1 and CDK7 knockdown protocol: For knockdown experiments, cells were seeded in six-well plates and transfected with 100 nM ON-TARGETplus SMARTpool siRNA (Dharmacon) targeting MED1 (Dharmacon, L-004126-00-0005),  CDK7 (Dharmacon, L-003241-00-005), and non-targeting Pool as a control (Dharmacon, D-001810-10-05) using lipofectamine RNAiMAX (Invitrogen,13778150) according to the manufacturer's instructions. Cells were then harvested 48/72h post-transfection and used in RNA-seq and other experiments.

value: Prostate Cancer

value: LNCaP


title: MED1-chip_LNCaP_DHT

description: MED1 ChIP DNA


title: AR-chip_LNCaP_DHTTHZ1

description: AR ChIP DNA

value: AR stimulation in presence of THZ1 (6h)


title: MED1-chip_LNCaP_VEH

description: MED1 ChIP DNA

value: Vehicle control


title: 1_E_CD_23


title: 1_E_CD_24


title: AR-chip_LNCaP_VEH

description: AR ChIP DNA


title: H3K27ac-chip_LNCaP

description: H3K27ac ChIP DNA

value: parental line


title: AR-chip_LNCaP_DHT

description: AR ChIP DNA

value: AR stimulation (6h)


title: 1_E_AS_41

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was removed and the remaining cells were manually dissociated in Neural Tissue Dissociation Buffer (P) (Miltenyi Biotec). Myelin was removed using a 25% Percoll gradient and astrocytes were captured using ACSA2 microbeads (Miltenyi Biotec). Cells were spun at 1,000 x g and flash frozen in liquid nitrogen.
Tissue isolation described in samples. RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

value: Astrocyte


title: 1_E_CD_06


title: 1_E_AS_40


title: 1_E_CD_08


title: H3K27ac-chip_VCaP_DHT

description: H3K27ac ChIP DNA

value: VCaP

value: AR stimulation (12h)


title: MED1-chip_VCaP_DHT

description: MED1 ChIP DNA


title: VCaP_DHTsiMED1_rep1

description:
processed data file:
fpkm_matrix_siknockdown.csv

data_processing:
Illumina Nextseq500 reads were demultiplexed using bcl2fastq
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner with the default setting in Illumina Basespace (https:// basespace.illumina.com/home/indexIllumina)
Aligned reads for RNA-seq samples were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis for RNA-seq was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values were generated for  each sample
fpkm_matrix_DHTstimulation.csv: FPKM matrix of all samples treated with DHT in absence or presence of THZ1
fpkm_matrix_24hTHZ1_treatment.csv: FPKM matrix of parental lines treated with THZ1 for 24hrs
fpkm_matrix_siknockdown.csv: FPKM matrix of siNT, siCDK7 and siMED1 knockdown

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: si knockdown of MED1


title: MED1-chip_VCaP_VEH

description: MED1 ChIP DNA


title: VCaP_DHTsiMED1_rep2


title: MED1-chip_VCaP_DHTENZA

description: MED1 ChIP DNA

value: AR stimulation in presence of enzalutamide (6h)


title: Hs746T PHA665752

city: Seoul

first: Sehui

last: Kim

address: 101, Daehak-ro Jongno-gu

department: Pathology

country: South Korea

institute: Seoul National University

description: MET inhibition

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: Data was extracted using GeneSpringGX 7.3 (Agilent Technology, USA). Raw intensity data was globally normalized (Cheadle et al.(2003).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Hs746T cells were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum.

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

treatment_protocol: Hs746T cells were treated with MET inhibitor (PHA665752) or transfected with MET siRNAs

value: MET inhibitor


title: Hs746T Met siRNA

description: MET Knockdown

source_name: Hs746T Met siRNA

value: MET siRNA


title: Hs746T DMSO

description: MET inhibition

source_name: Hs746T DMSO

value: DMSO


title: Hs746T SC siRNA

description: MET Knockdown

source_name: Hs746T SC siRNA

value: sc siRNA


title: VCaP_DHTsiNT_rep2

value: si knockdown non-target


title: 1_E_AS_24

value: Prefrontal cortex

value: Ethanol


title: 1_E_AS_08


title: 1_E_AS_26


title: 1_E_AS_23


title: LNCaP_DHTsiMED1_rep1

value: Prostate Cancer

value: LNCaP


title: LNCaP_DHTsiMED1_rep2


title: 1_E_AS_06


title: 1_E_AS_25


title: 1_E_AS_39


title: 1_C_TH_37

treatment_protocol: Mice exposed to fresh air in Plexiglass chambers 16 hr/day in 4 weekly cycles. Before entering chambers, mice administered saline and pyrazole (1mmol/kg).

value: Control (Air)

value: Total homogenate


title: LNCaP_DHTsiCDK7_rep2

value: si knockdown of CDK7


title: VCaP_DHTsiCDK7_rep2


title: VCaP_DHTsiCDK7_rep1


title: 1_C_TH_35


title: LNCaP_DHTsiCDK7_rep1


title: 1_C_TH_22


title: 1_C_TH_36


title: LNCaP_DHTsiNT_rep1


title: LNCaP_DHTsiNT_rep2


title: DU145_24hTHZ1_rep2

description:
processed data file:
fpkm_matrix_24hTHZ1_treatment.csv

value: 24h THZ1 treatment


title: 1_C_TH_05


title: VCaP_DHTsiNT_rep1

value: VCaP


title: 1_C_TH_20


title: 1_C_CD_37

value: Microglia


title: 1_C_TH_03


title: DU145_24hDMSO_rep1

value: 24h DMSO treatment


title: DU145_24hTHZ1_rep1


title: VCaP_24hTHZ1_rep2


title: VCaP_24hTHZ1_rep1


title: 1_C_CD_36


title: 1_C_CD_35


title: VCaP_24hDMSO_rep2


title: 1_C_CD_22


title: LNCaP_24hTHZ1_rep2


title: 1_C_CD_19


title: 1_C_CD_05


title: 1_C_CD_03


title: LNCaP_24hDMSO_rep2


title: LNCaP_24hTHZ1_rep1


title: 1_C_AS_37

value: Astrocyte


title: 1_C_TH_19


title: 1_C_AS_35


title: DU145_24hDMSO_rep2


title: 1_C_CD_20


title: VCaP_24hDMSO_rep1


title: VCaP_DHTTHZ1_rep1

description:
processed data file:
fpkm_matrix_DHTstimulation.csv

value: AR stimulation in presence of THZ1 (6h)


title: 1_C_AS_22


title: 1_C_AS_20


title: 1_C_AS_36


title: 1_C_AS_05


title: 1_C_AS_19


title: LNCaP_24hDMSO_rep1


title: VCaP_VEH_rep1

value: Vehicle control


title: LNCaP_DHTTHZ1_rep2


title: VCaP_DHT_rep1

value: AR stimulation (6h)


title: LNCaP_DHTTHZ1_rep1


title: LNCaP_DHT_rep1


title: VCaP_DHTTHZ1_rep2


title: N_2

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

data_processing:
Adapter trimmed, and alignment was performed using STAR, using mm10 as reference
Gene quantification was conducted using HTSeq, using the mouse GENCODE gene model
gene normalization was done using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix

source_name: Dorsal skin

extract_protocol:
Telogen dorsal skin was shaved and a ~4 x 4 cm region of skin was collected and incubated overnight in 0.25% trypsin at 4 degrees Celsius.  The next day, the epidermis were scraped from the dermis using a razor blade, minced in trypsin, and passed through a 100 um nylon mesh to remove hair shafts.  The cells were lysed in 350 uL RLT buffer per 5 x 10^6 cells, and processed using RNeasy Mini Kit (Qiagen).  1.5 ug of total RNA with RIN > 7 was submitted to Novogene Corporation for RNA-Seq, and ~20 x 106 reads were collected per sample.
After QC procedures, mRNA was enriched using oligo(dT) beads. Next, the mRNA was fragmented randomly by adding fragmentation buffer, then cDNA was synthesized by using mRNA template and random hexamers, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I were added to initiate second-strand synthesis. 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. The quality control of the library consisted of three steps:  (1) Qubit 2.0: tested the library concentration preliminarily.  (2) Agilent 2100: tested the insert size.  (3) Q-PCR: quantified the library effective concentration precisely. The qualified libraries were fed into HiSeq/MiSeq sequencers after pooling according to its effective concentration and expected data volume.

treatment_protocol: Mice were injected with tamoxifen to induce Cre-mediated deletion of Notch components in the skin.  Samples were harvested 10 weeks later.

value: Dorsal skin

tag: cage

tag: condition


title: N_3

tag: tissue


title: N_4


title: N_1


title: LNCaP_VEH_rep2


title: VCaP_DHT_rep2


title: LR_3

value: LR


title: MDA-MB-231 breast cancer cells coculture with 3T3-L1 adipocytes

city: Mysuru

first: Ravi

last: Kasiappan

state: Karnataka

address: Department of Biochemistry

department: Biochemistry

country: India

institute: CSIR-Central Food Technological Research Institute

description: Ad-BCa

data_processing:
The sequences were aligned using Bowtie 1.1.1 aligner against Homo sapiens GRCh38 build genome
3' Trueseq adapter sequences were restricted by using the small RNA-workbench V3.0_ALPHA and it was further trimmed based on the length criteria (minimum length 16 bp and maximum 40 bp) and distributed between 16 to 40 bp.
MiRNA analysis was carried out on an average 8.8 M high quality adapter free reads out of 13 M generated. Aligned reads were extracted and checked for ncRNA (rRNA, tRNA, snRNA and snoRNA) contamination. The unaligned reads to ncRNAs database were used for known miRNA prediction.
Homology search of these miRNAs was done against human mature miRNA sequences retrieved from miRbase-21 database using NCBI blast-2.2.30+ at e-3.
Genome_build: GRCh38 build
Supplementary_files_format_and_content: Excel files were generated using RPM count

source_name: human breast and mouse embryo

growth_protocol: MDA-MB-231 cells were routinely cultured on 100 mm dish with DMEM medium supplemnted with 10 % FBS and 100 U/mL penicillin, 100 mg/mL streptomycin.   3T3-L1 preadipocytes were maintained with DMEM medium and differentaiton was induced by adding 5 µg/ml insulin, 0.5 mM 3- isobutyl-1-methylxanthine and 1 µM dexamethasone.

extract_protocol:
Total RNA inclduing small RNA was extracted from MDA-MB-231 cells and subjected to small RNA deep sequencing
Small RNA sequencing libraries were prepared with TruSeq Small RNA Sample Preparation Guide at the Genotypic Technology Pvt. Ltd., Bangalore, India. Briefly, approx. 50 ng of RNA was used as starting material. 3’ adaptors were ligated to the specific 3’OH group of microRNAs followed by 5’ adaptor ligation. The ligated products were reverse transcribed with superscript III reverse transcriptase by priming with reverse transcriptase primers. The cDNA was enriched and barcoded by PCR (15 cycles) and cleaned using polyacrylamide gel. The library was size selected in the range of 140 bp– 160 bp followed by overnight gel elution and salt precipitation using glycogen, 3 M sodium acetate and absolute ethanol.The precipitate was re-suspended in nuclease free water. The Illumina-compatible sequencing library was initially quantified by qubit fluorometer and its fragment size distribution was analyzed on Agilent Bioanalyzer. Finally, the sequencing library was accurately quantified by quantitative PCR using Kapa Library Quantification Kit. The qPCR quantified library was subjected to sequencing on an Illumina NextSeq 500 sequencer for 75 bp single-end chemistry.

treatment_protocol: MDA-MB-231 were co-cultured with 3T3-L1 mature adipocytes by using a 6-well 0.4-μm pore size transwell system for 5 days

value: mammary gland/breast; derived from metastatic site:pleural effusion

tag: co-culture

value: 3T3-L1 mouse pre-adipocytes


title: LR_1


title: KR_5

value: KR


title: LR_2


title: VCaP_VEH_rep2

value: Prostate Cancer


title: MDA-MB-231 breast cancer cells

description: BCa

source_name: human breast


title: LNCaP_VEH_rep1

value: LNCaP


title: dgat1-1 16DAF rep3

city: Manhattan

first: Timothy

last: Durrett

state: KS

address: 1711 Claflin Road

department: Biochemistry and Molecular Biophysics

institute: Kansas State University

description: RNA-Seq data dgat1-1.txt

data_processing:
Raw fastq files were imported into CLC genomics workbench v7.5.1 platform using Illumina import. Reads were imported as paired reads, and reads which fail the quality score based on Illumina pipeline 1.8 and later were removed.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis genome assembly (Araport 11)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
To identify differentially expressed genes, the EDGE test (empirical analysis of differentially expressed genes) was used which is included in CLC genomics workbench. This test implements the “Exact test” for two-group comparisons. This test assumes that all samples have negative binomial distribution and accounts for the biological variability of replicates.
Paramteres used for EDGE test to identify differentially expressed (DE) genes: fold change greater than 2-fold , p value <=0.05 and only those genes were seleced which had RPKM value equal or higher than 0.1
Genome_build: Araport 11
Supplementary_files_format_and_content: Excel spreadsheet files include RPKM values for each sample

source_name: Late seed development

growth_protocol: Dry seeds were cold stratified for two days at 4˚C before growing on soil mixture (4:2:1 mixture of Metromix Professional Growing Mix: vermiculite: perlite) in growth chambers at 23 ˚C under long-day conditions (16 h light / 8 h dark)

extract_protocol:
Total RNA was extracted from the pooled seeds of 30-40 siliques using the RNeasy plant mini kit (Qiagen) according to the manufacturer’s instructions, followed by additional purification with sodium citrate to improve RNA quality. We obtained total RNA yields in the range of 1-3ug for ~50mg seeds. Using an Agilent Bioanalyzer, we confirmed that the RNA Integrity Number (RIN) for all samples was greater than 9.
Total RNA (500 ng) was sequenced at the Genomics Core at the University of Kansas Medical Center. The mRNA fraction was enriched with oligo dT capture, sized, reverse transcribed into cDNA and ligated with the appropriate indexed adaptors using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina). Following Agilent Bioanalyzer QC of the library preparation and library quantification using the Roche Lightcycler96 with KAPA SYBR Fast Universal qPCR kit (KAPA Biosystems), the RNA-Seq libraries were adjusted to a 4nM concentration and pooled for multiplexed sequencing. Libraries were denatured and based on qPCR results, diluted to the appropriate concentration, followed by clonal clustering onto the sequencing flow cell using the TruSeq Paired-End (PE) Cluster Kit v3-cBot-HS (Illumina). The clonal clustering procedure was automated using the Illumina cBOT Cluster Station. The clustered flow cell was sequenced on an Illumina HiSeq 2500 Sequencing System using the TruSeq SBS Kit v3-HS (Illumina) to obtain 100bp pair-end reads, which were trimmed and quality assessed before assembly against the Arabidopsis reference genome (Araport 11) using CLC genomics workbench (v 7.5.1).

treatment_protocol: To isolate seeds at different developmental stages, emerging flowers were tagged with the cotton thread at specific time intervals. Whole siliques were flash frozen in liquid nitrogen and stored at -80 ˚C. Seed harvesting from siliques was done on dry ice

tag: development stage

value: 16 days after flowering (DAF)

tag: background ecotype

value: Columbia

value: Seed


title: dgat1-1 16DAF rep2

description: RNA-Seq data dgat1-1.txt


title: 1_C_AS_03

value: Prefrontal cortex

value: Control (Air)


title: dgat1-1 16DAF rep1

description: RNA-Seq data dgat1-1.txt


title: LNCaP_DHT_rep2

tag: cell line


title: KR_1


title: KR_3


title: dgat1-1 12DAF rep2

description: RNA-Seq data dgat1-1.txt

source_name: Mid seed development

value: 12 days after flowering (DAF)


title: Cont_6

description: Control for KR (also known as Cont_62 below)

value: Cont

value: Control for KR


title: dgat1-1 12DAF rep3

description: RNA-Seq data dgat1-1.txt


title: dgat1-1 8DAF rep3

description: RNA-Seq data dgat1-1.txt

source_name: Early seed development

value: 8 days after flowering (DAF)


title: dgat1-1 12DAF rep1

description: RNA-Seq data dgat1-1.txt


title: dgat1-1 8DAF rep2

description: RNA-Seq data dgat1-1.txt


title: Cont_5

description: Control for LR (also known as Cont_52 below)

value: Control for LR


title: Cont_4

description: Control for KR (2 files:  Cont_4 and Cont_42 were from identical samples (the same mouse), below, sequenced on 2 separate occasions)

value: Dorsal skin


title: Cont_2

description: Control for LR


title: dgat1-1 8DAF rep1

description: RNA-Seq data dgat1-1.txt


title: Cont_1

description: Control for KN1 (2 files: Cont_1 and Cont_12 were from identical samples (the same mouse), below, sequenced on 2 separate occasions)

value: Control for KN1


title: WT 16DAF rep3

description: RNA-Seq data dgat1-1.txt

value: WT


title: WT 8DAF rep3

description: RNA-Seq data dgat1-1.txt


title: WT 12DAF rep2

description: RNA-Seq data dgat1-1.txt


title: WT 16DAF rep1

description: RNA-Seq data dgat1-1.txt


title: WT 12DAF rep1

description: RNA-Seq data dgat1-1.txt


title: KR_4


title: WT 16DAF rep2

description: RNA-Seq data dgat1-1.txt


title: H3K4me1_WT_e13.5_Input

city: Davis

first: Alex

middle: S.

last: Nord

address: 1544 Newton Court

department: Center for Neuroscience

institute: University of California Davis

description: H3K4me1 WT e13.5 Input

data_processing:
Alignment to the mouse genome (mm9) was performed on QC'd and adapter-trimmed reads (TrimGalore version 0.4.4-0.5.0) using bwa (0.7.16a). Duplicate removal and post-processing was carried out with Samtools (1.8-1.9)
Individual and differential peaks (bed) were called with MACS2 (2.1.1-2.1.2).
Binding coverage (bigWig) was determined using DeepTools (2.5-3.1).
bigWig files containing coverage, and bed files containing MACS2 peak calls.
Genome_build: mm9

source_name: ganglionic eminences

extract_protocol:
Transcription factor ChIP was performed using rabbit DLX1, DLX2 and DLX5 antibodies described in the paper. Basal ganglia (consisting of LGE, MGE and CGE progenitor and mantle zones) were dissected from e13.5 CD1 embryos, fixed in formaldehyde and lysed with a hypotonic buffer to obtain the nuclei; these were then lysed in 1% SDS buffer and the chromatin was sheared into 300-1000 bp fragments by sonicating using a bioruptor (Diagenode). Immunoprecipitation (IP) reactions were performed with the sheared chromatin diluted 1/10 times with dilution buffer usually in 6 ml.  Antibody was then added: 5 µg DLX specific Ab. Negative control CHIP reactions used either rabbit IgG (5µg) or blocking peptide (DLX antigen used for immunizing rabbits; 50x molar excess).  Antibody/chromatin complexes were purified using Dynabeads (Invitrogen) and washed extensively in wash buffer. Complexes were eluted, reverse crosslinked, treated with RNase  and Proteinase K and cleaned using a ChIP DNA Clean & Concentrator kit (Zymo Research). The chromatin was quality controlled (QC) using qPCR to check for enrichment of genomic DNA fragments that were expected, and not-expected, to have DLX binding.  Native histone ChIP was performed starting with ~250,000 nuclei from WT and Dlx1/2-/- E13.5 basal ganglia. Nuclei were extracted and digested with micrococcal nuclease (MNase, Sigma). A population of mono- and di-nucleosomes were used in Chromatin immunoprecipitation assays. Antibodies used were specific to H3 monomethyl lysine-4 (H3K4me1), H3 trimethyl lysine-4 (H3K4me3), H3 trimethyl lysine-27 (H3K27me3), and H3 acetylated lysine 27 (H3K27ac). Immunoprecipitated DNA was washed, isolated and cleaned as for the TF ChIP-Seq described above.
Libraries were prepared using an Ovation Ultralow DR Multiplex System (Nugen), size selected in the range of 300 bp on a chip from BluePippin (Sage Science) and lastly QC tested on a Bioanalyzer (Agilent). The libraries were sequenced as single 50-nucleotide reads on a HiSeq4000 (Illumina) at Center for Advanced Technology (UCSF).

tag: developmental stage


title: ribo-minus iRNAi mutant rrp41-i rep 3

city: Atlanta

first: Hsiao-Lin

middle: V.

last: Wang

state: GA

address: 615 Michael Street,, Whitehead Biomedical Research Building, Room 355,

department: School of Medicine, Department of Human Genetics

institute: Emory University

data_processing:
Each library was subjected to paired-end sequencing at 2 X 100 bp on an Illumina HiSeq2500 and demultiplex using CASAVA 1.8.2.
1. Each library was subjected to paired-end sequencing at 2 X 100 bp on an Illumina HiSeq2500 and demultiplex using CASAVA 1.8.2. The sequencing and pre-processing were performed by the Genomics Facility of the University of Chicago).
2. The RNA-seq data generated using filters to select for polyadenylated RNA and rRNA-depleted total RNA were referred to as poly(A)+ and ribo-minus datasets, respectively, in subsequent analysis. Therefore, a total of four series of RNA-seq data were generated in the study, including two types of libraries for the induced RRP41-iRNAi plants (rrp41-i) and corresponding control (RRP41). Each series contains three biological replicates (a total of 12 datasets).
3.  The Tuxedo protocol was used to map and align the RNA-seq reads in each dataset (a total of four data series, including both polyA(+) and ribo-minus) and to assemble the transcriptome. The same protocol were applied on all dataset in the four data series, including poly(A)+ and ribo-minus.
4. Custom in-house UNIX shell programming was used to bridge the subsequent steps. RNA-seq reads of each biological replicate were mapped independently to Arabidopsis TAIR10 genome assembly using the splice junction mapper TopHat (v2.0.9) with default parameters for stranded RNA-seq (--coverage-search --microexon-search --library-type=fr-firststrand).
5. The mapped reads of each biological replicate were independently assembled into transcripts using Cufflinks (v2.1.1).
6. The assembled transcripts were further processed using associated functions in the Cufflinks package (as described below). All transcripts assemblies from the same data series were processed through the Cuffmerge program. The Cuffmerge function was used to merge novel and known isoforms, and eliminating transcribed fragments (transfrags), which might be artifacts. The merged assemblies were quantified in each condition by Cuffdiff and tested for the statistical significance of each observed change in expression between induced rrp41-i and uninduced control RRP41. The differentially expressed transcripts were considered significant if the uncorrected p-value was greater than the false discovery rate after Benjamini-Hochberg correction for multiple-testing.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: bed file of raw abundance measurements per PE region for both forward and reverse RNA expression in bed file format. Column information: chromosome, start, strop, PE_ID, midpoint, strand, forward_RNA_Exp, reverse_RNA_Exp.

source_name: ribo-minus iRNAi mutant rrp41-i

extract_protocol:
The inducible RNA interference (iRNAi) line (rrp41-i) targeting the exosome subunit gene RRP41 (RRP41-iRNAi) was described in the associated publication. To induce iRNAi against RRP41, the seedlings were germinated and grown for 7 days on 1/2 MS plates with 8 mM 17b-estradiol, as described in the associated publication, the induced material/seedlings/sample is referred to as rrp41-i. The uninduced seedlings were referred to as RRP41 (WT), as the control for rrp41-i.
Three biological replicates, consisting of 7-day old seedlings, were prepared using the RRP41-iRNAi line. Two sets of samples, both the induced (rrp41-i) and the uninduced corresponding control (RRP41), were collect. Total RNA was extracted from each biological replica and polyadenylated RNA (poly(A)+) was prepared using the TruSeq Stranded mRNA Library Preparation Kit (catalog number: RS-122-2101, Illumina). The rRNA-depleted total RNA (ribo-minus) was prepared from the same total RNA sample using TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Plant (catalog number: RS-122-2401, Illumina).

value: induced iRNAi sample

value: 7-day old seedlings

tag: rna filtering

value: rRNA-depleted total RNA (ribo-minus)


title: H3K4me3_KO_e13.5_ChIP

description: H3K4me3 KO e13.5 ChIP

value: Abcam, ab8580

value: KO


title: H3K4me1_WT_e13.5_ChIP

description: H3K4me1 WT e13.5 ChIP

value: Abcam, ab8895


title: H3K4me3_WT_e13.5_ChIP

description: H3K4me3 WT e13.5 ChIP


title: H3K27me3_KO_e13.5_ChIP

description: H3K27me3 KO e13.5 ChIP


title: H3K27me3_WT_e13.5_ChIP

description: H3K27me3 WT e13.5 ChIP


title: H3K4me1_KO_e13.5_ChIP

description: H3K4me1 KO e13.5 ChIP


title: histone_WT_e13.5_Input

description: histone WT e13.5 Input


title: ribo-minus iRNAi mutant rrp41-i rep 2


title: H3K27ac_WT_e13.5_ChIP

description: H3K27ac WT e13.5 ChIP

value: Abcam, ab472


title: Cont_7

description: Control for KN1 (also known as Cont_72 below)


title: ribo-minus iRNAi mutant rrp41-i rep 1


title: Cont_3

description: Control for LR


title: WT 12DAF rep3

description: RNA-Seq data dgat1-1.txt

value: Columbia

value: Seed


title: ribo-minus control RRP41 rep 3

source_name: ribo-minus control RRP41

value: uninduced corresponding control


title: histone_KO_e13.5_Input

description: histone KO e13.5 Input


title: ribo-minus control RRP41 rep 2


title: H3K27ac_KO_e13.5_ChIP

description: H3K27ac KO e13.5 ChIP


title: polyA(+) iRNAi mutant rrp41-i rep 3

source_name: polyA(+) iRNAi mutant rrp41-i

value: polyadenylated RNA (poly(A)+)


title: Dlx5_BG_e13.5_Input

description: Dlx5 e13.5 Input


title: Dlx5_BG_e16.5_ChIP

description: Dlx5 e16.5 ChIP

value: lab-made (described in paper)


title: ribo-minus control RRP41 rep 1


title: WT 8DAF rep2

description: RNA-Seq data dgat1-1.txt

value: 8 days after flowering (DAF)


title: Dlx5_BG_e13.5_ChIP

description: Dlx5 e13.5 ChIP


title: polyA(+) iRNAi mutant rrp41-i rep 1


title: Dlx5_BG_e11.5_ChIP

description: Dlx5 e11.5 ChIP


title: Dlx2_BG_e16.5_ChIP

description: Dlx2 e16.5 ChIP


title: polyA(+) control RRP41 rep 2

source_name: polyA(+) control RRP41


title: polyA(+) control RRP41 rep 1


title: Dlx2_BG_e13.5_Input

description: Dlx2 e13.5 Input


title: Dlx2_BG_e13.5_ChIP

description: Dlx2 e13.5 ChIP


title: Dlx2_BG_e11.5_ChIP

description: Dlx2 e11.5 ChIP


title: BG_e16.5_Input

description: BG e16.5 Input


title: Dlx1_BG_e13.5_Input

description: Dlx1 e13.5 Input


title: Dlx1_BG_e13.5_ChIP

description: Dlx1 e13.5 ChIP


title: Dlx1_BG_e11.5_ChIP

description: Dlx1 e11.5 ChIP


title: polyA(+) iRNAi mutant rrp41-i rep 2


title: RNA-seq_KO_rep4

description: Dlx1/2 knock-out e13.5

data_processing:
Base calls were performed with bcl2fastq2.
FASTQ files were aligned to the mouse genome (mm9) using STAR (2.4.2a).
Genome_build: mm9

extract_protocol:
Total RNA from four embryos (e13.5, 2 males and 2 females) of either WT or Dlx1/2-/- was purified using RNeasy Mini Kit (Qiagen). The DNAse treated RNA was checked on Bioanalyzer and concentration was measured.
RNA sequencing libraries were generated using TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Mouse, according to the manufacturer’s protocol (Illumina, San Diego, CA, USA). Fragment size distribution was assessed using the Bioanalyzer 2100 and the DNA high-sensitivity chip (Agilent). Concentration of the libraries was measured using the Kapa library quantification kit (Kapa Biosystems, Woburn , MA, USA). Libraries were multiplexed, sequenced on the HiSeq 4000 and generated, roughly 814 million single-end 50bp reads.


title: bone human Mac DMSO 2

city: Cambridge

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were trimed with 8 bases in 5-prime and aligned to the human genome using Tophat2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: mm10 or hg19
Supplementary_files_format_and_content: tab-delimited text files include count values for each sample

source_name: bone

growth_protocol: mouse and human macrophages were sorted by flow cytometry based on expression of hCD45-F4/80+CD11b+ and hCD45+CD14+

extract_protocol:
Qiagen RNeasy Micro Kit
SMARTer Universal Low Input RNA Kit

value: macrophages

tag: patient

value: donor 2

value: DMSO

value: bone


title: spleen human Mac CTX 1

source_name: spleen

value: donor 1

tag: treatment

value: CTX

value: spleen


title: spleen human Mac DMSO 2


title: spleen human Mac DMSO 1


title: spleen human Mac CTX 2


title: bone human Mac CTX 1


title: RNA-seq_KO_rep2

description: Dlx1/2 knock-out e13.5


title: bone human Mac CTX 2


title: bone human Mac DMSO 1


title: polyA(+) control RRP41 rep 3

value: 7-day old seedlings


title: RNA-seq_KO_rep1

description: Dlx1/2 knock-out e13.5

value: KO


title: c26_5Hetero

city: seoul

first: Hyun-Seob

last: Lee

address: 71 Daehak-ro, Jongno-gu

department: Biomedical research institute

institute: Seoul national University Hospital

data_processing:
Illumina Casava1.9 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence (over Q10), then mapped to hg19  UCSC  using Transcriptome with novel splices
Fragments Per Kilobase of exon per Million (FPKM) were performed using cufflinks.
Genome_build: UCSC (hg19)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: ESCs

growth_protocol: All human ESC lines were grown on matrigel- with mTESR1-human ES medium.

extract_protocol:
total RNA were isolated from hESCs using Trizol reagent.  Lexogen SENSE total RNA Library Preparation Kit was used with 1 ug of total RNA for the construction of sequencing libraries..
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCs


title: c42_WT

value: Wild Type


title: Dlx1_BG_e16.5_ChIP

description: Dlx1 e16.5 ChIP

value: WT


title: RNA-seq_WT_rep4

description: Wild-type e13.5


title: PRMT3_rep2

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

description:
PRMT3merge_inputmerge_q0.01_peaks.txt
s4

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
Whole or any subsets of adaptor sequences were trimmed at 3'- end of the reads.
Clean reads were aligned to refference genome (hg19) using BWA.
Duplication reads were removed by MACS(v2) software.
Unique mapped and non-duplication reads were used to call peaks by MACS(v2) software
Genome_build: hg19
Supplementary_files_format_and_content: peak.txt files include the peaks called by MACS(v2)
Supplementary_files_format_and_content: bedgraph files include the information of modification enrichment which could be visualised in IGV software.

source_name: mesenchymal stem cell

growth_protocol: rimary hMSCs were purchased from ScienCell Research Laboratories (Carlsbad, CA, USA). Cells at passage 3 from 3 independent donors were used for the assays. Proliferation media (DMEM; 10% fetal bovine serum; 1% penicillin/streptomycin) and osteogenic media [Proliferation media containing 100 nM dexamethasone (Sigma-Aldrich, St. Louis, MO, USA), 0.2 mM ascorbic acid (Sigma-Aldrich), and 10 mM β-glycerophosphate (Sigma-Aldrich)] were used for cell culture and osteogenic induction respectively.

extract_protocol: Briefly, cells were cross-linked with 1% formaldehyde, resuspended in lysis buffer (1% SDS, 10 mM EDTA, and 50 mM Tris-HCl [pH 8.0]) on ice for 3 min, and fragmented by sonication in RIPA ChIP buffer (0.5 mM EGTA, 140 mM NaCl, 10 mM Tris-HCl, pH 7.5, 1% TritonX-100, 0.01% SDS, 1 mM EDTA and protease inhibitor). The samples were then incubated overnight with Protein A/G-beads bound with antibodies [PRMT3 (Abcam, Cambridge, UK), H4R3me2a (Active Motif, Carlsbad, CA), H3 (Cell Signaling)]. After the crosslinking was reversed, immune complexes containing DNA were purified and eluted. The precipitated DNA for sequencing, including H4R3me2a and PRMT3, were constructed into libraries with NEBNext DNA Library Prep Reagent Set for Illumina (NEB) as described by the manufacturer.

value: mesenchymal stem cell

value: PRMT3 (Abcam, Cambridge, UK)


title: RNA-seq_WT_rep2

description: Wild-type e13.5


title: RNA-seq_WT_rep1

description: Wild-type e13.5


title: H4R3_input


title: PRMT3_input


title: RNA-seq_WT_rep3

description: Wild-type e13.5


title: BG_e11.5_Input

description: BG e11.5 Input


title: RNA-seq_KO_rep3

description: Dlx1/2 knock-out e13.5


title: c38_Homo


title: PRMT3_rep1

description:
PRMT3merge_inputmerge_q0.01_peaks.txt
s3