title: Exp2_PolII_Vehicle

city: Bethesda

first: Pablo

last: Sandoval

state: Maryland

address: 31 Center Dr

department: NHLBI

institute: NIH

data_processing:
Align and transform the .fastq to .sam files using BWA program and mm10 mouse genome:  bwa samse mm10.fa sample7.sai sample7.fastq > sample7.sam bwa aln -t 8 mm10.fa  sample7.fastq > sample7.sai.
Convert format from Sam to Bam and index the files using Samtools: Samtools view –bhS sample7.sam > sample7.bam, samtools sort V1_mm10.bam V1_mm10.sorted; samtools index V1_mm10.sorted.bam.
Create bedgraph files using genomeCoverageBed -ibam Exp3_Vehicle.bam -bg -trackline -g mm10.chrom > Exp3_Vehicle.bedGraph
Create a coverage txt file using coverageBed -abam JP001_1_AAGGGA_L007_R1_concatenated.bam -b all_genes_refseq.bed > IGG_EXP1_dDAVP_coverage.txt
The IGG coverage txt was used to filter out the genes with low signal to noise
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph and txt files

source_name: mpkCCD cells

growth_protocol: Cultured mouse mpkCCD (clone 11) cells were grown as previously described (Yu MJ, Proc Natl Acad Sci U S A 106:2441-2446, 2009). After initial growth in flasks (at least 3 days) containing complete medium (DMEM/F12; containing 2% dialyzed serum), cells were transferred to permeable supports (Transwell), and grown until confluency as documented transepithelial resistance measurements (Epithelial Volt ohmmeter; WPI). At that point, the serum was removed, and cells were maintained for one more day in serum-free medium. The V2 receptor-selective vasopressin analog dDAVP (0.1 nM) or its vehicle was included throughout the entire procedure.  Cells were harvested 24 hr after serum removal.

extract_protocol:
The mpkCCD cells cross-linking (formaldehyde 1.11%), nuclei were isolated and then sheared into approximately 300-bp fragments (Covaris S2 SonoLAB).  Samples underwent chromatin immunoprecipitation  (SimpleChIP protocol (#9003, Cell Signaling Technology) using the anti-Polr2a antibody (Catalog #: MMS-126R, Covance). After the ChIP step, crosslinking was reversed and samples were processed for library construction.
The libraries were made using an Ovation Ultralow Library System (NuGen).  cDNAs ranging from 200 to 400 bp were selected on 2% agarose gel and sequenced on a HiSeq2000 platform (Illumina) to generate 50-bp  FASTQ sequences.  The raw FASTQ sequences were mapped to the mouse Reference Genome (mm10) using the Burrows-Wheeler Aligner  (BWA).

tag: cell type

value: cultured mouse collecting duct cells (mpkCCD)

tag: passages

value: transformed mouse renal principal cells

value: anti-Polr2a antibody (Catalog #:MMS-126R, Covance)

tag: treatment

value: wehicle


title: Exp3_PolII_dDAVP

status: Public on Jul 01 2016

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: chip antibody

value: dDAVP (0.1 nM)


title: Exp3_PolII_Vehicle


title: IGG_Vehicle_exp3

value: anti-IGG antibody (Catalog #:2729)


title: Exp1_PolII_dDAVP


title: P0 Cochlea DMSO GFP- 2

city: Houston

first: Andrew

last: Groves

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description: mRNA enriched ds cDNA was sequenced paired end

library_source: transcriptomic

data_processing:
RNA-seq reads were mapped to the mouse reference genome (mm9) using TopHat (v1.4.0) with default parameters except -G Ensembl GTF gene annotation.
Read counts for each gene were determined using htseq -count (python) function.
Reads were normalized across samples using DESeq Bioconductor package (v1.9.2).
Genome_build: mm9
Supplementary_files_format_and_content: Text files inclue read counts value for each gene; individual file for each sample.

molecule: total RNA

source_name: Purified LFng-GFP- cells from P0 mouse cochlea cultured for 24 hours in DMSO

growth_protocol: P0 and P5 cochleas were cultured in DMEM/F12 (buffered with Hepes; Thermo Fisher Scientific) supplemented with B27 (Thermo Fisher Scientific), 1mM N-acetylcysteine (Sigma), 5 ng/ml EGF and 2.5 ng/ml FGF2 and 67 µg/ml penicillin. For Notch inhibition experiments, cultures were treated with 10µM DAPT (Gamma secretase inhibitor IX, Calbiochem EMD) or 0.04% v/v DMSO (vehicle control; Thermo Fisher Scientific) for 24 hours

extract_protocol:
Total RNA was extracted using Trizol (Thermo Fisher Scientific) and PelletPaint (Novagen EMD Millipore). Briefly, samples were homogenized in 300µl of Trizol and shaken with 60µl chloroform and 2µl PelletPaint and centrifuged for 15 minutes. The supernatant containing RNA was precipitated with 1 volume of isopropanol, centrifuged for 30 minutes, washed in 75% ethanol, resuspended in 100µl water and re-precipitated with 10µl 3M sodium acetate and 250µl ethanol. After a final wash in 75% ethanol, the pellet was allowed to dry, resuspended in 20µl RNAse-free water and stored at -80°C.
cDNA libraries for RNAseq were generated using RNA Seq Truseq RNA sample preparation kit v2 (Illumina) following the “low sample” protocol according to the manufacturer's instructions for mRNA extraction, cDNA synthesis, indexing and amplification. cDNA generated from less than 20,000 cells received an initial amplification using the NuGen Ovation Kit.  The quality and integrity of RNA samples and the final quality of the sequencing libraries was checked by electrophenogram in an Agilent Bioanalyzer.
paired end 100bp sequencing

tag: agent

value: DMSO

value: LFng-GFP BAC Transgenic Mouse (B6;FVB-Tg(Lfng-EGFP)HM340Gsat/Mmucd)

tag: tissue type

value: P0  cochlea


title: Exp1_PolII_Vehicle


title: 1_oWT_10dBNF_2

city: Amsterdam

first: Martijn

last: Koppens

address: Plesmanlaan 121

department: Molecular Genetics

country: Netherlands

institute: NKI-AVL

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 0.12.9/1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Prior to analysis the provided processed data files were only normalized for sequencing depth, using the DESeq2 package, and normalized for batch effects (ex: sequencing run) if necessary using ComBat, as described in the paper.
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples; format: 2 tab-separated text files corresponding to the two sequencing runs, 385 and 440

source_name: oWT_10dBNF_small intestinal organoids

extract_protocol:
RNA was harvested from samples using TRIzol and further purified using the Qiagen MinElute Cleanup Kit.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E).

treatment_protocol: Organoids were grown from either isolated AhCre or AhCre;Eedf/f crypts and treated with bNF for 10 days, after which the organoids were removed from Matrigel with ice-cold medium, washed, and lysed in TRIzol.

tag: strain background

value: FVB

tag: genotype/variation

value: WT

tag: treated with

value: beta-naphthoflavone for 10 days

tag: tissue/cell type

value: small intestinal organoids

tag: run id

value: Run 385


title: IGG_Vehicle_exp2


title: IGG_dDAVP_exp3


title: 1_oWT_10dBNF_1


title: IGG_dDAVP_exp2


title: mpkCCD cells, DDAVP #8

data_processing:
Reads were mapped to mm10 genome using STAR 2.4.0.1
Samtools was used to process SAM, BAM, and BED files.
Reads mapping to RefSeq transcripts were counted using HTSeq-count
Transcripts per million (TPM) were calculated for each gene.
Genome_build: mm_10 refseq

growth_protocol: All experiments were performed in mpkCCD11 cells as previously described (Yu MJ). Briefly, cells were expanded to ~80% confluence on 25-cm2 plastic flasks (Corning), trypsinized (0.05% trypsin, 1.5 mM EDTA) and resuspended in 10 ml DMEM/F12, and then seeded on permeable supports (75-mm2 diameter, 0.4-μm pore size, Corning) at a ratio of 1:10 and grown in 1:1 DMEM/F12 (Invitrogen) containing 2% fetal bovine serum, insulin, dexamethasone, triiodothyronine, epidermal growth factor, selenium, and transferrin. Once cells reached confluence demonstrated by a transepithelial resistance (RTE) of ≥5 KΩ·cm2

extract_protocol:
Confluent mpkCCD cell monolayers were washed in ice-cold 1X PBS (Ca+2/Mg+2-free), total RNAs were isolated using QIAGEN RNeasy-mini and eluted in 50 uL of RNase-free water.
Library construction was performed on a NuGEN Mondrian SP+ instrument (NuGEN, San Carlos, CA) using the protocol and reagents outlined in the Ovation SP Ultralow Library Systems kit. Libraries were then enriched via PCR. Libraries were sequenced using an Illumina Hiseq2000 instrument to obtain single read data. For RNA-seq, 20 nanograms of total RNAs were used to start reverse transcription. RNA-seq library preparation was performed following a previously reported protocol for single-cell RNA-seq (Tang F, Nat Protoc 2010, PMID 20203668).
libraries were sequenced using an Illumina HiSeq 2000 machine to obtain 50-bp-long single-end sequences.

treatment_protocol: They were maintained in serum-free medium for 24 h prior to treatment with or without 0.1 nM dDAVP in serum-free medium for 24 h.

value: 0.1 nM dDAVP


title: IGG_Vehicle_exp1


title: mpkCCD cells, DDAVP #9


title: mpkCCD cells, DDAVP #5


title: mpkCCD cells, DDAVP #2


title: mpkCCD cells, DDAVP #6


title: mpkCCD cells, DDAVP #4


title: mpkCCD cells, control #9


title: mpkCCD cells, DDAVP #3


title: mpkCCD cells, DDAVP #7


title: mpkCCD cells, control #7


title: mpkCCD cells, control #6


title: mpkCCD cells, control #4


title: mpkCCD cells, control #5


title: Exp2_PolII_dDAVP


title: mpkCCD cells, control #3


title: mpkCCD cells, control #1


title: ChIP-Seq WCE_rep2

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). Differential expression test between different groups was performed with Cuffdiff module, and genes with p-value < 0.05 were selected as differentially expressed genes. The GTF annotation files for UCSC mm9 was used for gene annotation.
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were removed by samtools. Bed alignment files were generated using bedtools. Peak calling was also performed using dfilter.
Genome_build: mm9
Supplementary_files_format_and_content: bed format for ChIP-Seq called peaks, FPKM table format for RNA-Seq differentially expressed genes

source_name: hippocampus

growth_protocol: Tissue was extracted from mice at 12 weeks old.

extract_protocol:
For ChIPseq, frozen tissue was fixed with 2mM disuccinimidyl glutarate in PBS for 35 min, 1 % formaldehyde for 10 min, and quenched with 125 mM glycine. Fixed homogenate was washed twice, douce-homogenized, and resuspend in Lysis Buffer (1 mM EDTA, 0.5 mM EGTA, 10 mM Tris pH 8.0, 0.5 % sarcosyl) and chromatin sheared using a BioruptorPlus (Diagenode Inc, NJ) set to high for 40 cycles of 30 sec on, 30 sec off. About 3 µg chromatin was precleared and ChIP was performed using 5 µg HDAC3 antibody (Abcam, ab7030) overnight, followed by enrichment using protein A sepharose beads for 4 hours. Beads were washed 4 times with RIPA buffer and once with TE, then eluted and reverse-cross linked  in TE plus 1 % SDS at 65oC. Chromatin was subjected to RNase and proteinase K treatment, followed by DNA purification by phenol chloroform extraction and ethanol precipitation. DNA pellets were resuspended in 10 mM Tris. For RNAseq, RNA wwas extracted from frozen tissue using Trizol according to manufacturers protocol (Invitrogen). RNA (3 µg) was DNase I treated (4 U, Worthington Biochemical Corporation), purified using RNA Clean and Concentrator-5 Kit (Zymo Research) according to manufacturers’ instructions and eluted with 14 µl DEPC-treated water.
RNAseq libraries were prepared and sequenced as previously described (Gjorneska et al. Nature 2015).
ChIPseq libraries were prepared and sequenced as previously described (Gjorneska et al. Nature 2015).

treatment_protocol: No treatment

tag: antibody

value: WCE


title: ChIP-Seq HDAC3_rep2

value: HDAC3 Abcam ab7030


title: mpkCCD cells, control #2


title: ChIP-Seq WCE_rep3


title: ChIP-Seq HDAC3_rep3


title: ChIP-Seq WCE_rep1


title: RNA-Seq HDAC3_KO2

value: HDAC3c KO


title: mpkCCD cells, DDAVP #1


title: IGG_dDAVP_exp1

value: cultured mouse collecting duct cells (mpkCCD)

value: transformed mouse renal principal cells


title: RNA-Seq HDAC3_KO1


title: RNA-Seq WT1


title: RNA-Seq WT2


title: mpkCCD cells, control #8


title: FDR1G

city: Brisbane

first: Shuhong

last: Gao

state: QLD

address: Research Road, St Lucia

department: Advanced Water Management Centre

country: Australia

institute: The University of Queensland

data_processing:
NGS QC Toolkit (v2.3.3) was used to do the quality control and tag removal to generate the clean sequence reads; the resulting clean reads no shorter than 75 bp were used for downstream analyses.
The cleaned sequence reads for each sample were aligned to the PAO1 reference genome (NC_002937.3) using SeqAlto
Strand-specific coverage for each gene was calculated and differential expression analysis was conducted using the cuffdiff command in Cufflinks (version 2.2.1) on triplicated cultures
Statistic analyses and visualization were conducted using the cummeRbund package in R (http://compbio.mit.edu/cummeRbund/). Gene expression was calculated as reads per kilobase of a gene per million mapped reads (RPKM), a normalized value derived from the frequency of detection and the length of a given gene (Cole Trapnell, Nature Protocols, 2012) Differences in fold-change values were calculated between control and FNA-treated samples (4 μg-N/L) by determining the log2 fold-change (LFC) of the averaged RPKM values determined from triplicate experiments run on two separate occasions.
Genome_build: NC_002937.3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Nitratidesulfovibrio vulgaris

source_name: Bacteria

growth_protocol: For all the performed experiments, a defined lactate sulfate medium (LS4D medium) was used to cultivate the culture. The anaerobic LS4D medium was prepared and then gassed in serum bottles with nitrogen gas for 30 min before capping with butyl rubber stopper for autoclave. 1.5 mL of a glycerol preserved stock of D. vulgaris was used as inoculum to the serum bottles containing 140 mL medium. These were then cultivated at 37°C for 48 h to achieve the early stationary phase of growth (optical density at 600 nm [OD600] 0.9 to 1.0). OD600 of the culture was then adjusted to 0.5 before 10 mL of this culture was transferred into 140 mL of autoclaved anaerobic LS4D medium in serum bottles inside the anaerobic chamber. The cultures were then incubated at 30°C without shaking for further use of experiments.

extract_protocol:
For the extraction 5 mL of the bacterial suspension from each serum bottle was centrifuged at 13,000 x g for 2 minutes, the supernatant was discarded and the pellets were immediately frozen in the liquid nitrogen before storing at -80ºC prior to RNA extraction. Total RNA extraction was performed using the QIAGEN miRNeasy Mini Kit (Catalog number: 217004) according to the manufacturer’s instructions except for the addition of an extra bead-beating step to ensure the complete lysis of the cells.
Strand-specific cDNA library construction

treatment_protocol: After 26 h growth at 30°C the cultures were in early log phase (OD600 around 0.3), and nitrite was added to achieve the starting FNA concentrations of 0, 1.0, 4.0, and 8.0 μg N/L. Each FNA concentration was performed in triplicate.

value: Hildenborough

tag: genotype

value: wild type

tag: incubation time

value: 27 hours incubation after the standard inoculation, that is 1 hour after FNA addition

tag: fna level

value: 4 ug-N/L


title: FDR1I


title: WT rep 2

city: Boston

first: Marie-Anne

last: Goyette

address: 450 Brookline avenue

institute: DFCI

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were aligned to the GRCm38 genome with TopHat v2.0.10
Raw alignment counts were calculated with Htseq-count v0.5.3.
Differential expression measurements were performed with DESeq2 v1.4.5
Genome_build: GRCm38
Supplementary_files_format_and_content: Text files with reads for each samples

molecule: polyA RNA

source_name: epididymal white adipose tissue

extract_protocol:
Epididymal white adipose tissue total RNA was extracted using Trizol reagent and RNA samples were further purified using RNeasy columns (Qiagen). Illumina TruSeq RNA Sample Preparation kit, Illumina TruSeq SR cluster kit v2 and Illumina TruSeq SBS kit V2 (50 cycles) was used to generate expression libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mixed genetic background

tag: tissue

value: epididymal white adipose tissue


title: WT rep 1


title: Nck2 KO rep 2

value: Nck2 mutant


title: 1374 wor1 Glu

city: Beijing

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

country: China

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling.
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) according to Mortazavi, et al., Nature Methods, 2008, and the formula is shown as follows: RPKM=106C/(NL/103). C is the number of reads that uniquely aligned to a gene, N is total number of reads that uniquely aligned to all genes, and L is the number of bases on a gene.
Genome_build: C. tropicalis MYA-3404 genome
Supplementary_files_format_and_content: Tab-delimited text file contains RPKM values.

organism: Candida tropicalis MYA-3404

source_name: wor1 deletion mutant, glucose

growth_protocol: wor1 deletion mutant cells grown in Lee's glucose or Lee's GlcNAc medium.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

value: wor1 deletion mutant

tag: medium

value: Lee's glucose


title: LIR_04-LN_EM

city: BETHESDA

first: Jianfei

last: Hu

state: MD

address: 40 CONVENT DR

department: Vaccine Research Center

data_processing:
Illumina bcl2fastq-2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 repeat-masked  genome using tophat v2.0.13 with parameters  -p 4 --coverage-search --library-type fr-unstranded
Gene transcript isoform expression level was calculated by cufflinks v2.1.1
Genome_build: hg19
Supplementary_files_format_and_content: Gene transcript isoform expression file

organism: Homo sapiens

extract_protocol:
Sorted cells were lysed and total RNA was extracted using RNAzol RT (Molecular Research Center Inc., Cincinnati, OH). Poly-adenylated RNA was purified using Dynabeads oligo (dT)25 (Invitrogen, Carlsbad, CA) and fragmented
cDNA was synthesized and Illumina-ready libraries were generated using a modified Illumina TruSeq mRNA Library preparation protocol (paired end HiSeq 2x75 reads)

tag: cell type

tag: status

value: ex vivo; unstimulated

tag: sorting phenotype


title: LIR_04-LN_Tfh


title: FDR1B

tag: strain

value: 27 hours incubation after the standard inoculation


title: 1374 wor1 GlcNAc

source_name: wor1 deletion mutant, GlcNAc

value: Lee's GlcNAc


title: FDR1A


title: Argonaute IP

city: Munich

first: Anne

last: Dueck

state: Bavaria

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

country: Germany

institute: TUM

description: small RNA sequencing data

data_processing:
sequenced on a MiSeq; Kit version V1 1 x 50; 66x sequencing cycles
analysis pipeline: Miseq Control Software: Version 2.0.5; RTA-Version: 1.16.18; MiSeq Reporter: Version 2.0.26; MiSeq Recipes: 2.0.0.1
Barcode splitting was performed by the Illumina software; adapter trimming was performed using custom scripts.
Reads were mapped to V.carteri genome assembly using tophat.
Genome_build: Phytozome 9.0 v2.0
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads

organism: Volvox carteri

source_name: whole colonies (somatic cells and reproducitve cells (gonidia))

growth_protocol: Volvox carteri strain Vol6 was cultured under standard conditions.

extract_protocol:
myc-tagged Argonaute was transformed into vegetative growing Volvox carteri, strain Vol6. Colonies were pelleted and sheared to dissociate the cells from the extracellular matrix. After centrifugation, cells were lysed in lysis buffer with additional sonication. The immunoprecipitation (IP) was performed using the cleared lysate with anti-myc antibodies. After washing of the IP, the RNA was recovered by performing first a Proteinase K digest followed by a phenol/chloroform extraction. The RNA was precipiated over night with Ethanol, recovered by centrifugation and solved in ultra-pure water.
The Library was constructed according to Illumina's TruSeq small RNA cloning kit using the following adapters:  5′adapter 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; 3′adapter Phospho-TGGAATTCTCGGGTGCCAAGG-Amino-C7. The index was added by PCR later in the protocol: Used index:  Sample 1=Index 12; 5' PCR primer 5'-AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGA-3'; 3' PCR primer 5'-CAAGCAGAAGACGGCATACGAGATTACAAGGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3'

tag: developmental stage

value: vegetative (asexual)

value: Argonaute protein was myc-tagged


title: LIR_04-LN_nGC


title: ChIP-Seq HDAC3_rep1

value: WT

value: HDAC3 Abcam ab7030


title: LIR_04-PBMC_EM


title: LIR_04-LN_N


title: LIR_04-PBMC_TM


title: LIR_04-PBMC_CM


title: LIR_04-LN_CMPD1lo


title: LIR_03-LN_CMPD1lo57lo


title: Nck2 KO rep 1


title: LIR_03-LN_N


title: LIR_03-LN_nGC


title: LIR_03-LN_EM


title: LIR_04-PBMC_N


title: LIR_03-PBMC_EM


title: FDR1H


title: FDR1C


title: LIR_03-PBMC_CM


title: LIR_03-PBMC_TM


title: LIR_03-LN_Tfh


title: LIR_02-LN_nGC


title: LIR_02-LN_EM


title: LIR_03-PBMC_N


title: LIR_02-LN_CMPD1lo57hi


title: LIR_02-PBMC_TM


title: LIR_02-LN_N


title: LIR_02-PBMC_EM


title: LIR_02-PBMC_CM


title: LIR_02-LN_CMPD1lo57lo


title: LIR_01-LN_EM


title: LIR_01-LN_Tfh


title: LIR_01-LN_CMPD1lo57hi


title: LIR_01-PBMC_EM


title: LIR_01-LN_nGC


title: LIR_01-PBMC_TM


title: LIR_01-PBMC_CM


title: SCOPE_14952014-PBMC_TM


title: VRC200_907-PBMC_EM


title: SCOPE_14952014-PBMC_CM


title: LIR_01-PBMC_N


title: LIR_01-LN_N


title: VRC200_907-PBMC_N


title: LIR_01-LN_CMPD1lo57lo


title: VRC200_907-PBMC_TM


title: SCOPE_1270-PBMC_EM


title: SCOPE_14952014-PBMC_EM


title: SCOPE_1270-PBMC_TM


title: SCOPE_1788-PBMC_EM


title: VRC200_907-PBMC_CM


title: LIR_02-LN_Tfh


title: SCOPE_1270-PBMC_CM


title: SCOPE_14952014-PBMC_N


title: LIR_02-PBMC_N


title: SCOPE_1349-PBMC_EM


title: SCOPE_1788-PBMC_TM


title: SCOPE_1788-PBMC_N


title: SCOPE_1349-PBMC_TM


title: SCOPE_1349-PBMC_N


title: SCOPE_1270-PBMC_N


title: SCOPE_1349-PBMC_CM


title: SCOPE_1788-PBMC_CM


title: SCOPE_1541-PBMC_N


title: SCOPE_1541-PBMC_TM


title: SCOPE_1541-PBMC_CM


title: SCOPE_1548-PBMC_CM


title: SCOPE_1541-PBMC_EM


title: SCOPE_1548-PBMC_TM


title: SCOPE_1548-PBMC_N


title: SCOPE_14952010-PBMC_N


title: SCOPE_14952010-PBMC_EM


title: SCOPE_1492-PBMC_TM


title: SCOPE_14952010-PBMC_CM


title: SCOPE_1492-PBMC_EM


title: SCOPE_1492-PBMC_N


title: SCOPE_1492-PBMC_CM


title: VRC200_912-PBMC_TM


title: SCOPE_1475-PBMC_TM


title: VRC200_912-PBMC_N


title: SCOPE_14952010-PBMC_TM


title: VRC200_912-PBMC_EM


title: VRC200_912-PBMC_CM


title: SCOPE_1475-PBMC_CM


title: SCOPE_1548-PBMC_EM


title: SCOPE_1475-PBMC_N


title: SCOPE_1475-PBMC_EM


title: US-1421579_MK0646+MK8669_R1

city: Rochester

first: Marc

middle: A

last: Becker

state: MN

address: 200 First St SW

department: Medical Oncology

institute: Mayo Clinic

data_processing:
Next-generation sequencing was performed using the Illumina HiSeq 2000 platform.
RNA-seq data was analyzed with Partek Flow 3.0.
Reads were mapped to the human genome (Ensembl GRCh37) and quantified using the STAR aligner.
Aligned reads to genes using Partek E/M.
Differentially expressed genes determined using gene-specific analysis (GSA).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Xenograft tumor tissue

extract_protocol:
Xenograft tumors were rapidly excised, weighed and preserved in RNA Later (Invitrogen Life Technologies, Carlsbad, CA, USA). Total RNA was isolated using Trizol reagents (Cat#15596-026, Invitrogen, Carlsbad, CA). RNA integrity was confirmed using the Agilent 2100 Bioanalyser (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: time

value: Post treatment (Day 28)

tag: treatment


title: US-1419278_MK0646+MK8669_R2


title: US-1418854_MK8669_R1


title: US-1419317_MK0646_R3


title: US-1419319_MK0646_R1


title: US-1419285_MK8669_R2


title: US-1419253_MK0646_R2


title: US-1419309_LET+MK8669_R12


title: US-1419284_LET+MK8669_R11


title: US-1419271_LET+MK8669_R10


title: US-1419318_MK8669_R3


title: US-1419251_LET+MK8669_R8


title: US-1419236_LET+MK8669_R6


title: US-1419226_LET+MK8669_R5


title: US-1418923_LET+MK8669_R4


title: US-1419267_LET+MK8669_R9


title: US-1418864_LET+MK8669_R2


title: US-1418887_LET+MK8669_R3


title: US-1419241_LET+MK8669_R7


title: US-1418834_LET+MK8669_R1


title: US-1419315_LET+MK8669+MK0646_R7


title: US-1419312_MK0646+MK8669_R3


title: US-1419233_LET+MK8669+MK0646_R5


title: US-1419323_LET+MK8669+MK0646_R8


title: US-1418883_LET+MK8669+MK0646_R3


title: US-1418872_LET+MK8669+MK0646_R2


title: US-1418916_LET+MK8669+MK0646_R4


title: US-1418838_LET+MK8669+MK0646_R1


title: US-1419246_LET+MK0646_R3


title: US-1419235_LET_R2

value: LET


title: US-1419325_LET+MK0646_R2


title: US-1418862_LET_R3


title: US-1418847_Control_R7

value: Control


title: US-1419337_Control_R10


title: US-1419328_Control_R9


title: US-1419247_LET+MK0646_R1


title: US-1418890_LET_R1


title: US-1418826_Control_R4


title: US-1418845_Control_R6


title: US-1418825_Control_R2


title: US-1418907_Control_R1


title: US-1418837_Control_R5


title: US-1419330_Control_R3


title: US-1421650_LET+MK8669+MK0646_R9


title: US-1419275_LET+MK8669+MK0646_R6


title: D2DJAACXX_1

city: Ann Arbor

first: Ryan

last: Mills

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
Prior to adapter removal, an ambiguous nucleotide at the first position in human neuroblastoma ribosome profiling reads was trimmed.
Human neuroblastoma ribosome profiling reads were trimmed of adapters according to previously published methods (Ingolia, 2014).
For clipping, the following parameters of fastx_clipper were used:
-Q33 -a CTGTAGGCACCATCAAT -l 24 -c -n -v
For trimming, the following parameters of fastx_trimmer were used:
-Q33 -f 2 -m 24
Trimmed reads were aligned to a ribosomal RNA database, and unmapped reads were then aligned to the Ensembl v78 human transcriptome and genome reference using TopHat  v2.10.0 with the following parameters:
--bowtie1 --no-novel-juncs --library-type fr-unstranded --solexa-quals
Aligned reads were filtered based on a minimum mapping quality of filter of 10 using samtools v0.1.18 with the following parameters:
-b -q 10
The relative abundance of ribosome-protected fragments over each transcript was calculated using Cufflinks v2.1.1 with default parameters.
Genome_build: Ensembl v78 (GRCh38)
Supplementary_files_format_and_content: Tab-delimited gene and isoform-level output from Cufflinks.

source_name: Neuroblastoma cells

growth_protocol: The neuroblastoma SH-SY5Y cells were plated on 140mm dishes and allowed to propagate to 80% confluency.

extract_protocol:
Lysates from two plates were combined, RNase I treated, and the ribosome fraction of 300uL of lysate was extracted with a 1M sucrose cushion and high speed centrifugation.
RNA footprints in the range of 26-34nt were gel extracted, rRNA was depleted using the Ribo-Zero rRNA Removal Kit (Illumina), and the remaining RNA served as the template for constructing the amplified cDNA library. Sequencing was performed in a single lane on an Illumina HiSeq2000 with 50 cycles of single-end reads at the University of Michigan DNA Sequencing Core.

treatment_protocol: Cells were washed with PBS supplemented with cycloheximide (100ug/ml), then flash frozen and lysed on plate in the presence of cycloheximide in 500uL of ice-cold lysis buffer.

value: SH-SY5Y neuroblastoma cells


title: H3K36me3

city: Palo Alto

first: Li

last: Zhu

state: CA

address: 265 Campus Drive, Rm. G2035

department: Pathology

institute: Stanford University

data_processing:
Sequencing reads were mapped to the human reference genome (hg19) using Bowtie with parameters: -v 2 -k 2 -m 1 --best --strata.
Clonal reads were removed before enriched peaks/regions calling with MACS version2.1.0.
Enriched regions (fold-change ≥ 5) were filtered with false discovery rate ≤ 0.01 to be considered as statistically significant ChIP peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files represent statistically mapped ChIP-seq reads and scores were assigned for each mapped reads

source_name: MV4-11 human leukemia cells

extract_protocol:
Whole genome ChIP using MV4-11 cells was performed under conditions described previously (Boyer et al., 2005) using 2-4×107 cells per IP with specific antibodies
ChIP-seq libraries were prepared according to the Illumina protocol and sequenced using Illumina HiSeq.  Sequencing was carried out at the Stanford Genome Center using Illumina HiSeq 2000. The read length is 50bp.

value: H3K36me3 (Abcam ab9050)


title: LEDGF

value: LEDGF (Bethyl Laboratories A300-848A)


title: ASH1L

value: ASH1L (Bethyl Laboratories A301-749A)


title: MLLn

value: MLLn (Bethyl Laboratories A300-086A)


title: AF4

value: AF4 (Michael Cleary Lab C2-1)


title: H3K36me2

value: H3K36me2 (Active Motif 39255)


title: MLLc

value: MLLc (Millipore 05-765)


title: US-1418878_Control_R8


title: input


title: GR-KAN1.0.3_dexamethasone

city: Stanford

first: Samuel

last: Hokin

state: California

address: 260 Panama St

department: Plant Biology

institute: Carnegie Institution for Science

description:
Ot7960
Col KANADI1-GR

data_processing:
Alignment to genome with TopHat v2.0.10,  parameter --no-novel-juncs
Transcript abundances with Cufflinks
Merge transcript abundances with Cuffmerge
Determine differential expression with Cufflinks
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with geometric normalized FPKM values

organism: Arabidopsis thaliana

source_name: GR-KAN1 seedling, 0 mins, rep 3

growth_protocol: Seeds were surface sterilized in bleach and rinsed multiple times in sterile water.  Following two days of stratification at 4 degrees in the dark,50 seeds each were transferred to 250 ml ehrlenmeyer flasks containing 50 mls of sterile MS medium and capped loosely with aluminum foil.  Flasks were swirled gently on a platform shaker placed under a bank of cool white fluorescent lamps.

extract_protocol:
Frozen tissue was ground to a fine powder in liquid nitrogen and mRNA was extracted using Quiagen's RNEasy kit.
oligo dT primed cDNA was used as the basis for a library made using standard Illumina protocols.

treatment_protocol: After seven days of growth, dexamethazone was added to a final concentration of 50 microMolar to each flask. Plants were quickfrozen in liquid nitrogen 0, 30, 60 and 120 minutes after addition of dexamethazone.

tag: ecotype

value: Columbia

value: Dexamethasone

value: 0 mins

value: seedling


title: GR-KAN1.0.1_dexamethasone

description:
Ot7958
Col KANADI1-GR

source_name: GR-KAN1 seedling, 0 mins, rep 1


title: GR-KAN1.0.2_dexamethasone

description:
Ot7959
Col KANADI1-GR

source_name: GR-KAN1 seedling, 0 mins, rep 2


title: GR-KAN1.60.2_dexamethasone

description:
Ot7965
Col KANADI1-GR

source_name: GR-KAN1 seedling, 60 mins, rep 2

value: 60 mins


title: GR-KAN1.30.3_dexamethasone

description:
Ot7963
Col KANADI1-GR

source_name: GR-KAN1 seedling, 30 mins, rep 3

value: 30 mins


title: GR-KAN1.30.1_dexamethasone

description:
Ot7961
Col KANADI1-GR

source_name: GR-KAN1 seedling, 30 mins, rep 1


title: GR-KAN1.60.3_dexamethasone

description:
Ot7966
Col KANADI1-GR

source_name: GR-KAN1 seedling, 60 mins, rep 3


title: GR-KAN1.120.1_dexamethasone

description:
Ot7967
Col KANADI1-GR

source_name: GR-KAN1 seedling, 120 mins, rep 1

value: 120 mins


title: GR-REV.120.3_dexamethasone

description:
Ot7957
Col GR-REVOLUTA

source_name: GR-REV seedling, 120 mins, rep 3

value: GR-REVOLUTA


title: GR-REV.60.2_dexamethasone

description:
Ot7953
Col GR-REVOLUTA

source_name: GR-REV seedling, 60 mins, rep 2


title: GR-KAN1.120.2_dexamethasone

description:
Ot7968
Col KANADI1-GR

source_name: GR-KAN1 seedling, 120 mins, rep 2


title: GR-KAN1.60.1_dexamethasone

description:
Ot7964
Col KANADI1-GR

source_name: GR-KAN1 seedling, 60 mins, rep 1


title: GR-REV.60.3_dexamethasone

description:
Ot7954
Col GR-REVOLUTA

source_name: GR-REV seedling, 60 mins, rep 3


title: GR-REV.30.2_dexamethasone

description:
Ot7951
Col GR-REVOLUTA

source_name: GR-REV seedling, 30 mins, rep 2


title: GR-REV.120.2_dexamethasone

description:
Ot7956
Col GR-REVOLUTA

source_name: GR-REV seedling, 120 mins, rep 2


title: GR-REV.60.1_dexamethasone

description:
Ot7952
Col GR-REVOLUTA

source_name: GR-REV seedling, 60 mins, rep 1


title: GR-REV.120.1_dexamethasone

description:
Ot7955
Col GR-REVOLUTA

source_name: GR-REV seedling, 120 mins, rep 1


title: GR-KAN1.120.3_dexamethasone

description:
Ot7969
Col KANADI1-GR

source_name: GR-KAN1 seedling, 120 mins, rep 3


title: GR-REV.30.1_dexamethasone

description:
Ot7950
Col GR-REVOLUTA

source_name: GR-REV seedling, 30 mins, rep 1


title: GR-REV.0.2_dexamethasone

description:
Ot7948
Col GR-REVOLUTA

source_name: GR-REV seedling, 0 mins, rep 2


title: GR-STM.60.3_dexamethasone

description:
Ot7943
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 60 mins, rep 3

value: GR-SHOOT MERISTEMLESS


title: GR-REV.0.1_dexamethasone

description:
Ot7947
Col GR-REVOLUTA

source_name: GR-REV seedling, 0 mins, rep 1


title: GR-REV.0.3_dexamethasone

description:
Ot7949
Col GR-REVOLUTA

source_name: GR-REV seedling, 0 mins, rep 3


title: GR-KAN1.30.2_dexamethasone

description:
Ot7962
Col KANADI1-GR

source_name: GR-KAN1 seedling, 30 mins, rep 2


title: GR-STM.120.1_dexamethasone

description:
Ot7944
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 120 mins, rep 1


title: GR-STM.60.2_dexamethasone

description:
Ot7942
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 60 mins, rep 2


title: GR-STM.60.1_dexamethasone

description:
Ot7941
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 60 mins, rep 1


title: GR-STM.30.3_dexamethasone

description:
Ot7940
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 30 mins, rep 3


title: GR-STM.120.2_dexamethasone

description:
Ot7945
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 120 mins, rep 2


title: GR-STM.30.1_dexamethasone

description:
Ot7938
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 30 mins, rep 1


title: GR-STM.0.3_dexamethasone

description:
Ot7937
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 0 mins, rep 3


title: GR-AS2.120.1_dexamethasone

description:
Ot7932
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 120 mins, rep 1

value: GR-ASYMMETRIC LEAVES 2


title: GR-AS2.30.3_dexamethasone

description:
Ot7928
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 30 mins, rep 3


title: GR-STM.30.2_dexamethasone

description:
Ot7939
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 30 mins, rep 2


title: GR-AS2.60.3_dexamethasone

description:
Ot7931
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 60 mins, rep 3


title: GR-STM.0.1_dexamethasone

description:
Ot7935
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 0 mins, rep 1


title: GR-AS2.60.2_dexamethasone

description:
Ot7930
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 60 mins, rep 2


title: GR-AS2.30.2_dexamethasone

description:
Ot7927
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 30 mins, rep 2


title: GR-AS2.120.2_dexamethasone

description:
Ot7933
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 120 mins, rep 2


title: GR-AS2.120.3_dexamethasone

description:
Ot7934
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 120 mins, rep 3


title: GR-AS2.0.2_dexamethasone

description:
Ot7924
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 0 mins, rep 2


title: GR-STM.0.2_dexamethasone

description:
Ot7936
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 0 mins, rep 2


title: WT.120.6_dexamethasone

description:
OtA0259
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 6

value: wild-type


title: GR-AS2.0.3_dexamethasone

description:
Ot7925
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 0 mins, rep 3


title: GR-AS2.30.1_dexamethasone

description:
Ot7926
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 30 mins, rep 1


title: GR-STM.120.3_dexamethasone

description:
Ot7946
Col GR-SHOOT MERISTEMLESS

source_name: GR-STM seedling, 120 mins, rep 3


title: GR-AS2.60.1_dexamethasone

description:
Ot7929
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 60 mins, rep 1


title: WT.120.5_dexamethasone

description:
OtA0258
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 5


title: WT.120.2_dexamethasone

description:
Ot7921
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 2


title: GR-AS2.0.1_dexamethasone

description:
Ot7923
Col GR-ASYMMETRIC LEAVES 2

source_name: GR-AS2 seedling, 0 mins, rep 1


title: WT.120.3_dexamethasone

description:
Ot7922
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 3


title: WT.120.1_dexamethasone

description:
Ot7920
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 1


title: WT.60.6_dexamethasone

description:
Ot8699
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 6


title: WT.60.2_dexamethasone

description:
Ot7918
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 2


title: WT.60.3_dexamethasone

description:
Ot7919
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 3


title: WT.60.4_dexamethasone

description:
Ot8697
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 4


title: WT.30.6_dexamethasone

description:
Ot8696
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 6


title: WT.30.4_dexamethasone

description:
OtA0255
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 4


title: WT.30.3_dexamethasone

description:
Ot7916
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 3


title: WT.30.2_dexamethasone

description:
Ot7915
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 2


title: WT.0.4_dexamethasone

description:
Ot8691
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 4


title: WT.0.6_dexamethasone

description:
Ot8693
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 6


title: WT.30.1_dexamethasone

description:
Ot7914
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 1


title: WT.0.3_dexamethasone

description:
Ot7913
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 3


title: WT.0.1_dexamethasone

description:
Ot7911
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 1


title: WT.0.2_dexamethasone

description:
Ot7912
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 2


title: WT.120.4_dexamethasone

description:
OtA0257
Col wild-type

source_name: Wild-type seedling, 120 mins, rep 4


title: Dachshund-ChIPSeq

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

data_processing:
Cleaning (fastq-mcf)
Mapping to dm3 genome using bowtie2
Calling peaks using macs2
Calling differential peaks between Dac-ChIP and input (macs2)
Filtering out all promoter regions using Bedtools
Genome_build: Drosophila melanogaster FlyBase version 5
Supplementary_files_format_and_content: Bed file with Narrow peaks called by macs2; Bed file of filtered peaks ( no 5'UTR or 1kb upstream of TSS)

organism: Drosophila melanogaster

source_name: eye-antennal discs

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
Sonicated chromatin was extracted using an anti-GFP ab and immunocomplexes were recovered on A/G megnetic beads
ChIP libraries were prepared using the Truseq DNA library prep kit (Illumina)

treatment_protocol: Wandering 3rd instar larvae were dissected in PBS to extract the eye-antennal discs

value: Bloomington 42269

tag: genotype/variation

value: Grh-GFP

tag: age

value: 3rd instar

value: eye-antennal discs

tag: chip antibody

value: anti-GFP Ab (ab290, Abcam)


title: input DNA

city: Milano

first: Andrea

last: Brendolan

address: Via Olgettina 60

department: Experimental Oncology

country: Italy

institute: San Raffaele Scientific Institute

description: ChIP-seq analysis on untreated growing eSMC cells. Total chromatin (input).

data_processing:
Sequencing data generated from the Illumina platforms were aligned to mouse reference genome (mm9) using Bowtie version 0.12.7.
Only reads with unique alignment were retained for downstream analysis. Peak-calling was done using MACS 1.4.0 software
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files

source_name: spleen; Derived from embryonic spleens

growth_protocol: Cells were cultured in  DMEM supplemented with 10% fetal bovine serum and antibiotics.

extract_protocol:
CHIP followed by purification with Qiaquick PCR Purification kit (Qiagen)
The library was constructed using ChIPseq  Sample Prep Kit, Illumina, according to the manufacturer's recommendations

value: Immortalized embryonic Spleen Mesenchymal cell (eSMC)

tag: passages

tag: chip antibody provider

tag: chip antibody catalog


title: Meq-DF-1, biological rep2/Igg Ab

city: East Lansing

first: sugalesini

last: Subramaniam

address: 3606 E Mount Hope Rd

department: CMIB

institute: Michigan State University

data_processing:
ChIP-seq reads were aligned to the chicken genome assembly using Bowtie 0.12.5
ChIP-seq data were analyzed using the peak calling software QUEST
Peaks with high-confidence were defined by ChIP-enrichment of more than three-fold with an FDR <0.01 .
Genome_build: unknown to submitter/authors of this data

organism: Gallus gallus

growth_protocol: Cells were cultured in Lebowitz's L-15 and McCoy 5A media with 15% inactivated fetal bovine serum, 100 U of penicillin per ml, and maintained at 37 °C.

extract_protocol: unknown to submitters/authors of this data

value: Igg

value: Meq-DF-1 clone 5G


title: Meq-DF-1, biological rep1/Jun Ab

value: Jun


title: Meq-DF-1, biological rep2/Jun Ab


title: Meq-DF-1, biological rep1/Meq Ab

value: Meq


title: Meq-DF-1, biological rep1/Igg  Ab


title: Meq-DF-1, biological rep2/Meq Ab


title: Hox11_rep2

description: ChIP-seq analysis on untreated growing eSMC cells. Immunoprecipitation was performed using  anti-Hox11  antibody (Santa Cruz). Replicate 2.

tag: tissue

value: Santa Cruz


title: WT.60.5_dexamethasone

description:
Ot8698
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 5

value: Columbia

tag: genotype

value: Dexamethasone

value: 60 mins

value: seedling


title: 3KO_MEF

city: Columbus

first: Lindsey

middle: N

last: Kent

state: oh

address: 460 W 12th Ave

department: CCC

institute: OSU

data_processing:
Alignment was done using Bowtie2 setting number of mismatches with the -N flag to be 1
Multimapped reads were removed before peak calling utilizing the presence of the XS flag in the SAM files resulting from alignment
SAM files were converted to BAM format using samtools
Peaks were called used Macs1.4 (Harvard) with defaults to gauge peaks and using a WT Input ( with the -c flag)
Peaks found in knock-out MEF samples were deemed non-specific. Peaks from the 1-/- MEFs were subtracted from the E2F1 ChIP while 3-/- peaks were subtracted from the E2F3A and E2F3B ChIPs.
Genome_build: mm9
Supplementary_files_format_and_content: The bed files contain the coordinates and chromosomes of all peaks

source_name: mouse embryonic fibroblasts

growth_protocol: Mouse embryonic fibroblasts were cultured in 10%FBS DMEM. Samples from asynchronous populations of proliferating cells were used.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
E2F- ChIP DNA was processed to generate libraries using TruSeq ChIP DNA library prep kit (Illumina). Briefly, 10 ng of pull down DNA was used to ligate with barcoded adaptors, amplified with 14 cycles of PCR, and then a 200-300bp library was collected using E-gel (Invitrogen).

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)

tag: cell type

value: MEF

tag: antibody

value: anti-E2F3 (Santa Cruz, catalog# sc-878x, lot# E1712)


title: Hox11_rep1

description: ChIP-seq analysis on untreated growing eSMC cells. Immunoprecipitation was performed using  anti-Hox11  antibody (Santa Cruz). Replicate 1.


title: E2F3B_MEF

value: overexpressing E2F3B


title: 1KO_MEF

value: anti-E2F1 (Santa Cruz, catalog# sc-193x, lot# B0615)


title: WT.30.5_dexamethasone

description:
OtA0256
Col wild-type

source_name: Wild-type seedling, 30 mins, rep 5

value: wild-type

value: 30 mins


title: WT.60.1_dexamethasone

description:
Ot7917
Col wild-type

source_name: Wild-type seedling, 60 mins, rep 1


title: E2F3A_MEF

value: overexpressing E2F3A


title: WT.0.5_dexamethasone

description:
Ot8692
Col wild-type

source_name: Wild-type seedling, 0 mins, rep 5

value: 0 mins


title: Input-ChIPSeq

value: Bloomington 42269

value: Grh-GFP

value: 3rd instar

value: eye-antennal discs


title: Day3.5_60kPa rep1

city: San Francisco

first: Laralynne

last: Przybyla

address: 513 Parnassus Ave.

institute: UCSF

description: processed data file: processed data Day3_5.txt

data_processing:
Reads mapped to human reference genome and RPKM values generated with Cufflinks.
Genome_build: hg19
Supplementary_files_format_and_content: text file with FPKM values and statistics summarized across the two replicates.

source_name: H9 human embryonic stem cells_induced to mesoderm_60kPa

growth_protocol: Human embryonic stem cells were routinely cultured in KSR-DMEM and grown on gels in feeder-conditioned media. Differentiation was induced using a cocktail consisting of bFgf, Activin, VEGF, and BMP4.

extract_protocol:
Cells were lysed with TRIzol and total RNA was recovered according to manufacturer's instructions
Libraries were prepared according to Illumina Next Gen Sequencing (RNA) pipeline

tag: cell line source

value: H9 human embryonic stem cells

value: multipotent mesoderm progenitors

tag: substrate stiffness

tag: differentiation state

value: induced to mesoderm


title: Day3.5_400Pa rep2

source_name: H9 human embryonic stem cells_induced to mesoderm_400Pa


title: Day0_60kPa rep1

description: processed data file: processed data Day0.txt

source_name: H9 human embryonic stem cells_undifferentiated_60kPa

value: human embryonic stem cells

value: undifferentiated


title: Day0_400Pa rep1

source_name: H9 human embryonic stem cells_undifferentiated_400Pa


title: Day0_400Pa rep2


title: puro-WWTR1#2

city: Charlestown

first: Cyril

middle: H.

last: Benes

state: MA

address: 149 Thirteenth St

department: Cancer Center

institute: Massachusetts General Hospital/Harvard Medical School

description: WWTR1 overexpression

data_processing:
STAR aligner(Dobin et al., 2013) was used to map sequencing reads to transcripts. Read counts for individual transcripts were produced with HTSeq-count(Anders et al., 2015), followed by the estimation of expression values as RPKM (reads per kilobase per million) and detection of differentially expressed transcripts using EdgeR(McCarthy et al., 2012). Benjamini-Hochberg FDR (false discovery rate) was used as the estimate of statistical significance of expression difference.
Genome_build: hg19
Supplementary_files_format_and_content: differential expressed genes with change over 1.5-fold between vector group and WWTR1-overexpressing group listed in an excel file

growth_protocol: cells were grown in DMEM+5%FBS for 24 hours before haresting

extract_protocol:
Qiagen Rneasy minicolumn
Total RNA was prepared using Qiagen RNeasy mini kit, processed using TruSeq RNA sample preparation kit (Illumina) to generate libraries of sequencing molecules. samples were prepared from four biological replicates of viral infections, indexed, pooled, and sequenced. using Illumina HiSeq2500 instrument.
Both vector and WWTR1 were prepared with four biological replicates by lentivirus infection (bsd-, puro-, #1 and #2). Twelve indexed samples (including four from other projects) were pooled and sequenced in two HiSeq channels. Raw data were demultiplexed and pooled from two channels for differential expression analysis.

tag: cell line

value: melanoma cell line

value: WWTR1 cDNA plasmid

tag: wwtr1 expression level

value: high

tag: barcode

value: AGTTCC

tag: illumina truseq rna index


title: puro-WWTR1#1

description: WWTR1 overexpression

tag: genotype/variation

value: AGTCAA


title: Clone 34 hF Replicate2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: Expression profile of Human Fibroblast NHDF17914

data_processing:
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 and Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene were counted using  HTSeq
FPKM values were computed using R script
Mumber of SNP-overlapping reads for mjor and minor allele was obtained using SAMtools mpileup version 0.1.18
Genome_build: hg19 & mm9
Supplementary_files_format_and_content: hg19 FPKM values
Supplementary_files_format_and_content: Number of reads overlapping with major and minor alleles at selected SNPs on chrX

source_name: Limiting dilution of TERT-immortalised NHDF17914 fibrobalst (Lonza)

growth_protocol: Human fibrobalst (hF) clones were maintainedat 3% O2  in DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine and antibiotics (10 µg/ml penicillin and streptomycin). After hF x mESC fusion, cells were cultured in mouse ESC medium (KO-DMEM supplemented with 10% FCS, 1% non-essential amminoacids, 2mM L-glutammine, 50μM β-mercaptoethanol, antibiotics (10 µg/ml penicillin and streptomycin) and LIF) and selected 12hrs after by adding puromycin (1.5 μg/ml) and HAT (20μM hypoxantine, 0.08 mM aminopterin, and 3.2 mM thymidine; Sigma).

extract_protocol:
Total RNA was exacted by RNABee (Amsbio), treated with RNAse-free DNAseI (Ambion) and cleaned-up with RNAeasy Mini-elute columns.
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). For the ligation step, 2 μl of adaptors were used. Libraries were amplified 14 cycles before deep-sequencing.

treatment_protocol: hF clones were fused with mESC by PEG (Roche)

value: fibroblast clones derived from TERT-immortalised NHDF17914


title: Clone 34 hF Replicate1


title: puro-VEC#2

description: vector control

value: lentiviral vector controls

value: normal

value: GCCAAT


title: MV4-11-3_NEB

city: Salt lake city

last: O'Connell

state: UT

address: 15 N Medical Dr East

institute: University of Utah

description: Small RNA

data_processing:
Reads were aligned to mm10 using Novoalign (v2.08.03) using small RNA settings. If a read aligns to multiple locations, one was alignment was chosen randomly.
The USeq (v8.8.8) application DefinedRegionDifferentialSeq was used to generate counts and FPKM values for miRNA transcripts and mature miRNAs separately (miRBase v21).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing raw counts and FPKM for each miRNA (miRBase v21)

source_name: MV4-11 cells

growth_protocol: MV4-11 cells were infected with EV lentiviral CRISPR-Cas9 construct and allowed to grow 2 weeks prior to RNA extraction.

extract_protocol:
Total RNA was isolated from MV4-11 cell lines using the Qiagen miRNeasy spin column kit
RNA libraries were prepared for sequencing using NEB Illumina library prep protocol.

value: FLT3-ITD+ AML cell lines (MV4-11)

value: WT


title: puro-VEC#1

description: vector control

value: ACAGTG


title: bsd-WWTR1#1

description: WWTR1 overexpression

value: CAGATC


title: bsd-VEC#2

description: vector control

value: TGACCA


title: MV4-11-2_NEB

description: Small RNA


title: bsd-VEC#1

description: vector control

value: CGATGT


title: E2F1_MEF

tag: strain

value: mixed background (FVB/NT, 129S1/Svlmj,C57BL/6NT)

value: overexpressing E2F1

value: MEF

value: anti-E2F1 (Santa Cruz, catalog# sc-193x, lot# B0615)


title: S10_3

description:
S10_vs_EV.txt
S10_vs_S3.txt

data_processing:
Reads were aligned to hg19 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.8) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.8) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to determine differentially expressed genes.  The application determines the number of reads aligning to each gene and runs DESeq2 (v1.4.5) on the resulting count table.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing gene counts, FPKMs, log2 fold change and adjusted p-values (DESeq2)

growth_protocol: MV4-11 cells were infected with empty vector (EV) or miR-155 (S3 or S10) CRISPR-Cas9 lentiviral CRISPR-Cas9 construct and allowed to grow 2 weeks prior to RNA extraction.

extract_protocol:
Total RNA was isolated from MV4-11 cell lines using the Qiagen miRNeasy spin column kit
RNA libraries were prepared for sequencing using RiboZero Illumina library prep protocol.


title: S10_1

description:
S10_vs_EV.txt
S10_vs_S3.txt


title: S10_2

description:
S10_vs_EV.txt
S10_vs_S3.txt


title: S3_3

description:
S10_vs_S3.txt
S3_vs_EV.txt


title: MV4-11-1_NEB

description: Small RNA


title: Day3.5_60kPa rep2

value: H9 human embryonic stem cells

value: multipotent mesoderm progenitors

value: induced to mesoderm


title: S3_2

description:
S10_vs_S3.txt
S3_vs_EV.txt


title: Day3.5_400Pa rep1


title: S3_1

description:
S10_vs_S3.txt
S3_vs_EV.txt


title: EV_3

description:
S10_vs_EV.txt
S3_vs_EV.txt


title: EV_1

description:
S10_vs_EV.txt
S3_vs_EV.txt


title: EV_2

description:
S10_vs_EV.txt
S3_vs_EV.txt


title: Day0_60kPa rep2

value: human embryonic stem cells

value: undifferentiated


title: TP23_3

description:
Cell counts for amplified CRISPR-Cas9 guide RNA sequence
TP0vsTP23_gene_results.txt
TPOvsTP23_tag_results.txt
Illumina DNA sequencing.

data_processing:
Trim off primer sequence (GTGGAAAGGACGAAACACCG) using cutadapt (v1.6),retaining trimmed reads that were 20bp or longer.
Aligned the first 20bp of the trimmed read to of an index containing all guide RNAs separated by Ns. Alignments were only allowed to the forward strand and up to three mismatches were allowed.  Alignments were only reported if there was a single alignment location at the lowest observed mismatch level.
The alignment locations were used to generate a count table for each guide RNA.
Tags with very high or low counts in at the initial timepoint were removed.
Genes with FPKM values < 1 (GSE71541) and mature miRNAs with fewer than 10 counts (GSE71543) were removed.
The count table was run through DESeq2 to generate log2 Fold Change and adjusted p-value.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing raw and normalized read counts, log2Ratio, p-value and adjusted p-value (DESeq2)

growth_protocol: FLT3-ITD+ AML cells (MV4-11 cells) were infected with CRISPR-Cas9 library at 250x coverage. Cells were allowed to recover for 2 days following infection, and then selected with puromycin for 1 week. Puromycin was removed and cells were allowed to grow 16 more days before ending experiment.

extract_protocol:
DNA was isolated 2 days after initial infection (TP0) and at end of experiment (TP23) using Qiagen DNeasy Blood and Tissue Kit
A two-step PCR method was employed to amplify inserted CRISPR-Cas9 RNA guide sequences and append molecular barcodes and Illumina adapter sequences. We modified our method to be compatible with Illumina TruSeq sequencing and obtain sufficient sequence information from a single-end 50-cycle sequencing run.

tag: timepoint

value: Final 3

tag: days post-infection


title: TP23_1

value: Final 1


title: TP23_2

value: Final 2

value: FLT3-ITD+ AML cell lines (MV4-11)


title: TP0_2

value: Initial 2


title: TP0_1

value: Initial 1


title: TP0_3

value: Initial 3


title: bsd-WWTR1#2

description: WWTR1 overexpression

value: melanoma cell line

value: WWTR1 cDNA plasmid

value: high

value: CTTGTA


title: Exp1_LPS_rep2

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10

growth_protocol: Mature bone marrow-derived macrophages (BMDM) were differentiated from C57BL/6 bone marrow cells in the presence of 20 ng/ml murine recombinant M-CSF for seven days.

extract_protocol:
mRNA was extracted from cell lysates by means of oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrid was degraded with consecutive acid-alkali treatment.
For cDNA synthesis, custom oligo-dT primers were used with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis, samples were pooled together based on Actb qPCR values, and RNA-DNA hybrids degraded using consecutive acid-alkali treatment. A second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (NEB) followed by SPRI clean-up. The mixture was then PCR enriched for 12 cycles and SPRI purified to yield final strand specific RNA-seq libraries as previously described (Jha et al., 2015)

treatment_protocol: mature  WT BMDM were treated for 12h with 0.25 mM dimethyl itaconate (DI) or vehicle (Unst) and then stimulated with LPS (E. coli 0111:B4; 100 ng/ml, 4h) (DI+LPS; LPS)

tag: strain background

value: WT

value: Bone marrow-derived macrophages

tag: treated with

value: vehicle and then stimulated with LPS for 4h


title: Exp1_LPS_rep1


title: Exp2_Irg1KO_LPS_IFNg_rep2

treatment_protocol: mature  Irg1-/- BMDM were stimulated with LPS (E. coli 0111:B4; 100 ng/ml) and murine recombinant IFNg  (50 ng/ml) for 24h

value: LPS and IFNg for 24h


title: Exp2_Irg1KO_LPS_IFNg_rep1


title: Exp1_LPS_rep3


title: Exp2_WT_LPS_IFNg_rep1


title: Exp1_Unst_rep3

value: unstimulated


title: Exp1_DI_rep1

value: dimethyl itaconate


title: Exp2_WT_LPS_IFNg_rep2


title: Exp1_DI_rep3


title: Exp1_DI_LPS_rep2

value: dimethyl itaconate and then stimulated with LPS for 4h


title: Exp1_Unst_rep2


title: Exp1_DI_LPS_rep1


title: Exp1_Unst_rep1


title: egg cells

description: small RNA sequencing data

data_processing:
sequenced on a Hi-Seq 2000; 1 x 50
analysis pipeline: HiSeq Control Soft. v. 1.1.37.8; RTA 1.7.48; CASAVA 1.7
Barcode splitting and adapter trimming was performed using custom scripts.
Reads were mapped to V.carteri genome assembly using tophat.
Genome_build: Phytozome 9.0 v2.0
Supplementary_files_format_and_content: tab-delimited TXT-file; trimmed read sequence followed by a tab and the number of reads

source_name: reproducitve cells (egg cells)

growth_protocol: Volvox carteri strain HK10 was cultured under standard conditions.

extract_protocol:
Colonies were pelleted and sheared to separate the two different cell types. After size-selection by sieving, the cell preparations were pure. RNA was prepared by using Trizol according to manufacturer's instructions.
Libraries were constructed according to Illumina's small RNA cloning kit v1.5 using the following adapters:  5′adapter 5′-GUUCAGAGUUCUACAGUCCGACGAUC-3′; 3′adapter 5′-Phospho-T-4nt-Barcode-CGTATGCCGTCTTCTGCTTG-(C7amino)-3′. Used barcodes:  Sample 1=GTAA; Sample 2=TACA; Sample3=ACTA; Sample 4=GTAA; Sample 5=TACA

tag: developmental stage

value: female

value: reproducitve cells (egg cells)


title: induced somatic cells

description: small RNA sequencing data

source_name: somatic cells

value: induced with sex inductor for 16h

value: somatic cells


title: induced gonidia

description: small RNA sequencing data

source_name: reproducitve cells (gonidia)

value: reproducitve cells (gonidia)


title: female somatic cells

description: small RNA sequencing data


title: Exp1_DI_rep2


title: All_1574.AAGTAGAG ifnA-3

data_processing:
Second mate was used for sample demultiplexing
individual single-end fastqs were aligned to mm9 genome via TopHat
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Differentially expressed genes that were present in the database of interferon regulated genes (INTERFEROME) were identified
Overlapping genes were analyzed for GO biological processes using the online bioinformatics tool DAVID (https://david.ncifcrf.gov/)
Genome_build: mm9

source_name: Plasmacytoid dendritic cells

growth_protocol: DCs were generated from bone marrow using Flt3L as described (Naik et al., 2007). Briefly, bone marrow cells were differentiated in the presence of Flt3L (PeproTech, 160 ng/ml) in RPMI containing 10% fetal calf serum, 100 U/ml penicillin/ streptomycin, and 2 mM L-glutamine for 9 days.  CD11cintSiglec H+ B220+ pDCs, and CD11chiSIRPα+ cDCs were isolated by FACS using a BD FACSaria II.

extract_protocol:
mRNA was extracted from cell lysates by means of oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrid was degraded with consecutive acid-alkali treatment.
Then, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI clean-up. The mixture then was PCR enriched 12 cycles and SPRI purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: pDCs were cultured in complete DC media at 1.5 × 105 cells/well in 200 l, and where indicated pre-treated for 24 h with TLR9 agonist CpG-A (5 g/mL; InvivoGen) or IFNα (100U/ml, PBL Assay Science)


title: Exp2_Irg1KO_LPS_IFNg_rep3


title: Exp1_DI_LPS_rep3


title: All_1574.AACGCATT control 3


title: Exp2_WT_LPS_IFNg_rep3


title: All_1574.AACTTGAC control 2


title: All_1574.AGTTGCTT control 1


title: lane2.TCCTTGGT cpg


title: vegetative gonidia

description: small RNA sequencing data

value: vegetative (asexual)


title: lane2.CCTATGCC cpg


title: crypts-WT-H3K27ac_Sample#3

city: Amsterdam

first: Martijn

last: Koppens

address: Plesmanlaan 121

institute: NKI-AVL

data_processing:
description; output; software name version; parameters
base calling; $fastq; bcl2fastq2 2.17.1.14; --mask-short-adapter-reads 0 --runfolder-dir $runfolder --output-dir $outputdir --interop-dir $outputdir/InterOp --sample-sheet $samplesheet
alignment; pipe; bwa 0.7.10; mem -t 14 Mus_musculus.GRCm38.dna.primary_assembly.fa $fastq
single end sam; pipe; bwa 0.7.10; samse -r $readgroup Mus_musculus.GRCm38.dna.primary_assembly.fa - $fastq
sam to bam; pipe; samtools 0.1.19; view -Sbu -
sort; $bam; samtools 0.1.19; sort -m 3000000000 - $basename
view; pipe; samtools 0.1.19; view -bu $bam
genomecov; pipe; bedtools 2-2.20.1; genomecov -bg -ibam -
fix for downstream analysis; $bedGraph; GNU sed 4.1.5; -n -r "/^([0-9]+|[XY]|MT)/{s/^MT/M/;s/^/chr/;p}" > $bedGraph
fetchChromSizes; mm10.chrom.sizes; UCSC genome browser 'kent' bioinformatic utilities FetchChromSizes v1.2; mm10 > mm10.chrom.sizes
bedGraphToBigWig; $bigWig; bedGraphToBigWig v4; $bedGraph mm10.chrom.sizes
Genome_build: Ensembl GRCm38, primary assembly
Supplementary_files_format_and_content: bigwig

extract_protocol:
Protein A-G magnetic beads (Dynabeads, Thermo Fisher Scientific) were used to pull down immunocomplexes.
Illumina compatible libraries were prepared using Diagenode's MicroPlex v2 Library Preparation™ kit.

treatment_protocol: After treating 6 weeks old mice with beta-naphthoflavone for 6 weeks, crypts were isolated from the small intestine by scraping off villi and EDTA chelation, after which they were washed. Crypts were then lysed in TRIzol.

tag: genotype

value: wild type

tag: age

value: 6 weeks

value: beta-naphthoflavone for 6 weeks

value: small intestinal crypts

tag: chip antibody


title: crypts-WT-H3K27me3_Sample#9

tag: cell type


title: lane2.GACAGTAA ctrl


title: lane2.CAGCAAGG ctrl


title: crypts-WT-H3K27ac_Sample#2


title: crypts-WT-H3K27me3_Sample#8


title: 2_cEzh2KO_6w_3

data_processing:
The reads were sequenced using a stranded protocol and aligned against the mouse genome, build 38, using Tophat 2.0.12 with bowtie 0.12.9/1.1
The parameters used are --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were generated using a custom script based on the same strategy as HTSeq-count. Genes that have no expression across all samples are removed from the dataset.
Prior to analysis the provided processed data files were only normalized for sequencing depth, using the DESeq2 package, and normalized for batch effects (ex: sequencing run) if necessary using ComBat, as described in the paper.
Genome_build: Mus_musculus.GRCm38.dna.primary_assembly
Supplementary_files_format_and_content: readcountfiles: tab-separated gene counts and gene annotation for all samples; format: 2 tab-separated text files corresponding to the two sequencing runs, 385 and 440

source_name: cEzh2KO_6w_small intestinal crypts

extract_protocol:
RNA was harvested from samples using TRIzol and further purified using the Qiagen MinElute Cleanup Kit.
Strand-specific libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina Inc., San Diego, RS-122-2101/2) according to the manufacturer's instructions (Illumina, Part # 15031047 Rev. E).

value: C57BL/6-FVB mixed

tag: tissue/cell type

tag: run id

value: Run 440


title: Input#1+2+3_Sample#1

value: none (input)


title: 2_cEzh2KO_6w_2


title: All_1574.GTATAACA ifnA-2


title: 2_cEzh2KO_6w_1


title: Rodrigue_9-WT-phiNi-3

city: Villeurbanne

first: Agnès

last: Rodrigue

address: 10 rue Dubois

country: France

institute: INSA Lyon CNRS

description: growth in M63 minimal media plus 0.4% glucose

data_processing:
Basecalls performed using HCS 2.0.5 and RTA 1.17.20
RNA-seq reads were aligned to the W3110 genome  using CASAVA 1.8.2
Gene expression (based on known genes) was determined using Cufflinks 2.0.2, only PF reads were retained
Genome_build: W3110  (NC_007779)
Supplementary_files_format_and_content: excel file with coverage and FPKM measurements

organism: Escherichia coli

source_name: Escherichia coli_control condition

growth_protocol: Transcriptomic analyses were carried out after growing bacteria in minimal media supplemented with glucose. Several Ni concentrations and exposure times were assayed. rcnA gene expression was taken as an internal control to arbitrate between the different conditions. rcnA is induced by Ni when cells are overloaded with this ion and must detoxify the cytoplasm by extruding excess metal via the RcnAB efflux system. rcnA induction was maximised after culture incubation for 10 min, and longer periods of incubation lead to a decline in rcnA expression (Fig. S1). For the RNA-Seq experiments, bacteria were grown until O.D600nm = 0.3, were treated with 50 µM NiCl2 for 10 min and were frozen prior to RNA extraction.

extract_protocol:
Total RNA was extracted using the frozen acid-phenol method described by Maes and Messens (Maes and Messens, 1992) and then treated with RNase-free DNaseI according to the manufacturer’s recommendations (Ambion, USA).
Library preparation were performed with Epicentre ScriptseqTM v2 RNA-Seq Library preparation kit with 50 ng of depleted RNA; Strand orientated RNA-Seq

tag: growth phase

value: log phase


title: Rodrigue_10-WT-Ni-3

description: growth in M63 minimal media plus 0.4% glucose plus 50 µM NiCl2

source_name: Escherichia coli_nickel condition


title: Rodrigue_2-WT-Ni-1


title: Rodrigue_5-WT-Ni-2


title: 2_cEedKO_6w_1

source_name: cEedKO_6w_small intestinal crypts

value: Eed-/-


title: 2_cWT_6w_1

source_name: cWT_6w_small intestinal crypts

value: WT


title: Rodrigue_6-WT-phiNi-2


title: batch culture rep3, 2 min

city: Stuttgart

first: Joachim

last: von Wulffen

address: Waldburgstr. 19

department: Institute for System Dynamics

institute: University of Stuttgart

data_processing:
alignment: STAR 2.4.0i
gene counting: HTSeq-Count 0.6.0
Genome_build: NC007779.1 (UCSC Archaeal Genome Browser)
Supplementary_files_format_and_content: The file format is .xlsx. The file contains the raw gene counts of all samples.

source_name: batch culture

growth_protocol: Cell were grown in 3-liter stirred tank bioreactor anaerobically. The growth medium contained Na2H2PO4 (1.1 g/l), K2HPO4 (2.5 g/l), (NH4)2SO4 (9.0 g/l), Glucose (15.0 g/l), CaCl2 (2.2 mg/l), MgSO4 (0.55 g/l), NaH2-Citrate (234 mg/l), FeCl3*6 H2O (25.0 mg/l), ZnSO4*7 H2O (0.18 mg/l), MnSO4*7 H2O (0.1 mg/l), CuSO4*5 H2O (0.16 mg/l), CoCl2*6 H2O (0.18 mg/l).

extract_protocol:
Samples were treated with RNAprotect (Qiagen, Hilden, Germany) and stored at -80°C until preparation. rRNA was removed using RiboZero rRNA Removal Kit (Illumina, San Diego, CA), and sequencing libraries were prepared with TruSeq™ RNA Sample Preparation Kitv2 (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Aeration was initiated at 1 l/min when the culture reached an OD (600nm) of 3.

tag: replicate

tag: time

value: 2 min


title: batch culture rep3, 5 min

value: 5 min


title: Rodrigue_1-WT-phiNi-1


title: All_1574.CATGCTTA ifnA-1


title: Runx1Δ/Δ XMP_rep2

city: Hamburg

first: Kira

last: Behrens

address: Martinistrasse 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

description:
fl_CD150_CD16/32 - kbrs34
lin-sca-kit+CD41-CD105-CD16/32+CD150+
fl_CD150_CD16/32 - kbrs34_GAGTGG_L004_R1_001

data_processing:
base calling was performed using RTA 1.18.64.0
RNA-seq reads were aligned to the mm9 genome assembly using CLC Genomics Workbench v6.5.1 software (Qiagen) using default settings
No data filtering steps were used
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: Runx1Δ/Δ XMP

extract_protocol:
RNA was extracted using the peqGOLD TriFast kit (Peqlab) according to the manufacturer's instructions
Libraries were generated using the TruSeq: RNA Sample Preparation V2 Low Throughput (LT) Kit (Illumina) or the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (both from New England Biolabs)

tag: tissue

value: bone marrow

value: XMP


title: Runx1Δ/Δ MEP_rep2

description:
fl_MEP - kbrs33
lin-sca-kit+CD41-CD105-CD16/32-CD150+
fl_MEP - kbrs33_CGTACG_L005_R1_001 (GE)

source_name: Runx1Δ/Δ MEP

value: MEP

tag: genotype/variation


title: lane2.CCAGAGCT cpg

tag: strain


title: Runx1Δ/Δ MEP_rep1

description:
fl_MEP - kbrs28
lin-sca-kit+CD41-CD105-CD16/32-CD150+
fl_MEP - kbrs28_CCGTCC_L005_R1_001


title: batch culture rep3, 0.5 min

value: 0.5 min


title: batch culture rep3, 10 min

value: 10 min


title: batch culture rep3, 0 min

value: 0 min


title: Runx1wt/wt MEP_rep1

description:
wt_MEP - kbrs26
lin-sca-kit+CD41-CD105-CD16/32-CD150+
wt_MEP - kbrs26_AGTTCC_L003_R1_001

source_name: Runx1wt/wt MEP


title: Runx1wt/wt MEP_rep2

description:
wt_MEP - kbrs31
lin-sca-kit+CD41-CD105-CD16/32-CD150+
wt_MEP - kbrs31_GTGGCC_L005_R1_001


title: Runx1Δ/Δ GMP_rep2

description:
fl_GMP - kbrs27
lin-sca-kit+CD41-CD105-CD16/32+CD150-
fl_GMP - kbrs27_ATGTCA_L005_R1_001

source_name: Runx1Δ/Δ GMP

value: GMP


title: batch culture rep2, 2 min


title: Runx1Δ/Δ GMP_rep1

description:
fl_GMP - kbrs32
lin-sca-kit+CD41-CD105-CD16/32+CD150-
fl_GMP - kbrs32_GTTTCG_L005_R1_001


title: batch culture rep2, 0.5 min


title: batch culture rep2, 5 min


title: Runx1wt/wt GMP_rep1

description:
wt_GMP - kbrs25
lin-sca-kit+CD41-CD105-CD16/32+CD150-
wt_GMP - kbrs25_AGTCAA_L003_R1_001

source_name: Runx1wt/wt GMP


title: batch culture rep2, 1 min

value: 1 min


title: FDC-P1 Runx1_ChIPSeq

data_processing:
Basecalls performed using  RTA 1.13.48.0 (for HiSeq2000) or RTA 1.17.20.0 (for HiSeq2500)
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.8 with the following configurations: --threads 6 --best --strata –m 1
peaks were called using MACS version 1.4.1 using default setting
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated using MACS14

source_name: FDC-P1 RUNX1-ERt2

growth_protocol: FDCP1 and FDCP1_RUNX1-ERt2 cells were cultured in DMEM 10%FCS + IL3

extract_protocol:
ChIP was performed using the EZ-ChIP Kit (Upstate/Millipore) on murine FDCP1 cells. After chromatin-crosslinking with 1% formaldehyde, cells were lysed and nuclei were isolated by centrifugation. Chromatin was extracted from the isolated nuclei and fragmented by sonication to an average length of 200–500 bp. Material from 1x10e7 cells was pre-cleared with protein-G agarose beads to reduce non-specific background. Chromatin immunoprecipitation was performed with either rabbit anti-Runx1 antibody, generated against a C-terminal peptide,2 or rabbit IgG (Abcam). Bound protein-DNA complexes were captured with Protein G Sepharose 4 Fast Flow (GE Healthcare) and chromatin eluted according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts >70 bps. DNA fragments between 200-400 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 2100 using a High Sensitivity DNA Kit (Agilent)

treatment_protocol: FDCP1_RUNX1-ERt2 were treated with 1 µM 4-OHT for 48h prior to assay

tag: cell line

tag: infection

value: Runx1, rabbit (Aziz-Aloya R, 1998)


title: batch culture rep2, 10 min


title: Runx1Δ/Δ XMP_rep1

description:
fl_CD150_CD16/32 - kbrs29
lin-sca-kit+CD41-CD105-CD16/32+CD150+
fl_CD150_CD16/32 - kbrs29_GTCCGC_L005_R1_001


title: FDC-P1 IgG_ChIPSeq

value: Rabbit IgG (ab37415, Abcam)


title: batch culture rep3, 1 min


title: batch culture rep1, 5 min


title: batch culture rep1, 2 min


title: batch culture rep1, 10 min


title: batch culture rep1, 1 min


title: batch culture rep2, 0 min


title: Arid3a-/- E11.5 rep1

city: Boston

first: David

middle: T

last: Scadden

address: 185 Cambridge St

department: Center for Regenerative Medicine

institute: MGH

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using tophat.
RPKM were calculated using 'cuffdiff'.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each samples

source_name: Placenta

extract_protocol:
Placentas were removed, flash forzen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: WT E11.5


title: batch culture rep1, 0.5 min


title: Arid3a-/- E10.5 rep2


title: Runx1wt/wt GMP_rep2

description:
wt_GMP - kbrs30
lin-sca-kit+CD41-CD105-CD16/32+CD150-
wt_GMP - kbrs30_GTGAAA_L002_R1_001


title: batch culture rep1, 0 min


title: Arid3a-/- E10.5 rep1


title: WT E10.5


title: SH0003 30h

city: Suwon-si

first: Jinsuk

middle: J.

last: Lee

address: 130 Samsung-ro

country: South Korea

institute: Samsung Advanced Institute Technology

description: with vitamin B12

data_processing:
Illumina Casava 1.8.2 software used for basecalling with default parameter.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity sequence, then mapped to E.coli W3110 whole genome.
Data filtering was done with in-house script with the set value as follows: Removal if % of N nucleotide is more than 10%, if more than 40% of the nucleotide is Q20 or less, if average quality of the reads is less than Q20.
Read alignment was performed with BWA (version 0.6.2) with default parameter.
Transcript assembly an quantification was performed using a protocols from Trapnell et al., and Li et al. Fragments Per Kilobases of exon per million (FPKM) were calculated.
Genome_build: http://www.ncbi.nih.gov/nuccore/AP009048.1
Supplementary_files_format_and_content: Excel files include FPKM values for each sample.

source_name: bacterial cells

growth_protocol: SH0012 and SH0003 were fermented in a 5.0L jar-fermenter with a 2.0 working voulume of modified R medium (20g/L glucose, 80 g/L glycerol, 1.4g/L MgSDo4, 13.5 g/L KH2PO4, 4.0 g/L (NH4)2HPO4 and 1.7g/L citric acid at 35°C. The agitation was at 1200 rpm and pH was maintained at 7.0 with 5N NH4OH. with the depletion of initial glucose, feeding medium of glycerol (700g/L) was throughout fermentation.

extract_protocol:
The bacterial cells from 5L fermentation were collected at 20h, 30h, 40h and centrifuged for 5min to pellet the cells. The cells then mixed with 500mL of RNA protectant bacterial reagents to stabilize RNA and stored at -80°C until use. Total RNAs were isolated using RNeasy mini kit and were treated with DNase to remove DNA.
The RNA-Seq library was constructed with TruSeq RNA Preparation Kit.

treatment_protocol: Expression of introduced enzymes for 3-HP productionm was induced by 0.05mM IPTG and 50 µM vitamin B12 when the cell reached at the early-exponential growth phase. T

tag: fermentation time

tag: agitation speed

value: 600 rpm


title: SH0012 no rpm change

description: with vitamin B12


title: SH0012 no vitamin B12

description: without vitamin B12


title: WT2

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: RNAseq data

data_processing:
RTA (Illumina) is used for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat (version 2.0.4) infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Relative abundance (aka expression level) of genes and splice isoforms is estimated using cufflinks 2.0.2 with default settings.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: TXT files and reads

source_name: WT_Splenic germinal center (GC) B lymphocytes

extract_protocol:
Total RNA of ~6-40 x 10(4) cells was isolated using the Nucleospin RNA XS isolation kit (Macherey-Nagel) according to the manufacturer’s protocol. RNA integrity >8 was determined using a BioAnalyzer 2100 (Agilent Technologies).
RNA was amplified via the NuGEN Ovation RNA-Seq System V2 prior to RNA sequencing. Libraries were sequenced on the Illumina HiSeq2500 at the New York Genome Center.

treatment_protocol: B cells from 12-week old Relbfl/flnfkb2fl/flCg1-Cre and Cg1-Cre littermate mice were isolated by flow cytometric sorting from splenic mononuclear cells.

tag: gentotype/variation

value: WT; Cg1-Cre

value: 12 weeks

value: splenic mononuclear cells

tag: cell subtype

value: FACS-purified germinal center B cells


title: SH0012 30h

description: with vitamin B12


title: Sh0012 40h

description: with vitamin B12


title: SH0012 20h

description: with vitamin B12


title: DKO1

description: RNAseq data

source_name: DKO_Splenic germinal center (GC) B lymphocytes

value: DKO; relbfl/flnfkb2fl/flCg1-Cre

tag: age


title: WT3

description: RNAseq data


title: Arid3a-/- E11.5 rep2

tag: genotype


title: TATCre+hSS2 tumor 2

city: Salt Lake City

first: Kevin

middle: B

last: Jones

state: Utah

address: 2000 Circle of Hope Drive, Room 4263

department: Department of Orthopaedics

data_processing:
Reads were aligned to mm10 chromosome sequence + splice junction sequences using Novoalign (v2.08.03), allowing up to 50 alignments for each read. Splice junctions were created by running USeq (v8.8.8) MakeTranscriptome application using Ensembl transcript annotations.
The resulting alignment file was processed with the USeq (v8.8.8) application SamTranscriptomeParser, which selects the appropriate alignment location for each read and discards repetitive alignments or alignments with low qualities.  SamTranscriptomeParser also converts splice junction alignment coordinates back to genomic space.
USeq's DefinedRegionDifferentialSeq application was used to calculate FPKMs
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files containing FPKMs

source_name: TATCre+hSS2 tumor

growth_protocol: Mice with Cre-lox inducible alleles of either SS18-SSX1 or SS18-SSX2 were injected in the pre-tibial soft-tissues with TATCre protein to induce tumors, which were harvested approximately 1 year later from each.

extract_protocol:
Tumors were harvested and snap frozen. Total RNA was extracted using Rneasy kits from Qiagen.
Ribo-Zero method of coding sequence selection was used for library generation

treatment_protocol: No treatments

value: containing Cre-lox inducible allele of SS18-SSX2

tag: injected with

value: TATCre protein

tag: time point

value: 1 year after the injection

value: tumor from leg


title: TATCre+hSS2 tumor 1


title: TATCre+hSS1 tumor 1

source_name: TATCre+hSS1 tumor

value: containing Cre-lox inducible allele of SS18-SSX1


title: R848-1

city: Seattle

first: Scott

last: Presnell

state: WA

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically in Illumina BaseSpace after sequencing; FASTQ reads were trimmed in Galaxy in two steps: 1) hard-trimming to remove 1 3'-end base (FASTQ Trimmer tool, v.1.0.0); 2) quality trimming from both ends until minimum base quality for each read >= 30 (FASTQ Quality Trimmer tool, v.1.0.0).
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.5.0).
Reads representing potential PCR duplicates were removed in Galaxy using SAMTools rmdup (rmdup tool, v.1.0.1)
Read counts per Ensembl gene ID were estimated in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Genes expressed (trimmed mean of M-values >1) in less than 1 sample were removed. Data normalization (TMM) and differential expression analysis to compare R848 vs. MCSF were performed in R using the "edgeR" package.
Genome_build: GRCm38
Supplementary_files_format_and_content: R848vMCSFmacs_rawCounts.csv: comma-separated matrix – first column contains Ensembl gene ID, remaining columns include raw read counts assigned for each library. Data represents all processing steps up to read counting, not including gene filtering and analysis with edgeR.

source_name: Sorted CD11b+F4/80+ macrophages from cultured bone marrow CMP treated with SCF+R848 for 5 days

growth_protocol: Common myeloid progenitors (CMP) were sorted from Lineage depleted bone marrow (Miltenyi) as Lin-CD117+Sca-1-CD34+CD16/32- and cultured in StemPro 34 media (Gibco) with 20 ng/ml SCF (Peprotech) and either 1 μg/ml R848 (Invivogen) or 20 ng/ml MCSF (Peprotech) for 4 days. They were then washed and rested in DMEM/10%FCS for 24 hours, followed by sorting of live CD11b+F4/80+ cells.

extract_protocol:
CD11b+F4/80+ macrophages from the cultures were sorted directly into RLT Plus lysis buffer (Qiagen) and total RNA isolated using Rneasy Kit (Qiagen)
Sequencing libraries were constructed from total RNA using the TruSeq RNA Sample Preparation V2 kit (Illumina)

tag: treatment

value: 5 days

tag: cell population

value: CD11b+F4/80+ cells differentiated from CMP


title: WT1

description: RNAseq data

tag: cell type


title: DKO2

description: RNAseq data


title: MCSF-1

source_name: Sorted CD11b+F4/80+ macrophages from cultured bone marrow CMP treated with SCF+MCSF for 5 days

treatment_protocol: 1 μg/ml R848 (Invivogen) or 20 ng/ml MCSF (Peprotech) for 4 days

value: MCSF+SCF

tag: time


title: MCSF-3


title: MCSF-2


title: TATCre+hSS1 tumor 2

tag: tissue


title: R848-3


title: R848-2


title: MT2

city: bangkok

first: Sirirak

last: Supa-amornkul

address: 272 Payatai

department: Microbiology

country: Thailand

institute: Mahidol University

description: rRNA depleted RNA

data_processing:
.sff file from Ion torrent machine was converted to fastq file by sff2fastq code.
FastQC program was obtained to determine quality of output sequences.
GetSpecificLengthRead.cpp was used to trim the sequences before alignment.
EDGE-pro was obtained to align the sequences to 10403s reference genome and to detemine differentially expressed genes between the two stains of L. monocytogenes.
RPKM data from EDGE-pro were compared and sorted in Microsoft Excel.
Genome_build: NC_017544.1 (ASM16869v2)
Supplementary_files_format_and_content: RPKM values for each sample

organism: Listeria monocytogenes 10403S

source_name: 10403s null nmlR strain

growth_protocol: L. monocytogenes strains were grown until early stationary phase. Early stationary phase is defined as a culture incubated at 37C with 200 rpm agitation until OD 600 reached 1.0 with 3 additional hours of incubation.

extract_protocol:
RNA was obtained by Ribopure RNA extraction kit (Ambion).   rRNA in RNA samples was depleted by MICROBExpress bacterial mRNA enrichment kit.
The whole transcriptome library was constructed by Ion total RNAseq kit.

tag: genotype/variation

value: null nmlR


title: WT1

description: rRNA depleted RNA

value: wild type


title: A3 (LF-SO)

city: Jouy-en-Josas

first: Sylvain

last: Marthey

address: Domaine de Vilvert Bat 320

department: Animal Genetics

institute: INRA

description: pool of 2 biopsies from 2 dairy cows. LF diet with 4 g/100g of dry matter of sunflower oil substituting for corn grain (LF-SO)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for poly-A stretches, then filtered for their size (17-28 nt). The cleaned sequences were clustered into unique reads and then mapped to the bovine (UMD3.1.71) reference genomes using the mapper.pl module from miRDeep2 with defaut parameters.
Novel miRNA and precursors were identified using miRDeep2 core module miRDeep2.pl using defaut parameters. Then Novel miRNA datasets were created by adding to known miRNA of bovine (miRBase v20) miRNA predicted with a miRDeep2 score> 0.
Quantification was performed using quantifier.pl module from miRDeep2 with defaut parameters using the unique reads, novels miRNA datasets, precursor datasets and know miRNA. Results were then filtered with a custom perl script parse_miRDeep2_outputs.pl (https://mulcyber.toulouse.inra.fr/projects/bioinfoutils/) to eliminate redundancy between known and putative novel miRNA.
Genome_build: UMD3.1.71
Supplementary_files_format_and_content: Quantification files (*_quantification.txt) are the resulting files generated by the quantifier.pl module of miRDeep2. These tab-delimited text files include for each miRNA its associated precursor, raw abundance measurements, normalized abundance, and sequence.
Supplementary_files_format_and_content: Prediction files (*_prediction.txt) are the resulting files generated by the miRDeep2 prediction process (miRDeep2.pl). These tab-delimited text files include predicted miRNA and precursors, associated miRDeep2 scores, and their genome location.

organism: Bos taurus

source_name: Mammary biopsy

extract_protocol:
Total RNA were isolated from mouse tissue biopsies or from the samples obtained after AGO2 co-immunoprecipitation using the RNA NOW kit (Ozyme), with overnight precipitation so as to guarantee a maximum yield of small RNA. Bovine total RNA were prepared from about 50 mg mammary tissue using the Nucleospin® miRNA isolation kit (Macherey-Nagel Inc.) according to the manufacturer’s instructions. Both mouse and bovine samples were precipitated using sodium acetate 3M, 96% ethanol and 5 mg/mL glycogen.
Libraries were prepared using the Illumina small RNA kit (Illumina) from GATC Biotech Company, according to the manufacturer’s instructions.

value: Mammary biopsy

tag: breed

value: Holstein

tag: physiological stage

value: mid-lactation

tag: diet

value: low fat diet with 4 g/100g of dry matter of sunflower oil substituting for corn grain (LF-SO)


title: MT1

description: rRNA depleted RNA


title: WT2

description: rRNA depleted RNA


title: A377-75

city: Tjele

first: Peter

last: Sørensen

address: Blichers Alle 1

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
Sequence reads obtained for each sample were aligned separately to the Bovine genome assembly (UMD3.1).  Sequence alignment was conducted using an efficient and sensitive mapping paradigm based on seed-and-vote algorithm (Liao et al., 2013 Liao Y, Smyth GK and Shi W (2013).  implemented in the Rsubread package in R. The abundance of mRNAs for all genomic features (bovine Ensembl genes) was calculated for each sample. Procedures described by Lawrence et al. (2013)  were used to obtain the annotated bovine ensemble genes from the annotations available at the UCSC Genome Browser. The function ‘Feature Counts’ in the R package was used to count the number of reads that mapped to each feature using the default settings.
Genome_build: Bovine genome assembly (UMD3.1)
Supplementary_files_format_and_content: RPKM values

source_name: Udder

extract_protocol:
RNA extraction was performed as described previously (Kristensen et al., 2005).
Each sample was sequenced using a 100 bp paired approach with the Illumina Hiseq2000 sequencing technology by AROS Applied Biotechnology (Aarhus, Denmark). The standard Illumina TruSeq mRNA protocol was used with minor changes (fragmentation time was 1 minute and the number of PCR cycles was 13).

value: Udder

tag: ID

tag: type

value: HF

tag: infection

value: kontrol

tag: time (h)


title: A377-68

value: VF


title: TATCre+hSS2 tumor 3

value: containing Cre-lox inducible allele of SS18-SSX2

value: TATCre protein


title: A377-98


title: A377-65


title: A377-79


title: A377-67


title: A377-105


title: A377-73


title: A377-104


title: A1 (LF-SO)


title: A377-66


title: A377-72


title: A377-06

source_name: Liver

value: Liver

value: L


title: A377-103


title: A377-10


title: A377-71


title: A377-09


title: A377-116


title: A377-97


title: A377-115


title: A377-04


title: A377-05


title: A377-02


title: A377-37


title: A377-41


title: A377-111


title: A377-33


title: A377-44


title: A377-40


title: A377-36


title: A377-123


title: A377-54


title: A377-12


title: A377-03


title: A377-58


title: A377-08


title: Clone 34 day5 Replicate1

description: Expression profile of hF x mESC fuction, Day 5

data_processing:
Human fibroblast RNA-seq reads were aliged to the Human genome (hg19) using Tophat v2.0.8 and Ensembl gene v72 as gene model.
RNA-Seq reads from hF x mESC fusion were aligned independently to Human (hg19, Ensembl v72) and Mouse (mm9, Ensembl v67) using Tophat v2.0.8. Reads aligned to both Human and Mouse were excluded from the further anlaysis.
Reads overlapping with each gene were counted using  HTSeq
FPKM values were computed using R script
Mumber of SNP-overlapping reads for mjor and minor allele was obtained using SAMtools mpileup version 0.1.18
Genome_build: hg19 & mm9
Supplementary_files_format_and_content: hg19 FPKM values
Supplementary_files_format_and_content: Number of reads overlapping with major and minor alleles at selected SNPs on chrX

organism: Homo sapiens x Mus musculus hybrid cell line

source_name: hF x mESC fusion

extract_protocol:
Total RNA was exacted by RNABee (Amsbio), treated with RNAse-free DNAseI (Ambion) and cleaned-up with RNAeasy Mini-elute columns.
RNA-seq libraries were prepared from 0.6μg total RNA accordingly to Illumina True-seq RNA sample preparation v2 guide (Illumina). For the ligation step, 2 μl of adaptors were used. Libraries were amplified 14 cycles before deep-sequencing.

value: fibroblast clone (derived from TERT-immortalised NHDF17914) fused with mouse ESC (E14Tg2a:puroR)


title: A377-51


title: App3_RNA-seq

city: Wuhan

first: Lu

last: Li

email: sakura.tree@163.com, xuzf@mail.hzau.edu.cn, xuzhuofei@sohu.com, kobe2071@tom.com

state: Hubei

address: Shizishan Street 1

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.8.2 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Perl script was written to convert Illumina reads into fastq format.
The reads in fastq format were converted to Sanger fastq format with the script“fq_all2std.pl’’ from MAQ
All the reads in sanger fastq format were mapped to the A. pleuropneumoniae JL03 genome sequence (GenBank Accession number. CP000687) using the Burrows-Wheeler alignment tool (BWA) allowing for a maximum of two mismatches.The reads that map to more than one location were discarded.
Samtools was used for data format conversion into SAM/BAM format and to generate alignment results in a pileup format.
Genome_build: CP000687 [ASM1668v1]
Supplementary_files_format_and_content: BED file contains the count of reads per base aligned to each location across the genome.

organism: Actinobacillus pleuropneumoniae serovar 3 str. JL03

source_name: Actinobacillus pleuropneumoniae JL03 cell culture

growth_protocol: A. pleuropneumoniae JL03 was grown at 37℃ in tryptic soy broth (TSB) or on tryptic soy agar (TSA), supplemented with 10% (v/v) filtered cattle serum and 10 μg/ml nicotinamide adenine dinucleotide (NAD). The culture was adjusted to an OD600nm=1, supplemented with RNAprotect reagent, and cells harvested by centrifugation and stored at -80°C.

extract_protocol:
Total RNA was extracted using RNA Midiprep kit (Promega, Madison, USA) according to the manufacturer’s protocol. Total RNA was treated with RNase-free DNase (Invitrogen, Carlsbad, CA) to remove traces of genomic DNA. By using Agilient Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA), we checked the RNA integrity number (RIN) of total RNA to be greater than 8. Bacterial 16S and 23S ribosomal RNAs were removed with a MICROBExpress ™ kit (Ambion, TX, USA). Small RNAs (i.e., tRNA and 5S rRNA) were not removed with this enrichment step.
We used 100 ng enriched mRNA with Illumina mRNA-Seq sample preparation kit (Illumina,San Diego, CA) for library construction following manufacturer's protocols.

tag: isolate

value: clinical isolate of serovar 3

tag: culture condition

value: cultured in TSB medium to middle exponential phase