title: MCF10A MII_siJUNB, TGFβ 16h_RNA

city: Tokyo

first: Masato

last: Morikawa

address: 2-21-1 Kaga, Itabashi-ku

department: Advanced Comprehensive Research Organization

country: Japan

institute: Teikyo University

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
RNA-seq reads were aligned and gene expression levels in fragments per kilobase of exon per million fragments mapped (FPKM) were estimated using Tophat/Cufflinks (version 2.0.13 and 2.2.1, respectively) with the default parameter settings (Trapnell et al., 2012).
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
BAM to bigWig conversion was performed  using "samtools depth" combined with "UCSC wigToBigWig".
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file includes FPKM values of genes for each Sample, which was generated by Cufflinks; bigWig files were generated by Tophat and wigToBigWig.

source_name: Breast epithelial cell line, MCF10A MII

growth_protocol: MCF10A MII cells were obtained from Dr. Fred Miller (Barbara Ann Karmanos Cancer Institute, Detroit, USA) and maintained at 37°C and 5% CO2 in DMEM/F12 (Gibco), supplemented with 5% FBS (HyClone), 20 ng/ml epidermal growth factor (EGF) (PeproTech), 100 ng/ml cholera toxin (Sigma-Aldrich), 0.5 μg/ml hydrocortisone (Sigma-Aldrich), 10 μg/ml insulin (Sigma-Aldrich).

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen).
RNA-seq libraries were prepared essentially as described (Parkhomchuk et al., 2009). In short, mRNA was isolated from 1 μg total RNA using Dynabeads Oligo(dT)25 (Life Technologies) and fragmented to 150-200 nt in first strand buffer for 3 min at 94°C. Random hexamer primed first strand was generated in presence of dATP, dGTP, dCTP and dTTP. Second strand was generated using dUTP instead of dTTP to tag the second strand. Subsequent steps to generate the sequencing libraries were performed with the NEBNext kit for Illumina sequencing (New England Biolabs) with minor modifications; after indexed adapter ligation to the dsDNA fragments, the library was treated with USER (Uracil-Specific Excision Reagent) Enzyme (New England Biolabs) in order to digest the second strand derived fragments. After amplification of the libraries, samples with unique sample indexes were pooled and sequenced using HiSeq 2500 with TruSeq SBS Kit v4 reagent (Illumina) following the manufacturer's protocols.

treatment_protocol: Recombinant human TGFβ3 (a generous gift of Dr. K. Iwata, OSI Pharmaceuticals, Inc, New York, USA) was used for stimulation of cells. For siRNA-mediated knockdown, Dharmacon On Target Plus pools of four oligonucleotides (GE Healthcare Life Sciences) was transfected using siLentFect (Bio-Rad) transfection reagent according to manufacturer’s instructions at 25 nM final concentration.

value: MCF10A MII

value: Breast epithelial cell line

tag: transformation

value: H-Ras transformed

tag: treatment

value: TGFβ3, 5 ng/ml, 16h

tag: knockdown

value: siJUNB, final 25 nM


title: MCF10A MII_siJUNB, control_RNA

status: Public on Nov 15 2017

type: SRA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: untreated


title: MCF10A MII_siControl, TGFβ 16h_RNA

value: siControl, final 25 nM


title: MCF10A MII_siJUNB, TGFβ 1.5h_RNA

value: TGFβ3, 5 ng/ml, 1.5h


title: MTD control 0-2hr replicate4

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

department: Molecular Biology

country: USA

institute: Massachusetts General Hospital

data_processing:
RNAseq reads were aligned to the D. melanogaster genome (dm3) using TopHat version 2.0.13 with default parameters
Reads mapping to genes were counted using HTseq-count version 0.5.4p3 with parameters ‘-s no -a 10’
Differential expression analysis of the RNAseq was done using the DESeq tool
Genome_build: dm3
Supplementary_files_format_and_content: [.txt file] Fold changes and significance of changes in gene expression are given for each gene
Columns are:
id: gene id
baseMean: average of MTD control and clamp RNAi
baseMeanA: MTD control, average of replicates
baseMeanB: clamp RNAi, average of replicates
foldChange: fold change from MTD control to clamp RNAi
log2FoldChange: log2 of foldChange
pval: p-value
padj: adjusted p-value, FDR

molecule: total RNA

organism: Drosophila melanogaster

source_name: Mixed sex embryos

growth_protocol: 3-5 day old virgin females of the relevant genotypes were mated to yw males. Embryos were collected on standard grape juice plates with yeast paste.

extract_protocol:
Total RNA was extracted with trizol. RNAseq libraries were made using the NuGEN Ovation kit with Drosophila ribosomal RNA depletion.
Libraries were preapred as described in the NuGEN Ovation kit.

treatment_protocol: Embryos were dechorionated in bleach for 2-5 minutes and washed extensively with 1x PBS.

tag: genotype/variation

value: MTD control

tag: strain

tag: developmental stage

value: embryo

tag: time

value: 0-2 hour after egg lay


title: clamp RNAi 0-2hr replicate4

value: clamp RNAi


title: MTD control 2-4hr replicate4

value: 2-4 hour after egg lay


title: MCF10A MII_siControl, control_RNA


title: MCF10A MII_siControl, TGFβ 1.5h_RNA


title: clamp RNAi 0-2hr replicate3


title: MTD control 0-2hr replicate3


title: clamp RNAi 2-4hr replicate2


title: MTD control 2-4hr replicate3


title: clamp RNAi 2-4hr replicate3


title: clamp RNAi 0-2hr replicate2


title: ALP.2

city: Bethesda

first: Margaret

middle: C

last: Cam

state: MD

institute: NIH

data_processing:
Basecalling by RTA 1.18.64, Illumina instrument run time analysis software, Demultiplexing Bcl2fastq 1.8.4, Barcode demultiplexed allowing 1 mismatch
The raw RNA-Seq fastq reads were aligned to mouse genome (mm10) using STAR (v. 2.4.0h) on 2-pass mode with mouse gencode (release 4) gtf
Genes were subsequently counted using Rsubread and further normalized using TMM (edgeR) and analyzed for gene expression changes using limma-voom with quantile normalization.
Genome_build: mm10
Supplementary_files_format_and_content: Genes were subsequently counted using Rsubread and further normalized using TMM (edgeR) and analyzed for gene expression changes using limma-voom with quantile normalization. The gene and sample-specific normalization factors were then used to correct counts to generate bedgraph files used for further visualization.

organism: Mus musculus

source_name: ALP

growth_protocol: samples were isolated by cell sorting from bone marrow and thymus single cell suspensions

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen)
mRNA sequencing libraries were prepared using the SMARTer Ultra Low Input RNA Kit v3 (Clontech) and Nextera XT DNA library preparation kit (Illumina)

tag: genotype

tag: tissue

value: bone marrow

tag: sorting profile

value: linlow Ly-6Dlow Kitpos IL-7Rapos Flt3high

tag: batch


title: clamp RNAi 2-4hr replicate1


title: MTD control 2-4hr replicate2


title: MTD control 0-2hr replicate2


title: clamp RNAi 0-2hr replicate1


title: MTD control 0-2hr replicate1


title: dex2

city: Heidelberg

first: Jan

last: Lohmann

address: Im Neuenheimer Feld, 230

department: Stem Cell Biology

country: Germany

institute: Centre for Organismal Studies

data_processing:
Quality control: FastQC
Read alignment: TOPHAT2
BAM SAM conversion: samtools
Read table reconstruction: HT-seq
Genome_build: TAIR10
Supplementary_files_format_and_content: text file with normalized read count table

organism: Arabidopsis thaliana

source_name: inflorescence

growth_protocol: 23°C; 65% humidity;  16h light/8h dark; LED lights 200µE

extract_protocol:
RNAeasy plant mini kit according to manufacturer instructions (Qiagen, Hilden, Germany)
The RNA were poly A selected using the NEB Poly (A) Magnetic isolation module (7490), then the NEBnext Ultra Direction RNA Prep Kit (E7420) for Illumina with the NEBnext Multiplex Oligo's for Illumina (E7335). For RNA 1 µg inout was used.

treatment_protocol: 0.01% ethanol,0.015% Silwet, with or without 10µM dexamethasone,

tag: ecotype

value: inflorescence

tag: age

value: 30 days after germination

value: until flower stage 3-4


title: CCL5-rep 3

city: Toon

first: Ji-Won

last: Lee

address: Shitsukawa

department: Proteo-Science Center

institute: Ehime University

data_processing:
Sequence data were mapped on the mouse genome (mm10) using Tophat and anlyzed by Cufflinks.
Genome_build: mm10

source_name: bone marrow

growth_protocol: Mouse bone marrow cells isolated from 7 week old mice cultured in a-MEM were used.

extract_protocol:
Total RNA was extracted with an RNeasy spin column kit (Qiagen, USA), followed by treatment with DNase I (Qiagen). RNA samples with RNA integrity number (RIN) greater than 8 were normalized to 100 ng/μl before further analyses.
RNA-Seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit setA (Illumina, San Diego CA) according to the manufacturer's instructions and subsequently validated for an average size of about 330-340 bp using a 2100 Bioanalyzer and the Agilent DNA1000 kit.for the construction

treatment_protocol: Bone marrow macrophages were induced with 50ng/mL M-CSF for 24 hr. Then cells were incubated with RANKL alone and the combinationa of RANKL and CCL5 (100ng/mL) for 48 hr further.

value: 7 week-old

value: Primary bone marrow macrophages

tag: treated with

value: recombinant CCL5


title: CCL5-rep 2


title: CCL5-rep 1


title: dex1


title: clamp RNAi 2-4hr replicate4


title: ACs alone #2

city: Berkeley

first: Jeffery

middle: S

last: Cox

state: CA

address: University of California, Berkeley Dept. of Molecular and Cell Biology 142 Weill Hall #3200

institute: University of California, Berkeley

description: rRNA-depleted RNA

data_processing:
Basecalls performed using CASAVA version 2.7.
Sequenced reads were quality-trimmed (cut-off of 30) with cutadapt 1.1. Command line parameters: -m 35 -q 30,30
Aligned to the mouse transcriptome (GRCm38, release 79) with Kallisto 0.43.3. --single -l 200 -s 30 -b 60 (pseudoaligned using a 31-mer index).
Genome_build: GRCm38
Supplementary_files_format_and_content: *txt: Tab-delimited text files include TPMs.
Supplementary_files_format_and_content: *hdf5: hdf5 format, from Kallisto, contains pseudo alignment counts and bootstrapping estimates for analysis with Sleuth package.

source_name: irradiated thymocytes, +ACs

growth_protocol: Macrophages were cultured in complete RPMI media after isolation from mice.

extract_protocol:
Total RNA was prepared from cells using RNAzol, DNase treated and purified using RNA clean and concentrator columns. 1 ug of total RNA was subsequently used for rRNA depletion using the RiboZero depletion kit.
RNA-Seq library was prepared by using the TruSeq RNA sample prep kit (Illumina) according to manufacturer’s instructions.
50-cycle single-end RNA sequencing was performed on a HiSeq 4000 (Illumina).

tag: strain/background

value: wild type

value: irradiated thymocytes

tag: time in culture

value: + ACs


title: Control rep3

value: none (control)


title: mock3


title: Control rep2


title: ACs alone #1

description: rRNA-depleted RNA

tag: treatment


title: mock1


title: Control rep1


title: Deprogrammed macrophages + ACs #2

description: rRNA-depleted RNA

source_name: Tim-4+ peritoneal macrophages, 60 hours in culture, +ACs

treatment_protocol: Tim-4+ peritoneal macrophages were stimulated + apoptotic cells (ACs) immediately ex vivo or after tissue culture for 2 or 60 hours.

value: Tim-4+ peritoneal macrophages

value: 60 hours


title: Deprogrammed macrophages + ACs #1

description: rRNA-depleted RNA


title: cyc-dex3

treatment_protocol: 10µM cycloheximide, 0.01% ethanol,0.015% Silwet, with or without 10µM dexamethasone,


title: NGP TFAP4 KD RNASeq [SD006]

city: New York

first: Gonzalo

last: Lopez

state: NY

address: 1399 Park avenue

department: Genetics and Genomic Sciences

institute: Mount Sinai School of Medicine

data_processing:
We use RTA (Illumina) for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: txt files were generated containing gene level read count values, gene FPKM and isoform FPKM values

source_name: NGP TFAP4 KD RNASeq

growth_protocol: NGP was maintained in RPMI-40 medium supplemented with 10% FBS and 1% penicillin/streptomycin (Invitrogen)

extract_protocol:
Total RNA was extracted using RNEASY mini kit (Qiagen).
We use poly-A pull-down to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required) and proceed on library preparation by using Illumina TruSeq RNA prep kit.
Libraries are then sequenced using Illumina HiSeq2000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol:
1ug/ml Doxycycline adding into the medium to induce the shRNA
Lentiviral particles using shRNA (Dharmacon, V3THS_301154) against TFAP4.

value: NGP

tag: tissue source

value: bone marrow metastatic neuroblastoma

value: neuroblastoma cell line

value: Dox


title: cyc-dex2


title: Programmed macrophages + ACs #1

description: rRNA-depleted RNA

source_name: Tim-4+ peritoneal macrophages, 2 hours in culture, +ACs

value: 2 hours


title: MTD control 2-4hr replicate1

value: MTD control

value: embryo

value: 2-4 hour after egg lay


title: dex3

value: inflorescence

value: 30 days after germination

value: until flower stage 3-4


title: cyc-mock3


title: cyc-dex1


title: NGP Control RNASeq [SD005]

source_name: NGP Control RNASeq

treatment_protocol:
Control
Lentiviral particles using shRNA (Dharmacon, V3THS_301154) against TFAP4.

tag: cell line

value: control

value: Control


title: 60 hours in culture expt 2 #2

description: rRNA-depleted RNA

source_name: Tim-4+ peritoneal macrophages, 60 hours in culture

value: wild type

tag: cell type


title: cyc-mock2


title: cyc-mock1


title: 60 hours in culture expt 1 #2

description: rRNA-depleted RNA

tag: genotype/variation


title: SKNDZ TFAP4 KD RNASeq [SD002]

source_name: SKNDZ TFAP4 KD RNASeq

growth_protocol: SKNDZ was maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin (Invitrogen).

value: SK-N-DZ

value: shRNA (Dharmacon, V3THS_301154) against TFAP4


title: Immediately ex vivo expt 2

description: rRNA-depleted RNA

source_name: Tim-4+ peritoneal macrophages, immediately ex vivo

value: Tim-4+ peritoneal macrophages

value: 0 hours


title: SKNDZ Control RNASeq [SD007]

source_name: SKNDZ Control RNASeq

value: bone marrow metastatic neuroblastoma


title: mock2


title: 60 hours in culture expt 2 #1

description: rRNA-depleted RNA

value: 60 hours


title: 60 hours in culture expt 1 #1

description: rRNA-depleted RNA


title: Programmed macrophages - ACs #2

description: rRNA-depleted RNA

source_name: Tim-4+ peritoneal macrophages, 2 hours in culture, -ACs

value: - ACs


title: Immediately ex vivo expt 1

description: rRNA-depleted RNA


title: SKNDZ Control RNASeq [SD001]

value: neuroblastoma cell line


title: Unbound_free_dna_rep3

city: Munster

first: Veeramohan

last: Veerapandian

state: North Rhine-Westphalia

address: Röntgenstr. 20

department: Department Tissue Morphogenesis

institute: Max Planck Institute for Molecular Biomedicine

description: Contains dimer bound, two monomer bounds and unbound for downstream processing. Contains raw data from 2 replicates.

library_source: genomic

data_processing:
Raw reads were de –multiplexed using custom python scripts and imported into R (https://www.r-project.org/) and the Biostrings, data.table and ggplot2 packages were used for further analysis.
The 5-mers at the randomized positions were extracted with the extractAT function and counted using the oligonucleotideFrequency function (width =5) for each band and replicate.
Finally, the cooperativity factor  was calculated for each sequence using k-mer count data in dimer, monomer1, monomer2 and free DNA fractions followed by median normalization to account for technical variability
N/A
N/A
Genome_build: N/A
Supplementary_files_format_and_content: Tab delimited text files.

molecule: genomic DNA

organism: mixed DNA library

source_name: Synthesized DNA

extract_protocol: The Coop-seq experiment was performed following a previously reported workflow ( DOI:  https://doi.org/10.1093/nar/gkw1198  ) by mixing 200 nM of a 109 amino acids Sox2 HMG construct  and 300 nM Pax6 paired domain  with 250 nM randomized DNA library in CutSmart buffer (NEB). 10 l of the reaction were loaded onto 12% PAGE minigels and electrophoresed for 1 h at 200 V using a Tris-Glycine [25 mM Tris pH 8.3; 192 mM glycine] buffer system. The gel was stained with ethidium bromide and bands containing dimers, monomers and free DNA were excised with a disposable toothpick. The DNA was eluted from the gel, ethanol precipitated and PCR amplified using HotStart DreamTaq Green PCR Master Mix (2X) (ThermoFisher Scientific) and primers containing modified indexed-Illumina primers with barcodes in both directions PCR products were purified using the TIANquick Midi purification kit and submitted for sequencing using the HiSeq2000 system. Samples were sequenced in rapid mode in the presence of 15% PhiX genomic DNA with a read length of 125 bp.

tag: sample type

value: Library of DNA oligos


title: Colon/K562, replicate 1

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

description: Epithelial enrichment

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using inDrops pipeline (https://github.com/indrops/indrops). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods.
Human and mouse genes were separated and then human and mouse cells were deconvolved to observe doublet rate.
Mouse cells were selected for further analysis, and barcodes with number of unique UMIs greater than a threshold (Klein et al., 2015) were selected, resulting in the processed data table.
Genome_build: Human: GRCh38.85, Mouse: GRCm38.85 (mixed database)
Supplementary_files_format_and_content: *_colon_rnaseq.csv: Comma-delimited tables, with cells and genes, as columns and rows.

organism:
Homo sapiens
Mus musculus

growth_protocol: Primary cells/cell line mix.

extract_protocol:
Mouse epithelial cell suspensions were obtained by EDTA extraction and Collagenase/DNase dissociation. Viable cells were enriched with MACS. K562 cells were spiked in. Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of RNA/cDNA followed by index primer-based amplification.
RNA-Seq was performed on NextSeq500 with a 2 x 75 paired-end kit using custom read lengths.

treatment_protocol: None.

tag: mouse strain/background

tag: mouse genotype/variation

value: WT

tag: mouse cell type

value: Colonic epithelial cells

tag: human cell line


title: Pax6_monomer_rep3


title: Programmed macrophages + ACs #2

description: rRNA-depleted RNA

value: 2 hours

value: + ACs


title: Sox2_monomer_rep3

description: Contains dimer bound, two monomer bounds and unbound for downstream processing. Contains raw data from 5 replicates.


title: shMSK1_H3K27me3

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

data_processing:
ChIP-seq datasets were aligned to the human genome build hg19 using BowTie (version 1.0.1) (Langmead et al. 2009); the parameters used were –k 1, –m 1, and –n 2. UCSC browser tracks (Kent et al. 2002) were created from the mapped bam file after converting it to bedGraph (normalized to 10 million reads) and subsequently bigWig format. For histone marks, MACS version 2 was used with parameters –broad, -q 0.01, and –g mm. ChIP-seq peaks were annotated using the annotatePeaks.pl script of the HOMER suite (version 4.6)
For Histone Marks, MACS2 was used with parameters -broad, -q 0.01 -g hs.
Genome_build: hg19
Supplementary_files_format_and_content: The BED files were obtained from the output of MACS2.

source_name: dormant bone metastatic (DBM) derivatives of T47D cells

growth_protocol: Cells were grown in DMEM 4,5g/L D-glucose medium supplemeted with 10% FBS, 50 U/ml penicilin, 50μg/ml streptomycin and 5% glutamine.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with indicated antibody
Libraries for sequencing were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) following the manufacturer's instructions.

tag: transfection

tag: chip antibody

value: H3K27me3 (Abcam, ab6002)


title: shMSK1_input_DNA


title: shMSK1_H3K27ac

value: H3K27ac (Merck Millipore, 07-360)


title: 92 h

city: Jinan

first: Guangxiang

last: Cao

address: 18877 jingshi Road

country: China

institute: Shandong Academy of Medical Sciences

data_processing:
Basecalling were performed by Illumina GA Pipeline v1.5
raw reads were filtered to generate clean data
clean reads were aligned against genome by SOAP aligner/SOAP2 (Li， 2009）
Reads per kilobase transcriptome per million mapped reads(RPKM) was used to analyze the expression of genes
Genome_build: Reference Genome Sequence is NC_003888.3,NC_003903.1,NC_003904.1.
Supplementary_files_format_and_content: text files include RPKM values for each Sample .

organism: Microlunatus phosphovorus

growth_protocol: The bacteria were grown aerobically in the SBR at 28 oC for 74 h to reach the mid-exponential growth phase, and then alternating anaerobic and aerobic processes were operated.

extract_protocol:
the cell were collected at various times, ground in liquid nitrogen, and then dispensed into Rezol reagent (SBSBIO). Crude RNA samples were treated twice with ‘Turbo DNA-free’ DNase reagents (Ambion) to remove chromosomal DNA
The integrity of total RNA was determined using a Thermo NanoDrop, and the RNA Integrity Number value of each sample met the standard required for preparing a cDNA library. The cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

treatment_protocol: the total RNA of Microlunatus phosphovoruswas extracted from cultures in SBR for 86h  and 92 h, and then treated with RNase-free DNase I (Invitrogen) twice according to the recommended protocols.

tag: phenotype

value: anaerobic

tag: strain


title: Sox2Pax6_dimer_rep3


title: shMSK1_H3K9me3

value: H3K9me3 (Abcam, ab8898)


title: Unbound_free_dna_rep2


title: 86 h

value: aerobic


title: shMSK1_H3K9ac

value: H3K9ac (Abcam, ab4441)


title: Programmed macrophages - ACs #1

description: rRNA-depleted RNA

value: wild type

value: Tim-4+ peritoneal macrophages


title: shCTRL_input_DNA

value: shCTRL


title: shCTRL_H3K27me3


title: 30 degrees C replicate 3

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: Wildtype S. aureus USA300 NRS384 replicate 3 grown at 30 degrees C

data_processing:
Bioinformatic analyses were performed using R (http://r-project.org), and packages from the Bioconductor project (http://bioconductor.org).
RNA sequencing reads were processed using the HTSeqGenie package. Reads were aligned to the Staphylococcus aureus USA300 NRS384 genome sequence using the GSNAP algorithm. Uniquely aligned read pairs were tallied to estimate gene expression levels.
To determine differential expression of genes, we used the DESeq and DESeq2 algorithms with default parameters. To control for multiple testing, P values were adjusted using the Benjamini–Hochberg method. RPKMs were normalized using the library size normalization defined by Anders and Huber. Genes were considered differentially expressed if they differed between comparison groups by at least twofold, with an adjusted P < 0.05.
Genome_build: Staphylococcus aureus USA300 NRS384
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene counts, gene length, and RPKM values

organism: Staphylococcus aureus USA300-0114

source_name: USA300 cultures

growth_protocol: USA300 cultures were grown in TSB alone.

extract_protocol:
RNA was isolated from the bacteria using RNAeasy Mini Kit (Qiagen). Quality control of RNA samples was done to determine RNA quantity and quality prior to their processing by RNA-seq. The concentration of RNA samples was determined using NanoDrop 8000 (Thermo Scientific) and the integrity of RNA was determined by 2100 Bioanalyzer (Agilent Technologies).
Ribosomal RNA depletion was performed using a Ribo-Zero rRNA Removal Kit (Bacteria) (Illumina, San Diego, CA) according to the manufacturer’s instructions. RNA-seq library generation was continued using the TruSeq RNA protocol (Illumina) starting at the “Elute, Prime, Fragment” step and was completed according to the manufacturer’s instructions.

tag: genotype

value: Wildtype

tag: growth temp

tag: replicate

tag: growth phase

value: log, OD 0.5

tag: nacl pct


title: Pax6_monomer_rep2


title: shCTRL_H3K27ac


title: 30 degrees C replicate 2

description: Wildtype S. aureus USA300 NRS384 replicate 2 grown at 30 degrees C


title: Sox2Pax6_dimer_rep2

description: Conatins bound and unbound reads needed to calculate the relative binding energy.


title: Sox2_monomer_rep2


title: 30 degrees C replicate 1

description: Wildtype S. aureus USA300 NRS384 replicate 1 grown at 30 degrees C


title: Colon/K562, replicate 2

description: Epithelial enrichment

tag: treatment


title: Unbound_free_dna_rep1


title: shCTRL_H3K9ac


title: shCTRL_H3K9me3


title: Pax6_monomer_rep1


title: 37 degrees C replicate 3

description: Wildtype S. aureus USA300 NRS384 replicate 3 grown at 37 degrees C


title: input DNA, BT549

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command “-S -a --best --strata -v 1 -m 1”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
SMAD2/3 binding regions were identified using MACS software (Model based analysis of ChIP-seq) (version 1.4.2) (Zhang et al., 2008) with a p-value threshold of 1e-5.
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and WIG files were generated using MACS (version 1.4.2).

growth_protocol: Hs578T and BT-549 were obtained from ATCC, and maintained as recommended. Briefly, Hs578T cells were cultured at 37°C and 5% CO2 in DMEM (Gibco, Thermo Fisher Scientific) supplemented with 10% FBS (HyClone, GE Healthcare Life Sciences), and 10 μg/ml insulin (Gibco), and BT-549 cells were maintained in RPMI-1640, supplemented with 10% FBS (HyClone), and 0.023 IU /ml insulin (Gibco).

extract_protocol:
Chromatin isolation, sonication and immunoprecipitation using anti-SMAD2/3 antibody (#610843, BD Transduction Laboratories) were performed essentially as described (Isogaya et al., 2014; Morikawa et al., 2016).
The libraries were constructed as described (Murai et al, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: Recombinant human TGFβ3 (R&D Systems) was used for stimulation of cells.

tag: cell line

value: breast cancer cell line BT549

tag: disease state

value: Triple-negative breast cancer (TNBC)

value: untreated

tag: time

value: control


title: 37 degrees C replicate 1

description: Wildtype S. aureus USA300 NRS384 replicate 1 grown at 37 degrees C


title: WT 2C 10 uM Linoleic Acid

description: WT S. aureus USA300 NRS384 10 uM Linoleic Acid replicate 2C

source_name: S. aureus USA300 NRS384 cultures

growth_protocol: S. aureus USA300 NRS384 cultures were grown in TSB alone or supplemented with individual fatty acids (20µM, 10µM, 5µM, 2.5µM, 1.25µM, 0.625µM).

treatment_protocol: RNA-seq was performed using USA300 S. aureus in the presence and absence of 10 μM linoleic acid. For each condition we included three replicates thereby yielding a total of 6 samples.

tag: group

value: WT

value: 10 uM Linoleic Acid


title: Sox2Pax6_dimer_rep1

tag: sample type

value: Library of DNA oligos


title: MCF10A MII, TGFβ 1.5h_RNA

source_name: Breast epithelial cell line, MCF10A MII

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen).
RNA-seq libraries were prepared essentially as described (Parkhomchuk et al., 2009). In short, mRNA was isolated from 1 μg total RNA using Dynabeads Oligo(dT)25 (Life Technologies) and fragmented to 150-200 nt in first strand buffer for 3 min at 94°C. Random hexamer primed first strand was generated in presence of dATP, dGTP, dCTP and dTTP. Second strand was generated using dUTP instead of dTTP to tag the second strand. Subsequent steps to generate the sequencing libraries were performed with the NEBNext kit for Illumina sequencing (New England Biolabs) with minor modifications; after indexed adapter ligation to the dsDNA fragments, the library was treated with USER (Uracil-Specific Excision Reagent) Enzyme (New England Biolabs) in order to digest the second strand derived fragments. After amplification of the libraries, samples with unique sample indexes were pooled and sequenced using HiSeq 2000 with TruSeq SBS Kit v3 reagent (Illumina) following the manufacturer's protocols.

value: MCF10A MII

tag: cell type

value: Breast epithelial cell line

tag: transformation

value: H-Ras transformed

value: TGFβ3, 5 ng/ml, 1.5h

tag: knockdown


title: SMAD2/3, MCF10A MII, TGFβ 16h_ChIP

data_processing:
Reference files of the human genome hg19 (NCBI build 37, Feb. 2009) and GTF annotation file were obtained from iGenomes (http://support.illumina.com/sequencing/sequencing_software/igenome.html).
ChIP-seq data sets were aligned using Bowtie (version 1.1.0) (Langmead et al., 2009) with the command “-S -a --best --strata -v 1 -m 1”.
BAM files were sorted using Picard SortSam (http://picard.sourceforge.net/).
SMAD2/3 binding regions were identified using MACS software (Model based analysis of ChIP-seq) (version 1.4.2) (Zhang et al., 2008) with a p-value threshold of 1e-5.
WIG to bigWig conversion was performed  using UCSC wigToBigWig.
To reduce the size of the bigWig files, regions with value less than 2 were removed using bwtool (Pohl and Beato, 2014) with the command "remove less 2".
Genome_build: hg19
Supplementary_files_format_and_content: BED and WIG files were generated using MACS (version 1.4.2).

extract_protocol:
Chromatin isolation, sonication and immunoprecipitation using anti-SMAD2/3 antibody (#610843, BD Transduction Laboratories) were performed essentially as described (Isogaya et al., 2014; Morikawa et al., 2016).
The library was prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England Biolabs) or KAPA DNA Library Preparation Kits for Illumina (KAPA Biosystems).

treatment_protocol: Recombinant human TGFβ3 (a generous gift of Dr. K. Iwata, OSI Pharmaceuticals, Inc, New York, USA) was used for stimulation of cells.

value: TGFβ3, 5 ng/ml, 16h


title: SMAD2/3, BT549, TGFβ 16h_ChIP

tag: chip antibody

value: anti-SMAD2/3 antibody (BD Transduction Laboratories, catalog# 610843, lot# 2104740)


title: SMAD2/3, BT549, TGFβ 1.5h_ChIP


title: wt_rep2_RNA_seq

city: Norwich

first: David

middle: B.

last: Lyons

state: Norfolk

address: Colney Lane

country: United Kingdom

institute: John Innes Centre

description: ribo-depleted RNA

data_processing:
For all sequencing experiments, Illumina Hi-seq basecalls were converted to fastq with Illumina software 'bcl2fq' at the sequencing core facility
For bisulfite-seq, we used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 100 base reads were divided into the first 50 and the last 50 bases, 100 base reads were divided in half and 50 base reads were processed as single reads. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
For MNase-seq, paired-end reads were aligned using default bowtie2 settings and nucleosomes were identified with iNPS (Chen et al. 2014).   Group_1 is the best-positioned; Group_4 is the worst.
For RNA-seq, reads were mapped with Tophat and PCR duplicates were removed with samtools prior to identification of transcripts with cufflinks.  Transcript abundance estimates were made with kallisto/sleuth in the provided table, requires unaligned reads, which is why fastq and bam are both provided here.
Genome_build: TAIR10
Supplementary_files_format_and_content: bisulfite-seq single-c GFF files contain the per-base calculated methylated cytosine level; mnase-seq bigwig files are iNPS-smoothed read depth normalized to the library size (RPM) across the TAIR10 genome; bed files from MNase-seq are the nucleosome coordinates as called by iNPS (only 'MainPeaks') across the TAIR10 genome.

source_name: 1-month-old leaf

growth_protocol: ddm1-10 (Zhang et al., 2016), h1.1 (Zemach et al., 2013) and h1.2 (Zemach et al., 2013) Arabidopsis thaliana (Columbia ecotype) were crossed to generate h1ddm1 and siblings for this study. ddm1 was not homozygous at any point prior to the F2 reported herein.  For MNase-seq, RNA-seq, and bisulfite-seq samples, plants were germinated on agarose plates supplemented with Gamborg’s B-5 growth media (GBP07, Caisson Labs). Following germination, they were transferred to soil and grown on a 16hr-light/8hr-dark long-day schedule.

extract_protocol: Leaves (as above) were flash frozen in liquid nitrogen, pulverized with mortar and pestle on dry ice, and the resulting material was subjected to vortexing in Trizol (Invitrogen, cat. no. 15596-026). Chloroform was then added at one-fifth the total volume and further vortexing was carried out until the solution appeared homogenous. RNA was subsequently pelleted in ice-cold isopropanol. The resuspended RNA was subjected to rRNA removal with Ribo-zero plant kit (Illumina, MRZPL1224) according to the manufacturer’s protocol. 50 ng of ribo-depleted RNA was used for library preparation with the Scriptseq kit (Epicentre, cat. no. SSV21124) following the manufacturer’s protocol but with the following modifications: the RNA fragmentation step was extended to 10 minutes, and the temperature was increased to 90°C.

tag: tissue

value: rosette leaf

tag: genotype/variation

value: wt


title: Sox2_monomer_rep1


title: MCF10A MII, control_RNA


title: input DNA, Hs578T

value: breast cancer cell line Hs578T


title: WT 2B 10 uM Linoleic Acid

description: WT S. aureus USA300 NRS384 10 uM Linoleic Acid replicate 2B

tag: genotype


title: wt_rep1_RNA_seq

description: ribo-depleted RNA


title: SMAD2/3, Hs578T, TGFβ 1.5h_ChIP


title: WT 2A 10 uM Linoleic Acid

description: WT S. aureus USA300 NRS384 10 uM Linoleic Acid replicate 2A


title: ddm1_bsseq

extract_protocol: Genomic DNA (gDNA) was extracted from 1-month-old Arabidopsis thaliana rosette leaves with the DNeasy plant mini kit (Qiagen, cat. no. 69104) per the manufacturers’ instructions. Libraries were prepared from roughly 500ng of purified gDNA that was sheared to approximately 400bp on a Misonix water bath sonicator, then purified using 1.2X volume of Agencourt Ampure beads (referred to as “beads” henceforth, cat. no. A63881). Following ligation of methylated Truseq sequencing adapters (Illumina), bisulfite conversion of DNA was carried out according to manufacturer’s protocol (Qiagen Epitect Kit, cat. no. 59104) except without using carrier RNA. DNA was purified twice with 1.2X beads and converted a second time to ensure complete bisulfite conversion of unmethylated cytosine. NEB next indexing primers (cat. no. E7335S) were used for generating multiplexed libraries during PCR amplification of libraries.


title: WT_bsseq


title: h1_bsseq


title: SMAD2/3, MCF10A MII, TGFβ 1.5h_ChIP


title: input DNA, MCF10A MII


title: WT 1A No treatment

description: WT S. aureus USA300 NRS384 No treatment replicate 1A

value: No treatment


title: WT 1B No treatment

description: WT S. aureus USA300 NRS384 No treatment replicate 1B


title: 37 degrees C replicate 2

description: Wildtype S. aureus USA300 NRS384 replicate 2 grown at 37 degrees C

value: Wildtype

tag: growth temp

value: log, OD 0.5


title: hESC_day13_with_RP22_RNAseq_rep3

status: Public on Nov 14 2017

city: La Jolla

first: Evan

middle: Thomas

last: Powers

address: 10550 North Torrey Pines Rd

department: Chemistry

institute: The Scripps Research Institute

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Single end, 100 bp-long reads from RNA Seq experiments were aligned to the GRCh37.p13 human genome reference assembly using SeqMan NGen 11.2.1 or 12.2.0 (DNAStar Inc.) using default parameters.
The assembly data were imported into ArrayStar 12.2 with Qseq (DNAStar Inc.) to quantify the gene expression levels. The sequence counts were normalized to reads per kilobase per million (RPKM) after filtering out non-mRNA sequence features.
Genome_build: GRCh37.p13 human genome reference assembly
Supplementary_files_format_and_content: abundance measurements in RPKM, tab-delimited text
Supplementary_files_format_and_content: abundance measurements in raw counts, tab-delimited text

source_name: Human embyonic stem cells

growth_protocol: HUES9 were maintained on a feeder layer of Mito-C treated primary MEFs (EMD Millipore), with daily media changes of pre-warmed conditioned media supplemented with 6 ng/ml FGF2 (EMD Millipore). Conditioned media was prepared by incubating primary MEFS for 24hrs with hESC specific media (KnockoutTM DMEM (Life Technologies); 10% KnockoutTM Serum Replacement (Life Technologies); Human Plasmanate (Chapin Healthcare); 1% MEM Non-Essential Amino Acids Solution (Life Technologies); 1% Penicillin -Streptomycin (Life Technologies); 1% GlutaMAXTM (Life Technologies); 55 μM 2-mercaptoethanol (Fisher Scientific). hESCs were used between passages 36-46 for all experiments. hESCs were split every three days using accutase (Innovative Cell Technologies, Inc.), spun out at 200Åã x g for 5 min (Beckman, AllegraTM X-22) before re-plating on freshly prepared PMEF cells. Primary MEFs were plated on to 0.1% gelatine coated 10 cm dishes using PMEF media (DMEM (Corning Inc.; 10% FBS).

extract_protocol:
Samples for RNA-Seq analysis were collected at day 1 and 13 treated with 10 μM RP22 or 10 μM AA47. Three independent experiments were performed. Cells were lysed and total RNA was collected (RNeasy mini kit, Qiagen)
Libraries were constructed using standard Illumina protocols

treatment_protocol: HUES9 Cells were differentiated performing spin embryoid body (EB) formation, cells were treated with 5 mM StemoleculeTM (Stemgent) 24 hrs prior to the procedure. Accutase (Innovative Cell Technologies, Inc.) was used to detach cells before performing cell counting using a hemocytometer. 10,000 cells were plated into each well of a 96 V-shaped plate (VWR) in the absence of FGF2 using differentiation media (KnockoutTM DMEM (Life Technologies); 20% KnockoutTM Serum Replacement (Life Technologies); 1% MEM Non-Essential Amino Acids Solution (Life Technologies); 1% Penicillin –Streptomycin (Life Technologies); 1% GlutaMAXTM (Life Technologies); 55 μM 2-mercaptoethanol (Fisher Scientific). Plates were spun down at 950 x g for 5 min (Beckman, AllegraTM X- 22), before placing at 37C, 5% CO2 to encourage differentiation. Suspension cultures were prepared 24 hrs after EB preparation, and EBs were transferred into ultra low attachment 6-well microplates (Corning Inc.) for 5 days until EBs were plated on to Matrigel (Corning Inc.) coated dishes for further differentiation. Throughout differentiation, samples were collected at indicated time points. Differentiation media, containing required drug treatments or compounds was changed daily. ATF6 activating compound AA147 and its analogue RP22 was prepared in DMSO as stock solution of 10 mM, working aliquots were prepared and stored at -20C. The compound was used in differentiation media at final concentration of 10 μM. DMSO was used as drug solvent control, but was excluded from data presentation when AA147 and RP22 were used since no difference between RP22 and DMSO treated samples was detected.

value: Human Embryonic Stem Cell Line - HUES9

tag: passages

tag: sample collection day

tag: agent

value: 10 microM RP22 (Inactive Analogue)


title: MCF10A MII, TGFβ 16h_RNA

tag: treatment

value: control


title: hESC_day13_with_RP22_RNAseq_rep1

tag: cell line


title: hESC_day13_with_RP22_RNAseq_rep2


title: hESC_day13_with_AA147_RNAseq_rep2

value: 10 microM AA147 (ATF6 Activator)


title: hESC_day1_RNAseq_rep2


title: hESC_day1_RNAseq_rep3


title: SMAD2/3, Hs578T, TGFβ 16h_ChIP

source_name: SMAD2/3, Hs578T, TGFβ 16h_ChIP

tag: disease state

value: Triple-negative breast cancer (TNBC)


title: hESC_day13_with_AA147_RNAseq_rep1


title: NSCFoxp1

city: Utrecht

first: Paul

middle: J

last: Coffer

address: Uppsalalaan 6

department: Regenerative Medicine Center

country: Netherlands

institute: UMC Utrecht

description: anti-Foxp1 ChIP-seq

data_processing:
ChIP-sequencing reads were mapped with Bowtie 2.1.0 against the reference genome (mm10) using default settings (Langmead and Salzberg, 2012).
Peaks were called with HOMER software using the input as a control (Fold over local region=8, Fold over input=2) (Heinz et al., 2010).
Mapped fragments were extended according to the average fragment size and converted to TDF files, visualized with IGV tools v2.3.36 and represented as coverage normalized tracks (Robinson et al., 2011). SAMtools was used for manipulation of SAM and BAM files; manipulation of BED file format was performed with BEDtools (Li et al., 2009; Quinlan and Hall, 2010).
Motif discovery, peak annotation and generation of histograms were performed using HOMER software. For motif discovery the 200 bp sequence surrounding each peak was examined and motifs with length of 8, 10 and 12 nt were searched. Motifs were identified through de novo motif discovery.
For functional annotation of peaks the software GREAT was used, where genes that presented peaks within 1kb with Forkhead motif were selected (McLean et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Emrbyonic neural stem cells

growth_protocol: NSCs were grown as neurospheres in presence of EGF and bFGF

extract_protocol:
Crosslink was performed with disuccinimidyl glutarate (DSG) (Thermo Scientifis) for 45 minutes followed by 30 minutes incubation with formaldehyde 1%. The reaction was blocked with glycine 100 mM. Shearing was performed using Covaris S2 (Covaris, Woburn, MA) for 8 min at maximum intensity. The sonicated chromatin was incubated O/N at 4°C in presence of 5µg of anti-Foxp1 (ab16645, Abcam) coupled to A/G sepharose beads (Santa Cruz Biotechnology).
Kapa Hyper Prep Kit (Kapa Biosystems, Wilmington, MA) was used for End-repair, A-tailing and ligation of sequence adaptors. Samples were amplified by PCR and the libraries were size-selected in the 200-500 bp range.

tag: strain

tag: age

value: Embryonic neural stem cells

value: anti-Foxp1 (Abcam, catalog# ab16645, lot# GR55101-1)


title: NSCinput

description: input ChIP-seq


title: 022-NL

city: Beirut

first: Humam

last: Kadara

address: Riad El Solh Street

department: Department of Biochemistry and Molecular Genetics, Faculty of Medicine

country: Lebanon

institute: American University of Beirut

data_processing:
The Ion Torrent Suite 5.0 was used to assess the quality of the libraries and sequencing runs
Alignment of base calling filed to a reference file (hg19_ampliseq_transcriptome_ercc_v1.fasta) produced aligned BAM files within the Ion Torrent server
Transcripts were then quantified using a modified version of the expectation-maximization (E/M) algorithm
Resultant gene-based counts were normalized, log (base 2) transformed, and corrected for batch using the R limma package
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with TPM values for each sample. Data from all 48 samples are in one file

source_name: formalin fixed paraffin embedded lung tissue

extract_protocol:
RNA was extracted from all samples using the AllPrep DNA/RNA FFPE kit from Qiagen and suspended in nuclease free water (RNA) or AE buffer (DNA). Sample concentrations were measured using NanoDrop 1000 (Thermo Fisher Scientific), and RNA integrity numbers were obtained on the 2100 Bioanalyzer (Agilent Technologies) according to the manufacturer’s protocol
Approximately 30 ng of RNA was used based on sample concentrations obtained from the Qubit HS RNA assay (Thermo Fisher Scientific). All samples were reverse-transcribed to generate cDNA libraries using the Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific) adhering to the manufacturer’s protocol for FFPE samples with 16 cycles of target amplification. Library concentrations were determined by qPCR using an absolute quantitation method and the Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific) following the manufacturer’s protocol. Template reactions were carried out using the Ion PI Hi-Q OT2 200 Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions and then loaded onto Ion PI chips v3 using the Ion PI Hi-Q Sequencing 200 Kit based on the manufacturer’s protocol (Thermo Fisher Scientific).

tag: donor

value: cytologically-normal lung tissue


title: 022-LUAD

value: lung adenocarcinoma


title: 020-NL


title: 018-NL


title: 020-LUAD


title: 022-AAH

value: atypical adenomatous hyperplasia


title: WT 1C No treatment

description: WT S. aureus USA300 NRS384 No treatment replicate 1C

tag: group

tag: replicate

value: WT


title: hESC_day13_with_AA147_RNAseq_rep3


title: 018-AAH


title: 020-AAH


title: 017-LUAD


title: 016-AAH


title: 016-NL


title: 014-NL


title: 018-LUAD


title: 016-LUAD


title: 014-LUAD


title: 014-AAH


title: 010-NL


title: 012-AAH


title: hESC_day1_RNAseq_rep1


title: 017-AAH


title: 017-NL


title: 009-LUAD


title: 009-AAH


title: 009-NL


title: 008-LUAD


title: 008-AAH


title: 006-LUAD


title: 007-LUAD


title: 006-NL


title: panicle_R_postanthesis

city: Chesterfield

first: Ian

last: Davis

state: MO

address: 700 Chesterfield Pkwy W

department: Biotechnology

institute: Monsanto Company

data_processing:
RNA-STAR with default parameters (Dobin et al., 2013)
Calculate log2(1+Fragments_Per_Kilobase_of_exons_per_Million_mapped_reads) on a per-sample basis.
DESeq2 algorithm, as implemented in R/Bioconductor (Love et al., 2014)
TSS reads were identified by 5’ tag sequences from the SMARTer protocol. From these, transcription start sites were determined using a simple algorithm. For each gene, the TSS was considered to be the center of the 7 bp window containing the most 5’-tagged sequence reads. Only genes with at least 5 reads in the peak were considered for analysis. On the upstream (5’) side, TSSs were constrained to lie within 200 bp of the annotated TSS or less than halfway to the nearest upstream gene, whichever was less. On the downstream (3’) side, TSSs were constrained to precede the start codon or the first splice site, whichever was nearer to the annotated TSS. A gene was excluded from TSS analysis if any part of this region overlapped with any part of another gene.  TSS reads were pooled across all tissue samples.
Genome_build: Setaria italica genome (version 2.1) from Phytozome
Supplementary_files_format_and_content: all_gene_fpkms.csv: log2(1+Fragments_Per_Kilobase_of_exons_per_Million_mapped_reads) on a per-sample basis, in Comma-Separated Value format.
Supplementary_files_format_and_content: tss_offsets.txt: proposed changes to the Transcription Start Site for 4900 Setaria genes, in base pairs, relative to the TSS in the reference genome.  Negative numbers mean the TSS should move upstream, lengthening the gene;  positive numbers mean the TSS should move downstream, shortening the gene.

organism: Setaria viridis

source_name: Panicle post-anthesis

growth_protocol: Setaria viridis accession A10 seeds were surface sterilized with bleach, washed with sterile water, and germinated on sterile, wet filter paper. The seedlings were transferred after 3 days to a hydroponic apparatus (Araponics, Liege, Belgium) filled with Epstein’s media (4 mM KNO3, 4 mM Ca(NO3)2, 2.5 mM 2[N-morpholino]ethanesulfonic acid, 2 mM KH2PO4, 2 mM NH4NO3, 1 mM MgSO4, 50 μM FeEDTA, 50 μM KCl, 25 μM H3BO4, 2 μM MnSO4, 2 μM ZnSO4, 0.5 μM CuSO4, 0.5 μM (NH4)6Mo7O24, pH 6.0). The plants were grown in 8 hour days at 28°C under metal halide lamps and 16 hour nights at 22°C. Tissues were dissected as indicated in Table 1 and Figure 1, frozen in liquid nitrogen, and stored at -80°C prior to RNA extraction. Three independent biological replicates using plants grown at different times were performed and the samples were sequenced separately.

extract_protocol:
Tissues were homogenized in liquid nitrogen using a mortar and pestle. RNA was extracted using a Plant RNeasy kit (Qiagen). Genomic DNA was removed by digestion with RQ1 RNAse-free DNAse (Promega).
The integrity of the RNA was determined by Bioanalyzer (Agilent), and RNA with an RNA Integrity Number (RIN) of at least 7 was submitted to Otogenetics (Norcross, GA) for library preparation and sequencing. Briefly, this involved generating cDNA using the SMARTer cDNA kit (Clontech), followed by Illumina library preparation with NEBNext reagents (New England Biolabs). The libraries were sequenced on the Illumina HiSeq2000 platform generating paired-end 100 nt reads.

tag: accession

value: accession A10

tag: age (days after germination)

value: panicle


title: 006-AAH

tag: tissue


title: panicle_R_preanthesis

source_name: Panicle pre-anthesis


title: 005-NL


title: 005-AAH


title: 010-LUAD


title: 004-NL


title: shoot_V5_bulk

source_name: Bulk shoots

value: shoot


title: meristem_V5_inflorescence

source_name: Inflorescence meristem

value: meristem


title: root_V5_bulk

source_name: Bulk roots

value: root


title: 010-AAH


title: 005-LUAD


title: 003-NL


title: 003-LUAD


title: meristem_V3_vegetative

source_name: Vegetative meristem


title: leaf_V3_base

source_name: Leaf 3 base above ligule

value: leaf


title: leaf_V3_tip

source_name: Leaf 3 tip


title: 003-AAH


title: 007-NL


title: 007-AAH


title: leaf_V3_midsection

source_name: Leaf 3 mid section above leaf 2 ligule


title: leaf_V3_lowersection

source_name: Leaf 3 lower section below leaf 2 ligule


title: shoot_V3_bulk

source_name: Bulk shoot


title: 002-NL


title: shoot_VE_coleoptile

source_name: Coleoptile


title: 002-LUAD


title: 001-NL


title: shoot_R_bulk


title: Mterf4 (L/L) rep4

city: Bentley

first: Irina

last: Kuznetsova

state: WA

address: Building 304, Kent Street

department: The Centre for Crop and Disease Management

country: Australia

institute: Curtin University

data_processing:
HISAT2 version 2.0.4 (hisat2 -p 8 –dat) was used to perform alignment of paired-end reads to the Mus Musculus reference genome (GRCm38). The output files were sorted and indexed with SAMtools version 1.3.1
StringTie version 1.2.4  (stringtie -p 18 -e -B) was applied to estimate transcripts abundance
prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py) Python version 2.7.6 was used to extract raw counts
DESeq2 R package version 3.3.2 was used for differential expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: DESeq2 results

source_name: heart

extract_protocol:
Total RNA isolated from hearts
standard TruSeq library preparation

tag: strain background

tag: genotype/variation

value: Mterf4 (L/L)


title: Mterf4 (L/L) rep5


title: 001-LUAD


title: 004-LUAD


title: 004-AAH


title: Mterf4 (L/L, cre) rep3

value: Mterf4 (L/L, cre)


title: Mterf4 (L/L, cre) rep2


title: Mterf4 (L/L) rep3


title: Mterf4 (L/L, cre) rep1


title: 001-AAH


title: mouse.JNK.epithelium.susp.rep3.0

city: Worcester

first: Roger

address: 373 Plantation St Suite 309

institute: University of Massachusetts Medical School

data_processing:
Paired-end, 40-bp reads from each sample were aligned to the mouse genome (mm10) using TopHat and Bowtie.  Gene expression was quantified as fragments per kilobase of exon model per million mapped fragments (FPKM) using Cufflinks version 1.0.3.
Differential expression for Control and Jnk1-/- Jnk2-/- kidney epithelial cells in attached and suspended conditions was determined using the Cufflinks tool, Cuffdiff.
The processed data file is an Excel file in the format of Cufflinks output.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data file an Excel file in the format of Cuffdiff output. It contains FPKM values as well as differential expression.

source_name: Mouse Kidney Epithelial Cells

extract_protocol:
RNA was extracted from cultured kidney epithelial cells using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.  On-column DNA RNAse-free DNase digestion was performed to eliminate genomic DNA.  RNA quality was verified (RNA integrity number >9) using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Messenger RNA was isolated, converted to cDNA, and amplified using the mRNA Purification Kit (Illumina, San-Diego, CA) according to the manufacturer’s instructions. An Illumina library was constructed and run on a HiSeq 2000 (Illumina).

tag: culture

value: Suspended

tag: genotype


title: Polrmt (L/L) rep4

value: Polrmt (L/L)


title: mouse.JNK.epithelium.susp.rep1.0


title: mouse.JNK.epithelium.susp.rep2.0


title: mouse.rose.epithelium.susp.rep1.0

value: Rosa-CreER


title: Polrmt (L/L) rep2


title: Polrmt (L/L) rep3


title: mouse.rose.epithelium.susp.rep3.0


title: Polrmt (L/L) rep1


title: mouse.rose.epithelium.susp.rep2.0


title: mouse.rose.epithelium.rep2.0

value: Attached


title: 002-AAH


title: mouse.rose.epithelium.rep3.0


title: Polrmt (L/L, cre) rep3

value: Polrmt (L/L, cre)


title: mouse.JNK.epithelium.rep3.0


title: mouse.JNK.epithelium.rep2.0


title: Mterf4 (L/L) rep1


title: Mterf4 (L/L) rep2


title: Polrmt (L/L, cre) rep2


title: mouse.JNK.epithelium.rep1.0


title: 48 h infected-3

city: Wuhan

first: Junqin

last: Zhang

address: Shizishan Street

institute: Huazhong Agricultural university

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Seqtk (https://github.com/lh3/seqtk).
The clean reads were aligned and mapped to the chicken reference genome (Genome Assembly: Gallus_gallus-5.0 GCA_000002315.3) by using Hisat2 (version 2.0.4)
The expression abundance of the mapped gene reads were normalized by the fragments per kilobase of exon model per million mapped reads (FPKM) using StringTie (version: 1.3.0)
The differentially expressed genes (DEGs) were selected using edgeR.
Genome_build: NCBI Gallus_gallus-5.0 GCA_000002315.3
Supplementary_files_format_and_content: an EXCEL file include normalized FPKM values and raw fragment counts for each Sample

organism: Gallus gallus

source_name: LMH cells

growth_protocol: LMH cells were maintained in F12 medium supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin, and 0.1 mg/ml streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was purified by RNeasy micro kit (QIAGEN, Germany) and RNase-Free DNase Set (QIAGEN, Germany).
Following "TruSeq RNA Sample Preparation Guide".

treatment_protocol:
LMH cells were cultured by approximately 24 h to reach about 80% confluence. The cells were washed three times with PBS and infected with FAdV-4 isolated strain at a MOI of 5. After one-hour adsorption in serum-free medium at 37 °C, the medium was replaced with 2% FBS F12 medium.
12 h infected-1; 12 h infected-2; 12 h infected-3; 24 h infected-1; 24 h infected-2; 24 h infected-3; 48 h infected-1; 48 h infected-2; 48 h infected-3

value: Leghorn male hepatocarcinoma cells


title: 48 h infected-2


title: Polrmt (L/L, cre) rep1


title: 48 h infected-1


title: Twinkle (L/L) rep5

value: Twinkle (L/L)


title: 24 h infected-2


title: 24 h infected-1


title: 24 h infected-3


title: 12 h infected-3


title: mouse.rose.epithelium.rep1.0


title: Polrmt (L/L, cre) rep4


title: 12 h infected-1


title: 12 h infected-2


title: Twinkle (L/L) rep3


title: Twinkle (L/L) rep4


title: 48 h mock-3


title: 24 h mock-2


title: 48 h mock-1


title: 48 h mock-2


title: 24 h mock-1


title: Twinkle (L/L) rep2


title: Twinkle (L/L) rep1


title: Twinkle (L/L, cre) rep3

value: Twinkle (L/L, cre)


title: 12 h mock-2


title: 12 h mock-3


title: Lrpprc (L/L) rep4

value: Lrpprc (L/L)


title: Twinkle (L/L, cre) rep1


title: 12 h mock-1


title: Lrpprc (L/L) rep3


title: Twinkle (L/L, cre) rep2


title: Lrpprc (L/L) rep2


title: SCRp1

description: polyadenylated RNA

data_processing:
Sequencing reads were mapped against the reference genome (mm10 assembly) using TopHat v2.0.9 as previously described (Trapnell et al., 2012). Only uniquely mapped reads were selected for further analysis.
guide transcripts were assembled using CuffLinks v2.2.1. Reads were quartile normalized using the –library-norm-method quartile option.
Differential gene analysis was performed using CuffDiff. Cluster 3.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing  average differential gene expression FPKM normalized values
Supplementary_files_format_and_content: q1= shRNA scrambled; q2= shRNA against Foxp1

source_name: mouse E14.5 embryonic neural stem cells

growth_protocol: NSCs were growth as monolayer in poli-L-ornithine and laminin coated plates in presence of EGF and bFGF

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)
Sample preparation was performed using Poly(A)Purist MAG Kit (Thermo Scientific) according to manufacturers’ instructions. Isolated mRNA was subsequently repurified using mRNA-ONLY Eukaryotic mRNA Isolation Kit (Epicentre (Illumina, Inc.), Madison, WI, USA). Sequencing libraries were prepared using SOLiD Total RNA-Seq Kit (Applied Biosystems Life Technologies) according to the standard protocol recommendations

treatment_protocol: Upon lentiviral transduction NSCs were grown and expanded under puromycin selection before RNA-isolation (0.5 µg/mL)

tag: shRNA

value: scrambled

tag: name and source shrna

value: SHC002, Sigma Aldrich, St. Louis, MS

tag: developmental stage

tag: source cells

value: Mouse Cortical Stem Cells purchase from Systems, Minneapolis, MN.


title: SCRp2

description: polyadenylated RNA


title: Foxp1KDp2

description: polyadenylated RNA

value: targeting Foxp1

value: pLKO.1_sh_ex15, gift from Benjamin Blencowe, Addgene plasmid # 35166


title: Foxp1KDp1

description: polyadenylated RNA


title: Lrpprc (L/L) rep1


title: Lrpprc (L/L, cre) rep4

value: Lrpprc (L/L, cre)


title: 24 h mock-3

tag: cell line


title: Lrpprc (L/L, cre)rep2


title: Lrpprc (L/L, cre) rep1


title: 1084_TS_3

city: Baltimore

first: Suvarna

last: Nadendla

address: 670 W.Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description: Barcode: GATCAGA

data_processing:
Illumina reads were mapped to the Streptococcus agalactiae A909 (NC_007432) and 10/84 (CP006910) genomes using Bowtie v. 0.12.7
The mapped reads were counted using HTSeq and normalized and then the differential expression of each gene for one sample compared to another was determined using DESeq v. 1.5.24, and statistical analyses were performed using R-2.15.2, and was represented as the log2 of the fold-change values.
RPKMs for each gene were calculated for each sample.
Genome_build: CP006910 (ASM78285v1), NC_007432 (ASM1270v1)
Supplementary_files_format_and_content: RPKMs

organism: Streptococcus agalactiae

source_name: Bacterial outgrowth

growth_protocol: Stationary growth at 37 degrees C until mid-log phase

extract_protocol:
RNA extraction with Ambion ribopure kit followed by Dnase treatment
Strand specific RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Serine hydroxamate coincubation or control broth

tag: strain

tag: growth condition

value: TS media


title: 1084_SR_2

description: Barcode: GGCTACA

value: Serine hydroxamate


title: 1084_TS_2

description: Barcode: ACTTGAA


title: A909_SR_2

description: Barcode: ACAGTGA


title: A909_SR_1

description: Barcode: TGACCAA


title: 1084_TS_1

description: Barcode: CAGATCA


title: Lrpprc (L/L, cre) rep3

tag: age


title: 1084_SR_1

description: Barcode: TAGCTTA


title: A909_TS_2

description: Barcode: CGATGTA


title: A909_TS_3

description: Barcode: TTAGGCA


title: A909_TS_1

description: Barcode: ATCACGA


title: polyA_TMAC sample 15 - 1:50

status: Public on Nov 13 2017

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

institute: CRG

data_processing:
Demultiplexing using the batch barcode (index read). Perl 5.10.1
Demultiplexed using the sample barcode (first read). Python2.7/HTSeq
Trim off 8 bases of the first read (molecular barcode) and store with reverse read. Discard first read. Perl5
Trim off polyA from 3' end of reverse read. Discard reads not ending in a poly A tail. Python2.7/HTSeq
Align reads to hg19 genome. Gsnap
Filter out reads of non-unique alignment, low alignemt quality, alignment to A-rich genomic regions, A-rich reads. Python2.7/HTSeq
Count unique molecular barcodes aligning to different genomic features. Python2.7/HTSeq
Remove barcode counts stemming from similar molecular barcodes with a Hamming distance of less than 1. Perl5
Collapse putative polyadenylation sites stemming from genomic positions within 12bp distance. Perl5
Genome_build: hg19
Supplementary_files_format_and_content: *isoforms.counts.gz: comma-separated value files containing the ensembl gene ID of the closest genomic feature, the 3' alignment position (polyadenylation site), the Barcode Count, the Read Count, a brief description of the alignment site, the distance to the closest annotated transcript termination site

source_name: HeLa RNA

extract_protocol:
RNA was extracted from HeLa cell culture using TriZOL.
Full-length cDNA was amplified from 15 pg of HeLa RNA using a smart-seq2 protocol with an alternative 3' primer, which inclued a 8 nt UMI, a 6 nt cell identifier, and an 4 nt end-specific identifier. cDNA was  tagmented with a single adapter (loaded onto Tn5), technical replicates were performed on different cDNA samples. PCR was performed using specific i7 index primers complementary to the tagmentation adapter as well as a primer complementary to the 3' end specific adapter. Fragments were size selected to achieve an average  library size of 347 bp

value: HeLa

tag: smartseq2 replicate

value: HeLa RNA sample 15

tag: pcr additive

value: TMAC


title: polyA_TMAC sample 11 - 1:50

value: HeLa RNA sample 11


title: polyA_TMAC sample 13 - 1:50

value: HeLa RNA sample 13


title: A909_SR_3

description: Barcode: GCCAATA


title: polyA_TMAC sample 14 - 1:50

value: HeLa RNA sample 14


title: polyA_TMAC sample 12 - 1:50

value: HeLa RNA sample 12


title: polyA_TMAC sample 10 - 1:50

value: HeLa RNA sample 10


title: polyA_TMAC sample 16 - 1:50

value: HeLa RNA sample 16


title: 1084_SR_3

description: Barcode: CTTGTAA


title: polyA_TMAC sample 6 - 1:50

value: HeLa RNA sample 6


title: polyA_TMAC sample 8 - 1:50

value: HeLa RNA sample 8


title: polyA_TMAC sample 3 - 1:50

value: HeLa RNA sample 3


title: polyA_TMAC sample 4 - 1:50

value: HeLa RNA sample 4


title: polyA_TMAC sample 2 - 1:50

value: HeLa RNA sample 2


title: polyA_TMAC sample 1 - 1:50

value: HeLa RNA sample 1


title: polyA_TMAC sample 16


title: polyA_TMAC sample 14


title: polyA_TMAC sample 13


title: polyA_TMAC sample 15


title: polyA_TMAC sample 11


title: polyA_TMAC sample 12


title: polyA_TMAC sample 7

value: HeLa RNA sample 7


title: polyA_TMAC sample 10


title: polyA_TMAC sample 8


title: polyA_TMAC sample 4


title: polyA_TMAC sample 2


title: polyA_TMAC sample 3


title: polyA_TMAC sample 6


title: polyA_DMSO sample 9

value: HeLa RNA sample 9

value: DMSO


title: polyA_DMSO sample 10

value: HeLa


title: polyA_DMSO sample 15

value: HeLa RNA sample 15


title: polyA_DMSO sample 13


title: polyA_DMSO sample 11

value: HeLa RNA sample 11


title: polyA_TMAC sample 7 - 1:50

value: TMAC


title: polyA_DMSO sample 7


title: polyA_DMSO sample 6


title: polyA_DMSO sample 4


title: polyA_TMAC sample 1


title: polyA_DMSO sample 2


title: polyA_DMSO sample 1


title: polyA_DMSO sample 3


title: i5i7_lane3Fresh3

description: i5i7 standard protocol, reference for gylcerol stock and dilution 3

data_processing:
Demultiplexing. Perl 5.10.1
Trim off remaining poly-A tails, if applicable. Perl 5.10.1
Align reads to the human genome using GSNAP with default settings, expected paired-end length=400bp and allowable deviation from expected paired-end length=100bp. GSNAP version 2012-01-11
Count reads overlapping uniquely with mRNA genes. Python2.7/HTSeq
Genome_build: hg19
Supplementary_files_format_and_content: csv file with read counts

source_name: HeLa RNA sample 7

extract_protocol:
RNA was extracted from HeLa cell culture using TriZOL.
Full-length cDNA was amplified from 15pg of HeLa RNA using the smart-seq2 protocol. 75-225pg of cDNA was tagmented using various conditions as outlined in the sample specification. Samples were sequenced using a dual-indexed single read strategy, unless specified differently.

value: R27S,E54K,L372P-Batch 2

tag: inactivation

tag: pcr

value: ReadyMix


title: i5i7_lane3GlyDil3

description: i5i7 glycerol dilution of loaded Tn5 3


title: i5i7_lane3Fresh2

description: i5i7 standard protocol, reference for gylcerol stock and dilution 2


title: polyA_DMSO sample 8


title: i5i7_lane3Fresh1

description: i5i7 standard protocol, reference for gylcerol stock and dilution 1


title: polyA_TMAC sample 9


title: i5i7_lane3GlyStock3

description: i5i7 glycerol stock of loaded Tn5 3


title: i5i7_lane3GlyDil2

description: i5i7 glycerol dilution of loaded Tn5 2


title: i5i7_lane3GlyDil1

description: i5i7 glycerol dilution of loaded Tn5 1


title: i5i7_lane3GlyStock2

description: i5i7 glycerol stock of loaded Tn5 2


title: i5i7_lane2B1F3

description: i5i7 standard protocol with 14 month old Tn5 batch 3

source_name: HeLa RNA sample 6

value: R27S,E54K,L372P-Batch 1 14 month at -20°C


title: i5i7_lane2B1F1

description: i5i7 standard protocol with 14 month old Tn5 batch 1


title: i5i7_lane2B1F2

description: i5i7 standard protocol with 14 month old Tn5 batch 2


title: polyA_DMSO sample 14

value: HeLa RNA sample 14


title: i5i7_lane3GlyStock1

description: i5i7 glycerol stock of loaded Tn5 1


title: i5i7_lane2B3F3

description: i5i7 standard protocol, reference 14 month old first batch 3

value: R27S,E54K,L372P-Batch 3


title: i5i7_lane2B3F2

description: i5i7 standard protocol, reference 14 month old first batch 2


title: i5i7_lane2WT1

description: i5i7 Tn5-E54K, L372P 1

source_name: HeLa RNA sample 5


title: i5i7_lane2B3F1

description: i5i7 standard protocol, reference 14 month old first batch 1


title: i5i7_lane2WT2

description: i5i7 Tn5-E54K, L372P 2


title: i5i7_lane2B3H2

description: i5i7 standard protocol, reference for Tn5-E54K, L372P 2

value: KAPA Pol


title: i5i7_lane2WT3

description: i5i7 Tn5-E54K, L372P 3


title: i5i7_lane1Smartseq75pg1to40SDS3batch3

description: i5i7 75 pg/ul cDNA input 2

source_name: HeLa RNA sample 4

value: 75 pg


title: i5i7_lane1Smartseq225pg1to20SDS3batch3

description: i5i7 225 pg/ul cDNA input 3


title: i5i7_lane1Smartseq150pg20ulNextera3

description: i5i7 Nextera 3

value: Nextera

value: NT buffer


title: i5i7_lane1Smartseq75pg1to40SDS1batch3

description: i5i7 75 pg/ul cDNA input 1


title: i5i7_lane2B3H1

description: i5i7 standard protocol, reference for Tn5-E54K, L372P 1


title: i5i7_lane1Smartseq225pg1to20SDS1batch3

description: i5i7 225 pg/ul cDNA input 2


title: i5i7_lane1Smartseq150pg20ulNextera2

description: i5i7 Nextera 2


title: i5i7_lane1Smartseq225pg1to10SDS2batch3

description: i5i7 225 pg/ul cDNA input 1


title: i5i7_lane1Smartseq150pg1to5no3

description: i5i7 Ready Mix and 0.2% SDS 3


title: i5i7_lane1Smartseq150pg1to10SDS5batch3

description: i5i7 standard protocol 4.2 batch 3

source_name: HeLa RNA sample 3


title: i5i7_lane1Smartseq150pg1to5no1

description: i5i7 Ready Mix and 0.2% SDS 1


title: i5i7_lane1Smartseq150pg1to10SDS4batch3

description: i5i7 standard protocol 3.2 batch 3


title: i5i7_lane1Smartseq150pg1to10SDS2batch1

description: i5i7 standard protocol 2  batch 1

source_name: HeLa RNA sample 2

value: R27S,E54K,L372P-Batch 1


title: i5i7_lane1Smartseq150pg1to10SDS6batch3

description: i5i7 standard protocol 5.2 batch 3


title: i5i7_lane1Smartseq150pg1to10SDS2batch2

description: i5i7 standard protocol 2 batch 2


title: i5i7_lane1Smartseq150pg1to10SDS2

description: i5i7 standard protocol 2.1 batch 3

source_name: HeLa RNA sample 1


title: i5i7_lane1Smartseq150pg1to5no2

description: i5i7 Ready Mix and 0.2% SDS 2


title: i5i7_lane1Smartseq150pg20ulNextera1

description: i5i7 Nextera 1


title: i5i7_lane1Smartseq150pg1to10SDS1batch1

description: i5i7 standard protocol 1  batch 1


title: i5i7_lane1Smartseq150pg1to10SDS1batch3

description: i5i7 standard protocol 1.2 batch 3


title: i5i7_lane1Smartseq150pg1to10SDS1batch2

description: i5i7 standard protocol 1 batch 2


title: i5i7_lane1Smartseq150pg1to10SDS1

description: i5i7 standard protocol 1.1 batch 3


title: i5i7_lane1Smartseq150pg1to10heat2batch3

description: i5i7 heat inactivation 2

value: heat


title: i5i7_lane1Smartseq150pg1to10heat1batch3

description: i5i7 heat inactivation 1


title: T3_d

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

country: France

institute: Institut Pasteur

description: bisulfite converted genomic DNA

data_processing:
processed by trimGalore v. 0.4 with the --rrbs flag set
mapped with bismark v 0.14.4 agains mm10
processed with bismark_methylation_extractor with the -s --comprehensive flags set
CpG context files were processed by the bismark2bedGraph tool
CpG context bedgraph files were loaded and clustered with BiSeq v. 1.14.0, using standard parameters and. The clusterSites function was caled with perc.samples = 3/4, min.sites = 5 and max.dist = 100
Beta regression was done with BiSeq, with the parameters formula = ~ Condition, link = "probit" and type = "BR". Null model was obtained by swapping the labels on Fix1, Fix2, Live1 and Live2
DMRs were called with BiSeq, clusteres were tested with an FDR-cutoff of 1%, and then trimmed with a FDR-cutoff of 10%. DMRs were called with parameters max.dist = 100 and diff.dir = TRUE. Clusters with a median methylation change less than 10% were discarded.
DMRs were annotated with ChIPseeker v. 1.12.1
Genome_build: mm10
Supplementary_files_format_and_content: Two bed-files, one with non-significant and one with significant regions. One excel-file with the significant regions annotated with nearest gene.

source_name: Muscle Stem Cell

extract_protocol:
3-4x105 sorted T0-T3-SCs cells were lysed and their genomic DNA extracted using the RecoverAll Kit for FFPE (Ambion, AM1975) following the manufacturer’s guidelines (one animal per replicate, n=4). Genomic DNA samples were first concentrated with Genevac EZ-2 Evaporation System and diluted in water to reach 95ng in 26µl.
Sequencing library pool was prepared with the Premium Reduced Representation Bisulfite Sequencing (RRBS) Kit (Diagenode, C02030033) following manufacturer’s instructions, quantified with the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32854) and average size of DNA fragments was estimated with a 2100 Bioanalyzer instrument using Agilent High Sensitivity DNA Kit (5067-4626). Library pool was then denaturated in NaOH and diluted at 1.9pM with 20% of PhiX Control v3 (Illumina, FC-110-3001). To improve cluster density consistency, the diluted library pool was heat-denatured at 96°C for 2min, inverted twice to mix, and quickly moved to ice for 5min before loading onto the sequencer. The library pool was sequenced on a NextSeq 500 (Illumina) using the NextSeq 500/550 High Output v2 Kit, 75 cycles (Illumina, FC-404-2002). Sequencing was single-read, 76 cycles, index 1: 6 bases.

tag: cell type

value: skeletal muscle stem cells (MuSCs)

tag: treatment

value: Live


title: T3_c

description: bisulfite converted genomic DNA


title: T0_d

description: bisulfite converted genomic DNA

value: Fixated


title: T3_b

description: bisulfite converted genomic DNA


title: T0_c

description: bisulfite converted genomic DNA


title: T0_a

description: bisulfite converted genomic DNA


title: T0_b

description: bisulfite converted genomic DNA


title: i5i7_lane1Smartseq150pg1to10SDS2batch3

description: i5i7 standard protocol 1.3 batch 3

value: HeLa


title: Jan27_Cell_94

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Ly6G- Cd11b+CD115+Ly6CHi Gfi1 High Irf8 High

data_processing:
FASTQ sequence files were aligned to the mouse genome version 9 (mm9) using RSEM.
Single-cell were analyzed using RSEM to estimate transcripts per million mapped reads (TPM) for all genes.
Differentially expressed genes were identified using AltAnalyze using an empirical Bayes moderated t-test p<0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file of TPM RSEM expression values

source_name: bone marrow (femurs and tibias)

extract_protocol:
Cells were harvested from bone marrow.  Femurs, tibias and iliac crest were harvested immediately after euthanasia and put in cold PBS+2%FBS. Bones were crushed with mortar and pestle, filtered and washed in cold PBS+2%FBS. Ly6Chi monocytes (CD11b+ Ly6G– CD115+ F4/80– Ly6Chi cells) were isolated from the bone marrow of wild-type and Gfi1-Tomato IRF8-GFP mice by FACS sorting on BD FACSAria II with a 100μm nozzle.
cDNA was made with Clontech SMARTer® Kit “the mRNA Seq: RT + Amp (1771x), Libraries were constructed using Nextera XT DNA Library Preparation Kit
Single cells were separated using Fluidigm C1 system. Single-cell libraries were subjected to paired-end 75 bp RNA-sequencing on a HiSeq 2500 (Illumina Inc.). 96 scRNA-seq libraries were sequenced per HiSeq 2500 gel (~300 million bp per gel).

value: Wild-type

tag: differentiation

value: In vitro


title: Jan27_Cell_93

value: Ly6G- Cd11b+CD115+Ly6CHi Gfi1 High Irf8 High


title: Jan27_Cell_90


title: Jan27_Cell_91


title: Jan27_Cell_92


title: Jan27_Cell_89


title: Jan27_Cell_87


title: Jan27_Cell_88


title: Jan27_Cell_85


title: Jan27_Cell_84


title: Jan27_Cell_86


title: i5i7_lane1Smartseq150pg1to10heat3batch3

description: i5i7 heat inactivation 3


title: Jan27_Cell_83


title: Jan27_Cell_82


title: Jan27_Cell_81


title: Jan25_Chip320_Cell_79

description: Ly6G- Cd11b+CD115+Ly6CHi

value: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_78

description: Ly6G- Cd11b+CD115+Ly6CHi


title: T3_a

description: bisulfite converted genomic DNA


title: Jan27_Cell_96


title: Jan25_Chip320_Cell_76

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_74

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_77

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan27_Cell_95


title: Jan25_Chip320_Cell_72

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_73

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_71

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_70

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_69

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_68

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_65

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_67

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_66

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_64

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_80

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_63

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_61

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_58

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_62

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_60

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_57

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_59

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_55

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_54

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_52

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_56

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_51

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_75

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_48

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_49

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_47

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_50

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_46

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_45

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_44

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip320_Cell_43

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_8

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_7

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_6

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_42

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_5

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_37

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_38

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_39

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_9

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_41

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_35

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_33

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_36

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_4

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_34

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_32

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_3

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_40

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_29

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_28

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_26

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_27

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_24

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_25

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_22

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_20

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_21

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_2

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_14

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_16

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_31

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_1

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_10

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_13

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_11

description: Ly6G- Cd11b+CD115+Ly6CHi


title: T5_b_ii RNAseq

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using an in-house program (https://github.com/baj12/clean_ngs)
STAR version 2.5.0a [1], with default parameters, was used for alignment on the reference genome (GRCm38 from Ensembl database)
Genes were counted using featureCounts version 1.4.6-p3 [2] from Subreads package (parameters: -t gene -s 0 -O)
Count data were analyzed using R version 3.3.1 and the Bioconductor package DESeq2 version 1.12.3]. The normalization and dispersion estimation were performed with DESeq2 using the default parameters but statistical tests for differential expression were performed without applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between T0, T3 and T5. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: GRCm38 from Ensembl database version 74
Supplementary_files_format_and_content: matrix of count from featurecounts

source_name: Skeletal muscle stem cells from Tg:Pax7-nGFP mice

extract_protocol:
Total RNA was exrtacted from fixed MuSCs using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE, Ambion, AM1975. Modification: cells were incubated at 50°C for 1h in digestion buffer plus Proteases. No 80°C incubation was performed as recommended by the manufacturer as this deteriorated RNA quality.
Directional libraries were prepared using the Smarter Stranded Total RNA-Seq kit- Pico Input Mammalian   following the manufacturer’s instructions (Clontech 635005). The quality of all libraries was checked with the DNA-1000 kit (Agilent) on a 2100 Bioanalyzer and quantification was performed with Quant-It assays on a Qubit 3.0 fluorometer (Invitrogen).
Clusters were generated for the resulting libraries, with Illumina HiSeq SR Cluster Kit v4 reagents. Sequencing was performed with the Illumina HiSeq 2500 system and HiSeq SBS kit v4 reagents. Runs were carried out over 65 cycles, including seven indexing cycles, to obtain 65-bp single-end reads. Sequencing data were processed with Illumina Pipeline software (Casava version 1.9).

treatment_protocol: T0: muscles fixed with 0.5% paraformaldehyde (PFA), 1h, 4°C. T3: MuSCs fixed with 0.5% PFA, 30min on ice after FACS-isolation. T5: MuSCs fixed with 0.5% PFA, 30min on ice after dissected muscles were incubated in DMEM at 37°C for 2h and then MuSCs isolated by FACS.

tag: muscle stem cells manipulation

value: Standard MuSCs isolation; post-incubation and post-isolation fixed MuSCs.

tag: tissue

value: Pectoral, forelimb, and hindlimb muscles


title: T5_b_i RNAseq


title: Jan25_Chip170_Cell_30

description: Ly6G- Cd11b+CD115+Ly6CHi

tag: genotype


title: Jan25_Chip170_Cell_15

description: Ly6G- Cd11b+CD115+Ly6CHi


title: T5_a_i RNAseq


title: T3_b RNAseq

value: Standard MuSCs isolation; post-isolation fixed MuSCs.


title: T5_a_ii RNAseq


title: T3_c RNAseq


title: Untreated MoMF (second replicate)

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

data_processing:
Basecalling was performed with a pipeline, using HiSeq Control Software 2.2.58, RTA 1.18.64.0 and CASAVA-1.8.2
After quality assessment of the corresponding FASTQ files with FastQC v0.11.5 (1), adaptor sequences were trimmed from the reads.
Additionally, 10 bases were trimmed from the 5-prime end and 5 bases from the 3-prime end of each read.
Trimmed reads shorter than 50 nucleotides were discarded.
Low-quality sequences (Phred quality score < 30) were also removed.
These quality enhancement steps were performed using TrimGalore v0.4.1 (2).
The reads were subsequently aligned to the mm10 reference genome sequence using HISAT2 v2.0.5 (3) with default parameters.
In the quantification step, reads were counted with HTSeq v0.6.1p1 (4).
Finally fold changes and their corresponding p-values were computed for each condition using DESeq2 v1.10.1 (5).
Genome_build: mm10
Supplementary_files_format_and_content: Excel File for each condition containing FKPKM values, FoldChanges, Pvalues and Various annotations.
Supplementary_files_format_and_content: Tab delmited file for the pair (treated MOMF vs. Treated Kupffer Cells, containing fold changed andy very precise p-values as computed by the deseq package for the volcano plot.

source_name: MoMF cells

growth_protocol: 8 week old C57BL6/J mice were used for the experiments

extract_protocol:
Hepatic macrophages were isolated from MCD-treated mice and sorted by fluorescent activated cell sorting using an Aria-II (BD Biosciences). Total RNA of MoMF and Kupffer cells was isolated directly afterwards by using PeqGold (VWR Technologies).
Illumina TruSeq stranded mRNA kit, Library dilution at 10nM

treatment_protocol: treatment with methionine and choline deficient (MCD) diet started at week 8 for 4 weeks

tag: library type

value: untreated

tag: target population

value: MO


title: T3_a RNAseq


title: Jan25_Chip170_Cell_19

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Untreated MoMF (first replicate)


title: Treated MoMF (second replicate)

value: treated


title: Jan25_Chip170_Cell_18

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Untreated Kupffer (second replicate)

source_name: Kupffer cells

value: KC


title: Treated Kupffer (first replicate)


title: Treated Kupffer (second replicate)


title: Jan25_Chip170_Cell_17

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Jan25_Chip170_Cell_12

description: Ly6G- Cd11b+CD115+Ly6CHi


title: Treated MoMF (first replicate)


title: T3_d RNAseq


title: NYJ2_6

city: College Station

first: Cecilia

last: Tamborindeguy

address: Heep Center

institute: Texas A&M University

data_processing:
analyses was performed on CyVerse.org
The pre-filtered reads were quality-filtered using FASTQC tools.
The RNA-seq reads that passed the quality filters were mapped to the potato reference genome (PGSC_DM_v3.4 gene models ensemblv19-preinstalled in iplantcollaborative.org) using the Tuxedo RNA-seq pipeline (Trapnell et al., 2013, Trapnell et al., 2009, Trapnell et al., 2010).
The Tuxedo pipeline comprised TopHat2 (mapping), Cufflinks2 (transcript assembly), and Cuffmerge2 (transcript merging).
Identification of differential gene expression was conducted using Cuffdiff2, following the defaults parameters in CyVerse.
Supplementary_files_format_and_content: .gtf file

organism: Solanum tuberosum

source_name: psyllid with Liberibacter solanacearum

growth_protocol: Tubers were planted in one gallon pots each and grown in growth chmaber/controled condition at 24Celcius 16:8 day night light cycle

extract_protocol:
Plant Sample were collected and flash frozen in liquid nitrogen / extraction were made with Rneasy kit from qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: plant were treated either with J1: Lso minus potato psyllid or infected with Liberibacter solanacearum via insect (psyllid treatment) for a week

value: Leaf

value: 49 day old

tag: cultivar

value: psyllid with Liberibacter solanacearum


title: NYJ2_5


title: NYJ1_1

source_name: psyllid without Liberibacter solanacearum


title: NYJ1_3

value: psyllid without Liberibacter solanacearum


title: ATJ2_7

value: Atlantic


title: ATJ1_4


title: ATJ1_1


title: ATJ2_5


title: Mycobacerium smegmatis infected with mycobacteriophage L5 for 30min

city: Pittsburgh

first: Rebekah

middle: M

last: Dedrick

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

data_processing:
Basecalls performed with MiSeq Reporter
Reads were trimmed at both ends using cutadapt version 1.8.3 using a quality score cutoff of 30
Reads were aligned using bowtie2 version 2.2.6
Reads that did not uniquely align to reference genome were removed with sed command line utility using the "XS:I" flag in the bowtie alignment output
SAM converted to BAM using samtools version 1.2
BAM converted to BED using bedtools version 2.25.0
Expression levels were computerd as reads mapped per base pair per strand using the genomecov tool of bedtools version 2.25.0
Genome_build: NC_008596.1 (Mycobacterium smegmatis mc2155)
Genome_build: NC_001900.1 (Mycobacterium phage D29)
Genome_build: KX897981.1 (Mycobacterium phage StarStuff)
Genome_build: NC_001335.1 (Mycobacterium phage L5)
Supplementary_files_format_and_content: bedgraph formatted files containing strand-specific ("top" and "bottom" strands) expression coverage levels per base pair across the genome, computed by the genomecov tool in bedtools

organism: Fromanvirus L5

source_name: Cells grown in liquid media

growth_protocol: Cells were grown in 7H9 media to OD(600) of 0.7-1.0 (mid-log phase)

extract_protocol:
RNA was extracted using Rneasy Mini Kit (Qiagen), rRNA was depleated using RiboZero (Illumina)
Illumina TruSeq Stranded mRNA sample prep kit

tag: time

value: 30min post infection

tag: host

value: Mycobacterium smegmatis


title: mc2155(L5)

value: lysogen


title: Mycobacerium smegmatis infected with mycobacteriophage StarStuff for 60min

organism: Mycobacterium phage StarStuff

value: 60min post infection


title: Mycobacerium smegmatis infected with mycobacteriophage StarStuff for 150min

value: 150min post infection


title: Mycobacerium smegmatis infected with mycobacteriophage StarStuff for 30min


title: Mycobacerium smegmatis infected with mycobacteriophage D29 for 60min

organism: Fromanvirus D29


title: Mycobacerium smegmatis infected with mycobacteriophage D29 for 150min


title: Mycobacerium smegmatis infected with mycobacteriophage D29 for 15min

value: 15min post infection


title: NYJ2_7


title: UV_rep2

city: Ann Arbor

first: mehmet

last: tardu

state: MI

address: 930 N University Ave

institute: University of Michigan

data_processing:
Illumina data processing pipeline (v1.5) was used for base calling.
FastQC (v0.11.5) was used to evaluate the initial quality of the raw reads.
The following steps were performed to obtain high quality clean reads using Trimmomatic (v0.32) tool: (1) removing the reads with adaptor contamination; (2) filtering the low-quality reads with ambiguous sequences ‘N’; (3) removing the low-quality bases (quality score < Q30).
All downstream analyses were based on clean, high quality data. De novo assembly of the high quality reads was performed using Trinity, which is composed of three independent software modules: Inchworm, Chrysalis and Butterfly. By Inchworm, RNA-seq data was assembled into unique sequences through establishing a k-mer graph (K = 25). By Chrysalis, the contigs generated in the previous step were clustered, and a de Bruijn graph was constructed for each cluster. Subsequently, by Butterfly, these Bruijn graphs were processed in parallel and the paths were traced according to reads and pairs of reads within graphs to obtain full-length transcripts for alternative splicing isoforms and distinguish transcripts of paralogous genes. Finally, the distributed situation of length of result sequences was counted and analyzed using RSEM method. A Pearson’s correlation analysis was performed to obtain the transcript-level R2 between biological replicates.
For count-based differential expression testing between WT, UV-715 and EMS-25 cells, edgeR was used. We used min_rowSum_counts of 10, stringent q-value < 0.01 (false discovery rate, FDR) and the absolute value of | log2 fold change| ≥ 1 as the threshold to judge the significant differences in gene expression between WT and mutant cells.
Genome_build: De novo assembly
Supplementary_files_format_and_content: matrix text file (transcript count values of rsem output across samples)

organism: Chlorella vulgaris

source_name: UV

growth_protocol: Chlorella vulgaris (SAG 211-12) was obtained from the collection of algal cultures at the University of Göttingen, Germany. The inoculum was grown in Bold’s Basal medium consisting of (per liter): 0.25 g NaNO3, 0.075 g MgSO4.7H2O, 0.075 g K2HPO4, 0.175 g KH2PO4, 0.025 g NaCl, 0.025 g CaCl2.2H2O, 8.82 mg ZnSO4.7H2O, 0.44 mg MnCl2.4H2O, 0.71 mg MoO3, 1.57 mg CuSO4.5H2O, 0.49 mg CoCl2.6H2O, 11.42 mg H3BO3, 50 mg EDTA, 31 mg KOH, 4.98 mg feSO4.7H2O. Cultures were maintained at 25◦C under continuous illumination by four fluorescent lamps.

extract_protocol:
Total RNA was extracted from 14-days old stationary phase reached (OD680=5) 5 ml cell culture using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. Briefly, after quality and quantity measurement using 2100 BioAnalyzer (Agilent, USA), it was treated with RNase-free DNase I (Thermo Scientific, USA) at a concentration of 1 U/µg to remove residual genomic DNA. Then, RNA-seq library preparation was performed using TruSeq mRNA Sample Preparation Kit (Illumina, USA) according to the manufacturer’s instructions.
mRNAs were purified from the 1 µg of total RNA using oligo (dT) magnetic beads and fragmented using fragmentation buffer. Afterthat, the cleaved short RNA fragments were used for first-strand cDNA synthesis using first strand synthesis mix, and the second strand was synthesized using second strand marking master mix. The double strand cDNAs were purified with AMPure XP beads (Beckman Coulter, USA) and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. 75x2 paired-end sequencing of three cDNA libraries (WT, UV-715 and EMS-25) with two biological replicates were performed using the Illumina MiSeq sequencing platform (Illumina, USA). All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.

treatment_protocol: 250 µl culture of C. vulgaris with the cell count of   4×10e8 cells/ml was spread on solid Bold’s basal media and then exposed to UV irradiation (254 nm) with an intensity of 2.9 ×10-2 W/cm2 for 0.5 to 10 minutes at a distance of 15 cm. UVX Digital Radiometer (UVP, USA) was used to measure the UV-light intensity. The UV-irradiated plates were kept in dark for 24 h to prevent light-induced repair. The plates were then maintained under normal light for 2 weeks. Single colonies appearing on plates were selected and transferred individually into 2 ml Bold’s basal medium. After 10 days of culturing, the cell densities were determined by measuring OD at 680 nm.

tag: strain

value: UV mutant (UV-715)


title: NYJ1_2

tag: age


title: Col-0 seedling

city: Alicante

first: Angel

last: Barco

address: Ramon y Cajal

department: Neuro Plasticity

institute: NeuroSciences Institute of Alicante CSIC

data_processing:
Reads with total sequencing quality of less that 30 Phred or shorter than 10 nucleotides were discarded.
paired-end reads were mapped to the reference genome TAIR10 using bwa with default parameters.
Duplicated paired mappings were removed.
The annotated nuclear genome was divided into 1 Kb bins and the number of mapped reads falling into each bin were counted.
Bins containing less reads in Col than the tenth lower quantile of all bins were not considered for further analysis.
A bin-wise one-sided binomial test was used to test for reduced coverage in fas2.
Multiple testing correction was done by pFDR.
Bins were considered to have reduced coverage in fas2 if q<0.05 and log2FC < -1.5.
Genome_build: TAIR10
Supplementary_files_format_and_content: contains position of low coverage in fas2. They are excluded from nucleosomal analysis

source_name: seedling

growth_protocol: 10-day old seedlings were used

extract_protocol:
Seedlings were harvested and DNA was isolated using a MagJET Plant Genomic DNA Kit (Thermo Fisher Scientific) according to the manufacturer´s instructions.
Genomic DNA sequencing libraries were generated using a TruSeq DNA LT Library Preparation kit (Illumina Inc) and sequenced using 100 bp paired-end mode on an Illumina HiSeq 2000 system (Illumina Inc).

tag: biological replicate


title: fas2 seedling


title: UV_rep1


title: Mycobacerium smegmatis infected with mycobacteriophage StarStuff for 15min


title: ATJ1_3


title: EMS_rep1

source_name: EMS

value: EMS mutant (EMS-25)


title: Mycobacerium smegmatis infected with mycobacteriophage L5 for 150min