title: Stamen

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

data_processing:
Illumina 1.8 pipeline used for basecalling
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Base mean value was calculated for all the genes in each tissue sample using DESeq
Genome_build: Saffron Transcriptome v1.0 (http://nipgr.res.in/mjain.html?page=saffron)
Supplementary_files_format_and_content: tab delimited text files include base mean values for each sample

organism: Crocus sativus

source_name: Mature plant

growth_protocol: Plants grown in field

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma
Libraries were prepared using mRNA-Seq Sample Prep kit (Illumina) according to the manufacturer’s protocol

value: Stamen


title: Soybean Bert wild-type

status: Public on Mar 04 2016

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: Soybean leaf, wildtype

library_source: transcriptomic

data_processing:
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: JGI glyma v2
Supplementary_files_format_and_content: tag count file

molecule: total RNA

organism: Glycine max

source_name: Soybean leaf

extract_protocol:
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed using the Illumina TruSeq Small RNA sample preparation kit RS-200-0012 and RNA-Seq libraries were prepared using the Illumina TruSeq RNA sample preparation kit RS-122-2001.

tag: tissue

value: Soybean leaf

tag: genotype/variation

value: wildtype


title: Tepal

value: Tepal


title: Soybean dcl1a/dcl1b-1.1

description: Soybean leaf, dcl1a/dcl1b-1.1

value: mutant


title: Soybean leaf WT rep1

description: Soybean leaf, wildtype rep1


title: datL5-2 midbrain neurons

city: New York

first: Mary

middle: Alanna

last: Hynes

state: NY

address: 1230 York Ave

institute: Rockefeller University

description:
(DAT or Slc6a3 JD1640, JAX #905444)
ribosomal tagged mRNA

data_processing:
Reads were mapped to the mm10 mus musculus genome using STAR
genes in Gencode vM2 were quantified with featureCounts
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts output

organism: Mus musculus

source_name: midbrain dopamine neurons

growth_protocol: Normal BacTrap embryos were dissected at E15. E18 midbrain was dissected at E15 and aged in vitro for 3 days to assure identical dissections.

extract_protocol: First strand cDNA was initially amplified by long-distance PCR (LD-PCR) using hot-start amplification. 2-7 ng cDNA was sonicated (Covaris S2; Covaris Inc., Woburn, MA, USA) and  ~200 bp fragments end-repaired following adapter ligation, and enriched with 10 cycles of PCR for HiSeq 2500 technology (Ilumina Inc., San Diego, CA) using TruSeq DNA Sample kit (FC-121-2001, Illumina) following manufacturer`s instructions, and sequenced as 100 bp single reads at the RU Genomics Resource Center. The quality and quantity of the libraries were validated using Agilent’s High Sensitivity DNA Chip (Agilent) for the Agilent 2100 Bioanalyzer

value: midbrain

tag: transporter

value: dopamine


title: Leaf

value: Leaf


title: datM3-1 midbrain neurons


title: Stigma

value: Stigma


title: Corm

source_name: Corm

value: Corm


title: 6-C10+D1 CRISPR/Cas9 and a homologous donor template Experiment_2

city: boston

first: Luca

last: Pinello

state: MA

address: 450 brookline avenue

institute: Dana-Farber Cancer Institute

description:
6-C10+D1
http://www.bloodjournal.org/content/45/3/321.long?sso-checked=true
K562 subclone cells are a suspension cell line cultured in RPMI-1640 with 10% fetal bovine serum (FBS) and 1X Pencillin, Streptomycin, L-Glutamine

library_source: genomic

data_processing:
Before runnig CRISPResso, raw reads were trimmed for the HBB primers and merged using cutadapt (1.8) with  default parameters (" -g ^NNNNGGCAGAGCCATCTATTGCTT -G ^GGTCTCCTTAAACCTGTCTTG").
Merged file were processed using CRISPResso (0.9) with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: CRISPResso output  (tables only)

molecule: genomic DNA

organism: Homo sapiens

source_name: Subclone of K562 cells with genotype rs713040-A/A and rs334-A/A

growth_protocol: K562 subclone cells were cultured in RPMI with 10% fetal bovine serum and 1X penicillin/streptomycin/L-glutamine at a density of 1e5-1e6cells/ml. Cells were split every 3-4 days and given fresh medium.

extract_protocol:
Genomic DNA was extracted using the Invitrogen PureLink Genomic DNA Mini Kit (CA#K182002 ) according to the manufacturer's instructions
Genomic DNA samples were initially amplified outside the donor template with primers OuterFwd 5'-ATGCTTAGAACCGAGGTAGAGTTT-3' and OuterRev 5'-CCTGAGACTTCCACACTGATG-3'. 1ul of the PCR was run on a 1% agarose gel to confirm band size. 1ul of PCR product was then used for the "inner" PCR with primers HBB Fwd 5’ – ACACGACGCTCTTCCGATCTNNNNGGCAGAGCCATCTATTGCTT – 3’ and HBB Rev 5’ – GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTGGTCTCCTTAAACCTGTCTTG – 3’ to amplify the specific 198 bp region of HBB surrounding the sickle mutation along with primers to add Illumina adapters and indexes. 1ul of the second PCR product was run on a 2% agarose gel to confirm the band size was accurate. Quantification of individual samples was completed using densitometry and samples were pooled at equimolar ratios before being PCR purified using Ampure Beads. The final library was quantified using droplet digital PCR for the Illumina adapters and diluted to 10nM before being run on an Illumina HiSeq machine

treatment_protocol: K562 subclone cells were nucleofected with plasmids containing the CRISPR sgRNA and Cas9 (pX330, Addgene plasmid #42230) and, where applicable, a TOPO vector containing a homologous donor template containing ~1.1kb of the beta-globin locus surrounding the sickle mutation and containing the 4 base changes at positions 59, 67, 69, and 91 relative to the amplicon start. 2e5 cells were nucleofected using the Lonza Amaxa 4D Nucleofector with Cell Line Solution SF according to the manufacturer's protocol. 4 days following nucleofection, cells were harvested for genomic DNA extraction.

tag: cell line name

value: K562 cells

tag: source

value: Human erythroleukemia cell line derived from a 53-year-old female with chronic myelogenous leukemia, subcloned to be homozygous at rs713040-A/A and rs334-A/A


title: Soybean leaf dcl1a rep1-1

description: Soybean leaf, dcl1a rep1-1


title: N8-4

city: Cambridge

first: Diwakar

last: Pattabiraman

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing:
RNASeq paired-end reads from Illumina 1.5 encoding were aligned using TopHat (v 2.0.13) to the human genome (GRCh37) with Ensembl annotation (GRCh37.75) in gtf format: default parameters were used, except for base encoding. HTSeq-count was used to obtain counts with intersection-strict mode option, and unstranded.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw counts from HTSeq-count.

source_name: Mesenchymal derivatives of HMLE

growth_protocol: All cells were grown in mammary epithelial growth medium (MEGM; Lonza)

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus kit
Libraries were prepared using the TruSeq stranded mRNA protocol as described in the kit (Illumina; Catalog # RS-122-2101) manual
Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling was done using the Standard Illumina pipeline, and then demultiplexed into fastq files

treatment_protocol: N8-CTx cells were derived by treating NAMEC8 cells with cholera toxin every 2 days over a period of 14 days

tag: cell type


title: N8-CTx RNASeq

source_name: NAMEC8 induced to undergo an MET


title: N8-3_3

description:
Biological rep3
Technical rep 3


title: N8-3_1

description:
Biological rep3
Technical rep 1


title: N8-1_3

description:
Biological rep1
Technical rep 3


title: N8-2_1

description:
Biological rep2
Technical rep 1


title: N8-3_2

description:
Biological rep3
Technical rep 2


title: HMLE-3_3

description:
Biological rep3
Technical rep 3

source_name: Immortalized human mammary epithelial cells

value: HMLE


title: N8-1_2

description:
Biological rep1
Technical rep 2


title: N8-2_2

description:
Biological rep2
Technical rep 2


title: 3-C11-1 CRISPR/Cas9 alone Experiment_1

description:
3-C11-1
http://www.bloodjournal.org/content/45/3/321.long?sso-checked=true
K562 subclone cells are a suspension cell line cultured in RPMI-1640 with 10% fetal bovine serum (FBS) and 1X Pencillin, Streptomycin, L-Glutamine


title: N8-2_3

description:
Biological rep2
Technical rep 3


title: N8-1_1

description:
Biological rep1
Technical rep 1


title: HMLE-3_1

description:
Biological rep3
Technical rep 1


title: Ref

city: Freising

first: Juergen

last: Behr

state: Bavaria

address: Weihenstephaner Steig 16

department: Technische Mikrobiologie

country: Germany

institute: TU Muenchen

description: rRNA depleted mRNA

data_processing:
SOLiD sequencing was performed at CeGaT GmbH (Tübingen, Germany). Fragmentation, library preparation, templated bead preparation and sequencing followed standard Applied Biosystem protocols.
The SOLiD data as QUAL and CSFASTA files were mapped with Bowtie (version 1.1.2) to the reference genome of E. faecalis OG1RF with default settings. Resulting SAM files were filtered for mappable reads only, sorted and converted into BAM files using Samtools (version 0.1.18). Cufflinks, Cuffmerge and Cuffdiff release 2.0.2 were used to quantify transcript abundance as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and calculate log2-fold changes (logFC). According to the instructions of the programmers of the Cufflinks suite for bacterial RNA-Seq data, Cufflinks was run with a supplied reference genome annotation and as rRNA depleted samples were used for SOLiD sequencing a mask-file containing the locations of 5S, 16S and 23S rRNA genes was provided. The resulting GTF files were merged using Cuffmerge. Cuffdiff was run (with switched on upper quartile normalization in order to improve the robustness of differential expression calls for less abundant genes) for calculating significant differences in gene expression levels.
Genome_build: Sequence and annotation data for E. faecalis OG1RF under accession number CP002621 was downloaded from the NCBI database (http://ncbi.nlm.nih.gov/).
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for each sample and log2(fold_change) values.

organism: Enterococcus faecalis

source_name: BHI broth

growth_protocol: Nine germ-free wild type mice 129 SvEv TAC were monoassociated with E. faecalis strain OG1RF at an age of 11-12 weeks. Mice were fed standard autoclavable diet Prolab® RMH 3500 in which calories are provided by 26.20 % protein, 15.46 % fat and 58.34 % carbohydrates. The intestinal contents were collected and deep-frozen immediately after killing and dissection. For the reference RNA sample of E. faecalis OG1RF was extracted from a pure culture of OG1RF grown to mid exponential growth phase in BHI media under anaerobic conditions at 37 °C.

extract_protocol:
All buffers or pure water were treated with diethylpyrocarbonate (DEPC) to inactivate RNases and prevent RNA degradation. Mouse fecal samples were weighed in aliquots (each 0.1 g) and mixed with equal volume of phosphate-buffered saline (PBS: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4·H2O, 1.76 mM K2HPO4; pH 7.4). After centrifugation at 10,000 x g for 1 min the supernatant was discarded and the pellet was resuspended in equal volume of dissociation solution (DSS: 0.1 % (v/v) Tween 80, 1 % (v/v) methanol, 1 % tertiary butanol adjusted to pH 2 with HCl; Whitehouse et al., 1994). The samples were centrifuged for 3 min at 200 x g. Afterwards, the supernatant was collected and centrifuged at 10,000 x g for 1 min. The supernatant was discarded, the pellet was resuspended in 200 µl TE buffer and then 600 µl RLT buffer (including 10 µl/ml of β-mercaptoethanol) was added. RNA samples extracted from mouse fecal content from nine mice (five male and four female mice) were originated from all intestinal segments: jejunum, ileum, cecum and colon. These samples were pooled into one in vivo total RNA sample only if the quality requirements were met. It must be stressed that pooling of these samples is inevitable to receive any RNA sequencing result because of the very low amount of RNA, which can be isolated from enterococci residing in the fecal samples.The total RNA sample was depleted of rRNA using The Ribominus™ Transcriptome Isolation Kit (Invitrogen, Carlsbad, California, USA) according to the manufacturer’s instructions. Afterward the treated RNA was precipitated with ethanol in which the RNA sample was well mixed with 1 µl glycogen (20 µg/µl), 2.5 x sample volumes of 100 % ethanol and 1/10th sample volume of 3 M sodium acetate. After precipitation of RNA by incubation at -80 °C for 2 hours, the sample was treated with RNase-free DNase (TURBO DNA-freeTM Kit; Applied Biosystems Inc., Foster City, California, USA) to avoid DNA contamination in further analysis.
SOLiD sequencing was performed at CeGaT GmbH (Tübingen, Germany). Fragmentation, library preparation, templated bead preparation and sequencing followed standard Applied Biosystem protocols.

tag: strain

tag: growth environment

value: BHI broth


title: Efm

description: rRNA depleted mRNA

source_name: monoassociated mice fecal samples

value: monoassociated mice


title: HMLE-3_2

description:
Biological rep3
Technical rep 2


title: HMLE-1_3

description:
Biological rep1
Technical rep 3


title: HMLE-2_2

description:
Biological rep2
Technical rep 2


title: HMLE-2_1

description:
Biological rep2
Technical rep 1


title: HMLE-2_3

description:
Biological rep2
Technical rep 3


title: HMLE-1_2

description:
Biological rep1
Technical rep 2


title: 6-C11+D1 CRISPR/Cas9 and a homologous donor template Experiment_3

description:
6-C11+D1
http://www.bloodjournal.org/content/45/3/321.long?sso-checked=true
K562 subclone cells are a suspension cell line cultured in RPMI-1640 with 10% fetal bovine serum (FBS) and 1X Pencillin, Streptomycin, L-Glutamine


title: HMLE-1_1

description:
Biological rep1
Technical rep 1


title: Y7-2

city: Rongchang

first: Jie

last: Zhang

state: Chongqing

address: Xueyuan road #160

department: College of Animal Science

country: China

institute: Southwest University

description:
Digital gene expression tag profiling (DGE). Tag length = 21 nt.
Chinese indigenous pig breed.

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to pig whole genome using Sscrofa10.2.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: Tab-delimited text files include tag sequences, counts, and TPMs (number of transcripts per million tags).

organism: Sus scrofa

source_name: Adipose tissues, postnatal 7y

extract_protocol:
Subcutaneous adipose tissues were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: breed

value: Jinhua pig

value: subcutaneous adipose tissues

tag: developmental stage

value: postnatal 7 years


title: Y7-1


title: Y7-3


title: N8_CTx_WCE

description: WCE

data_processing:
ChIPSeq reads from Illumina 1.5 encoding were aligned to the human genome (GRCh37) using Bowtie2 (v 2.2.5), default parameters except for the encoding were used.
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig files

extract_protocol:
ChIP was performed using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (Cell Signaling Technology; #9005); PHF2 Antibody (Cell Signaling Technology, Catalog #3497 Lot#2)
To make libraries, TruSeq ChIP protocol was followed as described in the kit (Illumina; Catalog # IP-202-1012) manual
Libraries were pooled together and sequenced on the HiSeq 2500 sequencer using the Standard sequencing protocols. Images analysis and base calling was done using the Standard Illumina pipeline, and then demultiplexed into fastq files

tag: chip antibody


title: D180-1

source_name: Adipose tissues, postnatal 180d

value: postnatal 180 days


title: NAMEC8_PHF2_WCE

description: WCE

source_name: Mesenchymal derivatives of HMLE cells


title: N8-CTx_PHF2_ChIP

description: Chromatin IP against PHF2

value: PHF2 Antibody (Cell Signaling Technology, Catalog #3497, Lot#2)


title: D30-2

source_name: Adipose tissues, postnatal 30d

value: postnatal 30 days


title: D30-3


title: D30-1


title: D180-2


title: NAMEC8_WCE

description: WCE


title: NAMEC8_H3K9me3_ChIP

description: Chromatin IP against H3K9me3

value: H3K9me3 antibody


title: NAMEC8_PHF2_ChIP

description: Chromatin IP against PHF2


title: ZIKV2-2

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned using tophat v2.0.13 and differential RPKM expression values were extracted using cuffdiff v2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: text file with abundance values for combined replicates and statistical test for differential expression.

source_name: human Neural Progenitor cells

growth_protocol: Human iPSC lines (C1-2 and D3-2) were previously generated from skin biopsy samples and they had been fully characterized and passaged on MEF feeder layers (Wen et al., 2014). H9 hESCs (WA09 from WiCell) and iPSC line (DF19-9-11T.H.) were cultured on feeder free condition. All studies followed institutional IRB and ISCRO protocols approved by Johns Hopkins University School of Medicine and Florida State University. Human iPSCs (C1 and D3-2) were differentiated into forebrain specific hNPCs and immature neurons following previous protocols (Wen et al., 2014). Briefly, hiPSCs colonies were detached from the feeder layer with 1 mg/ml collagenase treatment for 1 hr and suspended in embryonic body (EB) medium, consisting of FGF-2-free iPSC medium supplemented with 2 µM Dorsomorphin and 2 µM A-83, in non-treated polystyrene plates for 4 days with a daily medium change. After 4 days, EB medium was replaced by neural induction medium (NPC medium) consisting of DMEM/F12, N2 supplement, NEAA, 2 µg/ml heparin and 2 µM cyclopamine. The floating EBs were then transferred to matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with NPC medium change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates (Corning) to form neurospheres in NPC medium containing B27. The neurospheres were then dissociated with Accutase at 37⁰C for 10 min and placed onto matrigel-coated 6-well plates at day 24 to form monolayer NPCs in hNPC medium containing B27. These hNPCs expressed markers for forebrain-specific progenitor markers, including NESTIN, PAX6, EMX-1, FOXG1 and OTX2 (Wen et al., 2014). For neuronal differentiation, monolayer hNPCs were dissociated with Accutase at 37⁰C for 10 min and placed onto Poly-D-Lysine/laminin-coated coverslips in the neuronal culture medium, consisting of Neurobasal medium supplemented with 2 mM L-glutamine, B27, cAMP (1 µM), L‐Ascorbic Acid (200 ng/ml), BDNF (10 ng/ml) and GDNF (10 ng/ml).

extract_protocol:
Total RNA was extracted from mESCs by RNeasy (Qiagen), and 1 μg total RNA was primed with Oligo(dT)20 primers (Invitrogen) for cDNA synthesis.
ZIKV infected hNPCs at 56 hrs and mock infected parallel cultures were used for global transcriptome analysis. RNA-seq libraries were generated from duplicated samples per condition using the Illumina TruSeq RNA Sample Preparation Kit v2 following manufacturer’s protocol. An Agilent 2100 BioAnalyzer was used to quantify amplified cDNA and qPCR was applied to accurately quantify library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle pair-end sequencings were performed using Illumina MISeq or HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline. RNA-seq reads were aligned using tophat v2.0.8 (Trapnell et al., 2012) and differential RPKM expression values were extracted using cuffdiff v2.2.1 (Trapnell et al., 2012). Statistical significance were determined by cuffdiff in duplicated samples per condition. Gene Ontology analyses were on biological process (BP) performed by The Database for Annotation, Visualization and Integrated Discovery (DAVID) v6.7 (Huang da et al., 2009).

treatment_protocol: A ZIKV stock with the titer of 1x105 TCID/ml in the form of culture fluid from an infected rhesus Macaca cell line, LLC-MK2, were originally obtained from ZeptoMetrix (Buffalo, NY). This virus stock was then used to infect the Aedes C3/C36 cells at a MOI of 0.02. Supernatant from the infected mosquito cells were collected 4-7 days post-infection and frozen in aliquots for both titering and infection of human cells. Infections of different cell types were performed at a low multiplicity of infection (MOI; MOI < 0.1) and the virus inoculum was removed after a 2-hour incubation with the cells. To determine whether infected hNPCs produce more infectious ZIKV particles, supernatant from hNPC cultures 72 hour after infection were added to Vero cells for 48 hours.

value: Neural Progenitor cells

tag: infection status

value: Zika infected


title: Mock2-2

value: mock infected


title: ZIKV1-2


title: Mock1-2


title: D0-2

source_name: Adipose tissues, postnatal 0d

value: postnatal 0 day


title: D0-1


title: WT, biol. replicate #1

status: Public on Mar 03 2016

city: Westmead

first: Julianne

middle: T

last: Djordjevic

state: NSW

address: 176 Hawkesbury Road

department: Centre for Infectious Diseases and Microbiology

country: Australia

institute: Westmead Institute for Medical Research

data_processing:
Casava 1.8.2 was used to de-multiplex and generate the fastq files. Only reads that passed Illumina's filter were extracted from the run.
The sequences were aligned to the genome (Broad Institute, "cryptococcus_neoformans_var._grubii_h99__cna3__3_transcripts.gtf") using TopHat for Illumina in Galaxy interface, default settings.
FPKM values determination and statistical analysis of gene expression were performed using Cuffdiff v2.1.1 , Galaxy interface, using default settings.
Genome_build: Cryptococcus neoformans var. grubii H99 Sequencing Project, Broad Institute of Harvard and MIT (http://www.broadinstitute.org/)
Supplementary_files_format_and_content: Tab-delimited text file containing FPKM values for each gene (generated by Cuffdiff)
Supplementary_files_format_and_content: Tab-delimited text file containing pairwise comparison of all strains and statistical significance values (generated by Cuffdiff)

organism: Cryptococcus neoformans H99

source_name: Fungal cells

growth_protocol: The cells were grown in YPD broth (shake culture) at 30 degrees for 22 hours.

extract_protocol:
The cells were homogenized in the presence of glass beads using bead beater. Total RNA was extracted with Trizol following manufacturer's protocol. RNA was further purified using Qiagen RNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq sample preparation kit)

treatment_protocol: No treatment

value: Parental strain


title: WT, biol. replicate #3


title: NAMEC8_H3K9me2_ChIP

description: Chromatin IP against H3K9me2

value: H3K9me2 antibody


title: N8-CTx_H3K9me2_ChIP

description: Chromatin IP against H3K9me2


title: kcs1, biol. replicate #3

value: IP6 kinase mutant


title: kcs1, biol. replicate #2


title: D180-3


title: ipk1, biol. replicate #2

value: IP5 kinase mutant


title: N8-CTx_H3K9me3_ChIP

description: Chromatin IP against H3K9me3


title: kcs1, biol. replicate #1


title: D0-3


title: ipk1, biol. replicate #1


title: WT, biol. replicate #2


title: arg1, biol. replicate #2

value: IP3 kinase mutant


title: arg1, biol. replicate #3


title: arg1, biol. replicate #1


title: Sgo1 4

city: Oklahoma City

first: Hiroshi

middle: Y

last: Yamada

state: Oklahoma

department: Medicine

institute: OUHSC

data_processing:
Paired fastq files were imported and aligned in Strand NGS software version 2.1  www.strand-ngs.com
The expression values were obtained by quantifying the association of reads to genes and exons as raw counts
The raw counts were normalized using DESeq and normalized signal counts were log transformed
Genome_build: mouse mm10 (UCSC) assembly   Genome Reference Consortium Mouse Build 38 GCA_000001635.5
Supplementary_files_format_and_content: raw and normalized counts

source_name: colonic mucosal tissue

extract_protocol:
Colonic mucosal tissues were extracted in Trizol, total RNA were precipitated, then mRNA were purified with mRNA puriification kit (Ambion).
Libraries were prepared according to Illumina's instructions accompanying the RNA TruSeq V2 Library construction kit.   Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.

treatment_protocol: All mice were treated with Azoxymethane (4mg/kg bw) twice a week from 8 weeks of age to 12 weeks of age. They were maintained without further treatments until 9 months of age, then samples were collected.

value: colon

tag: genotype


title: Sgo1 5


title: Sgo1 1


title: WT5

value: wild type


title: WT6


title: Sgo1 2


title: WT3


title: WT2


title: WT4


title: iXEN9x

city: East Lansing

first: Michael

last: Halbisen

state: MI

address: 603 Wilson Rd RM 419

department: Biochemistry and Molecular Biology

institute: Michigan State University

description: mRNA

data_processing:
Illumina base calling.
QC with FastQC (0.11.3).
Adapter trimming with Trimmomatic (0.32).
Alignment with TopHat (2.0.12).
Reads counted with HTSeq (0.6.1).
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Tab-delimited text files include raw count data for each sample.

source_name: iXEN grown in XEN cell medium

growth_protocol: 10 passages in ESC medium, then 5 passages in XEN cell medium.

extract_protocol:
Trizol (Invitrogen).
Illumina TruSeq mRNA kit (Illumina).

tag: strain/background

value: induced extraembryonic endoderm stem cell line

tag: treatment

value: grown in XEN cell medium


title: iXEN2x

description: mRNA


title: XEN7x

description: mRNA

source_name: XEN grown in XEN cell medium

value: extraembryonic endoderm stem cell line


title: iXEN1x

description: mRNA


title: iXEN6x

description: mRNA


title: XEN2x

description: mRNA


title: XEN1x

description: mRNA


title: ipk1, biol. replicate #3


title: iXEN6m

description: mRNA

source_name: iXEN grown in ES cell medium

growth_protocol: 10 passages in ESC medium, then 5 passages in ESC medium.

value: grown in ES cell medium


title: iXEN9m

description: mRNA


title: iXEN2m

description: mRNA


title: iXEN1m

description: mRNA


title: Sgo1 3


title: Sgo1 6


title: XEN2m

description: mRNA

source_name: XEN grown in ES cell medium


title: XEN7m

description: mRNA


title: XEN1m

description: mRNA


title: WT1


title: MEF3m

description: mRNA

source_name: MEF control

growth_protocol: 3 passages in MEF medium.

value: mouse embryonic fibroblasts

value: control


title: MEF2m

description: mRNA


title: MEF1m

description: mRNA


title: 16HBE14o- miRNA-1343 rep4

city: Cleveland

first: Ann

last: Harris

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University

description:
Ambion Pre-miR miRNA Precursors
16HBE gene_exp.diff

data_processing:
Paired-end reads (100bp) format were mapped to the reference human genome (hg19) with ENSEMBL Release 74 of human genome annotation as transcriptome mapping, using TopHat (v2.0.10)
The aligned reads were then processed by Cufflinks (v2.1.1) to assemble expressed genes and transcripts against the UCSC hg19 gene structure annotation, and estimate expression levels for each transcript.
The assembly files for each of the samples were then merged to create a single transcriptome annotation and differentially expressed genes identified by Cuffdiff.
Samples were then normalized and expressed as fragments per kilobase of transcript per million fragments mapped (FPKM) and both a test statistic (p-value) and an adjusted p-value (q-value) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each gene and fold difference between negative control and miR-1343

source_name: Human bronchial epithelial cells

growth_protocol: A549 and 16HBE14o- cells were grown in DMEM Low glucose media supplemented with 10% FBS

extract_protocol:
Trizol® (Life Technologies) was used for RNA extraction
RNA libraries were prepared from 2 ug of total RNA using TruSeq™ RNA sample preparation kit v2 as per the manufacturer's low-throughput protocol (Illumina)

treatment_protocol: Cells at 50% confluence were transfected with miRNA-1343 or negative control miRNA using Lipofectamine 2000 (Life Technologies) reagent to a final contentration of 20 nM.  At 48 h post-transfection, the cells were washed in PBS and immediately lysed in Trizol (Life Technologies) reagent to be harvested for RNA extraction.

value: 16HBE14o- cells

value: Precursor miR-1343 (Life Technologies)

value: Transient overexpression (20 nM)


title: 16HBE14o- miRNA-1343 rep1


title: A549 negative control rep1

description:
Ambion Pre-miR miRNA Precursors
A549_gene_exp.diff

source_name: Lung adenocarcinoma cells

value: A549 cells

value: Negative control Precursor miRNA #2 (Life Technologies)


title: 16HBE14o- miRNA-1343 rep2


title: A549 negative control rep4


title: 16HBE14o- negative control rep3


title: 16HBE14o- negative control rep1


title: A549 miRNA-1343 rep1


title: A549 miRNA-1343 rep4


title: 16HBE14o- miRNA-1343 rep3


title: A549 miRNA-1343 rep2


title: A549 miRNA-1343 rep3


title: 16HBE14o- negative control rep4


title: A549 negative control rep2


title: 16HBE14o- negative control rep2


title: A549 negative control rep3


title: HEK293T_Tet2_RRBS

city: Shanghai

first: Wei

last: Li

address: DongAn Road 130

institute: FuDan University

data_processing:
For ChIP-seq, sequenced were filtered based on a mean base quality score <20 and duplicate reads were removed. Filtered reads were then aligned to the human reference genome (UCSC assembly hg19, GRCh37) using the Bowtie short-read alignment program (v0.12.7) to retain reads mapped to unique genomic locations with at most 2 mismatches.Unique and monoclonal reads were used in subsequent peak calling analyses.Each sequence was extended to 400 bp according to the average DNA fragment length used in ChIP-seq. The peaks of Tet2 ChIP-seq are identified using the MACS software (version 1.4) with the default parameters except for the P-value cut-off which was set to <1e-5 and FDR <0.01
For hMeDIP-seq, we separated the raw sequence reads of hMeDIP and Input into different files according to the specific barcode sequence of each sample. Sequence reads were mapped onto the reference human genome using the Bowtie (v0.12.7) algorithm. Since the average DNA fragment length used in hMeDIP-seq was 450bp, each sequence was extended to 450 bp.The peaks of hMeDIP-seq are identified using the MACS software (version 1.4) with the default parameters except for the P-value cut-off which was set to <1e-5 and FDR <0.01.
For RRBS,  sequencing raw reads were trimmed with trim_galore (v0.4.0) with default parameters to remove adaptor sequence and low-quality sequence, and then the rest reads were aligned to human reference genome (hg19, downloaded from http://genome.ucsc.edu) using BSMAP (v2.6) with default parameters, finally a script, methratio.py was used for extracting methylation ratios from BSMAP mapping results
Genome_build: hg19
Supplementary_files_format_and_content: txt file was methylation ratio of RRBS datas generated by methratio.py;*peaks.bed: peaks bed files generated by Macs14, monoExt*.bed:mapped reads files in bed format, monoExt*.

growth_protocol: HEK293T cells were cultured in DMEM + serum at 37°C / 5% CO2

extract_protocol:
For ChIP-seq, cells were fixed with DSG (Disuccinimidyl glutarate) followed by formaldehyde. Chromatin was incubated with anti-HA antibody (Cell Signaling; C29F4) for overnight followed by incubation with Protein A magnetic beads (Millipore). ChIP DNA was reverse-crosslinked and purified with MinElute PCR purification kit (Qiagen); For hMeDIP-seq, genomic DNA was sonicated to <500 bp by Bioruptor sonicator (Diagenode; Belgium) and quantified using the NANODROP2000c (Thermo) according to the manufacturer’s manual. The sonicated DNA fragments (1ug of each sample) were end-repaired using the End-It DNA End Repair Kit (EPICENTRE Biotechnologies) according to the manufacturer’s instructions, followed by treatment with Klenow fragment 3’-5’exo (NEB) and dATP to generate a protruding 3’A for ligation with the adaptor containing a specific barcode sequence. The barcode sequence (four-base index: TTAGGC, GATCAG, AGTTCC, GTCCGC) within the adaptor. Then equal amount of bar-code tagged gDNA from Control, MBD3L2, Tet2, Tet2+MBD3L2 were mixed together in one tube and 10% DNA was taken as Input. The mixed DNA was then incubated with 5hmC antibody (Active Motif) for overnight followed by incubation with Protein A/G beads. The 5hmC binding DNA fragments were purified with MinElute PCR purification kit (Qiagen); For RRBS, 500 ng of genomic DNA was digested with the methylation insensitive restriction digest enzyme Msp1 (NEB), which cleaves DNA at CCGG sites creating fragments high in CpG content (Gu et al., 2011). The DNA was purified using the QIAquick PCR Purification Kit (Qiagen).
For ChIP-seq, library were performed using NEB Next ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions; For hMeDIP-seq, Library were performed using NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions; For RRBS, samples were end-repaired and A-tailed using a Klenow fragment (New England Biolabs, Inc). TruSeq™ adaptors (Illumina, Inc., San Diego, CA) were ligated to the modified DNA ends using T4 DNA ligase (New England Biolabs, Inc.). We excised the gel ranged from 150-400bp and purified the gel with the QIAquick Gel Extraction Kit (Qiagen). The sample was bisulfite modified and PCR amplified to enrich for fragments containing high CpG content. Samples were submitted for sequencing on the Illumina HiSeq™ instrument

treatment_protocol: Empty vector,HA-Tet2 or HA-MBD3L2 were transfected simultaneously or individually in HEK 293T cell line.

tag: cell line

tag: transfected with

tag: molecule subtype

value: Bisulfite treated DNA


title: HEK293T_Tet2+MBD3L2_RRBS

value: HA-Tet2 + HA-MBD3L2


title: HEK293T_Input_5hmC

value: empty vector


title: HEK293T_Control_RRBS


title: HEK293T_Tet2_5hmC

value: 5hmC mouse polyclonal antibody (Active Motif, catalog #39769)


title: HEK293T_Input_ChIPSeq


title: HEK293T_HA_Tet2_ChIP-Seq

value: HA beads


title: HEK293T_MBD3L2_5hmC


title: HEK293T_HA_MBD3L2_ChIPSeq


title: HEK293T_Control_5hmC


title: HEK293T_Tet2+MBD3L2_5hmC


title: T915

city: Toulouse

first: Frédéric

last: Chibon

address: 2 avenue Hubert Curien

department: Team 19 - INSERM UMR1037

country: France

institute: Cancer Research Center of Toulouse

data_processing:
Low-quality 5' and 3' ends were trimmed using Sickle (Phred score <20). Overlapping reads were merged using SeqPrep and split in half with a Awk routine. Paired-ends with one read shorter than 30 bp were discarded.
Transcriptomic (coding RefSeq genes from Hg19 UCSC Table Browser fixed on 2014/01) alignments were performed by TopHat2. Once aligned, paired-end reads that mapped at multiple locations on transcriptome, low-quality (score <20) and discordant paired-end reads were discarded using SAMtools. MarkDuplicates removed PCR duplicates.
Cufflinks estimated gene and transcript abundances.
Miscellaneous filters, statistics and plots were performed by R.
Genome_build: Hg19
Supplementary_files_format_and_content: Expression matrix generated by R.

source_name: Leiomyosarcoma

extract_protocol:
RNA extraction from frozen samples was performed using a standard TRIzol (Life Technologies) / chloroform extraction followed by 70% ethanol precipitation and RNA purification using the RNeasy Mini Kit (Qiagen) with a DNase treatment (RNase-Free DNase Set, Qiagen). RNA extraction from FFPE tissue was performed using a Deparaffinization Solution (Qiagen) as recommended by the manufacturer followed by a DNase treatment (RNase-Free DNase Set, Qiagen) and RNA purification using the RNeasy FFPE kit (Qiagen) according to the manufacturer’s recommendations. RNA were quantified using a Nanodrop 1000 spectrophotometer (Thermo Scientific) and were qualified with the Agilent 2100 Bioanalyzer (Agilent) using the Agilent RNA 6000 Nano Kit (Agilent) according to the manufacturer’s instructions. An ERCC RNA Spike-In Mix (Life technologies) was added to each RNA as recommended by the manufacturer.
The RNA-seq libraries from FFPE tissue samples total RNA were prepared using a modified TruSeq RNA Sample Prep Kit v2 protocol. Briefly, rRNA was depleted from 0.5 µg of total RNA using the RiboZero Magnetic Gold Kit (Human/Mouse/Rat, Epicentre). Ribosomal RNA-depleted RNA samples were purified using Agencourt RNA Clean XP beads (Beckman Coulter Genomics) and RNA was eluted with the Elute, Prime, Fragment Mix from the TruSeq RNA Sample Prep Kit v2 (Illumina Inc.). The RNA fragmentation time (2.5 to 5 minutes) varied depending on the quality of the initial total RNA (assessed by Eukaryote Total RNA Nano Bioanalyzer assay, Agilent). Following the fragmentation, first and second strand synthesis, the Illumina barcoded adapters were ligated at 1/10 dilution of the recommended concentration. Libraries were enriched with 15 cycles of PCR. The size and quality of the libraries were assessed in a High Sensitivity DNA Bioanalyzer assay (Agilent). Starting input material for the libraries construction was DNA free total RNA from frozen tissue using the TruSeq™ RNA Sample Prep Kit v2 (Illumina Inc.,) according to manufacturer’s protocol. In short, 0.5 μg of total RNA was used for poly-A based mRNA enrichment selection followed by fragmentation by divalent cations resulting into fragments of 80-250nt, with the major peak at 130nt. Double stranded cDNA was end repaired, 3´adenylated and the 3´-“T” nucleotide of barcoded Illumina adapters was used for the adapter ligation. The ligation product was amplified with 12 cycles of PCR and quality controlled in Agilent DNA 7500 Bioanalyzer assay (Agilent). Each library was sequenced using TruSeq SBS Kit v3-HS, in paired end mode with the read length 2x76bp. We generated minimally 23 million paired end reads passing filter for each FFPE RNA-seq library or at least 35 million paired end reads passing filter for each frozen tissue RNA-seq library in a fraction of a sequencing lane on HiSeq2000 (Illumina, Inc) following the manufacturer’s protocol. Image analysis, base calling and base quality scoring of the run were processed by integrated primary analysis software - Real Time Analysis (RTA 1.13.48) and followed by generation of FASTQ sequence files by CASAVA (v1.8).

tag: metastasis

value: No

tag: time

tag: paired microarray

tag: paired material support

tag: material support

value: FFPE block

tag: ffpe quality

tag: cinsarc


title: T909

source_name: Other


title: T917

source_name: Undifferentiated sarcoma


title: T918


title: T910

source_name: GIST

value: Yes


title: T916


title: T919


title: T912

source_name: Dedifferentiated liposarcoma


title: T914


title: T913


title: T911


title: T905


title: T907


title: T906


title: T908


title: T902


title: T904

source_name: Myxofibrosarcoma


title: T903


title: T901


title: T895


title: T898


title: T897


title: T894


title: T893


title: S962


title: T900


title: S960


title: S959


title: S958


title: S946


title: S945


title: S954


title: S941


title: S957


title: S947


title: S944


title: S955


title: S936

molecule: polyA RNA

value: Frozen tumor


title: S956


title: S938


title: S951


title: S933


title: S935


title: S931


title: S937


title: S932


title: S930


title: S929


title: S924


title: S927


title: S925


title: S928


title: S952


title: S926


title: S923


title: S942


title: S921


title: S919


title: S918


title: S917


title: S934


title: S916


title: S909


title: S910


title: S915


title: S913


title: S911


title: S903


title: S902


title: S899


title: S907


title: S900


title: S905


title: S904


title: S886


title: S901


title: S888


title: S887


title: S881


title: S880


title: S883


title: S885


title: S882


title: S884


title: S878


title: S920


title: S875


title: S908


title: S868


title: S866


title: S906


title: S876


title: S874


title: S872


title: S879


title: 13h-B2

city: Clermont-Ferrand

first: Damien

last: BALESTRINO

address: 28 Place Henri Dunant

institute: Université Clermont Auvergne

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software CASAVA. The quality of the data was assessed using the Illumina software SAV (Sequence Analysis Viewer), FastQC and FastQScreen (contaminant screening) from the Babraham Institute.
The BWA-backtrack mapper (version 0.7.12-r1039) was used to align RNA-seq reads to the Klebsiella pneumoniae genome (internal resource).
Counting was performed with HTSeq-count 0.6.1p1 using the union mode, with a set of gene model annotations (internal references). As data come from a strand-specific assay, the read has to be mapped to the opposite strand of the gene.
Differentially expressed genes were identified using the Bioconductor package DESeq (v1.16.0). Genes with less than 15 reads (cumulating all the analysed samples) were filtered and thus removed from the analysis. Data were normalized using Relative Log Expression (RLE) normalization factors. Genes with adjusted p-value less than 1% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: CH1034.fa, internal resource.
Supplementary_files_format_and_content: Table with a first column for gene identification. The next columns correspond to the normalized abundance measurements (RLE normalization using DESeq statistical package) for each sample.

organism: Klebsiella pneumoniae

growth_protocol:
Bacteria were grown in 0.4% glucose M63B1 minimal medium (M63B1) at 37°C in aerobic conditions
growth in flow-cell for 13 hours

extract_protocol:
Total RNA was harvested using Trizol reagent following the protocol described by Toledo-Arana et al., 2009 (Toledo-Arana et al., 2009 - Nature 459: 950-956). Ribosomal RNAs were removed using the Bacteria Ribo-Zero Magnetic kit (Epicentre Biotechnologies) according to manufacturer's instructions. Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina) was used with rRNA depleted RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the TruSeq Stranded mRNA Sample Preparation kit from Illumina according to the manufacturer's instructions.

treatment_protocol: Recovered cells from cultures were harvested by addition of RNAlater (Life Technologies) and centrifugation.

tag: strain

tag: cell type

value: sessile cells

tag: conditions


title: D2

growth_protocol:
Bacteria were grown in 0.4% glucose M63B1 minimal medium (M63B1) at 37°C in aerobic conditions
Self-dispersed from a 13 hours-old biofilm grown in flow-cell

value: biofilm-dispersed cells

value: Dispersed bacteria from 13 hours-old biofilm


title: D3


title: 13h-B3


title: 13h-B1


title: 7h-B2

growth_protocol:
Bacteria were grown in 0.4% glucose M63B1 minimal medium (M63B1) at 37°C in aerobic conditions
growth in flow-cell for 7 hours


title: S867


title: 7h-B1


title: 7h-B3


title: SP3

growth_protocol:
Bacteria were grown in 0.4% glucose M63B1 minimal medium (M63B1) at 37°C in aerobic conditions
overnight culture

value: planktonic cells

value: stationnary growth phase


title: S863


title: S865


title: S862


title: S859


title: S860


title: S861


title: SP1


title: S871


title: EP2

growth_protocol:
Bacteria were grown in 0.4% glucose M63B1 minimal medium (M63B1) at 37°C in aerobic conditions
OD600 of 0.25

value: exponential growth phase


title: SP2


title: S857


title: S858


title: D1


title: EP3


title: EP1


title: S853


title: S855


title: S856


title: S852


title: S847


title: S845


title: S849


title: S846


title: S844


title: S843


title: S850


title: S840


title: S839


title: S836


title: S837


title: S833


title: S830


title: S834


title: S838


title: S829


title: S827


title: S831


title: S828


title: S841


title: S854


title: S826


title: S824


title: EBNA2 ChIP-seq

city: London

first: Richard

last: Jenner

address: 72 Huntley Street

department: Cancer Biology

country: United Kingdom

institute: UCL Cancer Institute

data_processing:
Initial processing of sequencing images was carried out using the CASAVA pipeline. Base calling, and quality control statistics were performed using GOAT and Bustard modules.
Sequence reads were aligned to the hg19 release of the human genome with Bowtie (default parameters).
Bed files were generated using bamtobed
Peak calling was performed with MACS 1.4.2 with a p-value threshold of 10-7.
Genome_build: hg19
Supplementary_files_format_and_content: Peaks called by MACS 1.4.2 at p<10-7. CSV file.

source_name: EBV transformed B cell line

growth_protocol: Cells were cultured in RPMI 1640, 10% foetal bovine serum and antibiotics and passaged twice weekly.

extract_protocol:
Following cross-linking, glycine was added to a final concentration of 1.25 M and cells were washed in PBS and lysed in 300 ul of cell lysis buffer (85 mM KCl, 0.5% NP-40, 5 mM PIPES pH 8.0, 1 mM PMSF and EDTA-free protease inhibitor cocktail (Roche)) per 10 7 cells. Following a 10 minute incubation on ice, cell nuclei were pelleted by centrifugation at 8000 rpm for 5 minutes at 4ºC in a bench-top Microfuge. The nuclei were then resuspended in 200 µl of SDS lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH 8.0 plus protease inhibitors) per 10 7 cells and sonicated to reduce DNA length to between 200 and 600 bp. Each ChIP was carried out using 600 µl of chromatin from 30 x 10 6 cross-linked cells diluted 10-fold in IP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris pH 8.0, 167 mM NaCl) and pre-cleared with protein A sepharose beads. An input control sample was removed and EBNA 2 was precipitated using 48 µg EBNA 2-specific mouse monoclonal antibody (PE2) overnight at 4ºC with rotation followed by an additional 2 hr incubation with 60 µg rabbit anti-mouse antibodies (Dako). IgG control samples were incubated overnight with 48 µg of a 1:1 mix of sheep and mouse IgG (Santa Cruz Biotechnology). BSA-coated protein A sepharose beads were then added and immune complexes collected by rotation at 4ºC for 3 hrs. Beads were washed for 10 minutes at 4 ºC with rotation using a series of different wash buffers. Complexes were washed once in low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl), once in high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 500 mM NaCl), once in LiCl wash buffer (250 mM LiCl, 1% NP40, 1% Na deoxycholate, 1 mM EDTA, 10 mM Tris pH 8.0) and twice in TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). Immune complexes were eluted in TE elution buffer (10 mM Tris pH 8.0, 5 mM EDTA, 1% SDS) at 65 ºC for 15 minutes. TE elution buffer was added to the input control sample and all samples were then incubated at 65 ºC overnight to reverse the crosslinks and samples were treated with 0.2 µg/ml RNAse A for 1 hr at 37 ºC to remove RNA. DNA was purified using QIAquick gel extraction and PB buffer (Qiagen).
ChIP and input DNA (10 ng) was used to generate sequencing libraries with an NEBNext ChIP-seq library prep reagent set for Illumina using NEBNext Index primers. PCR-amplified samples (16-cycles) were separated on a 2% agarose gel in TAE buffer, visualized using SYBR-safe stain and a Dark Reader transilluminator (Clare Chemical Research). The region of the gel containing 150-350 bp DNA fragments was excised and DNA purified using a gel extraction kit (Qiagen). The library was quantified using an Agilent bioanalzer and subjected to 35bp single-end read sequencing with an Illumina Genome Analyzer IIx with 6 samples per lane.

treatment_protocol: GM12878 cells were diluted to 5x10 5 cells/ml 24 hrs prior to chromatin preparation. Cells were then resuspended at 1x10 7 cells/ml and formaldehyde was added to a final concentration of 1% (v/v) for 15 minutes at room temperature with rocking to cross-link proteins and DNA.

value: B cell

tag: antibody

value: EBNA2 mouse monoclonal antibody (PE2) plus secondary rabbit anti-mouse


title: S851


title: S848


title: IgG control ChIP-seq

value: 1:1 mix of mouse and sheep IgG (santa cruz)


title: S842


title: S835


title: input DNA


title: S822


title: S821


title: S820


title: S817


title: S825


title: S816


title: N008


title: N009


title: S815


title: 5H

city: Oxford

first: Helio

last: Pais

address: Jonh Radcliffe Hospital

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

data_processing:
Read trimming with Trim Galore, default settings
Alignment and transcript abundance estimation with Sailfish, default settings
Differential expression with DESeq2, default settings
Genome_build: human cDNA, Ensembl version 75
Supplementary_files_format_and_content: CSV, estimated transcripts per million (Sailfish estimate), cell type mean, standard deviation and log fold change (estimated by DESeq2)

source_name: MSC

growth_protocol: All Ewing’s sarcoma cell lines were kept in RPMI1640 medium supplemented with 10% FCS. The MSC lines 4+v and 5H [PMID:20466760] were grown in MesenCult MSC basal medium supplemented with 10% MesencCult stimulatory supplements (Stemcell Technologies)

extract_protocol:
total RNA was extracted from each cell line using Trizol RNA extraction reagent (Life Technologies), according to manufacturer’s recommendations and 75 µg was used in two rounds of polyA selection to purify the mRNA.
The mRNA was reverse transcribed into cDNA and made into dsDNA using Just cDNA Double Stranded cDNA Synthesis Kit (Stratagene). The double stranded products were fragmented using Covaris S2 System, size selected using Ampure XP beads (Beckman Coulter), then sequencing libraries prepared before single end deep sequencing was carried out with an Illumina GA IIx to obtain 80bp reads.

value: mesenchymal stem cell line


title: S813


title: 4+v


title: A673

source_name: EWS

value: Ewing's sarcoma cell line


title: S819


title: TC-32


title: N006


title: TTC-466


title: N004


title: S818


title: N003


title: N002


title: S814


title: M998


title: M999


title: S823


title: M997


title: M995


title: M994


title: N007


title: N005


title: N001


title: M992


title: M991


title: M989


title: M988


title: IRF1-/-_BMDM_RNA_UT_2

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

country: Canada

institute: McGill University

data_processing:
The quality of sequence reads obtained for each sequence reads was confirmed using FastQC tool (Babraham Bioinformatics).
Reads were mapped to the mouse UCSC mm9 reference assembly using TopHat v2.0.9 in conjunction with Bowtie 1.0.0 algorithm (Langmead et al., 2009; Trapnell et al., 2009; Kim et al., 2013)
gene expression was quantified by counting the number of uniquely mapped reads with featureCounts using default parameters (Liao et al., 2014).
Normalization and differential expression analysis was conducted using the edgeR Bioconductor package (Robinson and Oshlack, 2010).
We retained genes that had an expression level of minimum 5 count per million reads (CPM) in at least 2 of the 12 samples and pairwise differential gene expression analysis was performed by comparing IFNγ-treated samples vs untreated samples. Genes with changes in expression ≥ |2| and adjusted p value < 10-5 were considered significant.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample.

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow-derived macrophages (BMDMs) were differentiated from bone marrow isolated from femur and tibia of 8-16 week-old C57BL/6 (B6), BXH2 (Ifr8m/m) or Irf1-/- female mice (Jackson Laboratory). Briefly, bone marrow cells were cultured in DMEM containing 10% heat inactivated FBS, antibiotics and 20% L-cell-conditioned medium (LCCM) as a source of M-CSF on non-adherent Petri dishes. The cells were supplemented with 10% LCCM 4 days later and at day 6, cells were harvested by gentle washing of the monolayer with PBS-Citrate. Cells were plated in tissue culture-grade dishes in DMEM containing 10% FBS, 20% LCCM and antibiotics and used the next day.

extract_protocol:
Independent duplicates of 5x10^5 WT, Irf8m/m and Irf1-/- BMDM were treated or not with IFNγ (400 U/ml) for 3h and RNA was extracted using RNeasy columns (Qiagen). RNA integrity was assessed on a Bioanalyzer RNA pico chip.
RNA-seq libraries were prepared following poly-A enrichment using Illumina TruSeq RNA sample preparation kit. The RNA-seq libraries were sequenced on an Illumina HiSeq 2000 sequencer in paired-end 50bp configuration.

treatment_protocol: BMDMs were left untreated or treated for 3h with 400U/ml of recombinant mouse IFNg added to culture medium.

value: no treatment


title: IRF8m/m_BMDM_RNA_IFNg_3h_2

value: IFNg (400U/ml) 3h


title: IRF1-/-_BMDM_RNA_UT_1


title: IRF1-/-_BMDM_RNA_IFNg_3h_1


title: M985

value: No


title: M984


title: IRF8m/m_BMDM_RNA_UT_2


title: IRF8m/m_BMDM_RNA_UT_1


title: M986


title: B6_BMDM_RNA_IFNg_3h_2


title: M982


title: M987


title: M983


title: M981


title: B6_BMDM_RNA_UT_2


title: B6_BMDM_RNA_UT_1


title: IRF1-/-_BMDM_H3K27Ac_IFNg_3h

data_processing:
Reads quality filtered according to the Illumina pipeline
The sequence reads were mapped to the mouse mm9 reference genome assembly with Bowtie 1.0.0 using the following settings: --best --trim5 2 mm9 (Langmead et al., 2009).
To identify significant TF binding events, we processed the mapped sequence reads with MACS 1.4.1 using matching number of IgG control reads to TF samples (Zhang et al., 2008).
The resulting transcription factor peak lists were filtered to remove regions longer than 3kb because they were artifacts generated from high background sequences, and contiguous peaks were separated with PeakSplitter (Salmon-Divon et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.bed = list of transcription factor binding peaks called by MACS and splitted by PeakSplitter

extract_protocol:
Twenty million BMDMs per ChIP were crosslinked for 10 min at room temperature with 1% formaldehyde added in culture medium. Crosslink was stopped with ice-cold PBS containing 0.125M glycine for 5min. Nuclei were prepared by sequential incubation on ice for 5min in buffer A [10mM Tris-HCl (pH 8), 10mM EDTA, 0.25% Triton X-100], and for 30min in buffer B [10mM Tris-HCl (pH 8), 1mM EDTA, 200mM NaCl] (all buffers include proteases inhibitors). Nuclei were resuspended in sonication buffer [10mM Tris-HCl (pH 8), 1mM EDTA, 0.5% SDS, 0.5% Triton X-100, 0.05% NaDOC, 140mM NaCl] and sonicated with a Branson Digital Sonifier (Branson Ultrasonics) to an average size of 250bp. Sonicated chromatin was incubated overnight on a rotating platform at 4°C with a mixture of 20μl Protein A and 20μl Protein G Dynabeads (Invitrogen) pre-bound with 6μg of control IgG (sc-2028) or IRF8 (sc-6058), IRF1 (sc-640), PU.1 (sc-352) antibodies from Santa Cruz Biotechnologies or 3μg of H3 (ab1791), H3K27Ac (ab4729) from Abcam. Immune complexes were washed sequentially for 2min at room temperature with 1ml of the following buffers: Wash B [1% Triton X-100, 0.1% SDS, 150mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8]; Wash C [1% Triton X-100, 0.1% SDS, 500mM NaCl, 2mM EDTA, 20mM Tris-HCl pH 8), Wash D (1% NP-40, 250mM LiCl, 1mM EDTA, 10mM Tris-HCl pH 8]; and TEN buffer [50mM NaCl, 10mM Tris-HCl pH 8, 1mM EDTA]. After de-crosslinking by overnight incubation at 65°C, the DNA was purified with QIAquick PCR purification columns following manufacturer’s instructions (Qiagen).
ChIP-seq libraries were prepared using Illumina TruSeq kit and sequenced on a HiSeq 2000 in paired-end 50bp configuration following manufacturer’s recommendations.

treatment_protocol: BMDMs were left untreated or treated for 30 minutes or 3h with 400U/ml of recombinant mouse IFNg added to culture medium.

value: IRF1 KO

value: anti-H3K27Ac (Abcam, ab4729)


title: M980

value: Yes

value: Frozen tumor


title: IRF1-/-_BMDM_RNA_IFNg_3h_2


title: IRF1-/-_BMDM_H3K27Ac_UT


title: M977


title: M976


title: IRF8m/m_BMDM_H3K27Ac_IFNg_3h


title: IRF8m/m_BMDM_RNA_IFNg_3h_1


title: IRF8m/m_BMDM_H3K27Ac_UT


title: B6_BMDM_RNA_IFNg_3h_1


title: B6_BMDM_H3K27Ac_IFNg_3h


title: B6_BMDM_H3K27Ac_UT


title: PPARy-siRNA2

city: Helsinki

first: Oyediran

middle: Olulana

last: Akinrinade

address: Biomedicum Helsinki 2U, E107b

department: Institute of Clinical Medicine

country: Finland

institute: University of Helsinki, Finland

data_processing:
Sequenced reads  were subjected to adapters removal, quality trimming before PE-pairing; Paired quality-trimmed reads were mapped to hg19 whole genome using bwa in pair-end mode.
The abundance of mRNAs for all annotated genes from the ENSEMBL v72 annotation of the human genome (hg19) was calculated using an in-house R script.
The abundance of mRNA (read count) was normalized as Reads per Kilobase of feature(genemodel) per Million reads in the library (RPKM)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: endothelial cell (EC)

growth_protocol: Pulmonary microvascular ECs were grown in commercial EGM-2 media (Lonza Clonetics).

extract_protocol:
RNA was isolated and purified using the protocol of Nucleospin RNA II-kit and NucleoSpin® RNA Clean up-kit (Macherey-Nagel, BioTop Oy, Turku, Finland). RNA samples were prepared for Illumina RNA sequencing using instructions provided by New England BioLabs® Inc (NEB BioLabs, Ipswitch, MA, USA).
Total RNA of 1-5μg was used as starting material when isolating poly(A)+ RNA transcripts from total RNA for RNA library preparation and sequencing using instructions provided by New England BioLabs® Inc.

treatment_protocol: ECs were transfected with Con- and PPARy siRNAs for 6h using RNAiMAX Lipofectamine (Invitrogen) and OPTI-Mem (Gibco). Ecs were harvested 48h after the initation of transfections.

value: pulmonary microvascular EC

tag: passages

tag: transfection

value: PPARy-siRNA


title: PPARy-siRNA1


title: Con-siRNA3

value: Con-siRNA


title: B6_BMDM_PU1_IFNg_0.5h

value: anti-PU.1 (SantaCruz, sc-352x)

tag: treatment


title: B6_BMDM_PU1_IFNg_3h


title: B6_BMDM_IgG_control

value: IgG control Ab (SantaCruz, sc-2028)


title: PPARy-siRNA3


title: Con-siRNA4


title: Con-siRNA1


title: M979


title: Con-siRNA2


title: B6_BMDM_IRF1_IFNg_0.5h

value: anti-IRF1 (SantaCruz, sc-640x)


title: B6_BMDM_H3K4me1_UT

value: anti-H3K4me1 (Abcam, ab8895)


title: B6_BMDM_IRF1_UT


title: B6_BMDM_IRF1_IFNg_3h


title: B6_BMDM_IRF8_IFNg_3h

value: anti-IRF8 (SantaCruz, sc-6058x)


title: B6_BMDM_PU1_UT


title: Fft2D fft3D mononucleosomes

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

data_processing:
Alignment to the S. pombe genome was carried out using Bowtie2 with standard parameters for paired-end data.
Removal of clonal reads, read length adjustment, quantile normalization and calculation of differences in nucleosome occupancy were carried out with DANPOS (doi:10.1101/gr.142067.112)
Genome_build: Ensembl Genome Build ASM294v2.2, retrieved March 21, 2014, from http://www.pombase.org/downloads/datasets
Supplementary_files_format_and_content: Processed fixed step WIG files contain nucleosome occupancy scores (WT.wig and Fft2DFft3D.wig) and differential scores (+/- log10 of Poisson test p-values) as calculated by DANPOS with a step size of 10bp.

organism: Schizosaccharomyces pombe

source_name: log-phase liquid culture

extract_protocol:
Mononucleosomal DNA was prepared as described in Lantermann et al., Methods, 48(3), 218–225. doi:10.1016/j.ymeth.2009.02.004 .
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®

tag: genotype

value: h+ fft2D::kanMX fft3D::hphMX ura4D18 leu1-32 ade6-216


title: Wildtype mononucleosomes


title: B6_BMDM_IRF8_IFNg_0.5h


title: B6_BMDM_IRF8_UT


title: ATCC1_2

status: Public on Mar 02 2016

first: Hanqi

last: Yin

state: Shanghai

address: libing road 151

institute: shanghai biochip corporation

description:
methicillin susceptible
AT-2

data_processing:
whole transcriptome sequencing on the Illumina HiSeq2500 platform.Illumina Casava1.7 software used for basecalling.
Purified reads of ATCC29213 sample were aligned to all of the S. aureus genome sequences downloaded from NCBI database
first mapping by FANSe2 -E 12 -L 135 -S 10
Iterative Genome Correction method with FANSe2 to correct ATCC genome by seven mapping and correct
last mapping by FANSe2 -E 7 -L 135 -S 10. It was determined differentially expressed genes, expression of the each gene in different samples was transformed to CPM (counts per million) by edgeR package
Genome_build: S. aureus ED98 genome
Supplementary_files_format_and_content: tab-delimited text file contain expression level, fold change and annotations of the transcribed genes

organism: Staphylococcus aureus

source_name: ATCC

growth_protocol: The strains were cultured on selective Staphylococcus Chromogenic Medium (Qindao hope bio-technology limited company, China). Routinely, the isolates were cultured for 24-48 hours on Mueller-Hinton Agar supplemented with 5% sheep blood (Ruite bio-technology limited company, Guangzhou, China) at 37℃ under microaerobic conditions (5% O2, 10% CO2, and 85% N2).

extract_protocol:
Total RNAs were extracted with TRIzol (Invitrogen Inc., California, USA) from the selected bacterial isolate according to the manufacturer's instructions. Any possible genomic DNA contamination was removed by RNase-free DNase I (Ambion Inc., Texas, USA).
Ribosome RNA was removed from total RNA with Ribozero Kit and followed by strand specific RNA-seq protocol.RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition

tag: growth medium

value: MH Agar


title: ATCC1_1

description:
methicillin susceptible
AT-1


title: MRSA1679a_2

description:
methicillin resistant
33-2

source_name: Chicken


title: MRSA1679a_1

description:
methicillin resistant
33-1


title: vegetative somatic cells

city: Munich

first: Anne

last: Dueck

address: Biedersteiner Str.29

department: Institute of Pharmacology and Toxicology

institute: TUM

description: small RNA sequencing data

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

organism: Volvox carteri

source_name: somatic cells

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

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

tag: developmental stage

value: vegetative (asexual)

value: somatic cells


title: Pasteurella multocida VP161 wild-type replicate 2

city: Clayton

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

institute: Monash University

data_processing:
Reads were mapped with CLC genomics workbench v7.0
Mapped reads were converted to counts with CLC genomics workbench v7.0
Genome_build: VP161; The assembly is available on the series record in the file Pm_VP161.fa and the annotation is available on the series record in the file Pm_VP161.gff.
Supplementary_files_format_and_content: CSV file containing raw read counts per CDS feature

organism: Pasteurella multocida

source_name: Pasteurella multocida VP161 wild-type

growth_protocol: Experiments to examine the whole-genome transcriptional response of a Pasteurella multocida hfq mutant compared to the wild-type parent strain

extract_protocol:
The P. multocida strains AL2521 (VP161 hfq mutant) and VP161 (wild-type) were each grown in BHI broth to mid-exponential growth phase (OD600 = 0.6, approximately 1.0 x 10^9 CFU/ml). To each 25 ml culture, 2.5 ml of ice-cold killing buffer (containing 0.05 M Tris-HCl [pH 7.5], 15 mg/ml sodium azide and 0.6 mg/ml chloramphenicol) was added and the mixed sample cooled on ice before centrifugation at 9,000 x g for 10 min (4°C). Pelleted cells were then resuspended in 1 ml RNAlater Stabilisation reagent (Qiagen) and incubated for 5 min at room temperature before centrifugation at 5,000 x g for 10 min. Total RNA was purified using the RNeasy minikit (Qiagen) with DNase treatment according to the manufacturer’s instructions. RNA samples were quantified and analysed for DNA contamination using the Qubit kit (Invitrogen) and visualised by gel electrophoresis.
The construction of the cDNA library from purified RNA samples was performed using the Truseq RNA Preparation Kit (Illumina). Ribosomal RNA (rRNA) was removed from the samples using the Ribozero kit (Epicentre).

treatment_protocol: Both strains were grown in brain heart infustion broth to an optical density of 0.6 at 600 nm and samples taken without further treatment.

value: wild-type


title: Pasteurella multocida VP161 wild-type replicate 1


title: Pasteurella multocida VP161 hfq mutant replicate 3

source_name: Pasteurella multocida VP161 hfq mutant

value: hfq mutant


title: Pasteurella multocida VP161 hfq mutant replicate 2


title: Pasteurella multocida VP161 hfq mutant replicate 1


title: Kanamycin 1

city: Dublin

first: Brendan

middle: J.

last: Loftus

address: Conway Institute, University College Dublin

department: School of Medicine & Medical Science

country: Ireland

institute: University College Dublin

data_processing:
Adapters (first 10 bases of reads) were trimmed from Fastq files using the fastx_trimmer utility from FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Trimmed reads were reverse-complemented using the fastx_reverse_complement utility from FASTX-Toolkit, to obtain reads in the correct orientation (Illumina outputs the reverse complement)
Trimmed, reverse-complemented reads were aligned to the M. abscessus genome using bowtie, with the following parameters: --best -S -p 2
SAM format files were converted to BAM format using the import function of samtools
BAM files were sorted and indexed using the sort and index functions of samtools, respectively
Genome_build: NC_010397.1
Supplementary_files_format_and_content: Read counts per gene obtained using a custom python script, invoking samtools to count the numbers of reads from aligned BAM files. Genomic coordinates of genes were as specified in the PTT-format annotation file for M. abscessus from NCBI. Columns represent experimental conditions, rows represent genomic features.

organism: Mycobacteroides abscessus

source_name: M. abscessus grown in presence of 2 μM Kanamycin

growth_protocol: For Artificial Sputum and Sputum Control: bacterial cultures grown in Middlebrook 7H9 were grown till OD 1; for all other other conditions: bacterial cultures were grown till OD 0.8

extract_protocol:
Bacteria were recovered by centrifugation (10 min at 4000 x g) and re-suspended in TRI-Reagent (Sigma Aldrich). Following physical disruption using 0.1 mm zirconia-silica beads in a MagNA Lyzer (Roche Diagnostics). RNA was isolated using miRNeasy spin columns with an additional on-column DNase treatment, according to manufacturer’s instructions (Qiagen). RNA was quantified using NanoDrop 1000 spectrophotometer (Thermo Scientific) and sample quality was assessed using RNA Nano Chip on a Bioanalyzer 2100 instrument.
Sequencing libraries were generated with the TruSeq Stranded RNA kit according to manufacturer’s instructions (Illumina Inc.), validated using High Sensitivity DNA chip (Bioanalyzer 2100) and quantified using High Sensitivity DNA Quantification assay (Qubit Fluorometer).

treatment_protocol: For Artificial Sputum: The cultures were washed 2x with PBS and transferred to Artificial Sputum (stress condition) or Middlebrook 7H9 medium (control condition). Hypoxia was induced by 40 min incubation in the presence of 50 μM diethylenetriamine/nitric oxide (DETA/NO) adduct. For macrolide treatment, 1 μM Erythromycin was added to bacterial cultures and the exposure was carried out for 1 h. Kanamycin was added at a final concentration of 2 μM and cultures were incubated for 1 h.

tag: experimental group

value: Group 2

tag: experimental status

value: Group 2 Treatment

tag: grown in

value: presence of 2 μM Kanamycin


title: Hypoxia 3

source_name: M. abscessus grown in presence of 50 μM diethylenetriamine/nitric oxide (DETA/NO) adduct.


title: Hypoxia 2

value: presence of 50 μM diethylenetriamine/nitric oxide (DETA/NO) adduct.


title: Hypoxia 1


title: Erythromycin 1

source_name: M. abscessus grown in medium containing 1 μM Erythromycin

value: medium containing 1 μM Erythromycin


title: Erythromycin 2


title: Erythromycin 3


title: Kanamycin 2


title: Group 2 control 1

source_name: M. abscessus grown in absence of antibiotics (log phase)

value: Group 2 Control

value: absence of antibiotics (log phase)


title: Group 2 control 3


title: Middlebrook 3

source_name: M. abscessus grown in Middlebrook 7H9 broth

value: Group 1

value: Group 1 Control

value: Middlebrook 7H9 broth


title: Group 2 control 2


title: Artificial Sputum 2

source_name: M. abscessus grown in artificial sputum medium

value: Group 1 Treatment

value: artificial sputum medium


title: Middlebrook 2


title: RNAseq-T-ALL_10

city: Montreal

first: Daniel

last: Sinnett

state: Quebec

address: 3175 Cote-Sainte-Catherine

institute: CHU Sainte-Justine

data_processing:
AB SOLID data:  Primary alignment with Lifescope software version 2.1
ILLUMINA data: Primary alignment with STAR
Mark duplicate with PICARD version 1.107
SplitNCigar with GATK version 3.2-2
Read counts using HTSeq version 0.6.1p1 with Ensembl GRCH37 version 75
Genome_build: hg19
Supplementary_files_format_and_content: counts

source_name: Tumoral biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Total RNA was extracted from bone marrow samples at diagnosis for patients 432, 437, 547, 693, 716, 743, 744, 748, 791 and 849 using the mirVana Isolation kit (Ambion) according to the manufacturer’s protocol. The Allprep DNA/RNA Mini kit (Qiagen) was used for relapse samples in patients 791 and 879. For patient 744, mature RNA was also purified using the Ambion's MicroPoly(A)Purist kit (Small Scale mRNA Purification Kit P/N AM1919). Following a DNAse I treatment, total or mature RNA samples were quantified by NanoDrop ND1000 (Thermo-Fisher Scientific) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent). Ribosomal ribonucleic acid (rRNA) were depleted using the Invitrogen RiboMinus Eukaryote kit (Life Technologies). cDNA libraries were prepared using the SOLiD Total RNA-seq kit (diagnosis samples) and the Illumina TruSeq Stranded Total RNA kit (relapse samples) based on manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System or the Illumina HiSeq 2500 System.

tag: tissue

value: Bone marrow

tag: age diagnosis (month)

tag: patient id


title: Pasteurella multocida VP161 wild-type replicate 3

tag: strain


title: Artificial Sputum 3


title: RNAseq-T-ALL_8


title: RNAseq-T-ALL_9


title: Kanamycin 3


title: RNAseq-T-ALL_6


title: Mn_H

city: huzhou

first: ding

last: zhili

address: xueshi road

institute: Huzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then assembly use Trinity
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample; Trinity assembly fasta file

organism: Macrobrachium nipponense

source_name: oriental river prawn

extract_protocol: The RNA-Seq was conducted by LC-Bio Co. (Hangzhou, China). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

treatment_protocol: Juvenile oriental river prawn, M. nipponense were obtained from aquatic product market, Huzhou, China, and maintained in aerated freshwater for 72 h before tissues were collected. The hepatopancreas and muscle were ablated and stored in liquid nitrogen at -80°C until RNA extraction.

tag: development

value: juvenile

value: hepatopancreas


title: Mn_M

value: muscle


title: RNAseq-T-ALL_7.1

description: Mature RNA


title: WES-N-ALL_22

data_processing:
AB SOLID data: Primary alignment using the LifeScope software version 2.1 on human genome hg18
Illumina HiSeq data: Primary alignment with Bowtie2 on human genome hg19
Mark duplicate with PICARD version 1.107
Indel realignment with GATK version 3.2-2 (RealignerTargetCreator + IndelRealigner)
Genome_build: hg18 (SOLID), hg19 (ILLUMINA)

source_name: Control normal biospecimen

extract_protocol:
see Baccichet A, Qualman SK, Sinnett D. Allelic loss in childhood acute lymphoblastic leukemia. Leuk Res. 1997;21(9):817-23.
Whole exomes were captured in solution with Agilent’s SureSelect Human All Exon (38Mb or 50Mb), Nextera Rapid Capture Exome Enrichment kit (case 791) or SureSelectXT Clinical Research Exome (case 879) kits according to the manufacturer’s protocol and sequenced on the Life Technologies SOLiD 5500 System and for cases 791 and 879.

value: Blood


title: RNAseq-T-ALL_2


title: Middlebrook 1


title: WES-N-ALL_20


title: WES-N-ALL_18


title: WES-N-ALL_23


title: RNAseq-T-ALL_1


title: WES-N-ALL_19


title: Artificial Sputum 1


title: WES-N-ALL_14


title: WES-N-ALL_16


title: WES-N-ALL_17


title: WES-N-ALL_12


title: WES-N-ALL_21


title: WES-N-ALL_13


title: WES-N-ALL_10


title: WES-N-ALL_8


title: RNAseq-T-ALL_4


title: WES-N-ALL_7


title: WES-N-ALL_9


title: WES-N-ALL_11


title: WES-N-ALL_6


title: WES-N-ALL_4


title: WES-N-ALL_5


title: RNAseq-T-ALL_3


title: WES-N-ALL_2


title: WES-N-ALL_3


title: WES-N-ALL_1


title: WES-T-ALL_27


title: WES-T-ALL_24


title: WES-T-ALL_21


title: WES-T-ALL_20


title: WES-T-ALL_29


title: AstroEGFR_3_Zfp423

city: Milano

first: Pasquale

last: Laise

address: Via Adamello,16

country: Italy

institute: IEO

description: Astrocytes p16/p19 KO infected with a retroviral vector overexpressing human EGFRvIII and a lentiviral vector overexpressing Zfp423

data_processing:
Basecalling and filtering were perfomed according to the illumina protocol.
Sequenced reads were mapped to mm9 using tophat_v1.3.
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using cuffnorm function (cufflinks2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample.

source_name: Cerebral cortex, day P5

extract_protocol:
Cell were processed using Qiagen RNeasy Mini kit. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: astrocytes

tag: passage


title: AstroEGFR_2_Zfp423


title: WES-N-ALL_15


title: WES-T-ALL_28


title: WES-T-ALL_16


title: WES-T-ALL_19


title: WES-T-ALL_25


title: AstroEGFR_1_Zfp423


title: WES-T-ALL_15


title: WES-T-ALL_18


title: PT4

description: glioma propagating cells

source_name: Tumor (glioma)

value: C57BL/6 transplanted into CD1 Nude

value: glioma propagating cells


title: PT3

description: glioma propagating cells


title: WES-T-ALL_12


title: PT2

description: glioma propagating cells


title: WES-T-ALL_10


title: PT1

description: glioma propagating cells


title: WES-T-ALL_13


title: WES-T-ALL_14


title: AstroEGFR_3

description: Astrocytes p16/p19 KO infected with a retroviral vector overexpressing human EGFRvIII


title: AstroEGFR_2


title: WES-T-ALL_9


title: WES-T-ALL_8


title: WES-T-ALL_23


title: AstroEGFR_1


title: WES-T-ALL_7


title: INPUT_PT

description: glioma propagating cells

data_processing:
Basecalling and filtering were perfomed according to illumina protocol.
Sequenced reads were mapped to mm9 using bowtie version 0.12.9.
Peaks were identified using MACS version 1.4.1 (pval< 1e-7)
Genome_build: mm9
Supplementary_files_format_and_content: peaks.bed files generated with MACS version 1.4.1. Peaks were detected using a p-value <1e-7.

extract_protocol:
Lysates were sonicated using Covaris Sonicator and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: chip antibody


title: INPUT_AstroEGFR_3

description: astrocytes


title: WES-T-ALL_3


title: WES-T-ALL_6


title: INPUT_AstroEGFR_1

description: astrocytes


title: WES-T-ALL_1


title: H3K27me3_PT3

description: glioma propagating cells

value: H3K27me3 (Cell signaling, cat n. 9733BF)


title: WES-T-ALL_2


title: H3K27me3_PT4

description: glioma propagating cells


title: H3K27me3_AstroEGFR_3


title: H3K27me3_AstroEGFR_1


title: H3K27me3_PT1

description: glioma propagating cells


title: RNAseq-T-ALL_7


title: MacB3-3wk, replicate 2

city: Aurora

first: Joanna

last: Poczobutt

institute: University of Colorado Denver

data_processing:
Reads quality was checked using FastQC (http://www.bioinformatics. bbsrc.ac.uk/projects/fastqc).
Reads were processed and aligned to Mus musculus reference genome (build mm10) using TopHat v2, with default parameters.
The aligned read files were processed by Cufflinks v2.0.2. Reads were assembled into transcripts and their abundance was estimated. The unit of measurement is Fragments Per Kilobase of exon per Million fragments mapped (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file. File contains normalized abundance measurements (FPKM) for each sample.

source_name: tumor-bearing lung, 3 week

growth_protocol: C57BL/6 mice were obtained from Jackson Laboratory. Experiments were done in 10-16 week old males. LLC-Luc cells (1x10^5 in 25 µl per injection) were suspended in PBS containing 15% Growth Factor Reduced Matrigel (BD Biosciences, cat# 354230) and injected into the parenchyma of the left lung lobe through the rib cage using a 30G needle.

extract_protocol:
Tumor-bearing mice were sacrificed at 2 and at 3 weeks after cancer cell injection, together with control uninjected mice. The lung circulation was perfused with PBS/heparin (20 U/ml, Sigma). Left lung lobes containing tumors were harvested. For control mice, all the lung lobes were used. Tissues from 3-5 mice were pooled, mechanically dissociated and incubated for 30 min at 37°C with 3.2 mg/ml Collagenase Type 2 (Worthington, 43C14117B), 0.75 mg/ml Elastase (Worthington, 33S14652), 0.2 mg/ml Soybean Trypsin Inhibitor (Worthington, S9B11099N), and DNAse I 40µg/ml (Sigma). During incubation, samples were placed in a shaking water bath and dispersed by pipetting every 10 minutes. Resulting single-cell suspensions were filtered through 70 um cell strainers (BD Biosciences) and washed with staining buffer (PBS containing 1% FBS, 2mM EDTA, 10mM HEPES). Samples were subject to red blood cell lysis, washed with staining buffer and filtered through 40 um cell strainers (BD Biosciences). Prior to staining, FcgammaR was blocked with anti-CD16/CD32 antibody (BD Biosciences) for 10 minutes. Cells were stained for 30-45 min at 4°C with the following antibodies: CD11b-FITC (Clone M1/70, BD Biosciences), SiglecF-PE or AlexaFluor647 (Clone E50-2440, BD Biosciences), Ly6G-PE-Cy7 (Clone 1A8, BD Biosciences), CD64-PE or AlexaFluor647 (Clone X54-5/7.1, BD Biosciences), CD11c-APC-Cy7 (Clone HL3, BD Biosciences), CD11c-PerCP-Cy5.5 (Clone N418, BioLegend). Flow cytometry-based cell sorting was conducted using XDP-100 or Astrios (Beckman Coulter) cell sorters. The sorting strategy involved excluding debris and cell doublets by light scatter, and dead cells by DAPI (1 ug/ml). Total RNA was isolated from flow cytometry-sorted cells using the QIAshredder and RNeasy Plus Micro kit (Qiagen). RNA quality and quantity was analyzed using NanoDrop and Bioanalyzer.
Libraries were constructed using NuGen Ovation Human FFPE RNA-Seq Multiplex System kit customized with mouse specific oligos for rRNA removal.

tag: markers

tag: run lane

tag: multiplex index

value: TGGTGA


title: MacB3-3wk, replicate 3

value: GTCGTA


title: MacB2-3wk, replicate 1

value: AGTGAG


title: MacB3-2wk, replicate 3

source_name: tumor-bearing lung, 2 week

value: GTGCTT


title: MacB3-3wk, replicate 1

value: GCACTA


title: MacB3-2wk, replicate 2


title: MacB2-3wk, replicate 3

value: AAGCCT


title: MacB2-3wk, replicate 2

value: AACCAG


title: MacB2-2wk, replicate 3

value: ACCTCA


title: MacB3-2wk, replicate 1


title: MacB2-2wk, replicate 2


title: MacA-2wk, replicate 3


title: MacA-2wk, replicate 2


title: MacB2-2wk, replicate 1


title: MacB2-N, replicate 1

source_name: lung


title: MacB1-N, replicate 3


title: MacB2-N, replicate 3


title: MacA-2wk, replicate 1


title: MacB1-N, replicate 2


title: MacA-N, replicate 1


title: MacA-N, replicate 2


title: MT77: Tumor tissue

city: Edmonton

first: Sambasivarao

last: Damaraju

state: Alberta

address: 11560 University Ave

department: Laboratory medicine and pathology

institute: University of Alberta

description: Genomic small RNA (size selected from total RNA)

data_processing:
Base calling and demultiplexing were done using CASAVA 1.8.2 with default settings
Trimming of adapters using cutadapt software (http://code.google.com/p/cutadapt/). Options were given to retain sequences longer than 17 nucleotides. Quality trimming was performed to retain only reads with a Sanger quality score cut-off of 30
Quality of the sequenced reads after adapter trimming was assessed using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Trimmed sequences were then aligned to the reference genome using Bowtie (31) and allowed a maximum of 2 mismatches. Human, hg19 genomic assembly (UCSC) downloaded from Illumina iGenome repository was used as a reference for mapping
.bam files were analyzed using Partek Genomics Suite 6.6
Data was normalized using Reads per Kilobase per Million (RPKM)
Genome_build: hg 19, miRBAse v 20 for annotating miRNAs
Supplementary_files_format_and_content: tab-delimited txt files containing RPKM normalized values of all miRNAs before batch correction for normal and tumor tissues

source_name: Breast

growth_protocol: Normal tissues were preserved as Fresh frozen tissues and tumor tissues were preserved as FFPE tissue blocks

extract_protocol:
Total RNA from FF tissues (normal) was isolated using TRIzol and Qiagen RNeasy kit according to manufacturer’s instructions. Total RNA from FFPE blocks was isolated using RecoverAll Total Nucleic Acid Isolation Kit (Life Technologies). RNA quality and quantity were analyzed with Bioanalyzer 2100 and RNA Nano Chips (Agilent Technologies).
Small RNAs were sequenced using TruSeq Small RNA Sequencing Kit (Illumina), TruSeq SR Cluster Kit v5-CS-GA (Illumina), and TruSeq SBS Kit v5-GA (Illumina) according to manufacturer’s instructions. All the samples were sequenced on Illumina Genome Analyzer IIx with 36 cycles single end protocol.

value: Surgically resected tumor

tag: preservation type

value: Formalin fixed paraffin embedded (FFPE)

tag: tissue type

value: Invasive Ductal Carcinoma

tag: breast cancer subtype

value: Luminal A

tag: batch id

value: II


title: MT79: Tumor tissue

value: IV


title: MT979: Tumor tissue

value: Luminal B HER2+


title: MT990: Tumor tissue


title: MT895: Tumor tissue


title: MT75: Tumor tissue

value: Luminal B


title: MT689: Tumor tissue


title: MT750: Tumor tissue


title: MacB2-N, replicate 2


title: MT450: Tumor tissue

value: TNBC


title: MT359: Tumor tissue


title: MT578: Tumor tissue


title: MT518: Tumor tissue


title: MT469: Tumor tissue


title: MT53: Tumor tissue


title: MT658: Tumor tissue


title: MacB1-N, replicate 1


title: MacA-N, replicate 3


title: MT813: Tumor tissue


title: MT350: Tumor tissue


title: MT290: Tumor tissue


title: MT269: Tumor tissue


title: MT265: Tumor tissue


title: MT1847: Tumor tissue


title: MT1525: Tumor tissue


title: MT174: Tumor tissue

value: III


title: MT1643: Tumor tissue


title: MT1386: Tumor tissue


title: MT1315: Tumor tissue


title: MT1275: Tumor tissue


title: MT111: Tumor tissue


title: MT1310: Tumor tissue


title: MT1118: Tumor tissue


title: MT1266: Tumor tissue


title: MT1029: Tumor tissue


title: MT1023: Tumor tissue


title: MT1213: Tumor tissue


title: MT1584: Tumor tissue


title: MT1230: Tumor tissue


title: GT93: Tumor tissue


title: GT74: Tumor tissue


title: GT91: Tumor tissue


title: MT2385: Tumor tissue


title: MT219: Tumor tissue


title: MT237: Tumor tissue


title: GT07: Tumor tissue


title: GT141: Tumor tissue


title: MT1794: Tumor tissue


title: GT226: Tumor tissue


title: CT74: Tumor tissue


title: MT1337: Tumor tissue


title: C81: Tumor tissue


title: C75: Tumor tissue

value: I


title: C60: Tumor tissue


title: C704: Tumor tissue


title: C702: Tumor tissue


title: C533: Tumor tissue


title: C586: Tumor tissue


title: C56: Tumor tissue


title: C521: Tumor tissue


title: C494: Tumor tissue


title: C389: Tumor tissue


title: C49: Tumor tissue


title: C440: Tumor tissue


title: C451: Tumor tissue


title: C342: Tumor tissue


title: C340: Tumor tissue


title: RNAseq-T-ALL_9.1

description: Mature RNA

value: Bone marrow


title: C336: Tumor tissue


title: RNAseq-T-ALL_11


title: WES-N-ALL_24

value: Blood


title: C306: Tumor tissue


title: WES-N-ALL_22_mdup


title: WES-T-ALL_30


title: WES-T-ALL_28_mdup


title: MT196: Tumor tissue


title: 96h rep1

first: Mengzhu

last: Xue

address: No.100, Haike Road

institute: Shanghai Advanced Research Institute

description: TGF-beta induced EMT

data_processing: Reads were mapped to ENSEMBL release 75 transcripts by Bowtie, then TPM values were calculated by RSEM to characterize gene expression profiles.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols, and Illumina TruSeq RNA Sample Prep Kit was used for library construction.

tag: cell line

tag: time point


title: C537: Tumor tissue

tag: tissue


title: 96h rep2

description: TGF-beta induced EMT


title: C304: Tumor tissue


title: 72h rep2

description: TGF-beta induced EMT


title: C288: Tumor tissue


title: 72h rep1

description: TGF-beta induced EMT


title: C287: Tumor tissue


title: C363: Tumor tissue


title: 48h rep1

description: TGF-beta induced EMT


title: 36h rep1

description: TGF-beta induced EMT


title: 36h rep2

description: TGF-beta induced EMT


title: 24h rep2

description: TGF-beta induced EMT


title: C268: Tumor tissue


title: 24h rep1

description: TGF-beta induced EMT


title: 12h rep2

description: TGF-beta induced EMT


title: 12h rep1

description: TGF-beta induced EMT


title: 6h rep2

description: TGF-beta induced EMT


title: C257: Tumor tissue


title: 6h rep1

description: TGF-beta induced EMT


title: C250: Tumor tissue


title: 0h rep2

description: TGF-beta induced EMT


title: 0h rep1

description: TGF-beta induced EMT


title: 48h rep2

description: TGF-beta induced EMT


title: C249: Tumor tissue


title: C280: Tumor tissue


title: C234: Tumor tissue


title: 304M3-B lot2_ChIPSeq experiment 2

city: Chicago

first: Takamitsu

last: Hattori

state: IL

address: 900 E. 57th Street

department: Department of Biochemistry and Molecular Biology

institute: The University of Chicago

description:
Sample 10
Cell culture
Samples 9 and 10 are technical replicates.

data_processing:
Data analysis was performed with Galaxy (Blankenberg et al., 2010; Giardine et al., 2005; Goecks et al., 2010).
Raw reads in FastQ fromat were first submitted to FastQ Groomer.
Reads were mapped with Bowtie2 (Langmead et al., 2009) (sensitive preset option, end-to-end alignment), to human (hg19) reference genomes.
Resulting SAM files were then filtered using SAMtools (Li et al., 2009). Reads that were unmapped were removed from the set by this data analysis pipeline.
To remove noise coming from low-quality reads and contaminants, as well as to mask repeatable genomic sequences, reads with mapping quality lower 13 (p-value < 0.05) were removed.
BEDTools (Quinlan and Hall, 2010) were used to create genome coverage bedgraphs, which were converted into bigWig format.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigWig (Score); Score : Genome coverage.

source_name: HEK293, 304M3-B lot2 ChIP

growth_protocol: The HEK293 cells were grown in the DMEM media (Thermo) with 10% FBS and Penicillin-Streptomycin.

extract_protocol:
Native ChIP experiments using HEK293 cells were performed as previously described (Brand M. et al., Nat. Protoc., 3, 398-409 (2008) and Ruthenburg, A.J. et al., Cell, 145, 692-706 (2011)) except for the following modifications. Micrococcal nuclease-digested nuclei from HEK293 cells were purified using hydroxyapatite chromatography with stepwise elution in 50, 100, 200 and 500 mM sodium phosphate buffer (pH 7.2) containing 100 mM NaCl, 1 mM EDTA and 200 uM PMSF. The purity of nucleosomes in elution fractions was examined by SDS-PAGE and high-purity fractions were used for ChIP. The antibody-coated beads were prepared by incubating 132 uL of Dynabeads M280 streptavidin (Life Technology) and 3.3 ug of a biotinylated Fab antibody (molar equivalent to 1 ug of IgG antibody) for 1hr at 4 ˚C. Excess biotin-binding sites of streptavidin were blocked with biotin. The antibody-coated beads were incubated with 10 ug of purified nucleosomes at 4˚C for overnight. Washing, elution and DNA purification were performed as previously described (Brand M. et al., Nat. Protoc., 3, 398-409 (2008)).
Library preparation for sequencing was performed using TruSeq ChIP sample preparation Kit, Set A (Illumina) according to the manufacturer’s protocol.

value: anti-H3K4me3 (304M3-B lot 2)


title: WT-S

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
STAR_2.4.0a paired-end mapping versus mm10.
FeatureCounts transcripts quantification (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file.
Kallisto v0.42.3 transcripts quantification with Ensembl release 79 GTF file.
Genome_build: mm10
Supplementary_files_format_and_content: featurecounts_table.txt: raw counts from featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options and Mus_musculus.GRCm38.77 Ensembl GTF annotation file. Kallisto_estcounts_table.txt: estimate counts produce with kallisto v0.42.3 with Ensembl release 79 GTF file. Kallisto_tpm_table.txt: transcript counts per million produce with kallisto v0.42.3 with Ensembl release 79 GTF file. BigWig files has been generated using samtools to discriminate expression strand for paired-end reads then genomeCoverageBed and bedGraphToBigWig from bedtools 2 suite.

source_name: lymphoid tissue

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen) from either freshly purified splenic B cells, obtained after gradient separation using Lympholyte Mammal (Cedarlane) followed by CD43 negative selection (Miltenyi Biotec), or from purified splenic B cells stimulated in vitro (106 cells m/L) for 48 hours in RMPI 1640 medium (Lonza) supplemented with 10% fetal calf serum (Lonza) and with 5µg/mL LPS (Cayla Invivogen), separated on a Lympholyte Mammal gradient. For each genotype (wt, 3’PALD/D, hs3b-4D/D, 3’RRD/D), RNA sample was prepared from a pool of equivalent numbers of purified B cells from 4 animals
1 µg of total RNA were depleted from ribosomal RNA, ligated, reverse transcribed and amplified (14 cycles) with the reagents from the truseq stranded total RNA kit (illumina). Libraries were quantified with the Bioanalyzer DNA 1000 Kit (Agilent). 4nM of libraries were then diluted and denatured according to the Illumina recommendations.  Paired-end 150-bp reads were sequenced on an Illumina Nextseq 500 sequencer.

value: Activated B cells from the spleen (48 hours with LPS)

tag: passages

value: Primary cells activated in vitro

value: mixed background 129/C58BL/6

tag: genotype

value: wt mouse strain of mixed background 129/C58BL/6


title: 304M3-B lot2_ChIPSeq experiment 1

description:
Sample 9
Cell culture
Samples 9 and 10 are technical replicates.


title: C258: Tumor tissue

value: Surgically resected tumor

value: Formalin fixed paraffin embedded (FFPE)


title: PAL-R

value: Resting B cells from the spleen

value: Sorted (CD43 negative) primary cells

tag: strain

value: homozygous 3'PAL KO animals, unpublished at this time


title: PAL-S


title: 304M3-B lot1_ChIPSeq experiment 2

description:
Sample 8
Cell culture
Samples 7 and 8 are technical replicates.

source_name: HEK293, 304M3-B lot1 ChIP

value: anti-H3K4me3 (304M3-B lot 1)


title: WT-R


title: C225: Tumor tissue

value: Invasive Ductal Carcinoma

value: Luminal A

value: IV


title: 304M3-B lot1_ChIPSeq experiment 1

description:
Sample 7
Cell culture
Samples 7 and 8 are technical replicates.


title: Input for 304M3-B

description:
Sample 6
Cell culture
This is input sequencing for Samples 7-10.

source_name: HEK293, input


title: 309M3-A lot3_ChIPSeq experiment 2

description:
Sample 5
Cell culture
Samples 4 and 5 are technical replicates.

source_name: HEK293, 309M3-A lot3 ChIP

value: anti-H3K9me3 (309M3-A lot 3)


title: C204: Tumor tissue

value: III


title: C22: Tumor tissue

value: II


title: 309M3-A lot3_ChIPSeq experiment 1

description:
Sample 4
Cell culture
Samples 4 and 5 are technical replicates.


title: 309M3-B lot1_ChIPSeq experiment 2

description:
Sample 3
Cell culture
Samples 2 and 3 are technical replicates.

source_name: HEK293, 309M3-B lot1 ChIP

value: anti-H3K9me3 (309M3-B lot 1)


title: C201: Tumor tissue

value: TNBC


title: 3B4-R

value: homozygous hs3b-hs4 KO animals, ref Pinaud  et al. Immunity. 2001 Aug;15(2):187-99. PubMed PMID:11520455.s


title: C203: Tumor tissue


title: 3B4-S

value: Activated B cells from the spleen (48 hours with LPS)

value: Primary cells activated in vitro

value: mixed background 129/C58BL/6


title: 309M3-B lot1_ChIPSeq experiment 1

description:
Sample 2
Cell culture
Samples 2 and 3 are technical replicates.


title: C229: Tumor tissue

value: Surgically resected tumor

value: Formalin fixed paraffin embedded (FFPE)

value: I


title: Input for 309M3-B and 309M3-A

description:
Sample 1
Cell culture
This is input sequencing for Samples 2-5.


title: C23: Tumor tissue


title: spleen_naiv_ko_9

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Institute of Biochemistry, Medical Faculty

institute: Leipzig University

data_processing:
basecalling using freeIBIS
adapter were trimmed and reads were merged
reads were mapped using tophat 1.3.3 and bowtie 0.0.9v
aligned reads were filtered for quality (samtools view -q 255) and all reads mapping to the mitochondria genome were removed
readcounts were retrieved using intersectBED
differential expression analysis was performed using the Deseq package
Genome_build: mm9
Supplementary_files_format_and_content: readcounts are provided as space delimited text files for each sample

source_name: Spleen

growth_protocol: Bone marrow was isolated from femurs and tibiae of 8–16 week old male WT or KO mice. 4x106 cells were plated and further cultivated for 10 days at 37°C in a humidified atmosphere containing 5% CO2 in a 3:2 mixture of RPMI 1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin, 50 μM β-mercaptoethanol and a supernatant from a GM-CSF secreting X63 cell line.

extract_protocol:
Total RNA was extracted from DC cultures and spleen samples using the TRI REAGENT™ according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Dcs were harvested on day 10 and seeded (3x106 cells in 2.5 ml serum-free RPMI 1640) in 6-cm dishes. On day 11, Dcs were incubated with LPS for 8 h.

value: Spleen

tag: age

value: 12 weeks


title: C197: Tumor tissue

value: Invasive Ductal Carcinoma

value: Luminal B HER2+


title: C18: Tumor tissue

value: Luminal A


title: 3pRR-S

tag: cell type

value: homozygous 3'RR KO animals, ref Vincent-Fabert C et al. Blood. 2010 Sep 16;116(11):1895-8. doi:10.1182/blood-2010-01-264689.