title: 3D7-H3K9ac-Schizont

city: Melbourne

first: Michaela

last: Petter

state: VIC

address: 792 Elizabeth Street

department: Peter Doherty Institute

country: Australia

institute: University of Melbourne

data_processing:
All Samples were quality controlled using FastQC (version 0.11.2, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapter sequences were trimmed and reads were quality filtered using Trim Galore! (version 0.3.7, www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
ChIPseq: Sequence reads from ChIP and input samples were then mapped to the P. falciparum 3D7 strain genome assembly (PlasmoDB v12) using Subread (Liao et al., 2013)
Peaks were called using MACS2 q=0.01 (Zhang et al., 2008) using Bam files concatenated with Samtools (Li et al., 2009) from three biological replicates for schizonts and two for trophozoites for both ChIPseq and input libraries as per Zhang et al’s instructions (Zhang et al., 2008).
Genes closest to a ChIP peak were identified using the bedtools suite (Quinlan and Hall, 2010).
RNAseq: Sequence reads from RNASeq were mapped to the P. falciparum 3D7 strain genome assembly using Tophat2
The gene annotations are publicly available in the Plasmodium database PlasmoDB (http://plasmodb.org/plasmo/)
Transcript coverage normalised for gene and library size (fpkm) was determined using Cufflinks (Trapnell et al., 2012).
Genome_build: PlasmoDB v12
Supplementary_files_format_and_content: tab-delimited text files include FPKM (fragments per kilobase of exon per million fragments mapped) values for concatenated data sets
Supplementary_files_format_and_content: xls files include ChIP peaks called for concatenated data sets

organism: Plasmodium falciparum

source_name: P. falciparum in vitro culture

growth_protocol: Plasmodium falciparum parasites were cultured in RPMI-HEPES medium containing 5% O+ red blood cells, 0.2% sodium bicarbonate and 0.5% Albumax (Gibco). Parasitaemia was maintained at 0.5%-10%. Parasites cultures were incubated at 37ºC in 1% O2, 5% CO2 and 94% N2.

extract_protocol:
DNA was purified using Qiagen MinElute columns.
2ng of ChIP or Input material was used to prepare indexed Illumina sequencing libraries using the NEBNext Ultra DNA library prep kit (New England Biolabs). Adapter ligated ChIP DNA libraries were amplified for 15 cycles.

value: whole organism

tag: Stage

value: Schizont

value: rabbit anti-H3K9ac (Millipore)


title: TB progressor (040718PAXGENEDAY0_L8.LB2)

status: Public on Mar 22 2016

type: SRA

city: Seattle

first: Daniel

middle: Edward

last: Zak

state: WA

address: 307 Westlake Ave N, Suite 5

country: USA

institute: Seattle Biomedical Research Institute

description: Processed data: primarySampleJunctions.xlsx - Sheet1

library_source: transcriptomic

data_processing:
Alignment GSNAP version 2012-06-20
Sequenced reads were filtered for low-quality sequence and the presence of 'N's, then mapped to hg19 whole genome using gsnap v0.12.2
Junctions counts were calculated by using an in house script to count the number of reads mapped to all splice junctions in the genome
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited file including the raw junction counts for all the detected junctions in the genome (number of reads mapped to the splice junctions in all samples)

molecule: total RNA

organism: Homo sapiens

source_name: Blood, case

extract_protocol:
Paxgene RNA
GlobinClear Globin transcript reduction followed by Illumina mRNA-Seq

tag: group

value: case (TB progressor)

tag: bin

tag: age

tag: gender

value: female

tag: ethnicity

value: coloured

tag: previous diagnosis of tb

value: n

tag: tst

tag: qft

value: positive

tag: tissue

value: blood


title: 3D7-H3K9ac-Troph

library_source: genomic

molecule: genomic DNA

tag: strain

value: Troph

tag: chip antibody


title: BDP1-Schizont_4

value: rat anti-HA clone 3F10 (Roche)


title: Non-progressor (04_0699D025uL04_0699_L3.LB6)

source_name: Blood, control

value: control (non-progressor)


title: 3D7-Input-Troph


title: 3D7-Input-schizont


title: TB progressor (040238PAXGENEIC_L2.LB16)


title: TB progressor (040238PAXGENEDAY540_L3.LB18)


title: TB progressor (040511PAXGENEDAY360_L6.LB12)


title: TB progressor (04_0511D025uL04_0511_L6.LB9)

value: negative


title: TB progressor (040238PAXGENEDAY0_L2.LB15)


title: BDP1-Schizont_1


title: BDP1-Schizont_2


title: BDP1-Schizont_3


title: TB progressor (040152PAXGENEDAY540_L6.LB9)


title: TB progressor (040695PAXGENEDAY360_L7.LB20)

value: male

value: indeterminate


title: Input-Schizont_3


title: TB progressor (040152PAXGENEDAY360_L4.LB8)


title: TB progressor (040695PAXGENEDAY540_L7.LB21)


title: TB progressor (04_0152D020uL04_0152_L2.LB11)


title: Input-Schizont_2


title: TB progressor (040152PAXGENEDAY180_L4.LB7)


title: Non-progressor (030714PAXGENEDAY0_L3.LB21)

value: black


title: BDP1-Troph_2


title: Non-progressor (030711PAXGENEDAY0_L4.LB23)


title: Input-Schizont_1


title: BDP1-Troph_1


title: Non-progressor (030697PAXGENEDAY0_L2.LB11)


title: Input-Troph_2


title: TB progressor (01_0993D030uL01_0993_L8.LB8)


title: Input-Schizont_4


title: RNA-Schizont_4

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions
2 mg total RNA was depleted of Hb mRNA (GLOBINclear kit, Life Technologies) and other mRNAs purified using magnetic oligo dT beads. Indexed sequencing libraries were prepared using the NEBNext Ultra directional RNAseq kit (New England Biolabs). The PCR Library Enrichment step was replaced by a custom PCR protocol using the KAPA Hifi PCR system (KAPA Biosystems) for 12 cycles (Oyola et al., 2012).


title: RNA-Schizont_3

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies) following manufacturer's instructions
2 ug total RNA was depleted of Hb mRNA (GLOBINclear kit, Life Technologies) and other mRNAs purified using magnetic oligo dT beads. Indexed sequencing libraries were prepared using the NEBNext Ultra directional RNAseq kit (New England Biolabs). The PCR Library Enrichment step was replaced by a custom PCR protocol using the KAPA Hifi PCR system (KAPA Biosystems) for 12 cycles (Oyola et al., 2012).


title: Non-progressor (01_0940D030uL01_0940_L6.LB10)


title: Input-Troph_1


title: RNA-Schizont_2


title: RNA-Schizont_1


title: TB progressor (010757PAXGENEIC_L5.LB7)


title: RNA-Troph_2


title: RNA-Troph_1


title: TB progressor (01_0673D025uL01_0673_L6.LB7)


title: TB progressor (010757PAXGENEDAY0_L1.LB7)


title: TfoY-producing strain replicate 3

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

department: School of Life Sciences

country: Switzerland

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

data_processing:
Data processing was done by Microsynth (Balgach, Switzerland)
Reads were mapped onto the reference genome using the TopHat and Bowtie 2 software
Reads were counted using HTSeq
The counted transcripts were normalized and subjected to statistical analysis through the DESeq2 software package
Genome_build: Reference genome (NC_002505, NC_002506)
Supplementary_files_format_and_content: .counts.txt files; counts per locus tags

organism: Vibrio cholerae

source_name: bacterial in vitro culture

growth_protocol: V. cholerae strains were grown in 6 x 2.5 ml LB medium with 0.02% arabinose at 30C until an optical sensity at 600 nm (OD600) of 1.5-1.8 was reached. At this time, the bacteria were harvested by centrifugation at 4C.

extract_protocol:
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNAse treatment using a RNA clean-up procedure (GenElute Mammalian Total RNA miniprep kit; Sigma). Ribodepletion was performed using a Ribo-Zero Magnetic kit (Epicentre) for Gram-negative bacteria.
RNA libraries were prepared with a TruSeq Stranded mRNA sample prep kit (Illumina).

treatment_protocol: The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri reagent, and stored at -80C until their processing.

tag: genotype

value: A1552 with TntfoY transposon


title: TB progressor (01_0524D030uL01_0524_L8.LB7)


title: TB progressor (010524PAXGENEIC_L5.LB5)


title: CD6_MIGS

city: Houston

first: Angela

middle: H

last: Ting

state: Tx

address: 1881 East Road

department: Epigenetics and Molecular Carcinogenesis

institute: The University of Texas MD Anderson Cancer Center

data_processing:
For MiGS data, all reads with MAPQ < 10 were filtered. Remaining reads were aligned to hg19 with bowtie2 (options: -N 1 -L 20 -phred33). Average coverage in non-overlapping 50 bp bins were counted genome-wide, and served as input for a differentially methylated region (DMR) detection pipeline in R.
For RNA-seq data, reads were aligned to hg19 using GSNAP. Read counts for RefSeq genes were computed using HTSeq-count.
Genome_build: hg19
Supplementary_files_format_and_content: For MiGS data, rounded average coverage values within 50 bp non-overlapping windows have been provided for each sample as text files. The first column is the chromosome (hg19) followed by start and end coordinates in the second and third columns. The fourth column provides the average coverage within the window, rounded to the nearest integer. Bins with values of zero have been omitted. These were generated in the process of differentially methylated region (DMR) discovery using iDPT (http://idpt.github.io/dptscan/).
Supplementary_files_format_and_content: For RNA-seq data, reads were counted for RefSeq transcription units using HTSeq-count. The tab-delimited text file contains one row for each gene and one column containing the DESeq normalized read counts for each sample.

source_name: human intestinal fibroblasts (HIFs)

growth_protocol: Human intestinal fibroblasts (HIFs) were cultured and their purity confirmed by established methods.

extract_protocol:
Genomic DNA was purified using the Qiagen DNEasy kit.
Genome-wide DNA methylation was mapped using MBD-isolated genome sequencing (MiGS) (Serre, 2010), with the following differences. DNA (10 ug) was sheared on a Covaris S220 to an average fragment size of 120 bp and methylated fragments were purified on PrepEase DNA columns (USB). Methylated DNA sequences were captured with the methyl binding transcriptional repressor protein MBD2 MethylMiner Methylated DNA Enrichment kit #ME10025 (Invitrogen). A sequencing library for each sample was prepared from the immunoprecipitated DNA using Ilumina’s ChIP-seq DNA Sample Prep Kit and the quality of the DNA was assessed on an Agilent Bioanalyser.

value: Crohn's disease-associated fibrosis

value: colon

tag: cell type

value: intestinal fibroblast


title: TfoY-producing strain replicate 1


title: WT strain replicate 3


title: TfoY-producing strain replicate 2


title: WT strain replicate 2


title: WT strain replicate 1


title: CD7_MIGS


title: Input, replicate 2

first: Orla

last: Conneely

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
DNA libraries were sequenced on an Illumina Genome Analyzer II.
Sequences (36-nt reads) were aligned to the human genome (NCBI37/hg19) using the Burrows-Wheeler Aligner algorithm.
Aligns were extended in silico at their 3'-ends to a length of 150bp and assigned to 32-nt bins along the genome.
Peak locations were determined using MACS with a p value cutoff of 1e-10.
Genome_build: NCBI37/hg19
Supplementary_files_format_and_content: wig

source_name: acute myeloid leukemia

growth_protocol: RPMI 1640 with 20% FBS

extract_protocol:
Cells were lysed by Dounce homogenization and chromatin was sheared to an average length of 300-500bp.  30ug aliquots of lysates were pre-cleared with Protein A agarose beads and incubated with 2ug NR4A antibody (sc-990, Santa Cruz Biotechnology) overnight at 4ºC.
ChIP and input DNA were amplified using the Illumina ChIP-Seq DNA Sample Prep Kit.

tag: cell line

value: acute myeloid leukemia cell line Kasumi-1

tag: antibody

tag: treatment

value: NR4A1 mRNA electroporation

tag: genotype/variation


title: NR4A1 ChIP-seq, replicate 1

value: anti-NR4A1 (Santa Cruz, sc-990)


title: Input, replicate 1


title: VSMC at Passage 2 [002_C96]

city: Excelsior

first: Rod

middle: A.

last: Staggs

state: MN

address: 20040 Cottagewood Ave

institute: Minnesota Informatics

data_processing:
Aligned with BWA, redundant reads removed with Samtools
transcript abundance estimated using HT-seq
Genome_build: Ensembl Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Hall.project20.DeSeqNormData.txt
Supplementary_files_format_and_content: DeSeq normalized transcript counts

organism: Mus musculus

source_name: descending aorta

growth_protocol: Freshly isolated VSMCs from murine aorta were cultured in DMEM supplemented with 1% penicillin/streptomycinand 10% fetal bovine serum and plated in a 24-well tissue culture plates. The plates with VSMCs were incubated in a 37^C incubator with 5% CO2 and left undisturbed for 5 days. After day 5, the passage 1 (P1) cells were trypsinized and subcultured to obtain passage 2 (P2).

extract_protocol:
Fluidigm C1 Single-Cell Auto Prep System
dual indexed RNA-seq libraries were prepared using Nextera XT reagents.

value: adult 3-4 month old

tag: Sex

tag: passage

value: Passage 2


title: NR4A1 ChIP-seq, replicate 2


title: VSMC at Passage 2 [002_C91]

tag: age


title: VSMC at Passage 2 [002_C92]


title: TB progressor (010673PAXGENEIC_L6.LB11)

tag: group

value: case (TB progressor)

tag: bin

tag: gender

value: coloured

value: n

value: blood


title: VSMC at Passage 2 [002_C89]


title: VSMC at Passage 2 [002_C90]


title: CD8_MIGS


title: Non-progressor (01_0934D020uL01_0934_L1.LB1)

value: control (non-progressor)

value: female

tag: ethnicity

tag: previous diagnosis of tb

tag: tst


title: VSMC at Passage 2 [002_C86]

tag: strain

value: male


title: VSMC at Passage 2 [002_C87]


title: VSMC at Passage 2 [002_C79]


title: VSMC at Passage 2 [002_C83]


title: VSMC at Passage 2 [002_C82]


title: VSMC at Passage 2 [002_C85]


title: VSMC at Passage 2 [002_C80]


title: VSMC at Passage 2 [002_C77]


title: VSMC at Passage 2 [002_C78]


title: NL4_MIGS

value: control

tag: tissue


title: VSMC at Passage 2 [002_C76]


title: VSMC at Passage 2 [002_C74]


title: VSMC at Passage 2 [002_C94]


title: VSMC at Passage 2 [002_C71]


title: VSMC at Passage 2 [002_C73]


title: NL2_MIGS


title: VSMC at Passage 2 [002_C67]


title: VSMC at Passage 2 [002_C66]


title: VSMC at Passage 2 [002_C69]


title: VSMC at Passage 2 [002_C59]


title: VSMC at Passage 2 [002_C6]


title: VSMC at Passage 2 [002_C55]


title: VSMC at Passage 2 [002_C51]


title: VSMC at Passage 2 [002_C5]


title: VSMC at Passage 2 [002_C40]


title: VSMC at Passage 2 [002_C35]


title: VSMC at Passage 2 [002_C31]


title: VSMC at Passage 2 [002_C38]


title: VSMC at Passage 2 [002_C30]


title: VSMC at Passage 2 [002_C28]


title: VSMC at Passage 2 [002_C3]


title: VSMC at Passage 2 [002_C24]


title: VSMC at Passage 2 [002_C21]


title: VSMC at Passage 2 [002_C20]


title: VSMC at Passage 2 [002_C25]


title: VSMC at Passage 2 [002_C65]


title: VSMC at Passage 2 [002_C27]


title: VSMC at Passage 1 [001_C78]

value: Passage 1


title: VSMC at Passage 2 [002_C13]


title: VSMC at Passage 1 [001_C67]


title: VSMC at Passage 2 [002_C62]


title: VSMC at Passage 2 [002_C23]


title: VSMC at Passage 2 [002_C61]


title: VSMC at Passage 2 [002_C53]


title: VSMC at Passage 1 [001_C5]


title: VSMC at Passage 1 [001_C49]


title: VSMC at Passage 1 [001_C41]


title: Spermatid_H3K27me3_bound_rep3 Sample 127

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to X. Laevis genome 6.1 using TopHat 2.0.6
ChIP-seq  data have been aligned to X. Laevis genome 6.1 using BWA 0.6.2 with default options. Duplicate reads were then removed
Peaks were called using MACS2 2.0.9 with --broad options and q-value<0.01.
The list of confirmed peaks across replicates consisted of peaks with pvalue <0.01 detected in at least 2 out of 3 replicates.
MNase-seq data have been aligned to X. Laevis genome 6.1 with BWA with default options and duplicates reads were removed. Nucleosomes positions have been estimated on cell-specific merged bam files with NucHunter (-fLen = 150, -wrad 146)
MBD-seq data have been processed as ChIP-seq
Counts from RNA-seq data were extracted using HT-seq count
Differential analysis was conducted using EdgeR package
Supplementary_files_format_and_content: counts files contain counts generated using htseq-count
Supplementary_files_format_and_content: .cov files contain counts per million coverage normalized to total number of reads 1kb around TSS
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 200bp windows
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 50bp windows
Supplementary_files_format_and_content: bed files contains coordinate of features (i.e. for Nucleosome, putative locations of stable nucleosomes)

organism: Xenopus laevis

growth_protocol: no growth protocol

extract_protocol:
none provided by submitter
Illumina TruSeq RNA sample prep kit for RNA-seq,

tag: pairing of samples

value: spermatid chromatin

tag: starting material

value: 1M cells

value: H3K27me3 immunoprecipitation


title: Spermatid_H3K27me3_bound_rep2 Sample 125

tag: cell type


title: Spermatid_H3K27me3_bound_rep1 Sample 123


title: VSMC at Passage 1 [001_C38]


title: VSMC at Passage 1 [001_C39]


title: VSMC at Passage 1 [001_C36]


title: Spermatid_H3K9me3_bound_rep3 Sample 121

value: H3K9me3 immunoprecipitation


title: VSMC at Passage 1 [001_C31]


title: VSMC at Passage 1 [001_C3]


title: VSMC at Passage 1 [001_C28]


title: Spermatid_H3K4me3_bound_rep3 Sample 115

value: H3K4me3 immunoprecipitation


title: VSMC at Passage 1 [001_C23]


title: VSMC at Passage 1 [001_C22]


title: Spermatid_H3K4me3_bound_rep2 Sample 113


title: VSMC at Passage 1 [001_C16]


title: VSMC at Passage 1 [001_C14]


title: Spermatid_H3K4me3_input_rep1 Sample 110

value: 0.1M cells


title: VSMC at Passage 1 [001_C20]

value: adult 3-4 month old


title: VSMC at Passage 1 [001_C13]


title: VSMC at Passage 1 [001_C10]


title: KO_UTX_Male

city: Ottawa

first: Marjorie

last: Brand

state: Ontario

address: 501 Smyth Road

country: Canada

institute: Ottawa Hospital Research Institute

data_processing:
Sequenced reads were initially mapped to the known mm9 transcripts (GTF file from the UCSC) using Bowtie version 2.2.4 / TopHat 2.0.12 using default values. Unmapped reads were then mapped to the mm9 genome.
Splice junctions were determined with TopHat version 2.0.12 using default values.
Transcript quantification was performed with Cufflinks version 2.2.1 and HT-Seq 0.6.1.
Identification of differentially expressed genes was performed with the CuffDiff from Cufflinks version 2.2.1 and EdgeR bioconductor package.
Genome_build: mm9
Supplementary_files_format_and_content: WIG files represent the read per million mapped reads coverage of the RNA-Seq across the genome. The files were generated using the BEDTools suite (version 2.16.2) and UCSC genome browser standalone tools for Unix from the aligned reads output of TopHat version 2.0.12 using default values.
Supplementary_files_format_and_content: Text file contains quantification for each gene in Fragments Per Million Kilobase (FPKM).

source_name: Satellite cells from muscle

growth_protocol: SCs from UTXmKO/TdT or UTXWT/TdT mice were grown in in Ham's F10 modified media supplemented with 20 % fetal calf serum, 4 mM L-Glutamine, 1.5 g/L sodium bicarbonate, 2.5 ng/mL of  FGF, and 2.5 µM of 4-OH-Tamoxifen.

extract_protocol:
Total RNA was then isolated using RNAesay kit (Qiagen) using an on-column DNase digestion (RNase-Free DNase Set, Qiagen) to avoid genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Sorted TdT+ SCs from UTXmKO/TdT or UTXWT/TdT mice were induced to differentiate for 24 h.

value: Differentiating Myoblasts

value: Male


title: WT_UTX_Male


title: KI_UTX_Female_Rep2

value: Female


title: VSMC at Passage 1 [001_C25]


title: Ctrl-KI_UTX_Female_Rep2


title: KI_UTX_Female_Rep1


title: Spermatid_H3K4me2_input_rep2  Sample 106


title: Spermatid_H3K4me2_bound_rep2 Sample 107

value: H3K4me2 immunoprecipitation


title: Ctrl-KI_UTX_Female_Rep1


title: VSMC at Passage 1 [001_C27]


title: Baf250a_Hcn4

city: New York City

first: Yong

last: Zhao

state: NY

address: 1470 Madison Ave

department: Mindich Child Health and Development Institute

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Reads were aligned to the mouse reference genome using TopHat program (Bowtie algorithm)
Transcript assembles and identification of differentially expressed genes were achieved using Cufflinks package
To account for expression bias due to transcript length, each sample transcript expression was normalized by using cufflinks algorithm with a FDR of 0.05
genome build: mm9

source_name: 6 days

extract_protocol:
Total RNAs were extracted using TRIzol Reagent. mRNAs were purified using a poly-A selection approach.
Sequencing libraries were prepared according to a standard protocol. Barcode (Time series control): TGACCA; Barcode (16hr): ACAGTG; Barcode (20hr): GCCAAT; Barcode (24hr): CAGATC; Barcode (48hr): ACTTGA; Barcode (6-day control): CTTGTA; Barcode (6-day): GCCAAT

value: SAN

value: postnatal 3 weeks

tag: genotype


title: Spermatid_H3K4me2_input_rep3 Sample 108


title: Spermatid_H3K9me3_bound_rep2 Sample 119


title: Spermatid_H3K9me3_bound_rep1 Sample 117


title: VSMC at Passage 1 [001_C26]


title: Baf250a_Ctrl

source_name: Ctrl


title: 24h


title: Spermatid_H3K4me3_bound_rep1 Sample 111


title: Spermatid_H3K4me2_bound_rep3 Sample 109


title: Spermatid_H3K4me2_input_rep1 Sample 104


title: 48h


title: Sperm_H3K27me3_bound_rep2 Sample 101

value: sperm chromatin


title: 20h


title: ctrl

source_name: ctrl


title: 16h


title: Sperm_H3K9me3_bound_rep1 Sample 93


title: Sperm_H3K27me3_bound_rep1 Sample 99


title: Sperm_H3K9me3_bound_rep3 Sample 97


title: Sperm_H3K9me3_bound_rep2 Sample 95


title: VSMC at Passage 1 [001_C15]

value: male


title: Sperm_H3K4me3_bound_rep2 Sample 89


title: UMSCC25_GEFITINIB_3

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: kinome-shRNA library

data_processing:
alignment: Bowtie v1.0.0 that allows no mismatches
normalization : quartile normalization
comparison : fisher's exact test assuming negative binomial (edgeR)
gene collapsing : weighted z-transformation
Genome_build: hg19 (Ucsc) - TRC Kinome siRNA reference library
Supplementary_files_format_and_content: text file with read counts

source_name: Head and Neck Squamous Cell Carcinoma cell line

growth_protocol: Cells were maintained in Dulbecco's modified Eagle medium (UMSCC25, UMSCC8, UMSCC1) supplemented with 10% Fetal Bovine Serum and 1% penicillin-streptomycin at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total genomic DNA was extracted with the Quick-gDNA MiniPrep Kit (Zymo Research Corporation) according to manufacturer's instructions.
6x10^6 cells from each of the cell lines (UMSCC25, UMSCC8, UMSCC1) were plated into duplicate 15cm plates (3x106 cells/plate) and transduced 24 hours later with the kinome shRNA library containing viral supernatant and 8 μg/ml polybrene (Sigma-Aldrich). After 72 hours, transfected cells were selected with puromycin (1 μg/ml) for 5 days. The lentiviral preparation for the SBI genome-wide screen was reported in our previous publication

treatment_protocol: Cells were treated with DMSO or AZ8931 (30nM) or Gefitinib (300nM) as indicated for 72 hrs and allowed to recover in media for 72 hrs.

tag: agent

value: Gefitinib treated

tag: cell line

tag: treatment protocol

value: Cells were treated with 1.0 μM Gefitinib for a period of 72 hrs and allowed to recover in media for 72 hrs. Genomic DNA was isolated at 144 hrs.


title: Sperm_H3K4me3_input_rep2 Sample 88


title: Sperm_H3K4me3_bound_rep3 Sample 91


title: UMSCC25_GEFITINIB_2

description: kinome-shRNA library


title: UMSCC25_GEFITINIB_1

description: kinome-shRNA library


title: Sperm_H3K4me3_bound_rep1 Sample 87


title: Sperm_H3K4me3_input_rep3 Sample 90


title: Sperm_H3K4me2_bound_rep3 Sample 85


title: UMSCC25_AZD8931_2

description: kinome-shRNA library

value: AZD8931 treated

value: Cells were treated with 1.0 μM AZ8931 for a period of 72 hrs and allowed to recover in media for 72 hrs. Genomic DNA was isolated at 144 hrs.


title: UMSCC25_AZD8931_1

description: kinome-shRNA library


title: UMSCC25_AZD8931_3

description: kinome-shRNA library


title: Spermatid_H3K4me2_bound_rep1 Sample 105

value: spermatid chromatin

value: 1M cells


title: UMSCC25_DMSO_2

description: kinome-shRNA library

value: DMSO

value: Cells were treated with DMSO for a period of 72 hrs and allowed to recover in media for 72 hrs. Genomic DNA was isolated at 144 hrs.


title: Sperm_H3K4me2_input_rep3 Sample 84

value: 0.1M cells


title: UMSCC25_DMSO_1

description: kinome-shRNA library


title: Sperm_H3K4me2_bound_rep2 Sample 83


title: UMSCC8_GEFITINIB_3

description: kinome-shRNA library


title: Sperm_H3K4me2_bound_rep1 Sample 81


title: Sperm_H3K4me2_input_rep2 Sample 82


title: Sperm_H3K4me2_input_rep1 Sample 80


title: UMSCC8_GEFITINIB_1

description: kinome-shRNA library


title: UMSCC8_AZD8931_3

description: kinome-shRNA library


title: UMSCC8_GEFITINIB_2

description: kinome-shRNA library


title: UMSCC8_AZD8931_2

description: kinome-shRNA library


title: UMSCC8_AZD8931_1

description: kinome-shRNA library


title: Sperm_PE1_rep7 Sample 19

source_name: ICSI on UV radiated Eggs

value: Sperm-derived embryos

value: pool of 5 embryos

value: Haploid Embryo 10.5-11.5


title: UMSCC25_DMSO_3

description: kinome-shRNA library


title: UMSCC8_DMSO_3

description: kinome-shRNA library


title: Sperm_PE1_rep6 Sample 17


title: UMSCC1_GEFITINIB_1

description: kinome-shRNA library


title: Spermatid_PE1_rep7 Sample 15

value: Spermatid-derived  embryos


title: UMSCC1_GEFITINIB_2

description: kinome-shRNA library


title: UMSCC1_AZD8931_3

description: kinome-shRNA library


title: UMSCC8_DMSO_1

description: kinome-shRNA library


title: UMSCC1_AZD8931_2

description: kinome-shRNA library


title: Spermatid_PE1_rep6 Sample 13


title: UMSCC1_AZD8931_1

description: kinome-shRNA library


title: UMSCC1_DMSO_1

description: kinome-shRNA library


title: UMSCC1_DMSO_2

description: kinome-shRNA library


title: UMSCC1_DMSO_3

description: kinome-shRNA library


title: Spermatid_SE_rep5 Sample 12


title: Sperm_H3K27me3_bound_rep3 Sample 103

value: H3K27me3 immunoprecipitation


title: Sperm_SE_rep5 Sample 11


title: PY79 Day 13

city: Stanford

first: Stuart

state: CA

address: 279 Campus Drive

department: Developmental Biology

institute: Stanford University

data_processing:
Data were processed as in (Van Nostrand and Kim, 2013)
Reads with 10 or more consecutive A's or T's were removed as likely amplification artifacts, and reads were then mapped to the Wormbase reference WS220 genome and transcriptome using Bowtie version 0.12.7, using the options “-a –best –strata -v 2” to obtain all genomic position(s) to which the read mapped with the least number mismatches (up to 2 allowed).
Greater than 30 million reads for each independent replicate were obtained that mapped uniquely to the sense strand of WS215 annotated transcripts (with more than 85% of post-filter reads mapping to C. elegans in each experiment).
To determine expression for each transcript in the WS220 Wormbase annotation, we counted the number of reads that uniquely mapped to the sense strand (i.e., they did not map equally well elsewhere in the genome).
For genes with multiple annotated isoforms, only the transcript with the highest average expression across the six experiments was used for further analysis.
Genome_build: ws220
Supplementary_files_format_and_content: Excel file containing uniquely-mapping sense-strand read counts for each transcript

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: Whole-worm mRNA

growth_protocol: A synchronized population of approximately 10,000 N2 animals was fed either OP50 or PY79. Sample were collected on either Day 4 or Day 13 of adulthood.

extract_protocol:
Worms were pelleted into TRIzol.  Total RNA was extracted following the manufacturer's instructions.  Poly A-enriched RNA was isolated using the Qiagen OligoTex kit.
3’-end enriched RNA-sequencing (“3SEQ”) libraries were prepared as previously described (Van Nostrand and Kim, 2013, Beck et al., 2010). Briefly, barcoded sequencing adapters were ligated onto cDNA made from poly-A-enriched RNA. Libraries were pooled prior to sequencing.

tag: fed with

value: PY79 B. subtilis

tag: time point

value: Day 13 of adulthood

value: Whole-worm


title: OP50 Day 13

value: OP50 E. coli


title: UMSCC8_DMSO_2

description: kinome-shRNA library


title: Spermatid_SE_rep4 Sample 10


title: OP50 Day 4

value: Day 4 of adulthood


title: UMSCC1_GEFITINIB_3

description: kinome-shRNA library

value: Gefitinib treated

value: Cells were treated with 1.0 μM Gefitinib for a period of 72 hrs and allowed to recover in media for 72 hrs. Genomic DNA was isolated at 144 hrs.


title: PY79 Day 4


title: Sperm_SE_rep3 Sample 7


title: Sperm_SE_rep4 Sample 9


title: Spermatid_PE1_rep1 Sample 3


title: Sperm_SE_rep2 Sample 5


title: Sperm_PE1_rep1 Sample 1


title: DNA methylation porg rep3 bound Sample 79

source_name: Methyl Binding Domain (MBD) based enrichment

value: spermatid chromatin

value: 200ng DNA from Mnase digested chromatin

value: spermatid methylated DNA  captured by binding of MBD protein


title: elt-2_OE_Day13_B

data_processing:
Data were processed as in (Van Nostrand and Kim, 2013)
Reads with 10 or more consecutive A's or T's were removed as likely amplification artifacts, and reads were then mapped to the Wormbase reference WS220 genome and transcriptome using Bowtie version 0.12.7, using the options “-a –best –strata -v 2” to obtain all genomic position(s) to which the read mapped with the least number mismatches (up to 2 allowed).
Greater than 30 million reads for each independent replicate were obtained that mapped uniquely to the sense strand of WS215 annotated transcripts (with more than 85% of post-filter reads mapping to C. elegans in each experiment).
To determine expression for each transcript in the WS220 Wormbase annotation, we counted the number of reads that uniquely mapped to the sense strand (i.e., they did not map equally well elsewhere in the genome).
For genes with multiple annotated isoforms, only the transcript with the highest average expression across all experiments was used for further analysis.
To avoid differential expression of the most highly expressed genes skewing the relative abundance of other transcripts, the most highly expressed 3% of genes in each library were excluded from this analysis.
Genome_build: ws220
Supplementary_files_format_and_content: text file containing read counts for the most abundant transcript of each gene

growth_protocol: A synchronized population of approximately 10,000 N2 animals at the L1 stage was fed E. coli. Animals were washed from plates 28 hours later, when the animals had reached the L4 stage. The animals were pelleted and placed into TRIzol.  For old samples, a synchronized population of approximately 10,000 control or elt-2 overexpression animals was placed onto FUDR-containing plates at Day 1 of adulthood. On Days 2, 3, 4, 5, 7, 9, 11, and 13 of adulthood, worms were washed from plates onto nylon mesh to filter out eggs and potential progeny. On Day 13, dead animals were manually removed from the plates. The remaining animals were washed from the plates, pelleted, and placed into TRIzol. Five biological replicates were collected for each sample.

value: whole worm


title: Transgenic_Control_Day13_A


title: elt-2_OE_L4_D


title: elt-2_OE_Day13_C


title: Transgenic_Control_Day13_E


title: Transgenic_Control_Day13_D


title: elt-2_OE_L4_C


title: elt-2_OE_L4_E


title: elt-2_OE_Day13_E


title: elt-2_OE_Day13_A


title: elt-2_OE_Day13_D


title: Transgenic_Control_Day13_C


title: Spermatid_SE_rep3 Sample 8


title: elt-2_OE_L4_B


title: Transgenic_Control_Day13_B


title: NL3_MIGS

tag: group

value: control

value: colon

value: intestinal fibroblast


title: elt-2_OE_L4_A


title: DNA methylation prog rep2 input Sample 75

value: 20ng DNA from Mnase digested chromatin

value: Mnase digested spermatid  DNA


title: Spermatid_SE_rep2 Sample 6

value: Spermatid-derived  embryos

value: pool of 5 embryos

value: Haploid Embryo 10.5-11.5


title: DNA methylation prog rep1 input Sample 74


title: DNA methylation prog rep3 input Sample 76


title: DNA methylation sperm rep3 bound Sample 73

value: sperm chromatin

value: sperm methylated DNA  captured by binding of MBD protein


title: Transgenic_Control_L4_D


title: DNA methylation porg rep2 bound Sample 78


title: DNA methylation sperm rep2 bound Sample 72


title: Transgenic_Control_L4_C


title: Transgenic_Control_L4_B


title: DNA methylation sperm rep1 bound Sample 71


title: DNA methylation porg rep1 bound Sample 77


title: DNA methylation sperm rep3. input Sample 70

value: Mnase digested sperm DNA


title: DNA methylation sperm rep1. input Sample 68


title: elt-2 RNAi_L4_B

data_processing:
Data were processed as in (Van Nostrand and Kim, 2013)
Reads with 10 or more consecutive A's or T's were removed as likely amplification artifacts, and reads were then mapped to the Wormbase reference WS220 genome and transcriptome using Bowtie version 0.12.7, using the options “-a –best –strata -v 2” to obtain all genomic position(s) to which the read mapped with the least number mismatches (up to 2 allowed).
Greater than 30 million reads for each independent replicate were obtained that mapped uniquely to the sense strand of WS215 annotated transcripts (with more than 85% of post-filter reads mapping to C. elegans in each experiment).
To determine expression for each transcript in the WS220 Wormbase annotation, we counted the number of reads that uniquely mapped to the sense strand (i.e., they did not map equally well elsewhere in the genome).
For genes with multiple annotated isoforms, only the transcript with the highest average expression across the six experiments was used for further analysis.
Genome_build: ws220
Supplementary_files_format_and_content: text file containing read counts for the most abundant transcript of each gene

growth_protocol: A synchronized population of approximately 10,000 N2 animals at the L1 stage was fed either elt-2 RNAi or an empty vector control. Animals were washed from plates 28 hours later, when the animals had reached the L4 stage. The animals were pelleted and placed into TRIzol.


title: spermatid_rep3 Sample 67

source_name: MNase digested gDNA

value: 0.1M cells

value: MNase digested spermatid chromatin


title: sperm_rep2 Sample 63

value: MNase digested sperm chromatin


title: spermatid_rep2 Sample 66

value: spermatid chromatin


title: elt-2 RNAi_L4_C


title: sperm_rep3 Sample 64


title: Transgenic_Control_L4_A


title: DNA methylation sperm rep2. input Sample 69


title: elt-2 RNAi_L1_B

growth_protocol: A synchronized population of approximately 10,000 N2 animals was fed either elt-2 RNAi or an empty vector control on Day 1 of adulthood. After 24 hours of exposure to RNAi, adult animals were bleached. Embryos were synchronized by hatching overnight in S-Basal.


title: Control_L4_A


title: Control_L4_C


title: elt-2 RNAi_L4_A


title: elt-2 RNAi_L1_A


title: K6B Sample 59

source_name: IVM/ICSI

value: pool of 5-7 embryos

value: Embryo with overexpressed Kdm6b


title: K6B Sample 61


title: ctrl Sample 58

value: Embryo with overexpressed inactive Kdm6b


title: Control_L1_B

value: whole worm


title: ctrl Sample 60


title: Control_L1_C


title: Control_L1_A


title: Transgenic_Control_L4_E


title: ctrl Sample 56


title: K6B Sample 55


title: ctrl Sample 57


title: spermatid_rep1 Sample 65


title: Control_L4_B


title: elt-2 RNAi_L1_C


title: sperm_rep1 Sample 62


title: K6B Sample 46

value: Sperm derived embryos


title: K6B Sample 54


title: ctrl Sample 47


title: ctrl Sample 53


title: ctrl Sample 45

value: Embryo with injected RFP


title: K6B Sample 50


title: ctrl Sample 49


title: ctrl Sample 51


title: K6B Sample 52


title: ctrl Sample 44


title: K5B Sample 39

value: Embryo with overexpressed Kdm5b


title: ctrl Sample 38

value: Spermatid-derived  embryos


title: K5B Sample 40


title: ctrl Sample 42


title: ctrl Sample 36


title: K5B Sample 43


title: K5B Sample 34


title: K5B Sample 32


title: ctrl Sample 35


title: K5B Sample 37


title: RFP Sample 30


title: RFP Sample 28


title: K5B Sample 29


title: K5B Sample 26


title: ctrl Sample 33


title: RFP Sample 25


title: K6B Sample 48


title: RFP Sample 27


title: K5B Sample 41


title: Spermatid_rep3 Sample 23

source_name: Purified spermatids

value: Spermatid purified cells

value: 1 M cells

value: Spermatid


title: K5B Sample 24


title: KO_UTX_Female

value: Differentiating Myoblasts

tag: Sex

value: Female


title: Spermatid_rep2 Sample 22


title: VHL ChIP [CZE_028]

city: Singapore

first: Justin

middle: Jeyakani

last: Joseph Gnanakkan

state: Singapore

address: 60, Biopolis street

department: Computational and Systems Biology

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Basecalls using CASAVA (v 1.8.2, Illumina).
Alignment was carried out using CASAVA (v 1.8.2, Illumina) with danRer7-Zv9 as the build
Peaks were called using MACS  (version 1.4.2 20120305)  with peak density in ChIP vs input control, a threshold of p-value > 1x10-5 was applied.
Genome_build: danRer7-Zv9
Supplementary_files_format_and_content: bigwig files were generated from the alignments using bedtools genomeCoverageBed and ucsc utility bedGraphToBigWig. Peak files were generated by MACS program, it contains each peaks genomics location, tag counts and p-value.

organism: Danio rerio

source_name: Primary tissue from zebrafish larvae

growth_protocol: Embryos were incubated for 4 days at 28C

extract_protocol:
Embryos were de-yolked, macerated and then fixed using formaldehyde before being flash frozen using liquid nitrogen. Cells were then lysed, sonicated and incubated with antibody bound Dynabeads A for chromatin immunoprecipitation. Finally, samples were washed, eluted and crosslinking was reversed before cellular RNA and protein was degraded.
Libraries were prepared using 5ng of ChIP material and 10ng of input material for both wild-type and vhl mutants, library preparation was performed using the Illumina Truseq ChIP Sample Preparation Kit set A (REF: 15034288) in accordance with manufacturer’s instructions using the adapters 2, 7 for input in duplicate and 19 for the ChIP samples to allow multiplexing. End repair, converted overhangs into blunt ends using an End Repair Mix . The 3' to 5' exonuclease activity of this mix removes the 3'overhangs and the polymerase activity fills in the 5' overhangs. 3' Adenylation using A-tailing mix, adds a single ‘A’ nucleotide to the 3’ ends of the blunt fragments to prevent self-ligation. A single ‘T’ nucleotide on the 3’ end of the adapter provides a complementary overhang for ligating the adapter to the fragment. After adapter ligation, DNA was isolated from an agrose gel (~ 250bp) and then ampified using PCR for 10 cycles. The samples were then quanified using titatration PCR and pooled before multiplex sequencing. Sequencing was performed using the Illumina HiSeq 2000 (Illumina, USA) performing a single read with 3 samples per lane.

value: TL/LWT mix

tag: genotype/variation

value: von Hippel Lindau mutant

tag: developmental stage

tag: chip antibody

value: Hif-1α custom antibody


title: WT_UTX_Female

value: Pax7-CreER, Rosa26-Floxed-TdTomato


title: Wild-type Input [CZE_023]

value: wild type


title: Wild-type ChIP [CZE_025]


title: Input1-3

status: Public on Mar 21 2016

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
Samples were sequenced on Illumina HiSeq 2000
First 5 bases were trimmed for all the reads using Trimmomatic software and kept 49bp in length
Alignment to the mouse genome build mm9 was performed using Bowtie with parameters -n 2 -q -m 1 -l 49 -e 70 -k 1 --best
Peak calling was done using MACS14 1.4.2 with pvalue 1e-5
Wiggle files were normalized by dividing each fragment pile up by total number of mapped reads in million
Genome_build: MM9
Supplementary_files_format_and_content: wig files were generated using MACS14 1.4.2. Data values  represent normalized pile up.

source_name: Sheared Chromatin (biological replicate 1)

growth_protocol: Standard ESC conditions

extract_protocol:
Briefly, cells were crosslinked for 5 min at room temperature with 1% fresh formaldehyde. Reaction was quenched with glycine (125 mM final concentration) for 5 min at room temperature. Cells were lysed in 0.1% SDS lysis buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8.0,150 mM NaCl). Chromatin was sonicated to a mean size of 300-500bp. Lysed cells were cleared by centrifugation and anti-Ring1b (Active Motif 39664) was added to chromatin extracts and incubated overnight.  Protein A/G Dynal beads were added for 2 hours and beads were isolated with a magnet and then washed with 0.1% SDS Lysis Buffer, Low Salt Buffer ( 0.1% SDS, 1% Triton X-100, 2mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl),  LiCl Wash Buffer (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and TE x2. DNA was eluted and decrosslinked overnight at 65 oC in SDS Elution Buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH 8.0). The next day RNase A and proteinase K were added, and the DNA was precipitated in the presence of glycogen. DNA for downstream applications were quantitated by flourometry (Qubit, Invitrogen), and equal DNA was used for each ChIP-qPCR and normalized to sheared, non-IP’d genomic DNA (Input).
NEB ChIp-seq library prep kit (cat# E7645)

treatment_protocol:
Cells were infected with two different shRNAs to Wapal, or an Empty Vector control.
ESCs were infected and selected with puromcyin for 48hrs prior to chromatin generation

value: murine ESC-129 derived

tag: infected with

tag: chip-antibody


title: Input1-2


title: Input1-4


title: Input2-2

source_name: Sheared Chromatin (biological replicate 2)


title: Input2-3


title: Input2-4


title: Input1-1


title: Empty Vector 3

description: processed data file: EMPTYVECTOR_RING1B_VS_BothINPUT_normalized.wig

source_name: ESC infected with Empty Vector

value: Empty Vector

value: anti-Ring1b (Active Motif 39664)


title: Empty Vector 2


title: Empty Vector 1


title: Input2-1


title: Empty Vector 4


title: Wapal shRNA#2-4

description: processed data file: W_RING1B_VS_BOTHINPUT_normalized.wig

source_name: ESC infected with Wapal shRNA #2

value: Wapal shRNA #2


title: K5B Sample 31

value: Sperm derived embryos

value: pool of 5-7 embryos


title: Wapal shRNA#2-2


title: Wapal shRNA#2-3


title: Wapal shRNA#2-1


title: VHL input [CZE_026]

tag: strain


title: Spermatid_rep1 Sample 21


title: Wapal shRNA#1-2

source_name: ESC infected with Wapal shRNA #1

value: Wapal shRNA #1


title: Wapal shRNA#1-3


title: Wapal shRNA#1-4


title: Wapal shRNA#1-1


title: 0hDZ

city: shantou

first: chuping

last: xie

state: Guangdong

address: Guangdong shantou university road 243

country: China

institute: Shantou 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.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Supplementary_files_format_and_content: Expression analysis: Tab-delimited file with Reads Per Kilobase of exon per Megabase of library size (RPKM). Transcriptome analysis: Fasta file with contigs.

organism: Scylla paramamosain

source_name: 0 h (no V.parahaemolyticus injection)

growth_protocol: The mud crab S.paramamosain (100 g±10g) were purchased from a mariculture farm in Niutianyang, Shantou, China.The crabs were maintained at 25°C in aerated water tanks with a flow-through seawater supply. After 7 days of acclimation, these crabs were used for the infection experiments.

extract_protocol:
The hemocytes was collected from blood mixed with an equal volume of anti-coagulant solution, followed by centrifugation at800g at 4C for 20 min. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 7 days of acclimation, these crabs were used for the infection experiments. Twenty crabs were injected intramuscularly with V.parahaemolyticus at a dose of 1 × 108 cfu/100 g (This dose was chosen based on previous unpublished data) of crab. The strain of V.parahaemolyticus used in our manuscript was maintained in our lab. A second group of 20 mud crabs was injected with sterilized 0.7% NaCl at a dose of 0.1 ml/100 g of crab as a control.

tag: tissue

value: hemocytes


title: Mix

source_name: 0-24h after infection with V.parahaemolyticus (Mixture)


title: 24hVP

source_name: 24 h after V.parahaemolyticus injection


title: ER_LY2_Veh_02

city: Dublin

first: Leonie

last: Young

address: York Street

department: Surgery

country: Ireland

institute: Royal College of Surgeons, Ireland

data_processing:
The DNA sequencing was carried out on the Illumina GAII and Illumina HiSeq 2000
ChIP-seq reads were aligned to the hg19 genome using Bowtie (v0.12.9) with parameters "-m 1 -v 2 --strata --best"
Peak calling was carried out by MACS2 with a p-value cut off of 1e-03 and by linearly scaling the smaller dataset to the larger dataset (via the "--to-large" parameter).
Using the MACS2 results, a reliable peakset was produced by applying the Irreproducible Discovery Rate tool to the LetR replicates of the androstenedione treated and vehicle samples. The peak sets for the LetR androstenedione and vehicle samples were then assessed for overlapping peaks using bedtools (by at least 1bp).
Genome_build: hg19
Supplementary_files_format_and_content: There are the ChIP-seq data files in bedgraph format from the MACS2 peak calling software.

source_name: LY2 Breast Cancer Cell Line

growth_protocol: LY2 cells were grown in phenol red-free MEM with 2mM L-glutamine, 10% charcoal dextrin stripped fetal bovine serum, 50U/ml penicillin and 50ug/ml streptomycin in 37C incubator with 5% CO2.

extract_protocol: no entry

treatment_protocol: Cells were maintained in steroid depleted medium for 72 hours prior to treatment with Vehicle (10% ethanol) for 45minutes.

tag: treatment

value: Untreated

value: ER


title: 6861_methyl-seq_T cell

city: hackensack

first: Benjamin

last: Tycko

state: NJ

address: 40 prospect avenue

department: Epigenetics

institute: HUMC

description:
Bisulfite converted DNA
Targeted methyl-seq library

data_processing:
Basecalls was performed using illumina CASAVA
Trimming of adaptors, low quality base calls (quality score <30), and exclusion of short reads (<40 bp) using TrimGalore
Alignment against human reference genome GRCh37 was performed using Bismark Aligner
Read deduplication was performed using Samtools
Methylation calling was performed using Bismark Methyl Extractor
CpGs with less than 10X coverage were filtered out
SNP calling was performed using BisSNP. SNPs with less than 10X per allele, as well as C>T SNPs on negative strand were excluded, since >95% of the enriched DNA aligned to the negative strand.
ASM calling was performed with Bismark, after separating the valid SNP-containing reads by allele.
Genome_build: GRCh37
Supplementary_files_format_and_content: The methylation percentage bedgraph files were generated using Bismark Methyl Extractor outputs,   the values  represent the percentage of methylation, CpGs with less than 10X coverage were filtered out; the vcf files contains the heterozygous SNPs called by BisSNP including their coordinates,  reference and alternate alleles, as well the coverage for each allele.

source_name: T cell

extract_protocol:
Genomic DNA (500 ng) was extracted using Phenol-chloroform extraction protocol and bisulfite-converted using EZ DNA methylation kit (Zymo)
Target enrichment and libraries were prepared according to Agilent's instructions accompanying SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing kit.
Targeted bisulfite converted libraries, covering 84Mb and 3.7 million CpGs, using  SureSelectXT Methyl-Seq Target Enrichment System for Illumina Multiplexed Sequencing.

value: T cell

tag: diagnosis

value: normal


title: 7764_methyl-seq_T cell


title: ER_LY2_Veh_01


title: LY2_Input

extract_protocol:
Cells were treated and harvested for ChIP-seq as described previously (Schmidt et al, 2009, http://www.ncbi.nlm.nih.gov/pubmed/19275939). The anti-ER (sc-543) from Santa Cruz Biotechnologies was used as the antibody. Chromatin was extracted from the cells and the protein of interest, along with the DNA attached, was immunoprecipitated using the antibody attached to Dynal beads (Dynabeads® Protein A 10001D, Life Technologies). The proteins were then removed from the DNA by reverse crosslinking overnight and the DNA purified and amplified before being sequenced.
DNA libraries were generated from ChIP output DNA by adaptor ligation, gel purification, and cycles of PCR as described by Illumina.

treatment_protocol: Input libraries were harvested without further treatment


title: 5998_methyl-seq_Liver

source_name: Liver

value: Liver


title: 6788_methyl-seq_T cell


title: 5644_methyl-seq_Brain

source_name: Brain

value: Brain


title: 5984_methyl-seq_Brain

description:
Bisulfite converted DNA
Targeted methyl-seq library. Sequencing data for this library has been complemented with an additional MiSEQ run


title: 5176_methyl-seq_Placenta

source_name: Placenta

value: Placenta


title: 6003_methyl-seq_Liver


title: 5140_methyl-seq_Placenta


title: 3150_methyl-seq_Heart

source_name: Heart

value: Heart


title: 5753_methyl-seq_Brain


title: 2936_methyl-seq_Lung

source_name: Lung

value: Lung


title: 3147_methyl-seq_Heart


title: hydrostatic pressure plus perfusion replicate3

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilian University

data_processing:
Tophat v2.0, gtf from iGenomes
HTseq count
DEseq2, rlog transformed
Genome_build: hg19
Supplementary_files_format_and_content: raw count table from HTseq count and rlog transformed expression values from DEseq2

source_name: Human articular cartilage

growth_protocol: Human articular cartilage (triple arthrodesis, 16 y, male) was obtained. The study was approved by the responsible Ludwig-Maximilians-University medical center ethics committee. Chondrocytes were isolated by pronase (Roche Diagnostics GmbH, Mannheim, Germany) and collagenase (Sigma-Aldrich Co., St. Louis, USA). Isolated cells were cultured in a humidified atmosphere at 37° C, 5% CO2 until passage 2. Culture medium consisted of Dulbecco’s Modified Eagle Medium (DMEM)/F12 (1:1, Biochrom AG, Berlin, Germany), 10% fetal bovine serum (FBS) (Biochrom AG, Berlin, Germany), 1% MEM amino acids (Biochrom AG, Berlin, Germany), 25 µg/ml ascorbic acid (Sigma-Aldrich Co., St. Louis, USA), 50 IU/ml Penicillin/Streptomycin (Biochrom AG, Berlin, Germany) and 0.25 µg/ml Amphotericin B (Biochrom AG, Berlin, Germany). The cells were plated 24h prior to stimulation at a density of 106 cells/cm2 in 6-well plates

extract_protocol:
After 4 days of culture, total RNA was isolated using QiazolTM Lysis Reagent (Qiagen, Hilden, Germany) according to manufacturer’s introduction
An amount of 100 ng total RNA was first treated with double-strand specific DNAse (Fermentas Inc., Hanover. MD , United States) to remove any traces of genomic DNA. After heat-inactivation of the DNAse, cDNA was synthesized and converted to Illumina-compatible sequencing libraries with the Encore complete RNAseq kit from NuGen (NuGen, San Carlos, USA). Briefly, first strand cDNA was generated by selective priming, second strand cDNA was synthesized using dUTP and the generated double stranded cDNA was fragmented using a Covaris M220 sonicator (50W peak incident power, 20% duty factor, 200 cycles per burst, 160 sec treatment time). Then cDNA was end-repaired, ligated to Illumina-Adapters and the second-strand was selectively removed. After 18 cycles of PCR the final library was quantified

treatment_protocol: A simplified bioreactor (Fig.1) described earlier (Schröder et al., 2015), was used to culture human chondrocytes in high-density monolayer culture. In brief, loading and perfusion were applied through the same piping by pressurizing the medium directly. Parallel chambers were used for different stimulations: Perfusion (P) (n=6), hydrostatic pressure plus perfusion (HPP) (n=6) and control (C) (n=6), where cells were kept in static culture. For P and HPP, perfusion was applied with a medium flow rate of 2 ml/min for 20 h/day for 4 days. The perfusion flow rate of 2 ml /min was chosen according to cell viability tests (data not shown). In HPP, hydrostatic pressure of 0.1 MPa for 2 h (loading), followed by 2 h rest (off-loading), was applied each day. During this 4 h period perfusion was stopped in P simultaneously

tag: cell type

value: chondrocyte

tag: treatment perfusion

value: yes

tag: treatment pressure

tag: age

value: 16 years-old

tag: gender

value: male


title: HeLa; None

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
The Illumina basecalling and read generation algorithm versions were RTA 1.12.4.2 and CASAVA-1.8.2.
Gene model annotation for hg19 from Ensembl was provided to the aligner with the -G parameter.
Cufflinks v2.1.1 with hg19 UCSC genes from iGenomes was used to generate gene-level abundance estimates.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files contain Cufflinks output for gene expression

source_name: HeLa

growth_protocol: Cells were maintained according to standard procedures in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS), glucose (4.5 g/liter), and 5% CO2. Cells were split by trpsinization every 3 days. Primary cervical epithelial cells were grown in propriety Epi growth medium (Cell Applications Inc.) / 5% CO2. One day prior to lysis, Epi cells were transferred to DMEM and maintained under the same conditions as HeLa and D551 cells to account for differences arising from culture conditions.

extract_protocol:
Total cellular RNA was extracted with RNeasy Mini kit (Qiagen) in accordance with the manufacturer's instructions, prior to sequencing.
Ribosomal RNAs (rRNA) were removed from total RNA samples using Ribo-Zero™ rRNA Removal Kits (Epicentre). The total RNA samples (after depletion of rRNA) were size-fractionated on a 6% TBE-Urea polyacrylamide gel to enrich for molecules in the range of 50-400nt. Small RNA libraries and sequencing for each sample were performed by LC Sciences (Houston, TX). In brief, RNA fragments were dephosphorylated and ligated with 3′ RNA adaptor. The resulting ligated RNA fragments were reversed-transcribed and ligated with 5′ DNA/DNA adaptor and PCR amplified (15 cycles) using primers on both adaptors. Subsequently, PCR products were purified and small RNA library was sequenced on Illumina GAIIx (Illumina, Inc., Santa Clara, CA) for single-end 35-mers or on Illumina HiSeq for single-end 51-mers following the manufacturer’s protocol. Raw sequence FASTQ files were generated by using Illumina’s software pipeline..

treatment_protocol: Delivery of siRNA into HeLa cells was achieved using DharmaFECT 1 transfection reagent (Dharmacon Inc.) according to manufacturer’s instructions. TCAB1 siRNA was acquired from Qiagen (siTCAB1, SI00388941), USPL1 siRNA (sc-76875) and non-targeting control siRNA (siCon, sc-37007) from Santa Cruz. Briefly, 100nM siRNA was transfected on 2 consecutive days and cells were collected 24h after the second round of transfection.

tag: cell line

value: HeLa


title: hydrostatic pressure plus perfusion replicate1


title: hydrostatic pressure plus perfusion replicate2


title: Primary Cervical Epithelial Cells; None

source_name: Primary Cervical Epithelial Cells

value: Primary Cervical Epithelial Cells


title: HeLa; TCAB1 siRNA

value: TCAB1 siRNA


title: HeLa; Scrambled siRNA

value: Scrambled siRNA


title: perfusion replicate2

value: no


title: HeLa; USPL1 siRNA

value: USPL1 siRNA


title: perfusion replicate3


title: GH671; TCAB1kd; U1

data_processing:
Library strategy: 4C-Seq
The 4C libraries were barcoded and pooled together ran on a HiSeq2000 lane using V3 chemistry.
The barcoded samples are demultiplexed, and separated by each bait primer types.
Reads are filtered and trimmed based on bait sequences and followed the 4C data processing procedure that we have used for your previous data set.
The trimmed reads are aligned against hg19 reference genome using Bowtie V0.12.8 program with --phred33-quals -v2 --all --best --strata -m -q options. Only unique alignments are stored in the BAM files.
Genome_build: hg19

growth_protocol: Cells were maintained according to standard procedures in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% (v/v) fetal bovine serum (FBS), glucose (4.5 g/liter), and 5% CO2. Cells were split by trpsinization every 3 days.

extract_protocol:
Cultured HeLa cells were cross-linked in 2% formaldehyde at 37°C for 10min. After being quenched with glycine, cells were lysed using 10mM Tris-HCl, pH8.0, 10mM NaCl, 0.2% NP-40) supplemented with 1× complete protease inhibitors (Sigma) at 4°C for 1 h.
Cross-linked chromatin was digested overnight with an excess of HindIII enzyme (New England Biolabs), and then DNA ends were ligated under diluted conditions that favor junctions between cross-linked DNA fragments. NlaIII (New England Biolabs) was used in a second round of digestion, and DNA was re-ligated. 4C DNA samples were barcoded and sequenced on Illumina HiSeq 2000 according to the Illumina paired-end 100 bp sequencing protocol.

treatment_protocol: Delivery of siRNA into HeLa cells was achieved using DharmaFECT 1 transfection reagent (Dharmacon Inc.) according to manufacturer’s instructions. TCAB1 siRNA was acquired from Qiagen (siTCAB1, SI00388941) and non-targeting control siRNA (siCon, sc-37007) from Santa Cruz. Briefly, 100nM siRNA was transfected on 2 consecutive days and cells were collected 24h after the second round of transfection.

value: siRNA

tag: primer sequence

tag: bait type


title: perfusion replicate1


title: GH671; TCAB1kd; H3F3


title: D551; None


title: control replicate3


title: control replicate2


title: control replicate1


title: GH668; TCAB1kd; U1


title: OMT916645 exosome

first: Chi Lam

last: Au Yeung

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description: small RNA

data_processing:
Ion Torrent reads were collected using Ion Torrent Suite software, which also sorted the data according to the barcodes.
The software scores the quality of the reads by assigning Q17 and Q20 scores according to the quality scoring computation.
Fastq files from the Ion Torrent server were imported to the CLC Genomics Workbench (version 5.1; Life Technologies Corp.).
Sequence reads were trimmed to remove reads with ambiguous nucleotides and to create a sequence length of 15 to 55 nucleotides. Trimmed sequence reads were aligned to a miRNA database (miRBase, release 18). Mapped reads were annotated and counted.
Genome_build: hg19
Supplementary_files_format_and_content: Ion Torrent reads were then normalized to the number of cells in each cell line used for exosome collection and presented as the total reads per 1000 cells in xlsx files.

source_name: Cancer-associated adipocytes

extract_protocol:
Exosomes were isolated from the conditioned medium by differential ultracentrifugation. Total RNAs were extracted from purified exosomes using the RNAqueous-Micro kit (Thermo Fisher Scientific), and the amount and quality of small RNA in the total RNA samples were determined using the Agilent small RNA kit on an Agilent 2100 Bioanalyzer. Five nanograms of small RNAs were subjected to library construction.
Library was constructed using the Ion Total RNA-Seq kit v2 (Life Technologies Corp.), according to the small RNA protocol.

value: Cancer-associated adipocytes

tag: sample type

value: exosome


title: GH670; WT; U1


title: OMT924007 exosome

description: small RNA


title: GH667; WT; U1


title: GH667; WT; H3F3


title: Histamine blockade pre exercise [HIST_7_pre]

city: Eugene

first: John

last: Halliwill

state: OR

address: 1370 Franklin Blvd

institute: University of Oregon

data_processing:
.fastq.gz files: Raw, demultiplexed sequence files produced by Illumina HiSeq Control Software 2.2.58 and CASAVA 1.8.2
Sequencing and basecalling by Illumina HiSeq Control Software 2.2.58
BCL conversion and demultiplexing by Illumina CASAVA 1.8.2
FASTQ files aligned to Homo_sapiens.GRCh38.dna.toplevel.fa genome assembly obtained from ENSEMBL.  The Homo_sapiens.GRCh38.78.gtf file from ENSEMBL was used for annotation.  Alignments were performed with STAR 2.4.0i.
Gene count tables were generated from STAR-produced SAM files using HTSeq-count 0.6.1
Genome_build: Homo_sapiens.GRCh38.dna.toplevel.fa
Supplementary_files_format_and_content: .counts.txt files: Gene count tables generated by HTSeq-count from each .sam file for each sample

source_name: Histamine blockade subject biopsy pre exercise

extract_protocol:
Trizol RNA extraction protocol (Thermo Fisher)
Kapa Biosystems Stranded mRNA Seq kit

tag: subject id

value: subject 7

tag: subject group

value: received combined H1/H2-histamine receptor blockade prior to exercise

tag: time point

value: pre exercise

value: vastus lateralis muscle


title: CAF888242 exosome

description: small RNA

source_name: Cancer-associated fibroblasts

value: Cancer-associated fibroblasts


title: siCon_Replicate2

data_processing:
The Illumina basecalling and read generation algorithm versions were RTA 1.12.4.2 and CASAVA-1.8.2.
Raw reads were trimmed before alignment. The trimming software used was ea-utils FasqMcf software (http://code.google.com/p/ea-utils/wiki/FastqMcf Expression Analysis Inc., Durham, NC).  The trimming parameters used were: -l 15 -q 0 -u -P 33 (minimum retained sequence length = 15, quality threshold causing base removal = 0, enable Illumina PF filtering, Phred 33 scale).
Trimmed reads were mapped to the hg19 reference genome with TopHat v.2.0.860, accepting only unique alignments (parameters -g 1 -r 10 --mate-std-dev 100), with the Bowtie2 alignment engine
Gene model annotation for hg19 from Ensembl was provided to the aligner with the -G parameter.
Cufflinks v2.1.1 with hg19 UCSC genes from iGenomes was used to generate gene-level abundance estimates.
Genome_build: hg19
Supplementary_files_format_and_content: fpkm_tracking files contain Cufflinks output for gene expression

extract_protocol:
Total cellular RNA was extracted with RNeasy Mini kit (Qiagen) in accordance with the manufacturer's instructions, prior to sequencing.
Libraries were generated with the Illumina Truseq mRNA protocol (Illumina, San Diego, CA) and TruSeq sample prep kits (catalog ID: FC-122-1001). Libraries were sequenced on a HiSeq2000 instrument (Illumina, San Diego, CA) for 2x101 cycles, generating 101bp paired end reads. All samples were run on the same flowcell, multiplexed with 4 samples per lane.


title: siTCAB1_Replicate2


title: Histamine blockade immediately after exercise [HIST_7_immediate]

source_name: Histamine blockade subject biopsy immediately after exercise

value: immediately after exercise


title: Histamine blockade pre exercise [HIST_5_pre]

value: subject 5


title: CAF866652 exosome

description: small RNA


title: Histamine blockade post exercise [HIST_5_post]

source_name: Histamine blockade subject biopsy 3 hours after exercise

value: 3 hours after exercise


title: CAF869881 exosome

description: small RNA


title: Histamine blockade immediately after exercise [HIST_5_immediate]


title: NOF151 exosome

description: small RNA

source_name: Normal fibroblasts

value: Normal fibroblasts


title: Histamine blockade pre exercise [HIST_4_pre]

value: subject 4


title: siTCAB1_Replicate1

value: TCAB1 siRNA

value: HeLa


title: NOF810000 exosome

description: small RNA


title: GH670; WT; H3F3


title: SKOV3 exosome

description: small RNA

source_name: Ovarian cancer SKOV3 cells

value: Ovarian cancer SKOV3 cell line


title: Histamine blockade post exercise [HIST_4_post]


title: siCon_Replicate1

value: Scrambled siRNA


title: Histamine blockade post exercise [HIST_7_post]


title: OMN050312 exosome

description: small RNA

source_name: Normal adipocytes

value: Normal adipocytes


title: Histamine blockade immediately after exercise [HIST_4_immediate]


title: Histamine blockade pre exercise [HIST_2_pre]

value: subject 2


title: siUSPL1_Replicate2

value: USPL1 siRNA


title: A2780 exosome

description: small RNA

source_name: Ovarian cancer A2780 cells

value: Ovarian cancer A2780 cell line

value: exosome


title: ER_LET-R_Veh_02

data_processing:
The DNA sequencing was carried out on the Illumina GAIIx and Illumina HiSeq 2000
ChIP-seq reads were aligned to the hg19 genome using Bowtie (v0.12.9) with parameters "-m 1 -v 2 --strata --best"
Peak calling was carried out by MACS2 with a p-value cut off of 1e-03 and by linearly scaling the smaller dataset to the larger dataset (via the "--to-large" parameter).
Using the MACS2 results, a reliable peakset was produced by applying the Irreproducible Discovery Rate tool to the replicates of the androstenedione treated and vehicle samples. The peak sets for the androstenedione and vehicle samples were then assessed for overlapping peaks using bedtools (by at least 1bp).
This produced three peaks lists : 1) Androstenedione only peaks, 2) Vehicle only peaks and 3) Overlapping peaks between Androstenedione and Vehicle peaksets. They are represented as bed files
Genome_build: hg19
Supplementary_files_format_and_content: There are the ChIP-seq data files in bedgraph format from the MACS2 peak calling software.And there are bed files for the three peak lists: 1) Androstenedione only peaks, 2) Vehicle only peaks and 3) Overlapping peaks between Androstenedione and Vehicle peaksets

growth_protocol: Estrogen receptor positive MCF-7 breast cancer cells were obtained from American Type Culture Collection (ATCC). MCF-7 cells were stably transfected with the aromatase gene (CYP19) (Invitrogen, Paisley, UK) to generate aromatase inhibitor sensitive cells (Aro cells). Letrozole-resistant (LetR) cells were then generated by long-term (>3 months) culture of Aro cells with letrozole (10-6M; Novartis, Switzerland) and androstenedione (25 x 10-5 mol/L; Sigma Aldrich) in MEM supplemented with 10% charcoal-dextran-stripped FCS, 1% L-Glutamine, 1% Pen/Strep, and 200 mg/mL Geneticin (G418, Gibco Invitrogen).  All cells were maintained at 37degreesCelcius, 5% CO2 in a humidified incubator.

treatment_protocol: Cells were maintained in steroid depleted medium for 72 hours prior to treatment with androstenedione (10-7 M; Sigma Aldrich, St. Louis, MO, USA) or Vehicle (10% ethanol) for 45minutes.

value: Let-R

value: Letrozole-resistant breast cancer cells

tag: treated with

value: 10% ethanol (vehicle control) for 45min

tag: chip antibody

value: anti-ER

tag: chip antibody vendor

value: Santa Cruz Biotechnologies

tag: chip antibody cat. #


title: ER_LET-R_Veh_01


title: HeyA8 exosome

description: small RNA

source_name: Ovarian cancer HeyA8 cells

value: Ovarian cancer HeyA8 cell line


title: GH668; TCAB1kd; H3F3

tag: treatment

value: siRNA


title: Histamine blockade immediately after exercise [HIST_2_immediate]

value: received combined H1/H2-histamine receptor blockade prior to exercise

value: immediately after exercise

tag: tissue

value: vastus lateralis muscle


title: Histamine blockade post exercise [HIST_2_post]

value: 3 hours after exercise


title: OVCA433 exosome

description: small RNA

source_name: Ovarian cancer OVCA433 cells

tag: cell type

value: Ovarian cancer OVCA433 cell line


title: Histamine blockade post exercise [HIST_15_post]

value: subject 15


title: Histamine blockade pre exercise [HIST_12_pre]

value: subject 12

value: pre exercise


title: Histamine blockade immediately after exercise [HIST_15_immediate]


title: Histamine blockade pre exercise [HIST_17_pre]

value: subject 17


title: Histamine blockade post exercise [HIST_17_post]


title: siUSPL1_Replicate1

value: USPL1 siRNA

value: HeLa


title: Histamine blockade immediately after exercise [HIST_17_immediate]


title: Histamine blockade pre exercise [HIST_15_pre]


title: Histamine blockade immediately after exercise [HIST_12_immediate]


title: Histamine blockade post exercise [HIST_11_post]

value: subject 11


title: Histamine blockade immediately after exercise [HIST_11_immediate]


title: Histamine blockade post exercise [HIST_12_post]


title: Histamine blockade pre exercise [HIST_11_pre]


title: Control immediately after exercise [CON_9_immediate]

source_name: Control subject biopsy immediately after exercise

value: subject 9

value: control


title: Control pre exercise [CON_8_pre]

source_name: Control subject biopsy pre exercise

value: subject 8


title: Control post post exercise [CON_8_post]

source_name: Control subject biopsy 3 hours after exercise


title: Control post post exercise [CON_9_post]


title: Control pre exercise [CON_4_pre]

value: subject 4


title: Control immediately after exercise [CON_5_immediate]

value: subject 5


title: Control pre exercise [CON_5_pre]


title: Control immediately after exercise [CON_8_immediate]


title: Control post post exercise [CON_5_post]


title: Input_control

value: Let-R

value: Letrozole-resistant breast cancer cells


title: ER_LET-R_Andro_01

value: Androstenedione for 45min

value: anti-ER

value: Santa Cruz Biotechnologies


title: Control post post exercise [CON_4_post]

value: 3 hours after exercise

value: vastus lateralis muscle


title: Control immediately after exercise [CON_4_immediate]

value: immediately after exercise


title: Control post post exercise [CON_3_post]

value: subject 3


title: OMN923075 exosome

description: small RNA

value: Normal adipocytes

value: exosome


title: Control immediately after exercise [CON_3_immediate]


title: Rib cartilage from 8-week old mouse

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: mouse tissue

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
The sequence reads were mapped to mm9 reference genomes, downloaded on 25th April 2014, using Tophat v2.0.14. Calculation of gene expression value and normalization were performed by RPKMforgenes (10th, Dec, 2012).
Genome_build: mm9
Supplementary_files_format_and_content: Output from RPKMforgenes software.

source_name: rib cartilage

growth_protocol: Primary chondrocytes of Col11a2-CreER; Sik3flox/flox mice were cultured in DMEM, 10% FBS medium for 5 days on the culture dish.

extract_protocol:
RNAs was extracted from these cultured chondrocyte pellets using QIAzol Lysis Reagent (Qiagen) and the miRNeasy Mini Kit (Qiagen). RNAs were also extracted from various mouse tissues.
One hundred (rib cartliage) or two hundreds (the others) ng of total RNA was subjected to library preparation using KAPA stranded mRNA-seq Kits (KAPA Biosystems, Woburn, MA), according to manufacturer’s instruction. The libraries were sequenced in 101 cycle Single-Read mode of HiSeq2500.

treatment_protocol: These chondrocytes were centrifuged and incubated in the tubes for 3 days. The resulting cell pellets were incubated in the same medium in the presence or absence of 300 µM pterosin B for further 4 weeks.

value: rib cartilage

value: 8 weeks

tag: strain


title: Calvarium from 8-week old mouse

description: mouse tissue

source_name: cranial bone

value: cranial bone

tag: age


title: Control pre exercise [CON_20_pre]

value: subject 20

value: control

value: pre exercise


title: Control post post exercise [CON_20_post]


title: Control pre exercise [CON_9_pre]

value: subject 9


title: Skeletal muscle from 8-week old mouse

description: mouse tissue

source_name: skeletal muscle

value: skeletal muscle


title: Testis from 8-week old mouse

description: mouse tissue

source_name: testis

value: testis


title: Skin from 8-week old mouse

description: mouse tissue

source_name: skin

value: skin


title: Control immediately after exercise [CON_16_immediate]

value: subject 16


title: Small intestine from 8-week old mouse

description: mouse tissue

source_name: small intestine

value: small intestine


title: Kidney from 8-week old mouse

description: mouse tissue

source_name: kidney

value: kidney


title: ER_LET-R_Andro_02

value: Let-R

value: Letrozole-resistant breast cancer cells

value: Androstenedione for 45min

value: anti-ER

value: Santa Cruz Biotechnologies


title: Liver from 8-week old mouse

description: mouse tissue

source_name: liver

value: liver

value: 8 weeks


title: Control post post exercise [CON_13_post]

value: subject 13

value: 3 hours after exercise

value: vastus lateralis muscle


title: Heart from 8-week old mouse

description: mouse tissue

source_name: cardiac muscle

value: cardiac muscle


title: Control pre exercise [CON_13_pre]

value: control

value: pre exercise


title: Spinal cord from 8-week old mouse

description: mouse tissue

source_name: spinal cord

value: spinal cord


title: Control immediately after exercise [CON_13_immediate]

value: immediately after exercise


title: Control pre exercise [CON_3_pre]

value: subject 3


title: Brain from 8-week old mouse_2

description: mouse tissue

source_name: cartilage

value: cartilage


title: Brain from 8-week old mouse_1

description: mouse tissue

source_name: brain

value: brain


title: Control rep3

city: Nanjing

first: Bing-Mei

last: Zhu

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing university of Chinese Medicine

description: Sample 8

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC RN4 whole genome using tophat v2.0.6
Differential gene and transcript expression analysis using a protocol from Cole Trapnell et al., nature protocols, 2012.
Genome_build: Rattus_norvegicus_UCSC_rn4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Rattus norvegicus

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

tag: mouse weight

tag: gender

value: male

tag: sample group

value: heart; myocardium


title: Control rep1

description: Sample 6


title: Long bone from 8-week old mouse

description: mouse tissue

source_name: long bone

value: long bone


title: Mouse chondrocyte pellet culture in the presence of pterosin B, sample 2

description: Primary chondrocytes from Col11a2-CreER; Sik3flox/flox mice were used

value: chondrocyte

tag: genotype

value: Col11a2-CreER; Sik3flox/flox


title: Mouse chondrocyte pellet culture in the presence of pterosin B, sample 5


title: Control rep2

description: Sample 7


title: Control post post exercise [CON_16_post]

value: subject 16


title: Mouse chondrocyte pellet culture in the absence of pterosin B, sample 5


title: EA rep3

description: Sample 5

value: MI + electro-acupuncture (EA)


title: Mouse chondrocyte pellet culture in the absence of pterosin B, sample 2


title: EA rep2

description: Sample 4


title: MI rep1

description: Sample 1

source_name: myocardial ischemia_myocardium

value: myocardial ischemia (MI)


title: MI rep2

description: Sample 2


title: Mouse chondrocyte pellet culture in the presence of pterosin B, sample 1


title: Mouse chondrocyte pellet culture in the absence of pterosin B, sample 1


title: EA rep1

description: Sample 3


title: Taf4a-/- EB8 rep2

status: Public on Mar 20 2016

city: Illkirch

first: diana

last: langer

address: 1 rue laurent fries

country: France

institute: IGBMC

description: Sample 16

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.9 and CASAVA 1.7 (Samples 3,5 and 7) or CASAVA 1.8 (other samples)
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v2.0.10
Quantification : Gene expression was quantified using HTSeq v0.5.4p3 and annotations from Ensembl release 67
Normalization : Data normalization was performed with DESeq2 v1.0.19 Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, one column for each sample containing normalized read counts, gene name and description.

source_name: neural precursor cells

growth_protocol: ES cells were cultured on inactivated MEF feeders under standard conditions (DMEM 4.5g/l glucose/Glutamax supplemented with 15% heat inactivated FCS, LIF, nonessential amino acids and β-mercaptoethanol).

extract_protocol:
Total RNA from ES cells or embryoid bodies was isolated using the GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
Libraries of template molecules suitable for high throughput DNA sequencing were created using “TruSeq™ RNA Sample Preparation v2 Kit” (Illumina). Briefly, mRNA was purified from 120-150 ng of total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters were generated in the Cbot and sequenced in the Illumina GAIIx as single-end 54 base reads.

treatment_protocol: Cells were differentiated by RA into neurons as described (Bibel et al 2007).

tag: genotype/variation

value: neural precursor cells (EB8)


title: Control pre exercise [CON_16_pre]

source_name: Control subject biopsy pre exercise

tag: subject id

value: control

value: vastus lateralis muscle


title: Taf4a-/- EB5 rep2

description: Sample 14

source_name: differentiating ES cells

value: differentiating ES cells (EB5)


title: Taf4a-/- EB8 rep1

description: Sample 15


title: Taf4a-/- EB5 rep1

description: Sample 13


title: Taf4a-/- EB4 rep2

description: Sample 12

value: differentiating ES cells (EB4)


title: Taf4a-/- ES rep2

description: Sample 10

source_name: ES cells

value: ES cells


title: Taf4a-/- EB4 rep1

description: Sample 11


title: Taf4a-/- ES rep1

description: Sample 9


title: Wapal_rep2

data_processing:
Samples were sequenced on Illumina HiSeq 2000
Alignment to the mouse genome build mm9 was performed using Bowtie with parameters -n 2 -q  -m 1 -l 49 -e 70 -k 1 --best
Peak calling was done using MACS14 1.4.2 with pvalue 1e-5
Genome_build: mm9
Supplementary_files_format_and_content: bed and Wiggle files were generated using MACS14

source_name: Embryonic stem cells

extract_protocol:
Briefly, cells were crosslinked for 5 min at room temperature with 1% fresh formaldehyde.  Reaction was quenched with glycine (125 mM final concentration) for 5 min at room temperature.  Cells were lysed in 0.1% SDS lysis buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH8.0,150 mM NaCl).  Chromatin was sonicated to a mean size of 300-500bp. Lysed cells were cleared by centrifugation and added to to 50 μL of Streptavidin Dynal Beads (Life Techniologies, Cat #65601).  ψBeads were isolated with a magnet and then washed with SDS Buffer ( 2% SDS) x2, High Salt ( 0.1% Deoxycholate, 1% Triton X-100, 1mM EDTA, 50 mM Hepes, 7.5, NaCl 500 mM), LiCl wash (250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.0), and TE x2.  DNA was eluted and decrosslinked overnight at 65 oC in SDS Elution Buffer (1% SDS, 10mM EDTA, 50 mM Tris-HCl pH 8.0). The next day RNase A and proteinase K were added, and the DNA was precipitated in the presence of glycogen.  DNA for downstream applications were quantitated by flourometry (Qubit, Invitrogen), and equal DNA was used for each ChIP-qPCR and normalized to sheared, non-IP’d genomic DNA (Input).
The BioScientific NEXTFlex ChIp-seq kit was used.

treatment_protocol: ESCs were engineered to express a biotinylatable version of Wapal

value: ESC

tag: cell type modification

tag: chromatin pulldown


title: Input

value: engineered to express a biotinylatable version of Wapal


title: BirA

value: expresses BirA ligase (BirA cells are a negative control- they are equivalent to an IgG only control)


title: WT EB8 rep1

description: Sample 7


title: WT EB5 rep2

description: Sample 6


title: WT EB8 rep2

description: Sample 8


title: WT EB4 rep2

description: Sample 4


title: WT EB5 rep1

description: Sample 5


title: Wapal_rep1

value: Streptavidin Dynal Beads (Life Techniologies, Cat #65601)


title: WT EB4 rep1

description: Sample 3


title: Taf4a-/- Cardiac differentiation day 9 rep1

description: Sample 3

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.9 and CASAVA 1.8
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v1.3.3
Quantification : Gene expression was quantified using HTSeq v0.5.3p1 and annotations from Ensembl release 64
Normalization : Data normalization was performed with DESeq Bioconductor package
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, one column for each sample containing normalized read counts, gene name and description

source_name: cardiac cells

extract_protocol:
Total RNA was isolated using the GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich)
Libraries of template molecules suitable for high throughput DNA sequencing were created using “TruSeq™ RNA Sample Preparation v2 Kit” (Illumina). Briefly, mRNA was purified from 1 µg of total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 15 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 7pM concentration and clusters were generated in the Cbot.

treatment_protocol: For differentiation into cardiomyocytes, cells were grown as EBs in EB medium containing 20% heat inactivated FCS and cultured for 5 days. EBs were then transferred to gelatin-coated plates and cultured for 9 more days

tag: time

value: day 9 of the differentiation into the cardiac lineage

value: cardiac cells


title: WT ES rep2

description: Sample 2


title: WT ES rep1

description: Sample 1


title: Taf4a-/- Cardiac differentiation day 9 rep2

description: Sample 4


title: WT Cardiac differentiation day 9 rep1

description: Sample 1


title: WT Cardiac differentiation day 9 rep2

description: Sample 2


title: 287_ss_rt

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

institute: University of Alberta

data_processing:
Alignment to Genome with Tophat2
Alignment output piped to Ht-seq-count
Reads mapped were normlized into counts per million
Differential analysis was performed using edgeR
Functional anlaysis with Ingenuity Pathway Anlaysis
Genome_build: umd3.1
Supplementary_files_format_and_content: csv files, content is normalized expressional abundance of each gene each animal

organism: Bos taurus

source_name: rectal tissue

extract_protocol:
Two 2 cm2 biopsies 3-5 cm proximal to the rectal-anal junction were collected from each animal and immediately flash frozen in liquid nitrogen within 10 min after death of the animal. Samples were stored at -80 °C until RNA was extracted. 100 mg of powdered rectal tissue was used for RNA extraction using a mirVana total RNA Isolation Kit
Illumina truseq_stranded_total_rna_sample_preparation kit

treatment_protocol: Cattle with two phenotypes, one is negative for E. coli O157, one is shedding > 10^4 CFU E. coli O157/g of feces

value: rectum

tag: phenotypes

value: Super-shedders


title: 299_ss_rt


title: 310_ss_rt


title: 274_ss_rt


title: 242_ns_rt

value: negative for E. coli O157


title: F3m

city: Irvine

first: Geraint

last: Parfitt

state: California

address: 843 Health Sciences Rd

department: Ophthalmology

institute: University of California, Irvine

data_processing:
Fastq sequencing files were evaluated for quality using RobiNA software.
Using Tuxedo, sequences were aligned to the reference genome from using the TopHat module.
The Cufflinks module was then used to assemble transcripts.
Differential gene expression analysis was performed using CyberT.
Genome_build: mm10
Supplementary_files_format_and_content: Table S1_expressed genes.xlsx: Abundance measurements
Supplementary_files_format_and_content: Table S3 cyber Tresults.xlsx: Differential gene expression

extract_protocol:
Eyelids were excised, frozen in liquid nitrogen and RNA isolated using a Qiagen RNAeasy columns.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

value: Female

value: 3 months old

value: Lower Eyelid


title: M2y

value: Male

value: 2 years old


title: M3m


title: 165_ns_rt


title: H3K27ac_ESKO

first: Igor

last: Martianov

address: 1 rue Laurent Fries

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie v0.12.7 with the following parameters -m 1 --strata --best.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

source_name: TAF4-/- Escells

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent). The libraries were loaded in the flow cell at 8pM concentration and clusters were generated in the Cbot and sequenced in the Illumina Hiseq 2500 as single-end 50 base reads.

value: embryonic stem cells (ESC)

tag: chip antibody

value: H3K27ac (39133, Active Motif)


title: H3K4Me3_ESwt

source_name: wt ES cells

value: wt

value: anti-H3K4Me3 (04-745, Millipore)


title: H3K27ac_EB8wt

source_name: wt EB8

value: embryoid bodies (EB)


title: H3K4Me3_EB8wt


title: TBP_EB8wt

value: TBP (ab28175, Abcam)


title: H3K27ac_EB8KO

source_name: TAF4-/- EB8


title: TBP_EB8KO


title: F2y


title: 294_ss_rt


title: H3K4Me3_EB8KO


title: PolII_EB8KO

value: Pol II (sc-9001x, Santa Cruz)


title: TBP_ESwt


title: TBP_ESKO


title: PolII_EB8wt


title: H3K4Me3_ESKO


title: 108_ns_rt


title: 152_ns_rt


title: H3K27ac_ESwt


title: TFIIB_EB8KO

value: TFIIB (sc225x, Santa Cruz)


title: TFIIB_EB8wt


title: TFIIB_ESwt


title: TFIIB_ESKO


title: Emu-Myc 146a-/-, sample 2

city: LOS ANGELES

first: Dinesh

middle: S

address: 750 CHARLES E YOUNG DRIVE, 12-272 FACTOR

department: PATHOLOGY AND LABORATORY MEDICINE

institute: UCLA

data_processing:
Reads were aligned to the Mus musculus genome (mm10 build) using STAR v2.3.0 (Dobin et al. doi:10.1093/bioinformatics/bts635) in supervised mode using the Ensemble GRCm38.71 gene annotation as template. Relevant alignment parameters are: --outFilterMultimapScoreRange 0.75  --outFilterMultimapNmax 100 --outFilterMismatchNmax 25 --outFilterScoreMinOverLread 0.75 --outFilterMatchNminOverLread 0.75 --outFilterMismatchNoverLmax 0.25 --sjdbOverhang 99
HTSeq-count v0.5.4p3 (Simon Anders, http://www-huber.embl.de/users/anders/HTSeq/) was used to compute the matrix of raw counts (relevant paramters: --mode=intersection-strict). After pooling the counts for technical replicates, this matrix was used as input for DESeq v1.12.1 to assess pair-wise differential expression with "per-condition" expression estimates. Finally, moderate fold-changes (mfc) between two experimental conditions were computed from variance stabilized data (as provided by DESeq with "pooled" dispersion estimates). Genes were tagged as differentially expressed if abs(mfc)>.7 and Benjamini-Hochberg adjusted p-value <0.05.
Genome_build: GRCm38.71/mm10
Supplementary_files_format_and_content: Per sample expression estimates in units of RPKMs

source_name: Emu-Myc 146a-/-_tumor cells_thymic tumor

growth_protocol: Tumors were made into single cell suspensions, and were immediately frozen in Trizol.

extract_protocol:
Total RNA was isolated using Trizol extraction
Single-end RNA libraries were prepared for sequencing using standard Illumina protocols. Two technical replicates were generated for each individual tumor sample

treatment_protocol: Cells were lysed by resuspension in Trizol

value: female

value: Myc tg; miR-146a-/-

value: 10 weeks

tag: tumor site

value: thymus

value: tumor cells


title: Emu-Myc 146a-/-, sample 1

value: 11 weeks


title: Emu-Myc 146a+/+, sample 3

source_name: Emu-Myc 146a+/+_tumor cells_thymic tumor

value: male

value: Myc tg; miR-146a+/+


title: Emu-Myc 146a+/+, sample 4


title: NA  rep2

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC RN4 whole genome using tophat v2.0.6
Differential gene and transcript expression analysis using a protocol from Cole Trapnell et al., nature protocols, 2012.
Genome_build: rn4
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: myocardium

value: Sprague Dawley

value: heart

tag: weight


title: I/R  rep2

tag: tissue


title: EA  rep2


title: SO rep2


title: I/R  rep1


title: NA  rep1


title: Emu-Myc 146a+/+, sample 2

source_name: Emu-Myc 146a+/+_tumor cells_neck node

value: 16 weeks

value: neck node

tag: cell type


title: SO rep1

tag: strain


title: Emu-Myc 146a+/+, sample 1

tag: age

value: 18 weeks


title: PolII_ESKO

value: embryonic stem cells (ESC)


title: PolII_ESwt

value: wt


title: M12 cell line reverted to non-tumorigenic cell line through microcell-mediated chromosomal transfer

status: Public on Mar 19 2016

city: Richmond

first: Sarah

middle: J

last: Seashols-Williams

state: VA

address: 1015 Floyd Ave Box 843079

department: Forensic Science

institute: Virginia Commonwealth University

data_processing:
basecalling and demultiplexed by Illumina software
Quality and adaptor trimming in Partek Flow using an miRNA pipeline, increased match times to 3.
Sequences with PHRED score >30 and of appropriate size were aligned to the human genome (GRCh38) using Bowtie 1.0, seed mismatch of 1, alignments per read of 3.
Data annotated to miRbase 21, mature v2.
Genome_build: human genome GRCh38. miRbase v21, mature v2.
Supplementary_files_format_and_content: CSV file of all samples sequenced, raw aligned and annotated sequence reads

source_name: prostate tissue

growth_protocol: P69, M2182, M12 cell lines:  Bae et al.  Prostate. 1998 Mar 1;34(4):275-82.  F6 cell line: Astbury et al. Genes Chromosomes Cancer. 2001 Jun;31(2):143-55.

extract_protocol:
miRVANA RNA Isolation for small RNA, elution in 200 uL.  RNA concentration and quality determined through Bioanalyzer Small RNA chip.
Illumina TruSeq Small RNA sample preparation kits

tag: cell line

tag: tumorigenic

value: no

value: non-metastatic subline reverted from M12

tag: molecule subtype

value: small RNA


title: non-metastatic human prostate cell line, replicate 2

value: non-metastatic human prostate cell line


title: metastatic prostate subline, replicate 2

value: yes

value: tumorigenic derivative cell line


title: non-metastatic human prostate cell line, replicate 1


title: Sample uninfected (ISE6-U2)

city: Ciudad Real

first: Jose

last: De La Fuente

state: Ciudad Real

address: Ronda de Toledo s/n

country: Spain

institute: SaBio. Instituto de Investigación en Recursos Cinegéticos IREC-CSIC-UCLM-JCCM

data_processing:
Reads were mapped using Tophat 2.1.0
Small RNA library preparation but strand specific data for Ixodes scapularis unavailable, so the reads were mapped to the reference genome as if they were from a normal RNAseq experiment. Thus we obtained reads mapping to coding sequences (protein coding and miRNA coding as well) and also to non coding regions.
Transcripts assembly and abundance estimation performed using Cufflinks 2.2.1
Analysis of differentially expressed genes was performed using Cufflinks 2.2.1
Genome_build: JCVI_ISG_i3_1.0 (NZ_ABJB000000000)
Supplementary_files_format_and_content: GTF2 files generated with Cufflinks.  Columns: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> <FPKM values are included in the last column of the file>

organism: Ixodes scapularis

source_name: ISE6 cells, uninfected

growth_protocol: The I. scapularis embryo-derived tick cell line ISE6 was cultured in L-15B300 medium as described previously (Blouin et al. (2003) Vet. Parasitol 111, 247-260), except that the osmotic pressure was lowered by the addition of one-fourth sterile water by volume. Tick cells were inoculated with A. phagocytophilum (human NY18 isolate) cells as described previously (Munderloh et al. (1999) J. Clin. Microbiol 37, 2518-2524; de la Fuente et al. (2005) Cell. Microbiol 7, 549–559). Uninfected and infected cultures with approximately 107 cells each were sampled at 12 days post-infection (dpi) (percent infected cells 68-73% (Ave±SD, 70±3). The percentage of cells infected with A. phagocytophilum was calculated by examining at least 200 cells using a 100x oil immersion objective.

extract_protocol:
miRNA was extracted using a Purelink miRNA isolation kit (Invitrogen) following manufacturers recommendations. Quality check of all samples was carried out using the Agilent 2100 Bioanalyzer with the Small RNA kit (Agilent) to determine sample quality and concentration of miRNA in each sample. The four samples passed internal QC with good bioanalyzer profiles and enough miRNA in each sample to proceed with library construction.
The libraries were prepared using the TruSeq Small RNA Sample Prep Kit (Illumina), where the miRNA samples were subjected to ligation of the 3’ and 5’ adapters, and reverse transcription. Unique barcodes were incorporated during the PCR enrichment step to ensure sufficient amount of library is generated. Adapter dimers were removed and the small RNA libraries were purified by PAGE. Resulting libraries were run on the Agilent Bioanalyzer with the DNA High Sensitivity Chip to determine library concentration and size distribution profile. Real-time quantification (KAPA qPCR quantification for Illumina systems) was performed to quantify the libraries prior to sequencing on the the most advanced Illumina platform the NextSeq 500, which uses two channel chemistry to reduce the sequencing time while maintaining unparallel accuracies of the data. Samples with different barcodes are pooled together prior to sequencing but were be separated post sequencing through demutiplexing. Resulting miRNA-seq single end reads and Bcl files were converted to Fastq data immediately after the run and used to generate Cufflinks output

treatment_protocol: The cells were centrifuged at 10,000 g for 3 min, and cell pellets were frozen at -80C until used for miRNA extraction

tag: infection

value: uninfected


title: metastatic prostate subline, replicate 1


title: Sample uninfected (ISE6-U4)

value: I. scapularis embryo-derived tick cell line ISE6