title: shGFP

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

data_processing:
geneExpressionMatrix.xlsx: Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
repetitiveElementExpressionMatrix.xlsx: Helicos Basic pipeline for alignment to the genome followed by PASA method of coverage computation (Kim, Wittner, Amzallag, et al., in preparation) followed by summing coverage in regions and dividing by average read length
Genome_build: mm9
Supplementary_files_format_and_content: geneExpressionMatrix.xlsx: Transcript abundances as determined by smsDGE described in Pubmed ID 19581875 (i.e., the RMC column of the output of the Helicos Digital Gene Expression pipeline run using the Mouse.Txome reference file). Columns correspond to samples and rows correspond to genes.
Supplementary_files_format_and_content: repetitiveElementExpressionMatrix.xlsx: Estimate of number of reads originating from all genomic locations annotated by a certain repetitive element class. Columns correspond to samples and rows correspond to a repClass/repRamily/repName as defined by the mm9 table rmsk from UCSC's table browser. ID_REFs are annotated in repetitiveElementPlatform.xlsx.

source_name: embryonic stem cells

growth_protocol: Mouse embryonic stem cells ES-D3 were obtained from ATCC. ES-D3 cells were grown on γ-irradiated feeder layer in DMEM supplemented with 15% FBS, 10 ng/ml Leukemia Inhibitory Factor (LIF, Millipore), 1x MEM Non-Essential Amino Acids (Gibco), 0.1 mM β-Mercaptoethanol, 2 mM L-glutamine, and 50 units/mL penicillin/streptomycin. Feeder cells were depleted by trypsinization and replating on a plate for 30 min before extracting RNA.

extract_protocol:
RNA extraction and single molecular sequencing was described previously in PubMed ID 22763454
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: PubMed ID 18388294, 20133332

treatment_protocol: Lentiviral shRNA infection followed by puromyacin selection

tag: shRNA target

tag: cell line


title: AML-14355

status: Public on Apr 14 2015

type: SRA

city: New York

first: Yanwen

last: Jiang

state: NY

country: USA

institute: Weill Cornell Medical College

description: disease: acute myeloid leukemia

library_source: genomic

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: methycall files are in .txt format

molecule: genomic DNA

organism: Homo sapiens

source_name: Hematopoietic stem cells

growth_protocol: Primary, uncultured cells.

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

treatment_protocol: The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice and lin-cd34+cd38-cd90+ cells sorted from human AML samples

tag: cell type

value: hematopoietic stem cells

tag: cell markers

tag: genotype

value: Tet2 mutant; Flt3-ITD

tag: strain


title: ALS11

city: ILLKIRCH

first: nicolas

last: charlet

address: 1 Rue laurent Fries

country: France

institute: IGBMC

library_source: transcriptomic

data_processing:
FASTQ files were generated with CASAVA v1.8.2. (Illumina)
Reads were trimmed for adaptor,  low-quality sequences were removed and reads were mapped to hg19
Reads were counted using htseq-count
reads were calculated using DEXseq
Alternative splicing was analyzed using DEXSEQ and  KISSPLICE (http://kissplice.prabi.fr/)
Genome_build: hg19
Supplementary_files_format_and_content: txt

molecule: total RNA

source_name: Control

extract_protocol:
Total RNA from heart samples was extracted by Trizol
mRNA libraries were created using TruSeq RNA Sample Preparation v2 Kit (Illumina). Briefly, mRNA was purified from 1 µg 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 12 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), then sequenced at 7pM concentration using Hiseq 2000 (Illumina) as paired-end 2x100 base reads.

tag: tissue

value: left ventricle

tag: disease state

value: control


title: hs1.cb.1-3

city: Stanford

first: Cheryl

middle: L

last: Smith

state: CA

address: 300 Pasteur Dr.

department: Pathology

institute: Stanford University

description: library strategy: 3'-biased RNAseq (3SEQ)

data_processing:
Trimming: The first 18 bases and the last 7 bases of the HiSeq F1 reads were trimmed to make them the same length as the GAIIx reads; for all data, Prior to read mapping, 3' poly(A) sequences likely to be derived from the mRNA poly(A) tail were trimmed.
A Mus musculus castaneus genome was created in silico by applying the high-quality Cast SNPs [Keane, T. M. et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 477, 289-294, (2011).] to the reference C57BL/6 genome mm9. For B6, we used the mm9 genome. For each of these two reference genomes, a transcriptome was computed using RefSeq annotations, including spliced transcripts of all genes separated by 200 nucleotides, and each spliced transcriptome was added to its reference genome sequence.
Bowtie2 was used to align reads to composite genomes (Cast or B6 including spliced transcripts) with bowtie2 settings "“-k 200 --score-min L,0,-0.10 --rdg 2,2 --rfg 2,2 --mp 1,1"
Reads derived from repetitive regions of the genome were filtered as follows: If the difference in edit distance (1 for each mismatch and 2 for each indel) between a read’s best alignment and its second-best alignment was within 3, the read was discarded. Reads were also filtered out unless all best alignments in the composite genome corresponded to the same genomic position.
Each aligned read was then consolidated into a single genomic alignment, including intronic splice gaps.
Gene expression was quantified using only reads mapping to exons. Read counts were normalized by the total number of sequenced reads per library, multiplied by 1x106, resulting in reads per million.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include Total Reads: per sample measure of expression as number of reads mapped to any exon of a given gene; Cast Votes: per sample number of reads mapping to a given gene and containing Cast-specific snp(s); B6 Votes: per sample number of reads mapping to a given gene and containing B6-specific snp(s); N2 Genotypes: per sample inferred genotypes of homozygous (1) or heterozygous (0.5) at each gene locus
Supplementary_files_format_and_content: samp-expr_F1.tsv: Total Reads_F1
Supplementary_files_format_and_content: samp-allele-gene-c-votes_F1.tsv: Cast Votes_F1
Supplementary_files_format_and_content: samp-allele-gene-b-votes_F1.tsv: B6 Votes_F1
Supplementary_files_format_and_content: samp-expr_N2.tsv: Total Reads_N2
Supplementary_files_format_and_content: samp-allele-gene-c-votes_N2.tsv: Cast Votes_N2
Supplementary_files_format_and_content: samp-allele-gene-b-votes_N2.tsv: B6 Votes_N2
Supplementary_files_format_and_content: genotypes.tsv: N2 Genotypes

organism: Mus musculus

source_name: whole embryo

extract_protocol:
Whole embryos were separated from all extra-embryonic material and homogenized in Trizol; total RNA was extracted and mRNA subsequently purified using Qiagen Oligotex.
Libraries were prepared according to Beck, A. H. et al. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PloS one 5, e8768, (2010).

tag: generation

tag: maternal strain

value: Castaneus (Cast)

tag: paternal strain

tag: developmental stage

value: Embryonic day 11.5

tag: litter

tag: embryo id

tag: somite number

tag: sequencing run

tag: sequencing lane


title: hs1.cb.2-3


title: hs1.cb.1-2


title: hs1.bc.5-7


title: hs1.cb.1-1


title: NR7

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: hg19
Supplementary_files_format_and_content: methycall files are in .txt format

source_name: Diffuse Large B-cell Lymphoma

extract_protocol:
DNA was extracted from frozen solid tissue sections of DLBCL tumor samples.
ERRBS libraries were prepared according to a previously published protocol (Akalin et al., PLoSGenetics, 2012).

value: malignant mature B cells

tag: tumor stage

value: diagnosis


title: hs1.bc.5-5


title: NR5


title: hs1.bc.5-6


title: hs1.bc.5-4


title: NR3


title: NR2


title: hs1.bc.3-3


title: hs1.bc.5-3


title: ChIP-seq, Macrophage_Input

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
ChIP-seq reads were aligned to the mouse genome mm9 using Bowtie with options ‘-k 1 -m 1 --best -strata’. After the alignment, down-sampling was performed to avoid read saturation in highly enriched regions. Specifically, after randomly selecting 20 million reads from each ChIP-seq run, redundant reads were removed, and peak calling was performed against an input sample. Peaks were re-sized to 200 bp, and those meeting a threshold of 1 RPM were chosen for further study. Peaks located in the ENCODE blacklist regions were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq peak files in BED format

source_name: bone marrow-derived macrophages

growth_protocol: Mice were back-crossed for at least four generations to the BALB/c background. Primary macrophages were differentiated from bone marrow isolated from the femurs of twelve-week-old GRdim and GR+/+ litter-mate controls.

extract_protocol:
Macrophages were crosslinked in 1 % formaldehyde/PBS, Cell lysis and sonication was performed according to standard ChIP protocol.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols.

treatment_protocol: Primary macrophages were treated overnight with 1µM dexamethasone (Sigma) and/or lipopolysaccharide (LPS, 100ng/ml, Sigma) for 3 hours.

value: back-crossed to the BALB/c

tag: chip antibody

value: GR, sc-1004, Santa Cruz


title: ChIP-seq, Macrophage_GR_GRdim

tag: genotype/variation

value: GRdim


title: ChIP-seq, Macrophage_GR_WT


title: IC

source_name: Myotonic Dystrophy type 1

value: myotonic dystrophy


title: hs1.cb.1-4


title: NR8

tag: cell type


title: ChIP-exo, Liver_GR_WT_pred_6am

description:
library strategy: ChIP-exo
replicate 1 & 2

data_processing:
1) ChIP-seq: ChIP-seq reads were aligned to the mouse genome mm9 using Bowtie with options ‘-k 1 -m 1 --best -strata’. After the alignment, down-sampling was performed to avoid read saturation in highly enriched regions. Specifically, after randomly selecting 15 million reads from each ChIP-seq run, redundant reads were removed, and peak calling was performed using Homer with a previously published input sample [GSM1044696] (You et al., 2013). Peaks were re-sized to 200 bp, and those meeting a threshold of 2 RPM were chosen for further study. Peaks located in the ENCODE blacklist regions were discarded. Based on the initial peak calling results, reproducibility was confirmed using Spearman’s rank correlation coefficient. Replicate pairs were then pooled into a single data set for each condition, followed by final peak-calling.
2) ChIP-exo: ChIP-exo reads were aligned to the mouse genome mm9 like ChIP-seq samples. To define a preliminary set of ChIP-exo elementary peaks on the forward and reverse strands, initial peak calling was performed separately for each biological replicate by examining the 5‘ ends of reads using GeneTrack (Albert et al., 2008) with options, ‘-s 3 -e 10’. Peak calling was also performed after pooling replicates for each condition. Reproducible and strong elementary peaks were selected from pooled replicates if they overlapped peaks from each replicate by at least by 5 bp (out of 10 bp). Elementary peaks located within the ENCODE blacklist regions were discarded.
Genome_build: mm9
Supplementary_files_format_and_content: 1) ChIP-seq peak files in BED format 2) ChIP-exo peak files in txt format contaning elementary peaks from each strand

source_name: Liver tissue

growth_protocol: Mice were back-crossed for at least four generations to the BALB/c background. Twelve-week-old male GRdim and GR+/+ litter-mate controls were maintained in a 12 hour dark /light cycle, and 6 am and 6 pm tissues were collected at the beginning of the light and dark phases, respectively.

extract_protocol:
Liver tissue isolated from sacrificed mice was immediately frozen in liquid nitrogen. To process for ChIP, the tissue was thawed, minced and crosslinked in 1 % formaldehyde/PBS. Cells were disrupted and nuclei purified by dounce homogenization in a hypotonic buffer (20 mM HEPES/NaOH pH 7.5, 0.25 M sucrose, 3 mM MgCl2, 0.2% NP-40, 3 mM 2-mercaptoethanol, Complete protease inhibitor cocktail). To prepare ChIP extracts, nuclei were suspended SDS lysis buffer (50 mM HEPES/NaOH pH 7.5, 1% SDS, 10 mM EDTA, Complete protease inhibitor), incubated at 4 C for 10 min, and subjected to microtip probe sonication under conditions optimized for IP efficiency.
ChIP-Seq libraries were produced and sequenced according to Illumina protocols. ChIP-exo libraries were produced for Illumina sequencing. Libraries were multiplexed for sequencing.

treatment_protocol: Mice were treated for 24 hours with s.c. applied prednisolone pellets (12mg/kg; Innovative Research of America)

value: GR, PA1-511A, Pierce; sc-1004, Santa Cruz

tag: collection time


title: ChIP-exo, Liver_GR_GRdim_pred_6am

tag: strain


title: hs1.bc.3-4


title: NR6


title: ChIP-exo, Liver_GR_GRdim_6pm


title: 11D


title: ChIP-seq, Liver_CEBPb_WT_6pm

description: replicate 1 & 2

value: CEBPb, sc-150, Santa Cruz


title: 9R

value: relapse


title: hs1.bc.3-1


title: ChIP-seq, Liver_RNAPII_WT_6am

description: replicate 1 & 2

value: RNAPII, sc-899, sc-9001, Santa Cruz


title: 8R


title: 9D


title: 10R


title: NR1


title: ChIP-exo, Liver_GR_GRdim_6am


title: ChIP-exo, Liver_GR_WT_6pm


title: 8D


title: 11R


title: ChIP-seq, Liver_GR_WT_pred_6am

description: replicate 1 & 2


title: ChIP-seq, Liver_GR_WT_6am

description: replicate 1 & 2


title: ChIP-seq, Liver_GR_GRdim_pred_6am

description: replicate 1 & 2


title: 6R


title: ChIP-seq, Liver_GR_WT_6pm

description: replicate 1 & 2


title: ChIP-seq, Liver_RNAPII_WT_pred_6am

description: replicate 1 & 2


title: ChIP-exo, Liver_GR_WT_6am


title: 10D


title: ChIP-seq, Liver_GR_GRdim_6am

description: replicate 1 & 2


title: 5R


title: 6D


title: 5D


title: T2F3-LSK-3

treatment_protocol: The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice.

tag: cell markers

value: lin-Sca+cKit+

tag: genotype


title: T2F3-LSK-2

value: hematopoietic stem cells


title: 4D


title: TET2-LSK-3


title: T2F3-LSK-1


title: 7R


title: TET2-LSK-2


title: 4R


title: 3D


title: 2R


title: 7D


title: 1R3


title: FLT3-LSK-2


title: 1R2


title: FLT3-LSK-1


title: WT-LSK-4

value: wide type


title: 1R1


title: WT-LSK-3


title: WT-LSK-2


title: TET2-LSK-1


title: 3R


title: willow 24 h  B replicate

status: Public on Apr 13 2015

city: Nottingham

first: David

middle: B

last: Archer

address: University Park

department: School of Life Sciences

country: United Kingdom

institute: University of Nottingham

data_processing:
The Life Technologies LifeScope (v2.5.1) Whole Transcriptome (WT) Pipeline was used to filter, then map the SOLiD reads to the reference genome sequence using the mate-pair read WT pipeline.
Reads were initially filtered against library adaptor and barcode sequences as well as A. niger rRNA 5.8S, 16S, 18S & 28S sequences obtained from Genbank.
Reads that passed the filter were then mapped to the reference genome sequence, and to a library of exon junction sequences derived from the genome sequence using known exon coordinates. This allowed reads that spanned exon junctions (spliced reads) to be determined.
Read counts per gene were determined using the program Htseq-count (http://www-huber.embl.de/users/anders/HTSeq) using uniquely aligned reads with ≥MAPQ20. For paired read alignments from this dataset, only the forward read (F3) were counted. The count information was then used to calculate normalized gene expression values as RPKM (Mortazavi et al., 2008).
Genome_build: The reference genome and gene models used here are mainly from the genome sequence and gene models of the Aspergillus niger ATCC1015 strain version 3 from the JGI. This was supplemeted with gene models and sequence from the CBS513.88 strain where the gene model and/or genomic sequence was absent from the ATCC1015 strain genome sequence and/or gene models.
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPKM values for each sample

organism: Aspergillus niger

source_name: mycelia from A. niger cultured in willow medium

growth_protocol: A. niger strain N402 (Bos et al., 1988) was routinely grown on potato dextrose agar (PDA, Oxoid) (Delmas et al., 2012). Medium contained 1 % (w/v) glucose or 1 % ball milled willow as the sole carbon source. Fungal strains were grown on agar slopes at 28 °C to produce spores, which were harvested using 0.1% (v/v) Tween 20. For liquid cultures, 100 ml medium in a 250 ml flask was inoculated with 1x10^6 spores ml-1 and incubated at 28 °C, 150 RPM. For cultivation on willow, AMM containing glucose was inoculated with spores and incubated for 48 h to generate mycelium. Mycelium was collected by filtration over Miracloth (Calbiochem), washed with AMM without carbon source and subsequently 1.5 g wet weight of mycelium was transferred to a flask with the appropriate medium [PMID:  3224384; 22912594]

extract_protocol:
Total RNA was extracted from mycelia using the Plant/Fungi total RNA Purification Kit (Norgen Biotek, Canada) including the on-column DNAase treatment step.
10 ug of Total RNA was depleted of ribosomal RNA using the Ribominus Eukaryotic kit (Invitrogen). The KAPA library quantification kit for Applied Biosystems SOLiD platform was used to quantify the libraries by qPCR. SOLiD whole transcriptome libraries were made as outlined in the SOLiD Whole transcriptome kit protocol (Applied Biosystems). Emulsion PCR and bead-based enrichment was carried out using the SOLiD EZ bead system. Using a SOLiD 5500xl ABi sequencer, 50bp/35bp paired-end reads were generated in colour space.

tag: culture condition

value: willow 24 h

tag: tissue

value: mycelia


title: glucose 48 h A replicate

source_name: mycelia from A. niger cultured in glucose medium

value: glucose 48 h


title: willow 24 h + glucose 5 h A replicate

source_name: mycelia from A. niger cultured in willow medium for 24 h and then glucose is added and culturing continued for a further 5 h

value: willow 24 h + glucose 5 h


title: glucose 48 h B replicate


title: willow 24 h + glucose 5 h B replicate


title: 2D

value: malignant mature B cells


title: FLT3-LSK-3


title: 1D

value: diagnosis


title: willow 24 h A replicate


title: zf3_dis_S366

city: New York City

first: Rahul

last: Satija

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
To map reads, we slightly modified the Zv9 reference transcriptome, since our reads were expected to originate from the 5’ end of each mRNA molecule, which could cause problems if the reference gene models had an incorrect annotation for the transcription start site (TSS). To address this, we extended the TSS for all Zv9 genes by 100 bases upstream to allow for minor fluctuations. We then aligned read-pairs directly to this modified reference transcriptome, using Bowtie with the following parameters: -q --phred33-quals -n 2 -l 25 -I 1 -X 2000 -a -m 200. As expected, following mapping, our reads overwhelmingly originated from near the TSS.
To quantify gene expression, we leveraged the 5 bp Random Molecular Tags (RMTs) that were associated with each sequencing read pair. For each annotated gene in Zv9, we identified all read-pairs that mapped to the correct strand, and collected each of the 5 bp RMTs that were associated with these reads. We collapsed duplicate RMT sequences together, in order to calculate the number of distinct RMTs associated with each gene. We quantified gene expression for 1,152 single cell libraries, and identified a subset of 207 failed/low-quality libraries with poor transcriptome complexity (< 2,000 genes detected per cell). After excluding these (remaining dataset of 945 cells), on average, we identified 47,000 unique molecules per sequencing library, corresponding to the detection of 3,400 genes per single cell.
Supplementary_files_format_and_content: zdata.expMatrix.txt --Expression matrix for all samples

organism: Danio rerio

source_name: 50% Epiboly stage

growth_protocol: Fertilized eggs from TL/AB in-crosses were incubated in 1 mg/ml pronase (Protease from Streptomyces griseus, Sigma-Aldrich) in a glass dish for 4–5 minutes until the chorion began to blister. The embryos were submerged in ~200 ml of embryo medium in a glass beaker without allowing them to contact air or plastic (both of which will cause the embryos to burst). The medium was poured off and new medium was vigorously added (again without allowing embryos to contact air) twice, in order to mechanically remove the chorions. The embryos were cultured in petri dishes coated with 2% agarose (to avoid contact with plastic) either at 23°C or 28°C until they reached 50% epiboly (about 6 hours post-fertilization at 28°C). At 50% epiboly, single embryos were visually confirmed to be at the correct stage

extract_protocol:
Two pairs of watchmaker forceps were used to dissect the blastula cap of the embryo away from the yolk. First, one pair of forceps was used to hold and rotate the cap, while the other was used to cut and pinch away the yolk that extended below the blastula cap. Then, the blastula cap was cut slightly up the side, which exposed the yolk that was inside of the blastula cap, which could then be gently peeled away. The blastula cap was transferred by pipette into a microfuge tube that contained 60 μl of DMEM/F12 media. The cells were dissociated by vigorously flicking the tube 10 times, and then pipetting the entire volume twice while visually confirming that dissociation had occurred. A timer was started at this time to track the amount of time the embryo had been dissociated. If cell clumps were still visible, the tube was flicked again. 180 μl of DMEM/F12 was added to dilute the cell mixture, then 120 μl of the diluted cell mixture was pipetted across the surface of a new agarose-coated dish filled with DMEM/F12 media. To collect cells, a P2 pipettor was used, while observing the cells under the dissecting scope, to collect 0.5 μl of media that contained a single cell. This was pipetted into 3 μl of TCL lysis buffer (Qiagen) in the lid of a PCR strip and mixed 3 times to ensure that lysis occurred. After collection of 8 cells, the entire strip of lids was snapped into a 96-well plate and kept on dry ice.
We used a modified strand-specific single-cell RNA-seq protocol based on the SMART template switching method, where the template- switch oligonucleotide included a stretch of 5 randomized nucleotides, thereby tagging each mRNA molecule with a random molecular tag (RMT) prior to PCR to mitigate amplification bias. Furthermore, we used a modified library preparation protocol that shares similarities with Soumillon et al. and is based on the Nextera Sample Preparation Kit. It selectively amplifies the 5’ transcript end, retains strand information, and is compatible with standard Illumina sequencing primers.

tag: group

value: experimental batch 3


title: zf3_dis_S365


title: zf3_dis_S362


title: zf3_dis_S361


title: zf3_dis_S359


title: zf3_dis_S360


title: zf3_dis_S364


title: zf3_dis_S357


title: zf3_dis_S358


title: zf3_dis_S355


title: zf3_dis_S353


title: zf3_dis_S352


title: zf3_dis_S356


title: zf3_dis_S351


title: zf3_dis_S354


title: zf3_dis_S349


title: zf3_dis_S350


title: zf3_dis_S363


title: zf3_dis_S347


title: zf3_dis_S346


title: zf3_dis_S348


title: zf3_dis_S345


title: zf3_dis_S1800


title: zf3_dis_S343


title: zf3_dis_S344


title: zf3_dis_S1799


title: zf3_dis_S1798


title: zf3_dis_S1797


title: zf3_dis_S1792


title: zf3_dis_S1796


title: zf3_dis_S1793


title: zf3_dis_S1791


title: zf3_dis_S1788


title: zf3_dis_S1787


title: zf3_dis_S1795


title: zf3_dis_S1784


title: zf3_dis_S1785


title: zf3_dis_S1783


title: zf3_dis_S1789


title: zf3_dis_S1790


title: zf3_dis_S1782


title: zf3_dis_S1781


title: zf3_dis_S1786


title: zf3_dis_S1780


title: ChIP-seq, Liver_GR_GRdim_6pm

description: replicate 1 & 2

value: back-crossed to the BALB/c


title: zf3_dis_S1778


title: zf3_dis_S1794


title: zf3_dis_S1776


title: zf3_dis_S1774


title: zf3_dis_S1777


title: zf3_dis_S1773


title: zf3_dis_S1775


title: zf3_dis_S1772


title: zf3_dis_S1764


title: zf3_dis_S1763


title: zf3_dis_S1771


title: zf3_dis_S1770


title: zf3_dis_S1768


title: zf3_dis_S1769


title: zf3_dis_S1765


title: zf3_dis_S1757


title: zf3_dis_S1758


title: zf3_dis_S1760


title: zf3_dis_S1766


title: zf3_dis_S1759


title: zf3_dis_S1761


title: zf3_dis_S1762


title: zf3_dis_S1755


title: zf3_dis_S1753


title: zf3_dis_S1779


title: zf3_dis_S1751


title: zf3_dis_S1756


title: zf3_dis_S1750


title: zf3_dis_S1752


title: zf3_dis_S1749


title: zf3_dis_S1767


title: zf3_dis_S1747


title: zf3_dis_S1745


title: zf3_dis_S1746


title: zf3_dis_S1744


title: zf3_dis_S1741


title: zf3_dis_S1742


title: zf3_dis_S1739


title: zf3_dis_S1738


title: zf3_dis_S1737


title: zf3_dis_S1734


title: zf3_dis_S1735


title: zf3_dis_S1730


title: zf3_dis_S1733


title: zf3_dis_S1731


title: zf3_dis_S1736


title: zf3_dis_S1732


title: zf3_dis_S1729


title: zf3_dis_S1727


title: zf3_dis_S1726


title: zf3_dis_S1728


title: zf3_dis_S1724


title: zf3_dis_S1748


title: zf3_dis_S1754


title: zf3_dis_S1725


title: zf3_dis_S1721


title: zf3_dis_S1720


title: zf3_dis_S1722


title: zf3_dis_S1719


title: zf3_dis_S1723


title: zf3_dis_S1740


title: zf3_dis_S1718


title: zf3_dis_S1743


title: zf3_dis_S1717


title: zf3_dis_S1715


title: zf3_dis_S1713


title: zf3_dis_S1712


title: zf3_dis_S1711


title: zf3_dis_S1703


title: zf3_dis_S1705


title: zf3_dis_S1709


title: zf3_dis_S1702


title: zf3_dis_S1707


title: zf3_dis_S1710


title: zf3_dis_S1704


title: zf3_dis_S1701


title: zf3_dis_S1699


title: zf3_dis_S1700


title: zf3_dis_S1698


title: zf3_dis_S1716


title: zf3_dis_S1695


title: zf3_dis_S1696


title: zf3_dis_S1691


title: zf3_dis_S1694


title: zf3_dis_S1692


title: zf3_dis_S1693


title: zf3_dis_S1689


title: zf3_dis_S1690


title: zf3_dis_S1708


title: zf3_dis_S1706


title: zf3_dis_S1714


title: zf3_dis_S1686


title: zf3_dis_S1688


title: zf3_dis_S1685


title: zf3_dis_S1687


title: zf3_dis_S1683


title: zf3_dis_S1697


title: zf3_dis_S1684


title: zf3_dis_S1681


title: zf3_dis_S1682


title: zf3_dis_S1679


title: zf3_dis_S1680


title: zf3_dis_S1678


title: zf3_dis_S1674


title: zf3_dis_S1673


title: zf3_dis_S1677


title: zf3_dis_S1676


title: zf3_dis_S1675


title: zf3_dis_S1672


title: zf3_dis_S1669


title: zf3_dis_S1668


title: zf3_dis_S1670


title: zf3_dis_S1665


title: zf3_dis_S1666


title: zf3_dis_S1671


title: zf3_dis_S1661


title: zf3_dis_S1663


title: zf3_dis_S1664


title: zf3_dis_S1662


title: zf3_dis_S1667


title: zf3_dis_S1660


title: zf3_dis_S1658


title: zf3_dis_S1659


title: zf3_dis_S1657


title: zf3_dis_S1656


title: zf3_dis_S1655


title: zf3_dis_S1654


title: zf3_dis_S1653


title: zf3_dis_S1652


title: zf3_dis_S1651


title: zf3_dis_S1650


title: zf3_dis_S1647


title: zf3_dis_S1649


title: zf3_dis_S1644


title: zf3_dis_S1642


title: zf3_dis_S1641


title: zf3_dis_S1646


title: zf3_dis_S1643


title: zf3_dis_S1639


title: zf3_dis_S1640


title: zf3_dis_S1638


title: zf3_dis_S1645


title: zf3_dis_S1636


title: zf3_dis_S1634


title: zf3_dis_S1632


title: zf3_dis_S1635


title: zf3_dis_S1631


title: zf3_dis_S1633


title: zf3_dis_S1629


title: zf3_dis_S1628


title: zf3_dis_S1627


title: zf3_dis_S1648


title: zf3_dis_S1624


title: zf3_dis_S1626


title: zf3_dis_S1625


title: zf3_dis_S1622


title: zf3_dis_S1621


title: zf3_dis_S1637


title: zf3_dis_S1619


title: zf3_dis_S1615


title: zf3_dis_S1618


title: zf3_dis_S1612


title: zf3_dis_S1611


title: zf3_dis_S1614


title: zf3_dis_S1616


title: zf3_dis_S1617


title: zf3_dis_S1613


title: zf3_dis_S1630


title: zf3_dis_S1607


title: zf3_dis_S1610


title: zf3_dis_S1608


title: zf3_dis_S1605


title: zf3_dis_S1606


title: zf3_dis_S1609


title: zf3_dis_S1604


title: zf3_dis_S1603


title: zf3_dis_S1623


title: zf3_dis_S1620


title: zf3_dis_S1602


title: zf3_dis_S1601


title: zf3_dis_S1597


title: zf3_dis_S1595


title: zf3_dis_S1598


title: zf3_dis_S1596


title: zf3_dis_S1599


title: zf3_dis_S1600


title: zf3_dis_S1594


title: zf3_dis_S1593


title: zf3_dis_S1577


title: zf3_dis_S1588


title: zf3_dis_S1589


title: zf3_dis_S1579


title: zf3_dis_S1578


title: zf3_dis_S1586


title: zf3_dis_S1583


title: zf3_dis_S1581


title: zf3_dis_S1582


title: zf3_dis_S1584


title: zf3_dis_S1591


title: zf3_dis_S1573


title: zf3_dis_S1576


title: zf3_dis_S1574


title: zf3_dis_S1592


title: zf3_dis_S1575


title: zf3_dis_S1580


title: zf3_dis_S1572


title: zf3_dis_S1590


title: zf3_dis_S1571


title: zf3_dis_S1587


title: zf3_dis_S1585


title: zf3_dis_S1570


title: zf3_dis_S1569


title: zf3_dis_S1568


title: zf3_dis_S1567


title: zf3_dis_S1565


title: zf3_dis_S1563


title: zf3_dis_S1566


title: zf3_dis_S1561


title: zf3_dis_S1559


title: zf3_dis_S1560


title: zf3_dis_S1564


title: zf3_dis_S1557


title: zf3_dis_S1553


title: zf3_dis_S1558


title: zf3_dis_S1554


title: zf3_dis_S1556


title: zf3_dis_S1550


title: zf3_dis_S1549


title: zf3_dis_S1548


title: zf3_dis_S1546


title: zf3_dis_S1541


title: zf3_dis_S1538


title: zf3_dis_S1537


title: zf3_dis_S1552


title: zf3_dis_S1536


title: zf3_dis_S1542


title: zf3_dis_S1535


title: zf3_dis_S1534


title: zf3_dis_S1551


title: zf3_dis_S1545


title: zf3_dis_S1540


title: zf3_dis_S1555


title: zf3_dis_S1562


title: zf3_dis_S1547


title: zf3_dis_S1544


title: zf3_dis_S1533


title: zf3_dis_S1539


title: zf3_dis_S1532


title: zf3_dis_S1530


title: zf3_dis_S1529


title: zf3_dis_S1531


title: zf3_dis_S1528


title: zf3_dis_S1527


title: zf3_dis_S1526


title: zf3_dis_S1525


title: zf3_dis_S1522


title: zf3_dis_S1523


title: zf3_dis_S1524


title: zf3_dis_S1519


title: zf3_dis_S1521


title: zf3_dis_S1520


title: zf3_dis_S1517


title: zf3_dis_S1513


title: zf3_dis_S1515


title: zf3_dis_S1514


title: zf3_dis_S1511


title: zf3_dis_S1512


title: zf3_dis_S1509


title: zf3_dis_S1507


title: zf3_dis_S1508


title: zf3_dis_S1504


title: zf3_dis_S1506


title: zf3_dis_S1500


title: zf3_dis_S1501


title: zf3_dis_S1503


title: zf3_dis_S1502


title: zf3_dis_S1498


title: zf3_dis_S1499


title: zf3_dis_S1518


title: zf3_dis_S1516


title: zf3_dis_S1495


title: zf3_dis_S1494


title: zf3_dis_S1491


title: zf3_dis_S1492


title: zf3_dis_S1488


title: zf3_dis_S1493


title: zf3_dis_S1490


title: zf3_dis_S1497


title: zf3_dis_S1510


title: zf3_dis_S1487


title: zf3_dis_S1496


title: zf3_dis_S1486


title: zf3_dis_S1485


title: zf3_dis_S1484


title: zf3_dis_S1483


title: zf3_dis_S1505


title: zf3_dis_S1482


title: zf3_dis_S1543


title: zf3_dis_S1481


title: zf3_dis_S1479


title: zf3_dis_S1480


title: zf3_dis_S1477


title: zf3_dis_S1476


title: zf3_dis_S1473


title: zf3_dis_S1475


title: zf3_dis_S1474


title: zf3_dis_S1471


title: zf3_dis_S1470


title: zf3_dis_S1472


title: zf3_dis_S1466


title: zf3_dis_S1489


title: zf3_dis_S1467


title: zf3_dis_S1465


title: zf3_dis_S1461


title: zf3_dis_S1469


title: zf3_dis_S1468


title: zf3_dis_S1463


title: zf3_dis_S1459


title: zf3_dis_S1464


title: zf3_dis_S1458


title: zf3_dis_S1456


title: zf3_dis_S1462


title: zf3_dis_S1457


title: zf3_dis_S1460


title: zf3_dis_S1453


title: zf3_dis_S1452


title: zf3_dis_S1451


title: zf3_dis_S1455


title: zf3_dis_S1454


title: zf3_dis_S1450


title: zf3_dis_S1478


title: zf3_dis_S1449


title: zf3_dis_S1448


title: zf3_dis_S1446


title: zf3_dis_S1445


title: zf3_dis_S1444


title: zf3_dis_S1443


title: zf3_dis_S1442


title: zf2_dis_S342

value: experimental batch 2


title: zf3_dis_S1441


title: zf2_dis_S336


title: zf2_dis_S339


title: zf2_dis_S341


title: zf2_dis_S338


title: zf2_dis_S335


title: zf2_dis_S337


title: zf2_dis_S333


title: zf2_dis_S331


title: zf2_dis_S334


title: zf2_dis_S330


title: zf2_dis_S332


title: zf2_dis_S329


title: zf3_dis_S1447


title: zf2_dis_S327


title: zf2_dis_S325


title: zf2_dis_S323


title: zf2_dis_S326


title: zf2_dis_S322


title: zf2_dis_S324


title: zf2_dis_S328


title: zf2_dis_S319


title: zf2_dis_S318


title: zf2_dis_S340


title: zf2_dis_S320


title: zf2_dis_S316


title: zf2_dis_S315


title: zf2_dis_S314


title: zf2_dis_S317


title: zf2_dis_S313


title: zf2_dis_S311


title: zf2_dis_S309


title: zf2_dis_S310


title: zf2_dis_S308


title: zf2_dis_S302


title: zf2_dis_S301


title: zf2_dis_S304


title: zf2_dis_S303


title: zf2_dis_S305


title: zf2_dis_S321


title: zf2_dis_S300


title: zf2_dis_S299


title: zf2_dis_S297


title: zf2_dis_S295


title: zf2_dis_S294


title: zf2_dis_S296


title: zf2_dis_S298


title: zf2_dis_S293


title: zf2_dis_S290


title: zf2_dis_S288


title: zf2_dis_S312


title: zf2_dis_S292


title: zf2_dis_S285


title: zf2_dis_S284


title: zf2_dis_S286


title: zf2_dis_S287


title: zf2_dis_S306


title: zf2_dis_S282


title: zf2_dis_S283


title: zf2_dis_S280


title: zf2_dis_S279


title: zf2_dis_S278


title: zf2_dis_S277


title: zf2_dis_S276


title: zf2_dis_S273


title: zf2_dis_S275


title: zf2_dis_S274


title: zf2_dis_S307


title: zf2_dis_S271


title: zf2_dis_S272


title: zf2_dis_S291


title: zf2_dis_S269


title: zf2_dis_S267


title: zf2_dis_S268


title: zf2_dis_S270


title: zf2_dis_S289


title: zf2_dis_S266


title: zf2_dis_S264


title: zf2_dis_S262


title: zf2_dis_S265


title: zf2_dis_S263


title: zf2_dis_S261


title: zf2_dis_S260


title: zf2_dis_S258


title: zf2_dis_S257


title: zf2_dis_S281


title: zf2_dis_S255


title: zf2_dis_S256


title: zf2_dis_S251


title: zf2_dis_S252


title: zf2_dis_S254


title: zf2_dis_S253


title: zf2_dis_S259


title: zf2_dis_S249


title: zf2_dis_S248


title: zf2_dis_S250


title: zf2_dis_S240


title: zf2_dis_S245


title: zf2_dis_S239


title: zf2_dis_S244


title: zf2_dis_S247


title: zf2_dis_S241


title: zf2_dis_S237


title: zf2_dis_S238


title: zf2_dis_S242


title: zf2_dis_S243


title: zf2_dis_S236


title: zf2_dis_S235


title: zf2_dis_S233


title: zf2_dis_S234


title: zf2_dis_S232


title: zf2_dis_S230


title: zf2_dis_S226


title: zf2_dis_S229


title: zf2_dis_S228


title: zf2_dis_S227


title: zf2_dis_S246


title: zf2_dis_S224


title: zf2_dis_S225


title: zf2_dis_S222


title: zf2_dis_S219


title: zf2_dis_S220


title: zf2_dis_S221


title: zf2_dis_S218


title: zf2_dis_S231


title: zf2_dis_S216


title: zf2_dis_S214


title: zf2_dis_S209


title: zf2_dis_S212


title: zf2_dis_S205


title: zf2_dis_S210


title: zf2_dis_S207


title: zf2_dis_S204


title: zf2_dis_S1400


title: zf2_dis_S215


title: zf2_dis_S217


title: zf2_dis_S208


title: zf2_dis_S1399


title: zf2_dis_S1398


title: zf2_dis_S223


title: zf2_dis_S1397


title: zf2_dis_S1396


title: zf2_dis_S1394


title: zf2_dis_S1393


title: zf2_dis_S1391


title: zf2_dis_S1392


title: zf2_dis_S1389


title: zf2_dis_S1388


title: zf2_dis_S1387


title: zf2_dis_S1386


title: zf2_dis_S1385


title: zf2_dis_S1381


title: zf2_dis_S1382


title: zf2_dis_S1383


title: zf2_dis_S1380


title: zf2_dis_S1379


title: zf2_dis_S1377


title: zf2_dis_S1376


title: zf2_dis_S1378


title: zf2_dis_S1374


title: zf2_dis_S1373


title: zf2_dis_S1371


title: zf2_dis_S1372


title: zf2_dis_S1395


title: zf2_dis_S1390


title: zf2_dis_S1369


title: zf2_dis_S1370


title: zf2_dis_S1367


title: zf2_dis_S1368


title: zf2_dis_S1365


title: zf2_dis_S1366


title: zf2_dis_S1364


title: zf2_dis_S1363


title: zf2_dis_S1360


title: zf2_dis_S1384


title: zf2_dis_S1359


title: zf2_dis_S1375


title: zf2_dis_S1357


title: zf2_dis_S1358


title: zf2_dis_S1355


title: zf2_dis_S1354


title: zf2_dis_S1353


title: zf2_dis_S1356


title: zf2_dis_S1352


title: zf2_dis_S1349


title: zf2_dis_S1351


title: zf2_dis_S1350


title: zf2_dis_S1347


title: zf2_dis_S1346


title: zf2_dis_S1345


title: zf2_dis_S1343


title: zf2_dis_S1344


title: zf2_dis_S1341


title: zf2_dis_S1339


title: zf2_dis_S1342


title: zf2_dis_S1340


title: zf2_dis_S1361


title: zf2_dis_S1362


title: zf2_dis_S1338


title: zf2_dis_S1337


title: zf2_dis_S1336


title: zf2_dis_S1335


title: zf2_dis_S1333


title: zf2_dis_S1348


title: zf2_dis_S1332


title: zf2_dis_S1331


title: zf2_dis_S1327


title: zf2_dis_S1330


title: zf2_dis_S1329


title: zf2_dis_S1319


title: zf2_dis_S1320


title: zf2_dis_S1322


title: zf2_dis_S1326


title: zf2_dis_S1323


title: zf2_dis_S1324


title: zf2_dis_S1317


title: zf2_dis_S1316


title: zf2_dis_S1309


title: zf2_dis_S1313


title: zf2_dis_S1310


title: zf2_dis_S1312


title: zf2_dis_S1311


title: zf2_dis_S1315


title: zf2_dis_S1307


title: zf2_dis_S1308


title: zf2_dis_S1334


title: zf2_dis_S1306


title: zf2_dis_S1314


title: zf2_dis_S1305


title: zf2_dis_S1325


title: zf2_dis_S1328


title: zf2_dis_S1321


title: zf2_dis_S1303


title: zf2_dis_S1302


title: zf2_dis_S1304


title: zf2_dis_S1300


title: zf2_dis_S1299


title: zf2_dis_S1301


title: zf2_dis_S1318


title: zf2_dis_S1297


title: zf2_dis_S1296


title: zf2_dis_S1295


title: zf2_dis_S1298


title: zf2_dis_S1294


title: zf2_dis_S1293


title: zf2_dis_S1292


title: zf2_dis_S1291


title: zf2_dis_S1289


title: zf2_dis_S1288


title: zf2_dis_S1290


title: zf2_dis_S1285


title: zf2_dis_S1286


title: zf2_dis_S1284


title: zf2_dis_S1280


title: zf2_dis_S1282


title: zf2_dis_S1281


title: zf2_dis_S1279


title: zf2_dis_S1278


title: zf2_dis_S1277


title: zf2_dis_S1276


title: zf2_dis_S1274


title: zf2_dis_S1273


title: zf2_dis_S1272


title: zf2_dis_S1271


title: zf2_dis_S1269


title: zf2_dis_S1270


title: zf2_dis_S1268


title: zf2_dis_S1265


title: zf2_dis_S1287


title: zf2_dis_S1263


title: zf2_dis_S1264


title: zf2_dis_S1283


title: zf2_dis_S1261


title: zf2_dis_S1262


title: zf2_dis_S1260


title: zf2_dis_S1259


title: zf2_dis_S1258


title: zf2_dis_S1257


title: zf2_dis_S1256


title: zf2_dis_S1255


title: zf2_dis_S1254


title: zf2_dis_S1252


title: zf2_dis_S1253


title: zf2_dis_S1275


title: zf2_dis_S1249


title: zf2_dis_S1250


title: zf2_dis_S1251


title: zf2_dis_S1248


title: zf2_dis_S1246


title: zf2_dis_S1247


title: zf2_dis_S1267


title: zf2_dis_S1266


title: zf2_dis_S1242


title: zf2_dis_S1244


title: zf2_dis_S1243


title: zf2_dis_S1240


title: zf2_dis_S1238


title: zf2_dis_S1239


title: zf2_dis_S1237


title: zf2_dis_S1235


title: zf2_dis_S1236


title: zf2_dis_S1233


title: zf2_dis_S1234


title: zf2_dis_S1231


title: zf2_dis_S1228


title: zf2_dis_S1232


title: zf2_dis_S1230


title: zf2_dis_S1226


title: zf2_dis_S1227


title: zf2_dis_S1225


title: zf2_dis_S1221


title: zf2_dis_S1223


title: zf2_dis_S1224


title: zf2_dis_S1222


title: zf2_dis_S1241


title: zf2_dis_S1229


title: zf2_dis_S1245


title: zf2_dis_S1220


title: zf2_dis_S1217


title: zf2_dis_S1216


title: zf2_dis_S1215


title: zf2_dis_S1218


title: zf2_dis_S1219


title: zf2_dis_S1213


title: zf2_dis_S1212


title: zf2_dis_S1211


title: zf2_dis_S1210


title: zf2_dis_S1209


title: zf2_dis_S1207


title: zf2_dis_S1205


title: zf2_dis_S1208


title: zf2_dis_S1204


title: zf2_dis_S1202


title: zf2_dis_S1199


title: zf2_dis_S1200


title: zf2_dis_S1201


title: zf2_dis_S1198


title: zf2_dis_S1195


title: zf2_dis_S1197


title: zf2_dis_S1196


title: zf2_dis_S1203


title: zf2_dis_S1193


title: zf2_dis_S1192


title: zf2_dis_S1189


title: zf2_dis_S1214


title: zf2_dis_S1191


title: zf2_dis_S1187


title: zf2_dis_S1188


title: zf2_dis_S1190


title: zf2_dis_S1186


title: zf2_dis_S1185


title: zf2_dis_S1194


title: zf2_dis_S1183


title: zf2_dis_S1181


title: zf2_dis_S1184


title: zf2_dis_S1206


title: zf2_dis_S1180


title: zf2_dis_S1179


title: zf2_dis_S1178


title: zf2_dis_S1177


title: zf2_dis_S1173


title: zf2_dis_S1175


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title: zf2_dis_S1171


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title: zf2_dis_S1163


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title: zf1_p8_S94

value: experimental batch 1


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title: zf1_p8_S93


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title: zf2_dis_S1153


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title: zf1_p6_S83


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title: zf1_p5_S87


title: zf1_p5_S84


title: zf1_p5_S83


title: zf1_p6_S48


title: zf1_p5_S89


title: zf1_p5_S82


title: zf1_p5_S81


title: zf1_p5_S94


title: zf1_p5_S80


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title: zf1_p5_S8


title: zf1_p5_S77


title: zf1_p5_S76


title: zf1_p6_S44


title: SLK_polyA_mRNAseq_rep1 [mRNA]

city: Bethesda

first: Coralie

last: Viollet

state: MD

address: 10 Center Dr

institute: NIH/NCI

description: Total RNA enriched for polyadenylated RNA

data_processing:
For mRNA sequencing: Adapter sequences were trimmed using the Fastx toolkit. Reads were aligned against two target genomes, human (hg19) and KSHV (Genbank accession number NC_009333.1) using TopHat (Trapnell, Pachter, & Salzberg, 2009) to generate spliced alignments. Transcripts were assembled using Cufflinks and Cuffdiff (Trapnell et al., 2010) in order to reveal differentially expressed genes. Significant mRNA fold change was determined by an adjusted p-value lower than 0.05 based on the Benjamini and Hochberg multiple testing correction.
Genome_build: Human genome (hg19) and KSHV genome (Genbank accession number NC_009333.1)
Supplementary_files_format_and_content: bedGraph files were generated using BEDtools

molecule: polyA RNA

source_name: SLK cells

growth_protocol: Human KS-derived SLK and SLKK cells (also known as SLK+rKSHV.219) (Herndier et al., 1994; Stürzl, Gaus, Dirks, Ganem, & Jochmann, 2013; Jeffrey Vieira & O’Hearn, 2004; Ziegelbauer, Sullivan, & Ganem, 2009) were  maintained in Dulbecco’s Modified Eagle medium supplemented with 10% v/v fetal bovine serum and 1% Penicillin/streptomycin/glutamine solution. Additionally, KSHV-positive SLKK cells were periodically grown under selection with 10mg/mL puromycin to maintain the viral episome. Experiments were done in triplicate independent cell cultures maintained at 37°C in humidified 5% CO2.

extract_protocol:
Total RNA was extracted from cells using miRVana miRNA isolation kit (Ambion, Life Technologies) according to manufacturer instructions. RNA abundance and integrity were determined after isolation using a Nanodrop-ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer, respectively.
For mRNA-Seq: Total RNA of samples used for small RNA-Sequencing was treated with Turbo DNA-free DNase I and Dynabeads to deplete samples from the residual DNA and to isolate the polyadenylated mRNA transcriptome, respectively. PolyA+ RNA libraries were then prepared with the ScriptSeq v2 RNA-Seq kit (Epicentre). The final concentration and size distribution of the RNA libraries were measured by using a Nanodrop-ND-1000 spectrophotometer, and by running a DNA 100 chip on an Agilent 2100 Bioanalyzer. Finally, a total of 6 polyadenylated mRNA libraries (3 SLK and 3 SLKK samples) were sequenced using the Illumina HiSeq platform.

tag: infection status

value: Not infected

tag: cell line

value: SLK cells


title: SLK_polyA_mRNAseq_rep3 [mRNA]


title: zf1_p5_S74


title: zf1_p5_S85


title: zf1_p6_S28


title: zf1_p5_S73


title: zf1_p5_S71


title: SLK_microRNAseq_rep3 [microRNA]

description: Total RNA containing short RNA fraction

data_processing:
For small RNA sequencing: Reads were aligned against known miRNAs from miRbase (version 19.0) using the software package SHRIMP (Rumble et al., 2009) (http://compbio.cs.toronto.edu/shrimp/README) with miRNA specific settings (-o 1 -n 2  -r 30% -h 50% --local -Q --qv-offset 32 --sam). To process paired-end sequencing, reads were aligned separately covering the mature miRNA both on the forward and reverse read and the obtained number of matches were averaged. The match counts were normalized and tested for differential expression using the edgeR package (McCarthy, Chen, & Smyth, 2012) with default settings.
Genome_build: Human genome (hg19) and KSHV genome (Genbank accession number NC_009333.1)
Supplementary_files_format_and_content: bedGraph files were generated using BEDtools

growth_protocol: Human KS-derived SLK and SLKK cells (also known as iSLK and iSLK.219/rKSHV.219) (Herndier et al., 1994; Stürzl, Gaus, Dirks, Ganem, & Jochmann, 2013; Jeffrey Vieira & O’Hearn, 2004; Ziegelbauer, Sullivan, & Ganem, 2009) were  maintained in Dulbecco’s Modified Eagle medium supplemented with 10% v/v fetal bovine serum and 1% Penicillin/streptomycin/glutamine solution. Additionally, KSHV-positive SLKK cells were periodically grown under selection with 10mg/mL puromycin to maintain the viral episome. Experiments were done in triplicate independent cell cultures maintained at 37°C in humidified 5% CO2.

extract_protocol:
Total RNA was extracted from cells using miRVana miRNA isolation kit (Ambion, Life Technologies) according to manufacturer instructions. RNA abundance and integrity were determined after isolation using a Nanodrop-ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent 2100 Bioanalyzer, respectively.
For microRNA-Seq: Small RNA libraries were constructed using the Illumina TruSeq RNA Sample Prep kit. Briefly, after running 2μg of total RNA in a 15% urea-TBE gel for 1hr at 200V, the 20 to 30 nucleotide RNA fraction was excised and eluted in 0.3M NaCl.  Following separation of the elute from the gel debris using a Spin-X-column, the small RNA samples were precipitated in 100% ethanol and 1mg.mL-1 glycogen, incubated at -80°C for 30 minutes, centrifuged at 14,000rpm for 25 minutes, washed with 75% ethanol, air dried and resuspended in RNAse-free water. Illumina TruSeq libraries were then prepared according to the manufacturer’s protocol and the final RNA library concentration was measured by a Qubit 2.0 fluorometer using Qubit dcDNA HS Assay kit. We verified the size of the products contained in the libraries using a high sensitivity DNA chip and an Agilent 2100 Bioanalyzer. Finally, a total of 6 miRNA libraries (3 SLK and 3 SLKK samples) were sequenced using the Illumina HiSeq platform.


title: SLK_microRNAseq_rep1 [microRNA]

description: Total RNA containing short RNA fraction


title: zf1_p5_S70


title: zf1_p5_S7


title: KARPAS422_H3K27me3

city: Cambridge

first: Barbara

middle: M

last: Bryant

address: 215 First Street

institute: Constellation Pharmaceuticals

data_processing:
50-nucleotide sequence reads were aligned to the hg19 genome using the BWA algorithm with default settings. Only reads that passed Illumina’s purity filter, aligned with no more than 2 mismatches and mapped uniquely to the genome, were used in subsequent analyses.
The aligned read files were sorted and duplicates removed using sort and rmdup functions from samtools version 0.1.18 (Li et al., 2009).
WIG files were generated using IGVTools (version 2.2.2) count function with a window size of 25 nucleotides, an extension of 100 beyond the 50-nucleotide read length, and genome hg19 (Robinson et al., 2011; Thorvaldsdottir et al., 2013). The WIG files were scaled assuming an effective genome length of 2.79B base pairs, so that the mean signal would be 1.0.
Genome_build: hg19

source_name: Diffuse large B cell lymphoma

growth_protocol: KARPAS-422 cell line was grown in Roswell Park Memorial Institute (RPMI) GlutaMAX medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (Invitrogen).

extract_protocol:
genomic DNA
Sample processing, library generation and deep sequencing were carried out using the services of Active Motif.


title: KARPAS422_Input


title: zf1_p6_S24


title: zf1_p5_S69


title: KARPAS-GSK126-1

data_processing:
Sequencing was performed on an Illumina HiSeq 2000.
Tophat 1.4.1 was used to perform sequence alignment, with UCSC human (hg19) as the reference genome.
The Normalized counts of sequence reads (FPKM) mapped to annotated UCSC genes were determined using Cufflinks software.
The data was filtered to keep genes with at least one sample above a 50-read threshold. Samples with fewer than 10 reads FPKM are replaced with the average across samples of 10 reads FPKM, to generate the final gene counts for each sample and gene.
Data processing was performed by Ocean Ridge Biosystems.
Genome_build: hg19

extract_protocol: Cell samples were collected and total RNA was prepared using TRIzol (Life Technologies). RNA-sequencing from total RNA samples was carried out using the services of Ocean Ridge Biosciences.

treatment_protocol: KARPAS-422 cells treated for 4 days with 1.5 μM of one of three EZH2 inhibitors: CPI-360, GSK-126, and EPZ-6438.

tag: treatment


title: KARPAS-EPZ6438-2


title: zf1_p5_S68


title: zf1_p5_S75


title: zf1_p6_S15


title: zf1_p5_S78


title: zf1_p5_S66


title: KARPAS-CPI360-2


title: zf1_p5_S65


title: SLK_microRNAseq_rep2 [microRNA]

description: Total RNA containing short RNA fraction


title: zf1_p5_S64


title: KARPAS-CPI360-1


title: zf1_p5_S63


title: KARPAS-DMSO-1

value: DMSO


title: zf1_p5_S62


title: zf1_p5_S61


title: zf1_p5_S59


title: zf1_p5_S60


title: zf1_p5_S58


title: SLK_polyA_mRNAseq_rep2 [mRNA]


title: EpiSC OPCs - 12hrs Miconazole rep1

city: Clev

first: Paul

middle: J.

last: Tesar

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Sciences

institute: Case Western Reserve University School of Medicine

description:
EpiSC-OPC-diff_12hrMico
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with miconazole (1μM) for 12 hours prior to RNA isolation.

data_processing:
Reads were aligned to mm9 genome build (retrieved from http://cufflinks.cbcb.umd.edu/igenomes.html), using Tophat v2.0.6 (Trapnell et al., 2009) with default settings.
FPKM values for RefSeq genes were calculated using Cufflinks v2.0.2 (Trapnell et al., 2010) provided with the GTF file via the -G (known genes only) option.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks v2.0.2 (Trapnell et al., 2010). A detailed description of the file format can be found at http://cufflinks.cbcb.umd.edu/manual.html under the subheading "Cufflinks Output"

source_name: EpiSC OPCs

growth_protocol: OPCs used in this study were grown in culture conditions described previously (Najm, F. J. et al., Nature methods, 2011). Cultures were regularly tested and shown to be mycoplasma free.

extract_protocol:
Cells were lysed directly in 1ml TRIzol (Invitrogen) and stored in -80 degrees C. Once all samples were collected, samples were thawed on ice and separated with chloroform using Phase Lock Gel tubes (5 PRIME). RNA was isolated using the miRNeasy Plus Mini Kit (Qiagen) according to the manufacturer's protocol.
1ug of each sample was poly-A selected, fragmented, and library prepped using the TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's protocol. Samples were indexed using TruSeq adapters. 100 base-pair paired end reads were generated for each sample on an Illumina HiSeq 2500 instrument at the Case Western Reserve University Genomics Core facility.

value: 129O1 EpiSC derived oligodendrocyte progenitor cells


title: zf1_p5_S57


title: EpiSC OPCs - 12hrs Miconazole rep2


title: compete_library

city: Gainesville

first: Eric

middle: T

last: Wang

state: FL

address: 2033 Mowry Rd

institute: University of Florida

data_processing:
Reads were analyzed for motif enrichment according to Lambert et al, Mol Cell 2014.
Genome_build: n/a
Supplementary_files_format_and_content: Excel file of hexamer R values for each library.

organism: synthetic construct

source_name: in vitro library of RNA

extract_protocol: in vitro library


title: EpiSC OPCs - 12hrs Clobetasol rep2

description:
EpiSC-OPC-diff_12hrClob
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with clobetasol (5μM) for 12 hours prior to RNA isolation.


title: EpiSC OPCs - 12hrs DMSO rep2

description:
EpiSC-OPC-diff_12hrDMSO
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with DMSO for 12 hours prior to RNA isolation.


title: zf1_p5_S56


title: Celf1-130nM_Mbnl1-1000nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 1000 nM MBNL1 protein.


title: zf1_p5_S55


title: zf1_p6_S1


title: EpiSC OPCs - 6hrs Miconazole rep2

description:
EpiSC-OPC-diff_6hrMico
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with miconazole (1μM) for 6 hours prior to RNA isolation.


title: EpiSC OPCs - 6hrs Miconazole rep1


title: zf1_p5_S6


title: Celf1-130nM_Mbnl1-500nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 500 nM MBNL1 protein.


title: zf1_p5_S53


title: EpiSC OPCs - 12hrs Clobetasol rep1


title: zf1_p5_S52


title: EpiSC OPCs - 6hrs Clobetasol rep2

description:
EpiSC-OPC-diff_6hrClob
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with clobetasol (5μM) for 6 hours prior to RNA isolation.


title: zf1_p5_S50


title: zf1_p5_S51


title: EpiSC OPCs - 6hrs Clobetasol rep1


title: zf1_p5_S5


title: zf1_p5_S49


title: Celf1-130nM_Mbnl1-250nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 250 nM MBNL1 protein.


title: Celf1-130nM_Mbnl1-130nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 130 nM MBNL1 protein.


title: EpiSC OPCs - 6hrs DMSO rep2

description:
EpiSC-OPC-diff_6hrDMSO
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with DMSO for 6 hours prior to RNA isolation.


title: zf1_p5_S47


title: Celf1-130nM_Mbnl1-64nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 64 nM MBNL1 protein.


title: EpiSC OPCs - 6hrs DMSO rep1


title: Celf1-130nM_Mbnl1-0nM

source_name: in vitro library of RNA, pulled down with 130 nM CELF1 protein in the presence of 0 nM MBNL1 protein.


title: zf1_p5_S46


title: KARPAS-GSK126-2


title: zf1_p5_S45


title: EpiSC OPCs - 2hrs Miconazole rep2

description:
EpiSC-OPC-diff_2hrMico
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with miconazole (1μM) for 2 hours prior to RNA isolation.


title: zf1_p6_S35


title: res

city: West Lafayette

first: Damon

last: Lisch

state: IN

address: 915 West State Street

institute: Purdue University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR9 cDNA using BWA with parameters -e 60 -i 15 -q 10 -t 4
Reads Per Kilobase of transcript per Megabase of library size (RPKM) were calculated.
Genome_build: TAIR9
Supplementary_files_format_and_content: spreadsheet include numbers of mapped reads,RPKM values for each Sample as well as log2 RPKM ratios, p-values and FDR for 9 pairwise comparisons

organism: Arabidopsis thaliana

growth_protocol: Seeds pretreated with stratification for 2-4 days at 4°C were kept in the greenhouse for another 6 days (22°C, 16 h/8 h photoperiod) before transferring the seedlings to the soil for another 12 days.Aerial tissues were collected from the 18-day-old adult plants.

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and RNA was harvested using the RNeasy Plant Mini RNA Extraction Kit (Qiagen). Enriched mRNA using the Epicentre Ribo-Zero™ rRNA Removal Kits (Plant Leaf) from 10 μg total RNA was sheared before random-primed cDNA synthesis and amplification using the TruSeq mRNA preparation kit (Illumina) following the standard protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 18-day-old adult plant

value: aerial tissue


title: zf1_p5_S44


title: r


title: zf1_p5_S43


title: zf1_p5_S54


title: zf1_p5_S41


title: zf1_p5_S48


title: EpiSC OPCs - 2hrs Clobetasol rep2

description:
EpiSC-OPC-diff_2hrClob
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with clobetasol (5μM) for 2 hours prior to RNA isolation.


title: zf1_p5_S40


title: zf1_p5_S4


title: EpiSC OPCs - 2hrs Clobetasol rep1


title: es

source_name: ein5-1 ski2-3

value: ein5-1 ski2-3


title: s


title: zf1_p5_S39


title: zf1_p5_S72


title: EpiSC OPCs - 2hrs DMSO rep2

description:
EpiSC-OPC-diff_2hrDMSO
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours, then treated with DMSO for 2 hours prior to RNA isolation.


title: zf1_p5_S37


title: e


title: zf1_p5_S36


title: EpiSC OPCs - 2hrs Miconazole rep1


title: zf1_p5_S35


title: zf1_p5_S42


title: EpiSC OPCs - 12hrs DMSO rep1


title: C


title: zf1_p5_S34


title: zf1_p5_S33


title: EpiSC OPCs - 0hr treatment rep2

description:
EpiSC-OPC-diff_0hr
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies. Cells were plated in differentiation conditions (see Najm, F. J. et al., Nature methods, 2011) for 1.5 hours prior to RNA isolation (time 0).


title: EpiSC OPCs - 0hr treatment rep1


title: zf1_p5_S32


title: zf1_p5_S30


title: zf1_p5_S3


title: EpiSC OPCs - 2hrs DMSO rep1


title: EpiSC OPCs

description:
EpiSC-OPC
EpiSC-derived OPCs were generated from EpiSCs using in vitro differentiation protocols described previously (Najm, F. J. et al., Nature methods, 2011). To ensure uniformity EpiSC OPCs were sorted to purity by FACS at passage 5 with conjugated CD140a-APC (eBioscience, San Diego, CA) and NG2-AF488 (Millipore, Billerica, MA) antibodies.


title: zf1_p5_S29


title: zf1_p5_S28


title: zf1_p5_S38


title: zf1_p5_S26


title: rdr6-11 ein5-1 ski2-3_replicate_3

description: small RNA ( < 200 nt)

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to tair 10.0 genomic sequence using Bowtie with parameters bowtie2 --very-sensitive-local -k 50
The 21-22 nt clean reads after adaptor-removal and filtering were mapped to the reference (main gene models, TAIR 10.0 release) using the Bowtie program. Stringent mapping of the short reads was performed with a mismatch penalty of 10000 and no gaps allowed.
Reads mapped to each gene model were counted, then followed by normalization and differential expression analysis (DESeq,  es/c AND es/res, > 2 fold change,p < 0.005,q < 0.1)
Genome_build: tair 10.0
Supplementary_files_format_and_content: spreadsheets include numbers of mapped reads and normalized expression levels for each Sample

source_name: plant

extract_protocol:
Plant tissues were flash frozen in liquid nitrogen, and RNA was harvested using the microRNA Purification Kit (Norgen). Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: zf1_p5_S25


title: rdr6-11 ein5-1 ski2-3_replicate_2

description: small RNA ( < 200 nt)


title: zf1_p5_S24


title: zf1_p5_S23


title: rdr6-11 ein5-1 ski2-3_replicate_1

description: small RNA ( < 200 nt)


title: zf1_p5_S22


title: zf1_p5_S67


title: rdr6-11_replicate_3

description: small RNA ( < 200 nt)


title: zf1_p5_S21


title: rdr6-11_replicate_2

description: small RNA ( < 200 nt)


title: zf1_p5_S31


title: zf1_p5_S18


title: zf1_p5_S20


title: zf1_p5_S19


title: rdr6-11_replicate_1

description: small RNA ( < 200 nt)


title: zf1_p5_S16


title: zf1_p5_S17


title: KARPAS-EPZ6438-1


title: P7 brain OPCs

description:
P7brain-OPC
PDGFRa+ cells were immunopanned from the CNS of postnatal day 7 mouse pups as described previously (Cahoy, J. D. et al., The Journal of Neuroscience, 2008).

source_name: P7 mouse brain OPCs

value: brain oligodendrocyte progenitor cells


title: zf1_p5_S15


title: zf1_p5_S27


title: ein5-1 ski2-3_replicate_3

description: small RNA ( < 200 nt)


title: zf1_p5_S14


title: DnmtTKO

last: Karnik

address: 419 Broadway

description: original data source: Meissner Lab in house

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using MAQ bisulfite alignment mode.
Aligned bam files were processed using custom software (PMID:20852634).
Genome_build: mm9
Supplementary_files_format_and_content: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand

source_name: Mouse ES cells (Dnmt3a/3b KO, Dnmt1 knockdown)

extract_protocol:
Please see Gu et al., 2011 and Smith et al., 2012
RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)

value: embryonic stem cells

value: Dnmt3a/3b KO, Dnmt1 knockdown

tag: passage


title: zf1_p5_S13


title: zf1_p5_S12


title: Col-0_replicate_3

description: small RNA ( < 200 nt)


title: Dnmt1KO_P17

source_name: Mouse ES cells (Dnmt1 KO)

value: Dnmt1 KO


title: zf1_p5_S11


title: Dnmt1KO_P7


title: zf1_p5_S2


title: Dnmt3a3bKO_P13

source_name: Mouse ES cells (Dnmt3a/3b KO)

value: Dnmt3a/3b KO


title: Col-0_replicate_1

description: small RNA ( < 200 nt)


title: Col-0_replicate_2

description: small RNA ( < 200 nt)


title: Dnmt3a3bKO_P3


title: zf1_p5_S1

source_name: 50% Epiboly stage


title: Dnmt3bKO_P3

source_name: Mouse ES cells (Dnmt3b KO)

value: Dnmt3b KO


title: Dnmt3bKO_P13


title: SLKK_polyA_mRNAseq_rep3 [mRNA]

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: SLKK cells

value: Chronically KSHV-infected

value: SLKK cells


title: Dnmt3aKO_P13

source_name: Mouse ES cells (Dnmt3a KO)

value: Dnmt3a KO


title: SLKK_polyA_mRNAseq_rep1 [mRNA]


title: SLKK_polyA_mRNAseq_rep2 [mRNA]


title: SLKK_microRNAseq_rep3 [microRNA]

description: Total RNA containing short RNA fraction


title: WT_P14

source_name: Mouse ES cells (wild-type)

value: wild-type


title: ein5-1 ski2-3_replicate_2

description: small RNA ( < 200 nt)


title: SLKK_microRNAseq_rep1 [microRNA]

description: Total RNA containing short RNA fraction


title: Dnmt3aKO_P3


title: SLKK_microRNAseq_rep2 [microRNA]

description: Total RNA containing short RNA fraction


title: WT_P4


title: ein5-1 ski2-3_replicate_1

description: small RNA ( < 200 nt)


title: zf1_p5_S10

value: experimental batch 1


title: K180B rep2

status: Public on Apr 12 2015

first: Nicholas

middle: D

last: Socci

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls done with Torrent Suite Software Basecaller
We performed differential expression analysis looking for genes that varied significantly between parental and resistant cell lines: CAL33 and KYSE180. The analysis was done jointly resulting in genes that largely agreed on fold change in both cell types.
For gene expression quantifications, first we converted the BAM files to FASTQ format. Reads were then quality trimmed using the fastx toolkit to remove bases that had a base quality score less than 10 and then reads shorter than 50bp were discarded. We did a two pass mapping procedure that first mapped with rnaStar,that maps reads genomically and resolves reads across splice junctions. Any reads that did not map in this pass were re-mapped using BWA MEM method. We merged the output BAM files from these two steps and then counted gene level expression with htseq-count (-s yes -m intersection-strict) and exon level expression was quantitate with DEXSeq. For the analysis we considered only coding genes.
After quantification of gene expression we assessed replicate quality in the different cell types and conditions and removed replicates that showed considerable amount of variation in gene expression ('CAL33_2', 'KYSE180B_1', 'KYSE180_1').
For the differential analysis we used the DESeq2 package in R. DESeq2 performs differential analysis using raw read counts, under a Negative Binomial noise model. Our linear model explained gene expression by cell-line type and whether it is parental or resistant off-drug.
For every gene G we fitted the model and tested whether  was statistically significant, ie. was there a statistically significant change between parental and resistant cell lines. Model fitting was followed by FDR (BH) correction for multiple hypothesis testing.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file with raw gene counts. Genes are labeled with ENSEMBL Gene ID Symbols

growth_protocol: KYSE180 cultured in RPMI 10%FCS, CAL33 cultured in DMEM-F12 10%FCS.

extract_protocol:
RNA was extracted by Rneasy mini kit (Qiagen). After ribogreen quantification and quality control of Agilent BioAnalyzer(RIN>7), poly(A) RNA was isolated using Dynabeads® mRNA DIRECT™ Micro Kit(Life Technologies)from 1ug of total RNA. mRNA was then fragmentated using RNaseIII and purified . The Fragmented Samples quality and yield were evaluated using Agilent BioAnalyzer.
Fragmented material underwent Whole transcriptome Library preparation according to the Ion Total RNA-Seq Kit v2 protocol(Life Technologies), with 16 cycles of PCR. Samples were barcoded, template-positive Ion PI™ Ion Sphere™ Particles (ISPs) were prepared using the ion one touch system II and Ion PI™Template OT2 200kit v2 Kit (Life Technologies). Enriched particles were sequenced on a Proton sequencing system using   200bp version 2 chemistry. An average of 70 to 80 million reads per sample were generated.

treatment_protocol: Parental and acquired resistant were treated for 24 hours with 1uM BYL719 or DMSO.

tag: resistant

value: Yes


title: K180B rep1


title: K180 rep2

value: No


title: zf1_p6_S18


title: K180 rep1


title: CAL33B rep3


title: CAL33B rep2


title: Tet1 knockout mouse 1 hmc

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: GTM test for HELP-GT

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (versions 1.3-1.4).  Initial data processing was performed using the default read length of 36 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the mm9 freeze of the human genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include hydroxymethylation scores (5-hmc) for each Sample

source_name: Tet1 knockout mouse cells

extract_protocol:
Genomic DNA was isolated from purified LSK cells of 6-month old WT and Tet1 KO mice by Puregene Core Kit A (Qiagen)
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII and MspI in separate 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA or 1 μg of MspI-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

value: LSK cells

value: Tet1 knockout

tag: age

value: 6 months


title: Tet1 knockout mouse 2 hmc

description: GTM test for HELP-GT


title: CAL33 rep1


title: CAL33 rep2


title: CAL33B rep1


title: wild type mouse 2 hmc

description: GTM test for HELP-GT

source_name: wild type mouse cells

value: wildtype


title: wild type mouse 1 hmc

description: GTM test for HELP-GT


title: Th17 5hmC (Sample 12)

city: Seattle

first: Raymond

last: Doty

state: WA

department: Division of Hematology

institute: University of Washington

data_processing:
Basecalls performed using CASAVA version 1.7.0 pipeline.
ChIP-seq reads were aligned to the mm9 genome assembly using ELAND_EXTENDED.
Reads with multiple mappings were filtered out.
To identify those differentiated 5hmC/5mC targets, we used the area under the sequencing depth curve within a gene as the 5hmC/5mC modification intensity for the gene.
Genome_build: mm9
Supplementary_files_format_and_content: In sample_all_gene_area.txt (linked as a supplementary file on the Series record), the area under the sequencing depth curve within a gene was calculated for each of the 12 samples separately, including the input and IgG samples.

source_name: Th17 cells, 5hmC

extract_protocol:
The genomic DNA was purified and sonicated. DNA fragments (4 μg) were denatured and incubated with antibodies against 5mC, 5hmC or control IgG at 4°C overnight.
The DIP DNA fragments were prepared and amplified using the Illumina ChIP-seq DNA preparation kit (Cat#1003473).

value: Th17 cells

tag: chip antibody

value: anti-5hmC (5-hydroxymethylcytosine)

tag: chip antibody details

value: Active Motif, Catalog# 39770


title: iTreg 5hmC (Sample 11)

source_name: iTreg cells, 5hmC

tag: cell type

value: iTreg cells


title: naïve 5hmC (Sample 8)

source_name: naive T cells, 5hmC

value: naive T cells


title: Th2 5hmC (Sample 10)

source_name: Th2 cells, 5hmC

value: Th2 cells


title: Th17 5mC (Sample 7)

source_name: Th17 cells, 5mC

value: anti-5mC (5-Methylcytosine)

value: Eurogentec, catalog# A-1014-010


title: iTreg 5mC (Sample 6)

source_name: iTreg cells, 5mC


title: input DNA (Sample 1)

source_name: Th17 cells, input DNA


title: naïve 5mC (Sample 3)

source_name: naive T cells, 5mC


title: Th1 5mC (Sample 4)

source_name: Th1 cells, 5mC

value: Th1 cells


title: Th1 5hmC (Sample 9)

source_name: Th1 cells, 5hmC


title: IgG (Sample 2)

source_name: Th17 cells, control IgG

value: anti-IgG

value: BioXCell, Catalog# BE0083


title: 5hmC.Th1.Tet2KO

data_processing:
Basecalls performed using CASAVA version 1.6 and 1.8.1
MeDIP-seq reads were aligned to the mm9 genome assembly using Bowtie 1.0.1 using -p 4 -v 2 -m 1
The unique reads for 5mC and 5hmC were mapped into non-overlapping 200 bp windows (400 bp gap size) of mouse genome (mm9). The peaks were called using SICER (Zang et al., 2009), with the Input DNA sample as a control and a FDR of 0.01 as the cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using SICER.

source_name: CD4+ T cells, 5hmC.Th1.Tet2KO

growth_protocol: Naive T cells were isolated by sorting CD4+CD25-CD62LhighCD44low cells from spleens and lymph nodes, differentiated under several Th cell conditions, and analyzed as described. The naive T cells (5 x 105 cells/well) were cultured at 37oC (5% CO2) in RPMI-1640 (Invitrogen Life Technologies). The medium was supplemented with 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin, 100  g/ml streptomycin, and 50  M 2-mercaptoethanol. The cells were stimulated with the plate-bound a-CD3 (1  g/ml) and the soluble a-CD28 (1  g/ml). For Th0 differentiation, the cells were treated with 5  g/ml  -IFN-  (XMG1.2; BioXCell), 5  g/ml  -IL-4 (11B11; BioXCell) and 30 U/ml IL-2. For Th1 differentiation, the cells were treated with 10 ng/ml mIL-12 (Peprotech), 5  g/ml  -IL-4 and 30 U/ml IL-2. For Tr1 differentiation, the cells were treated with 50 ng/ml mIL-27 (R&D Systems), 2 ng/ml TGF- 1 (Peprotech) and 30 U/ml IL-2. When indicated, irradiated wild-type splenic antigen-presenting cells (APCs) were used for optimal Tr1 cell differentiation. For Th2 differentiation, the cells were treated with 10 ng/ml mIL-4 (Peprotech), 5  g/ml  -IFN- . For iTreg differentiation, the cells were treated with 1 ng/ml TGF- 1 (Peprotech), 5  g/ml  -IFN- , 5  g/ml  -IL-4 and 30 U/ml IL-2. For Th17 differentiation, the cells were treated with 0.5 ng/ml TGF- 1, 10 ng/ml IL-6 (Peprotech), 5  g/ml  -IFN- , and 5  g/ml  -IL-4. When indicated, 10 ng/ml IL-23 and 10 ng/ml IL-1  (Peprotech) were used for optimal Th17 cell differentiation.

extract_protocol:
the genomic DNA was purified and sonicated. DNA fragments (4 ug) were denatured and incubated with antibodies against 5mC (Eurogentec) and 5hmC (Active Motif) at 4 degree overnight. Antibody-DNA complexes were captured by protein A agarose/Salmon sperm DNA. The immunoprecipitated DNA was purified. The results were normalized relative to the input control.
Libraries were prepared using Illumina ChIP-seq DNA preparation kit (IP-202-1012) according to the manufacture's instruction.

tag: cell population

value: CD4+ T cells


title: 5hmC.Th1.Tet2WT

source_name: CD4+ T cells, 5hmC.Th1.Tet2WT

tag: strain


title: KARPAS-DMSO-2

source_name: Diffuse large B cell lymphoma

value: DMSO


title: TCF21 Ab1 r2

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

description:
initial TCF21 ChIPseq
TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project. Peak file for Ab1 is available on record GSM1503214.

data_processing:
Alignment: Sequences were aligned to hg19 using BWA set to default parameters.
Peak-calling: Peaks were called with MACS2 for HG 19, set to default parameters using IgG samples as background control
Replicate consolidation: For TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project. For JUN JUND no replicates.
Genome_build: hg19
Supplementary_files_format_and_content: bed files standard format

source_name: HCASMC Lonza 0000200212

growth_protocol: Human coronary artery smooth muscle cells were obtained from Lonza and grown as suggested in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics (Lonza, #CC-3182).

extract_protocol:
Ten million HCASMC cells per condition were crosslinked for 10 min with 1% formaldehyde. Cells were lysed for 10 min on ice, and nuclei were then lysed for 10 min on ice. Crosslinked chromatin was sheared for 3x5 min by sonication using a Bioruptor and pre-cleared with 10 µg anti-rabbit IgG pre-immune serum. TCF21 ChIP was performed overnight in IP dilution buffer using anti-TCF21 (Sigma-Aldrich, St. Louis, MA, USA, #HPA013189, Lot. No. R02939 (Ab1) or Abcam, Cambridge, UK, #ab49475, Lot No. 153899 (Ab2)) or anti-rabbit IgG respectively. JUN and JUND ChIP was performed with Santa Cruz Biotechnology sc-1694 and Santa Cruz Biotechnology sc-74 respectively.
After reverse-crosslinking, RNaseA and proteinase K digestion, chromatin was cleaned up using the Qiagen PCR purification kit

value: coronary artery smooth muscle

tag: chip antibody manufacturer and catalog number

value: Sigma HPA013189


title: 5hmC.iTreg

description: Reads obtained from two instruments: Illumina Genome Analyzer IIx and Illumina HiSeq 2500

source_name: CD4+ T cells, 5hmC.iTreg


title: TCF21 Ab2 r1

description:
initial TCF21 ChIPseq
TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project. Peak file for Ab2 is available on this record.


title: TCF21 Ab1 r1

description:
initial TCF21 ChIPseq
TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project. Peak file for Ab1 is available on this record.


title: 5hmC.Th17.Tet2WT

source_name: CD4+ T cells, 5hmC.Th17.Tet2WT


title: TCF21 Ab2 r2

description:
initial TCF21 ChIPseq
TCF21 Ab1 and Ab2 replicates were consolidated to produce one set of peaks per antibody using the IDR pipeline developed by the ENCODE project.  Peak file for Ab2 is available on record GSM1503216.


title: 5hmC.Th2

source_name: CD4+ T cells, 5hmC.Th2


title: 5hmC.Th1

source_name: CD4+ T cells, 5hmC.Th1


title: 5hmC.Th17

source_name: CD4+ T cells, 5hmC.Th17


title: 5mC.Th1

source_name: CD4+ T cells, 5mC.Th1


title: 5mC.iTreg

source_name: CD4+ T cells, 5mC.iTreg


title: 5mC.Naive

source_name: CD4+ T cells, 5mC.Naive


title: 5mC.Th2

source_name: CD4+ T cells, 5mC.Th2


title: 5hmC.Naive

source_name: CD4+ T cells, 5hmC.Naive


title: 5mC.Th17

source_name: CD4+ T cells, 5mC.Th17


title: IgG control 1

description: IgG control 1

value: IgG


title: Th2 5mC (Sample 5)

source_name: Th2 cells, 5mC


title: Input

source_name: CD4+ T cells, Input


title: LSK WT replicate 3

first: Luisa

last: Cimmino

address: 550 First Avenue

institute: NYU

description:
Sample name: LSK WT-3
RRBS from WT mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt

data_processing:
Reads were aligned to whole genome using the bismark alignment software. In silico MspI fragment library was constructed by cutting the reference genome to fragments from MspI sites. Bisulfite converted reads are aligned to in silico bisulfite converted MspI fragments using ELAND aligner. CpG islands, refseq genes and repeat sequences were downloaded from the UCSC genome browser. Percent methylation values for CpG dinucleotides are calculated by dividing number of methylated Cs by total coverage on that base.
Genome_build: mm9
Supplementary_files_format_and_content: TAB-delimited text, lsk25pHypo.anno.txt are regions with greater than 25% hypomethylation in KO vs WT and lsk25pHyper.anno.txt are regions with greater than 25% hypermethylation

source_name: LSK WT

growth_protocol: Ex vivo flow sorted LSKs from 6-month old mouse bone marrow

extract_protocol:
Bisulphite treatment was performed using the EZ DNA Methylation Kit (Zymo Research) and upon addition of the CT conversion reagent, the incubation was conducted in a thermocycler (Eppendorf MasterCycler). Purified products were subjected to PCR amplification using the FastStart High Fidelity PCR System (Roche). PCR products were isolated using AMPure XP beads (Life Sciences).
Library amplification and quality was determined AMPure XP beads (Life Sciences) and the Agilent 2100 Bioanalyzer. The amplified libaries were sequenced on an Illumina HiSeq2500 with 50 bp single-end reads following standard Illumina sequencing protocols

treatment_protocol: DNA was isolated from purified LSK cells of 6-month old WT and Tet1 KO mice.

value: bone marrow

value: LSK hematopoietic stem cells

tag: genotype/variation

value: WT


title: LSK KO replicate 2

description:
Sample name: LSK KO-2
RRBS from KO mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt

source_name: LSK KO

value: Tet1 KO


title: LSK KO replicate 1

description:
Sample name: LSK KO-1
RRBS from KO mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt


title: LSK WT replicate 2

description:
Sample name: LSK WT-2
RRBS from WT mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt


title: MPP KO replicate 2

description:
Sample name: MPP_KO_2
Gene expression data from KO mouse MPP
processed data file: mpp-TET1.txt

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were aligned to the mm9 genome assembly using Tophat
Differential gene expression analysis was performed using cuffdiffv2.1
Genome_build: mm9
Supplementary_files_format_and_content: TAB-delimited text, normalized abundance measurements

source_name: MPP KO

growth_protocol: Ex vivo flow sorted LT-HSC and MPP from 6-month old mouse bone marrow

extract_protocol:
10,000 purified long-term HSCs and100,000 purified MPPs from WT and Tet1 KO mice were used for RNA isolation. RNA was extracted using RNeasy kit (Qiagen) and PolyA selection using oligo-dT beads (Life Technologies) was performed according to the manufacturer’s instructions. RNA libraries were then sequenced on the Illumina HiSeq 2000 using 50bp paired-end reads.
Libraries were generated as described before, including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification.

treatment_protocol: LT-HSC and MPP cells were purified from mice 20 weeks post-transplant with WT and Tet1 KO bone marrow. RNA was extracted using RNeasy kit (Qiagen)

value: Hematopoietic multipotent progenitor (MPP)


title: LSK WT replicate 1

description:
Sample name: LSK WT-1
RRBS from WT mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt


title: 5hmC.Th17.Tet2KO

source_name: CD4+ T cells, 5hmC.Th17.Tet2KO


title: MPP KO replicate 1

description:
Sample name: MPP_KO_1
Gene expression data from KO mouse MPP
processed data file: mpp-TET1.txt


title: IgG control 2

description: IgG control 2

source_name: HCASMC Lonza 0000317155


title: MPP WT replicate 2

description:
Sample name: MPP_WT_2
Gene expression data from WT mouse MPP
processed data file: mpp-TET1.txt

source_name: MPP WT


title: MPP WT replicate 1

description:
Sample name: MPP_WT_1
Gene expression data from WT mouse MPP
processed data file: mpp-TET1.txt


title: JUND ChIPseq

description:
Follow-up JUND ChIPseq
These ChIPseqs were done on a different machine as paired ends, no replicates, sequences combined in a bam file which was used to create the bed file provided, otherwise handled as noted for the other ChIPseqs.

value: JUND

value: Santa Cruz sc-74


title: LT-HSC KO replicate 2

description:
Sample name: LT-HSC_KO_2
Gene expression data from KO mouse LT-HSC
processed data file: lt-TET1.txt

source_name: LT-HSC KO

value: long-term hematopoietic stem cell (LT-HSC)


title: LT-HSC WT replicate 2

description:
Sample name: LT-HSC_WT_2
Gene expression data from WT mouse LT-HSC
processed data file: lt-TET1.txt

source_name: LT-HSC WT


title: LT-HSC KO replicate 1

description:
Sample name: LT-HSC_KO_1
Gene expression data from KO mouse LT-HSC
processed data file: lt-TET1.txt


title: LT-HSC WT replicate 1

description:
Sample name: LT-HSC_WT_1
Gene expression data from WT mouse LT-HSC
processed data file: lt-TET1.txt


title: LSK KO replicate 3

description:
Sample name: LSK KO-3
RRBS from KO mouse LSKs
processed data file: lsk.25pHyper.anno.txt, lsk.25pHypo.anno.txt


title: Uninfected_mouse_vagina.rep1

status: Public on Apr 11 2015

city: Baltimore

first: Amol

middle: Carl

last: Shetty

state: Maryland

address: 670 W. Baltimore Street, Floor 3

department: Institute for Genome Sciences

institute: University of Maryland Baltimore

description: control sample

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse (GRCm38) and/or Candida (sc5314) reference using the TopHat splice-aware aligner
Reads Per Kilobase of gene per Million mapped reads (RPKM) were calculated for each sample.
Differential expression of genes were computed between infected and uninfected samples
Genome_build: M. musculus (GRCm38), C. albicans (sc5314); Regarding the Candida genome assembly, we used the Candida albican sc5314 assembly 21 from the Candida Genome Database (http://www.candidagenome.org) which is a haploid assembly similar to ?ASM18296v2?.
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each sample

source_name: Mouse vagina

growth_protocol: C. albicans cells were injected into the vagina of a mouse

extract_protocol:
RNA was isolated from the infected mouse vaginal tissues using the Qiagen Rneasy mini kit (Cat#74104)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: infection

value: Vagina

tag: time point

value: day 3 uninfected


title: Sufficient iron condition 1

city: Porto Alegre

first: Edilena

middle: Reis

last: Sperb

state: RS

address: Bento Gonçalves

department: Genética

country: Brazil

institute: UFRGS

data_processing:
Remove adaptors and trim 15 bp off of the 3'-end.
Comparison and mapping to the P. riograndensis SBR5 genome database located on the Aramis platform (http://aramis.genopar.org/bacteria/PR/) using CLC Genome Workbench 5.5 software.
Library normalization and analysis performed using the RPKM method as described by Mortazavi et al. (2008).
Supplementary_files_format_and_content: *unique.tab: Tab-delimited text files with abundance of unique sequences.
Supplementary_files_format_and_content: *RPKM.txt: Tab-delimited text files with gene-level RPKM values.

organism: Paenibacillus riograndensis SBR5

source_name: bacterial culture, sufficient iron

growth_protocol: SBR5 grown in KB media.

extract_protocol: Total RNA was extracted from bacterial cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. RNA integrity was verified by electrophoresis on a 1% agarose gel. After the samples were treated with DNase I (Invitrogen), the concentration and purity were determined by spectrophotometer readings at 260 nm and 280 nm using a NanoDrop 2000 (Thermo Scientific). To remove ribosomal RNA, total RNA was processed using a MICROB Express Bacterial mRNA Enrichment Kit (Ambion from Life Technologies), precipitated with ethanol and resuspended in nuclease-free water. cDNA libraries were constructed using a Whole Transcriptome Analysis Kit (Life Technologies) followed by full-scale emulsion PCR according to the supplier’s instructions.

treatment_protocol: SBR5 grown in sufficient or limited iron condition.

tag: strain/background

tag: growth phase

value: stationary

tag: condition

value: sufficient iron


title: Infected_mouse_vagina.rep1

description: infected sample

value: Candida albicans SC5314

tag: tissue

value: day 3 post innoculation