title: Oocyte #1

data_processing:
Reads mapping:We used Burrows-Wheeler Aligner (BWA, Version 0.5.9-r16) to align the clean reads to the hg19 Refseq, with the options "aln -o 1 -e 60 -i 15 -q 10 -t 8". [Ref: Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60]
Expression level analysis : The gene expression level was calculated by using RPKM method, We used all genes with RPKM ≥ 0.1 as expressed genes in the following analysis.
Use BEDTools(Version-2.16.2) to transform *.bam files into *.bed files.[Ref: Aaron R. Quinlan and Ira M. Hall. (2010) BEDTools: a flexible suite of utilities for comparing genomic features,Bioinformatics (2010), 26: 841-842]
Merge the *.bed files from samples in the same stage [available on Series records]
Use IGVtools to transform the merged *.bed files into *.tdf files for visualization [available on Series records]
Genome_build: hg19
Sample_M21.expression.txt: hg19

value: early blastomere

value: human preimplantation embryos


title: seq-AB2621_H3K79me3:361576_N2_L3_Input_Rep2

status: Public on Aug 10 2013

type: SRA

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: input DNA

library_source: genomic

data_processing:
ChIP-seq_alignment-BWA:JL:1 protocol. BWA is a fast light-weighted tool that aligns relatively short sequences to a sequence database. The algorithms is based on Burrows-Wheeler Transform (BWT). This protocal, was ran as DEFAULT for both bwa aln and bwa samse.bwa aln: Find the SA coordinates of the input reads. Maximum maxSeedDiff differences are allowed in the first seedLen subsequence and maximum maxDiff differences are allowed in the whole sequence.OPTIONS:-n NUM
Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]-o INT
Maximum number of gap opens [1]-e INT
Maximum number of gap extensions, -1 for k-difference mode (disallowing long gaps) [-1]-d INT
Disallow a long deletion within INT bp towards the 3?-end [16]-i INT
Disallow an indel within INT bp towards the ends [5]-l INT
Take the first INT subsequence as seed. If INT is larger than the query sequence, seeding will be disabled. For long reads, this option is typically ranged from 25 to 35 for ?-k 2?. [inf]-k INT
Maximum edit distance in the seed [2]-t INT
Number of threads (multi-threading mode) [1]-M INT
Mismatch penalty. BWA will not search for suboptimal hits with a score lower than (bestScore-misMsc). [3]-O INT
Gap open penalty [11]-E INT
Gap extension penalty [4]-R INT
Proceed with suboptimal alignments if there are no more than INT equally best hits. This option only affects paired-end mapping. Increasing this threshold helps to improve the pairing accuracy at the cost of speed, especially for short reads (~32bp).-c
Reverse query but not complement it, which is required for alignment in the color space.-N
Disable iterative search. All hits with no more than maxDiff differences will be found. This mode is much slower than the default.-q INT
Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0] bwa samse:Generate alignments in the SAM format given single-end reads. Repetitive hits will be randomly chosen.OPTIONS:-n INT
Maximum number of alignments to output in the XA tag for reads paired properly. If a read has more than INT hits, the XA tag will not be written. [3]  Processed data are obtained using following parameters: genome version is ce6   BEADS_Normalization protocol. Bias Elimination Algorithm for Deep Sequencing (BEADS): Sequence biasesin the Input and ChIP samples were normalized to remove: GC contentbiases, mappability biases, and regional biases. The originalPython/Java implementation can be accessed athttp://beads.sourceforge.net. Histone_Replicates_QC protocol. After BEADS normalization, genome wide correlation of BEADS signal was calculated in 1 kb windows, with a requirement for replicate correlation of at least 0.7. Signal tracks of biological replicates were also inspected visually for reproducibility.

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: Worm_L3_growth_and_harvest_vPK1. About 2-7 million of worms are bleached and then hatched in M9 for 24-42 hrs. About 100 embryos are seeded onto the plate to test for contamination and hatching efficiency. Remaining hatched L1 larvae are inoculated in a proper volume of liquid culture. Next day when larvae reach the L3 stage they are cleaned by M9 washes and sucrose gradient and collected by freezing in liquid nitrogen. Just before collection DIC pictures are taken and about 50ul of worms are stained for DAPI to assess the stage.

extract_protocol:
Worm_L3_extraction_vPK1. Worms are frozen, ground, and crosslinked for 10 minutes in 1% formaldehyde. Formaldehyde is quenched and cross-linked tissue washed, then resuspended in FA buffer and subjected to sonication in Bioruptor (14 pulses of 30 seconds with 1 minute rests in between). Extracts are then spun down and soluble fraction is stored for quality tests and future ChIP.
Worm_chromatin_immunoprecipitation_vIL2. Appropriate amount of extract is incubated overnight with a proper amount of antibody (exceptional antibodies due to better results are incubated 2hrs). Afterwards, 40ul of equilibrated magnetic beads (either protein A or G, depending on antibody) are added and incubated for 2 hrs. Later, washes with FA, 500mM-salt FA, 1M salt FA, TEL, and TE buffer are performed and DNA is eluted in elution buffer (1% SDS in TE with 250 mM NaCl) ? two times with 57 ?l volume each, at 65°C. Samples are treated with RNAse, proteinase K and then crosslinks are reversed overnight at 65°C. DNA is purified on Qiagen PCR purification columns, tested by q-PCR for ChIP quality, and stored at -20°C for future applications.
ChIP or input DNA is blunt ended, A-tailed, ligated to adaptors, amplified by PCR, then size selected using AMPure beads.  The protocol uses the Illuimina TruSeq DNA Sample Prep Kit.
Prepared sample are sequenced using Illumina GAII or HiSeq2000 at the High Throughput Sequencing Facility of University of North Carolina at Chapel Hill or Cambridge.

tag: strain

tag: developmental stage

value: L3 Larva

tag: genotype

value: wild type

tag: sex type

value: mixed Male and Hermaphrodite population


title: Nr106 MNA rep2

status: Public on Aug 09 2013

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

library_source: transcriptomic

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Tophat (v1.4.1) vs. the C. elegans genome (WS220)
For counting the reads per gene (raw counts) the Python package HTSeq was used in mode ‘union’ together with the Ensembl gene annotation. Only uniquely mapable reads were regarded.
Raw counts were analyzed using the R Statistical Computing Environment. RPKM values were calculated for each gene from the annotation (see ce_Nr101-109_counts_rpkm.xls)
Genome_build: WS220

molecule: total RNA

source_name: total RNA from whole animals, 1-MNA 1µM

growth_protocol: Nematodes were grown and maintained on NGM agar plates according to standard protocol as described (Brenner et al. 1974)

extract_protocol:
Total RNA was isolated using QIAzol (Qiagen, Hilden, Germany) based on the phenol/chloroform extraction method.  Afterwards the RNA was quantified photometrically with a NanoDrop 1000 (PeqLab, Erlangen, Germany) and stored at -80 °C until use.
For library preparation an amount of 2 μg of total RNA per sample was processed using Illumina’s TruSeqTM RNA Sample Prep Kit (Illumina; San Diego; CA, USA) following the manufacturer’s instruction.

treatment_protocol: Treatment of C. elegans was carried out on NGM agar plates containing 1nM nicotinic acid, 1 µM 1-MNA or the respective solvent control (H2O). All agar plates were prepared from the same batch of NGM agar, whereas treatment plates were supplemented with the respective compound and control plates with water.

tag: tissue

value: whole animal

value: Adult (48 hours after L4)

tag: agent

value: 1-MNA 1µM


title: Nr108 H20 rep3

source_name: total RNA from whole animals, control plate

value: control plate


title: Nr105 H20 rep2


title: Nr107 NA rep3

source_name: total RNA from whole animals, nicotinic acid 1mM

value: nicotinic acid 1mM


title: Nr109 MNA rep3


title: Nr104 NA rep2


title: Nr102 H20 rep1


title: Nr103 MNA rep1


title: Nr101 NA rep1


title: ThioMac-H4K8ac-KLA-1h-Inhibitors-group-2

city: Kuopio

first: Minna

middle: U

last: Kaikkonen

department: A.I. Virtanen Institute, Department of Biotechnology and Molecular Medicine

country: Finland

institute: University of Eastern Finland

description: H4K8ac nucleosomal DNA, KLA 1h

data_processing:
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
Gro-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9

organism: Mus musculus

source_name: Primary thioglycollate-elicited peritoneal macrophages

growth_protocol:
Growth-ThioMac
Growth-ThioMac: Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 10 min ? 48 hours. For inhibitor experiments, the inhibitors were added one hour prior to KLA, except ?-amanitin pretreatment was 4h due to its slow uptake. Final concentrations of the drugs were 30 µM of Inhibitor of IKK II (IKKi), 10 ?g/ml of alpha-amanitin, 5 ?g/ml of actinomycin D, 1µM of IBET151 (GSK), flavopiridol and triptolide
Growth-BMDM: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FBS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.
Growth-PUER: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.
Growth-PU.1-null: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

extract_protocol:
Extraction-ChIP-Seq
Extraction-Gro-Seq: Nuclei were extracted from 8-12 million cells grown on 10 cm plates and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 10-16 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina Genome Analyzer II or HiSeq 2000.
Extraction-ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, lysates clarified from isolated nuclei were treated with MNase and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3? end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere?s instructions.

tag: cell type

value: Macrophage

tag: treatment

value: Kdo2 Lipid A (KLA) 1h

tag: chip antibody

value: H4K8ac (Millipore 07-328)


title: ThioMac-H4K8ac-Amanitin-5h-KLA-1h-Inhibitors-group-2

description: H4K8ac nucleosomal DNA, Amanitin 1h

value: alpha-Amanitin 1h


title: ThioMac-notx-siCtl-input

description: ThioMac genomic DNA, notx siCtl (input)

value: siCtl


title: ThioMac-H4K8ac-notx-Inhibitors-group-2

description: H4K8ac nucleosomal DNA, notx


title: ThioMac-H4K8ac-Amanitin-5h-KLA-1h-Inhibitors-group-1

description: H4K8ac nucleosomal DNA, Amanitin 1h


title: ThioMac-KLA-6h-siCtl-input

description: ThioMac genomic DNA, KLA 6h siCtl (input)

value: Kdo2 Lipid A (KLA) 6h, siCtl


title: ThioMac-KLA-1h-input

description: ThioMac genomic DNA, KLA 1h (input)


title: ThioMac-H4K8ac-notx-Inhibitors-group-1

description: H4K8ac nucleosomal DNA, notx


title: ThioMac-H3K4me2-Amanitin-5h-KLA-1h-Inhibitors-group-2

description: H3K4me2 nucleosomal DNA, Amanitin 1h

value: H3K4me2 (Millipore 07-030)


title: ThioMac-H4K8ac-KLA-1h-Inhibitors-group-1

description: H4K8ac nucleosomal DNA, KLA 1h


title: ThioMac-H3K4me2-KLA-1h-Inhibitors-group-1

description: H3K4me2 nucleosomal DNA, KLA 1h


title: ThioMac-H3K4me2-KLA-1h-Inhibitors-group-2

description: H3K4me2 nucleosomal DNA, KLA 1h


title: ThioMac-H3K4me2-notx-Inhibitors-group-2

description: H3K4me2 nucleosomal DNA, notx


title: ThioMac-H3K4me2-Amanitin-5h-KLA-1h-Inhibitors-group-1

description: H3K4me2 nucleosomal DNA, Amanitin 1h


title: ThioMac-H3K4me2-notx-Inhibitors-group-1

description: H3K4me2 nucleosomal DNA, notx


title: ThioMac-H3K4me2-KLA-6h-siSmyd3

description: H3K4me2 nucleosomal DNA, KLA 6h siSmyd3

value: Kdo2 Lipid A (KLA) 6h, siSmyd3


title: ThioMac-H3K4me1-KLA-6h-siSmyd2

description: H3K4me1 nucleosomal DNA, KLA 6h siSmyd2

value: Kdo2 Lipid A (KLA) 6h, siSmyd2

value: H3K4me1 (Abcam ab8895)


title: ThioMac-H3K4me1-notx-siSmyd2

description: H3K4me1 nucleosomal DNA, notx siSmyd2


title: ThioMac-H3K4me1-KLA-6h-siSmyd3

description: H3K4me1 nucleosomal DNA, KLA 6h siSmyd3


title: ThioMac-H3K4me1-KLA-6h-siSmyd1

description: H3K4me1 nucleosomal DNA, KLA 6h siSmyd1

value: Kdo2 Lipid A (KLA) 6h, siSmyd1


title: ThioMac-H3K4me2-KLA-6h-siSmyd2

description: H3K4me2 nucleosomal DNA, KLA 6h siSmyd2


title: ThioMac-H3K4me2-KLA-6h-siSet1b

description: H3K4me2 nucleosomal DNA, KLA 6h siSet1b

value: Kdo2 Lipid A (KLA) 6h, siSet1b


title: ThioMac-H3K4me2-KLA-6h-siSmyd1

description: H3K4me2 nucleosomal DNA, KLA 6h siSmyd1


title: ThioMac-H3K4me2-notx-siSmyd3

description: H3K4me2 nucleosomal DNA, notx siSmyd3


title: ThioMac-H3K4me2-KLA-6h-siSet1a

description: H3K4me2 nucleosomal DNA, KLA 6h siSet1a

value: Kdo2 Lipid A (KLA) 6h, siSet1a


title: ThioMac-H3K4me2-notx-siSmyd2

description: H3K4me2 nucleosomal DNA, notx siSmyd2


title: ThioMac-H3K4me1-notx-siSmyd3

description: H3K4me1 nucleosomal DNA, notx siSmyd3


title: ThioMac-H3K4me2-KLA-6h-siSetd7

description: H3K4me2 nucleosomal DNA, KLA 6h siSetd7

value: Kdo2 Lipid A (KLA) 6h, siSetd7


title: ThioMac-H3K4me2-notx-siSet1b

description: H3K4me2 nucleosomal DNA, notx siSet1b


title: ThioMac-H3K4me2-notx-siSetd7

description: H3K4me2 nucleosomal DNA, notx siSetd7


title: ThioMac-H3K4me2-notx-siSet1a

description: H3K4me2 nucleosomal DNA, notx siSet1a


title: ThioMac-H3K4me1-notx-siSetd7

description: H3K4me1 nucleosomal DNA, notx siSetd7


title: ThioMac-H3K4me1-notx-siSet1b

description: H3K4me1 nucleosomal DNA, notx siSet1b


title: ThioMac-H3K4me1-KLA-6h-siSetd7

description: H3K4me1 nucleosomal DNA, KLA 6h siSetd7


title: ThioMac-H3K4me1-KLA-6h-siSet1a

description: H3K4me1 nucleosomal DNA, KLA 6h siSet1a


title: ThioMac-H3K4me2-KLA-6h-siMll3

description: H3K4me2 nucleosomal DNA, KLA 6h siMll3

value: Kdo2 Lipid A (KLA) 6h, siMll3


title: ThioMac-H3K4me1-KLA-6h-siSet1b

description: H3K4me1 nucleosomal DNA, KLA 6h siSet1b


title: ThioMac-H3K4me2-KLA-6h-siCtl

description: H3K4me2 nucleosomal DNA, KLA 6h siCtl


title: ThioMac-H3K4me2-notx-siMll1

description: H3K4me2 nucleosomal DNA, notx siMll1


title: ThioMac-H3K4me1-KLA-6h-siMll3

description: H3K4me1 nucleosomal DNA, KLA 6h siMll3


title: ThioMac-H3K4me2-KLA-6h-siMll1

description: H3K4me2 nucleosomal DNA, KLA 6h siMll1

value: Kdo2 Lipid A (KLA) 6h, siMll1


title: ThioMac-H3K4me1-notx-siSet1a

description: H3K4me1 nucleosomal DNA, notx siSet1a


title: ThioMac-H3K4me2-notx-siMll2-4

description: H3K4me2 nucleosomal DNA, notx siMll2 4


title: ThioMac-H3K4me1-KLA-6h-siMll2-4

description: H3K4me1 nucleosomal DNA, KLA 6h siMll2 4

value: Kdo2 Lipid A (KLA) 6h, siMll2/4


title: ThioMac-H3K4me1-notx-siMll3

description: H3K4me1 nucleosomal DNA, notx siMll3

value: Macrophage


title: ThioMac-H3K4me1-KLA-6h-siMll1

description: H3K4me1 nucleosomal DNA, KLA 6h siMll1


title: ThioMac-H3K4me1-KLA-6h-siCtl

description: H3K4me1 nucleosomal DNA, KLA 6h siCtl


title: ThioMac-H3K4me1-notx-siMll2-4

description: H3K4me1 nucleosomal DNA, notx siMll2 4


title: ThioMac-H3K4me1-notx-siMll1

description: H3K4me1 nucleosomal DNA, notx siMll1


title: ThioMac-H3K27ac-notx

description: H3K27ac nucleosomal DNA, notx

value: H3K27ac (Abcam ab4729)


title: ThioMac-H3K4me1-notx-siCtl

description: H3K4me1 nucleosomal DNA, notx siCtl


title: ThioMac-p65-IBET-2h-KLA-1h

description: p65 ChIP-Seq, ChIP-seq, IBET 2h KLA 1h

value: IBET 2h, Kdo2 Lipid A (KLA) 1h

value: p65 (Santa Cruz sc-372)


title: ThioMac-H3K27ac-KLA-1h

description: H3K27ac nucleosomal DNA, KLA 1h

value: Kdo2 Lipid A (KLA) 1h


title: ThioMac-p65-DMSO-2h-KLA-1h

description: p65 ChIP-Seq, DMSO 2h KLA 1h

value: DMSO 2h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-H3K4me2-KLA-6h-siMll2-4

description: H3K4me2 nucleosomal DNA, KLA 6h siMll2 4

value: H3K4me2 (Millipore 07-030)


title: ThioMac-PU1-DMSO-2h-KLA-1h

description: PU.1 ChIP-Seq, DMSO 2h KLA 1h

value: PU.1 (Santa Cruz sc-352)


title: ThioMac-H3K4me2-notx-siMll3

description: H3K4me2 nucleosomal DNA, notx siMll3


title: ThioMac-H3K4me2-notx-siCtl

description: H3K4me2 nucleosomal DNA, notx siCtl

value: siCtl


title: ThioMac-p65-Flavopiridol-7h-KLA-6h

description: p65 ChIP-Seq, Flavopiridol 7h KLA 6h

value: Flavopiridol 7h, Kdo2 Lipid A (KLA) 6h


title: ThioMac-PU1-DMSO-7h-KLA-6h

description: PU.1 ChIP-Seq, DMSO 7h KLA 6h

value: DMSO 7h, Kdo2 Lipid A (KLA) 6h


title: ThioMac-CEBPa-KLA-1h

description: CEBPa ChIP-Seq, KLA 1h

value: C/EBPa (Santa Cruz sc-61)


title: ThioMac-p65-DMSO-7h-KLA-6h

description: p65 ChIP-Seq, DMSO 7h KLA 6h


title: ThioMac-CEBPa-notx

description: CEBPa ChIP-Seq, notx


title: ThioMac-p65-KLA-1h-group-1

description: p65 ChIP-Seq, KLA 1h


title: ThioMac-p65-notx-group-2

description: p65 ChIP-Seq, notx


title: ThioMac-p65-KLA-6h-group-1

description: p65 ChIP-Seq, KLA 6h

value: Kdo2 Lipid A (KLA) 6h


title: ThioMac-p65-notx-group-1

description: p65 ChIP-Seq, notx


title: ThioMac-p65-KLA-24h-group-1

description: p65 ChIP-Seq, KLA 24h

value: Kdo2 Lipid A (KLA) 24h


title: ThioMac-PU1-KLA-24h

description: PU.1 ChIP-Seq, KLA 24h


title: ThioMac-PU1-KLA-12h

description: PU.1 ChIP-Seq, KLA 12h

value: Kdo2 Lipid A (KLA) 12h


title: ThioMac-PU1-IBET-2h-KLA-1h

description: PU.1 ChIP-Seq, IBET 2h KLA 1h


title: ThioMac-PU1-KLA-6h

description: PU.1 ChIP-Seq, KLA 6h


title: ThioMac-PU1-KLA-1h

description: PU.1 ChIP-Seq, KLA 1h


title: ThioMac-H4K8ac-Flavopiridol-2h-KLA-1h-group-2

description: H4K8ac nucleosomal DNA, Flavopiridol 2h KLA 1h

value: Flavopiridol 2h, Kdo2 Lipid A (KLA) 1h

value: H4K8ac (Millipore 07-328)


title: ThioMac-H4K8ac-DMSO-2h-KLA-1h-group-1

description: H4K8ac nucleosomal DNA, DMSO 2h KLA 1h

value: Macrophage


title: ThioMac-H4K8ac-Flavopiridol-2h-KLA-1h-group-1


title: ThioMac-H4K8ac-IBET-2h-KLA-1h-group-1

description: H4K8ac nucleosomal DNA, IBET 2h KLA 1h


title: ThioMac-H4K8ac-DMSO-2h-group-2

description: H4K8ac nucleosomal DNA, DMSO 2h

value: DMSO 2h


title: ThioMac-PU1-notx

description: PU.1 ChIP-Seq, notx


title: ThioMac-H4K8ac-DMSO-2h-KLA-1h-group-2

description: H4K8ac nucleosomal DNA, DMSO 2h KLA 1h


title: ThioMac-H4K8ac-DMSO-2h-group-1

description: H4K8ac nucleosomal DNA, DMSO 2h


title: ThioMac-PU1-Flavopiridol-7h-KLA-6h

description: PU.1 ChIP-Seq, Flavopiridol 7h KLA 6h


title: ThioMac-H4K8ac-IBET-2h-group-1

description: H4K8ac nucleosomal DNA, IBET 2h

value: IBET 2h


title: ThioMac-H4K8ac-Flavopiridol-2h-group-1

description: H4K8ac nucleosomal DNA, Flavopiridol 2h

value: Flavopiridol 2h


title: ThioMac-p65-KLA-1h-group-2

description: p65 ChIP-Seq, KLA 1h

value: Kdo2 Lipid A (KLA) 1h

value: p65 (Santa Cruz sc-372)


title: ThioMac-H3K4me2-IBET-7h-KLA-6h

description: H3K4me2 nucleosomal DNA, IBET 7h KLA 6h

value: IBET 7h, Kdo2 Lipid A (KLA) 6h

value: H3K4me2 (Millipore 07-030)


title: ThioMac-H3K4me2-Flavopiridol-7h-KLA-6h

description: H3K4me2 nucleosomal DNA, Flavopiridol 7h KLA 6h


title: ThioMac-H3K4me2-DMSO-7h-KLA-6h

description: H3K4me2 nucleosomal DNA, DMSO 7h KLA 6h


title: PUER-GroSeq-Tamoxifen-24h-KLA-1h

description: Gro-Seq for nascent RNA in PUER cells, Tamoxifen 24h KLA 1h

data_processing:
Library strategy: GRO-Seq
Libraries were sequenced for 36 or 50 cycles on an Illumina Genome Analyzer II or HiSeq 2000, respectively, according to the manufacturer’s instructions.
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome (NCBI build using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.
Gro-Seq results were trimmed to remove A-stretches originating from the library preparation. Data analysis was performed using HOMER and the detailed instructions for analysis can be found at http://biowhat.ucsd.edu/homer/
For ChIP-Seq, Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped. UCSC Genome Browser BigWig or BigWig hub text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.
Genome_build: mm9

source_name: PUER cells

growth_protocol:
Growth-PUER
Growth-ThioMac: Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 10 min ? 48 hours. For inhibitor experiments, the inhibitors were added one hour prior to KLA, except ?-amanitin pretreatment was 4h due to its slow uptake. Final concentrations of the drugs were 30 µM of Inhibitor of IKK II (IKKi), 10 ?g/ml of alpha-amanitin, 5 ?g/ml of actinomycin D, 1µM of IBET151 (GSK), flavopiridol and triptolide
Growth-BMDM: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FBS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.
Growth-PUER: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.
Growth-PU.1-null: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

extract_protocol:
Extraction-Gro-Seq
Extraction-Gro-Seq: Nuclei were extracted from 8-12 million cells grown on 10 cm plates and nuclear run-on reactions were performed for 5 minutes at 30°C in the presence of Sarkosyl and BrUTP. RNA was extracted with Trizol, DNase-treated, base-hydrolyzed and dephosphorylated with PNK. BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads and precipitated overnight. Poly(A)-tailing was followed by cDNA synthesis using complementary poly(T)-primers. Excess oligo was removed by Exonuclease I and cDNA fragments of were purified on a denaturing 10% polyacrylamide TBE-urea gel. The recovered cDNA was circularized, linearized, amplified for 10-16 cycles. The final product was ran on 10% TBE gel, gel purified and cleaned-up using ChIP DNA clean & Concentrator Kit. The final libraries were sequenced using an Illumina Genome Analyzer II or HiSeq 2000.
Extraction-ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody. Alternatively, lysates clarified from isolated nuclei were treated with MNase and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3? end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere?s instructions.

value: PUER cells

value: Tamoxifen 24h, Kdo2 Lipid A (KLA) 1h


title: PUER-GroSeq-Tamoxifen-24h

description: Gro-Seq for nascent RNA in PUER cells, Tamoxifen 24h

value: Tamoxifen 24h


title: PU1-null-GroSeq-KLA-1h

description: Gro-Seq for nascent RNA in PU.1 null cells, KLA 1h

source_name: PU.1-/- myeloid cell

growth_protocol:
Growth-PU.1-null
Growth-ThioMac: Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 10 min ? 48 hours. For inhibitor experiments, the inhibitors were added one hour prior to KLA, except ?-amanitin pretreatment was 4h due to its slow uptake. Final concentrations of the drugs were 30 µM of Inhibitor of IKK II (IKKi), 10 ?g/ml of alpha-amanitin, 5 ?g/ml of actinomycin D, 1µM of IBET151 (GSK), flavopiridol and triptolide
Growth-BMDM: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FBS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.
Growth-PUER: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.
Growth-PU.1-null: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

value: PU.1-/- myeloid cell


title: ThioMac-GroSeq-Triptolide-2h-KLA-1h-Inhibitors-group-3

description: Gro-Seq for nascent RNA, Triptolide 2h KLA 1h

value: Triptolide 2h, Kdo2 Lipid A (KLA) 1h


title: PU1-null-GroSeq-notx-1h

description: Gro-Seq for nascent RNA in PU.1 null cells, notx 1h


title: ThioMac-GroSeq-ActinomycinD-2h-KLA-1h-Inhibitors-group-3

description: Gro-Seq for nascent RNA, ActinomycinD 2h KLA 1h

value: ActinomycinD 2h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-GroSeq-Flavopiridol-2h-KLA-1h-Inhibitors-group-2

description: Gro-Seq for nascent RNA, Flavopiridol 2h KLA 1h. Note: For controls, use ThioMac-GroSeq-notx-group-4-1.fastq.gz and ThioMac-GroSeq-KLA-1h-group-4-1.fastq.gz


title: ThioMac-GroSeq-DMSO-2h-Inhibitors-group-3

description: Gro-Seq for nascent RNA, DMSO 2h


title: ThioMac-GroSeq-DMSO-2h-KLA-1h-Inhibitors-group-3

description: Gro-Seq for nascent RNA, DMSO 2h KLA 1h

value: DMSO 2h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-GroSeq-IBET-2h-KLA-1h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, IBET 2h KLA 1h

value: IBET 2h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-GroSeq-Flavopiridol-2h-KLA-1h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, Flavopiridol 2h KLA 1h

value: Flavopiridol 2h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-H3K4me2-IKKi-7h-KLA-6h

description: H3K4me2 nucleosomal DNA, IKKi 7h KLA 6h

value: Macrophage

value: IKKi 7h, Kdo2 Lipid A (KLA) 6h


title: Whole Cell Extract Wapl -/delta

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

data_processing:
Alignment: Reads that passed the Illumina quality filtering were considered for alignment. The remaining reads were aligned against the mouse genome assembly version July 2007 (NCBI37/mm9) using the BOWTIE program version 12.5 [Langmead, 2009], allowing up to two mismatches, and ignoring any read that would match more than once.
Peak calling: Peaks were called using the MACS program version 1.3.6.1 [Zhang et al.] with default parameters and appropriate tag size, mm9 genome size (2654911517), sample and input read files. In cases where the read shifting model could not be build with the default mfold parameter (32), the mfold cutoff was lowered up to the point where sufficient high quality peaks could be found to build the model (100). Peaks were further filtered for p-values lower than 1e-10. This cutoff is more conservative than the default (1e-5), and worked well in removing false positive (=unique) peaks of technical replicates [data not shown].
Genome_build: mm9
Supplementary_files_format_and_content: BED files contain all uniquely aligned reads or called peaks

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were starved in OptMEM containing 2% serum for seven days

extract_protocol:
Samples were sonicated for 12 x 60 second pulses with a Covaris sonicator; DNA was purified with Phase lock gel tubes (5PRIME)
Single read - Illumina

treatment_protocol: 4-OHT was added to the starvation medium to a final concentration of 500 nM

value: embryonic fibroblast

value: Wapl -/delta

tag: genetic background

value: mixed C57BL/6 and 129 background

value: rabbit anti-Smc3

tag: chip antibody manufacturer

value: Bethyl

tag: chip antibody catalog #


title: CTCF Wapl -/delta

value: Wapl +/delta

value: rabbit anti-CTCF

value: Upstate


title: Whole Cell Extract Wapl +/delta


title: Smc3 Wapl -/delta rep2


title: CTCF Wapl +/delta


title: ThioMac-GroSeq-DMSO-2h-KLA-1h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, DMSO 2h KLA 1h


title: Smc3 Wapl -/delta rep1


title: ThioMac-GroSeq-IBET-2h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, IBET 2h

value: IBET 2h


title: ThioMac-GroSeq-DMSO-2h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, DMSO 2h

value: DMSO 2h


title: ThioMac-GroSeq-Flavopiridol-2h-Inhibitors-group-1

description: Gro-Seq for nascent RNA, Flavopiridol 2h

value: Flavopiridol 2h


title: Smc3 Wapl +/delta rep2


title: Colon_Primary_Normal

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

institute: Max Planck Institute of Psychiatry

description: original data source: Meissner Lab in house

data_processing:
BiSeq raw sequencing reads were aligned using maq in bisulfite mode (Li et al. 2008) or bsmap 2.7 (Xi et al. 2009) against human genome version hg19/GRCh37, discarding duplicate reads. DNA methylation calling was performed based on an extended custom software pipeline published previously for RRBS (Gu et al., 2010).
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads is listed in the score column

organism: Homo sapiens

source_name: primary colon adjacent to tumor tissue, matching control for tumor; BioChain Institute, INC(Catalog no D8235090-pp-10, lot no A704198)

extract_protocol: Bisulfite-Seq:Genomic DNA was fragmented to 100-500 bp using a Covaris S2 sonicator. DNA fragments were cleaned-up, end-repaired, A-tailed, and ligated with methylated paired-end adapters (purchased from ATDBio). Bisulfite conversion and sequencing was done as previously described (Zhong et al. 2011)

tag: disease type

tag: culture medium and passage number

tag: race

tag: gender

value: male

tag: cogdx (cognitive impairment)

tag: gpath (global pathology)

tag: nft (neurofibrillary tangles)

tag: np (neuritic plaques)

tag: age at death


title: ThioMac-GroSeq-KLA-1h-group-5

description: Gro-Seq for nascent RNA, DMSO 2h KLA 1h

tag: strain

value: Kdo2 Lipid A (KLA) 1h


title: Smc3 Wapl +/delta rep1

tag: genotype


title: Colon_Tumor_Primary

source_name: colon primary tumor


title: ThioMac-GroSeq-KLA-1h-group-4

description: Gro-Seq for nascent RNA, DMSO 2h KLA 1h

tag: cell type


title: ThioMac-GroSeq-KLA-6h-group-4

description: Gro-Seq for nascent RNA, DMSO 2h KLA 6h

tag: treatment

value: Kdo2 Lipid A (KLA) 6h


title: IMR90

source_name: IMR90 immortalized fibroblast cell line

value: MEM + Glutamax (Invitrogen:41090-036)+ 10% FBS+ 1% NEAA, Pen/Strep and Sodium pyruvate  passag number 8


title: ThioMac-GroSeq-notx-group-5

description: Gro-Seq for nascent RNA, DMSO 2h

value: Macrophage


title: ThioMac-GroSeq-Amanitin-5h-KLA-1h-Inhibitors-group-3

description: Gro-Seq for nascent RNA, Amanitin 5h KLA 1h

value: alpha-Amanitin 5h, Kdo2 Lipid A (KLA) 1h


title: ThioMac-GroSeq-notx-group-4

description: Gro-Seq for nascent RNA, DMSO 2h


title: ThioMac-GroSeq-KLA-24h-group-2

description: Gro-Seq for nascent RNA, KLA 24h

value: Kdo2 Lipid A (KLA) 24h


title: HepG2

source_name: HepG2 cell line

value: HepG2 cells were cultured using the ENCODE guide lines:DMEM + 10% FBS + 1%pen/strep +1%glutamax   passage number 9


title: Frontal_cortex_AD_2

source_name: human frontal cortex Alzheimer

value: Alzheimer

value: White

value: Female


title: ThioMac-GroSeq-KLA-12h-group-2

description: Gro-Seq for nascent RNA, KLA 12h

value: Kdo2 Lipid A (KLA) 12h


title: Frontal_cortex_AD_1


title: ThioMac-GroSeq-KLA-1h-group-2

description: Gro-Seq for nascent RNA, KLA 1h


title: ThioMac-GroSeq-KLA-10m-group-2

description: Gro-Seq for nascent RNA, KLA 10m

value: Kdo2 Lipid A (KLA) 10m


title: Frontal_cortex_normal_2

source_name: human frontal cortex normal


title: ThioMac-GroSeq-KLA-6h-group-2

description: Gro-Seq for nascent RNA, KLA 6h


title: HKC8-H3K36me3

city: Philadelphia

first: Yi-An

last: Ko

state: Pennsylvania

address: 415 curie blvd

department: Genetics & Gene Regulation

country: USA

institute: UPeenn

data_processing:
Basecalls performed using CASAVA version 1.7.0
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 0.12.7 with the following configurations --phred33-quals -k 1 --sam --tryhard -p 8
Peaks were called usingMACS version 1.4.1 with the following setting: macs --treatment=<bam file for IP sample> --control=<bam file for INPUT sample> --name=<sample name> --format=BAM --gsize=2.7e9  --wig --space=100
Genome_build: hg19
Supplementary_files_format_and_content: bed files with called peaks

source_name: human kidney proximal tubule cells (HKC8 cells)

growth_protocol: Human proximal tubular epithelial cells (HKC-8) were maintained in DMEM/F12 medium with supplemented with 2.5% fetal bovine serum, antibiotics and insulin, transferrin and selenium.

extract_protocol:
HKC8 cell were collected when it reached to 80% confluence. Media were changed before fixing the cells to remove the dead cells. Cells were cross-linked with formaldehyde in a final concentration of 1% for 10 mins at room temperature.  A final concentration of 0.125M glycine was used in room temperature for 10 minutes to stop the reaction. Cells were scraped with ice cold PBS containing protease inhibitor.  The chromatin immunoprecipitation procedure was done with Invitrogen MAGnify™ Chromatin immunoprecipitation System following the manufacturer's protocols.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit  (Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation.

tag: cells

value: HKC8 cells

tag: antibodies


title: HKC8-Input

treatment_protocol: HKC8 cell were collected when it reached to 80% confluence. Media were changed before fixing the cells to remove the dead cells. Cells were cross-linked with formaldehyde in a final concentration of 1% for 10 mins at room temperature.  A final concentration of 0.125M glycine was used in room temperature for 10 minutes to stop the reaction. Cells were scraped with ice cold PBS containing protease inhibitor.  The chromatin immunoprecipitation procedure was done with Invitrogen MAGnify™ Chromatin immunoprecipitation System following the manufacturer's protocols.


title: ThioMac-GroSeq-notx-group-2

description: Gro-Seq for nascent RNA, notx


title: HKC8-H3K27me3


title: HKC8-H3K27ac


title: ThioMac-notx-input

description: ThioMac genomic DNA, notx (input)


title: HKC8-H3K4me2


title: HKC8-H3K4me1


title: ThioMac-PolII-serine2-DMSO-2h-KLA-1h

description: PolII serine2 ChIP-Seq, DMSO 2h KLA 1h

value: DMSO 2h, Kdo2 Lipid A (KLA) 1h

tag: chip antibody

value: RNA polymerase II CTD phsophoSerine 2 (Abcam  5095)


title: BMDM-H4K5ac-KLA-18h

description: H4K5ac nucleosomal DNA, KLA 18h

source_name: Bone marrow derived macrophages

growth_protocol:
Growth-BMDM
Growth-ThioMac: Primary cells were isolated from 6-8 week-old C57Bl/6 (Harlan Laboratories) male mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium. The following day fresh medium containing 0.5% fetal bovine serum was added to the cells and serum starvation was carried overnight. After serum starvation the cells were treated with 100 ng/ml of Kdo2-Lipid A for 10 min ? 48 hours. For inhibitor experiments, the inhibitors were added one hour prior to KLA, except ?-amanitin pretreatment was 4h due to its slow uptake. Final concentrations of the drugs were 30 µM of Inhibitor of IKK II (IKKi), 10 ?g/ml of alpha-amanitin, 5 ?g/ml of actinomycin D, 1µM of IBET151 (GSK), flavopiridol and triptolide
Growth-BMDM: Bone marrow was harvested and washed once with PBS, seeded/cultured in DMEM containing 20 % FBS, 30 % L-cell conditioned media (as source of macrophage colony stimulating factor, M-CSF), and 100 U/ml penicillin/streptomycin in non-tissue culture-treated petri dishes. After 6-8 days of culture, non-adherent cells were washed off with room temperature PBS and macrophages were obtained as a homogeneous population of adherent cells which were scraped and subsequently seeded onto tissue culture-treated petri dishes overnight in RPMI 1640 containing 10% FCS, 100 U/ml penicillin/streptomycin, and 10ng/ml M-CSF.
Growth-PUER: PUER cells were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 1 µg/ml puromycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4. The PU.1-ER fusion protein was activated by adding 4-hydroxy-tamoxifen at a final concentration of 100 nM to the media.
Growth-PU.1-null: PU.1-/- were propagated in 10 % FCS/Iscove's Modified Dulbecco's Medium (IMDM) supplemented with 100 U/ml penicillin/streptomycin, 2 mM L-glutamine and 5 ng/ml recombinant mIL-4.

value: Kdo2 Lipid A (KLA) 18h

value: H4K8ac (Millipore 07-327)


title: ThioMac-PolII-serine2-DMSO-2h

description: PolII serine2 ChIP-Seq, DMSO 2h

value: DMSO 2h


title: HKC8-H3K4me3


title: ThioMac-H3K4me2-KLA-48h

description: H3K4me2 nucleosomal DNA, KLA 48h

value: Kdo2 Lipid A (KLA) 48h

value: H3K4me2 (Millipore 07-030)


title: ThioMac-H3K4me2-KLA-6h

description: H3K4me2 nucleosomal DNA, KLA 6h

value: Macrophage

value: Kdo2 Lipid A (KLA) 6h


title: BMDM-H4K5ac-KLA-6h

description: H4K5ac nucleosomal DNA, KLA 6h


title: BMDM-H4K5ac-KLA-1h

description: H4K5ac nucleosomal DNA, KLA 1h

value: Kdo2 Lipid A (KLA) 1h


title: BMDM-H4K5ac-notx

description: H4K5ac nucleosomal DNA, notx


title: ThioMac-H3K4me2-KLA-24h

description: H3K4me2 nucleosomal DNA, KLA 24h

value: Kdo2 Lipid A (KLA) 24h


title: ThioMac-H3K4me2-notx

description: H3K4me2 nucleosomal DNA, notx


title: ThioMac-GroSeq-KLA-1h-group-3

description: Gro-Seq for nascent RNA, KLA 1h


title: Frontal_cortex_normal_1


title: ThioMac-H3K27me3-notx

description: H3K27me3 nucleosomal DNA, notx

value: H3K27me3 (Millipore 07-449)


title: ThioMac-GroSeq-notx-group-3

description: Gro-Seq for nascent RNA, notx


title: ThioMac-GroSeq-KLA-24h-group-1

description: Gro-Seq for nascent RNA, KLA 24h


title: ThioMac-GroSeq-KLA-12h-group-1

description: Gro-Seq for nascent RNA, KLA 12h


title: fly_input_shEll_ChIP_3

status: Public on Aug 08 2013

city: Kansas CIty

first: Alexander

middle: (Garrett)

last: Garruss

state: Missouri

address: 1000 East 50th Street

institute: Stowers Institute for Medical Research

description: Input DNA from whole cell extract following Ell RNAi

data_processing:
Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bedGraph files were created at 25bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.1 (20110622) using the indicated criteria.
RNA-seq alignments were done using TopHat v1.4.1 Differential expression analysis was done using DESeq corresponding to bioconductor version for R v2.11.1
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Genome_build: UCSC hg19 and UCSC dm3

organism: Drosophila melanogaster

source_name: S2 cell culture

growth_protocol: Drosophila chromatin immunoprecipitation was performed with S2 cells grown in Schneider's media with 10% FBS at room temperature.

extract_protocol: ChIP libraries were prepared with the TruSeq DNA Sample Kit (Illumina #FC-121-2001) according to Illumina's instructions.

treatment_protocol: Cells were fixed for 10 minutes in 1% formaldehyde, quenched with the addition of 1/10 volume of 2.5 M Glycine in PBS for 10 minutes, cells were washed twice in PBS, resuspended in hypotonic buffer and nutated for 10 minutes.3x10e7 cells were pelleted and resuspended in 1.3 ml RIPA buffer with 0.5% Sarkosyl.Cells were sonicated in polyethylene 15 ml tubes for 15 minutes, high output, in a Bioruptor Diagenode) at 4 degrees. Debris was pelleted 10 minutes at 20,000 x g 4° C. ChIP was performed with 200 µl of chromatin and 5 µg of antibodies, and scaled up 10 fold for ChIP-seq.  Drosophila Ice1, Ell, and non-targeting RNAi was performed as previously described (Smith et al., Mol Cell. 2011 Dec 23;44(6):954-65) except that S2 cells were grown in SFX serum-free media from HyClone (Thermo/HyClone #SH30278.02).

value: S2; Schneider's Drosophila Line 2;  Marco Blanchette's Lab

tag: antibody


title: fly_PolII_nont_ChIP_3

description: Chromatin IP of Pol II following non-targeting RNAi

data_processing:
MACS peak detector v1.4.1 20110622; associated IP and input samples were configured with appropriately sized genome.  Provided are bed file format for peaks meeting criteria: FDR < 5% and fold enrichment > 5.
Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bedGraph files were created at 25bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.1 (20110622) using the indicated criteria.
RNA-seq alignments were done using TopHat v1.4.1 Differential expression analysis was done using DESeq corresponding to bioconductor version for R v2.11.1
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Genome_build: UCSC hg19 and UCSC dm3

value: Drosophila Rpb1 antibody (Smith et al., Mol Cell. 2011 Dec 23;44(6):954-65)


title: ThioMac-GroSeq-KLA-6h-group-1

description: Gro-Seq for nascent RNA, KLA 6h


title: ThioMac-GroSeq-KLA-1h-group-1

description: Gro-Seq for nascent RNA, KLA 1h


title: ThioMac-GroSeq-notx-24h-group-1

description: Gro-Seq for nascent RNA, notx 24h


title: ThioMac-GroSeq-notx-12h-group-1

description: Gro-Seq for nascent RNA, notx 12h


title: fly_PolII_shIce1_2_ChIP_2

description: Chromatin IP of Pol II after Ice1 RNAi #2


title: fly_input_shIce1_1_ChIP_1

description: Input DNA from whole cell extract following Ice1 RNAi #1


title: fly_Ice1_shIce1_1_ChIP_1

description: Chromatin IP of Ice1 after Ice1 RNAi #1


title: fly_PolII_shEll_ChIP_3

description: Chromatin IP of Pol II following Ell RNAi


title: fly_input_non_ChIP_3

description: Input DNA from whole cell extract following non-targeting RNAi


title: fly_input_shIce1_2_ChIP_2

description: Input DNA from whole cell extract following Ice1 RNAi #2


title: ThioMac-GroSeq-notx-1h-group-1

description: Gro-Seq for nascent RNA, notx 1h


title: fly_PolII_shIce1_1_ChIP_1

description: Chromatin IP of Pol II after Ice1 RNAi #1


title: fly_Ice1_shIce1_2_ChIP_2

description: Chromatin IP of Ice1 after Ice1 RNAi #2


title: ThioMac-GroSeq-notx-6h-group-1

description: Gro-Seq for nascent RNA, notx 6h


title: fly_Ice1_nont_ChIP_0

description: Chromatin IP of Ice1 following non-targeting RNAi


title: ThioMac-H3K4me2-KLA-1h

description: H3K4me2 nucleosomal DNA, KLA 1h


title: fly_PolII_nont_ChIP_0


title: IgG_control_ChIP-seq_1

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

country: United Kingdom

institute: University of Warwick

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters
Peaks were called using MACS2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: bed files contain the peak coordinates called by MAC2 for each anti-GFP ChIP replicate over its paired anti-mIgG control ChIP.  Wig file contains the qpois background corrected track for the four merged ChIP replicates.

extract_protocol:
Lysates were precleared with Protein G Dynabeads.  Complexes were then isolated with 6µg anti-GFP monoclonal antibody (Invitrogen A11120, clone 3E6, IgG2a) or control Mouse IgG (Santa Cruz sc-2025, Mouse IgG) linked to Protein G Dynabeads.
Sequencing libraries were then prepared using the Illumina ChIP-seq DNA Sample Prep Kit.  Libraries were size selected at ~200bp and four libraries were multiplexed per lane on a HiSeq 2000.

tag: strain background

tag: cell line

value: CCE

value: mouse embryonic stem cells

tag: genotype/variation

value: expressing Prdm4-EGFP

value: normal mouse IgG

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Prdm4-EGFP_ChIP-seq_3

value: GFP (clone 3E6) Mouse IgG2a, Monoclonal Antibody

value: Invitrogen


title: IgG_control_ChIP-seq_4


title: IgG_control_ChIP-seq_3


title: Prdm4-EGFP_ChIP-seq_4


title: IgG_control_ChIP-seq_2


title: Prdm4-EGFP_ChIP-seq_1


title: human_ICE1KD_RNAseq

description: RNAseq after ICE1 RNAi

data_processing:
Reads were aligned using Ensembl 66 GTF human annotations using TopHat v.1.4.1 and Bowtie v0.12.7.  Alignments were not extended.  UCSC bedGraph files were created at 10bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.7, allowing unique reads only and up to three mismatches of a 50bp seed length.
Peak detection was done using MACS, version 1.4.1 (20110622) using the indicated criteria.
RNA-seq alignments were done using TopHat v1.4.1 Differential expression analysis was done using DESeq corresponding to bioconductor version for R v2.11.1
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
Genome_build: UCSC hg19 and UCSC dm3

source_name: HCT116 cell culture

growth_protocol: For HCT116 cells, 5x10^7 cells were grown according to previously described protocols (Lee et al., 2006).

extract_protocol: 2 µg of total RNA was depleted of ribosomal RNA with the Ribo Zero kit (Epicentre #MRZG12324) and libraries were made with the TruSeq RNA sample Pre Kit (Illumina #RS-122-2001).

treatment_protocol: HCT116 cells were infected with lentivirus harboring either Non-targeting shRNA or ICE1 shRNA in the presence of 8 µg/ml of polybrene (Sigma #H9268) for 24 hours (Target sequence for ICE1 sh1: 5’-ATAAGAGTCGTTTGCGAAATA-3’, Target sequence for ICE1 sh2: 5’-GCCTAATCAAGTATCAGTTAT-3’). The infected cells were selected with 2 µg/ml puromycin for extra 48 h before harvesting the cells for RNA extraction. Total RNA was extracted with Trizol (Invitrogen #15596-018), treated with DNase I (NEB #M03035) for 20 min at room temperature and precipitated with sodium acetate/ethanol in the presence of 1 µg/ml glycogen and dissolved again in RNase-free water.


title: human_WT_RNAseq_repB

description: RNAseq after non-targeting-RNAi; Replicate B


title: fly_input_nont_ChIP_0


title: SyKOyNyiPS2

city: Atlanta

first: Tao

last: Wang

state: GA

address: 615 Michael Street

department: Human Genetics

institute: Emory University

data_processing:
Library strategy: 5hmC-Seq
Bowtie aligned
remove duplicate reads
MACS peak calling
Genome_build: hg18/NCBI36
Supplementary_files_format_and_content: bed files with 5hmC enrichment peaks

source_name: mouse iPSCs

growth_protocol: For OG2-MEFs, the above medium was further supplemented with 0.055 mM β-mercaptoethanol (Gibco), 2 mM L-GlutaMax (Gibco) and 0.1 mM non-essential amino acids (NEAA; Gibco), and for iPSC generation, 50 µg/ml vitamin C (Sigma) and 1000 U/ml LIF (Millipore) were added. iPSCs were maintained on mitomycin C-treated MEF feeder cells knockout DMEM supplemented with 15% knockout serum replacement, 100 U/ml penicillin, 100 μg/ml streptomycin (Gibco), 0.055 mM β-mercaptoethanol (Gibco), 2 mM L-GlutaMax (Gibco), 0.1 mM NEAA (Gibco), and 1000 U/ml leukemia inhibitory factor (Millipore).

extract_protocol:
The captured DNA fragments were used for generation of libraries following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A). A total of 25 ng input genomic DNA, 5hmC-captured DNA or ChIP-DNA was used to initiate the protocol.
DNA fragments (~150–300 bp) were selected using AMPure beads after the adaptor ligation step. PCR-amplified DNA libraries were quantified on an Agilent 2100 Bioanalyzer and diluted to 6–8 pM for cluster generation and sequencing

treatment_protocol: Genomic DNA sonicated to fragments shorter than 500 bp was labeled with azide UDPG catalyzed by beta-glucosyl transferase for 1 h at 37C. The labeled DNA fragments were purified using a PCR purification kit (Qiagen), and then eluted in nuclease-free water. The labeled DNA fragments were biotinylated with a biotin-bisulfide linker at 37C for 2 h. After purification with the PCR purification kit and elution in 100 ul nuclease-free water, the biotinylated DNA was incubated with Dynabeads MyOne Streptavidin C1 (Cat#: 650.02; Invitrogen) in binding buffer containing 10 mM Tris-HCl, pH 7.5, 1 M NaCl, 1 mM EDTA, and 0.5% Tween 20 at room temperature for 15 min. After thorough washing with binding buffer, the captured DNA was eluted with 50 mM fresh DTT at room temperature for 2 h. A Bio-spin 6 Tris column (Cat#: 732-6227; Bio-Rad) was used to remove the DTT from the elution buffer, followed by purification using a Qiagen MinElute PCR Purification Kit, and then the captured DNA was eluted in 10 ul elution buffer.

value: mouse iPSCs

tag: modification

value: 5hmC-chemical label pull down


title: human_PolII_shICE1_ChIP_2

description: Chromatin IP of Pol II following RNAi of ICE1

growth_protocol: For HCT116 cells, 5x10^7 cells were grown and used for each ChIP assay according to previously described protocols (Lee et al., 2006).

treatment_protocol: HCT116 cells were crosslinked with 1% formaldehyde for 10 min at room temperature with rotation and then crosslinking was quenched by the addition of glycine. Fixed chromatin was sonicated on a Misonix 3000 and used for immunoprecipitation with the indicated antibody. HCT116 cells were washed with cold phosphate-buffered saline (PBS) twice and lysed in RIPA buffer (20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1% NP40, 1% sodium deoxycholate, 0.1% SDS, 1 mM dithiothreitol [DTT]) containing proteinase inhibitors (Sigma) for 30 min at 4°C. After centrifugation at 13,000 rpm for 30 min, the supernatant was incubated with the indicated antibodies and protein A/G PLUS agarose (Santa Cruz sc-2003) at 4 °C overnight with gentle rotation. The beads were spun down and washed three times with wash buffer (10 mM HEPES [pH7.4], 1 mM MgCl2, 300mM NaCl, 10mM KCl, 0.2%TritonX-100) before boiling in sodium dodecyl sulfate (SDS) loading buffer.  HCT116 cells harvested following RNAi were infected with lentivirus harboring either Non-targeting shRNA or ICE1 shRNA in the presence of 8 µg/ml of polybrene (Sigma) for 24 hours (Target sequence for ICE1 sh1: 5’-ATAAGAGTCGTTTGCGAAATA-3’, Target sequence for ICE1 sh2: 5’-GCCTAATCAAGTATCAGTTAT-3’). The infected cells were selected with 2 µg/ml puromycin for extra 48 h before harvesting the cells.

value: Pol II N-20 (Santa Cruz catalog #sc-899)


title: SyKOyNyD1

source_name: Reprogramming intermediates

value: Reprogramming intermediates

tag: reprogramming method

value: OySyNyK


title: SyKOyNyD5


title: human_input_shICE1_ChIP_2

description: Input DNA from whole cell extract following RNAi of ICE1


title: SKOND5

value: OSNK


title: human_input_shGFP_ChIP_1

description: Input DNA from whole cell extract following RNAi of GFP (non-targeting)


title: human_ICE1_shICE1_ChIP_2

description: Chromatin IP of ICE1 following RNAi of ICE1

value: ICE1-CT (aa 1872-2266; developed in this study)


title: SKOND1


title: MEFP3

source_name: Mouse Embryonic Fibroblast

value: Mouse Embryonic Fibroblast


title: Small RNAs in pepper (Root samples)

city: SEOUL

first: Chanseok

last: Shin

address: Gwanak-gu Daehak-dong

country: South Korea

institute: Seoul National University

data_processing:
Removed adaptors. Sequences without adapters were discarded. Small RNA sequences that did not match tRNA and rRNA sequences were selected.
Adaptor trimming: Fastx toolkit
rRNA, tRNA, snRNA/snoRNA masking: Blast
Data processing: Python script

organism: Capsicum annuum

source_name: pepper root

extract_protocol: A small RNA sequencing library was constructed using the TruSeq Small RNA Sample Preparation Kit (Illumina, CA, US), according to the manufacturer's instructions. Briefly, 5ug of total RNAs from each sample were ligated to a 3' adaptor and a 5' adaptor sequentially and then converted to cDNA by RT-PCR. The resulting cDNAs were then amplified by PCR, gel-purified and submitted for sequencing.

tag: tissue

value: root


title: human_PolII_shGFP_ChIP_1

description: Chromatin IP of Pol II following RNAi of GFP (non-targeting)


title: Small RNAs in pepper (FruitB+10 samples)

source_name: pepper fruit

value: fruit


title: Small RNAs in pepper (Leaf samples)

source_name: pepper leaf

value: leaf


title: Small RNAs in pepper (Stem samples)

source_name: pepper stem

value: stem


title: human_ICE1_shGFP_ChIP_1

description: Chromatin IP of ICE1 following RNAi of GFP (non-targeting)


title: Prdm4-EGFP_ChIP-seq_2

value: CCE

value: mouse embryonic stem cells

value: expressing Prdm4-EGFP


title: human_input_ChIP_0

description: Input DNA from whole cell extract


title: Small RNAs in pepper (FruitB+5 samples)


title: human_ZC3H8_ChIP_0

description: Chromatin IP of ZC3H8

value: ZC3H8 (full length; developed in this study)


title: Small RNAs in pepper (Fruit4 samples)


title: Small RNAs in pepper (FruitB samples)


title: SyKOyNyD3


title: human_WT_RNAseq_repA

description: RNAseq after non-targeting-RNAi; Replicate A


title: SKOND3


title: human_ICE1_ChIP_0

description: Chromatin IP of ICE1


title: Small RNAs in pepper (Fruit1 samples)


title: Giant_Cells_rice_root_time_point_1-replicate_2

status: Public on Aug 07 2013

city: Brussels

first: Simon

middle: Lieven Imanuel Johannes

last: Denil

address: Laarbeeklaan 101

department: University Hospital Brussels

country: Belgium

institute: VUB/ULB

data_processing:
base-calling: all reads were acquired by using the Genome Analyzer Data Collection Software SCS version 2.6
alignment: Reads were mapped to the Oryza sativa subsp. Japonica reference genome (build MSU7.0) in two phases using TopHat version 1.3.1 and Cufflinks, version 1.0.3, a detailed description of the workflow and settings used in the data analysis can be found in the description of GEO-submission GSE35843
quantification: Expression was quantified per sample and per annotated or unannotated transcript as the sum of all reads mapped to the respective gene exons with a 16 base pair tolerance on either side to compensate for potential errors in the gene annotation.
Genome_build: MSU7
Supplementary_files_format_and_content: tab separated values, gene names (known and novel) with location information and reads per sample

organism: Oryza sativa Japonica Group

source_name: Rice root

growth_protocol: Oryza sativa cv. ‘Nipponbare’ (GSOR-100, USDA) was germinated for 6 days at 30°C, transferred to SAP-substrate (Reversat et al., 1999) and further grown at 26°C under a 16h/8h light-regime.

extract_protocol:
Captured cells were infiltrated in RNA extraction lysis buffer (Stratagene). RNA from LCM-isolated giant cells was extracted with the Absolutely RNA Nanoprep Kit (Agilent), followed by cDNA amplification using the Ovation RNA-Seq System (NuGEN).
The full length cDNA was fragmented by sonication with a Covaris S2 (Covaris). The mRNA-Seq library was constructed according to the NEB protocols E6040 (New England BioLabs). We used the multiplexing sequencing adapters provided in the Multiplexing Sample Preparation Oligo Kit (Illumina). Size selection of the library was performed on a 2% agarose gel (Low Range Ultra agarose Biorad 161-3107) , fragment size was selected by excision from gel around 300 bp with a margin of 50 bp on either side. The denatured library was diluted to a final concentration of 6 pM and loaded on a paired-end read flow cell (TruSeq v5 kit, Illumina). To minimize lane effects the samples were multiplexed. Each sample was sequenced in duplicate in 2 different lanes (4 lanes total with 8 MID tags per lane).

treatment_protocol: When 12 days old, plants were inoculated with 250 stage 2 juveniles of Meloidogyne graminicola per plant. Control plants were mock-inoculated. Infected and control tissues were collected at 7 and 14 days after inoculation (dai) and fixed in Farmer’s fixative (3:1 Ethanol: Acetic Acid). The material was then cryosectioned with a cryostat at -20°C. Giant cells and vascular cells were captured using a Zeiss PALM Laser Microbeam according to the manufacturer’s instructions.

value: cv. Nipponbare (GSOR-100)

tag: infection

value: Meloidogyne graminicola

value: whole organism

tag: origin

value: Philipines


title: Giant_Cells_rice_root_time_point_2-replicate_2

tag: strain


title: human_ELL1_ChIP_0

description: Chromatin IP of ELL1


title: human_ICE2_ChIP_0

description: Chromatin IP of ICE2

value: ICE2 NT (aa 1-261; developed in this study)


title: Vascular_Cells_uninfected_rice_root_time_point_2-replicate_1

value: Vascular cells


title: Nedd4-/-

city: New York

first: Jiguang

state: NY

department: Department of microbiology and immunology

institute: Columbia University

description: Sample 2

data_processing:
Sequenced reads were mapped to mm9 whole genome using Tophat.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: Reads Per Kilobase of exon per Megabase of library size (RPKM); normalized abundance measurements

source_name: Nedd4-/- B cells

growth_protocol: B cells grown in 15% RPMI with LPS and IL4 for 72 hours

extract_protocol:
Total rRN-depleted RNA isolated with Ribo-Zero™ rRNA Removal Kits (epicentre)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: B6:129-backcrossed to B6

tag: cell type

value: Splenic B cells


title: Giant_Cells_rice_root_time_point_1-replicate_1


title: Phosphate-independent sRNAs in WT C. elegans by high-throughput sequencing

description:
Small RNA sequencing
C. elegans_sRNA_WT

data_processing:
All small-RNA data were mapped to the genome and exon-junction regions, allowing no mismatches and at most 10 multiple mapping loci.
If a read mapped to multiple loci, the read number was normalized to the number of loci. 9,298,952 and 9,232,069 reads from wild type adult and mir-249 mutant adult, respectively, were mapped to C. elegans genome (ce6).
After excluding rRNAs, miRNAs, 21U RNAs, and other structural ncRNAs, the remaining small RNAs were classified into 22G RNAs and 26G RNAs based on their length and 5′ terminal nucleotide.
To identify targets, we used RefSeq gene annotations (ce6) updated with new 3′ UTR annotations based on 3P-Seq data.
Genome_build: C. elegans genome (ce6)
Supplementary_files_format_and_content: The *bed files represent only the 22G-RNAs. The main purpose of employing the phosphate-independent small RNA sequencing was to analyze and compare the 22G-RNA populations in wild-type C. elegans versus mir-249 knockout mutant C. elegans.  Abundance measurements are present in the *bed files (ie, in the 4th of 9 fields).

source_name: Whole organ

extract_protocol:
Worms were harvested at the appropriate stage, washed twice with M9 buffer, and frozen in liquid nitrogen. For RNA preparation, worms were thawed at 37°C for 10min, and total RNA was extracted using Tri-Reagent (Ambion). Isolated total RNA was subjected to DNAse treatment (Takara) and further purified with phenol:chloroform followed by precipitation with ethanol.
Small RNA sequencing library construction was performed using ScriptMiner™ Small RNA-Seq Library Preparation Kit, according to manufacturer's instruction (Illumina). 5ug of total RNA from adult C. elegans was ligated to the 3' adaptor oligo, treated Tobacco Acid Pyrophosphatase (TAP), and subsequently ligated to the 5' adaptor oligo. Di-tagged RNA was then purified using Zymo RNA Clean & Concentrator Kits (Zymo Research). Reverse transcription was performed with MMLV Reverse Transcriptase for 15min at 37°C followed by heat inactivation for 15min at 85°C. The resulting cDNA was PCR-amplified for 18 cycles, with the ScriptMiner Multiplex Forward PCR primer and ScriptMiner Reverse PCR primer. The purified PCR product was submitted for sequencing.

value: Wild-type

tag: developmental stage

value: Adult

value: whole worm


title: Small RNAs in pepper (Flower samples)

source_name: pepper flower

value: flower


title: Vascular_Cells_uninfected_rice_root_time_point_1-replicate_2


title: Nedd4+/+

description: Sample 1

source_name: Nedd4+/+ B cells


title: Vascular_Cells_uninfected_rice_root_time_point_1-replicate_1


title: human_AFF4_ChIP_0

description: Chromatin IP of AFF4

treatment_protocol: HCT116 cells were crosslinked with 1% formaldehyde for 10 min at room temperature with rotation and then crosslinking was quenched by the addition of glycine. Fixed chromatin was sonicated on a Misonix 3000 and used for immunoprecipitation with the indicated antibody. HCT116 cells were washed with cold phosphate-buffered saline (PBS) twice and lysed in RIPA buffer (20 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1% NP40, 1% sodium deoxycholate, 0.1% SDS, 1 mM dithiothreitol [DTT]) containing proteinase inhibitors (Sigma #P8340) for 30 min at 4°C. After centrifugation at 13,000 rpm for 30 min, the supernatant was incubated with the indicated antibodies and protein A/G PLUS agarose (Santa Cruz sc-2003) at 4 °C overnight with gentle rotation. The beads were spun down and washed three times with wash buffer (10 mM HEPES [pH7.4], 1 mM MgCl2, 300mM NaCl, 10mM KCl, 0.2%TritonX-100) before boiling in sodium dodecyl sulfate (SDS) loading buffer.  HCT116 cells harvested following RNAi were infected with lentivirus harboring either Non-targeting shRNA or ICE1 shRNA in the presence of 8 µg/ml of polybrene (Sigma #H9268) for 24 hours (Target sequence for ICE1 sh1: 5’-ATAAGAGTCGTTTGCGAAATA-3’, Target sequence for ICE1 sh2: 5’-GCCTAATCAAGTATCAGTTAT-3’). The infected cells were selected with 2 µg/ml puromycin for extra 48 h before harvesting the cells.


title: T16_Day8 [PBMC]

city: Rochester

first: Stephen

last: Welle

address: 601 Elmwood Avenue

institute: University of Rochester

description: processed data file: T16_pbmc.txt

data_processing:
CASAVA version 1.7 pipeline was used to call bases, demultiplex indexes, align reads to the genome, and count the number of reads aligned with each annotated gene transcript.
RefSeq gene annotations ( hg19 refFlat.txt.gz) were downloaded from UCSC genome broswer and modified to add hg19 loci for constant regions of IGHA2 (chr14:106053890-106054215), IGHG4 (chr14:106090816-106091565), IGHG2 (chr14:106109959-106110289), IGHA1 (chr14:106173508-106173900,106174696-106174994), IGHG1 (chr14:106207813-106208562), IGHG3 (chr14:106235440-106235898), IGHD (chr14:106306703-106307026,106307237-106307563), IGHM (chr14:106320321-106320843) & IGKC (chr2:89156874-89157196).
Base counts per gene (i.e. bases aligned with RefSeq transcripts) were divided by 65 (read length) to obtain reads per gene.
Reads per gene were divided by the total number of RefSeq reads to obtain reads per gene per total reads.
Reads per million RefSeq reads (RPM) were obtained by multilying reads per total reads by one million.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain data from an individual subject (specified in file name), tab delimited text with 12 columns and 21967 rows. The first column contains official gene symbols. The first row indicates study day (0-10). Matrix contains RPM values as defined in description of data processing steps.

molecule: polyA RNA

source_name: T16_Day 8 post-vaccine_PBMCs

extract_protocol:
RNA was extracted with the Qiagen RNeasy micro kit. Concentrations were determined by UV spectrophotometry (Nanodrop) and integrity of ribosomal RNA was confirmed with an Agilent Bioanalyzer.
Polyadenylated RNA was extracted from total RNA, fragmented, ligated to sequencing and indexing adapters, and PCR amplified using Illumina TruSeq RNA kits as recommended by the kit instructions.

treatment_protocol: Blood was collected in heparinized tubes and a portion was removed for PBMC analysis. Lymphocytes were isolated using discontinuous Ficoll gradient centrifugation from buffy coat samples. Magnetic anti-CD235 immunoaffinity beads (Miltenyi Biotec, Auburn, CA) were used to remove RBC contaminants.

tag: subject id

tag: time point

value: Day 8 post-vaccine

value: peripheral blood mononuclear cells (PBMCs)


title: Phosphate-independent sRNAs in mir-249 mutant C. elegans by high-throughput sequencing

description:
Small RNA sequencing
C. elegans_sRNA_mir-249_Mutant

value: mir-249 knockout mutant


title: T16_Day6 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 6 post-vaccine_PBMCs

value: Day 6 post-vaccine


title: Giant_Cells_rice_root_time_point_2-replicate_1


title: MEF_L307R_Ring1B

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

country: Japan

institute: RIKEN

data_processing:
ChIP-seq reads were aligned to mouse genome (mm9) using Bowtie 0.12.7.
Accumulated tags around TSS were processed and counted using in-house software.
Genome_build: NCBI Build 37
Supplementary_files_format_and_content: Wiggle files were converted from aligned sequence using in-house programs.

source_name: MEF

growth_protocol: MEFs from a 12.5-dpc embryo were plated on a 10cm-dish and then expanded up to 15 x 15cm-dishes by 3 time-passages.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with the Ring1B antibody.
Libraries were prepared according to Illumina's instructions accompanying NEBNext ChIP-Seq Library set (NEB #E6200).

value: mouse embryonic fibroblasts

tag: genotype

value: Phc2 mutant (L307R)

value: embryonic day 12.5


title: T16_Day10 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 10 post-vaccine_PBMCs

value: Day 10 post-vaccine


title: Small RNAs in pepper (Fruit2 samples)

value: fruit


title: MEF_WT_Ring1B

value: WT


title: T16_Day7 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 7 post-vaccine_PBMCs

value: Day 7 post-vaccine


title: T16_Day5 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 5 post-vaccine_PBMCs

value: Day 5 post-vaccine


title: T16_Day4 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 4 post-vaccine_PBMCs

value: Day 4 post-vaccine


title: T16_Day9 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 9 post-vaccine_PBMCs

value: Day 9 post-vaccine


title: Vascular_Cells_uninfected_rice_root_time_point_2-replicate_2

value: Vascular cells

value: cv. Nipponbare (GSOR-100)


title: T16_Day3 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 3 post-vaccine_PBMCs

value: Day 3 post-vaccine


title: T16_Day1 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 1 post-vaccine_PBMCs

value: Day 1 post-vaccine


title: Stanford_ChipSeq_MEL_H3K27me3_IgG-rab

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

source_name: MEL

extract_protocol: Instrument model unknown. ("Illumina Genome Analyzer" specified by default). For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodeSydhHist

tag: lab

value: Stanford-m

tag: lab description

value: Snyder - Stanford University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: rabbit polyclonal. Antibody Target:H3K27me3

tag: antibody targetdescription

value: Trimethylated histone H3 (Lys27). Broad species cross-reactivity expected.

tag: antibody vendorname

value: Millipore

tag: antibody vendorid

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: control

value: IgG-rab

tag: control description

value: Input signal from Normal Rabbit IgG ChIP-seq.

tag: age

value: immortalized

tag: age description

value: Immortal cells

tag: controlid

value: MEL/None/Input/IgG-rab

tag: labversion

value: Unknown

tag: strain description

value: Unknown strain origin


title: T15_Day9 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 9 post-vaccine_PBMCs

tag: subject id

tag: time point

value: Day 9 post-vaccine

tag: cell type

value: peripheral blood mononuclear cells (PBMCs)


title: T16_Day0 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 0 (pre-vaccine)_PBMCs

value: Day 0 (pre-vaccine)


title: T15_Day8 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 8 post-vaccine_PBMCs

value: Day 8 post-vaccine


title: T15_Day6 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 6 post-vaccine_PBMCs

value: Day 6 post-vaccine


title: T15_Day7 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 7 post-vaccine_PBMCs

value: Day 7 post-vaccine


title: T15_Day5 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 5 post-vaccine_PBMCs

value: Day 5 post-vaccine


title: T15_Day4 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 4 post-vaccine_PBMCs

value: Day 4 post-vaccine


title: T15_Day1 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 1 post-vaccine_PBMCs

value: Day 1 post-vaccine


title: T15_Day0 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 0 (pre-vaccine)_PBMCs


title: T14_Day10 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 10 post-vaccine_PBMCs

value: Day 10 post-vaccine


title: T14_Day9 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 9 post-vaccine_PBMCs


title: T14_Day8 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 8 post-vaccine_PBMCs


title: T14_Day6 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 6 post-vaccine_PBMCs


title: T15_Day3 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 3 post-vaccine_PBMCs

value: Day 3 post-vaccine


title: T15_Day2 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 2 post-vaccine_PBMCs

value: Day 2 post-vaccine


title: T16_Day2 [PBMC]

description: processed data file: T16_pbmc.txt

source_name: T16_Day 2 post-vaccine_PBMCs


title: T14_Day4 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 4 post-vaccine_PBMCs


title: T14_Day3 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 3 post-vaccine_PBMCs


title: T14_Day2 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 2 post-vaccine_PBMCs


title: T14_Day0 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 0 (pre-vaccine)_PBMCs


title: T14_Day1 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 1 post-vaccine_PBMCs


title: T14_Day5 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 5 post-vaccine_PBMCs


title: T13_Day10 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 10 post-vaccine_PBMCs


title: T13_Day9 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 9 post-vaccine_PBMCs


title: T15_Day10 [PBMC]

description: processed data file: T15_pbmc.txt

source_name: T15_Day 10 post-vaccine_PBMCs


title: T13_Day8 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 8 post-vaccine_PBMCs


title: T13_Day6 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 6 post-vaccine_PBMCs


title: T13_Day7 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 7 post-vaccine_PBMCs


title: T13_Day5 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 5 post-vaccine_PBMCs


title: T13_Day2 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 2 post-vaccine_PBMCs


title: T13_Day0 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 0 (pre-vaccine)_PBMCs


title: T14_Day7 [PBMC]

description: processed data file: T14_pbmc.txt

source_name: T14_Day 7 post-vaccine_PBMCs


title: T12_Day9 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 9 post-vaccine_PBMCs


title: T12_Day6 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 6 post-vaccine_PBMCs


title: T12_Day5 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 5 post-vaccine_PBMCs


title: T12_Day8 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 8 post-vaccine_PBMCs


title: T12_Day7 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 7 post-vaccine_PBMCs


title: T12_Day10 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 10 post-vaccine_PBMCs


title: T12_Day2 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 2 post-vaccine_PBMCs


title: T12_Day3 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 3 post-vaccine_PBMCs


title: T16_Day10

description: processed data file: T16_bcel.txt

source_name: T16_Day 10 post-vaccine_circulating B cells

treatment_protocol: B cell samples were enriched from heparinized whole blood with RosetteSep Immunodensity separation (Stemcell Technologies, Vancouver, BC, Canada). Negative magnetic immunoaffinity bead separation columns (Miltenyi Biotec, Auburn, CA) were used with anti-CD3 (BD Bioscience, San Diego, CA) and anti-CD235 beads (Miltenyi Biotec, Auburn, CA) to further purify total Bc. Flow cytometric analysis was performed on all isolates, showing >90% purity of the isolates.

value: circulating B cells


title: T12_Day0 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 0 (pre-vaccine)_PBMCs


title: T12_Day4 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 4 post-vaccine_PBMCs


title: T12_Day1 [PBMC]

description: processed data file: T12_pbmc.txt

source_name: T12_Day 1 post-vaccine_PBMCs


title: T16_Day8

description: processed data file: T16_bcel.txt

source_name: T16_Day 8 post-vaccine_circulating B cells


title: T16_Day9

description: processed data file: T16_bcel.txt

source_name: T16_Day 9 post-vaccine_circulating B cells


title: T16_Day4

description: processed data file: T16_bcel.txt

source_name: T16_Day 4 post-vaccine_circulating B cells


title: T16_Day5

description: processed data file: T16_bcel.txt

source_name: T16_Day 5 post-vaccine_circulating B cells


title: T16_Day7

description: processed data file: T16_bcel.txt

source_name: T16_Day 7 post-vaccine_circulating B cells


title: T16_Day2

description: processed data file: T16_bcel.txt

source_name: T16_Day 2 post-vaccine_circulating B cells


title: T13_Day3 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 3 post-vaccine_PBMCs


title: T13_Day4 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 4 post-vaccine_PBMCs


title: T16_Day1

description: processed data file: T16_bcel.txt

source_name: T16_Day 1 post-vaccine_circulating B cells


title: T16_Day0

description: processed data file: T16_bcel.txt

source_name: T16_Day 0 (pre-vaccine)_circulating B cells


title: T13_Day1 [PBMC]

description: processed data file: T13_pbmc.txt

source_name: T13_Day 1 post-vaccine_PBMCs


title: T15_Day10

description: processed data file: T15_bcel.txt

source_name: T15_Day 10 post-vaccine_circulating B cells


title: T15_Day9

description: processed data file: T15_bcel.txt

source_name: T15_Day 9 post-vaccine_circulating B cells


title: T15_Day7

description: processed data file: T15_bcel.txt

source_name: T15_Day 7 post-vaccine_circulating B cells


title: T15_Day8

description: processed data file: T15_bcel.txt

source_name: T15_Day 8 post-vaccine_circulating B cells


title: T15_Day6

description: processed data file: T15_bcel.txt

source_name: T15_Day 6 post-vaccine_circulating B cells


title: T15_Day3

description: processed data file: T15_bcel.txt

source_name: T15_Day 3 post-vaccine_circulating B cells


title: T15_Day5

description: processed data file: T15_bcel.txt

source_name: T15_Day 5 post-vaccine_circulating B cells


title: T15_Day0

description: processed data file: T15_bcel.txt

source_name: T15_Day 0 (pre-vaccine)_circulating B cells


title: T16_Day6

description: processed data file: T16_bcel.txt

source_name: T16_Day 6 post-vaccine_circulating B cells


title: T14_Day7

description: processed data file: T14_bcel.txt

source_name: T14_Day 7 post-vaccine_circulating B cells


title: T14_Day9

description: processed data file: T14_bcel.txt

source_name: T14_Day 9 post-vaccine_circulating B cells


title: T14_Day4

description: processed data file: T14_bcel.txt

source_name: T14_Day 4 post-vaccine_circulating B cells


title: T16_Day3

description: processed data file: T16_bcel.txt

source_name: T16_Day 3 post-vaccine_circulating B cells


title: T14_Day6

description: processed data file: T14_bcel.txt

source_name: T14_Day 6 post-vaccine_circulating B cells


title: T14_Day8

description: processed data file: T14_bcel.txt

source_name: T14_Day 8 post-vaccine_circulating B cells


title: T15_Day1

description: processed data file: T15_bcel.txt

source_name: T15_Day 1 post-vaccine_circulating B cells


title: T14_Day0

description: processed data file: T14_bcel.txt

source_name: T14_Day 0 (pre-vaccine)_circulating B cells


title: T13_Day10

description: processed data file: T13_bcel.txt

source_name: T13_Day 10 post-vaccine_circulating B cells


title: T13_Day9

description: processed data file: T13_bcel.txt

source_name: T13_Day 9 post-vaccine_circulating B cells


title: T14_Day5

description: processed data file: T14_bcel.txt

source_name: T14_Day 5 post-vaccine_circulating B cells


title: T13_Day7

description: processed data file: T13_bcel.txt

source_name: T13_Day 7 post-vaccine_circulating B cells


title: T13_Day8

description: processed data file: T13_bcel.txt

source_name: T13_Day 8 post-vaccine_circulating B cells


title: WT root

city: Hong Kong

first: Anna

last: Liu

state: Hong Kong

address: Pokfulam Road

department: CS

country: Hong Kong

institute: HKU

data_processing: Potentially novel miRNAs were identified by folding the flaking genome sequence of unique small RNAs using MIREAP (http://sourceforge.net/projects/mireap/).

organism: Arabidopsis thaliana

source_name: Root

growth_protocol: Arabidopsis seeds of WT, T-DNA and OE lines were surface sterilized with 20% (v/v) bleach for 15~20 minutes and then washed with sterilized water for 4~5 times. The seeds were plated on Murashige and Skoog medium supplemented with 2% (w/v) sucrose for 10 days and then the seedling were transferred to soil under 16 hours light (22℃) / 8 hours dark (18℃) period. 20-day-old Arabidopsis shoot and root without bolting were immediately frozen in liquid Nitrogen for RNA extraction. For every plant line, individual shoot /root were mixed as one sample.

extract_protocol:
Total RNA of 20-day-old shoot and root were extracted with DNase I digestion according to the manufacturer’s instructions (RNeasy Plant Mini Kit, Qiagen, Hong Kong). The preliminarily quality was detected by running 1% (w/v) agarose gel stained by GelRed (Biotium, USA). The quality of RNA samples was tested with Agilent 2100 Bioanalyzer RNA Nanochip. At least 10 µg of total RNA at a concentration of ≥ 400 ng/µl, OD260/280=1.8~2.2 were used for cDNA library preparation.
Total RNA was sent to Beijing Genomics Institute (BGI) (Shenzhen, Guangdong province, China) and small RNAs were sequenced using Illumina HiSeqTM 2000 high throughput sequencing technology. SRNAs with the length of 18-30 nt were first separated from total RNA by running on 15% (w/v) TBE urea polyacrylamide gel. The excised gel with sRNAs from 18 to 30 nt in length were submerged in 600 μL of 0.3 M sodium chloride overnight at 4℃. The sRNA fragments were dissolved in diethylpyrocarbonate treated water (Ambion, Austin, TX, USA). The sRNAs were then added 5’ adaptor by T4 RNA ligase (Takara, Dalian, China) in the presence of RNase OUT Recombinant Ribonuclease Inhibitor (Invitrogen, China) overnight at 4℃ according to the manual. After obtaining the 5’ ligation products, a 3’adaptor was also added to the selecting 5’adaptor sRNAs following the same procedures as the 5’adaptor ligation. Finally, both 3’ and 5’ adaptors ligated sRNAs were run on a 10% (w/v) TBE urea polyacrylamide gel and then the 44 nt RNAs were excised. The sRNA were reversely transcribed to cDNA with the RT primer by Superscript II reverse transcriptase (Invitrogen, China). The cDNA was further quantified by Agilent 2100 and sequenced by the Illumina 1G Genome Analyzer.

tag: ecotype

tag: genotype/variation

value: Wild type


title: T13_Day6

description: processed data file: T13_bcel.txt

source_name: T13_Day 6 post-vaccine_circulating B cells


title: OE7 root

value: Overexpression line 7


title: T15_Day4

description: processed data file: T15_bcel.txt

source_name: T15_Day 4 post-vaccine_circulating B cells


title: T13_Day4

description: processed data file: T13_bcel.txt

source_name: T13_Day 4 post-vaccine_circulating B cells


title: T15_Day2

description: processed data file: T15_bcel.txt

source_name: T15_Day 2 post-vaccine_circulating B cells


title: T13_Day5

description: processed data file: T13_bcel.txt

source_name: T13_Day 5 post-vaccine_circulating B cells


title: T14_Day3

description: processed data file: T14_bcel.txt

source_name: T14_Day 3 post-vaccine_circulating B cells


title: OE21 root

value: Overexpression line 21


title: T14_Day2

description: processed data file: T14_bcel.txt

source_name: T14_Day 2 post-vaccine_circulating B cells


title: WT shoot

source_name: Shoot


title: T13_Day2

description: processed data file: T13_bcel.txt

source_name: T13_Day 2 post-vaccine_circulating B cells


title: T14_Day10

description: processed data file: T14_bcel.txt

source_name: T14_Day 10 post-vaccine_circulating B cells


title: T-DNA shoot


title: T13_Day1

description: processed data file: T13_bcel.txt

source_name: T13_Day 1 post-vaccine_circulating B cells


title: T14_Day1

description: processed data file: T14_bcel.txt

source_name: T14_Day 1 post-vaccine_circulating B cells


title: T13_Day3

description: processed data file: T13_bcel.txt

source_name: T13_Day 3 post-vaccine_circulating B cells


title: cr_20_27_bap-2

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Sample name: PJ-20

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Hepa-1 cells

growth_protocol: Cells were grown in a-MEM with 5% FBS.  Cells were passaged every 3 days.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in the presence of 0.5 mM Cr(VI) or grown normally for 20 or 25 passages.  After Cr(VI) growth treatment cells were treated with 5 mM B[a]P

tag: cell line

value: Grown for 20 passages with 0.5mM Cr(VI) followed by 5 without Cr(VI) and then treated for 8 hours with B[a]P

tag: passage


title: OE21 shoot


title: T13_Day0

description: processed data file: T13_bcel.txt

source_name: T13_Day 0 (pre-vaccine)_circulating B cells


title: T12_Day10

description: processed data file: T12_bcel.txt

source_name: T12_Day 10 post-vaccine_circulating B cells


title: OE7 shoot


title: T12_Day9

description: processed data file: T12_bcel.txt

source_name: T12_Day 9 post-vaccine_circulating B cells

value: Day 9 post-vaccine


title: T12_Day7

description: processed data file: T12_bcel.txt

source_name: T12_Day 7 post-vaccine_circulating B cells


title: T12_Day8

description: processed data file: T12_bcel.txt

source_name: T12_Day 8 post-vaccine_circulating B cells


title: T-DNA root

source_name: Root


title: cr_27_dmso-2

description: Sample name: PJ-17

value: Grown for 25 passages with 0.5mM Cr(VI) and then treated for 8 hours with DMSO


title: cr_27_bap-2

description: Sample name: PJ-18

value: Grown for 25 passages with 0.5mM Cr(VI) and then treated for 8 hours with B[a]P


title: cr_20_27_dmso-2

description: Sample name: PJ-19

value: Grown for 20 passages with 0.5mM Cr(VI) followed by 5 without Cr(VI) and then treated for 8 hours with DMSO


title: B6 9hr rep3

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

institute: Case Western Reserve University

description: Isolated whole eye mRNA

data_processing:
Base-calling was performed using the Illumina pipeline software ELAND v1.7
Data were processed and aligned with the University of California-Santa Cruz (UCSC) mouse genome assembly and transcript annotation (mm9) using Genomic Short-read Nucleotide Alignment Program (GSNAP),.
Manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation were done to generate reads per kilobase per million reads (RPKM) statistics by gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

source_name: Eye Tissue-B6 9.0 hr-3

extract_protocol:
Mice were euthanized by cervical dislocation. Eyes were enucleated and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity for whole eye runs.
One mouse eye or two retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the eye tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA samples of 5 female mice 4 weeks of age were used for each whole eye library preparation.  For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip prior to sequencing by using the Illumina Genome Analyzer IIx.

tag: strain

tag: tissue

value: Whole Eye

tag: timepoint

value: 9.0 hours after light onset (15:00)


title: bap_27-2

description: Sample name: PJ-16

tag: treatment

value: Treated with B[a]P for 8 hours


title: T12_Day6

description: processed data file: T12_bcel.txt

source_name: T12_Day 6 post-vaccine_circulating B cells

value: Day 6 post-vaccine


title: T12_Day5

description: processed data file: T12_bcel.txt

source_name: T12_Day 5 post-vaccine_circulating B cells

value: Day 5 post-vaccine


title: T12_Day4

description: processed data file: T12_bcel.txt

source_name: T12_Day 4 post-vaccine_circulating B cells

value: Day 4 post-vaccine


title: B6 9hr rep1

description: Isolated whole eye mRNA

source_name: Eye Tissue-B6 9.0 hr-1


title: T12_Day3

description: processed data file: T12_bcel.txt

source_name: T12_Day 3 post-vaccine_circulating B cells

value: Day 3 post-vaccine


title: dmso_27-2

description: Sample name: PJ-15

value: Treated with DMSO for 8 hours


title: B6rep3

description: Isolated whole eye mRNA

source_name: Eye Tissue-B6 1.5 hr-3

value: 1.5 hours after light onset (07:30)