title: Nab3_4

city: Edinburgh

first: Rebecca

middle: Katharine

last: Holmes

state: Midlothian

address: Max Born Crescent

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: Edinburgh University

data_processing:
Raw data files: Reads were demultiplexed by assigning samples to experiments using 5' barcodes. The barcode information is retained in the reads.
Processed data files: Reads were pre-processed as follows: 1. Data demultiplexed using pyBarcodeFilter.py from pyCRAC (Webb, Kudla and Granneman, Genome Biology 2014); 2. Quality filtering and adapter removal using flexbar version 2.4: flexbar -t '{output_prefix}' -f sanger -r '{input_filepath}' -q 30 -as 'TGGAATTCTCGGGTGCCAAGGC' -ao 4 -u 3 -m 17 -n 32; 3. PCR duplicates collapsed using pyFastqDuplicateRemover.py from pyCRAC.
Reads were mapped to the S. cerevisiae genome (SGDv64) using Novoalign with the following settings: -r Random -s 1
Subsequent analyses were performed using custom python, R and AWK scripts, and the pyCRAC package.
Genome_build: SGDv64
Supplementary_files_format_and_content: SGR files generated using pyCRAC (Granneman, Webb and Kudla, submitted); these are pileups of all mapped reads across the genome; these are not normalised to the total number of reads in each library.

source_name: BY4741 grown in SD (-TRP) medium

growth_protocol: Yeast cultures were grown in SD (-TRP or complete) medium at 30C to OD=0.5.

extract_protocol:
Cell lysate.
Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNase digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).

treatment_protocol: Yeast cultures were irradiated with UV light, to fix protein:RNA interactions.

value: BY4741 (MATa; his3delta1; leu2delta0; met15delta0; ura3delta0)

tag: tag

value: NAB3-C-HTP (C-terminal HTP tag)::URA


title: Sto1

status: Public on Dec 03 2015

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Saccharomyces cerevisiae

tag: strain/background

value: STO1-C-HTP (C-terminal HTP tag)::URA


title: Nab3_Dnpl3_4

tag: genotype/variation


title: Nab3_Dnpl3_1


title: day31 Cold4 cecum

city: Genève

first: Ozren

last: Stojanovic

address: 1, rue Michèl-Servet

department: Faculté de Médecine, Dept. PHYM

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
Library strategy: 16S rRNA gene V4-region miSeq
Using QIIME and custom scripts, sequences were quality filtered and demultiplexed using exact matches to the supplied DNA barcodes.
Resulting sequences were then searched against the Greengenes reference database of 16S rRNA gene sequences, clustered at 97% by uclust (closedreference OTU picking).
The longest sequence from each Operation Taxonomic Unit (OTU) thus formed was then used as the OTU representative sequence, and assigned taxonomic classification via mothur's bayesian classifier, trained against the Greengenes database clustered at 98%.
Taxa are filtered to those present in at least one of the samples (Filter-1), or to taxa significantly increased in their abundance in one category compared to the alternate categories (Filter-5). For Filter-5, ANOVA (analysis of variance) was employed to calculate p-values. Additionally, q-values were calculated using the Benjamini-Hochberg procedure to correct p-values, controlling for false discovery rates.
Supplementary_files_format_and_content: processed_counts.xlsx containes abundance of each OUT in every sample with taxonomical classification.

molecule: genomic DNA

organism: mouse gut metagenome

source_name: cecum

extract_protocol:
Bacterial DNA content was extracted using QIAamp Fast DNA stool Mini Kit (Qiagen). 40 DNA isolates from mice feces and 9 biospecimens of mice cecal content were received in Second Genome’s service laboratory on March 28 and April 2, 2014. The samples arrived intact, frozen and according to specification, and were immediately stored at -20°C. The biospecimen’s DNA are isolated using the MoBio PowerMag DNA isolation kit as per vendor’s protocol. The combined DNA samples ranged in concentration of 25-159.8 ng/μl. All samples were quantified via the Qubit® Quant-iT dsDNA Broad-Range Kit (Invitrogen, Life Technologies, Grand Island, NY) to ensure that they met minimum concentration and mass of DNA. The sample set met specifications.
To enrich the sample for bacterial 16S V4 rDNA region, DNA was amplified utilizing fusion primers designed against the surrounding conserved regions which are tailed with sequences to incorporate Illumina (San Diego, CA) flow cell adapters and indexing barcodes. Each sample was PCR amplified with two differently bar coded V4 fusion primers. 49 samples met the post-PCR quantification minimum and were advanced for pooling and sequencing.

treatment_protocol: 31 day on 6 C (Cold) or room temperature (RT)

tag: tissue

value: cecum of C57BL6/J mouse

tag: collection day

tag: temperature

value: cold


title: RAB2

description: whole tissue

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
The reads were mapped using TopHat v.2 to the UCSC mm10 genome release.
The gene features were counted with HTSeq v0.5.3p9 (htseq-count). Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: mm10
Supplementary_files_format_and_content: excel file, edgeR normalized counts

molecule: polyA RNA

organism: Mus musculus

source_name: room temp + antibiotics 30 days

extract_protocol:
RNA extracted by Trizol (Invitrogen) according to manufacturer's instructions
The libraries were prepared with 300 ng of total RNA as starting material and processed with the Illumina Truseq mRNA stranded kit according to the manufacturer instruction.

treatment_protocol: Mice were kept 30 days at room temperature or at 6C, 2 per cage, under SPF conditions, with or without administration of antibiotic coctail in drinking water. Fasted 5h before sacrifice.

value: jejunum

tag: strain


title: liver JM107 12weeks normal aging

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
FASTQ files were extracted using Illumina CASAVA v1.8.0 (Sample 1-50), CASAVA v1.8.2 (Sample 51-95) or bcl2fastq v1.8.4 (Sample 96-185) software.
FASTQ files were mapped using Tophat (v2.0.6) vs. the N. furzeri genome.
Uniquely mapped reads were counted for each gene_id using featureCounts v1.4.3-p1 (featureCounts -T 8 -a $GTF -s 0 -t exon -g gene_id -o featureCounts_gene.txt $SAMFILE) .
RPKM values were computed using exon lengths provided by featureCounts and the sum of all mapped reads per sample according to Mortazavi et al. (2008).
Genome build: Genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/). In addition, 18 mitochondrial genes were included.
Supplementary_files_format_and_content: Text files including raw counts and RPKM values of each sample.

organism: Nothobranchius furzeri

source_name: total RNA extracted from liver

growth_protocol: Animal maintenance was performed as described by Terzebasi et al., 2008 and 2009.

extract_protocol:
For library preparation an amount of around 2.5 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.
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.

value: liver

tag: age

value: 12 weeks

tag: age at death

tag: treatment

tag: FISH id


title: Nab3_1


title: day31 Cold3 cecum


title: RAB1

description: whole tissue


title: day31 Cold2 cecum


title: Rpo21_Dnpl3_4

value: RPO21-C-HTP (C-terminal HTP tag)::URA


title: CT3

description: whole tissue

source_name: 6 C 30 days


title: liver JM105 12weeks normal aging


title: Rpo21_Dnpl3_1


title: CT2

description: whole tissue


title: liver JM104 12weeks normal aging


title: liver JM106 12weeks normal aging


title: day31 RT4 cecum

value: room temperature


title: liver JM98 5weeks normal aging

value: 5 weeks


title: Rpo21_4


title: day31 Cold5 cecum


title: day31 RT3 cecum


title: CT1

description: whole tissue


title: day31 RT2 cecum


title: liver JM97 5weeks normal aging


title: RT3

description: whole tissue

source_name: room temp 30 days


title: day31 RT1 cecum


title: liver JM103 5weeks normal aging


title: RT2

description: whole tissue


title: Npl3_1

source_name: BY4727 grown in SD (complete) medium

value: BY4727 (MATalpha; his3delta200; leu2delta0; lys2delta0; met15delta0; trp1delta63; ura3delta0)

value: PTH-N-NPL3 (N-terminal PTH tag)


title: RT1

description: whole tissue


title: liver JM100 5weeks normal aging


title: day31 Cold8 feces

source_name: feces

value: feces of C57BL6/J mouse


title: BY_2


title: day31 Cold7 feces


title: BY_1


title: day31 Cold6 feces


title: CstF77 RNA pol II ChIP-seq S194 5'SP R1

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

country: USA

institute: U. Colorado School of Medicine

description: Chromatin IP against CstF77

data_processing:
Single-end 50 base reads (after removing barcodes) were mapped to the mm10 UCSC mouse genome  with Bowtie version 0.12.5
Genome_build: GRCm38/mm10 assembly
Supplementary_files_format_and_content: BigWig files; custom .bw files were made by mapping to the sequence of theIgM-Svneo insert in the integrated plasmid pR-SP6 (Ochi et al PNAS 80:6351, 1983)

source_name: S194 Myeloma B Cells

growth_protocol: S194 and M12  cell lines were grown in DMEM 10% HI-FCS, and pen/strep

extract_protocol:
cross-linked Chromatin was sonicated with a Bioruptor
IPs from 1-2 mg of cross-linked extract were immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, gel purification of ~200bp fragments, and amplification (18cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.
ChIP-seq 1X 50 base reads

treatment_protocol: cells were grown to densities of  1-1.5x10^6 before cross-linking and harvesting for ChIP-seq.

tag: cell line

value: Myeloma B cell line S194

tag: chip target

tag: chip antibody

value: rabbit anti-human CstF77 (this work)


title: BMDC footprints, cycloheximide-treated, 8 h mock

city: San Francisco

first: Alexander

middle: P

last: Fields

state: CA

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

institute: University of California San Francisco

description:
ribosomal profiling
DC_ORFs.bed.gz
B_all_pos.bedgraph.gz
B_all_neg.bedgraph.gz

data_processing:
Base-calling performed on-line by HiSeq Control Software 2.0.12.0
Sequenced reads were trimmed for adapter sequence
Trimmed reads were filtered for rRNA, snoRNA, snRNA, miRNA, tRNA, mitochondrial rRNA, and mitochondrial tRNA using Bowtie2 in --local mode
Remaining reads were aligned to a custom BMDC transcriptome with tophat using parameters '--b2-very-sensitive --transcriptome-only --no-novel-juncs --max-multihits=64'
Aligned reads were assigned to the ribosome p-site position and converted to bedgraphs for visualization purposes. Time courses were collapsed to single bedgraphs for ease of visualization.
The ORF-RATER pipeline was applied to aligned reads to identify high-confidence sites of translation
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph files indicate number of p-site-mapped RPFs at each position
Supplementary_files_format_and_content: bed file indicates ORFs identified by ORF-RATER as potentially translated; score column indicates confidence rating (scaled to 0-1000) assigned to each

source_name: Dendritic cells

growth_protocol: At day 0, BMDCs were collected from femora and tibiae and plated on twenty (per mouse), 100 mm non-tissue culture-treated plastic dishes using 10 mL medium per plate. At day 2, cells were fed with another 10 mL medium per dish. At day 5, cells were harvested from 15 mL of the supernatant by spinning at 1,400 rpm for 5 minutes; pellets were resuspended with 5 mL medium and added back to the original dish. Cells were fed with another 5 mL medium at day 7. At day 8, all non-adherent and loosely bound cells were collected and harvested by centrifugation. Cells were then resuspended with medium, plated at a concentration of 10×106 cells in 10 mL medium per 100 mm dish.

extract_protocol:
Following treatment with indicated ribosome inhibitors, cells were lysed by triturating 10 times with 400 μL lysis buffer (20 mM Tris pH 7.56, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100 [Sigma], 1 mM DTT [Sigma], 8% glycerol, 100 μg/mL CHX, 12 units/mL Turbo DNase [Life Technologies]). Lysates were clarified by centrifuging at 20,000×g for 10 min at 4°C. Clarified lysate was flash frozen in liquid nitrogen. Clarified cell lysates were treated with RNase I (Life Technologies) to digest RNA not protected by ribosomes. High molecular weight species were isolated by centrifuging lysates through a 34% sucrose cushion at 200,000×g for 4 hours at 4°C. Pellets were resuspended in Trizol (Life Technologies) and the RNA fraction isolated. Contaminant rRNA was removed using the listed strategies.
Total RNase I-treated RNA was size-separated by gel electrophoresis, and RNAs of size 28–34 nucleotides were purified. These ribosome protected fragments were cloned and sequenced via a single-end run on an Illumina HiSeq 2500 sequencer.

treatment_protocol: At day 9, cells were stimulated with LPS (100 ng/mL, rough, ultrapure E. coli K12 strain, Invitrogen) or mock treatment

tag: cell type

value: Bone marrow-derived dendritic cells

value: 6-8 weeks

tag: stimulation

value: 8 h mock

tag: ribosome inhibitor treatment

value: 100 ug/mL cycloheximide, 1 min

tag: rrna subtraction strategy

value: Subtractive hybridization


title: day31 Cold4 feces

value: cold


title: BMDC footprints, cycloheximide-treated, 9 h mock

value: 9 h mock


title: day31 Cold5 feces


title: Ser2P RNA pol II ChIP-seq S194 5'SP R1

description: Chromatin IP against Ser2P pol II CTD

value: Ser2P pol II CTD

value: rat anti Ser2P-CTD 3E10 Chromotek  cat. no. 3e10


title: BMDC footprints, cycloheximide-treated, 6 h mock

value: 6 h mock


title: Ser2P RNA pol II ChIP-seq S194 5'SP R2

description: Chromatin IP against Ser2P pol II CTD


title: BMDC footprints, cycloheximide-treated, 4 h mock

value: 4 h mock


title: Total RNA pol II ChIP-seq S194 5'SP R2

description: Chromatin IP against RNA pol II

value: RNA pol II

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Npl3_2

tag: strain/background

value: BY4727 (MATalpha; his3delta200; leu2delta0; lys2delta0; met15delta0; trp1delta63; ura3delta0)

tag: tag

value: PTH-N-NPL3 (N-terminal PTH tag)


title: day31 Cold3 feces

tag: tissue

value: feces of C57BL6/J mouse


title: Rpo21_1

value: BY4741 (MATa; his3delta1; leu2delta0; met15delta0; ura3delta0)

value: RPO21-C-HTP (C-terminal HTP tag)::URA


title: BMDC footprints, cycloheximide-treated, 2 h mock

value: Bone marrow-derived dendritic cells

value: 6-8 weeks

value: 2 h mock


title: day31 Cold1 feces

tag: collection day


title: day31 Cold2 feces

tag: temperature


title: liver JM101 5weeks normal aging

value: liver

value: 5 weeks


title: Total RNA pol II ChIP-seq S194 5'SP R1

description: Chromatin IP against RNA pol II

value: Myeloma B cell line S194

tag: genotype/variation


title: day31 RT6 feces

value: room temperature


title: CstF77 RNA pol II ChIP-seq S194 pA21 R1

description: Chromatin IP against CstF77

value: rabbit anti-human CstF77 (this work)


title: Ser2P RNA pol II ChIP-seq S194 pA21 R2

description: Chromatin IP against Ser2P pol II CTD

value: Ser2P pol II CTD

value: rat anti Ser2P-CTD 3E10 Chromotek  cat. no. 3e10


title: BMDC footprints, cycloheximide-treated, 1 h mock

tag: age

value: 1 h mock

value: 100 ug/mL cycloheximide, 1 min

value: Subtractive hybridization

tag: strain


title: BMDC footprints, cycloheximide-treated, 0.5 h mock

value: 0.5 h mock


title: BMDC footprints, cycloheximide-treated, 12 h mock

value: 12 h mock


title: Ser2P RNA pol II ChIP-seq S194 pA21 R1

description: Chromatin IP against Ser2P pol II CTD


title: day31 RT5 feces

value: feces of C57BL6/J mouse


title: day31 RT3 feces


title: day31 RT4 feces


title: Total RNA pol II ChIP-seq S194 pA21 R1

description: Chromatin IP against RNA pol II

value: RNA pol II

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: CstF77 RNA pol II ChIP-seq S194 WT R1

description: Chromatin IP against CstF77

value: WT


title: BMDC footprints, cycloheximide-treated, 9 h LPS, replicate 2

description:
ribosomal profiling
DC_ORFs.bed.gz
C_all_pos.bedgraph.gz
C_all_neg.bedgraph.gz

value: Bone marrow-derived dendritic cells

value: 6-8 weeks

value: 9 h LPS


title: BMDC footprints, cycloheximide-treated, 8 h LPS, replicate 2

value: 8 h LPS


title: day11 Cold8 feces

value: cold


title: BMDC footprints, cycloheximide-treated, 9 h LPS, replicate 1


title: Ser2P RNA pol II ChIP-seq S194 WT R1

description: Chromatin IP against Ser2P pol II CTD

value: Myeloma B cell line S194


title: day31 RT1 feces

value: room temperature


title: BMDC footprints, cycloheximide-treated, 8 h LPS, replicate 1


title: Total RNA pol II ChIP-seq S194 WT R2

description: Chromatin IP against RNA pol II


title: day31 RT2 feces


title: day11 Cold6 feces


title: BMDC footprints, cycloheximide-treated, 12 h LPS, replicate 2

value: 12 h LPS


title: Total RNA pol II ChIP-seq S194 WT R1

description: Chromatin IP against RNA pol II


title: BMDC footprints, cycloheximide-treated, 6 h LPS, replicate 1

value: 6 h LPS


title: day11 Cold4 feces


title: Total RNA pol II ChIP-seq M12 WT R2

description: Chromatin IP against RNA pol II

source_name: M12 B Lymphomas

value: B Lymphoma cell line M12


title: Total RNA pol II ChIP-seq M12 WT R1

description: Chromatin IP against RNA pol II


title: day11 Cold7 feces


title: BMDC footprints, cycloheximide-treated, 4 h LPS, replicate 2

value: 4 h LPS

value: 100 ug/mL cycloheximide, 1 min

value: Subtractive hybridization


title: BMDC footprints, cycloheximide-treated, 4 h LPS, replicate 1


title: day11 Cold2 feces

value: feces of C57BL6/J mouse


title: BMDC footprints, cycloheximide-treated, 12 h LPS, replicate 1


title: Total RNA pol II ChIP-seq S194 pA21 R2

description: Chromatin IP against RNA pol II

value: RNA pol II


title: day11 Cold3 feces


title: BMDC footprints, cycloheximide-treated, 2 h LPS, replicate 2

value: 2 h LPS


title: BMDC footprints, cycloheximide-treated, 6 h LPS, replicate 2


title: day11 Cold1 feces


title: BMDC footprints, cycloheximide-treated, 2 h LPS, replicate 1


title: Ser2P RNA pol II ChIP-seq S194 WT R2

description: Chromatin IP against Ser2P pol II CTD

value: WT

value: Ser2P pol II CTD

value: rat anti Ser2P-CTD 3E10 Chromotek  cat. no. 3e10


title: day11 RT6 feces


title: day11 RT5 feces


title: BMDC footprints, cycloheximide-treated, 1 h LPS, replicate 2

value: Bone marrow-derived dendritic cells

value: 6-8 weeks

value: 1 h LPS


title: day11 RT3 feces


title: BMDC footprints, cycloheximide-treated, 1 h LPS, replicate 1


title: BMDC footprints, cycloheximide-treated, 0.5 h LPS, replicate 2

value: 0.5 h LPS


title: BMDC footprints, cycloheximide-treated, 0.5 h LPS, replicate 1


title: day0 Cold7 feces

value: cold


title: day11 RT2 feces

value: room temperature


title: day11 RT1 feces


title: BMDC footprints, cycloheximide-treated, naïve, replicate 1


title: BMDC footprints, no drug treatment, 12 h LPS

description:
ribosomal profiling
DC_ORFs.bed.gz
N_all_pos.bedgraph.gz
N_all_neg.bedgraph.gz

value: 12 h LPS

value: RiboZero


title: BMDC footprints, cycloheximide-treated, naïve, replicate 2


title: day0 Cold5 feces


title: day0 Cold4 feces


title: day0 Cold6 feces


title: BMDC footprints, no drug treatment, 8 h LPS

value: 8 h LPS


title: BMDC footprints, no drug treatment, 6 h LPS

value: 6 h LPS


title: day0 Cold3 feces


title: day0 Cold2 feces


title: BMDC footprints, no drug treatment, 4 h LPS

value: 4 h LPS


title: BMDC footprints, no drug treatment, 9 h LPS

value: 9 h LPS


title: day0 Cold1 feces

value: feces of C57BL6/J mouse


title: BMDC footprints, no drug treatment, 2 h LPS

value: 2 h LPS


title: day0 RT6 feces


title: BMDC footprints, no drug treatment, 1 h LPS


title: day0 RT4 feces


title: day0 RT5 feces


title: BMDC footprints, no drug treatment, 0.5 h LPS


title: BMDC footprints, no drug treatment, naïve


title: day0 RT3 feces


title: BMDC footprints, lactimidomycin-treated, LPS stimulated

description:
ribosomal profiling
DC_ORFs.bed.gz

value: 50 ug/mL lactimidomycin, 30 min


title: day0 RT2 feces


title: BMDC footprints, harringtonine-treated, LPS stimulated

description:
ribosomal profiling
DC_ORFs.bed.gz

value: Mix of 0, 2, 4, 6, and 9 h LPS

value: 1 ug/mL harringtonine, 5 min

value: Subtractive hybridization


title: Sample_KO1

status: Public on Dec 02 2015

city: Dallas

first: Eric

middle: N

last: Olson

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: University of Texas Southwestern Medical Center at Dallas

data_processing:
QC using NGS-QC-Toolkit
High quality reads were aligned to mm10 using tophat2.0.0 using default setting
Reads count per gene were generated using HTSeq-count
Diffrenetial gene expression were done using DEseq (v 1.10.1) with filtering criteria p value <= 0.01, fold change >=1.5 and both samples have base Mean at least 1
Genome_build: mm10
Supplementary_files_format_and_content: Gene reads count generated by HTSeq-count, txt file

source_name: MRTFA/B double knockout_heart

extract_protocol:
Hearts were snap frozen in liquid nitrogen. Hearts were resuspended and homogenized in TRIZOL followed by chloroform extraction. RNAeasy mini-columns (Qiagen) were used for RNA purification. RNA-seq was performed using an Illumina HiSeq2500.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: Mixed

value: MRTFA/B double knockout

tag: developmental stage

value: heart


title: Sample_KO2


title: Sample_WT1

value: ICR

value: wild type


title: Sample_WT2


title: Tu-TErep1

city: Chongqing

first: Lu

last: Wencai

address: 216 Tiansheng Road

country: China

institute: Southwest University

data_processing:
Processing of raw data, removal of the adapter sequences,  base-calling and quality value calculations were performed  using Torrent Suite™ Software 4.0 (Ion torrent, Life technologies,  CA).
The whole transcriptome cDNA library was prepared  using Ion Total RNA-Seq kit V2 (Life Technologies  Corporation, CA).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the T. urticae genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Clean reads are the high quality sequences after data cleaning, on which all following analyses are based.
The entire assembled genes were used to search for the best-hit homologous proteins (BLASTX cut-off e-value 1.0E-5) in the T. urticae genome
For interlibrary comparison, read numbers were normalized to relative abundance as reads per kilobase transcriptome per million mapped reads (RPKM).
Genome_build: Tetranychus urticae genome (database web link: http://bioinformatics.psb.ugent.be/orcae/overview/Tetur)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Tetranychus urticae

source_name: T. urticae_tebufenpyrad_2d-old adult mite tissue

extract_protocol:
Total RNA was extracted from 2 day-old adult mites using the RNeasy plus Micro Kit (Qiagen, Hilden, Germany). Genomic DNA was removed using a genomic DNA elimination column supplied with the kit.
The Ribosomal RNA depletion was carried out using  RiboMinus RNA plant kit for RNA-Seq (Life Technologies,  CA). The whole transcriptome cDNA library was prepared  using Ion Total RNA-Seq kit V2 (Life Technologies  Corporation, CA).

tag: treated with

value: tebufenpyrad (18mg/L) for 6 h

tag: strain phenotype

value: tebufenpyrad-tolerant strain

tag: developemental stage

value: 2-day old adult mite


title: Tu-TErep3


title: Tu-TErep2


title: Tu-CKrep2

source_name: T. urticae_control_2d-old adult mite tissue

value: none (field population control)

value: susceptible strain


title: Tu-AVrep2

source_name: T. urticae_abamectin_2d-old adult mite tissue

value: abamectin (10 mg/L) for 6 h

value: abamectin-tolerant strain


title: Tu-FErep2

source_name: T. urticae_fenpropathrin_2d-old adult mite tissue

value: fenpropathrin (376mg/L) for 6 h

value: fenpropathrin-tolerant strain


title: Tc-TErep2

organism: Tetranychus cinnabarinus

source_name: T. cinnabarinus_tebufenpyrad_2d-old adult mite tissue


title: Tu-FErep1


title: Tu-AVrep3


title: Tu-CKrep3


title: Tc-TErep3


title: Tu-FErep3


title: Tu-AVrep1


title: E13.5_PGC_female_2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
3'-RNAseq amplified from 1ng RNA
expression_E10_E13_PGC.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10

source_name: primordial germ cells

growth_protocol:
The Prdm1(flox/flox); Rosa26(neo-EYFP/neo-EYFP) females were mated with the Dppa3-MCMP(TG/0); Prdm1(flox/flox) males to obtain Prdm1 CKO PGCs and control of them.
The wild type female mice were mated with the Dppa3-EGFP mice to obtain wild type PGCs.

extract_protocol:
Total RNAs from collected primordial germ cell were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
cDNA synthesis and amplification from isolated RNAs/single cells were perfomed essentially as reported in [Kurimoto, K.et.al., Nucleic Acids Research, 34(5), e42.] The numbers of PCR cycles were employed for 11 cycles. 5 ng of amplified and quality-checked cDNAs were added to the pre-amplification buffer [1 × ExTaq buffer [Takara Bio (RR006), Shiga, Japan], 0.2 μM of each dNTP [Takara Bio (RR006)], 0.01 μg/μl of the N-V3 (dT)24 primer (HPLC-purified, attachment of amine at the 5-prime end), 0.01 μg/μl of the V1(dT)24 primer (HPLC-purified), and 0.025 U/μl of ExTaqHS [Takara Bio (RR006)]], and were amplified by four cycles of PCR. The surplus primers and PCR byproducts such as primer dimers were removed by size selection through three rounds of purification using a 0.6 × volume of AMPureXP beads for each  round [Beckman Coulter (A63881), Tokyo, Japan] according to the manufacturer’s instructions. The purified cDNAs were diluted to 130 μl by double-distilled water (DDW) and fragmented by shearing with Covaris S2 or E210 (duty cycle: 10%; intensity: 5; cycles per burst: 200; duration: 50 seconds; an intensifier was installed in the case of E210) [Covaris, Woburn, MA], and then end-polished in the End-polish buffer [1 × NEBnext End Repair Reaction buffer [NEB (B6052S), Ipswich, MA], 0.01 U/μl of T4 DNA polymerase [NEB (M0203)], and 0.033 U/μl of T4 polynucleotide kinase [NEB (M0201)]] for 30 min at 20oC. After incubation, a 0.8 × volume of the AMPureXP was immediately added, the solution was mixed for more than 20 min, and then the supernatant was transferred to a 1.2 × volume of the AMPureXP reagent and the cDNAs were purified. Next, to provide the purified cDNAs with an Int-adaptor sequence, the cDNAs were incubated in 30 μl of the Internal adaptor extension buffer [1 × ExTaq Buffer, 0.23 mM of each dNTP, 0.67 μM of the IntV1 (dT)24 primer (HPLC-purified), 0.033 U/μl of ExTaqHS] using the following thermal cycler program: 95℃ for 3 min, 67℃ for 2 min, and 72℃ for 2 min. The reactions were terminated by chilling in an ice-block, and after the addition of 20 μl of the P1-adaptor ligation buffer [a mixture of 10 μl of 5 × NEBNext Quick Ligation Reaction Buffer [NEB (B6058S)], 0.6 μl of 5 μM of the P1-T adaptor [Life Technologies (4464411)], and 1 μl of T4 ligase [NEB (M0202M)]], the solution was incubated for 15 min at 20℃ and for 20 min at 72℃. After two rounds of cDNA purification by adding a 1.2 × volume of AMPure XP, the cDNAs were added into the Final amplification buffer [1 × ExTaq buffer, 0.2 mM of each dNTP, 1 μM of the P1 primer, 1 μM of the BarT0XX_IntV1 primer (HPLC-purified), 0.025 U/μl of ExTaqHS] and amplified by PCR using the following thermal cycler program: 95oC for 3 min; followed by 9 cycles of 95℃ for 30 sec, 67℃ for 1 min and 72℃ for 1 min; with a final extension of 72℃ for 3 min. Finally, the cDNA libraries were purified two times by using a 1.2 × volume of AMPureXP and dissolved in 20 μl of TE buffer. The quality and quantity of the constructed libraries were evaluated by LabChip GX or Bioanalyzer 2100, a Qubit dsDNA HS assay kit [Life Technologies (Q32851)], and a SOLiD Library TaqMan Quantitation kit [Life Technologies (4449639)]. The cDNA libraries were sequenced with an ABI SOLiD 5500XL system (Applied Biosystems) for 50-bp single-end reads according to the instructions of the manufacturer.

treatment_protocol:
To induce Cre-loxP recombination , pregnant female mice with floxed Prdm1 allele were injected intraperitoneally with 3 mg 4-OHT per 25g body weight at 10.5 dpc.
sample collection protocol: The pregnant females were sacrificed at designated stages, the embryos were isolated, and the gonads were isolated.  The gonads were dissociated into single cells by incubating with 0.05% Trypsin-EDTA in PBS at 37℃ for 10 min and to remove the cell clamps and tissue debris, the cell suspensions were filtered through a cell strainer (Falcon; 08-771-23).  The EYFP-positive cells were sorted and collected by fluorescence activated cell sorting (FACS) (Becton Dickinson; FACS ARIA III).  The cells  were labeled with Alexa Fluor 647-conjugated anti-SSEA-1 antibody (eBioscience; 51-8813), washed with PBS, suspended in 0.1% BSA-PBS, and sorted by FACS.

tag: developmental stages

value: primordial germ cells

tag: genotype


title: Tc-TErep1


title: Tc-FErep3

source_name: T. cinnabarinus_fenpropathrin_2d-old adult mite tissue

value: fenpropathrin (569mg/L) for 6 h


title: E13.5_PGC_female_1


title: day0 RT1 feces

value: feces of C57BL6/J mouse

value: room temperature


title: Tc-FErep1


title: RISC-associated small RNA from NoDice(4-25)ΔPKR expressing N-terminally truncated Dicer N1 transfected with pCD-Rluc

city: Durham

first: Edward

middle: Matthew

last: Kennedy

state: NC

address: Department of Molecular Genetics and Microbiology, Box 3025

department: Molecular Genetics and Microbiology

institute: Duke University

description:
RISC-associated small RNA from NoDice(4-25)ΔPKR expressing N-terminally truncated human Dicer N1 transfected with pCD-Rluc
NoDiceΔPKR_CD_Rluc_N1_RISC_RIPSeq
RISC-associated small RNA

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences (Kozomara and Griffiths-Jones, 2014), Ensembl noncoding RNA database release 70 (Flicek et al., 2014), human functional RNA database version 3.4 (Mituyama et al., 2009), the vector or viral sequence of interest, and finally human genome 19.  No mismatches were allowed for alignments to the different references except the human genome for which two mismatches were allowed.
Genome_build: Human PV1 strain Sabin 1 (accession AY184219.1) was used for alignment as well as the reference sequence for pcDNA3 and human genome 19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.  The fasta files with the insert sequences for pCDRLuc and pcDNA-3476 are available on the series record.

organism: Homo sapiens

source_name: Dicer-deficient NoDice(4-25) HEK-293T cells (Bogerd, H.P., Whisnant, A.W., Kennedy, E.M., Flores, O., Cullen, B.R. (2014). Derivation and characterization of Dicer- and microRNA-deficient human cells.  RNA 20(6): 923--937)

growth_protocol: Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum and Gentamicin

extract_protocol:
RISC-bound miRNAs 48 transfection were isolated by immunoprecipitation using a monoclonal antibody that recognizes all human Argonaute proteins (Abcam: AB 57113), TRIzol, Illumina TruSeq kit
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

tag: rna substrate investigated

value: pCD-Rluc

tag: cell line

tag: parental cell line

tag: illumina index number

tag: rip antibody

value: Ago2 Ig (Abcam, catalog# AB57113, lot# G111546-1)


title: E13.5_PGC_male_2

tag: tissue


title: RISC-associated small RNA from NoDice(4-25)ΔPKR expressing Dicer transfected with pCD-Rluc

description:
RISC-associated small RNA from NoDice(4-25)ΔPKR expressing human Dicer transfected with pCD-Rluc
NoDiceΔPKR_CD_Rluc_WT_RISC_RIPSeq
RISC-associated small RNA


title: Tc-AVrep3

source_name: T. cinnabarinus_abamectin_2d-old adult mite tissue

value: abamectin (1 mg/L) for 6 h


title: E13.5_PGC_male_1


title: Tu-CKrep1


title: E11.5_PGC_1


title: E11.5_PGC_2


title: E10.5_PGC_2


title: E10.5_PGC_1


title: Tc-AVrep1


title: NoDice(4-25)ΔPKR expressing N-terminally trunctated Dicer N1 infected with IAV PR8

description:
NoDice(4-25)ΔPKR expressing N-terminally trunctated human Dicer N1 infected with IAV PR8
NoDiceΔPKR_PVS1_N1_TotalRNA
Total small RNA

extract_protocol:
small RNAs (<200 nt) purified using the mirVana Kit (Ambion)
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

value: Influenza A Virus PR8


title: Tc-AVrep2


title: Tc-FErep2


description:
Total small RNA
pcDNA3 is from Oligoengine
NoDice(4-25)ΔPKR cells expressing human Dicer and transfected with pcDNA-3476

data_processing:
Initial reads were quality filtered with Cassava 1.8.2.
Reads >15 nt were collapsed into FASTA format with the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html) using the following pipeline: fastq_quality_filter –Q 33| fastq_to_fasta –Q 33 | fastx_clipper -a TruSeq-Index# -l 15 –c | fastx_collapser.
All reads were then subject to alignment using Bowtie v.0.12.7 (Langmead et al., 2009) with the following options: –a --best --strata –m 25.  The reads were sequentially aligned and filtered to adapter sequences, miRBase v. 20 annotations of miRNA hairpins or mature miRNA sequences (Kozomara and Griffiths-Jones, 2014), Ensembl noncoding RNA database release 70 (Flicek et al., 2014), human functional RNA database version 3.4 (Mituyama et al., 2009), the vector or viral sequence of interest, and finally human genome 19.  No mismatches were allowed for alignments to the different references except the human genome for which two mismatches were allowed.
Genome_build: Human PV1 strain Sabin 1 (accession AY184219.1) was used for alignment as well as the reference sequence for pcDNA3 and human genome 19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.   The fasta files with the insert sequences for pCDRLuc and pcDNA-3476 are available on the series record.

source_name: Dicer-deficient NoDice(4-25) HEK-293T cells (Bogerd, H.P., Whisnant, A.W., Kennedy, E.M., Flores, O., Cullen, B.R. (2014). Derivation and characterization of Dicer- and microRNA-deficient human cells.  RNA 20(6): 923--937,)

extract_protocol:
Total small RNA was directly harvested and isolated with the mirVana miRNA isolation kit (Ambion)
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.


title: Tc-CKrep2

source_name: T. cinnabarinus_control_2d-old adult mite tissue


title: Tc-CKrep3


title: Prdm1 CKO_3

description:
3'-RNAseq amplified from bulk RNA
expression_Blimp1Tg.txt


title: Prdm1 CKO_2


title: Prdm1 CKO_1


description:
NoDice(4-25)ΔPKR transfected with vector control infected with IAV PR8
NoDiceΔPKR_PVS1_pK_TotalRNA
Total small RNA


title: Tc-CKrep1


title: Control_4

value: Prdm1(flox/flox); Rosa26(neo-EYFP/+)


description:
Total small RNA
pcDNA3 is from Oligoengine
NoDice(4-25)ΔPKR cells transfected with vector control and pcDNA-3476


title: E18.5_RNASeq

city: Cambridge

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

data_processing:
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore (v0.3.7, default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/<http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>). Trimmed reads were aligned to the mouse genome in paired-end mode (with parameters: --bowtie2 --bam --pbat and --unmapped) and then the singleton unmapped reads were aligned in single-end mode to maximise the number of hits (read1 was aligned with --bam --bowtie2 and --pbat, while read2 aligned with  --bam --bowtie2) . Alignments were carried out with Bismark v0.13.1 (Krueger and Andrews, 2011). Reads were then deduplicated with deduplicate_bismark selecting a random alignment for position that were covered more than once. CpG methylation calls were extracted from the deduplicated mapping output using the Bismark methylation extractor (v0.13.1) with the following parameters: --bedGraph --counts --gzip --report and -s for single-end and -p for paired-end.

Raw ChIP reads were trimmed to remove poor quality calls and adapters using TrimGalore. ChIP-Seq libraries were mapped using Bowtie1, 'unique' parameters.

Raw E18.5 RNA-Seq reads were trimmed to remove poor quality calls and adapters using TrimGalore. RNA-Seq libraries were mapped using TopHat v2.0.9 (option -g 1). RNA-seq reads were assembled into the E18.5 transcriptome using Cufflinks (Trapnell et al. 2010; 2012). The E18.5 transcriptome was assembled using Cufflinks v2.1.1 with default parameters.

Raw KDM1B/AOF1 RNA-Seq reads were trimmed to remove poor quality calls and adapters using TrimGalore. RNA-Seq libraries were mapped using TopHat v2.0.9 (option -g 1).

References:
Krueger F, Andrews SA. 2011. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics 27: 1571-1572.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. 2012. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7: 562-578.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology 28: 511-515.

Genome_build: GRCm38
-Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>. It combined both the single-end and paired-end alignments.
-Supplementary_files_format_and_content: The RNA-seq processed data contains corrected read counts for Ensembl genes.
-Supplementary_files_format_and_content: The ChIP-seq processed data contains corrected read counts for 1 kilobase windows across the genome.

source_name: Oocyte

extract_protocol:
RNA-Seq
RNA from sorted E18.5 oocytes was extracted using the RecoverAll Total Nucleic Acid Isolation Kit (Ambion/ Thermo Scientific, AM1975) and purified using the RNA Clean & Concentrator-5 Kit (Zymo, R1013) with on-column DNAse treatment (RNase-free DNase I, Thermo Scientific, AM2222). Ribosomal RNA was depleted from total RNA using the Ribo-Zero Magnetic Kit (Human/Mouse/Rat – Low Input, Epicentre, SCL24G). To generate RNA-seq libraries, RNA was reverse-transcribed using SuperScript III (Life Technologies, 18080044), with the second DNA strand synthesized using dUTPs and DNA polymerase I (NEB, M0210S). Libraries were constructed using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB, E6040S), with an additional step of dUTP excision by USER Enzyme (NEB, M5505S) before PCR amplification.

tag: background strain

tag: antibody

value: Oocytes (E18.5)

value: Wild-type


title: p10_H3_2

extract_protocol:
ChIP-Seq
postnatal day 10 oocyte nuclei were obtained through enzymatic digestion of CD1 ovaries, nuclei extraction, and subsequent FACS sorting. ChIP lysis and immunoprecipitation were performed using the True MicroChIP kit (Diagenode AB-002- 0016), with modifications. ChIP-Seq libraries were generated from immunoprecipitated DNA using the NEBNext Ultra End Repair/dA-Tailing Module (E7742) followed by adaptor ligation, DNA purification and library amplification.

value: Rabbit IgG, Abcam ab1791

value: Oocyte nuclei (p10)


description:
Total small RNA
pCD-RLuc was generated from the pSuper vector (Invitrogen).
NoDice(4-25)ΔPKR cells expressing human Dicer and transfected with pCD-RLuc

value: pCD-RLuc


title: NoDice(4-25)ΔPKR expressing Dicer infected with IAV PR8

description:
NoDice(4-25)ΔPKR expressing human Dicer infected with IAV PR8
NoDiceΔPKR_PVS1_WT_TotalRNA
Total small RNA


description:
Total small RNA
pCD-RLuc was generated from the pSuper vector (Invitrogen).
NoDice(4-25)ΔPKR cells expressing N-terminally truncated human Dicer N1 and transfected with pCD-RLuc


title: Control_3


title: Control_2


title: Prdm1 CKO_4


description:
Total small RNA
pCD-RLuc was generated from the pSuper vector (Invitrogen).
NoDice(4-25)ΔPKR cells transfected with vector control and pCD-RLuc


title: p10_H3_1


title: p10_K36me3_2

value: Rabbit IgG, gift of Robert Klose


title: p10_K36me3_1


description:
Total small RNA
NoDice(4-25) cells expressing N-terminally truncated human Dicer F1

extract_protocol:
Total RNA was isolated using TRIzol and small RNAs (<200 nt) purified using the mirVana Kit (Ambion)
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

value: endogenous microRNAs


title: p10_K4me3_1

value: Rabbit IgG, Diagenode pAb-003-050


description:
Total small RNA
NoDice(4-25) cells expressing N-terminally truncated human Dicer N3


description:
Total small RNA
NoDice(4-25) cells expressing N-terminally truncated human Dicer N1


title: p10_K4me2_1

value: Rabbit IgG, Abcam ab32356


title: p10_K4me2_2


description:
Total small RNA
pcDNA3 is from Oligoengine
NoDice(4-25)ΔPKR cells expressing N-terminally truncated human Dicer N1 and transfected with pcDNA-3476


description:
Total small RNA
NoDice(4-25) cells transfected with vector control


title: E18.5_H3_2

extract_protocol:
ChIP-Seq
Embryonic day 18.5 oocytes were obtained through enzymatic digestion of CD1 ovaries and FACS sorting. ChIP lysis and immunoprecipitation were performed using the True MicroChIP kit (Diagenode AB-002- 0016), with modifications. ChIP-Seq libraries were generated from immunoprecipitated DNA using the NEBNext Ultra End Repair/dA-Tailing Module (E7742) followed by adaptor ligation, DNA purification and library amplification.


title: E18.5_K36me3_1


title: E18.5_K4me3_2


title: E18.5_K36me3_2


title: E18.5_K4me3_1


title: E18.5_H3_1


title: E18.5_K4me2_2


title: E18.5_K4me2_1


title: Control_1

value: primordial germ cells


title: LSD1_KO_2

extract_protocol: To obtain MII oocytes, 6-8-week-old mice were injected intraperitoneally with 5 IU of pregnant mare’s serum gonadotrophin (PMSG, Sigma) and, 48 hours later, with 5 IU of human chorionic gonadotrophin (hCG, Sigma). Superovulated mice were euthanized 16 hours after hCG injection, and oocytes collected from the oviducts and released into a hyaluronidase/M2 solution for removal of cumulus cells. Genome-wide methylation maps in KDM1A/LSD1- and KDM1B/AOF1-deficient MII oocytes and controls were generated using the PBAT method. For each genotype, triplicate PBAT libraries were generated, with ~100 MII oocytes per library.

value: Oocytes (ovulated, metaphase II)

value: LSD1 fl/fl, ZP3-Cre+


title: LSD1_KO_1


title: LSD1_WT_3

value: LSD1 fl/+, ZP3-Cre-


title: LSD1_KO_3


title: LSD1_WT_2


description:
Total small RNA
NoDice(4-25) cells expressing human Dicer


title: AOF1_KO_3

value: AOF1 1lox/1lox


title: p10_K4me3_2


title: AOF1_KO_2


title: AOF1_WT_3


title: INPUT-P21-r1

city: Memphis

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA
BWA (version 0.5.9-r26-dev, default parameter) to align the reads to mouse genome mm9(MGSCv37 from Sanger),
Picard(version 1.65(1160)) then have been used for marking duplicated reads. Before further analysis, only non-duplicated reads with have been kept by samtools (parameter “-q 1 -F 1024” version 0.1.18 (r982:295)). To quality control(QC) the data and estimated the fragment size, non-duplicated version of SPP(version 1.11) have been used to draw cross-correlation under support of R (version 2.14.0) with packages caTools(version 1.17) and bitops(version 1.0-6). All our data passed QC following ENCODE criterion. Upon manually inspect the cross-correlation plot generated by SPP, the best fragment size estimated (the smallest fragment size estimated by SPP in all our cases) were used to extend each reads and generate bigwig file to view on IGV (version 2.3.40), we scaled the bigwig files to normalized to 15M reads so tracks are comparable.
For point-source factors (BRG1-FLAG, H3K4me1, H3K4me3, H3K27Ac), MACS2 ( version 2.0.9 20111102, nomodel with extsize defined as fragment size estimated above ) have been used to call peaks and peaks within 100bp have been merged by bedtools (version 2.17.0). For broad peaks (H3K27me3), SICER (version 1.1 redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp, FDR 0.00001 with fragment size defined above) have been used for domain calling.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bed format and pk call (text file)

extract_protocol:
MinElute PCR-purification kit (QIAGEN)
ChIP was performed using the iDeal ChIP-seq kit (Diagenode).

value: retina

value: wildtype

value: none (INPUT)

tag: age


title: AOF1_WT_1


title: INPUT-P0-r2


title: INPUT-P12-CKO-r1


title: INPUT-P12-r1


title: INPUT-P12-CKO-r2


title: H3K4me3-AB2-P21-r1


title: INPUT-P14-r1


title: H3K4me3-AB2-P12-r2


title: AOF1_WT_2


title: H3K4me3-AB2-P21-r2


title: LSD1_WT_1


title: H3K4me3-AB2-P14-r2


title: H3K4me3-AB2-P0-r1


title: H3K27me3-AB3-P12-r1


title: INPUT-BRG1-FLAG-P0-r1

value: BRG-FLAG


title: H3K4me3-AB2-P14-r3


title: H3K27me3-AB3-P12-CKO-r1


title: H3K27me3-AB1-P21-r1


title: H3K27me3-AB3-P12-r2


title: H3K27me3-AB1-P0-r2


title: H3K27me3-AB1-P21-r2


title: AOF1_KO_1


title: H3K27me3-AB1-P14-r1


title: H3K27me3-AB1-P0-r1


title: INPUT-P0-r1


title: H3K27me3-AB1-P14-r2


title: H3K27Ac-AB2-P21-r1


title: H3K27Ac-AB2-P14-r2


title: H3K27Ac-AB2-P12-r1


title: H3K27Ac-AB2-P14-r1


title: H3K27Ac-AB2-P12-CKO-r2


title: H3K27Ac-AB2-P0-r1


title: H3K4me3-AB2-P12-CKO-r1


title: H3K4me3-AB2-P0-r2


title: BRG1-FLAG-P0-r1


title: RISC-associated small RNA from NoDice(4-25) expressing truncated human Dicer N1 infected with Polio Virus Sabin 1

description:
RISC-associated small RNA
RIP antibody: Abcam: AB 57113
RISC-associated small RNA from NoDice(4-25) expressing N-terminally truncated human Dicer N1 infected with Polio Virus Sabin 1

organism:
Homo sapiens
Human poliovirus 1 strain Sabin

extract_protocol:
RISC-bound miRNAs 16 h postinfection were isolated by immunoprecipitation using a monoclonal antibody that recognizes all human Argonaute proteins (Abcam: AB 57113), and proteins were removed by digestion with proteinase K. Recovered small RNAs were then isolated using a mirVana kit (Ambion). The immunoprecipitated RNA (RIP-Seq) cDNA library was constructed using an Illumina TruSeq small RNA kit.
All small RNA input was processed with the TruSeq Small RNA Sample Preparation Kit (Illumina). Adapter-ligated RNA was reverse transcribed using SuperScript III (Life Technologies) and amplified using GoTaq green PCR master mix (Promega) with TruSeq 3′ indices.  DNA bands corresponding to ~145 bp were isolated by gel electrophoresis on 10% polyacrylamide gels.

value: Poliovirus 1 Sabin 1


description:
RISC-associated small RNA
RIP antibody: Abcam: AB 57113
RISC-associated small RNA from NoDice(4-25) expressing human Dicer infected with Polio Virus Sabin 1


description:
Total small RNA
NoDice(4-25) expressing N-terminally trunctated human Dicer N1 infected with Polio Virus Sabin 1


description:
Total small RNA
NoDice(4-25) expressing human Dicer infected with Polio Virus Sabin 1


description:
Total small RNA
NoDice(4-25) transfected with vector control infected with Polio Virus Sabin 1


title: H3K27Ac-AB2-P21-r2


title: AOF1_KO_3 (RNA-Seq)

extract_protocol:
RNA-Seq
To obtain MII oocytes, 6-8-week-old mice were injected intraperitoneally with 5 IU of pregnant mare’s serum gonadotrophin (PMSG, Sigma) and, 48 hours later, with 5 IU of human chorionic gonadotrophin (hCG, Sigma). Superovulated mice were euthanized 16 hours after hCG injection, and oocytes collected from the oviducts and released into a hyaluronidase/M2 solution for removal of cumulus cells. For RNA-Seq , three biological replicates were prepared for each genotype. Each sample, which contained 100 GV oocytes collected from 2-3 mice, was lysed directly in 1 μl of prelude direct lysis buffer (Nugen). RNA was then subject to amplification using the ovation RNA-seq system v2 (Nugen). Amplified cDNA was fragmented using Covaris and paired-end libraries were then constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) starting from end repair.


title: AOF1_KO_1 (RNA-Seq)


title: AOF1_KO_2 (RNA-Seq)


title: G3T3a

city: Ste-Anne-de-Bellevue

first: Timothy

middle: G.

last: Geary

state: Quebec

address: 21,111 Lakeshore Rd

department: Parasitology

country: Canada

institute: McGill University

data_processing:
unaligned fastq files were groomed using Fastq Groomer (v 1.0.4)
quality control statistics were verified using FastQC: Reads QC (version 0.52).
Quality and adapter trimming was performed using Fastq Quality Trimmer (v 1.0.0) and Trim Galore (v 0.2.8.1)
Tophat2 (v 0.6) was used for mapping gapped reads to the B. malayi reference genome (Bmalayi V3 243 reference)
HTSeq-count (version 1.0.0) was used to count the number of reads per transcript
edgeR (version 0.0.1)  was used to perform differential expression analysis between time points
Genome_build: Bmalayi V3 243 reference
Supplementary_files_format_and_content: txt file containing read counts matrix ; txt file containing normalized expression matrix

organism: Brugia malayi

source_name: jird 3; RNA extraction after 48h in culture

growth_protocol: Groups were incubated 1 worm per well of a 12-well plate (Costar) containing 6 ml RPMI 1640 (Sigma-Aldrich, St. Louis MO) supplemented with 10% v/v heat-inactivated fetal bovine serum (Sigma-Aldrich, F1051), 5% penicillin/streptomycin (Sigma–Aldrich) and 2% gentamycin (Gibco, 15750-060)

extract_protocol:
RNA extracted using Trizol method.
Messenger RNA (mRNA) was enriched with a NEBNext® Poly (A) mRNA Magnetic Isolation Module (NEB, E7490, Ipswich, MA). Using the enriched mRNA as template, cDNA libraries were constructed using the NEBNext® Ultra RNA Library Prep Kit Illumina (NEB, E7530, Ipswich, MA) and NEBNext® Multiplex Oligos for Illumina (Index Primer 1-12) (NEB, E7600, Ipswich, MA) following the manufacturer’s instructions. To verify the quality, DNA concentration and product size of the cDNA libraries, a Qubit® 2.0 Fluorometer (Life Technologies, Q32866), Qubit® dsDNA BR assay kit (Life Technologies, Q32850), High Sensitivity DNA Analysis Kit (Agilent, 5067-4626) and Bioanalyzer were used. cDNA libraries were sequenced on an Illumina MiSeq® Platform employing a 150 base pair single-end NGS setting.

treatment_protocol: No groups were treated.

tag: Sex

value: female

value: adult


title: G2T4b

source_name: jird 2; RNA extraction after 5d in culture


title: AOF1_WT_3 (RNA-Seq)

value: Wild-type


title: G3T4a

source_name: jird 3; RNA extraction after 5d in culture


title: G2T4a


title: G1T4b

source_name: jird 1; RNA extraction after 5d in culture


title: G3T3b


title: G2T3b

source_name: jird 2; RNA extraction after 48h in culture


title: AOF1_WT_2 (RNA-Seq)


title: G3T4b


title: G2T3a


title: H3K27Ac-AB2-P0-r2


title: H3K27Ac-AB2-P12-CKO-r1


title: AOF1_WT_1 (RNA-Seq)


title: G1T3b

source_name: jird 1; RNA extraction after 48h in culture


title: TA biological rep3 (rna-seq)

city: New York

first: Sebastian

last: Poliak

state: NY

address: 701 West 168st

department: Neuroscience and Biochemistry and Molecular Biophysics

institute: Columbia University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.9 with parameters -X 20000 -k 2 -m 2 -q -p
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. Differenetial gene expression was calculated using the R statistical package DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: [seq_TAvsGS_GS_up.txt, seq_TAvsGS_TA_up.txt] tab-delimited text files include RPKM values and differenetial gene expression for the samples
Supplementary_files_format_and_content: [TA_GS_rpkm6samples.txt] tab-delimited text file includes reads and RPKM values for the samples  across all gene models

source_name: proprioceptors supplying TAmuscle

growth_protocol: Dissection and purification of individual proprioceptors, following TA or GS ctb-555 muscle injections,  were done follwing Malin et al., 2007; and Hempel et al., 2007

extract_protocol:
RNA was extracted with a PicoPure RNA isolation kit (Arcturus).
cDNA was synthesized using the Ovation RNA-Seq System V2 kit (Nugen)
cDNA libraries were constructed using the Nextera DNA Sample Prep Kit (Illumina) and sequenced on an Illumina HiSeq 2000 to a depth of 25-30 million paired-end reads per sample

value: TA muscle

tag: cell type

value: neuron


title: G2T2b

source_name: jird 2; RNA extraction upon arrival at McGill

tag: developmental stage


title: G3T2b

source_name: jird 3; RNA extraction upon arrival at McGill


title: G3T2a


title: G1T3a


title: TA biological rep2 (rna-seq)

source_name: proprioceptors supplying TA muscle


title: TA biological rep1 (rna-seq)


title: G1T4a


title: G2T2a


title: GS biological rep3 (rna-seq)

source_name: proprioceptors supplying GS muscle

value: GS muscle


title: GS biological rep2 (rna-seq)


title: G1T2b

source_name: jird 1; RNA extraction upon arrival at McGill


title: GS biological rep1 (rna-seq)


title: G3T1b

source_name: jird 3; RNA extraction upon jird dissection


title: G1T2a


title: G3T1a


title: G2T1b

source_name: jird 2; RNA extraction upon jird dissection


title: G2T1a


title: GR siNS rep1

status: Public on Dec 01 2015

city: Los Angeles

first: Dai-Ying

last: Wu

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

institute: University of Southern California

description:
spp.optimal.bf.GR_siNS_rep0_VS_Input_siNS_rep1_rajas.regionPeak
shifted2_siNS_rep0.bedgraph

data_processing:
bwa 0.7.5a-r405
SPP+IDR ENCODE workflow
convert bam to tagAlign
shift tagAlign by estimated avg fragment size
merge replicates and convert to bedgraph
Genome_build: hg19 w/out chrM
Supplementary_files_format_and_content: spp files contain spp+idr output

source_name: U2OS (GR alpha)

growth_protocol: A clonal line of U2OS cells that stably express wild-type rat GR alpha were plated into 15 cm plates dishes and grown for 72h DMEM (low glucose) supplemented with 5% FBS

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 1 hour, quenched with 0.125M Glycine and washed with PBS. Chromatin was isolated using a lysis buffer containing 1% SDS, 50 mM Tris-HCl (pH 8.0), and 10 mM EDTA. The chromatin extracts were sonicated for 20 min (in repeated cycles of 30-s on/30-s off) using a Bioruptor (Diagenode) kept at 4 °C with a circulating water bath to achieve a DNA fragment size of 300–400 bp.
Standard protocol at Next-Generation Sequencing Core of USC Norris Comprehensive Cancer Center

treatment_protocol: Cells were treated with 100nM Dexamethasone

tag: chip antibody

value: GR (Santa Cruz)

tag: sirna

value: siNS

tag: hormone

value: 100nM dex for 1h


title: GR siHic5 rep2

description:
spp.optimal.bf.GR_siHic5_rep0_VS_Input_siHic5_rep1_rajas.regionPeak
shifted2_siHic5_rep0.bedgraph


title: GR siNS rep2


title: Input siNS


title: Input siHic5


title: G1T1a

source_name: jird 1; RNA extraction upon jird dissection


title: X9017

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from this additional RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)
Supplementary_files_format_and_content: *fastq_bismark.sam_methpcNF2t10.txt files provide a fragment-based DNA methylomes in .txt format (contains chromosome, start, end, length of the fragment, number of CpG site in the fragment, count of methylated and methylated CPGs and percentage methylation of the fragment). We selected the fragments having 10 or more reads at 2 CpG sites in each sample to provide fragment-based methylomes for these individuals (F2 t10 switch in the diffmeth program of DMAP tool, Reference: Stockwell, P. A., Chatterjee, A., Rodger, E. J. & Morison, I. M. DMAP: differential methylation analysis package for RRBS and WGBS data. Bioinformatics 30, 1814-1822, doi:10.1093/bioinformatics/btu126 (2014)."

source_name: Neutrophil

extract_protocol:
Neutrophils were extracted from peripehral blood of healthy individuals with Ficoll-Paque method.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.

value: Neutrophil isolated from peripheral blood


title: 32

data_processing:
RNA-seq library from 4 individuals were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Alignment of the sequenced reads were perfromed using Tophat package
Differential expression analysis was perfomed using cufflink and cuffdiff packages
Exon usage analysis was perfromed using DEXSeq R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains FPKM values of 4 samples (excel)

extract_protocol:
For each participant 20 mL of peripheral blood was collected into heparinized tubes. Enrichment for neutrophil was performed by a Dextran-Ficoll sedimentation and centrifugation method60. Briefly, 20 mL of peripheral blood was mixed with  Dextran-RPMI media in a 4:1 ratio. After 40 minutes incubation at RT, the upper layer (white blood cell-rich plasma) was layered onto Ficoll (aspirate: Ficoll of 2:1 ratio) and centrifuged for 15 min at 2500 rpm. To remove the remaining erythrocytes, the cell pellet was treated with 2 mL ddH2O for 10-15 seconds, after which 25 mL of RPMI was added. The suspension was centrifuged for 5 min at 1400 rpm and the cell pellet was resuspended in 20 mL phenol red-free RPMI-1640. An aliquot of this suspension was used to check presence of dead cells with trypan blue staining.  This preparation contained > 98% neutrophils.
Total RNA was isolated with RNeasy Mini Kit (Qiagen) following manufacturer’s protocol. Two rounds of RNase-free DNase I digestion (Qiagen) was performed to eliminate genomic DNA during the extraction process. RNA concentrations were determined using NanoDrop 2000 (Thermo Scientific). The quality and integrity of the RNA was determined using the RNA 6000 Pico chip on 2100 Bioanalyzer (Agilent Technologies). The median RNA integrity number (RIN) for the 4 samples was 8.05. RNA libraries were constructed using 1 µg of total RNA with TruSeq stranded mRNA Sample Preparation kit (Illumina, USA) following the manufacturer’s protocol.


title: 30


title: 31


title: 29


title: X9015

data_processing:
DNA from 12 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
DNA methylation analysis was perfromed using a fragment based approach using our own in house developed pipeline called DMAP (Stockwell et al Bioinformatics, 2014).
Unix scripts and Epiexplorer ( for overlapping ENCODE data) was used for further processing of data.
Genome_build: GRCh37
Supplementary_files_format_and_content: Excel file contains variably methylated fragment details (excel)
Supplementary_files_format_and_content: *fastq_bismark.sam_methpcNF2t10.txt files provide a fragment-based DNA methylomes in .txt format (contains chromosome, start, end, length of the fragment, number of CpG site in the fragment, count of methylated and methylated CPGs and percentage methylation of the fragment). We selected the fragments having 10 or more reads at 2 CpG sites in each sample to provide fragment-based methylomes for these individuals (F2 t10 switch in the diffmeth program of DMAP tool, Reference: Stockwell, P. A., Chatterjee, A., Rodger, E. J. & Morison, I. M. DMAP: differential methylation analysis package for RRBS and WGBS data. Bioinformatics 30, 1814-1822, doi:10.1093/bioinformatics/btu126 (2014)."


title: X9018


title: X9019


title: X9020


title: X9012_replicate


title: X9016


title: X9014


title: X9021


title: X9006


title: X9010


title: X9012


title: X9007


title: GR siHic5 rep1


title: G1T1b


title: META-3

city: Brussels

first: Manuel

last: Saiselet

address: 808 route de Lennik

country: Belgium

institute: ULB - IRIBHM

data_processing:
3-prime adaptor trimming (part of BGI small RNA sequencing pipeline)
collapse reads by sequence to produce compact fasta files (part of BGI small RNA sequencing pipeline)
read-mapping using a custom approach described in the related publication
count mapped reads for each mature miRNA listed in miRBase v19 and used as input for DESeq R package (which requires raw read count instead of normalized expression such as FPKM)
Genome_build: hg19
Supplementary_files_format_and_content: .fa collapsed by sequence : usual fasta format, including the count for each sequence in the sequence description
Supplementary_files_format_and_content: .txt tab-separated: expression matrices for mature miRNA and isomiR in raw read counts. Column description is provided in the header of each file

source_name: lymph node metastasis

extract_protocol:
Total RNA was extracted from tissues using Qiazol, followed by purification on miRNeasy columns (Qiagen) according to the manufacturer’s recommendations.
Deep sequencing (miRSeq) of the 3 PTC and their related samples from the Bordet Institute were performed by the Beijing Genomics Institute (BGI) using the TruSeq Small RNA Sample Prep Kit (Illumina).

value: lymph node

tag: tumor stage

value: nodal metastasis

tag: patient

tag: gender


title: META-2

value: male


title: META-1


title: TUMOR-1

source_name: papillary thyroid carcinoma classical form


title: NORMAL-3

source_name: normal thyroid

value: thyroid

value: normal sample


title: NORMAL-1


title: NORMAL-2


title: TUMOR-2

value: papillary thyroid carcinoma classical form


title: FadU parental cells

city: Taipei

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

country: Taiwan

institute: National Yang Ming Chiao Tung University

description: FadU parental cells

data_processing:
3’ adaptors of the FASTQ raw data were trimmed, and trimmed data were collapsed by the FASTX toolkit (http://hannonlab.cshl.edu/fastx_toolkit).
For all datasets, reads that shorter than 17 nt or longer than 30 nt were filtered out.
Genome_build: hg19
Supplementary_files_format_and_content: miRNA RPKM

source_name: HNSCC

growth_protocol: Cells were cultured under RPMI-1640 (10%FBS, 1% penicillin-streptomycine). Atmosphere: air, 95%; carbon dioxide (CO2), 5%. Temperature, 37.0°C

extract_protocol:
TruSeq Small RNA Sample Prep Kit (Cat# RS-200-0012) was used with 1 ug of total RNA for the construction of sequencing libraries
miRNA-Seq
size fractionation

value: HNSCC cell line, FadU

tag: cell line

value: FadU


title: FadU sphere cells

description: FadU sphere cells (sphere-derived cancer stem cells)

growth_protocol: Cells were cultured in tumor sphere medium composed of DMEM-F12 with N2 Plus Supplement, 10 ng/ml recombinant bFGF , 10 ng/ml EGF  and 1% penicillin-streptomycine for enriching spheroid cells.


title: Bio-ChIP-seq Blimp1 PB [9544]

city: Vienna

first: Moritz

middle: M

last: Gaidt

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

data_processing:
For determining the regulatoy landscape and overall number of peaks, we used the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mixture of pro-B and mature B cell input control sample. For H3K27me3 ChIP-seq samples, we used SICER () and for de novo motif prediction analysis, we used SISSRS ().
For analysis of differential gene expression, the RNA-seq samples were cut down to a read length of 44 bp and aligned to the mouse transcriptome using the TopHat version 1.4.1. The number of reads per gene was counted using the HTseq version 0.5.3 with the overlap resolution mode option set to ‘union’. Between-batch variation was reduced with applying the R package EDAseq 1.0.0 (ref. 29). Genes with less than 10 counts per sample on average were excluded. For the remaining genes, all RefSeq transcripts assigned to the same gene were investigated, and cases, where the GC content differed by 10% or more between transcripts assigned to the same gene, were removed. If the difference was smaller than 10%, the average GC content across the transcripts were used as GC content input to EDASeq. EDASeq was run with default parameters. The GC-normalized EDAseq output was rounded, and the results were used as input for the downstream count-based analysis. The ex vivo samples showed no batch effect, and no GC normalization was performed. The ex vivo and in vitro data were analyzed separately using the R package DESeq version 1.8.3. To this end, the samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.1 were called as differentially expressed. Due to the strong batch effects in the in vitro data set, RPM and RPKM were not calculated. Instead, the GC-normalized rounded counts (EDAseq output) were used to calculate the GC-normalized RPM and GC-normalized RPKM. The calculations were done as for RPM and RPKM with the only difference that the GC-normalized data was used instead of the raw counts.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base; text tab delim = RPKM values in ASCII text format tab delimited

source_name: Bio-ChIP-seq Blimp1 PB

extract_protocol:
phenol-chloroform extraction
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.

tag: strain background

tag: genotype/background

value: Blimp1(Bio/Bio) R26(BirA/BirA)

tag: cell preparation

value: 4-day LPS stimulation

value: PB

tag: cell sorting strategy

value: Streptavidin


title: Fur IP ChIP-Seq Anaerobic A

city: Madison

first: Patricia

middle: J

last: Kiley

state: WI

address: 420 Henry Mall, Room 1135 Biochemistry Building

department: Biomolecular Chemistry

institute: University of Wisconsin - Madison

data_processing:
Reformat Illumina files to Sanger format, FASTQ Groomer
Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
Call peaks to and FDR 0.1, MOSAiCs
Deconvolute peaks in close proximity, dPeak
Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
Scale data set to 20 million reads
Genome_build: Escherichia coli MG1655 K-12 genome version U00096.2
Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Anaerobic cultures

growth_protocol: Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of ~0.3-0.35).

extract_protocol:
Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.

treatment_protocol:
Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.

tag: genotype/variation

value: Wild-type

tag: growth medium

value: MOPS minimal glucose media containing 10 µM FeSO4

value: Custom anti-Fur polyclonal antibody


title: Fur IP ChIP-Seq Aerobic A

source_name: Aerobic cultures


title: TUMOR-3

tag: tissue

value: female

tag: age


title: Nr13 danrer skin 42months rep3

city: Jena

last: Project

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

data_processing:
Illumina Casava software used for extraction of FASTQ files
FASTQ files were mapped using Bowtie vs. the respective genomic sequence and a splice site data set created using UCSC's RefSeq annotation for each species
Counting of uniquely mapped reads and assignment to RefSeq transcripts/genes using R Statistical Language and Bioconductor
Calculation of RPKM values for each transcript and gene from the corresponding RefSeq annotation
Genome_build: D. rerio: danRer7; M. musculus: mm9
Supplementary_files_format_and_content: Excel file include raw counts and RPKM values for each sample

organism: Danio rerio

source_name: total RNA extracted from skin

extract_protocol:
D. rerio: Skin tissue from male zebrafish was dissected and stored in RNAlater (Qiagen, Hilden, Germany) at 80 °C. Total RNA was isolated with TRIzol (Life Technologies, Darmstadt, Germany) according to the instructions of the manufacturer. M. musculus: The isolated skin was homogenized in 500 μl QIAzol (Qiagen) by subsequently adding 100 μl chloroform. Following phase separation, the aqueous phase was transferred into a fresh tube, then 0.16 volume NaAc (2 M, pH 4.0) and 1.1 volume isopropanol were added. The RNA was precipitated by centrifugation and the pellet was washed with 75% ethanol. Total RNA was resuspended in 20 μl water (GIBCO) and stored at –80°C until use.
D. rerio: 5 µg of total RNA was used for preparation of libraries using Illumina’s mRNA-Seq sample prep kit (Illumina, San Diego, CA, USA) following the manufacturer’s instruction. M. musculus: 2.5 µg of total RNA was used with Illumina’s TruSeq RNA sample prep kit.

tag: strain

value: TuAB

value: 42 months

value: skin


title: Nr11 danrer skin 42months rep1


title: Nr14 danrer skin 42months rep4


title: Nr18 danrer skin 42months rep5


title: e7.5 EPC Input (1)

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
Read alignment: Sequencing output was analyzed using the Illumina Genome Analyzer Pipeline. Sequence tags that aligned uniquely to the reference genome with zero, one, or two mismatches, according to the ELAND alignment algorithm, were used for further analysis.
Sequence tags from biological replicates were combined prior to peak calling.  Peak calling was performed using GLITR  (Tuteja et al. 2008 Nucleic Acid Research 36(12): 4149-4157)  with default parameters, a 5% false discovery rate cutoff, and a maximum peak height ≥20.  Data were further filtered to remove peaks that were also identified in input control data, and to remove peaks that overlapped exons (using the UCSC mm9.knownGene table) or that were within 2.5kb of a gene transcriptional start site.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files that have the coordinates of each called peak.

source_name: Placenta

extract_protocol:
Ectoplacental cone (EPC) tissue was dissected from embryos at e7.5 and e9.5, obtained from timed pregnant CD-1 mice (Charles Rivers Labs).   The EPC was separated from the maternal decidua, embryo, and other extraembryonic tissue.  Chromatin isolation and immunoprecipitation were carried out as previously described (Tuteja et al. 2008 Nucleic Acid Research 36(12): 4149-4157)  but with 5μg chromatin and 1.2μg of H3k27ac antibody (Abcam ab4729, lot: GR24371-1) for the immunoprecipitation assay.
For each sample of immunoprecipitated DNA, 2ng were modified for sequencing following the Illumina's protocol (Preparing Sample for ChIP Sequencing of DNA (11257047 Rev A)).

value: placenta


title: e9.5 EPC Input (2)


title: e7.5 EPC Input (2)


title: Nr73 danrer skin 24months rep4

first: JenAge

address: Beutenbergstr. 11

value: 24 months


title: Nr76 danrer skin 24months rep6


title: e7.5 EPC H3k27Ac (2)


title: e7.5 EPC H3k27Ac (1)


title: Nr75 danrer skin 24months rep5


title: e9.5 EPC H3k27Ac (1)


title: Nr12 danrer skin 42months rep2


title: e9.5 EPC Input (1)


title: Nr70 danrer skin 24months rep1


title: e9.5 EPC H3k27Ac (2)


title: Nr28 danrer skin 5months rep7

value: 5 months


title: Nr29 danrer skin 5months rep8


title: Nr27 danrer skin 5months rep6


title: Nr72 danrer skin 24months rep3


title: Nr71 danrer skin 24months rep2


title: Nr23 danrer skin 5months rep3


title: Nr26 danrer skin 5months rep5


title: Nr25 danrer skin 5months rep4


title: human epididymis

city: Yantai

first: Yan

last: Li

state: Shandong

address: 20th, Yu Dong Road, Zhifu Area

institute: Shandong  Research  Centre  for  Stem  Cell  Engineering

description: Sample 1

data_processing: Sequence tags from the Solexa sequencing went through data cleaning, which included filtering out low quality tags and several contaminants. High quality reads were defined as no N (unknown nucleotide base) in the sequences, no more than 4 bases whose quality score was lower than 10 and no more than 6 bases whose quality score was lower than 13. The SOAP program was then used to map the small RNA tags to the genome. Thereafter all the tags were aligned with non-coding RNAs registered in GenBank (http://www.ncbi.nlm.nih.gov/) and Rfam (http://www.sanger.ac.uk/software/Rfam). After discarding the tags that matched rRNA (ribosomal RNA), tRNA (transfer RNA), repeat sequences, as well as mRNAs, the rest were searched for miRNAs in miRBase 17.0 (http://www.mirbase.org/index.shtml) and piRNAs (Piwi-interacting RNA) in Genebank by using programs developed by BGI. Mireap software developed by BGI was used to predict novel miRNA candidates on the basis of their secondary structure, the Dicer cleavage site and the minimum free energy of the un-annotated small RNA tags that could be mapped to the genome. The secondary structures were predicted by the MFOLD program [PMID:12824337].

source_name: epididymis from a healthy and fertile man

extract_protocol: Briefly, total RNA was size-fractionated on a 15% (w/v) PAGE gel and then the 15-30 nt fraction was excised and purified with a 14-30nt ssRNA ladder (TaKaRa, Dalian, China) as molecular marker. After dephosphorylation by alkaline phosphatase, the small RNA was ligated sequentially to 5'- and 3'-adapters, followed by RT-PCR to produce the sequencing library. The PCR products were purified and sequenced with Solexa 1G Genome Analyzer (San Diego, USA).

treatment_protocol: The whole epididymis was immediately frozen in liquid nitrogen and stored at -80C for RNA extraction

value: male

value: epididymis


title: Nr22 danrer skin 5months rep2


title: 12085

city: Decatur

first: Aliza

middle: P.

last: Wingo

state: GA

address: 1670 Clairmont Rd

department: Psychiatry

institute: Atlanta VAMC/Emory University

data_processing:
Adapters were trimmed using cutadapt
After adapter trimming, sequences shorter than 14 nucleotides were discarded.
Trimmed reads were aligned to the miRbase v.21 using SHRiMP aligner; only reads with a minimum average PHRED score of 10 were considered for alignment
Genome_build: miRBase v.21
Supplementary_files_format_and_content: raw counts in .txt format

source_name: whole blood

extract_protocol:
total RNA was extracted from whole blood using the Norgen protocol; small RNA was size fractionated from total RNA using polyacrylamide gel
small RNA was used as the starting material to generate small RNA libraries following the Illumina TruSeq Small RNA protocol

tag: Sex

value: low

tag: case/control status

value: case


title: 11953

value: high

value: control


title: 11922


title: 11903


title: 11800


title: 11683


title: 11766

value: mid


title: 10608


title: 11294


title: 11423


title: 10306


title: 12026


title: 10923


title: 11307


title: 11539


title: 10541


title: Nr30 danrer skin 5months rep9


title: 10175


title: 10230


title: 10170


title: 10036


title: ChIP-seq_Mouse_E2F1

city: lausanne

first: Pierre-Damien

last: Denechaud

address: Rue du Bugnon 7

department: Physiology

institute: UNIL

data_processing:
Mapping and peaks finding were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie2 version 2.1.0 with parameters --end-to-end --sensitive -k 20. Only reads with less that 5 hits were retained.
If read length was shorter than 100 bp, reads were extended to 100 bp. Reads mapping to top and bottom strand were shifted 45 bp to compensate for average fragment length. Genome coverage densities were calculated for each strand separately and normalized by the total number of mapped reads (times 10^-7).
ChIP-seq peaks detection was done with MACS software (v1.4.0) via the ChIP-seq module of HTSstation. A deconvolution algorithm (described in David et al, 2014 PLoS ONE) was run to refine the list of peaks found.
Genome_build: mm9
Supplementary_files_format_and_content: density files (bigWig), peaks (tab-delimited text file with peaks annotations, MACS results and deconvolution scores)

source_name: primary culture of hepatocytes

extract_protocol:
Fixation: 10 min 1% formaldehyde. Nuclear extracts sonication: Bioruptor 14 time 30s on / 30s off and cleared by centrifugation. Precleared: protein A agarose / salmon sperm DNA. Immunoprecipitation: anti–E2F1 c-20 antibody (santa cruz sc-193). Washed: low salt, high salt, LiCl and TE buffer. Elution: NaHCO3 1% SDS buffer. Decrosslinking 65°C overnight. DNA purification: minielute (Qiagen). DNA quantification: Qubit  (Life Technology).
Illumina TruSeq ChIP Sample Prep reagents, according to the provider's protocol

treatment_protocol: Mouse hepatocytes cells were harvested 36h after adenofection with Ad-E2F1

tag: cell type

value: hepatocytes

tag: antibody

value: E2F1 c20 ( santa cruz sc193)


title: RICE-H4K16ac

first: Xuehua

last: Zhong

address: 330 N. Orchard St.

department: Epigenetics

institute: Wisconsin Institute for Discovery

description: Genomic DNA isolated from immnuoprecipitated chromatin using H4K16ac antibody (07-329 Millipore)

data_processing:
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10/MSU7.0 genome, with default parameters. Reads mapping to identical positions in the genome  were collapsed into one read.
Genome_build: TAIR10 for Arabidopsis; MSU7.0 for Rice
Supplementary_files_format_and_content: bigwig file generated by UCSC "bedGraphToBigWig" scipts

organism: Oryza sativa

source_name: leaf

growth_protocol: Arabidopsis plants were grown on soil at 21 degree under continuous light for 2 weeks. Oryza sativa was grown on MS medium at 28 degree under short day condition (8hrs light and 16hrs dark)

extract_protocol:
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850
ChIP library was constructed by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)

tag: cultivar

value: Nipponbare

value: leaf


title: RICE-H3K23ac

description: Genomic DNA isolated from immnuoprecipitated chromatin using H3K23ac antibody (07-355 Millipore)


title: 10101


title: ChIP-seq_Mouse_Input

extract_protocol:
Fixation: 10 min 1% formaldehyde. Nuclear extracts sonication: Bioruptor 14 time 30s on / 30s off and cleared by centrifugation. Decrosslinking 65°C overnight. DNA purification: minielute (Qiagen) . E2F1 ChIP, samples were precleared with protein A agarose / salmon sperm DNA and chromatin was immunoprecipitated with anti–E2F1 c-20 antibody (santa cruz sc-193). Immunoprecipitated chromatin was washed (low salt, high salt, LiCl and TE buffer), reverse-crosslinked (65°C overnight) and purified with mini elute columns (Qiagen). Qubit fluorometric quantification (Life Technology) was used to quantify DNA.
Illumina TruSeq ChIP Sample Prep reagents, according to the provider's protocol

value: none (input)


title: 11864

value: female


title: H3K9ac PB [17017]

source_name: H3K9ac PB

value: 4-day LPS stimulation, FACS sorted

value: PB

value: B220intGFP+ FACS sorted

tag: chip antibody

value: H3K9ac Ab (07-352 Millipore)


title: 10992


title: Nr21 danrer skin 5months rep1

value: TuAB

value: 5 months

value: skin


title: H3K9ac Act B cell [17018]

source_name: H3K9ac Act B cell

value: Act B cell

value: B220+GFP- FACS sorted


title: H3K27me3 Pre-PB [24482]

source_name: H3K27me3 Pre-PB

value: Pre-PB

value: CD138–GFP+CD22- FACS-sorted

value: H3K27me3 cell signaling


title: H3K27me3 Pre-PB [24484]

value: Blimp1(GFP/fl) Cd23(Cre/+)

value: CD138–GFP+CD22hi FACS-sorted


title: ATAC-seq Pre-PB [25430]

data_processing:
library strategy: ATAC-seq
For determining the regulatoy landscape and overall number of peaks, we used the MACS program version 1.3.6.1 with default parameters, a genome size of 2,654,911,517 bp (mm9) and a mixture of pro-B and mature B cell input control sample. For H3K27me3 ChIP-seq samples, we used SICER () and for de novo motif prediction analysis, we used SISSRS ().
For analysis of differential gene expression, the RNA-seq samples were cut down to a read length of 44 bp and aligned to the mouse transcriptome using the TopHat version 1.4.1. The number of reads per gene was counted using the HTseq version 0.5.3 with the overlap resolution mode option set to ‘union’. Between-batch variation was reduced with applying the R package EDAseq 1.0.0 (ref. 29). Genes with less than 10 counts per sample on average were excluded. For the remaining genes, all RefSeq transcripts assigned to the same gene were investigated, and cases, where the GC content differed by 10% or more between transcripts assigned to the same gene, were removed. If the difference was smaller than 10%, the average GC content across the transcripts were used as GC content input to EDASeq. EDASeq was run with default parameters. The GC-normalized EDAseq output was rounded, and the results were used as input for the downstream count-based analysis. The ex vivo samples showed no batch effect, and no GC normalization was performed. The ex vivo and in vitro data were analyzed separately using the R package DESeq version 1.8.3. To this end, the samples were normalized, and the dispersions were estimated using the default DESeq settings. DESeq was then used to identify differentially expressed genes for each pairwise comparison of interest. Genes with an adjusted P value of < 0.1 were called as differentially expressed. Due to the strong batch effects in the in vitro data set, RPM and RPKM were not calculated. Instead, the GC-normalized rounded counts (EDAseq output) were used to calculate the GC-normalized RPM and GC-normalized RPKM. The calculations were done as for RPM and RPKM with the only difference that the GC-normalized data was used instead of the raw counts.
Genome_build: MM9
Supplementary_files_format_and_content: bigwig = bigWig Track format of read counts per base; text tab delim = RPKM values in ASCII text format tab delimited

source_name: ATAC-seq Pre-PB

extract_protocol:
Qiagen MinElute Kit
About 1-5 ng of cDNA or ChIP-precipitated DNA were used as starting material for the generation of sequencing libraries with the NEBNext Quick Ligation Module, NEBNext Endrepair Module and NEBNext dA-Tailing module or NEBNext Ultra Ligation Module and NEBNext Ultra End Repair/dA-Tailing module. DNA fragments of the following sizes were selected for the different experiments: 200–500 bp for ChIP-seq and 150–700 bp for RNA-seq with AMPure XP beads (Beckman Coulter). For strand-specific RNA-sequencing, the uridines present in one cDNA strand were digested with uracil-N-glycosylase (New England Biolabs) followed by PCR amplification with the KAPA Real Time Amplification kit (KAPA Biosystems). Completed libraries were quantified with the Agilent Bioanalyzer dsDNA 1000 assay kit and Agilent QPCR NGS Library Quantification kit. Cluster generation and sequencing was carried out by using the Illumina HiSeq 2000 system with a read length of 50 nucleotides according to the manufacturer’s guidelines.


title: H3K27me3 PB [24483]

source_name: H3K27me3 PB

value: CD138+GFP+ FACS-sorted


title: Bio-ChIP-seq Blimp1 PB [21480]

value: Blimp1(Bio/Bio) R26(BirA/BirA)

value: 4-day LPS stimulation

value: Streptavidin


title: ATAC-seq PB [25428]

source_name: ATAC-seq PB

value: Blimp1(GFP/+) Cd23(Cre/+)

value: 4-day LPS stimulation, FACS sorted

value: PB


title: ChIP-seq IRF4 PB [25441]

source_name: ChIP-seq IRF4 PB

value: Wild-type

value: 4-day LPS stimulation, MACS sorted

value: CD138+ MACS sorted

value: Irf4 Ab, SantaCruz SC6059X, lot:E0608


title: H3K27me3 Act B cell [24481]

source_name: H3K27me3 Act B cell

value: Act B cell

value: CD138–GFP– FACS-sorted


title: ChIP-seq IRF4 Act B cell [25439]

source_name: ChIP-seq IRF4 Act B cell

value: 2-day LPS stimulation, MACS sorted


title: ATAC-seq Act B cell [25426]

source_name: ATAC-seq Act B cell


title: H3K27me3 Act B cell [24485]

value: H3K27me3 cell signaling


title: ATAC-seq Act B cell [25429]

value: Blimp1(GFP/fl) Cd23(Cre/+)


title: Limb Mesenchyme Even

city: Porltand

first: Herman

middle: Scott

last: Stadler

state: OR

address: 3101 SW Sam Jackson Park Rd

institute: Shriners Hospital

description: ChIRP seq file using Hotchon even probeset

data_processing:
library strategy: chromatin isolation by RNA purification sequencing (ChIRP-seq)
Fastq files were assembled against MM9 mouse reference genome using using bowtie-0.12.9 (Langmead et al., 2009) and normalized to the total read count.  Even and odd Hotchon ChIRP samples were merged by taking the minimum value of the even and odd tracks at each genomic position.  The mouse glial cell line that does not express Hotchon was used as a control to identify false hybridization peaks detected by the Hotchon-specific even and odd probe pools.  Peaks were called by MACS (Zhang et al., 2008) using the Hotchon ChIRP merge sample and the DNA input, with an initial threshold p-value ≤ 5.9 x 10-57 corresponding to 775 peaks based on visual inspection of the peaks using the UCSC Genome Browser.
Genome_build: mm9
Supplementary_files_format_and_content: Called peaks were processed as big wig files and converted to bed file format for viewing in the UCSC genome browser

source_name: Mouse limb bud

extract_protocol:
Twenty five oligonucleotide probes corresponding to the murine Hotchon transcript were selected using the Stellaris Probe Designer Software set to masking level 5 to ensure the maximal level of probe specificity (biosearchtech.com) (Supplemental File).  The oligonucleotide sequences selected by the software were synthesized with an 18-atom hexa-ethyleneglycol spacer followed by a biotin tag located at the 3’ end of each oligonucleotide and purified by HPLC by Integrated DNA Technologies (Corallville, IA).   The distal half of mouse embryonic limb buds at embryonic day (E) 11 were dissected and digested for 10 minutes in sterile PBS containing 0.1% trypsin and 0.1% collagenase at 37 degrees Celsius as described (Owens and Solursh, 1982).  The digested limb buds were dissociated into a single cell suspension by passing them through a 70 µm nylon mesh and fixed in 1% glutaraldehyde as described (Chu et al., 2011.  Approximately 2000 embryonic limb buds were required to produce the 200mg cells needed for each for each ChIRP assay (Chu et al., 2011).  Cell lysis and chromatin shearing were accomplished using a Bioruptor instrument (Diagenode Denville, NJ) as previously described (Chu et al., 2011).  Once sheared, the chromatin was hybridized with the biotin-tagged Hotchon oligonucleotide probes which were divided into even and odd probe pool sets as described (Chu et al., 2012).  As a control, chromatin from E15.5 murine glial cells (a kind gift from Dr. Peter Hurlin), that do not express the Hotchon, were used in parallel assays and hybridized with the same Hotchon even and odd probe pool sets.   After hybridization the chromatin-Hotchon probe complexes were isolated using magnetic streptavidin beads as described (Chu et al., 2011).  DNA from isolated chromatin was purified using phenol/chloroform extraction followed by DNA precipitation as described (Chu et al., 2011).  The precipitated DNA was quantified using a Qubit 2.0 DNA fluorometer (Life Technologies) and submitted to Elim Biopharm (Hayward, CA) for library preparation and next generation sequencing using an Ilumina HiSeq 2500 sequencer (Illumina San Diego, CA).
Libraries were constructed for next generation sequencing using the Illumina library preparation kit as described by the manufacturer.

value: Swiss Webster

tag: developmental stage

tag: tissue source

value: limb bud


title: Glial cell line

description: Input Glial cell chromatin

source_name: Mouse brain

value: embryonic mouse brain


title: Limb Mesenchyme Input

description: Input Limb chromatin