title: subject 58, ADEH-, sham treatment, rep 5

city: Aurora

first: Michael

last: Edwards

state: CO

address: 12700 East 19th Avenue, Box C272

department: Pulmonary

institute: UC Denver

data_processing:
After sequencing, the samples were demultiplexed and the indexed adapter sequences were trimmed using the CASAVA v1.8.2 Software (Illumina).
The RNA-seq sequencing data were mapped and aligned using the computational pipeline of Bowtie and Tophat.
After mapping and aligning, the resulting .BAM files were imported into Partek Genomics Suite v6.6 (www.partek.com) and converted into gene transcript levels as reads per kilobase of exon per million mapped reads (RPKM) using a mixed-model approach (http://www.partek.com/Tutorials/microarray/User_Guides/RNASEQ.pdf).
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited matrix file containing the official gene symbol on rows and the associated RPKM values for each sample in the study in the corresponding column.  Only genes with 5 or more reads in at least one sample are given in the table.

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was isolated from PBMCs using RNeasy Mini Kits (Qiagen, Valencia, CA) according to the manufacturer’s guidelines. RNA concentration and purity were determined using Nano Drop-1000 Spectrophotometer and Agilent 2100 Bioanalyzer RNA Nano Chip (Agilent Technol., Palo Alto, CA).  Library preparation and HiSeq sequencing were performed at The University of Colorado Denver Genomics and Microarray Core facility. A total of 200-1000 ng of total RNA was used to prepare the Illumina HiSeq libraries according to manufacturer’s instructions for the TruSeq RNA kit.  In brief, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.  Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature.  The cleaved RNA fragments were converted into first strand cDNA using reverse transcriptase and random primers.  This was followed by second strand cDNA synthesis using DNA polymerase I and RNase H. These cDNA fragments then went through an end repair process, the addition of a single “A” base, and then ligation of the adapters.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human PBMCs were isolated using Ficoll-Hypaque® density gradient centrifugation of heparinized venous blood from donors. Briefly, heparinized blood (< 25 ml/tube) was transferred to ficoll tubes (Greiner® Leucosep tubes prepared with 15ml Ficoll-Hypaque) and centrifuged for 15 min at 2000 rpm.  The white blood cells were washed three times with 1x phosphate buffered saline and the cells were re-suspended in RPMI 1640 containing 10% heat inactivated fetal bovine serum, 40 µmol/L L-glutamine, 100 U/mL penicillin, 100 U/mL streptomycin, and 20 mmol/L HEPES buffer solution (GIBCO BRL Life Technologies).   One million PBMCs in 200µl culture media were stimulated with sham or HSV-1(VR-733, ATCC, Manassas, VA) at a multiplicity of infection (MOI) of 0.1 for 21 hours as our pilot experiments demonstrated that PBMCs stimulated with MOI of 0.1 of HSV-1 gave optimal cytokine induction (data not shown).

tag: subject #

tag: ad type

value: ADEH-

value: sham

value: PBMCs


title: subject 88, ADEH-, sham treatment, rep 6

status: Public on Aug 18 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: treatment

tag: cell type


title: WT NO 1

city: Princeton

first: Mark

last: Brynildsen

state: NJ

address: 25 William Street

department: Chemical and Biological Engineering

institute: Princeton University

data_processing:
base-calling was performed with RTA version 1.17.21.3
Split multiplexed single-end sequencing data using a separate index read (standard Illumina TruSeq protocol), reads were mapped to the E. coli MG1655 genome (NCBI NC_000913.3) using TopHat (v2.0.9), and counted for each gene using htseq-count (version 0.6.0) from the HTSeq Python package .
Raw gene counts were analyzed and evaluated for differential expression in R (version 3.1.0) using DESeq2 (version 1.4.5).
Genome_build: NCBI NC_000913.3
Supplementary_files_format_and_content: text files containing the raw counts for each gene; xlsx containing summary DESeq2 output

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

source_name: wild type_DPTA treated

growth_protocol: E. coli from a -80°C frozen stock were grown in LB for 4 h (37°C and 250 r.p.m.), and MOPS minimal media (Teknova) + 10 mM glucose for 16 h (37°C and 250 r.p.m.). The overnight culture was inoculated into 20 ml of fresh MOPS + glucose media in a 250 ml baffled shake flask, and grown at 37°C and 250 r.p.m. until OD600 = 0.2. The culture was centrifuged for 3 min at 15,000 r.p.m., resuspended in fresh pre-warmed (37°C) MOPS + glucose, centrifuged for an additional 3 min at 15,000 r.p.m., and again resuspended in pre-warmed MOPS + glucose. The resuspension was delivered to 10 ml fresh pre-warmed (37°C) MOPS + glucose in a stirred, aerobic batch bioreactor to a final OD600 of 0.05.

extract_protocol:
10 min after inoculation & treatment, 3 ml of culture was removed and immediately mixed with 6 ml of RNAprotect Bacteria Reagent (Qiagen). Purification was performed using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s protocol. Briefly, after 5 min incubation with the RNAprotect reagent, the sample was centrifuged for 10 min at 5000×g, and the supernatant carefully discarded. Cell pellets were stored at −80 °C until all replicates and conditions for that particular experiment were completed, allowing simultaneous purification of all samples. To eliminate potential DNA contamination, an on-column DNase digestion was performed using RNase-free DNase I (Qiagen).
Half a microgram of total RNA from each sample was subject to ribosomal RNA depletion using RiboZero Bacteria kit (Illumina, CA) and then converted to strand-specific RNA-seq library using the automated Apollo 324TM NGS Library Prep System and associated kits (Wafergen, CA) according to the manufacturer’s protocol, utilizing different DNA barcodes for each library. The libraries were examined on Bioanalyzer (Agilent, CA) DNA HS chips for size distribution, and quantified by Qubit fluorometer (Invitrogen, CA). The 12 RNA-seq libraries were pooled together at equal amounts and sequenced on Illumina HiSeq 2500 in Rapid mode as one lane of single-end 67 nt reads following the standard protocol.

treatment_protocol: Immediately after inoculation of cells into the bioreactor, the culture was either treated with 250 μM DPTA, or an equal volume of only the DPTA solvent (20 μM NaOH) as an untreated control.

tag: genotype/variation

value: wild-type

tag: treated with

value: 250 μM DPTA

tag: sample type

value: bacterial liquid cell culture


title: clpP NO 2

source_name: ΔclpP_DPTA treated

value: [Delta]lpP


title: clpP NO 3


title: subject 17, ADEH-, sham treatment, rep 2


title: subject 88, ADEH-, HSV-1 treatment, rep 6


title: subject 169, ADEH-, sham treatment, rep 1


title: subject 329, ADEH-, sham treatment, rep 3


title: subject 58, ADEH-, HSV-1 treatment, rep 5


title: subject 329, ADEH-, HSV-1 treatment, rep 3


title: subject 373, ADEH-, HSV-1 treatment, rep 4


title: subject 373, ADEH-, sham treatment, rep 4


title: WT untr 3

source_name: wild type_untreated

value: 20 μM NaOH (DPTA solvent; untreated control)


title: subject 17, ADEH-, HSV-1 treatment, rep 2


title: subject 169, ADEH-, HSV-1 treatment, rep 1


title: subject 35, ADEH+, sham treatment, rep 5

value: ADEH+


title: subject 130, ADEH+, sham treatment, rep 1


title: subject 152, ADEH+, sham treatment, rep 2


title: subject 24, ADEH+, HSV-1 treatment, rep 3


title: 14SC16a

city: Munich

first: Charissa

last: de Bekker

state: Bayern

address: Goethestrasse 31

department: Institute for Medical Psychology

country: Germany

institute: Ludwig Maximilian University

description:
Ophiocordyceps unilateralis s.l. strain SC16a
PolyA RNA
Processed data: Ophio1_1.gene_exp

data_processing:
Mapping to respective parasite and host genomes using TopHat version 2.0.11 and Bowtie version 2.2.2. Default settings, intron length settings: minimum 5, maximum 1000. Microexon-search enabled.
Differential expression using Cuffdiff version 2.2.1. Default settings with bias correction method. Normalization to FPKM.
Genome_build: Camponotus floridanus: CamFlo_1.0 (AEAB00000000.1)
Genome_build: Ophiocordyceps unilateralis s.l. SC16a: LAZP00000000.1
Supplementary_files_format_and_content: Camfl1.gene_exp.diff: cuffdiff output for all Camponotus castaneus reads in this study.
Supplementary_files_format_and_content: Ophio1_1.gene_exp.diff: cuffdiff output for all Ophiocordyceps unilateralis s.l. reads in this study.

organism: Ophiocordyceps unilateralis

source_name: Fungal culture

growth_protocol: Fungal cultures were grown in 250 mL shaking flasks holding 50 mL supplemented insect medium (Grace's insect cell culture media with 10% FBS) shaken at 150 rpm at 28C.

extract_protocol:
Ants and fungal cultures were flash frozen in liquid nitrogen. Ants heads were cut off. The RNA was extracted using TRIzol reagent and subsequently cleaned up with RNeasy MinElute columns (Qiagen).
mRNA-Seq libraries were constructed using a TruSeq Stranded mRNA Sample Prep Kit (Illumina).
Samples were sequenced on an Illumina HiSeq 2500 using 100 x 100 paired-end sequencing in Rapid Run mode.

treatment_protocol: Ants were infected by ways of injection with 1uL of disrupted fungal tissue in Grace's insect medium supplemented with 10% FBS.

tag: tissue

value: fungal tissue

value: fungal culture control


title: subject 25, ADEH+, sham treatment, rep 4


title: subject 35, ADEH+, HSV-1 treatment, rep 5


title: 15SC16a


title: 90d

city: Guang zhou

first: Liu

last: Jing

address: Wushan street 483#

country: China

institute: south china agricultural university

data_processing:
After removal of impurities, the remaining reads were matched to the rRNA sequence of sow by SOAP (http://soap.genomics.org.cn/index.html) to screen out the clean reads that could not match for the next step.
Sequenced reads were mapped to swine genome to annotate the location in the chromosomes using TopHat (http://ccb.jhu.edu/software/tophat/index.shtml).
For the alignment results, fragments shorter than 200 bp and transcripts with low expression were filtered to build a transcript by cufflinks (http://cpc.cbi.pku.edu.cn/)
Genome_build: Sscrofa_Sscrofa10.2

organism: Sus scrofa

source_name: Ovary

growth_protocol: The six swine were reared in the same environment and fed the same diet ad libitum.

extract_protocol:
Genomic RNA of ovaries from each individual from the same group of gilts was extracted and equal amounts were pooled together.
Two libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Ovary samples were quickly frozen in liquid nitrogen after slaughter and stored at −80 °C.

tag: strain

value: Landrace x Yorkshire crossbred swine

value: ovary

tag: age

value: 90 days postnatal


title: subject 25, ADEH+, HSV-1 treatment, rep 4


title: 30d

value: 30 days postnatal


title: 13SC16a


title: subject 152, ADEH+, HSV-1 treatment, rep 2


title: subject 130, ADEH+, HSV-1 treatment, rep 1


title: subject 24, ADEH+, sham treatment, rep 3


title: ChIP-Tagmentation of PBMC cells with H3K4ME3 antibody with 100pg of starting DNA - replicate 1

status: Public on Aug 17 2015

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

library_source: genomic

data_processing:
Library strategy: ChIP-Tagmentation
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
For ATAC-seq, ChIPmentation and ChIP-Tagmentation samples, reads aligning to the plus strand were offset by +4 bp, and reads aligning to the minus strand were offset by -5 bp
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Genome_build: hg19
Supplementary_files_format_and_content: Fastq files contain raw reads, bigWig files contain counts of reads per basepair per million

molecule: genomic DNA

source_name: peripheral blood mononucleated cells

growth_protocol: K562 cells were cultured in RPMI medium supplemented with 10% FCS and antibiotics. They were analyzed with a CASY cell counter to determine cell numbers. Peripheral blood was obtained from healthy volunteers as approved by the ethics committee at the Medical University of Vienna. Coagulation was prevented with EDTA or heparin, peripheral blood was diluted 1:1-1:3 in PBS, and peripheral blood mononuclear cells (PBMCs) were isolated with Lymphoprep density gradient (Axis-Shield) following manufacturer instructions. Purified cells were suspended in RPMI supplemented with 10% FBS and penicillin-streptomycin.

extract_protocol:
Three alternative chromatin immunoprecipitation (ChIP) protocols were successfully tested in combination with ChIPmentation. These protocols use different fixation, sonication, lysis, and washing conditions, making it possible to use ChIPmentation with essentially any ChIP-grade antibody; ChIP version 1 (H3K4me3, H3K27me3): Cells were washed once with PBS and fixed with 1 % paraformaldehyde in up to 1 ml PBS for 5 minutes at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 x g for 10 minutes at 4 °C and washed twice with up to 1 ml ice-cold PBS supplemented with 1 μM PMSF. The pellet was lysed in Cell Lysis Buffer (50mM HEPES/KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 % Glycerol, 0.5 % NP-40, 0.25 % Triton X-100, 1x protease inhibitors (Sigma)) for 10 minutes on ice. Nuclei were isolated by spinning the lysed cells for 10 minutes at 1000 x g at 4 °C, the supernatant was discarded and the pellet was resuspended in Sonication Buffer (10 mM Tris-HCl pH 7.6, 1mM EDTA, 0.1 % SDS) and sonicated in a 130 μl microTUBE (for up to 3 x 106 cells) on a Covaris S220 for 12 minutes until most of the fragments were 200-700 base pairs long (settings: duty cycle 2 %, peak incident power 105 Watts, cycles per burst 200). Lysates were centrifuged at full speed for 5 minutes at 4 °C and the supernatant was transferred to a new tube. The lysate was diluted to 200 μl per IP to a buffer composition of 20 mM HEPES, 0.1 % SDS, 1 %Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and incubated with an antibody against H3K4me3 (1 μg/IP, Diagenode C15410003-50) or H3K27me3 (1 μg/IP, Millipore 07-449) over night at 4 °C on a rotator. 20 μl of Protein A Magnetic Beads were blocked over night with 0.1 % BSA in PBS and added to the IP the next day for 2 hours on a rotator at 4 °C to capture the immunoprecipitated fragments. The immunoprecipitated chromatin was washed subsequently with WBI (20mM HEPES, 150mM NaCl, 0.1 % SDS, 0.1 % DOC, 1 % Triton X-100, 1 mM EDTA, 0.5mM EGTA) (twice), WBII (20 mM HEPES, 500 mM NaCl, 0.1 % SDS, 0.1 % DOC, 1 % Triton X-100, 1 mM EDTA, 0.5 mM EGTA) (once), WBIII (20 mM HEPES, 250 mM LiCl, 0.5 % DOC, 0.5 % NP-40, 1 mM EDTA, 0.5 mM EGTA) (once) and WBIV (20 mM HEPES, 1 mM EDTA, 0.5 mM EGTA) (twice). Then beads were incubated with 70 μl elution buffer (0.5 % SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl pH 8.0) containing 2 μl of Proteinase K (NEB). Beads in Elution Buffer were incubated for 1 hour at 55 °C and 8 hours at 65 °C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55 °C. Finally, DNA was purified with SPRI AMPure XP beads (ratio sample:beads 1:2) or Qiagen MinElute columns; ChIP version 2 (H3K4me1, and H3K36me3 and REST): Cells were washed once with PBS and fixed with 1 % paraformaldehyde in up to 1.5 ml PBS for 10 minutes at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 x g for 10 minutes at 4 °C and washed twice with up to 1 ml μl ice-cold PBS supplemented with 1 μM PMSF. The pellet was lysed in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 140 mM NaCl, 1 % Triton x-100, 0.1 % SDS, 0.1 % DOC, 1x protease inhibitors (Sigma)) and sonicated in a 1 ml milliTUBE in a Covaris S220 for 30 minutes until most of the fragments were 200-700 base pairs long (settings: duty cycle 5 %, peak incident power 140 Watts, cycles per burst 200). Lysates were centrifuged at full speed for 5 minutes at 4 °C. In the meantime, 50 µl beads (10 µl for low-input ChIPmentation) were blocked and conjugated to an antibody by washing and resupsending them 2 times in PBS/0.5 % BSA/0.5 % Tween-20). A specific antibody was added and bound to the beads by rotating > 1 h at room temperature. Antibodies used in this study were H3K4me1 (1 µg/IP, Diagenode pAb-194-050), H3K36me3 (1 µg/IP, Diagenode pAb-192-050) and REST (10 µg/IP, Millipore 07-579). The supernatant was transferred to a 0.5 PCR tube and per ChIP 50 μl of blocked antibody conjugated magnetic protein A beads were added and incubated for 3 hours at 4 °C. Immunoprecipitation beads were washed subsequently with 150 μl RIPA (twice), RIPA-500 (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 500 mM NaCl, 1 % Triton x-100, 0.1 % SDS, 0.1 % DOC,) (twice), RIPA-LiCl (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, pH 8.0, 250 mM LiCl, 1 % Triton x-100, 0.5 % DOC, 0.5 % NP40) and TE pH 8.0 (twice). Then beads were then incubated with 70 μl elution buffer (0.5 % SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris-HCl pH 8.0) containing 2 μl of Proteinase K (NEB). Beads in Elution Buffer were incubated for 1 hour at 55 °C and 8 hours at 65 °C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Finally, DNA was purified with SPRI AMPure XP beads (ratio sample:beads 1:2) or Qiagen MinElute columns; ChIP version 3 (H3K27ac, PU.1, CTCF and GATA1): Cells were washed once with PBS and fixed with 1% paraformaldehyde in up to 1.5 ml PBS for 5-10 minutes at room temperature. Glycine was added to stop the reaction. Cells were collected at 500 x g for 10 minutes at 4 °C and washed twice with up to 1 ml μl ice-cold PBS supplemented with 1 μM PMSF. The pellet was lysed in buffer L3B (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1 % Na-Deoxycholate, 0.5 % N-lauroylsarcosine, 1 x protease inhibitors (Sigma)) and sonicated in a 1ml milliTUBE in a Covaris S220 for 20 minutes until most of the fragments were 200-700 base pairs long (settings: duty cycle 5 %, peak incident power 140 Watts, cycles per burst 200). Lysates were supplemented with 1 % Triton-X-100 and centrifuged at full speed for 5 minutes at 4 °C. In the meantime, beads were blocked and conjugated to an antibody by washing them 2 times in PBS/0.5 % BSA and resuspending 50 μl of beads per IP (10 µl beads for low-input ChIPmentation) in 200 μl of PBS/0.5 % BSA. A specific antibody was added and bound to the beads by rotating >1h at room temperature. Antibodies used in this study were H3K27ac (2 µg, Diagenode pAb-196-050) PU.1 (5 μg/IP, Santa Cruz sc-352), CTCF (10 μl/IP, Millipore 07-729) and GATA1 (4 µg/IP and 2µg for low-input, Abcam ab11852). The supernatant was transferred to a 0.5 PCR tube and per ChIP 50 μl of blocked antibody conjugated magnetic protein A beads were added and incubated for 3 hours at 4 °C. Immunoprecipitation beads were washed subsequently with 150 μl TF-WBI (20 mM Tris-HCl/pH 7.4, 150 mM NaCl, 0.1 % SDS, 1 % Triton X-100, 2 mM EDTA) (twice), TF-WBIII (250 mM LiCl, 1 % Triton X-100, 0.7 % DOC, 10 mM Tris-HCl, 1 mM EDTA) (twice) and TET (0.2 % Tween-20, 10 mM Tris-HCl/pH 8.0, 1 mM EDTA) (twice). Then beads were incubated with 70 μl elution buffer (0.5 % SDS, 300 mM NaCl, 5 mM EDTA, 10 mM Tris HCl pH 8.0) containing 2 μl of Proteinase K (NEB). Beads in Elution Buffer were incubated for 1 hour at 55 °C and 8 hours at 65 °C to revert formaldehyde crosslinking, and supernatant was transferred to a new tube. Another 30 μl of elution buffer was added to the beads for 1 minute and eluates were combined and incubated with another 1 μl of Proteinase K for 1 hour at 55 °C. Finally, DNA was purified with SPRI AMPure XP beads (ratio sample:beads 1:2) or Qiagen MinElute columns.
Standard ChIP-seq library preparation: Purified ChIP DNA was end-repaired using the NEBNext End Repair Module (NEB) according to manufacturer’s instruction. Clean-up was done using Ampure XP beads (Agencourt) according to manufacturer’s instruction. Fragments were A-tailed using Klenow (3′→ 5′ exo-) polymerase (Enzymatics), and TruSeq-compatible adapters were ligated using T4 DNA Ligase (Enzymatics). The final library was size-selected using Ampure XP beads to remove adapter dimers.

value: peripheral blood


title: ChIP-Tagmentation of PBMC cells with H3K4ME3 antibody with 10pg of starting DNA - replicate 1


title: ChIP-Tagmentation of PBMC cells with H3K4ME3 antibody with 2pg of starting DNA - replicate 1


title: ChIP-seq of nan PBMC cells with H3K4ME3 - replicate 1

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
For ATAC-seq, ChIPmentation and ChIP-Tagmentation samples, reads aligning to the plus strand were offset by +4 bp, and reads aligning to the minus strand were offset by -5 bp
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Genome_build: hg19
Supplementary_files_format_and_content: Fastq files contain raw reads, bigWig files contain counts of reads per basepair per million


title: Input of ChIP-Tagmentation of PBMC cells 100pg of starting DNA - replicate 1


title: ChIPmentation of 500 thousand K562 cells with PU1 antibody - replicate 1

description: ChIPmentation of 500K K562 cells with PU1 antibody - replicate 1

data_processing:
Library strategy: ChIPmentation
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
For ATAC-seq, ChIPmentation and ChIP-Tagmentation samples, reads aligning to the plus strand were offset by +4 bp, and reads aligning to the minus strand were offset by -5 bp
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Genome_build: hg19
Supplementary_files_format_and_content: Fastq files contain raw reads, bigWig files contain counts of reads per basepair per million

source_name: K562 cells

tag: cell line


title: Input of ChIP-seq of nan PBMC cells with  - replicate 1


title: ChIPmentation of 500 thousand K562 cells with PU1 antibody - replicate 2

description: ChIPmentation of 500K K562 cells with PU1 antibody - replicate 2


title: ATAC-seq of 50 thousand K562 cells - replicate 2

description: ATAC-seq of 50K K562 cells - replicate 2

data_processing:
Library strategy: ATAC-seq
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences
Reads were mapped to hg19 whole genome using bowtie2 v2.2.4 with the –very-sensitive parameter
Duplicate reads were marked and removed with picard tools version 1.118
For ATAC-seq, ChIPmentation and ChIP-Tagmentation samples, reads aligning to the plus strand were offset by +4 bp, and reads aligning to the minus strand were offset by -5 bp
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair per million created
Genome_build: hg19
Supplementary_files_format_and_content: Fastq files contain raw reads, bigWig files contain counts of reads per basepair per million


title: ChIPmentation of 500 thousand K562 cells with PU1 antibody - replicate 3

description: ChIPmentation of 500K K562 cells with PU1 antibody - replicate 3


title: ATAC-seq of 50 thousand K562 cells - replicate 1

description: ATAC-seq of 50K K562 cells - replicate 1


title: Input of ChIP-Tagmentation of PBMC cells 10pg of starting DNA - replicate 1


title: ChIPmentation of 500 thousand K562 cells with IGG antibody - replicate 3

description: ChIPmentation of 500K K562 cells with IGG antibody - replicate 3


title: ChIPmentation of 500 thousand K562 cells with IGG antibody - replicate 2

description: ChIPmentation of 500K K562 cells with IGG antibody - replicate 2


title: ChIPmentation of 500 thousand K562 cells with IGG antibody with 1 ul of Tn5 - replicate 1

description: ChIPmentation of 500K K562 cells with IGG antibody with 1 ul of Tn5 - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 antibody - replicate 2

description: ChIPmentation of 500K K562 cells with H3K4ME3 antibody - replicate 2


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 antibody - replicate 1

description: ChIPmentation of 500K K562 cells with H3K4ME3 antibody - replicate 1


title: Input of ChIP-Tagmentation of PBMC cells 2pg of starting DNA - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K27ME3 antibody - replicate 2

description: ChIPmentation of 500K K562 cells with H3K27ME3 antibody - replicate 2


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 with 1ul of Tn5 - replicate 1

description: ChIPmentation of 500K K562 cells with H3K4ME3 with 1ul of Tn5 - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 with 0.2ul of Tn5 - replicate 1

description: ChIPmentation of 500K K562 cells with H3K4ME3 with 0.2ul of Tn5 - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K27ME3 antibody - replicate 1

description: ChIPmentation of 500K K562 cells with H3K27ME3 antibody - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 with 0.5ul of Tn5 - replicate 1

description: ChIPmentation of 500K K562 cells with H3K4ME3 with 0.5ul of Tn5 - replicate 1


title: ChIP-seq of 500 thousand K562 cells with IGG antibody - replicate 2

description: ChIP-seq of 500K K562 cells with IGG antibody - replicate 2


title: ChIP-Tagmentation of 500 thousand K562 cells with H3K4ME3 with 0.1ul of Tn5 - replicate 1

description: ChIP-Tagmentation of 500K K562 cells with H3K4ME3 with 0.1ul of Tn5 - replicate 1


title: ChIP-seq of 500 thousand K562 cells with IGG antibody - replicate 1

description: ChIP-seq of 500K K562 cells with IGG antibody - replicate 1


title: ChIPmentation of 500 thousand K562 cells with CTCF antibody - replicate 2

description: ChIPmentation of 500K K562 cells with CTCF antibody - replicate 2


title: ChIPmentation of 500 thousand K562 cells with IGG antibody - replicate 1

description: ChIPmentation of 500K K562 cells with IGG antibody - replicate 1


title: ChIP-seq of 500 thousand K562 cells with H3K4ME3 antibody - replicate 2

description: ChIP-seq of 500K K562 cells with H3K4ME3 antibody - replicate 2


title: ChIPmentation of 500 thousand K562 cells with CTCF antibody - replicate 1

description: ChIPmentation of 500K K562 cells with CTCF antibody - replicate 1


title: ChIP-seq of 500 thousand K562 cells with H3K4ME3 antibody - replicate 1

description: ChIP-seq of 500K K562 cells with H3K4ME3 antibody - replicate 1


title: ChIP-seq of 500 thousand K562 cells with H3K27ME3 antibody - replicate 2

description: ChIP-seq of 500K K562 cells with H3K27ME3 antibody - replicate 2


title: ChIP-seq of 500 thousand K562 cells with H3K27AC antibody - replicate 1

description: ChIP-seq of 500K K562 cells with H3K27AC antibody - replicate 1


title: ChIP-seq of 500 thousand K562 cells with H3K27ME3 antibody - replicate 1

description: ChIP-seq of 500K K562 cells with H3K27ME3 antibody - replicate 1


title: ChIPmentation of 10 million K562 cells with PU1 antibody - replicate 1 - paired end

description: ChIPmentation of 10M K562 cells with PU1 antibody - replicate 2


title: ChIPmentation of 10 million K562 cells with PU1 antibody - replicate 1 - single end

description: ChIPmentation of 10M K562 cells with PU1 antibody - replicate 1


title: ChIPmentation of 10 million K562 cells with PU1 antibody - replicate 2 - single end


title: ChIPmentation of 10 million K562 cells with REST antibody - replicate 2

description: ChIPmentation of 10M K562 cells with REST antibody - replicate 2


title: (-) MET PolyA+ RNAseq rep2

city: Durham

first: Jason

middle: W

last: Locasale

state: NC

address: LSRC C270A

department: Pharmacology and Cancer Biology

institute: Duke University School of Medicine

description: (-) MET PolyA+ RNAseq rep2

data_processing:
Basecalls for RNA-seq were performed using CASAVA version 1.4
Basecalls for ChIP-seq were performed using Illumina pipeline software v1.8
Adapter sequences were trimmed (FASTQ Quality Trimmer) then mapped to hg19 using Bowtie2.2.4 (ChIP-seq) or TopHat2.07 (RNA-seq) all in the Galaxy software suite (https://usegalaxy.org) using the default parameters
MACS2 was used to call peaks from ChIP-seq data using the -broad option with the following parameters: -t [experimental file] -c [input file] -n [output file name] -f BAM -g hs --broad -browd-cutoff 0.1
Count tables were generated from the accepted hits bam files using Htseq with the following parameters: htseq-count -f bam -s yes [input bam] [hg19genes.gtf]
Normalized counts and differential expression were calculated in edgeR and DEseq2 for both RNA-seq and ChIP-seq data
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files, comma separated values files are counts per gene for each sample; text files are output from MACS2 and columns include: chr, start, end, length, tags, log10.pvalue, fold enrichment (FE), and log10.qvalue

molecule: polyA RNA

growth_protocol: HCT116 were grown ~80% confluency then split

extract_protocol:
Cells grown on 10cm plates were flash frozen in liquid nitrogen and total RNA was isolated with the Invitrogen PARIS Kit (cat# AM1921)
Libraries were prepared according to standard Illumina protocols

treatment_protocol: After two days in full RPMI media, media is replaced withl +MET or -MET conditional media for 24 hours, then collected

value: human colon cancer

tag: chip antibody

tag: culture media

value: (-) Methionine


title: ChIPmentation of 10 million K562 cells with IGG antibody - replicate 5

description: ChIPmentation of 10M K562 cells with IGG antibody - replicate 5


title: ChIPmentation of 10 million K562 cells with REST antibody - replicate 1

description: ChIPmentation of 10M K562 cells with REST antibody - replicate 1


title: (+) MET PolyA+ RNAseq rep2

description: (+) MET PolyA+ RNAseq rep2

value: (+) Methionine


title: ChIPmentation of 10 million K562 cells with IGG antibody - replicate 4

description: ChIPmentation of 10M K562 cells with IGG antibody - replicate 4


title: (+) MET PolyA+ RNAseq rep1

description: (+) MET PolyA+ RNAseq rep1


title: ChIPmentation of 10 million K562 cells with IGG antibody - replicate 3

description: ChIPmentation of 10M K562 cells with IGG antibody - replicate 3


title: ChIPmentation of 10 million K562 cells with IGG antibody - replicate 2

description: ChIPmentation of 10M K562 cells with IGG antibody - replicate 2


title: (-) MET Input DNA rep1

description: (-) MET Input DNA rep1

extract_protocol:
Cells grown on 15cm plates were crosslinked with 1% formaldyhyde in culture media.  Cross-linked chromatin was collected and flash frozen before sonication with the Covaris M2.  Lysates were clarified and protein-DNA complexes were immunoprecipitated with H3K4me3 antibody.
Libraries were prepared according to standard Illumina protocols


title: ChIPmentation of 10 million K562 cells with IGG antibody - replicate 1

description: ChIPmentation of 10M K562 cells with IGG antibody - replicate 1


title: (-) MET Input DNA rep2

description: (-) MET Input DNA rep2


title: ChIPmentation of 10 million K562 cells with H3K4ME1 antibody - replicate 1 - paired end

description: ChIPmentation of 10M K562 cells with H3K4ME1 antibody - replicate 2


title: (+) MET Input DNA rep1

description: (+) MET Input DNA rep1


title: (+) MET Input DNA rep2

description: (+) MET Input DNA rep2


title: (-) MET_H3K4me3 ChIP rep2

description: (-) MET_H3K4me3 ChIP rep2

value: ChIPAb+ Anti-H3K4me3 (Millipore #17-614)


title: ChIPmentation of 10 million K562 cells with H3K4ME1 antibody - replicate 1 - single end

description: ChIPmentation of 10M K562 cells with H3K4ME1 antibody - replicate 1


title: (-) MET H3K4me3 ChIP rep1

description: (-) MET H3K4me3 ChIP rep1


title: (+) MET H3K4me3 ChIP rep2

description: (+) MET H3K4me3 ChIP rep2


title: ChIPmentation of 10 million K562 cells with H3K36ME3 antibody - replicate 2

description: ChIPmentation of 10M K562 cells with H3K36ME3 antibody - replicate 2


title: (-) MET PolyA+ RNAseq rep1

description: (-) MET PolyA+ RNAseq rep1


title: ChIPmentation of 10 million K562 cells with H3K4ME1 antibody - replicate 2 - single end


title: ChIPmentation of 10 million K562 cells with H3K36ME3 antibody - replicate 1

description: ChIPmentation of 10M K562 cells with H3K36ME3 antibody - replicate 1


title: ChIPmentation of 10 million K562 cells with GATA1 antibody - replicate 2

description: ChIPmentation of 10M K562 cells with GATA1 antibody - replicate 2


title: (+) MET H3K4me3 ChIP rep1

description: (+) MET H3K4me3 ChIP rep1


title: ChIPmentation of 10 million K562 cells with CTCF antibody - replicate 2

description: ChIPmentation of 10M K562 cells with CTCF antibody - replicate 2


title: ChIPmentation of 10 million K562 cells with CTCF antibody - replicate 1

description: ChIPmentation of 10M K562 cells with CTCF antibody - replicate 1


title: ChIPmentation of 10 million K562 cells with GATA1 antibody - replicate 1

description: ChIPmentation of 10M K562 cells with GATA1 antibody - replicate 1


title: ChIPmentation of 10 million K562 cells with H3K27AC antibody - replicate 1

description: ChIPmentation of 10M K562 cells with H3K27AC antibody - replicate 1


title: ChIPmentation of 500 thousand K562 cells with H3K4ME3 with 5ul of Tn5 - replicate 1

description: ChIPmentation of 500K K562 cells with H3K4ME3 with 5ul of Tn5 - replicate 1


title: ChIP-seq of 10 million K562 cells with GATA1 antibody - replicate 2

description: ChIP-seq of 10M K562 cells with GATA1 antibody - replicate 2


title: ChIPmentation of 10 million K562 cells with H3K27AC antibody - replicate 2

description: ChIPmentation of 10M K562 cells with H3K27AC antibody - replicate 2


title: Input of ChIP-Tagmentation of 500 thousand K562 cells with 0.1ul of Tn5 - replicate 1

description: Input of ChIP-Tagmentation of 500K K562 cells with 0.1ul of Tn5 - replicate 1


title: ChIP-Tagmentation of 10 million K562 cells with PU1 antibody - replicate 1

description: ChIP-Tagmentation of 10M K562 cells with PU1 antibody - replicate 1


title: ChIP-seq of 10 million K562 cells with REST antibody - replicate 2

description: ChIP-seq of 10M K562 cells with REST antibody - replicate 2


title: ChIP-seq of 10 million K562 cells with CTCF antibody - replicate 2

description: ChIP-seq of 10M K562 cells with CTCF antibody - replicate 2


title: ChIP-seq of 10 million K562 cells with REST antibody - replicate 1

description: ChIP-seq of 10M K562 cells with REST antibody - replicate 1


title: ChIP-Tagmentation of 10 million K562 cells with H3K4ME1 antibody - replicate 1

description: ChIP-Tagmentation of 10M K562 cells with H3K4ME1 antibody - replicate 1


title: ChIP-seq of 10 million K562 cells with PU1 antibody - replicate 2

description: ChIP-seq of 10M K562 cells with PU1 antibody - replicate 2


title: ChIPmentation of 100 thousand K562 cells with GATA1 antibody - replicate 1

description: ChIPmentation of 100K K562 cells with GATA1 antibody - replicate 1


title: ChIP-seq of 10 million K562 cells with IGG antibody - replicate 1

description: ChIP-seq of 10M K562 cells with IGG antibody - replicate 1


title: ChIP-seq of 10 million K562 cells with PU1 antibody - replicate 1

description: ChIP-seq of 10M K562 cells with PU1 antibody - replicate 1


title: ChIPmentation of 100 thousand K562 cells with GATA1 antibody - replicate 2

description: ChIPmentation of 100K K562 cells with GATA1 antibody - replicate 2


title: 15DAS_Ler_RepB_Bottom

city: Canberra

first: Li

last: Wang

state: ACT

address: North-Science Road, Acton ACT 2601

country: Australia

institute: CSIRO

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed and mapped to the TAIR10 reference genome using BioKanga align (http://sourceforge.net/projects/biokanga/) using default settings and additionally implementing parameters -A5000 and -M5.
Mapped reads were allocated to genomic features (as per TAIR10 annotations) using BioKanga maploci on default settings.
Supplementary_files_format_and_content: Text File - Gene ID and counts of associated aligned reads (pre-normalised counts) for all samples

organism: Arabidopsis thaliana

source_name: Whole aerial tissue 15 day old seedlings

growth_protocol: Arabidopsis thaliana accessions C24 and Landsberg erecta (Ler) were used as parental lines. Reciprocal C24 x Ler hybrids were generated by hand pollination. Seeds were sterilized and sown onto plates containing MS medium supplemented with 1% (w/v) sucrose and 0.6% agar. After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22 °C/18 °C (day/night) and 16h light/8h dark cycle. The first batch including samples C24 (RepA and RepB), Ler (RepA and RepB), C24 x Ler F1 (RepA and RepB), F4-L1-1(RepA and RepB), F4-L1-2 (RepA and RepB), F4-L2-1 (RepA and RepB), F4-L2-2 (RepA and RepB) and F4-S-1 (RepA and RepB) were grown under Philips Cool Daylight TLD 58W/840 fluorescent tubes providing a photosynthetic photon flux density of 130 - 150μmol photons m-2·s-1 as measured using a quantum meter (Model MQ-200 calibrated for electric light source, Apogee), we also sampled the five smallest C24 seedlings and five smallest Ler seedlings among the population (n = 50); the second batch including C24 (RepC and RepD), Le r(RepC and RepD), Ler x C24 F1 Hybrid (RepA and RepB), F4-L3-1 (RepA and RepB), F4-L3-2 (RepA and RepB), F4-L4-1 (RepA and RepB) and F4-L4-2  (RepA and RepB) were grown in the same light intensity as above but under different light tubes (SYLVANIA PREMIUM extra FL36W/865 Super Daylight deluxe light tube).

extract_protocol:
The aerial tissues of 15 day seedlings were sampled. Total RNA was isolated using QIAGEN RNeasy MiniKitTM following the product instructions.
illumina True-seq kit

treatment_protocol: No treatment

value: aerial tissues of 15 day seedlings

tag: genotype

value: Ler


title: ChIPmentation of 100 thousand K562 cells with CTCF antibody - replicate 2

description: ChIPmentation of 100K K562 cells with CTCF antibody - replicate 2


title: ChIPmentation of 100 thousand K562 cells with REST antibody - replicate 2

description: ChIPmentation of 100K K562 cells with REST antibody - replicate 2


title: 15DAS_Ler_RepA_Bottom


title: 15DAS_C24_RepB_Bottom


title: ChIP-seq of 10 million K562 cells with IGG antibody - replicate 2

description: ChIP-seq of 10M K562 cells with IGG antibody - replicate 2


title: ChIP-seq of 10 million K562 cells with H3K4ME1 antibody - replicate 2

description: ChIP-seq of 10M K562 cells with H3K4ME1 antibody - replicate 2


title: 15DAS_C24_RepA_Bottom


title: ChIP-seq of 10 million K562 cells with IGG antibody - replicate 3

description: ChIP-seq of 10M K562 cells with IGG antibody - replicate 3


title: ChIPmentation of 100 thousand K562 cells with REST antibody - replicate 1

description: ChIPmentation of 100K K562 cells with REST antibody - replicate 1


title: 15DAS_S2-1_RepA


title: ChIP-seq of 10 million K562 cells with H3K36ME3 antibody - replicate 1

description: ChIP-seq of 10M K562 cells with H3K36ME3 antibody - replicate 1


title: 15DAS_S2-1_RepB


title: 15DAS_S1-1_RepB


title: ChIP-seq of 10 million K562 cells with H3K4ME1 antibody - replicate 1

description: ChIP-seq of 10M K562 cells with H3K4ME1 antibody - replicate 1


title: 15DAS_S1-1_RepA


title: ChIP-seq of 10 million K562 cells with CTCF antibody - replicate 1

description: ChIP-seq of 10M K562 cells with CTCF antibody - replicate 1


title: 15DAS_L4-1_RepA


title: ChIPmentation of 10 thousand K562 cells with IGG antibody - replicate 4

description: ChIPmentation of 10K K562 cells with IGG antibody - replicate 4


title: ChIPmentation of 10 thousand K562 cells with H3K27ME3 antibody - replicate 2

description: ChIPmentation of 10K K562 cells with H3K27ME3 antibody - replicate 2


title: 15DAS_L3-2_RepA


title: 15DAS_L2-2_RepB


title: 15DAS_L3-2_RepB


title: 15DAS_L1-1_RepB


title: ChIPmentation of 10 thousand K562 cells with H3K4ME3 antibody - replicate 3

description: ChIPmentation of 10K K562 cells with H3K4ME3 antibody - replicate 3


title: ChIPmentation of 10 thousand K562 cells with H3K4ME3 antibody - replicate 4

description: ChIPmentation of 10K K562 cells with H3K4ME3 antibody - replicate 4


title: 15DAS_L4-1_RepB


title: ChIPmentation of 10 thousand K562 cells with H3K27ME3 antibody - replicate 1

description: ChIPmentation of 10K K562 cells with H3K27ME3 antibody - replicate 1


title: ChIPmentation of 10 thousand K562 cells with IGG antibody - replicate 5

description: ChIPmentation of 10K K562 cells with IGG antibody - replicate 5


title: ChIPmentation of 10 thousand K562 cells with IGG antibody - replicate 3

description: ChIPmentation of 10K K562 cells with IGG antibody - replicate 3


title: ChIP-seq of 10 million K562 cells with H3K27AC antibody - replicate 1

description: ChIP-seq of 10M K562 cells with H3K27AC antibody - replicate 1


title: 15DAS_L1-2_RepB


title: ChIP-seq of 10 million K562 cells with GATA1 antibody - replicate 1

description: ChIP-seq of 10M K562 cells with GATA1 antibody - replicate 1


title: Control_H_PMA

city: Dublin

first: Emma

middle: Marie

last: Quinn

state: Leinster

address: Institute of Molecular Medicine, St James's hospital Campus

department: Clinical Medicine

country: Ireland

institute: Trinity College Dublin

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence data quality control was evaluated using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and any reads with a substandard quality or adapter contamination were removed
Reads were aligned to the UCSC hg19 human reference genome using Tophat2 v2.0.3, up to two mismatches were allowed per uniquely aligned read
Alignment metrics were then collected using the PICARD CollectRNASeqMetrics (http://broadinstitute.github.io/picard/).
Read counts for each gene were summarized using the program Htseq-count from the HTseq package
Genome_build: UCSC Hg19
Supplementary_files_format_and_content: tab deliminated files containing the gene ID and raw read count per sample as determined by HTSeq-count

source_name: CD4+ T cells

growth_protocol: 30mls of blood was collected from each coeliac patient and control subjects with 24mls used for CD4+ T-cell isolation and subsequent RNA extraction. CD4+ T cells were isolated from each blood sample using CD4+ microbeads under standard procedures (Milteny Biotech GmBH).

extract_protocol:
CD4+ T-cells were then divided into 3 separate groups and stimulated with either 10ul anti-CD3 antibody(CD3 clone HIT3a, 1mg/ml) and 1ul anti-CD28 antibody (CD28 clone CD28.2 ,1mg/ml) for 24 hours at 37°C, 1ug (1mg/ml) Phorbal 12-myristate 13-acetate (PMA) for 4 hours at 37°C or left unstimulated (UNS) to represent basal conditions and incubated for 24 hours at 37°C.
RNA libraries were prepared for sequencing using standard Illumina protocols for sequencing on an Illumina HiSeq™ 2000 using 50 base pair single end reads (GATC Biotech, Konstanz, Germany).

tag: cell stimulation

value: Phorbal myristate acetate (PMA) stimulation

tag: phenotype

value: Control individual


title: 15DAS_L2-1_RepA


title: 15DAS_L1-2_RepA


title: 15DAS_L2-1_RepB


title: 15DAS_L2-2_RepA


title: 15DAS_C24xLer_RepB


title: 15DAS_L1-1_RepA


title: Control_H_UNS

value: Unstimulated


title: 15DAS_C24xLer_RepA


title: Control_G_UNS


title: Control_G_PMA


title: ChIPmentation of 100 thousand K562 cells with CTCF antibody - replicate 1

description: ChIPmentation of 100K K562 cells with CTCF antibody - replicate 1


title: 15DAS_Ler_RepB


title: Control_G_CD3

value: anti-CD3/anti-CD28 stimulation


title: 15DAS_C24_RepB


title: 15DAS_Ler_RepA


title: Control_F_UNS


title: Control_F_CD3


title: 15DAS_C24_RepA


title: F6-L4-2-1-2 sib.3

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed and mapped to the TAIR10 reference genome using BioKanga align (http://sourceforge.net/projects/biokanga/) using default settings and additionally implementing parameters -A5000 and -M5.
Mapped reads were allocated to genomic features (as per TAIR10 annotations) using BioKanga maploci on default settings.
Genome_build: TAIR10
Supplementary_files_format_and_content: Text File - Gene ID and counts of associated aligned reads (pre-normalised counts) for all samples

growth_protocol: Arabidopsis thaliana accessions C24 and Landsberg erecta (Ler) were used as parental lines. Reciprocal C24 x Ler hybrids were generated by hand pollination. Seeds were sterilized and sown onto plates containing MS medium supplemented with 1% (w/v) sucrose and 0.6% agar. After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22 °C/18 °C (day/night) and 16h light/8h dark cycle. Plants were grown under controlled light conditions (OSRAM L 36W/865 LumLux Daylight, 130 - 150μmol photons·m-2·s-1).


title: F6-L3-1-1-2 sib.3


title: Control_F_PMA


title: F6-L4-2-1-2 sib.2


title: F6-L3-1-1-2 sib.2


title: F6-L3-1-1-2 sib.1


title: Control_H_CD3


title: Control_E_PMA


title: Control_E_UNS


title: Control_C_UNS


title: LerxC24_RepB


title: Control_E_CD3


title: Control_C_PMA


title: Control_C_CD3


title: Control_B_UNS


title: UWOPS_A

city: New York

first: Isabel

last: Lam

state: New York

address: 1275 York Avenue

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

description: digested with 10 units Mnase

data_processing:
Reads were first clipped to remove any Illumina adapter sequences present and reads shorter than 35 bp were discarded (both ends of paired end reads were discarded). The clipped reads were then mapped to the proper target genome using BWA MEM (default options). The output SAM files were coordinate sorted and read groups added and merged into single sample BAM files using the PICARD toolkit. The output BAM files were then post-processed with a series of custom scripts to filter for uniquely mapping and properly paired reads. Proper pairing was defined as reads where the chromosome of each pair is the same, insert size was less than 250 bp, and strands were in opposite/inward orientation (==> <==). This was done using bedtools to convert the BAM files to Paired BED files (bedpe) and then filtering. The filtered read pairs were used to compute genome-wide coverage using the bedtools genomecov program.
Reads were mapped to each species'/strains' specific genome assembly.
Genome_build: For wild-derived S. cerevisiae strains YPS128 and UWOPS03-461.4, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for S. paradoxus YPS138, reads were mapped to the strain's genome assembly from SGRP (Saccharomyces Genome Resequencing Project, Wellcome Trust Sanger Institute); for S. mikatae IFO1815 and S. kudriavzevii ZP591, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: Tab delimited text files include raw paired-end coverage map at each base position in the genome (reads were extended to mononucleosome DNA length, then occupancy calculated by summing at each base pair the number of extended reads that overlapped that base pair)

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol:
Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 23°C, harvested, resuspended in 1% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 23°C.
see SAMPLES section

extract_protocol: Based on Pan et al. 2011 Cell 144:719-731. Samples were harvested at the indicated time-points after transfer to sporulation conditions, crosslinked with 1% formaldehyde, spheroplasted, chromatin extracted, treated with a dilution series of micrococcal nuclease (MNase) from 5 to 80 units, and DNA purified, as described in Pan et al. 2011. Mononucleosome-sized DNA was then purified by size fractionation on agarose gels and libraries prepared for Illumina sequencing.

tag: meiotic time-point

value: 6 hr in meiosis


title: UWOPS_B

description: digested with 10 units Mnase


title: YPS128_B_40

description: digested with 40 units Mnase

value: 4 hr in meiosis


title: Control_B_PMA


title: LerxC24_RepA


title: YPS128_B_20

description: digested with 20 units Mnase


title: Ler_RepB


title: UWOPS_2

description: Spo11-associated DNA oligonucleotides

data_processing:
Base calls perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500
Adapters (AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) were clipped from reads using fastx_clipper, part of the FASTX Toolkit 0.0.13.2, with parameters -l 15 -n -v -Q33 -i
First five bases (diffusion primer added in library prep) in each sequence were trimmed and trimmed sequence was recorded in the FASTQ ID tag for downstream tracking
Clipped reads were mapped using SHRiMP 2.1.1b with parameters -N 15 -U -g -1000 -q -1000 -m 10 -i -20 -h 100 -r 50% -n 1 -s 1111111111,11110111101111,1111011100100001111,1111000011001101111 -o 1001 -Q -E --sam-unaligned --strata
Sequences clipped from a read during mapping should be polyC on the 3' end or polyG on the 5' end. If clipped bases were not polyC or polyG the alignment score was corrected by deducting the mismatch score for each non-C,G base in the clipped sequence.
Maps of 5' ends of sequence reads were compiled and analyzed in R (RStudio version 0.98.1091, R version 3.0.1)
Genome_build: For wild-derived S. cerevisiae strains YPS128 and UWOPS03-461.4, reads were mapped to the SGD assembly released in June 2008, called "sacCer2" by UCSC: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=340067645; for S. paradoxus YPS138, reads were mapped to the strain's genome assembly from SGRP (Saccharomyces Genome Resequencing Project, Wellcome Trust Sanger Institute); for S. mikatae IFO1815 and S. kudriavzevii ZP591, reads were mapped to the strains' genome assemblies from Scannell et al. 2011 G3 1: 11-25, available on http://www.saccharomycessensustricto.org.
Supplementary_files_format_and_content: wig files include RPM (reads per million mapped) for each sample at each non-zero base position in the genome

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 23°C, harvested, resuspended to OD600=6.0 in 1% potassium acetate, 0.2 × supplements (2 μg/mL adenine, 2 μg/mL histidine, 6 μg/mL leucine, 2 μg/mL tryptophan, 2 μg/mL uracil) and sporulated at 23°C.

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors

tag: epitope tag

value: epitope tag:Spo11-Flag


title: YPS128_2

description: Spo11-associated DNA oligonucleotides


title: UWOPS_1

description: Spo11-associated DNA oligonucleotides


title: C24_RepB


title: Control_A_PMA


title: Ler_RepA


title: YPS128_1

description: Spo11-associated DNA oligonucleotides


title: F6-L4-2-1-2 sib.1


title: C24_RepA


title: 15DAS_L4-2_RepB

growth_protocol: Arabidopsis thaliana accessions C24 and Landsberg erecta (Ler) were used as parental lines. Reciprocal C24 x Ler hybrids were generated by hand pollination. Seeds were sterilized and sown onto plates containing MS medium supplemented with 1% (w/v) sucrose and 0.6% agar. After 2 days at 4°C, the plates were transferred to a growth room with conditions of 22 °C/18 °C (day/night) and 16h light/8h dark cycle. At 18 days after sowing, the plants were transferred to soil and grown to the reproductive stage. Plants were grown under controlled light conditions (OSRAM L 36W/865 LumLux Daylight, 130 - 150μmol photons•m-2•s-1).

extract_protocol:
Total RNA was isolated using QIAGEN RNeasy MiniKitTM following the product instructions.
illumina True-seq kit


title: Control_9_PMA


title: 15DAS_L4-2_RepA


title: Control_9_UNS


title: CA1_OldSAHA_sRNA_1

city: Goettingen

first: Eva

last: Benito Garagorri

state: Niedersachsen

address: Von Siebold Strasse 3A

department: Epigenetics of Aging

institute: DZNE Goettingen

description: small RNA-Seq

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were first trimmed for adaptor contamination with cutadapt using the following options: -m 15 -M 32; Mapping was done to mm10 with STAR with the following options: --outFilterMismatchNmax 0.05; --outFilterMatchNmin 15; --alignIntronMax 1; counting was done with htseq on miRbase in the "intersection non-empty" mode
miRNA counts were generated using htseq over miRbase in the "intersection non-empty" mode
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing miRNA reads

organism: Mus musculus

source_name: 20 month old animals treated with SAHA

extract_protocol:
CA1 was microdissected under a microscope and snap-frozen in liquid nitrogen. RNA was extracted with Tri reagent (Sigma) and treated with DNAse I (Life Technologies) according to manufacturer's instructions.
Libraries were prepared using Illumina's TruSeq standard protocols starting from 1µg total RNA

value: 20 months

value: CA1 hippocampal subregion

value: WT

tag: drug treatment

value: SAHA:(18g cyclodextrin + 0.67g SAHA)/L water


title: CA1_OldSAHA_sRNA_5

description: small RNA-Seq


title: CA1_OldSAHA_sRNA_3

description: small RNA-Seq


title: Control_9_CD3


title: CA1_OldSAHA_sRNA_6

description: small RNA-Seq


title: CA1_OldSAHA_sRNA_4

description: small RNA-Seq


title: CA1_YoungVeh_sRNA_8

description: small RNA-Seq

source_name: 3 month old animals treated with vehicle

value: 3 months

value: Vehicle:18g cyclodextrin/L water


title: CA1_YoungVeh_sRNA_5

description: small RNA-Seq


title: Control_B_CD3


title: CA1_YoungVeh_sRNA_6

description: small RNA-Seq


title: Control_4_UNS


title: YPS128_A

description: digested with 20 units Mnase


title: Control_A_CD3


title: CA1_YoungVeh_sRNA_4

description: small RNA-Seq


title: CA1_OldSAHA_sRNA_2

description: small RNA-Seq


title: Control_4_PMA


title: CA1_YoungVeh_sRNA_2

description: small RNA-Seq


title: CA1_YoungVeh_sRNA_3

description: small RNA-Seq


title: Control_4_CD3


title: Control_3_UNS


title: 15DAS_L3-1_RepB


title: CA1_OldVeh_sRNA_5

description: small RNA-Seq

source_name: 20 month old animals treated with vehicle


title: CA1_YoungVeh_sRNA_1

description: small RNA-Seq


title: 15DAS_LerxC24_RepA


title: 15DAS_Ler_RepD


title: CA1_OldVeh_sRNA_4

description: small RNA-Seq


title: CA1_YoungVeh_sRNA_7

description: small RNA-Seq


title: 15DAS_L3-1_RepA


title: CA1_OldVeh_sRNA_3

description: small RNA-Seq


title: Control_3_CD3


title: 15DAS_C24_RepD


title: 15DAS_Ler_RepC


title: CA1_APPSAHA_8

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were aligend to mm10 using STAR with following parameters: outStd SAM; outFilterMismatchNmax 2; outSAMstrandField intronMotif; sjdbOverhang 49
Gene or exon counts were generated using htseq in the "intersection non-empty" mode
Genome_build: mm10
Supplementary_files_format_and_content: txt file containing gene or exon counts

source_name: 10 month old APP/PS1-21 animals treated with SAHA

extract_protocol:
CA1 was microdissected under a microscope and snap-frozen in liquid nitrogen. A small cube of liver was removed and snap frozen in liquid nitrogen. RNA was extracted with Tri reagent (Sigma) and treated with DNAse I (Life Technologies) according to manufacturer's instructions.
Libraries were constructe from 500ng of RNA according to standard Illumina protocols.

value: 10 months

value: APP/Ps1-21 transgenic


title: CA1_APPSAHA_7


title: 15DAS_LerxC24_RepB

value: aerial tissues of 15 day seedlings


title: Control_1_PMA


title: CA1_APPSAHA_5


title: Control_1_UNS


title: CA1_APPSAHA_4


title: CA1_APPSAHA_3


title: 28DAS_L4-2_RepB


title: CA1_OldVeh_sRNA_1

description: small RNA-Seq


title: 28DAS_L4-2_RepA

source_name: Expanded mature leaves from 28 day old plants


title: Control_3_PMA


title: Coeliac_15_UNS

value: Coeliac Individual


title: CA1_APPSAHA_2


title: CA1_OldVeh_sRNA_2

description: small RNA-Seq


title: 28DAS_L4-1_RepA

value: Expanded mature leaves from 28 day old plants


title: 28DAS_L4-1_RepB


title: CA1_APPveh_8

source_name: 10 month old APP/PS1-21 animals treated with vehicle


title: Coeliac_15_CD3


title: Coeliac_15_PMA

value: Phorbal myristate acetate (PMA) stimulation


title: CA1_APPSAHA_1


title: CA1_APPveh_9


title: CA1_APPveh_7


title: 15DAS_C24_RepC


title: CA1_APPSAHA_6


title: CA1_APPveh_6


title: CA1_APPveh_5


title: 28DAS_L3-2_RepB


title: CA1_APPveh_4


title: Coeliac_14_PMA


title: 28DAS_L3-2_RepA


title: CA1_APPveh_3


title: CA1_APPveh_2


title: Coeliac_14_CD3


title: Control_1_CD3

value: Control individual


title: 28DAS_L3-1_RepB


title: Coeliac_13_UNS

value: Unstimulated


title: CA1_Wtveh_11

source_name: 10 month old  vehicle-treated WT littermates of APP/PS1-21 animals


title: CA1_APPveh_1


title: Coeliac_13_PMA


title: CA1_Wtveh_9


title: 28DAS_L3-1_RepA


title: 28DAS_L2-2_RepB


title: Coeliac_13_CD3

value: anti-CD3/anti-CD28 stimulation


title: CA1_Wtveh_6


title: CA1_Wtveh_8


title: CA1_Wtveh_2


title: CA1_Wtveh_7


title: Coeliac_12_PMA


title: Coeliac_12_UNS


title: 28DAS_L1-2_RepB


title: CA1_Wtveh_4


title: 28DAS_L2-1_RepB


title: 28DAS_L2-1_RepA


title: Coeliac_12_CD3


title: 28DAS_L1-2_RepA


title: Coeliac_11_UNS


title: Liver_OldSAHA_6

value: Liver


title: Liver_OldSAHA_8


title: CA1_Wtveh_5


title: CA1_Wtveh_3


title: Coeliac_11_PMA


title: CA1_Wtveh_1


title: Liver_OldSAHA_7


title: CA1_Wtveh_10


title: Coeliac_11_CD3


title: 28DAS_L2-2_RepA


title: Liver_OldSAHA_5


title: Liver_OldSAHA_4


title: 28DAS_L1-1_RepB


title: Liver_OldSAHA_3


title: Coeliac_10_UNS


title: 28DAS_L1-1_RepA


title: 28DAS_LerxC24_RepB


title: Liver_OldSAHA_1


title: 28DAS_LerxC24_RepA


title: Liver_YoungVeh_6


title: Coeliac_10_PMA


title: Coeliac_10_CD3


title: Liver_YoungVeh_3


title: Liver_YoungVeh_5


title: 28DAS_C24xLer_RepB


title: Coeliac_9_UNS


title: 28DAS_Ler_RepD

value: Ler


title: Coeliac_9_PMA


title: Liver_YoungVeh_1


title: Liver_OldVeh_7


title: Liver_OldVeh_6

value: 20 months


title: Coeliac_9_CD3


title: Liver_OldVeh_4


title: Liver_OldVeh_3


title: 28DAS_Ler_RepC


title: Liver_OldSAHA_2


title: Coeliac_8_UNS


title: Liver_OldVeh_2


title: Liver_OldVeh_1


title: Coeliac_8_PMA


title: 28DAS_C24xLer_RepA


title: Liver_YoungVeh_2


title: 28DAS_Ler_RepA


title: CA1_OldSAHA_5

value: CA1 hippocampal subregion


title: 28DAS_C24_RepD


title: Coeliac_7_UNS


title: CA1_OldSAHA_2

value: WT


title: Coeliac_8_CD3


title: CA1_OldSAHA_3

value: SAHA:(18g cyclodextrin + 0.67g SAHA)/L water


title: 28DAS_C24_RepC


title: 28DAS_C24_RepB


title: CA1_YoungVeh_8

value: 3 months


title: Coeliac_7_PMA


title: CA1_OldSAHA_6


title: 28DAS_Ler_RepB


title: Coeliac_7_CD3


title: 28DAS_C24_RepA


title: Liver_YoungVeh_4

value: Vehicle:18g cyclodextrin/L water


title: CA1_YoungVeh_6


title: CA1_OldSAHA_1


title: Coeliac_6_UNS


title: CA1_YoungVeh_5


title: CA1_YoungVeh_7


title: Scm3_FLAG_10min_IP_(20140502_9)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: Immunoprecipitation of Scm3-FLAG from N-ChIPed chromatin, 10 minutes MNase.

data_processing: 1. We used Novoalign 2.08 (http://www.novocraft.com) to map paired-end 25bp reads to release 2.20 of the S. pombe genomic sequence obtained from http://www.pombase.org . If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads (Supplementary file .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)

organism: Schizosaccharomyces pombe

source_name: Immunoprecipitated DNA

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1988457) and subjected to MNase digestion. Resulting chromatin solution was needle extracted and soluble chromatin was subjected to native chromatin immunoprecipitation as described previously (PMID: 22184235).

tag: cell part

value: nuclei

tag: strain genotype

value: h minus (h- scm3-FLAG[hph])

value: Anti-FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823)


title: Coeliac_6_PMA

value: Coeliac Individual


title: Coeliac_6_CD3


title: CA1_OldSAHA_4


title: CA1_YoungVeh_2


title: Coeliac_5_CD3


title: H4_20min_cleavage_(20140725_2)

description: Immunuprecipitation of chemically cleaved DNA after 20 minutes.

source_name: Chemically cleaved chromatin

extract_protocol: Samples were prepared as described in PMID: 24277842. Chemical cleavage reaction was performed for 20 min.

value: spheroplasts

value: H4S48C:hhf1S48C, hhf2S48C


title: CA1_YoungVeh_3


title: Mis6_HA_10min_IP_(20140502_8)

description: Immunoprecipitation of Mis6-HA from N-ChIPed chromatin, 10 minutes MNase.

value: h minus (leu1 mis6-HA[LEU2])

value: Anti-HA (MBL anti-HA-tag mAB magnetic beads, catalog #M132-9)


title: H4_15min_cleavage_2_(20140725_3)

description: Immunoprecipitation of H4 from chemically cleaved DNA after 15 minutes. Replicate.

extract_protocol: Samples were prepared as described in PMID: 24277842. Chemical cleavage reaction was performed for 15 min.


title: H4_15min_cleavage_1_(20140725_1)

description: Immunoprecipitation of H4 from chemically cleaved DNA after 15 minutes.


title: Mis6_GFP_10min_XIP_(20140502_7)

description: Immunoprecipitation of Mis6-GFP from X-ChIPed chromatin, 10 minute MNase.

extract_protocol: ChIP assays were performed using a protocol described previously (PMID: 22536162) with slight modifications. Briefly an exponentially growing culture of S. pombe strain was fixed with 1% formaldehyde for 15 min and the reaction was quenched for 5 min at room temperature using glycine to a final concentration of 125 mM. Cells were resuspended in resuspension buffer (0.2 mM Tris-HCl pH, 9.4, 10 mM DTT) and incubated at 37degC for 15 min on a shaker at 180 rpm. Spheroplasting (95%) was performed using Zymolyase-100T (amsbio, Cat # 120493-1) in spheroplasting buffer (1.2 M Sorbitol, 20 mM Na-HEPES, pH 7.5) at 37degC at low speed (80 rpm). Spheroplasting was terminated by adding ice-cold post-spheroplasting buffer (1.2 M Sorbitol, 1mM Mgcl2, 20 mM Na-PIPES, pH 6.8). Spheroplasts were pelleted at low speed and subsequently washed with ice-cold 1xPBS, Buffer I (0.25% TritonX-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Na-HEPES, pH 6.5), Buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Na-HEPES). Washed spheroplasts were resuspended in extraction buffer (140 mM NaCl, 1 mM EDTA, 50 mM K-HEPES, 0.1% sodium deoxycholate, 1% Triton X-100, pH 7.5) with protease inhibitor cocktail to release chromatin. Released chromatin was digested with MNase in the presence of 3mM CaCl2 at 37degC for 10 min. Next, Chromatin was further sheared using bioruptor and the soluble fraction was obtained by centrifuging the chromatin solution at 13000 rpm for 15 min at 4degC. Soluble chromatin solution was diluted 5-fold with IP dilution buffer (167 mM NaCl, 1.1 mM EDTA, 1.1% Triton X-100, 167 mM Tris-HCl, pH 8.0). Antibody magnetic beads were added and the sample was incubated at 4degC for 3 hrs.  Next, beads were sequentially washed twice with extraction buffer, and once each with extraction buffer+500 mM NaCl, LiCl wash buffer (10 mM Tris-HCl, pH 8, 250 mM LiCl, 1 mM NP40, 0.5% sodium deoxycholate, 1 mM EDTA) and TE. Dynabeads were resuspended in equal volumes of elution buffer I (1/10 volume of IP dilution buffer) and elution buffer II (10 mM Tris-HCl, pH 8, 1 mM EDTA, 0.67% SDS) and incubated at 65degC overnight to reverse crosslinking. Decrosslinked solution was treated with RNase A (Roche # 1119915) at 37degC for 1 hr and Proteinase K (Roche Cat # 1 000 144) at 55degC for 3 hr. The DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol and precipitated in 100% ethanol overnight at 20degC. Precipitated DNA was resuspended in TE.

value: h minus (leu1 ura4 mis6-GFP[LEU2)

value: Anti-GFP (Abcam catalog #ab290)


title: Coeliac_5_UNS

value: Unstimulated


title: CA1_YoungVeh_1


title: Coeliac_4_PMA

value: Phorbal myristate acetate (PMA) stimulation


title: CA1_OldVeh_6

value: 20 months

value: CA1 hippocampal subregion


title: CA1_YoungVeh_4

value: WT


title: CA1_OldVeh_5


title: Coeliac_4_CD3

value: anti-CD3/anti-CD28 stimulation


title: CA1_OldVeh_4

value: Vehicle:18g cyclodextrin/L water


title: Cnp3_Myc_10min_XIP_(20140521_15)

description: Immunoprecipitation of Cnp3-Myc from X-ChIPed chromatin, 10 minute MNase.

value: nuclei

value: h minus (leu1-32 ura4DS/E ade6-210 cnt1::ura4+ pREP41-myc-Cnp3)

value: Anti-Myc (Santa cruz catalog #Sc-40)


title: Cnp20_FLAG_5min_XIP_(20140725_11)

description: Immunoprecipitation of Cnp20-FLAG from X-ChIPed chromatin, 5 minute MNase.

value: h minus (leu1 ade6 cnp20+-FLAG[KanR])

value: Anti-FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823)


title: Cnp20_FLAG_5min_XIN_(20140725_10)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp20-FLAG, 5 minute MNase.

source_name: DNA

extract_protocol: ChIP assays were performed using a protocol described previously (PMID: 22536162) with slight modifications. Briefly an exponentially growing culture of S. pombe strain was fixed with 1% formaldehyde for 15 min and the reaction was quenched for 5 min at room temperature using glycine to a final concentration of 125 mM. Cells were resuspended in resuspension buffer (0.2 mM Tris-HCl pH, 9.4, 10 mM DTT) and incubated at 37degC for 15 min on a shaker at 180 rpm. Spheroplasting (95%) was performed using Zymolyase-100T (amsbio, Cat # 120493-1) in spheroplasting buffer (1.2 M Sorbitol, 20 mM Na-HEPES, pH 7.5) at 37degC at low speed (80 rpm). Spheroplasting was terminated by adding ice-cold post-spheroplasting buffer (1.2 M Sorbitol, 1mM Mgcl2, 20 mM Na-PIPES, pH 6.8). Spheroplasts were pelleted at low speed and subsequently washed with ice-cold 1xPBS, Buffer I (0.25% TritonX-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM Na-HEPES, pH 6.5), Buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM Na-HEPES). Washed spheroplasts were resuspended in extraction buffer (140 mM NaCl, 1 mM EDTA, 50 mM K-HEPES, 0.1% sodium deoxycholate, 1% Triton X-100, pH 7.5) with protease inhibitor cocktail to release chromatin. Released chromatin was digested with MNase in the presence of 3mM CaCl2 at 37degC for 10 min. Next, Chromatin was further sheared using bioruptor and the soluble fraction was obtained by centrifuging the chromatin solution at 13000 rpm for 15 min at 4degC. To about 1/20 of total soluble chromatin equal volume of elution buffer I (50 mM Tris-HCl, pH 8, 10 mM EDTA, 1% SDS) was added and incubated at 65degC overnight to reverse crosslinking. Decrosslinked solution was treated with RNase A (Roche # 1119915) at 37degC for 30 min and Proteinase K (Roche Cat # 1 000 144) at 55degC for 1 hr. The DNA was extracted with an equal volume of phenol/chloroform/isoamyl alcohol and precipitated with ethanol. The DNA pellet was resuspended in TE.


title: Coeliac_3_UNS

value: Coeliac Individual


title: Coeliac_4_UNS


title: CA1_OldVeh_2


title: Cnp20_FLAG_20min_XIN_(20140725_18)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp20-FLAG, 20 minute MNase.


title: Coeliac_3_CD3


title: input to Sample 18

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with default options
Coverage was calculated from -2000 to +2000 from the TSS of all genes using the function coverage within R's package Iranges
Coverage was normalized to total aligned read counts in the library
Genome_build: mm10
Supplementary_files_format_and_content: Normalized coverage files

source_name: Non-neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals

extract_protocol:
Nuclei were fixed, extracted in RIPA buffer, and sonicated to achieve an average fragment size of ~300bp. For ChIP 0.5µg of antibody were used with 500ng of chromatin
Libraries were constructed according to standard Illumina protocols using NEB's kits Ultra DNA Library Prep Kit (Ref: E7370L) and Multiplex Oligos for Illumina Index Primer Set (E7335L)

tag: cellular population

value: non-neuronal

value: 10 months

value: APP/Ps1-21 transgenic

value: SAHA:(18g cyclodextrin + 0.67g SAHA)/L water


title: CA1_OldVeh_3


title: Coeliac_2_PMA


title: CA1_OldVeh_1


title: Coeliac_2_CD3


title: input to Sample 16

source_name: Non-neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals


title: Coeliac_3_PMA


title: Cnp20_FLAG_10min_XIN_(20140725_12)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp20-FLAG, 10 minute MNase.


title: Cnp20_FLAG_20min_XIP_(20140725_19)

description: Immunoprecipitation of Cnp20-FLAG from X-ChIPed chromatin, 20 minute MNase.


title: Cnp20_FLAG_10min_XIP_(20140725_16)

description: Immunoprecipitation of Cnp20-FLAG from X-ChIPed chromatin, 10 minute MNase.


title: Coeliac_1_UNS

value: Unstimulated


title: Cnp20_FLAG_10min_IP_(20140408_1)

description: Immunoprecipitation of Cnp20-FLAG from N-ChIPed chromatin, 10 minutes MNase.

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1976213) and subjected to MNase digestion. Resulting chromatin solution was needle extracted and soluble chromatin was subjected to native chromatin immunoprecipitation as described previously (PMID: 22184235).


title: input to Sample 15

source_name: Neuronal nuclei from 10 month old APP/PS1-21 SAHA-treated animals

value: neuronal


title: Coeliac_1_PMA

value: Phorbal myristate acetate (PMA) stimulation


title: input to Sample 14

source_name: Neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals


title: Cnp20_FLAG_10min_IN_(20140408_2)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp20-FLAG, 10 minutes MNase.

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1976213) and subjected to MNase digestion. Resulting chromatin solution was subjected to needle extraction followed by DNA isolation as described previously (PMID: 22184235).


title: Cnp20_FLAG_10min_150salt_IN_(20140408_4)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp20-FLAG, 10 minutes MNase, 150mM NaCl.

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1976213) and subjected to MNase digestion. Resulting chromatin solution was needle extracted and the insoluble pellet was solublilized with 150 mM NaCl containing extraction buffer (0.1% Triton X-100, 10 mM phosphate buffer, 0.75 mM EDTA, 150mM NaCl) for 4 hrs at 4 degree Celsius. DNA was extracted from the solublie fraction as described previously(PMID: 22184235).


title: Cnp20_FLAG_10min_150salt_IP_(20140408_3)

description: Immunoprecipitation of Cnp20-FLAG from N-ChIPed chromatin, 10 minutes MNase, 150mM NaCl.

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1988457) and subjected to MNase digestion. Resulting chromatin solution was needle extracted and the insoluble pellet was solublilized with 150 mM NaCl containing extraction buffer (0.1% Triton X-100, 10 mM phosphate buffer, 0.75 mM EDTA, 150mM NaCl) for 4 hrs at 4 degree Celsius. The solubilized chromatin was subjected to native chromatin immunoprecipitation as described previously (PMID: 22184235).


title: H4K12ac ChIP-Seq (Sample 18)

value: Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5)


title: Cnp1_HA_5min_XIP_(20140725_5)

description: Immunoprecipitation of Cnp1-HA from X-ChIPed chromatin, 5 minute MNase.

value: h minus (Lys::Cnp1HALys+)

value: Anti-HA (MBL anti-HA-tag mAB magnetic beads, catalog #M132-9)


title: input to Sample 13

source_name: Neuronal nuclei from 10 month old vehicle-treated WT littermates of APP/PS1-21 animals

value: WT

value: Vehicle:18g cyclodextrin/L water


title: input to Sample 17

source_name: Non-neuronal nuclei from 10 month old APP/PS1-21 vehicle-treated animals


title: H4K12ac ChIP-Seq (Sample 16)


title: Coeliac_1_CD3

source_name: CD4+ T cells

value: anti-CD3/anti-CD28 stimulation


title: Cnp1_HA_5min_XIN_(20140725_4)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp1-HA, 5 minute MNase.

value: nuclei


title: Cnp1_HA_5min_IP_(20140521_16)

description: Immunoprecipitation of Cnp1-HA from N-ChIPed chromatin, 5 minutes MNase.


title: H4K12ac ChIP-Seq (Sample 15)


title: Liver_OldVeh_5

value: 20 months

value: Liver


title: H4K12ac ChIP-Seq (Sample 13)


title: H4K12ac ChIP-Seq (Sample 14)


title: H4K12ac ChIP-Seq (Sample 17)


title: Cnp1_HA_20min_XIP_(20140725_9)

description: Immunoprecipitation of Cnp1-HA from X-ChIPed chromatin, 20 minute MNase.


title: Cnp1_HA_20min_XIN_(20140725_8)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp1-HA, 20 minute MNase.


title: input to Sample 4

source_name: Non-neuronal nuclei from 3 month old vehicle-treated animals

value: 3 months


title: Cnp1_HA_5min_150salt_IP_(20140521_20)

description: Immunoprecipitation of Cnp1-HA from N-ChIPed chromatin, 5 minute MNase, 150mM NaCl.


title: Cnp1_HA_10min_XIP_(20140725_7)

description: Immunoprecipitation of Cnp1-HA from X-ChIPed chromatin, 10 minute MNase.


title: input to Sample 3

source_name: Neuronal nuclei from 20 month old SAHA-treated animals


title: Cnp1_HA_10min_XIN_(20140725_6)

description: Input X-ChIPed chromatin for immunoprecipitation of Cnp1-HA, 10 minute MNase.

value: h minus (Lys::Cnp1HALys+) deg


title: Cnp1_GFP_15min_IP_(20140725_21)

description: Immunoprecipitation of Cnp1-GFP from N-ChIPed chromatin, 15 minute MNase.

value: h minus (scm3-19-HA[kanR] lys1+:cnp1-GFP)

value: Anti-GFP (Abcam catalog #ab290)


title: input to Sample 2

source_name: Neuronal nuclei from 20 month old vehicle-treated animals


title: Cnp1_FLAG_5min_IP_2_(20140731_11)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 5 minutes MNase. Replicate.

value: h minus (Cnp1-FLAG::kanR)

value: Anti-FLAG (Sigma anti-FLAG M2 magnetic beads, catalog #8823)


title: input to Sample 5

source_name: Non-neuronal nuclei from 20 month old vehicle-treated animals

value: non-neuronal


title: Cnp1_GFP_15min_IN_(20140725_20)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp1-GFP, 15 minute MNase.

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1988457) and subjected to MNase digestion. Resulting chromatin solution was subjected to needle extraction followed by DNA isolation as described previously (PMID: 22184235).


title: Spar_B

description: digested with 20 units Mnase

organism: Saccharomyces paradoxus

source_name: meiotic culture

value: 4 hr in meiosis


title: Cnp1_FLAG_5min_IP_1_(20131220_6)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 5 minutes MNase.


title: Spar_A_40

description: digested with 40 units Mnase


title: H4K12ac ChIP-Seq (Sample 6)

source_name: Non-neuronal nuclei from 20 month old SAHA-treated animals

value: Anti-Histone H4 (acetyl K12) antibody (Abcam, catalog# ab61238, lot# GR38757-5)

value: SAHA:(18g cyclodextrin + 0.67g SAHA)/L water


title: Spar_A_20

description: digested with 20 units Mnase


title: H4K12ac ChIP-Seq (Sample 4)


title: input to Sample 1

source_name: Neuronal nuclei from 3 month old vehicle-treated animals

value: neuronal


title: Spar_2

description: Spo11-associated DNA oligonucleotides

value: epitope tag:Spo11-Flag


title: Cnp1_FLAG_5min_150salt_IP_(20140731_14)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 5 minutes MNase, 150mM NaCl N-ChIP.

source_name: Immunoprecipitated DNA


title: H4K12ac ChIP-Seq (Sample 5)

value: WT

value: Vehicle:18g cyclodextrin/L water


title: Cnp1_FLAG_5min_IN_(20131220_5)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp1-FLAG, 5 minutes MNase.

value: nuclei


title: input to Sample 6

value: 20 months


title: Cnp1_FLAG_20min_150salt_IP_(20140731_16)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 20 minutes MNase, 150mM NaCl N-ChIP.


title: Cnp1_FLAG_20min_IP_(20140731_13)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 20 minutes MNase.


title: H4K12ac ChIP-Seq (Sample 2)


title: H4K12ac ChIP-Seq (Sample 3)


title: Skud_B

description: digested with 20 units Mnase

organism: Saccharomyces kudriavzevii

value: 9 hr in meiosis


title: H4K12ac ChIP-Seq (Sample 1)

value: 3 months


title: Skud_A

description: digested with 20 units Mnase


title: Spar_1

description: Spo11-associated DNA oligonucleotides


title: Cnp1_FLAG_1min_IP_(20131220_4)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 1 minute MNase.


title: Cnp1_FLAG_10min_IN_(20131220_7)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp1-FLAG, 10 minutes MNase.


title: Cnp1_FLAG_10min_IP_1_(20131220_8)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 10 minutes MNase.


title: Smik_A

description: digested with 5 units Mnase

organism: Saccharomyces mikatae

growth_protocol:
Cells were grown in a 7 h starter culture in SPS (0.5% yeast extract, 1% peptone, 0.67% yeast nitrogen base without amino acids, 1% potassium acetate, 0.05 M potassium biphthalate, pH 5.5), which was used to inoculate a 16 h pre-sporulation culture in SPS, and sporulation was done in 1% potassium acetate, 0.001% polypropylene glycol supplemented with 0.32% amino acid complementation medium (1.5% lysine, 2% histidine, 2% arginine, 1% leucine, 0.2% uracil, 1% tryptophan).
see SAMPLES section


title: Cnp1_FLAG_10min_IP_2_(20140731_12)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 10 minutes MNase. Replicate.


title: Cnp1_FLAG_10min_150salt_IP_2_(20140731_15)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 10 minute MNase, 150mM NaCl N-ChIP. Replicate.


title: Cnp1_FLAG_1min_IN_(20131220_3)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp1-FLAG, 1 minute MNase.


title: Smik_B

description: digested with 10 units Mnase


title: Cnp1_FLAG_10min_150salt_IP_1_(20140224_4)

description: Immunoprecipitation of Cnp1-FLAG from N-ChIPed chromatin, 10 minute MNase, 150mM NaCl N-ChIP.


title: -77 mutant Q

status: Public on Aug 15 2015

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

data_processing:
Illumina Casava-1.8.2 base calling
RSEM reference preparation: RSEM v1.2.18 with Bowtie v1.1.1, rsem-prepare-reference run with options "--bowtie --gtf" Gene annotation: Ensembl v76 filtered for genes of type "protein_coding" or "lincRNA" on standard chromosomes
RSEM abundance estimation: RSEM v1.2.18 with Bowtie v1.1.1, rsem-calculate-expression run with options "--no-bam-output --time -p 10"
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values and counts for each Sample

source_name: E13.5 CMP

extract_protocol:
Cells lysed in Trizol. RNA was purified by aqueous phase separation in chloroform, and isolated in isopropanol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CMPs were purified from disaggregated E13.5 fetal liver by FACS stained lineage-negative (B220, CD3, CD4, CD5, CD8, CD41, CD48, Gr-1, and TER-119), CD34+, FcRlow, c-kit+, Sca-1-.

tag: developmental stage

tag: genotype/variation

tag: cell type

value: common myeloid progenitor


title: -77 mutant C

tag: strain


title: -77 mutant D


title: wild type L


title: wild type F


title: wild type A


title: Hnf1b rep1

city: Dallas

first: Min Soo

last: Kim

state: Texas

address: 5323 Harry Hines Blvd.

department: Department of Clinical Sciences

institute: University of Texas Southwestern

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were filtered using FASTQC with default settings.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie 0.12.7 using default configurations.
peaks were called using QuEST 2.4
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated for each sample alignment file using bowtie

growth_protocol: IMCD3 cells were plated in T75 flask (~4 million cells) cultured in low glucose DMEM media supplimented with 10% FBS

extract_protocol:
Cells were sonicated and lysate cleared and Immunoprecipitated with the indicated anitbody
ChIP-seq libraries were prepared for sequencing using Illumina ChIP-Seq DNA Sample Prep Kit (IP-102-1001)

tag: cell line sournce

value: mouse kidney

value: mouse Inner medullary collceting duct cells

tag: passages

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Hnf1b rep2

tag: cell line

tag: chip antibody


title: IgG rep2

value: rabbit IgG


title: IgG rep1


title: Cnp1_FLAG_10min_150salt_IN_(20140224_3)

description: Input N-ChIPed chromatin for immunoprecipitation of Cnp1-FLAG, 10 minutes MNase, 150mM NaCl.

source_name: DNA

extract_protocol: Cells were grown in YES media. Nuclei were prepared following previously published protocol (PMID: 1988457) and subjected to MNase digestion. Resulting chromatin solution was needle extracted and the insoluble pellet was solublilized with 150 mM NaCl containing extraction buffer (0.1% Triton X-100, 10 mM phosphate buffer, 0.75 mM EDTA, 150mM NaCl) for 4 hrs at 4 degree Celsius. DNA was extracted from the solublie fraction as described previously(PMID: 22184235).

value: h minus(Cnp1-FLAG::kanR)


title: Skud_2

description: Spo11-associated DNA oligonucleotides

extract_protocol:
Based on Pan et al. 2011 Cell 144:719-731. Whole cell extracts were prepared by grinding frozen cells in a bead mill and resuspending powder in 10%TCA. Pellets were then extracted with SDS and soluble protein was subjected to affinity purification of Spo11-Flag fusion with Protein-G Dynabeads. Protein was digested with proteinase K and Spo11-associated oligonucleotides were recovered by ethanol precipitation.
Based on Pan et al. 2011 Cell 144:719-731. Oligonucleotides were tailed with ribo-G using rGTP and terminal transferase, then ligated to duplex DNA adaptors with a dC overhang using T4 RNA ligase 2. Complementary strands were synthesized with Klenow, then purified by denaturing polyacrylamide electrophoresis. Purified complementary strands were subjected to 3' tailing with ribo-G using rGTP and terminal transferase, then another duplex adaptor was ligated using T4 RNA ligase 2. Ligated material was amplified with 16 cycles of PCR to add Illumina HiSeq adaptors


title: csMed1-/- (5 mice)

city: Chicago

first: Navin

last: Viswakarma

state: IL

address: 303 E Chicago Ave

department: Pathology

institute: Northwestern University

data_processing:
Reads were aligned to mm10 (UCSC) using TopHat v2.0.8b with default parameters with the following exceptions: -g 1 -G genes.gtf -p 12.  Alignment to mm10 was also performed with STAR 2.4.0h with the following parameters: --readFilesCommand zcat --outFilterType BySJout --outSJfilterCountUniqueMin -1 2 2 2 --outSJfilterCountTotalMin -1 2 2 2 --outFilterIntronMotifs RemoveNoncanonical --runThreadN 20 --outReadsUnmapped Fastx
Unaligned reads from STAR were aligned to mm10 using Bowtie2 with the following parameters: --local --very-sensitive -p 7
Differential expression was performed on the TopHat results with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Differential expression was performed on the STAR results using DESeq2 using a cutoff of FDR-adjusted p-value <0.05.
The significantly differentially expressed genes from cuffdiff and DESeq2 were compared, and only genes within the intersection were considered for further analysis.
Common genes between cuffdiff results and STAR results were used in a pathway analysis using GeneCoDis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Mice were housed in animal house and maintained on a 12-h light-dark cycle. They received food and water ad libitum.

extract_protocol:
RNA was extracted with Trizol reagent. RNA quality and quantity were first determined with the Agilent Bioanalyzer 2100, accepting RNA integrity numbers (RIN) of >7 and quantities of 100 nanograms or more per sample.  Samples were enriched for mRNA using oligo-dT columns.
RNA libraries were prepared for sequencing using standard Illumina protocols.  mRNA was enriched prior to library preparation using oligo-dT.

treatment_protocol: No treatment. RNA was isoltaed from the heart of 23 day old Med1fl/fl and csMed1-/- mice.

tag: strain background

tag: age

value: 23 days old

tag: gender

value: mixed

tag: tissue

value: heart


title: Ph_Ch rep1

status: Public on Aug 14 2015

city: Beijing

first: Yanping

last: Li

address: No 38 Xueqing Road, Haidian Distric

institute: Novogene institue

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008)
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/Chinese_long/v2/cucumber_ChineseLong_v2_genome.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Cucumis sativus

source_name: leaves

growth_protocol: The treated seeds were placed in Petri dishes with filter paper at the bottom and two layers of gauze above. Seeds were incubated at 25◦C constant temperature for 24h. When the buds grew about 5mm long, then sown them in plastic pots containing sterilized soil (200 mm in diameter, ten plants per pot) in a growth chamber at 25◦C. When the fourth leaves were fully expanded, the plants were ready for compound treatment and conidium inoculation.

extract_protocol:
Cucumber leaves were sampled, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Physcion, chrysophanol alone and in combination treatment were applied to the cucumber plants before inoculation at concentrations of 10 mg/L and the surfactant Tween 20 was added in the final dilutions at a concentration of 0.25 g/L, respectively, and solvent-treated (contained 0.5% DMSO and 0.25% Tween 20) plants were used as controls. Inoculated plants were sprayed with a fine mist of S. fuliginea spore suspension eight hours after treatment. After inoculation, plants were incubated at 25◦C and 70% relative humidity until sampling. The fourth leaves of cucumber plants were collected immediately 3 days post-inoculation (dpi) until Solvent-treated plants disease. Each treatment had two or three biological replicates.

tag: cultivar

value: Changchunmici

value: leaves

tag: inoculant

value: Sphaerotheca fuliginea


title: Phy rep3


title: Smik_2

description: Spo11-associated DNA oligonucleotides

growth_protocol: Cells were grown in a 7 h starter culture in SPS (0.5% yeast extract, 1% peptone, 0.67% yeast nitrogen base without amino acids, 1% potassium acetate, 0.05 M potassium biphthalate, pH 5.5), which was used to inoculate a 16 h pre-sporulation culture in SPS, and sporulation was done in 1% potassium acetate, 0.001% polypropylene glycol supplemented with 0.32% amino acid complementation medium (1.5% lysine, 2% histidine, 2% arginine, 1% leucine, 0.2% uracil, 1% tryptophan) at OD600=6.0.

tag: epitope tag

value: epitope tag:Spo11-Flag

tag: meiotic time-point

value: 4 hr in meiosis


title: Ph_Ch rep3


title: Skud_1

description: Spo11-associated DNA oligonucleotides


title: Ph_Ch rep2


title: Med1fl/fl (5 mice)

tag: genotype/variation


title: TGF-β +IL-4 stimulated  CD4+ T cell

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: ChIP-seq

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
ChIP-Seq reads were mapped to the mouse genome (mm9, or NCBI 37) using Bowtie2, reads with MAPQ<10 were removed. Redundant reads were removed from each ChIP-Seq library.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.
Supplementary_files_format_and_content: bedGraph: the 4 column are chrom, chromStart, chromEnd, RPBM

source_name: CD4+CD25–CD62L+ T cells

growth_protocol: Naive CD4+CD25–CD62L+ cells were purified by magnetic cell sorting (Miltenyi Biotec) and were cultured at 37 °C at a density of 0.5 × 106 cells per well in 24-well plates with plate-bound anti-CD3 (1 μg/ml) plus soluble anti-CD28 (1 μg/ml) (both identified above) and TGF-β1 (2 ng/ml) with or without IL-4 (10 ng/ml).

extract_protocol:
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

value: C57BL/6 mice

tag: cell type

value: CD4+ T cell

tag: treatment

value: TGF-β +IL-4


title: Smik_1

description: Spo11-associated DNA oligonucleotides

tag: strain


title: Phy rep2


title: Chr rep2


title: Chr rep1


title: Con rep2


title: CD4+ T cells

description: ChIP-seq

treatment_protocol: soluble anti-CD28 (1 μg/ml) (both identified above) and TGF-β1 (2 ng/ml) with or without IL-4 (10 ng/ml).


title: Phy rep1


title: Con rep1


title: Lhx5-FLAG Input

city: Heidelberg

first: Gonzalo

last: Alvarez-Bolado

address: Im Neuenheimer Feld 307

institute: Institute for Anatomy and Cell Biology

data_processing:
Sequences were mapped to the mouse genome (mm9) with Bowtie for Illumina (Galaxy Project)
Unmapped reads were removed (Galaxy Project)
Peak calling was performed with MACS using a MFOLD of 10 and a p-value cutoff 1e-05 (Galaxy Project)
Peaks were annotated with PeakAnalyzer 1.4 by using the nearest dowstream gene method
Genome_build: mm9
Supplementary_files_format_and_content: bed files presenting the gene annotation for the identified peaks with the position on the chromosome and the distance to the next gene

source_name: Neuro2a cells expressing doxycycline-dependent Lhx5

extract_protocol:
Cell lysates were sonicated and Lhx5-bound DNA isolated with an anti-FLAG antibody. Cellular protein and RNA was digested and the DNA was purified
Libraries were constructed with the NEB CHIPseq Master Mix Prep Kit for Illumina

value: Lhx5-FLAG expression with Doxycycline induced


title: Lhx5-FLAG ChIP-Seq

value: anti-FLAG antibody (Sigma, F2426)


title: FLAG Input

source_name: Neuro2a cells transfected with a FLAG-tag expressing vector

value: transfected with FLAG-tag control construct


title: 12-OPDA - 1

status: Public on Aug 13 2015

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

description: Stranded mRNA-seq

data_processing:
Raw fastq reads were trimmed for adapters, preprocessed to remove low quality reads using Trimmomatic v0.32
Genome_build: Z. mays AGPv3.25
Supplementary_files_format_and_content: tab delimited text file, see metafile for column headers

organism: Zea mays

source_name: Emergent but non-fully-expanded 4th leaf

growth_protocol: Zea mays Var. Golden Queen seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol: RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity.

tag: developmental stage

value: Leaf

tag: agent

value: cis-12-oxo-phytodienoic acid

value: Golden Queen


title: FLAG ChIP-Seq


title: 5%DMSO/0.1%Tween 20 in H20 - 2

description: Stranded mRNA-seq

value: Dimeythl sulfoxide/Tween 20/H2O


title: 12-OPDA - 4

description: Stranded mRNA-seq


title: 5%DMSO/0.1%Tween 20 in H20 - 3

description: Stranded mRNA-seq


title: 12-OPDA - 3

description: Stranded mRNA-seq


title: 5%DMSO/0.1%Tween 20 in H20 - 4

description: Stranded mRNA-seq


title: 12-OPDA - 2

description: Stranded mRNA-seq


title: 10-OPEA - 4

description: Stranded mRNA-seq

value: 10-oxo-11-phytoenoic acid


title: 10-OPEA - 3

description: Stranded mRNA-seq


title: 10-OPEA - 2

description: Stranded mRNA-seq


title: 10-OPEA - 1

description: Stranded mRNA-seq