title: P.t. Input DNA

city: Thuwal

first: Alaguraj

last: Veluchamy

address: Thuwal

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

data_processing:
The reads were mapped onto the P. tricornutum genome V2.0 using Bowtie [61]
To identify regions that were significantly enriched, we used MACS and SICER with parameters of W:200 (Window length), G:200 (Gap size) for H3K4me2, H3K9_14Ac;  W:200, G:600 for H3K27me3, H3K9me2, H3K9me3 and  FDR <1E-2. Enriched regions were detected against the islands of background control with the same parameter.
Genome_build: Phatr V2
Supplementary_files_format_and_content: gff3 files were intervals of peaks

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum tricornutum Bohlin Clone Pt1 8.6 (CCMP2561) cells in low N at 75 µM

growth_protocol: Grow P. tricornutum culture in 400 ml artificial sea water under the standard conditions until cell density reaches around 1 million cells/ml.

extract_protocol:
Details are in: Tirichine L, Lin X, Thomas Y, Lombard B, Loew D, Bowler C: Histone extraction protocol from the two model diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana. Mar Genomics 2014, 13:21-25.
Single-end sequencing of the five ChIP samples was performed using Illumina GAIIx with a read length between 36 bp and 50 bp. This yielded an average of approximately 37 million reads each

treatment_protocol: For each IP, mix 45 μl beads A and 45 μl DNA beads G in siliconized tubes. Wash DNA beads twice with ChIP Dilution buffer and resuspend beads in 90 μl Chip dilution buffer. Split the 90 μl resuspended beads into 30 and 60 μl volumes. Add 5 μl of your antibody to the siliconized eppendorf tube that contains mixed 60 μl beads for Ig capturing. Add the diluted chromatin solutions into the tubes that contain 30 μl mixed beads for preclearing. Leave tubes with gentle rotation at 4°C for 2 hours.

value: Bohlin Clone Pt1 8.6

value: Input DNA


title: P.t. H3AcK9/14_lowN

status: Public on May 05 2015

type: SRA

library_source: genomic

molecule: genomic DNA

tag: cell type

tag: strain

tag: chip antibody

value: H4K9/14Ac (005-044) from Diagenode


title: P.t. H3K9me3_lowN

value: H3K9me3 (8898) from Abcam


title: P.t. H3K4me2_lowN

value: H3K4me2 (32356),from Abcam


title: P.t. H3K9me2

source_name: Phaeodactylum tricornutum Bohlin Clone Pt1 8.6 (CCMP2561) cells

value: H3K9me2 (17–681) from Millipore


title: P.t. H3K27me3

value: H3K27me3 (07-449) from Millipore


title: P.t. H3AcK9/14


title: P.t. H3K9me3


title: P.t. H3K4me2

value: H3K4me2 (07–030) from Millipore


title: GROseq siYAP Wnt3a+Activin (- chain)

status: Public on May 04 2015

city: La Jolla, San Diego

first: conchi

last: estaras

state: CA

address: 10010 N Torrey Pines Rd

department: Regulatory Biology

country: USA

institute: The Salk Institute

description:
Nascent RNA
Gro-seq

library_source: transcriptomic

data_processing:
Peak calling was performed using Homer software
Genome_build: hg19
Supplementary_files_format_and_content: wig

molecule: total RNA

organism: Homo sapiens

source_name: H1 human ESCs

growth_protocol: H1 hESCs grown in mTeSR media

extract_protocol:
For ChIPseq, DNA was extracted Qiaquick PCR extraction kit (cat 28106, Qiagen). For GROseq, nascent RNA purification was done using Trizol LS (Invitrogene).
For ChIPseq, libraries were done with Illumina reagents. For GROseq, libraries were prepared with NEBnext kit (E7300S)

treatment_protocol: H1 hESCs were left untreated, or treated with Wnt3a (200ng/ml), Activin (100ng/ml), or both cytokines together for 4h (ChIPseq) or 6h (GRO-seq). For siRNA-GROseq experiments, hESCs were transfected with specific siRNAs (using RNAimax) 48h before adding cytokine treatments.

value: embryonic stem cells

tag: passages/media

tag: treatment

value: Wnt3a+Activin A (WA) 6h

tag: sirna

value: Yap1 (Silencer Select Life Tech)


title: GROseq siYAP Wnt3a+Activin (+ chain)

description:
Nascent RNA
Gro-seq


title: YC

city: Guangzhou

first: Ruisong

last: Ye

state: Guangdong

address: 483 Wushan Tianhe

country: China

institute: South China Agricultural University

data_processing:
the library products were prepared for sequencing analysis via an Illumina HiSeq™ 2000, in order to obtain raw sequence data. To obtain clean reads, adaptor contamination, those in which unknown bases numbered more than 10, and low-quality reads (where the percentage of low-quality bases of quality value ≤ 5 was more than 50% in a read) were removed. Clean reads were further mapped to reference genome (ftp://ftp.ensembl.org/pub/release-65/fasta/sus_scrofa/dna/Sus_scrofa.Sscrofa9.65.dna.toplevel.fa.gz) and gene databases (ftp://ftp.ensembl.org/pub/release-65/fasta/sus_scrofa/cdna/Sus_scrofa.Sscrofa9.65.cdna.all.fa.gz) using SOAPaligner/soap2; mismatches of no more than two bases were allowed in the alignment. After assessment of sequencing (including sequence read quality, statistics of alignment analysis, sequencing saturation analysis, distribution of reads on reference genes/genome), the gene-expression level was calculated using the RPKM method (Reads Per kb per Million reads)
Genome_build: Sscrofa9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: polyA RNA

organism: Sus scrofa

source_name: Anterior pituitary

extract_protocol:
Total RNA was extracted from the anterior pituitary tissue using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions.
After extracting the total RNA from the samples, mRNA of eukaryotes is enriched by using the oligo(dT) magnetic beads and mRNA of prokaryotes is enriched just by removing rRNAs from the total RNA. Adding the fragmentation buffer, the mRNA is interrupted to short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to sythsize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors are ligated to the fragments. The required fragments is purified by agrose gel electrophoresis and enriched by PCR amplification. The library products are ready for sequencing analysis via Illumina HiSeq™ 2000.

tag: developmental stage

value: 20-day after birth

tag: breed

value: Landrace pig

tag: tissue

value: anterior pituitary


title: YB

value: Bama minipigs


title: GROseq siYAP untreated (- chain)

description:
Nascent RNA
Gro-seq

value: untreated


title: HSC 1

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

country: Australia

institute: St Vincent's Institute of Medical Research

description: Sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. The HSC population was defined as Lin- c-Kit+ Sca-1+ Flt3R-.

data_processing:
Base calling
Barcode deconvolution and stripping
Alignment to mature miRNA database (miRBase)
Alignment of remaining reads to miRNA precursor database (miRBase)
Read abundance counting and normalization to library read size
Genome_build: Genome_build: miRBase 17
Supplementary_files_format_and_content: miRNA_processed_expression_atlas.xls containing miRNA identity and counts

organism: Mus musculus

source_name: Bone marrow stem cell

extract_protocol:
Chloroform (1:5 vol/vol) was added to cell suspensions in TRI homogenate (thawed on ice) before vigorously mixing.  This was allowed to settle for 15 minute at 4oC. Phases were then separated by centrifugation 15 minutes at 4oC. An ethanol precipitation was then performed by adding co-precipitate (e.g. glycoblue (Invitrogen)) to the removed aqueous phase prior to addition of two times volume of ethanol. The solution is then precipitated at -80oC for 25 minutes before centrifugation for 15 minutes at 4oC. The supernatant is then discarded and the pellet washed in 70% ethanol. All supernatant is removed following a final centrifugation step and the pellet resuspended in RNase-free water.
microRNA libraries were constructed as previously described (Chong et al., 2010), adapted from (Hafner et al, 2008). Briefly, total RNA was resolved on a polyacrylamide/urea gel and the 19- to 24- nt small RNA fraction was isolated after each of two adaptor ligations. This fraction was tracked on the gel by the inclusion of radiolabeled 19- and 24-nt synthetic oligoribonucleotides. The first ligation, to the 3’ end of the RNA library, ligated a 5’ preadenylated and 5’-hydroxyl-blocked universal adaptor (miRNA cloning linker 1; Integrated DNA Technologies) facilitated by an RNA ligase 2 truncated mutant (1–249) K227Q (Hafner et al. 2008) in the absence of ATP. An Illumina-compatible adapter was then ligated to the 5’ end of the library, which subsequently allowed for deep sequencing on the Illumina GAII platform. In order to multiplex the sequencing runs, one of four barcodes (AGCCTAAGCT, CATTGTTAGC, TCAACGGTAG or GTGCATCCTA) was added to the 5’ end of each library. The nature of these two ligations dictate that only small RNAs with 5’ phosphate and 3’ hydroxyl termini were cloned.

treatment_protocol: Progenitor populations were sorted from the CD3, CD8, Mac1, Ter-119, CD19 and Gr-1 depleted fraction (Lin-) of bone marrow from the femur and tibula. The HSC population was defined as Lin- c-Kit+ Sca-1+ Flt3R-. CMPs were defined as c-Kit- Sca-1+ FcR- CD34+, while CLPs were c-Kitint Sca-1+ IL7R+ Flt3R+. CDPs were identified by expression of c-Kitint Sca-1- M-CSFR+ Flt3R+. Mature DCs were obtained ex vivo from collagenase-digested spleens. The cDC population was defined as CD11c+ CD4+ SiglecH- while pDCs were CD11c int SiglecH+ CD11b-.

tag: tissue origin

value: Bone marrow

value: Bone marrow stem cell

tag: barcode label

value: AGCCTAAGCT

tag: molecule subtype

value: 19-24nt RNA


title: GROseq siYAP untreated (+ chain)

description:
Nascent RNA
Gro-seq


title: GROseq siC Wnt3a+Activin (- chain)

description:
Nascent RNA
Gro-seq

value: control (Silencer Select Life Tech)


title: GROseq siC untreated (+ chain)

description:
Nascent RNA
Gro-seq


title: GROseq siC Wnt3a+Activin (+ chain)

description:
Nascent RNA
Gro-seq


title: GROseq Wnt3a (- chain)

description:
Nascent RNA
Gro-seq

value: Wnt3a 6h


title: GROseq Wnt3a+Activin (+ chain)

description:
Nascent RNA
Gro-seq


title: GROseq Wnt3a+Activin (- chain)

description:
Nascent RNA
Gro-seq


title: GROseq Wnt3a (+ chain)

description:
Nascent RNA
Gro-seq


title: P.t. H3

value: Bohlin Clone Pt1 8.6


title: GROseq Activin (+ chain)

description:
Nascent RNA
Gro-seq

value: Activin A 6h


title: GROseq Activin (- chain)

description:
Nascent RNA
Gro-seq


title: Nipbl Activin

value: Activin A 4h

tag: antibody

value: Nipbl (Bethyl a301-779a)


title: GROseq siC untreated (- chain)

description:
Nascent RNA
Gro-seq

value: embryonic stem cells


title: GROseq untreated (- chain)

description:
Nascent RNA
Gro-seq


title: Total-RNAPII Wnt3a

value: Wnt3a 4h

value: Total RNAPII (N20) (Santa Cruz sc-899)


title: Nipbl untreated


title: Total-RNAPII Wnt3a+Activin

value: Wnt3a+Activin A (WA) 4h


title: Nipbl Wnt3a


title: Nipbl Wnt3a+Activin


title: Maf1 KO rep3

city: Bronx

first: Ian

last: Willis

state: NY

address: 1300 Morris Park Ave

department: Biochemsitry

institute: Albert Einstein College of Medicine

description: Supplementary table S2 from Bonhoure et al. contains raw Htseq-count data, normalized Htseq-count data and EdgeR output

data_processing:
Illumina Casava software was used for basecalling and TrueSeq demultiplexing.
Sequenced reads were mapped to the mouse mm9 whole genome using GSNAP version 2012-06-12 with parameters -d mouse_refseq -A sam -B 4 -t 8
Uniquely mapped reads were counted using Htseq-counts version v0.5.3p3 with the parameters -s reverse -a 10 -t exon -m union
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet GSE65976_TableS2.xlsx contains raw Htseq-count data, normalized Htseq-count data and EdgeR output
Supplementary_files_format_and_content: Excel spreadsheet GSE65976_TableS3.xlsx contains Pol III transcriptome RNA-seq scores calculated as reported in the published Experimental Procedures. Briefly, reads corresponding to the loci in the table were summed after a sequential genome alignment procedure. Tag counts were scaled to the total number of tags aligning to pol II genes in each sample.  Multiple matches in the genome were given a weight corresponding to the number of matches divided by the number of times they were sequenced. Scores corresponding to the log2  of tags per gene were then calculated. Criteria for defining precursor and mature tRNA tags are given in the manuscript.

source_name: epididymal white adipose tissue

growth_protocol: Wild-type (C57Bl6/J) and Maf1 KO mice were ad libitum fed on a breeder chow diet (PicoLab Rodent Diet 20, #5058).

extract_protocol:
Total RNA was prepared (Qiagen miRNeasy), digested with DNase 1 and RNA quality was assessed by capilliary electrophoresis (Agilent 2100 Bioanalyzer).
A directional transcriptome RNA-seq protocol was employed. This included RiboZero treatment of the RNA, first strand synthesis primed with random hexamers and oligo(dT), second strand synthesis in the presence of dUTP, fragmentation, end repair, dA tailing, ligation of Illumina indexed adapters, UNG treatment and PCR amplification (18 cycles).

treatment_protocol: Three male mice (22-24 weeks of age) of each genotype were fasted overnight.  Epididymal adipose tissue was harvested and freeze-clamped in liquid nitrogen.

value: epididymal white adipose tissue

tag: metabolic state

value: overnight fasted

tag: genotype

value: Maf1 KO


title: SMRT-sequencing

city: Bad Nauheim

first: Lei

last: Gu

state: MASSACHUSETTS

address: parkstreet 1

country: Germany

institute: Max Planck Institute for heart and lung research

data_processing:
mapping using pbalign
The polymerase kinetics information was further loaded after alignment by loadChemistry.py and loadPulses scripts
post-aligned datasets were merged and sorted by using cmph5tools
m6A was identified using ipdSummary.py
Genome_build: ce10
m6A.gff
column: description
chr: chrromosome name
source: Name of tool -- "kinModCall"
type: Modification type -- a generic tag "modified_base" is used for unidentified bases. For identified bases, m6A, m4C, and m5C are used
start: start
end: end
score: -10 log (p-value) score for the detection of this event. Analogous to a Phred quality score. A value of 20 is the minimum default threshold for this file, and corresponds to a p-value of 0.01. A score of 30 corresponds to a pvalue of 0.001.
strand: Native sample strand where kinetics were generated. "+" is the strand of the original FASTA and "-" is the reverse complement of the strand. Note that in the .csv file these are marked "0" and "1" respectively.
phase: Not applicable
attibutes: Contains extra fields. IPDRatio is traditional IPD Ratio, context is the reference sequence -20bp to +20bp around the modification plus the base at this location as the 21st character, and sequencing coverage of that position. Context is always written in 5" -> 3" orientation of the template strand.

organism: Caenorhabditis elegans

source_name: whole worm WT gDNA

growth_protocol: Mixed stage WT (N2) worms were grown at 20 degrees

extract_protocol:
Worms were washed several times with M9 buffer and snap frozen in liquid nitrogen. Pellets were sent to Umass Medical School Deep Sequencing Core for gDNA extraction and SMRT sequencing
Library was constructed by Umass Medical School Deep sequencing core. Single Molecule Real Time Sequencing

treatment_protocol: Worms were fed dam-dcm- bacteria

value: WT (N2) mixed stage worms


title: NM1

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
For sequencing data alignment and analysis, the current assembly of mouse reference genome is missing the ribosomal rDNA repeats, of which there are approximately 400, located on chromosomes 12, 14 and 15. To compensate for this we utilized the procedure of Zentner et al (2011) and constructed a custom reference sequence that contained a non-masked rDNA repeat, taken from BK000964, which was added to the end of chromosome 12 of the MM9 assembly.
The analysis procedure involved the use of the SOAP2 program to map the reads to the constructed reference genome. Sequences with more than two mismatches were discarded from further analysis. The resulting individual sequences were remapped back to the annotated UCSC MM9 reference sequence which allows for the identification of peaks corresponding to the levels of association of the ChIP target with those loci.
Sequence data was filtered to obtain clean data which was then mapped to the reference genome. Only cleanly mapped sequences were used in further analysis.
The distribution of sequence hits along each chromosome is shown in the WIG file output.
Genome_build: mm9
Supplementary_files_format_and_content: wig

source_name: Mouse Embryonic Fibroblasts

growth_protocol: Mouse embryonic fibroblasts cells were grown in DMEM medium (Gibco), supplemented with 10% foetal bovine serum (Gibco) and a 1% penicillin/streptomycin cocktail

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with an NM1 antibody.
5 ng of precipitated DNA was used to prepare sequencing libraries at the Bejing Genome Institute (Hong Kong) using the Illumina HiSeq 2000 platform. Briefly, ChIP DNA was fragmented to 100-500bp by sonication. DNA-end was repaired to overhang a 3’-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification. Finally we got qualified library for sequencing.

value: Mouse Embryonic Fibroblasts

tag: passages


title: Maf1 KO rep1


title: Ser7P-RNAPII Activin

value: Ser7P-RNAPII (Active Motif 61087)


title: Ser7P-RNAPII Wnt3a+Activin


title: GROseq untreated (+ chain)

description:
Nascent RNA
Gro-seq

value: untreated


title: WT rep3

value: wild-type


title: WT rep2


title: Ser7P-RNAPII Wnt3a


title: Ser5P-RNAPII Wnt3a

value: Ser5P-RNAPII (Millipore 05-623)


title: H3K27me3 Wnt3a

value: H3K27me3 (Millipore 07-449)


title: Ser5P-RNAPII Wnt3a+Activin


title: Ser7P-RNAPII untreated


title: WT rep1


title: Ser5P-RNAPII Activin


title: Ser5P-RNAPII untreated


title: H3K27me3 untreated


title: Beta-catenin untreated

value: beta-catenin (Santa Cruz sc7199)


title: H3K27ac Wnt3a

value: H3K27ac (Abcam ab4729)


title: H3K27ac untreated


title: LEF-1 untreated

value: LEF-1 (homemade)


title: Beta-catenin Wnt3a

value: embryonic stem cells


title: Total-RNAPII untreated


title: Total-RNAPII Activin

value: Activin A 4h


title: MNase-Seq H9

city: Irvine

first: Puya

last: Yazdi

state: Ca

address: University of California at Irvine

institute: University of California at Irvine

description: FC1/2 Lanes 7-8

data_processing:
FastQ aligned with Bowtie2
Aligned reads processed using DANPOS
Genome_build: hg19
Supplementary_files_format_and_content: wig file of nucleosome occupancy; bed file of dyads coordinates with average nucleosome occupancy

source_name: human embryonic stem cell

extract_protocol:
Cells digested with MNase followed by extraction of ~150 bp DNA, prepared library using Illumina Paired-End DNA Sample Prep Kit
Contructed as per MFG instructions, except two PCR rxn's with product combined

tag: cell line

value: embryonic stem cell


title: MNase-Seq H1

description: FC1/2 Lanes 1-6

tag: cell type


title: LEF-1 Wnt3a

value: Wnt3a 4h


title: S5A [sequencing]

status: Public on May 03 2015

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

description: Technical replicate 1 of 2.

data_processing:
Adapter sequences from reads were removed with Cutadapt software.
Processed reads were mapped to miRBase 17 with Bowtie 1 and miRDeep2.
Genome_build: miRBase version 17
Supplementary_files_format_and_content: Read_count_per_miRNA.txt: Tab-delimited text file includes raw read counts per miRNA.

source_name: Liver tumour tissue

extract_protocol:
Total RNA was extracted using the RecoverAll Total Nucleic Acid Isolation kit (Ambion) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols and the TruSeq RNA Sample Preparation kit.

value: hepatoblastoma

tag: patient


title: S4B [sequencing]

description: Technical replicate 2 of 2.


title: S4A [sequencing]

description: Technical replicate 1 of 2.


title: S5B [sequencing]

description: Technical replicate 2 of 2.


title: RNA_4_Mouse_Liver_M_20w_NORMAL

city: Jerusalem

first: Howard

last: Cedar

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University

data_processing:
RNA-seq 50 bp single-end reads were obtained from the Hiseq 2500 and analyzed by TopHat2.  Differential expression between male and female mice was analyzed by CuffDiff v2.1.1 (using default parameters, q-value<=0.01).
Genome_build: mm9 for mouse samples; hg19 for human samples
Supplementary_files_format_and_content: 100bpTiles_RRBS_Mouse.txt.gz (contains 100bp tiles methylation data of all the RRBS Mouse samples); 400bpTiles_WG_Mouse.bed.gz (contains 400bp tiles methylation data of all the WGBS Mouse samples); gene_exp.diff.gz (contains the expression data as processed by Cuffdiff).

source_name: Liver

growth_protocol: C57/bl mice were sacrificed at different ages and their liver, spleen, cerebellum and muscle were isolated.  Mice were anesthetized and either sham operated or castrated by removal of the gonads at the age of 3 or 20 weeks.  Testosterone (5 mg/ml) or vehicle alone was dissolved and then injected into an osmotic pump (Alzet, Model 2004) which was incubated for 48 h in saline at 37°C and then implanted subcutaneously into castrated males or females.  For long-term testosterone administration, the pumps were replaced every 28 days.

extract_protocol:
RNA was isolated using miRNeasy (Qiagen).
TruSeq RNA Sample Preparation Kit v2 (Illumina) was used for Library preparation.

value: Liver

tag: strain

tag: gender

value: M

tag: age

tag: condition

value: NORMAL


title: RNA_2_Mouse_Liver_M_20w_NORMAL


title: RNA_1_Mouse_Liver_F_20w_NORMAL

value: F


title: RNA_3_Mouse_Liver_F_20w_NORMAL


title: RNA_1_Mouse_Liver_M_20w_NORMAL


title: WGBS_20w_male

data_processing:
Quality score recalibration, local realignment, and methylation calling were performed using the Bis-SNP v. 0.82.1 pipeline. Average bisulfite conversion was determined to be greater than 99.65% for all libraries. After removing PCR duplicates and improperly paired read pairs, genomic coverage was determined to be 14.2x (20 d male), 14.7x (20 wk female), and 14.9x (20 wk male). 100 bp tiles and methylation levels were calculated as was done for the RRBS data and the methylation difference (20 wk male minus 20 wk female) profile (DMRs) determined.  In order to reduce noise we analyzed 400 bp tiles and required a minimum coverage of 20 and a threshold of 35%.  We marked a DMR as valid only if the 20 days male methylation level was at least 25% higher than the lower methylation level.
Genome_build: mm9 for mouse samples; hg19 for human samples
Supplementary_files_format_and_content: 100bpTiles_RRBS_Mouse.txt.gz (contains 100bp tiles methylation data of all the RRBS Mouse samples); 400bpTiles_WG_Mouse.bed.gz (contains 400bp tiles methylation data of all the WGBS Mouse samples); gene_exp.diff.gz (contains the expression data as processed by Cuffdiff).

extract_protocol:
DNA was isolated from snap-frozen mouse tissues or from frozen human samples (purchased from Cancer Center Tissue and Tumor Bank of UMass Medical School) and incubated in lysis buffer (25  mM Tris-HCl (pH  8), 2  mM EDTA, 0.2% SDS, 200  mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
Unmethylated lamba phage DNA was spiked in for a final concentration of 0.5%. 1 μg of gDNA was sonicated using The Covaris S2 Sonicator (Covaris Inc, Woburn MA) to the desired size range of approximately 125 bp median size, with the majority of insert sizes falling within the range of 100-200bp as determined by Agilent Bioanalyzer examination and quantified using the Kapa Biosystems kit. End repair, A-tailing, and adapter ligation are carried out using the standard Illumina TruSeq protocol.  Adapters used were the methylated bar coded adapters included in the Illumina TruSeq DNA sample preparation kit.  Sodium bisulfite conversion of all DNA samples following adapter ligation was performed using the EZ DNA Methylation-Gold Kit or the EZ DNA Methylation-Lightning kit  (Zymo Research). 4-8 rounds of PCR were performed using the KAPA HiFi +Uracil DNA polymerase (Kapa Biosystems). AMPure XP purification (Agencourt) was used to retain fragments with insert sizes between 100-200bp, and this insert size range was verified post-sequencing.


title: RNA_2_Mouse_Liver_F_20w_NORMAL


title: WGBS_3w_male


title: S6B [sequencing]

description: Technical replicate 2 of 2.


title: RRBS_6_Mouse_Cerebellum_M_20w_NORMAL

data_processing:
100 bp paired-end sequencing reads from RRBS were obtained using the Hiseq 2500.  Adapter trimming and quality filtering was performed with the trim_galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)23using default parameters for RRBS analysis.  BSMAP24 was used for read alignment (using genome builds mm9 and hg19) and extraction of single base-resolution methylation levels.  100 bp tiles and DMRs were calculated with the MethylKit package25 using a minimum coverage of 10 per tile, methylation difference of 25%, and q value <= 0.01.  In order to increase sensitivity, DMRs were further filtered for multiple alignments in the genome using blat26 and excluding tiles that were mapped more than once.  The statistical significance of the DMR set was calculated by repeating the above steps on random permutations of male and female samples.  For each permutation the number of DMRs was calculated and a p-value was obtained by measuring the quantile of the original DMRs.  For tissues with at least 8 samples (Liver and Muscle) we included the condition that the difference between the second highest and second lowest values will not exceed 30%.
Genome_build: mm9 for mouse samples; hg19 for human samples
Supplementary_files_format_and_content: 100bpTiles_RRBS_Mouse.txt.gz (contains 100bp tiles methylation data of all the RRBS Mouse samples); 400bpTiles_WG_Mouse.bed.gz (contains 400bp tiles methylation data of all the WGBS Mouse samples); gene_exp.diff.gz (contains the expression data as processed by Cuffdiff).

source_name: Cerebellum

extract_protocol:
DNA was isolated from snap-frozen mouse tissues or from frozen human samples (purchased from Cancer Center Tissue and Tumor Bank of UMass Medical School) and incubated in lysis buffer (25  mM Tris-HCl (pH  8), 2  mM EDTA, 0.2% SDS, 200  mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
RRBS libraries were prepared as described (Boyle, P. et al. 2012)

value: Cerebellum


title: RRBS_5_Mouse_Cerebellum_M_1w_NORMAL


title: RRBS_11_Mouse_Cerebellum_F_20w_NORMAL


title: RRBS_7_Mouse_Cerebellum_M_20w_NORMAL


title: RRBS_8_Mouse_Cerebellum_F_20w_NORMAL


title: WGBS_20w_female


title: RRBS_4_Mouse_Cerebellum_M_1w_NORMAL


title: RRBS_9_Mouse_Cerebellum_F_20w_NORMAL


title: S6A [sequencing]

description: Technical replicate 1 of 2.


title: RRBS_93_Mouse_Spleen_M_20w_NORMAL

source_name: Spleen

value: Spleen


title: RRBS_91_Mouse_Spleen_M_20w_NORMAL


title: RRBS_92_Mouse_Spleen_M_20w_NORMAL


title: RRBS_94_Mouse_Spleen_M_20w_NORMAL


title: RNA_4_Mouse_Liver_F_20w_NORMAL


title: RNA_3_Mouse_Liver_M_20w_NORMAL


title: Maf1 KO rep2

value: epididymal white adipose tissue

value: overnight fasted

value: Maf1 KO


title: RRBS_90_Mouse_Spleen_F_20w_NORMAL


title: RRBS_95_Mouse_Spleen_F_20w_NORMAL


title: RRBS_87_Mouse_Spleen_M_1w_NORMAL


title: RRBS_153_Mouse_Muscle_M_20w_young_control_castrated

source_name: Muscle

value: Muscle

value: young control castrated


title: RRBS_89_Mouse_Spleen_F_20w_NORMAL


title: RRBS_151_Mouse_Muscle_M_20w_young_control_castrated


title: RRBS_145_Mouse_Muscle_M_20w_young_castrated

value: young castrated


title: RRBS_143_Mouse_Muscle_M_20w_young_castrated


title: RRBS_144_Mouse_Muscle_M_20w_young_castrated


title: RRBS_152_Mouse_Muscle_M_20w_young_control_castrated


title: RRBS_142_Mouse_Muscle_M_20w_young_castrated


title: RRBS_141_Mouse_Muscle_M_20w_young_castrated


title: RRBS_77_Mouse_Muscle_M_3w_NORMAL


title: RRBS_80_Mouse_Muscle_M_3w_NORMAL


title: RRBS_76_Mouse_Muscle_M_3w_NORMAL


title: RRBS_74_Mouse_Muscle_M_20w_NORMAL


title: RRBS_69_Mouse_Muscle_M_20w_NORMAL


title: RRBS_73_Mouse_Muscle_M_20w_NORMAL


title: RRBS_78_Mouse_Muscle_M_3w_NORMAL


title: RRBS_67_Mouse_Muscle_M_20w_NORMAL


title: RRBS_61_Mouse_Muscle_M_20w_NORMAL


title: RRBS_62_Mouse_Muscle_M_20w_NORMAL


title: RRBS_84_Mouse_Muscle_F_3w_NORMAL


title: RRBS_85_Mouse_Muscle_F_3w_NORMAL


title: RRBS_83_Mouse_Muscle_F_3w_NORMAL


title: RRBS_64_Mouse_Muscle_M_20w_NORMAL


title: RRBS_82_Mouse_Muscle_F_3w_NORMAL


title: RRBS_63_Mouse_Muscle_M_20w_NORMAL


title: RRBS_75_Mouse_Muscle_F_20w_NORMAL


title: RRBS_71_Mouse_Muscle_F_20w_NORMAL


title: RRBS_72_Mouse_Muscle_F_20w_NORMAL


title: RRBS_81_Mouse_Muscle_F_3w_NORMAL


title: RRBS_79_Mouse_Muscle_M_3w_NORMAL


title: RRBS_150_Mouse_Muscle_M_20w_young_control_castrated


title: RRBS_68_Mouse_Muscle_F_20w_NORMAL


title: RRBS_66_Mouse_Muscle_F_20w_NORMAL


title: RRBS_148_Mouse_Liver_M_20w_young_control_castrated


title: RRBS_149_Mouse_Liver_M_20w_young_control_castrated


title: RRBS_147_Mouse_Liver_M_20w_young_control_castrated


title: RRBS_140_Mouse_Liver_M_20w_young_castrated


title: RRBS_70_Mouse_Muscle_M_20w_NORMAL


title: RRBS_146_Mouse_Liver_M_20w_young_control_castrated


title: RRBS_139_Mouse_Liver_M_20w_young_castrated


title: RRBS_137_Mouse_Liver_M_20w_young_castrated


title: RRBS_138_Mouse_Liver_M_20w_young_castrated


title: RRBS_134_Mouse_Liver_F_20w_vehacle_+_castration

value: vehicle + castration


title: RRBS_135_Mouse_Liver_F_20w_vehacle_+_castration


title: RRBS_132_Mouse_Liver_F_20w_vehacle_+_castration


title: RRBS_131_Mouse_Liver_F_20w_vehacle_+_castration


title: RRBS_129_Mouse_Liver_M_20w_testosterone_control

value: testosterone control


title: RRBS_130_Mouse_Liver_F_20w_vehacle_+_castration


title: RRBS_133_Mouse_Liver_F_20w_vehacle_+_castration


title: RRBS_128_Mouse_Liver_M_20w_testosterone_control


title: RRBS_125_Mouse_Liver_F_20w_testosterone_+_castaration

value: testosterone + castaration


title: RRBS_127_Mouse_Liver_M_20w_testosterone_control


title: RRBS_123_Mouse_Liver_F_20w_testosterone_+_castaration


title: RRBS_121_Mouse_Liver_F_20w_testosterone_+_castaration


title: RRBS_120_Mouse_Liver_F_20w_testosterone_+_castaration


title: RRBS_65_Mouse_Muscle_F_20w_NORMAL


title: RRBS_118_Mouse_Liver_M_20w_testosterone

value: testosterone


title: RRBS_119_Mouse_Liver_M_20w_testosterone


title: RRBS_117_Mouse_Liver_M_20w_testosterone


title: RRBS_116_Mouse_Liver_M_20w_testosterone


title: RRBS_114_Mouse_Liver_M_31w_old_castration_control

value: old castration control


title: RRBS_115_Mouse_Liver_M_31w_old_castration_control

value: Liver


title: RRBS_136_Mouse_Liver_M_20w_young_castrated

value: M


title: RRBS_113_Mouse_Liver_M_28w_old_castration_control


title: RRBS_110_Mouse_Liver_M_28w_old_castration_control


title: RRBS_112_Mouse_Liver_M_28w_old_castration_control


title: RRBS_109_Mouse_Liver_M_28w_old_castration_control


title: RRBS_126_Mouse_Liver_M_20w_testosterone_control


title: RRBS_106_Mouse_Liver_M_20w_old_castration_control


title: RRBS_99_Mouse_Liver_M_31w_old_castration

value: old castration


title: RRBS_124_Mouse_Liver_F_20w_testosterone_+_castaration

value: F


title: RRBS_9_Human_Liver_M_Adult_NORMAL

value: Adult

value: NORMAL


title: RRBS_96_Mouse_Liver_M_28w_old_castration


title: RRBS_97_Mouse_Liver_M_28w_old_castration


title: RRBS_105_Mouse_Liver_M_28w_old_castration


title: RRBS_104_Mouse_Liver_M_28w_old_castration


title: RRBS_103_Mouse_Liver_M_28w_old_castration


title: RRBS_6_Human_Liver_F_Adult_NORMAL


title: RRBS_98_Mouse_Liver_M_28w_old_castration


title: RRBS_102_Mouse_Liver_M_28w_old_castration


title: RRBS_100_Mouse_Liver_M_31w_old_castration


title: RRBS_111_Mouse_Liver_M_28w_old_castration_control


title: RRBS_5_Human_Liver_F_Adult_NORMAL


title: RRBS_101_Mouse_Liver_M_28w_old_castration


title: RRBS_3_Human_Liver_F_Adult_NORMAL


title: RRBS_2_Human_Liver_F_Adult_NORMAL


title: RRBS_3_Mouse_Liver_F_20w_castration

value: castration


title: RRBS_1_Mouse_Liver_F_20w_castration


title: RRBS_54_Mouse_Liver_M_8w_NORMAL


title: RRBS_108_Mouse_Liver_M_28w_old_castration_control


title: RRBS_53_Mouse_Liver_M_8w_NORMAL


title: RRBS_8_Human_Liver_M_Adult_NORMAL


title: RRBS_2_Mouse_Liver_F_20w_castration


title: RRBS_107_Mouse_Liver_M_28w_old_castration_control


title: RRBS_50_Mouse_Liver_M_3w_NORMAL


title: RRBS_48_Mouse_Liver_M_3w_NORMAL


title: RRBS_7_Human_Liver_M_Adult_NORMAL


title: RRBS_4_Human_Liver_M_Adult_NORMAL


title: RRBS_51_Mouse_Liver_M_8w_NORMAL


title: RRBS_49_Mouse_Liver_M_3w_NORMAL


title: RRBS_42_Mouse_Liver_M_3w_NORMAL


title: RRBS_55_Mouse_Liver_M_8w_NORMAL


title: RRBS_47_Mouse_Liver_M_3w_NORMAL


title: RRBS_1_Human_Liver_F_Adult_NORMAL


title: RRBS_52_Mouse_Liver_M_8w_NORMAL


title: RRBS_35_Mouse_Liver_M_20w_NORMAL


title: RRBS_24_Mouse_Liver_M_20w_NORMAL


title: RRBS_34_Mouse_Liver_M_20w_NORMAL


title: RRBS_38_Mouse_Liver_M_20w_NORMAL


title: RRBS_23_Mouse_Liver_M_20w_NORMAL


title: RRBS_28_Mouse_Liver_M_20w_NORMAL


title: RRBS_26_Mouse_Liver_M_20w_NORMAL


title: RRBS_21_Mouse_Liver_M_1w_NORMAL


title: RRBS_29_Mouse_Liver_M_20w_NORMAL


title: RRBS_122_Mouse_Liver_F_20w_testosterone_+_castaration


title: RRBS_14_Mouse_Liver_M_1w_NORMAL


title: RRBS_31_Mouse_Liver_M_20w_NORMAL


title: RRBS_13_Mouse_Liver_M_1w_NORMAL


title: RRBS_19_Mouse_Liver_M_1w_NORMAL


title: RRBS_20_Mouse_Liver_M_1w_NORMAL


title: RRBS_60_Mouse_Liver_F_8w_NORMAL


title: RRBS_40_Mouse_Liver_M_20w_NORMAL


title: RRBS_59_Mouse_Liver_F_8w_NORMAL


title: RRBS_56_Mouse_Liver_F_8w_NORMAL


title: RRBS_44_Mouse_Liver_F_3w_NORMAL


title: RRBS_41_Mouse_Liver_F_20w_NORMAL


title: RRBS_57_Mouse_Liver_F_8w_NORMAL


title: RRBS_36_Mouse_Liver_F_20w_NORMAL


title: RRBS_43_Mouse_Liver_F_3w_NORMAL


title: RRBS_58_Mouse_Liver_F_8w_NORMAL


title: RRBS_45_Mouse_Liver_F_3w_NORMAL


title: RRBS_33_Mouse_Liver_F_20w_NORMAL


title: RRBS_27_Mouse_Liver_F_20w_NORMAL


title: RRBS_30_Mouse_Liver_F_20w_NORMAL


title: RRBS_46_Mouse_Liver_F_3w_NORMAL


title: RRBS_25_Mouse_Liver_F_20w_NORMAL


title: RRBS_17_Mouse_Liver_F_1w_NORMAL


title: RRBS_18_Mouse_Liver_F_1w_NORMAL


title: RRBS_16_Mouse_Liver_F_1w_NORMAL


title: RRBS_15_Mouse_Liver_F_1w_NORMAL


title: MCF10A rep2

status: Public on May 02 2015

city: Göttingen

first: Steven

middle: A

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

description:
Cells were crosslinked with 1 % formaldehyde for 10 minutes.
MCF10A_H4K12ac.bigwig

data_processing:
The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
DeepTools (Ramírez et. al., 2014) was used to create bigwigs by normalizing the ChIP-seq sample with the input samples of each cell line and obtaining the ratio of the reads using bamCompare function.  sample.
Normalization was done using read counts of each ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were made from bamCompare function of deepTools.  Scores represent ratio of the number of reads relative to input.

source_name: MCF10A breast epithelial cells

growth_protocol: MCF10A cells were grown in phenol-red free DMEM/F12 medium supplemented with 5% horse serum, 20 ng/mL epidermal growth factor, 0.1 µg/mL Cholera toxin, 10 µg/mL insulin, 0.5 µg/mL hydrocortisone, 1% penicillin/streptomycin at 37°C.

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10  minutes and quenched with 1.25 M Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

treatment_protocol: No special treatment.

value: Breast epithelial cells

tag: chip-seq antibody

value: Anti-acetyl-histone H4 (Lys12) (07-595; EMD Millipore) (1 µg used)


title: MCF10A Input

description: Cells were crosslinked with 1 % formaldehyde for 10 minutes.


title: MCF10A rep1


title: MCF7 E2 rep2

description:
Cells were crosslinked with 1 % formaldehyde for 10 minutes.
MCF7_H4K12ac_E2.bigwig

source_name: MCF7 breast cancer cells

growth_protocol: MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) with 10% bovine growth serum (Thermo Scientific) and 1% penicillin/streptomycin. After one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Biochrome).

treatment_protocol: After 2 days of hormone deprivation, MCF7 cells were treated with 10 nmol/L 17-β-estradiol (E2) (Sigma-Aldrich) treatment for 2 hours.

value: Human breast adenocarcinoma cell line


title: MCF7 E2 rep1


title: MCF7 E2 rep3


title: MCF7 Veh rep2

description:
Cells were crosslinked with 1 % formaldehyde for 10 minutes.
MCF7_H4K12ac_Veh.bigwig

treatment_protocol: After 2 days of hormone deprivation, vehicle (ethanol - Veh) was added as negative control for 2 hours.


title: RRBS_39_Mouse_Liver_F_20w_NORMAL


title: RRBS_37_Mouse_Liver_F_20w_NORMAL


title: RRBS_32_Mouse_Liver_F_20w_NORMAL


title: MCF7 Veh rep1

treatment_protocol: After 2 days of hormone deprivation, vehicle (ethanol - Veh) was added as negative control.


title: CB_Exp_Rep1

status: Public on May 01 2015

city: winnipeg

first: Riffat

last: Munir

state: MB

address: dafoe road

department: biosystems

country: Canada

institute: University of manitoba

data_processing:
The sequencing platform is illumina HiSeq 2000. Basecalls performed using CASAVA version 1.8
Raw Illumina R2 read sets are exactly aligned against a non-redundant 100mer alignment database using an in-house package
Expression values are the sum of alll 100-mer RNA  read alignments per gene, and mapped to a log2 scale.
Genome_build: SAMN02471873 (Biosample number)
Supplementary_files_format_and_content: tab-delimited text files include the sum of all 100-mer RNA alignments per gene mapped to a log2 scale

organism: Ruminiclostridium cellobioparum subsp. termitidis CT1112

source_name: Whole cell extract

growth_protocol: C.termitidis was cultured in was cultured anaerobically in complex 1191 medium containing 2 g/L each of cellobiose, xylose, α-cellulose and beechwood xylan respectively at 37 0C

extract_protocol:
RNA was extracted by using the ChargeSwitch magnetic bead based technique for RNA extraction (Life Technologies, Burlington, Canada) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: samples were drawn at exponential phase of growth and centrifuged to collect pellets

value: cellobiose

value: wild type

tag: time

value: Mid-log phase sample


title: AC_EXP_Rep2

value: α-cellulose


title: Xylose_EXP_Rep2

value: Xylose


title: Xylan_Exp_Rep2

value: Xylan


title: AC_EXP_Rep1


title: Xylose_EXP_Rep1


title: RRBS_22_Mouse_Liver_F_20w_NORMAL

tag: tissue


title: CB_Exp_Rep2


title: WG_Sta_Rep2

city: Winnipeg

first: Parveen

last: Sharma

state: Manitoba

address: 75A Chancellor's Circle

department: Biosystem Engineering

institute: University of Manitoba

data_processing:
Basecalls performed using CASAVA version 1.8
Raw Illumina R2 read sets are exactly aligned against a non-redundant 100mer alignment database using an in-house package
Expression values are the sum of alll 100-mer RNA  read alignments per gene, andmapped to a log2 scale.
Genome_build: ASM29444v2
Supplementary_files_format_and_content: tab-delimited text files include the sum of all 100-mer RNA alignments per gene mapped to a log2 scale (abundance measurements)

organism: Pseudomonas putida

growth_protocol: The cell was growing in 1X of Ramsay's medium supplimented with  30g/L of glycerol equilvalent of pure glycerol, waste glycerol culture or 1%v/v of waste fatty acids. Grwoth of the P.putida LS46 was monitered via spectro photometer at 600nm or total protein concentration for waste glycerol culture or waste fatty acid culture respectively.

extract_protocol:
The pelleted cell was subjected to total RNA isolation by using PureLink® RNA Mini Kit (Ambion, Life Technologies, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols. Library size selection: 300bp.

treatment_protocol: The cell was pelleted by centrifuging at 4,000 x g

tag: culture

value: waste glycerol

tag: growth phase

value: stationary phase

value: 32 hours post inocula


title: WG_Exp_Rep2

value: exponential phase

value: 8 hours post inocula


title: WG_Exp_Rep1


title: WG_Sta_Rep1


title: PG_Exp_Rep2

value: pure glycerol


title: Pool of mature seeds from berries in V, MR,R stages

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

description:
small RNA
Seed_M
Seeds collected from mature berries at V, MR, and R stages

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 18 and 34 nucleotides. Small RNA reads were mapped to the grapevine genome.
Genome_build: The International Grape Genome Project (IGGP)12X version 1
Supplementary_files_format_and_content: Text containing distinct smallRNAs with their raw abundance after removing the adapter sequences

organism: Vitis vinifera

source_name: Grapevine seeds

growth_protocol: All samples of Vitis vinifera L. cv Corvina were collected from a 7-year-old vineyard in Montorio, province of Verona, Italy (latitude 45˚ 27’ 17” N, longitude 11˚ 03’ 14”) during 2008/2009 growing seasons. The vineyard is at 130 m above sea level, planted on a soil with the following composition: 36% sand, 36% say and 28% silt. The grapevine plants clone PN40024 were grown in vitro on half strength MS medium with 15 g/l sucrose, at 25°C with a 16 h light cycle

extract_protocol:
Small RNA from green tissues such as leaf, stem, flower, tendril, anther, carpel, was extracted with mirPremierTM microRNA Isolation kit from Sigma, following manufacture’s protocol. Small RNA from bud, berries and rachis, was extracted using the Plant RNA Isolation Reagent (PRIR) method from Invitrogen, followed by the mirPremierTM microRNA isolation kit. A total of 100 mg of ground tissue was used as input material for small RNA extraction in both methods.
Small RNA libraries of Corvina's samples were constructed as previously described (Mica et al., 2010) following the Truseq small RNA sample preparation guide (Illumina, USA). Briefly, 50 ng of small RNA was used as input material and ligated first with the 3' RNA adaptor and then with 5' RNA adapter, followed by reverse transcription and 15 cycles of PCR amplification with unique barcoded indexes. Small RNA libraries from the clone PN40024 were constructed following the Small RNA Sample Prep kit (Illumina, USA), starting from 2 µg of small RNAs. The amplified libraries were run on a 6% PAGE gel and purified.

tag: developmental stage

value: Mature

tag: cultivar

value: Corvina

value: seeds


title: PG_Exp_Rep1


title: Pool of green seeds from berries in FS, PFS, PV stages

description:
small RNA
Seed_G
Seeds collected from green berries at FS, PFS, and Pre-V stages

value: Green


title: WFA_Exp_Rep2

value: waste free fatty acids


title: Root collected from in vitro cultivation replicate 1

description:
small RNA
Root_1
Roots were collected from in vitro growing cuttings

source_name: Grapevine in vitro roots

value: In vitro cultivation

value: in vitro roots


title: Root collected from in vitro cultivation replicate 2

description:
small RNA
Root_2
Roots were collected from in vitro growing cuttings


title: Rachis collected at Ripening replicate 2

description:
small RNA
Rachis_R_2
Rachis collected when berries were at R developmental stage

source_name: Grapevine rachis

value: Ripening

value: rachis


title: Rachis collected at Mid-ripening replicate 2

description:
small RNA
Rachis_MR_2
Rachis collected when berries were at MR developmental stage

value: Mid-ripening


title: Rachis collected at Ripening replicate 1

description:
small RNA
Rachis_R_1
Rachis collected when berries were at R developmental stage


title: Rachis collected at post-fruit set replicate 1

description:
small RNA
Rachis_PFS_1
Rachis collected when berries were at PFS developmental stage

value: Post-fruit set


title: Rachis collected at Veraison replicate 2

description:
small RNA
Rachis_V_2
Rachis collected when berries were at V developmental stage

value: Veraison


title: Rachis collected at Veraison replicate 1

description:
small RNA
Rachis_V_1
Rachis collected when berries were at V developmental stage


title: Rachis collected at post-fruit set replicate 2

description:
small RNA
Rachis_PFS_2
Rachis collected when berries were at PFS developmental stage


title: Xylan_Exp_Rep1

value: Xylan

value: wild type

value: Mid-log phase sample


title: Rachis collected at fruitset replicate 2

description:
small RNA
Rachis_FS_2
Rachis collected when berries were at FS developmental stage

value: Fruit set


title: WFA_Exp_Rep1

value: exponential phase

value: 8 hours post inocula


title: Post-harvest withering (3rd month) replicate 2

description:
small RNA
Berry_PHWIII_2
Withering stage III, characterized by weight reduction of 32.7% and 26.7 ˚Brix

source_name: Grapevine withering berries

value: Post-harvest (3rd month)

value: Corvina

value: withering berries


title: Post-harvest withering (2nd month) replicate 1

description:
small RNA
Berry_PHWII_1
Withering stage II, characterized by weight reduction of 30.3% and 25.9 ˚Brix

value: Post-harvest (2nd month)


title: Post-harvest withering (2nd month) replicate 2

description:
small RNA
Berry_PHWII_2
Withering stage II, characterized by weight reduction of 30.3% and 25.9 ˚Brix


title: Berries at Mid-ripening replicate 2

description:
small RNA
Berry_MR_2
Berries collected at mid-ripening stage (84 DAF; 15.5 ˚Brix)

source_name: Grapevine berries

value: berries


title: Berries at Mid-ripening replicate 1

description:
small RNA
Berry_MR_1
Berries collected at mid-ripening stage (84 DAF; 15.5 ˚Brix)


title: Post-harvest withering (3rd month) replicate 1

description:
small RNA
Berry_PHWIII_1
Withering stage III, characterized by weight reduction of 32.7% and 26.7 ˚Brix


title: Rachis collected at fruitset replicate 1

description:
small RNA
Rachis_FS_1
Rachis collected when berries were at FS developmental stage


title: Berries at Ripening replicate 1

description:
small RNA
Berry_R_1
Berries collected at last stage of ripening (115 DAF; 15.5 ˚Brix)


title: Berries at Veraison replicate 1

description:
small RNA
Berry_V_1
Berries collected when they change colour (10.4 ˚Brix,70 DAF)


title: Berries at Veraison replicate 2

description:
small RNA
Berry_V_2
Berries collected when they change colour (10.4 ˚Brix,70 DAF)


title: Berries at Ripening replicate 2

description:
small RNA
Berry_R_2
Berries collected at last stage of ripening (115 DAF; 15.5 ˚Brix)


title: Berries at Post-fruit set replicate 2

description:
small RNA
Berry_PFS_2
Berries collected when they reach >7 mm diam


title: Berries at Pre-veraison replicate 1

description:
small RNA
Berry_PV_1
Berries collected when they begin to soften and Sugar starts increasing

value: Pre-veraison


title: Berries at Pre-veraison replicate 2

description:
small RNA
Berry_PV_2
Berries collected when they begin to soften and Sugar starts increasing


title: Rachis collected at Mid-ripening replicate 1

description:
small RNA
Rachis_MR_1
Rachis collected when berries were at MR developmental stage


title: Berries at Post-fruit set replicate 1

description:
small RNA
Berry_PFS_1
Berries collected when they reach >7 mm diam


title: Post-harvest withering (1st month) replicate 2

description:
small RNA
Berry_PHWI_2
Withering stage I, characterized by a weight reduction of 23.6% and 24.5 ˚Brix

value: Post-harvest (1st month)


title: Berries at Fruitset replicate 1

description:
small RNA
Berry_FS_1
Berries collected 15 days after flowering


title: Pollen replicate 1

description:
small RNA
Pollen_1
Pollen was collected from disclosed flowers at more than 50% caps off

source_name: Grapevine pollen

value: disclosed flowers (> 50% caps off )

value: pollen


title: Post-harvest withering (1st month) replicate 1

description:
small RNA
Berry_PHWI_1
Withering stage I, characterized by a weight reduction of 23.6% and 24.5 ˚Brix


title: Berries at Fruitset replicate 2

description:
small RNA
Berry_FS_2
Berries collected 15 days after flowering


title: Pool of stamens replicate 2

description:
small RNA
Stamen_2
Stamens collected from undisclosed flowers  at 10% and 50% open flowers

source_name: Grapevine stamens from undisclosed flowers

value: undisclosed flowers

value: stamens from undisclosed flowers


title: Pollen replicate 2

description:
small RNA
Pollen_2
Pollen was collected from disclosed flowers at more than 50% caps off


title: Pool of stamens replicate 1

description:
small RNA
Stamen_1
Stamens collected from undisclosed flowers  at 10% and 50% open flowers


title: Flowering replicate 2

description:
small RNA
Flower_F_2
Flowering phase  (50% caps off)

source_name: Grapevine flowers

value: Flowering

value: flowers


title: Pool of Carpels replicate 1

description:
small RNA
Carpel_1
Pool of carpels collected from undisclosed flowers at 10% and 50% open flowers

source_name: Grapevine carpels from undisclosed flowers

value: carpels from undisclosed flowers


title: Flowering replicate 1

description:
small RNA
Flower_F_1
Flowering phase  (50% caps off)


title: Pool of carpels replicate 2

description:
small RNA
Carpel_2
Pool of carpels collected from undisclosed flowers at 10% and 50% open flowers


title: Flowering begins replicate 2

description:
small RNA
Flower_FB_2
Beginning of flowering  (10% caps off)

value: Beginning of flowering


title: Flowering begins replicate 1

description:
small RNA
Flower_FB_1
Beginning of flowering  (10% caps off)


title: Well developed Inflorescence replicate 1

description:
small RNA
Inf_WD_1
Well-developed inflorescence with single flower separated

source_name: Grapevine Inflorescences

value: Well-developed

value: Inflorescences


title: Well developed Inflorescence replicate 2

description:
small RNA
Inf_WD_2
Well-developed inflorescence with single flower separated


title: Young Inflorescence replicate 1

description:
small RNA
Inf_Y_1
Young inflorescence with single flower in compact groups

value: Young


title: Well developed Tendril replicate 1

description:
small RNA
Tendril_WD_1
Pool of well-developed tendrils collected when the shoot contains 12 separated leaves

source_name: Grapevine tendril

value: Corvina

value: tendril


title: Young Tendril replicate 2

description:
small RNA
Tendril_Y_2
Pool of tendrils from shoot bearing of 7 separated leaves


title: Young Inflorescence replicate 2

description:
small RNA
Inf_Y_2
Young inflorescence with single flower in compact groups


title: Green Stem replicate 1

description:
small RNA
Stem_G_1
pool of stems collected from the second node from the tip

source_name: Grapevine stem

value: Green

value: stem


title: Green Stem replicate 2

description:
small RNA
Stem_G_2
pool of stems collected from the second node from the tip


title: Well developed Tendril replicate 2

description:
small RNA
Tendril_WD_2
Pool of well-developed tendrils collected when the shoot contains 12 separated leaves


title: Woody Stem replicate 2

description:
small RNA
Stem_W_2
pool of woody stems (cane) collected at latent and winter bud stages

value: Woody


title: Laten bud replicate 2

description:
small RNA
Bud_L_2
first season latent bud

source_name: Grapevine buds

value: Latent

value: buds


title: Bud burst replicate 1

description:
small RNA
Bud_B_1
bud burst showing green tip

value: Burst


title: Winter bud replicate 1

description:
small RNA
Bud_W_1
winter dormant bud

value: Winter


title: Winter bud replicate 2

description:
small RNA
Bud_W_2
winter dormant bud


title: Woody Stem replicate 1

description:
small RNA
Stem_W_1
pool of woody stems (cane) collected at latent and winter bud stages


title: Young Tendril replicate 1

description:
small RNA
Tendril_Y_1
Pool of tendrils from shoot bearing of 7 separated leaves


title: Bud burst replicate 2

description:
small RNA
Bud_B_2
bud burst showing green tip


title: Bud after burst replicate 1

description:
small RNA
Bud_AB_1
final bud stage after burst

value: After Burst


title: Senescencing leaf replicate 2

description:
small RNA
Leaf_S_2
leaves in senescence, collected before the beginning of leaf fall

source_name: Grapevine leaves

value: Senescence

value: leaves


title: Bud after burst replicate 2

description:
small RNA
Bud_AB_2
final bud stage after burst


title: Senescencing leaf replicate 1

description:
small RNA
Leaf_S_1
leaves in senescence, collected before the beginning of leaf fall


title: Mature leaf replicate 1

description:
small RNA
Leaf_M_1
mature leaves collected when the berry size was about 4 mm in diameter

value: Mature


title: Young leaf replicate 1

description:
small RNA
Leaf_Y_1
young leaves collected when the shoot contains about 5 well separated leaves


title: GRA23-knockout

city: Cambridge

first: Daniel

last: Gold

state: Massachusetts

address: 77 Massachusetts Ave 68-264d

department: Biology

institute: MIT

description: as decribed in http://www.ncbi.nlm.nih.gov/pubmed/23231500

data_processing:
Illumina Offline BaseCaller1.9.3  software used for basecalling.
Sequence reads were mapped to either mm9 whole genome using Tophat 2.0.4 with the following parameters --genome-read-mismatches 2 --read-mismatches 3 --min-intron-length 70 --max-intron-length 500000 --solexa1.3-quals --no-coverage-search --segment-length 20 --mate-inner-dist 220 --mate-std-dev 30 --min-anchor-length 4 --b2-sensitive or to ME49v8.0 whole genome using  Tophat 2.0.4 --no-coverage-search --max-coverage-intron 2000 --max-segment-intron 2000 --segment-length 20 --mate-std-dev 80 -a 8 -i 70 -I 2000
Gene expression was calculated as Fragments per Kilobase of modeled exon per Million mapped reads (FPKM) using Cufflinks 2.0.2
Genome_build: mm9 or ME49v8.0
Supplementary_files_format_and_content: A tab-delimited text file that includes FPKM values for each Sample.

organism:
Mus musculus
Toxoplasma gondii RH

source_name: infected BMMs

growth_protocol: Cells were grown in R20 media (RPMI Glutamax +20% L929 sup+ 10% FCS +10uM HEPES +50uM B-ME + Pen.Strep )

extract_protocol: Total RNA was isolated using QIAGEN® RNeasy plus kit according the manufacturer’s instructions. Sequencing libraries were prepared according to Illumina RNA-Seq library kit with minor modifications. Briefly, mRNA was isolated using Dynabeads® mRNA Purification Kit (Invitrogen) followed by fragmentation (Ambion) and ethanol precipitation. First and second strand synthesis were performed followed by end repair, A-tailing, paired end adapter ligation and size selection on agarose gels. 200-400 bp dsDNA was enriched by 15 cycles of PCR with Phusion® High-Fidelity DNA Polymerase (NEB) followed by gel purification of ~250 bp fragments from the amplified material. Amplified libraries were sequenced on an Illumina GAII or GAIIx sequencer, alternatively.

treatment_protocol: Cells were infected with indicated Toxplasma strains for 4 hours at an intended MOI of 5

tag: pathogen

value: Toxoplasma gondii strain Rh

tag: mouse strain

value: Bone marrow

value: macrophages

value: week 4-6 mice

tag: toxoplasma gondii genotype


title: GRA17-knockout


title: GRA17-knockout+GRA17-HA


title: Young leaf replicate 2

description:
small RNA
Leaf_Y_2
young leaves collected when the shoot contains about 5 well separated leaves

value: Young

value: Corvina


title: Wild-type


title: Laten bud replicate 1

description:
small RNA
Bud_L_1
first season latent bud


title: Mature leaf replicate 2

description:
small RNA
Leaf_M_2
mature leaves collected when the berry size was about 4 mm in diameter


title: Ch1

city: Canberra

first: Sylvain

last: Foret

state: ACT

address: Gould Building #116

department: Research School of Biology

institute: The Australian National University

description: Primary polyps exposed 9 days at 750 ppm

data_processing:
Basecalls performed using CASAVA 1.2
Sequencing reads were mapped onto the A. millepora transcriptome assembly (Moya et al. 2012) using the Bowtie mapping software v0.12.7, allowing up to 2 mismatches. Reads mapping to more than 10 references were discarded.
Counts per reference summarized using in-house scripts
Genome_build: NCBI transcriptome assembly, shotgun assembly database numbers JR970414-JR999999 and JT000001-JT023377
Supplementary_files_format_and_content: Processed data file column headers: Reference transcript name, count

organism: Acropora millepora

growth_protocol: Fifteen adult colonies of Acropora millepora were collected off the coast of Orpheus Island, Queensland, Australia (under GBRMPA Permit No G10/33174.1), prior to the spawning event in November, 2010 and transported to the aquaculture facilities at James Cook University in Townsville where they were maintained in outdoor flow-through aquaria filled with 5 μm filtered seawater. Eggs and sperm from these colonies were collected immediately after spawning and used to make 3 independent crosses (3 x 5 colonies) corresponding to 3 biological replicates.

extract_protocol:
The primary polyps (~50 per condition) were carefully removed from the tiles with a sterile scalpel, immediately snap-frozen in liquid nitrogen and stored at -80°C until further processed. Total RNA was extracted from the samples using Trizol Reagent (Invitrogen) and dissolved in RNAse free water. RNA quantity and quality were assessed using a NanoDrop ND-1000 spectrometer and denaturing gel electrophoresis. Before being shipped on dry ice to the Macrogen sequencing facilities in Seoul, South Korea, each RNA sample was precipitated in ethanol and sodium-acetate (2x and 0.1x sample volume respectively), and stored at -80°C.
mRNA isolation and library construction were performed by Macrogen (South Korea)

treatment_protocol: Embryos were transferred immediately after fertilization to seawater that had been equilibrated with air containing 380 ppm (pHNBS~8.16) or 750 ppm (pHNBS~7.96) CO2, reflecting the control condition and medium CO2 scenario for the 21st century. Settlement was induced 5 d after fertilization by the introduction of unglazed terracotta tiles that had been conditioned with crustose coralline algae and then autoclaved.

value: primary polyp

tag: treatment

value: 750 ppm CO2

value: 9 days

value: whole polyps


title: Leaf_Stage8_rep1

city: West Lafayette

first: Karen

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

data_processing:
Aligned to Gmax189 transcriptome using Bowtie
Removed reads that matched mutliple transcript models
Removed reads with <10 hits per stage
Normalization using Deseq 1.0
Genome_build: Glycine max 189
Supplementary_files_format_and_content: .csv files with RPKM values for each sample

organism: Glycine max

source_name: 7 weeks after V3 stage

growth_protocol: Plants were grown in growth chambers at 12hr light:12 hr dark photoperiod with light provided by a combination of fluorescent and incandescent lighting at an intensity of 350 μmol m-2 s-1, constant temperature of 25 C and 75% relative humidity. Samples were collected at peak time in the afternoon to avoid changes due to day.

extract_protocol:
RNA was extracted from cotyledons and leaves using Phenol-cholorform method.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Time course study of normal development

tag: develomental stage

value: 7 weeks after V3 stage

value: Leaf


title: Leaf_Stage7_rep2

source_name: 6 weeks after V3 stage

value: 6 weeks after V3 stage


title: Leaf_Stage5_rep2

source_name: 4 weeks after V3 stage

value: 4 weeks after V3 stage


title: Leaf_Stage5_rep3


title: Ch3

source_name: Primary polyps exposed 9 days at 750 ppm


title: Leaf_Stage7_rep1


title: Leaf_Stage7_rep3


title: Leaf_Stage1_rep3

source_name: V3 stage

value: V3 Stage


title: Leaf_Stage1_rep2


title: Cotyledon_Stage3_rep3

source_name: 27 days after planting

value: 27 days after planting

value: Cotyledon


title: Leaf_Stage8_rep2


title: Leaf_Stage3_rep1

source_name: 2 weeks after V3 stage

value: 2 weeks after V3 stage


title: C2

description: Primary polyps exposed 9 days at 380 ppm

value: 380 ppm CO2 (control)


title: Leaf_Stage8_rep3


title: Ch2


title: Leaf_Stage1_rep1


title: Leaf_Stage3_rep2


title: Leaf_Stage5_rep1


title: Cotyledon_Stage3_rep2


title: C3

source_name: Primary polyps exposed 9 days at 380 ppm


title: C1


title: Cotyledon_Stage2_rep3

source_name: 15 days after planting

value: 15 days after planting


title: Cotyledon_Stage3_rep1


title: Cotyledon_Stage2_rep2


title: Cotyledon_Stage2_rep1


title: Leaf_Stage3_rep3


title: Cotyledon_Stage1_rep2

source_name: 4 days after planting

value: 4 days after planting


title: Cotyledon_Stage1_rep3


title: Cotyledon_Stage1_rep1


title: ELS rep2

city: Hangzhou

first: Gulei

last: Jin

state: Zhejiang

address: Yuhangtang Road 388#

institute: Zhejiang University

description: Sample name: ELS-2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using Tophat v2.0.9 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks v2.0.2. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Shoot

growth_protocol: Seeds were surface-sterilized, and germinated on nylon net with proper porosity floating on half-strength nutrient solution as presented in Niu et al. (2014). The composition of the Hydroponics culture solution was as follows (in µM): 1,500 KNO3, 1000 MgSO4, 1,000 CaCl2, 500 NaH2PO4, 250 (NH4)2SO4, 10 H3BO3, 0.5 MnSO4, 0.5 ZnSO4, 0.1 CuSO4, 0.1 (NH4)6Mo7O24 and 25 Fe-EDTA. The solution pH was adjusted daily to 6.0 using 1 M NaOH. At the end of the 5 weeks, CO2 treatments commenced. Plants were grown in chambers with a CO2 concentration of either 350 ± 50 (ambient) or 800 ± 50 µL L−1 (elevated CO2). At the same time, Mg treatments were initiated. The Mg treatments were commenced by growing plants in the nutrient solution with concentrations of 1 (L, low), 1000 (C, control), 10000 (H, high) µM Mg2+ as MgSO4 in each CO2 treatment. Concentrations of Mg in the medium were adjusted by manipulating the concentration of MgSO4. Meanwhile, the medium with lower concentrations of SO42- were made by substituting sodium sulfate for the sodium dihydrogen phosphate so that the level of SO42- in the medium equal to the control and decreasing the difference of SO42- concentration among the treatments. Though such differences were present among the P and Mg treatments, such differences in SO42- ion did not affect root morphogenesis of Arabidopsis (Gruber et al., 2013; Niu et al., 2014). The solution pH was buffered with was buffered with 0.5% 2-(-N-morpholino) ethanesulfonic acid (MES) at pH 5.8 to minimize pH change before autoclaving.

extract_protocol:
Retinas were removed, 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 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 1 (L, low) µM MgSO4

value: 800 ± 50 µL L−1 (elevated CO2)

value: Shoot


title: ELS rep1

description: Sample name: ELS-1


title: ELR rep2

description: Sample name: ELR-2

source_name: Root

value: Root


title: EHR rep2

description: Sample name: EHR-2

value: 10000 (H, high) µM MgSO4


title: Pool of in vitro grown roots

description:
small RNA
Root_PN
Leaf tissues collected at juvenile stage

source_name: Grapevine roots

value: in vitro

value: roots


title: EHS rep2

description: Sample name: EHS-2


title: ECS rep1

description: Sample name: ECS-1

value: 1000 (C, control) µM MgSO4


title: ECS rep2

description: Sample name: ECS-2


title: Pool of in vitro grown leaves

description:
small RNA
Leaf_PN
Root tissues collected at juvenile stage

value: leaves


title: EHS rep1

description: Sample name: EHS-1


title: AHS rep2

description: Sample name: AHS-2

value: 350 ± 50 (ambient CO2)


title: ALR rep1

description: Sample name: ALR-1


title: ECR rep1

description: Sample name: ECR-1


title: ELR rep1

description: Sample name: ELR-1


title: ALS rep1

description: Sample name: ALS-1


title: ACS rep2

description: Sample name: ACS-2


title: AHS rep1

description: Sample name: AHS-1


title: ALS rep2

description: Sample name: ALS-2


title: ACS rep1

description: Sample name: ACS-1


title: ECR rep2

description: Sample name: ECR-2


title: EHR rep1

description: Sample name: EHR-1


title: T2F3_2_LSK

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw fastq files were trimmed using cutadapt cutadapt (v1.2rc2) -f fastq -g GGCCAAGGCA -m 35 --too-short-output
Reads were mapped using TopHat (ver 2) -p 20 --library-type fr-secondstrand \ -G Mus_musculus.BCNIM37.67 --transcriptome-index transMM9/Ensembl -T mm9
Remaining unmapped reads were then aligned to the same ref as in prev step using bwa (ver 0.5.9) using default paramaters.
TopHat and BWA outputs were merged using Picard MergeSamFiles using default parameters.
Read counts were generated from mapped reads using HT-Seq count.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: Counts.txt file contains total raw read counts per gene from HT-Seq counts using mode = "union".

source_name: bone marrow, LSK, Tet2-/-Flt3ITD

growth_protocol: Cells were harvested from sacrificed animals treated as described in the methods section of the associated manuscript.

extract_protocol:
Cells were lysed directly in Trizol (Life Technologies).
Follow Ion Torrent protocol, start with 100ng RNA using Ambion Low Input RiboMinus Eukaryote System v2 kit + LifeTech Ion Total RNA seq kit V2.

treatment_protocol: Freshly dissected femurs and tibias were isolated from mice. Bone marrow was flushed with a syringe into RPMI 10%FCS media. Cells were passed through a 70um strainer. Red blood cells were lysed in ammonium chloride-potassium bicarbonate lysis buffer for 10 minutes on ice. Lineage depletion was performed using the EasySep® Mouse Hematopoietic Progenitor Cell Enrichment Kit. Granulocyte-Macrophage Progenitors (GMPs, lineage- c-Kit+ Sca-1-, FcγR+ CD34+) and LSK (lineage- cKit+ Sca-1-) were sorted on the FACS Aria. Antibodies used for flow cytometry were as follows: anti-Gr1 (Ly6G), anti-B220 (RA3-682), anti-CD34 (RAM34), FCR (93) anti-Sca-1 (D7), phospho-Stat5 from eBioscience; anti-c-Kit (2B8), anti-Mac-1 (CD11b) (M1/70), anti-NK1.1 (PK136), anti-Ter119 (Ter119,553673), anti-CD3 (145-2C11), CD45.1 (A20), CD45.2 (104) all from BD Biosciences); and anti-CD150 (TC-15-12F2.2) and CD48 (HM48-1; both from Biolegend. Both the bone marrow and spleen 'lineage cocktail' included anti-CD3, anti-Gr-1, anti-Mac-1 (CD11b), anti-NK1.1, anti-B220, and anti-Terr-119.

tag: strain/background

tag: genotype/variation

tag: cell type

value: LSK

tag: donor age (years)


title: WT3_LSK

source_name: bone marrow, LSK, WT

value: WT


title: AHR rep2

description: Sample name: AHR-2


title: AHR rep1

description: Sample name: AHR-1


title: T2F3_2_GMP

source_name: bone marrow, GMP, Tet2-/-Flt3ITD

value: GMP


title: ACR rep1

description: Sample name: ACR-1


title: ACR rep2

description: Sample name: ACR-2


title: T2F3_3_GMP


title: WT1_GMP

source_name: bone marrow, GMP, WT


title: ALR rep2

description: Sample name: ALR-2


title: WT1_LSK


title: WT2_LSK


title: WT3_GMP


title: HeLa_Inf_Mut1

city: Philadelphia

first: Diana

last: Bernstein

address: 3400 Civic Center Blvd Bldg 421

department: Department of Genetics, IDOM

institute: University of Pennsylvania

description: BisPCRSeq

data_processing:
DNA libraries were sequenced on the Illumina MiSeq with 150 base pair paired-end reads
DNA sequencing data was aligned to an in silico bisulfite converted human genome with the BS Seeker program, and was processed by the Next Generation Sequencing Core at the University of Pennsylvania (Philadelphia, PA)
Data was reported as the fraction of reads that were methylated, calculated as the ratio of cytosine bases (indicating methylated CpGs) to total reads for each CpG coordinate.  Unmethylated cytosines are ultimately converted to thymine bases during the bisulfite conversion process.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files of loci, fraction of methylated Cytosines and total read count.

source_name: HeLa cells

extract_protocol:
genomic DNA was extracted using the Qiagen AllPrep DNA/RNA Micro kit, and was then bisulfite converted with the Qiagen Epitect Bisulfite Kit.
Libraries were prepared following manufacturer's instructions using the Ovation® SP+ Ultralow DR Multiplex System (NuGEN Technologies Inc.) and were sequenced on an Illumina MiSeq with 150 base pair paired-end reads.  Data was analyzed by the Next Generation Sequencing Core at the University of Pennsylvania (Philadelphia, PA)
DNA sequencing libraries were prepared from PCR-amplified bisulfite converted genomic DNA

treatment_protocol: Human cells were infected with lentivirus encoding TALE-DNMT fusion proteins

value: p16 TALE-DNMT mutant infection

tag: cell line

value: HeLa cells


title: HeLa_Inf_WT3

description: BisPCRSeq

value: p16 TALE-DNMT wild-type infection


title: HeLa_Inf_WT2

description: BisPCRSeq


title: HeLa_Sort_WT3

description: BisPCRSeq


title: T2F3_1_GMP


title: HeLa_Uninf2

description: BisPCRSeq


title: WT2_GMP


title: HeLa_Inf_Mut2

description: BisPCRSeq


title: HeLa_Sort_Mut1

description: BisPCRSeq


title: HeLa_Sort_Mut2

description: BisPCRSeq


title: hFib_TALB_Mut2_Set2

description: BisPCRSeq

source_name: primary human fibroblasts

value: primary human fibroblasts


title: HeLa_Uninf3

description: BisPCRSeq


title: T2F3_3_LSK


title: hFib_TALB_Mut1_Set2

description: BisPCRSeq


title: hFib_TALB_WT2_Set2

description: BisPCRSeq


title: hFib_TALB_WT3_Set2

description: BisPCRSeq


title: HeLa_Uninf1

description: BisPCRSeq


title: HeLa_Sort_Mut3

description: BisPCRSeq


title: HeLa_Sort_WT1

description: BisPCRSeq


title: hFib_TALB_WT1_Set2

description: BisPCRSeq


title: T2F3_1_LSK


title: HeLa_Inf_Mut3

description: BisPCRSeq


title: hFib_TALC_Mut3

description: BisPCRSeq


title: hFib_TALC_WT3

description: BisPCRSeq


title: hFib_TALC_Mut1

description: BisPCRSeq


title: HeLa_Inf_WT1

description: BisPCRSeq


title: hFib_TALC_Mut2

description: BisPCRSeq


title: hFib_TALC_WT2

description: BisPCRSeq


title: hFib_TALC_WT1

description: BisPCRSeq


title: hFib_TALB_Mut3_Set2

description: BisPCRSeq


title: HeLa_Sort_WT2

description: BisPCRSeq


title: hFib_TALB_Mut2_Set1

description: BisPCRSeq


title: hFib_TALB_WT3_Set1

description: BisPCRSeq


title: hCASMC_Uninf3

description: BisPCRSeq

source_name: primary coronary artery smooth muscle cells


title: hFib_TALB_Mut3_Set1

description: BisPCRSeq


title: hFib_TALB_WT1_Set1

description: BisPCRSeq


title: hCASMC_Uninf2

description: BisPCRSeq

value: primary coronary artery smooth muscle cells


title: hCASMC_Mut3

description: BisPCRSeq


title: hCASMC_WT1

description: BisPCRSeq


title: hCASMC_WT3

description: BisPCRSeq


title: hFib_TALB_Mut1_Set1

description: BisPCRSeq


title: hCASMC_WT2

description: BisPCRSeq


title: small pre-B cell (Control)

city: Chicago

first: John

last: Crispino

state: IL

institute: The University of Chicago

data_processing:
Adapters were removed and reads were removed that had either more than 5% unknown bases, or more than 50% of the reads had a phred score less than 10
The remaining reads were aligned to mm10 (UCSC) with TopHat v2.0.8b with parameters -p 12 -G genes.gtf
Differential expression was performed with cuffdiff v2.1.1 using parameters -p 12 -b genome.fa.  FPKM values were extracted from the cuffdiff results.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: bone marrow

growth_protocol: mice were housed in barrier facility and analyzed at 4 weeks of age

extract_protocol:
total RNA was extracted using Qiagen RNeasy kits
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: single (nucleated) cell suspensions were prepared from bone marrow and thymus, stained for surface markers, and labeled with nucleic acid dyes

tag: strain

tag: age

value: 4 weeks

tag: genotype

value: Dyrk1a flox/flox, Mx1-Cre-

value: small pre-B cell


title: small pre-B cell (CKO)

value: Dyrk1a -/-, Mx1-Cre+


title: large pre-B cell (CKO)

value: large pre-B cell


title: hCASMC_Uninf1

description: BisPCRSeq


title: large pre-B cell (Control)


title: mature granulocytes (CKO)

value: mature granulocytes


title: mature granulocytes (Control)


title: quiescent CD4+CD8+ thymocyte (CKO)

source_name: thymus

value: quiescent CD4+CD8+ thymocyte


title: quiescent CD4+CD8+ thymocyte (Control)


title: cycling CD4+CD8+ thymocyte (Control)

value: cycling CD4+CD8+ thymocyte


title: cycling CD4+CD8+ thymocyte (CKO)


title: hFib_TALB_WT2_Set1

description: BisPCRSeq


title: Myb_ChIP-Seq rep1

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

description: ChIP-Seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie with default parameters.
To call the peaks, MACS 1.4 software was used.
After calling the peaks, peaks whose FDR(%) lower than 1.0 and fold enrichment over input lower than 5 were filtered, based on MACS peak calling results.
Datasets from C646 treatment were normalized to read depth (total mapped tag counts) of DMSO treatment.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were converted from wiggle files generated by MACS 1.4 software.

source_name: MLL-AF9/NrasG12D murine cell line

growth_protocol: Cultures were maintained in RPMI medium 1640 supplemented with 10% FBS, 1% Pen/Strep.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with appopriate sizes were prepared for sequencing.
These libraries were made following the instructions of illumina Truseq DNA sample prep kit v2.

treatment_protocol: Cells were treated with DMSO (2 hour) or C646 (10uM, 2 hour) or nothing before crosslinking. In brief, cells were crosslinked using 1% formaldehyde for 20 min at room temperature.

value: Acute myeloid leukemia

tag: antibody

value: Myb (sc-7874; Santa Cruz)

value: no treatment


title: Myb_ChIP-Seq rep2

description: ChIP-Seq


title: C/EBPb_ChIP-Seq rep1

description: ChIP-Seq

value: C/EBPβ (sc-150; Santa Cruz)


title: hCASMC_Mut2

description: BisPCRSeq

value: p16 TALE-DNMT mutant infection


title: hCASMC_Mut1

description: BisPCRSeq


title: Erg_ChIP-Seq rep2

description: ChIP-Seq

value: Erg (sc-354; Santa Cruz)


title: C/EBPa_ChIP-Seq rep2

description: ChIP-Seq

value: C/EBPα (sc-61; Santa Cruz)


title: Pu1_ChIP-Seq rep2

description: ChIP-Seq

value: Pu.1 (sc-352; Santa Cruz)


title: H4K8ac_DMSO ChIP-Seq rep2

description: ChIP-Seq

value: H4K8ac (ab15823; Abcam)

value: DMSO for 2 hours


title: H4K8ac_DMSO ChIP-Seq rep1

description: ChIP-Seq


title: Pu1_ChIP-Seq rep1

description: ChIP-Seq


title: p300_ChIP-Seq

description: ChIP-Seq

value: p300 (sc-584; Santa Cruz)


title: H3_ChIP-Seq rep2

description: ChIP-Seq

value: Histone H3 (ab1791; Abcam)


title: Fli1_ChIP-Seq rep1

description: ChIP-Seq

value: Fli1 (ab15289; Abcam)


title: H4K8ac_C646 ChIP-Seq rep2

description: ChIP-Seq

value: C646 (10uM) for 2 hours


title: H3_ChIP-Seq rep1

description: ChIP-Seq


title: Erg_ChIP-Seq rep1

description: ChIP-Seq


title: Fli1_ChIP-Seq rep2

description: ChIP-Seq


title: H4K8ac_C646 ChIP-Seq rep1

description: ChIP-Seq


title: H3K27ac_C646 ChIP-Seq rep1

description: ChIP-Seq

value: H3K27ac (ab4729; Abcam)


title: H3K27ac_DMSO ChIP-Seq rep2

description: ChIP-Seq


title: Brd4_C646 ChIP-Seq rep2

description: ChIP-Seq

value: Brd4 (A301-985A; Bethyl)


title: Brd4_C646 ChIP-Seq rep1

description: ChIP-Seq


title: C/EBPb_ChIP-Seq rep2

description: ChIP-Seq


title: Brd4_DMSO ChIP-Seq rep2

description: ChIP-Seq


title: H3K27ac_DMSO ChIP-Seq rep1

description: ChIP-Seq


title: C/EBPa_ChIP-Seq rep1

description: ChIP-Seq


title: PolyA+_TF screening_C/EBPb

description: RNA-Seq

data_processing:
Sequenced reads were trimmed for adaptor sequence to map with mouse genome (mm9) using Tophat with default parameters.
Cufflinks software was used to compare gene expression profiles by calculting Reads Per Kilobase of exon per Megabase of library size (RPKM) for each sample.
For biological replicates of experiments, two individual shRNAs (for HAT and TF knockdown RNA-Seq) or two independent drug treated cells (for JQ1 and C646 RNA-Seq) were used to prepare total RNA.
To define the expressed genes in further analysis of PolyA+ RNA-Seq, only the genes over RPKM=1 and status=OK from Cuffdiff analysis were considered.
Processed data files contain a list of filtered genes with averaged RPKM from two biological replicates.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

extract_protocol:
Total RNAs were extracted using Trizol reagent.
These libraries were made following the instructions of illumina Truseq RNA sample prep kit v2.

treatment_protocol: To profile the basal transcription level, we performed PolyA+ (illumina TruSeq) in a murine AML RN2 cell lines. To define the genes affected by target TF knockdown, RN2 cells which express dox-inducible shRNAs were cultured with Doxycyclin for 48 hour before harvest. To define the rapid downregulated genes in response to JQ1 and C646 in RN2 cell, we performed RNA-seq in RN2 exposing to each 500nM JQ1 or 10uM C646 for 6 hour. Especially, 10uM of C646 was replenished every 2 hour with unstable nature of C646 in this culture.

tag: shRNA

value: shC/EBPb.1459 (C/EBPb_1), shC/EBPb.1460 (C/EBPb_2)


title: PolyA+_TF screening_Erg

description: RNA-Seq

value: Acute myeloid leukemia


title: PolyA+_TF screening_Pu1

description: RNA-Seq


title: PolyA+_Drug screening_C646

description: RNA-Seq

value: C646 (10uM) for 6 hours (drugs in media were changed every 2 hours)


title: Input_DMSO ChIP-Seq

description: ChIP-Seq


title: PolyA+_TF screening_Fli1

description: RNA-Seq


title: Input_C646 ChIP-Seq

description: ChIP-Seq


title: PolyA+_Drug screening_DMSO

description: RNA-Seq

value: DMSO for 6 hours


title: H3K27ac_C646 ChIP-Seq rep2

description: ChIP-Seq


title: mESC(LIF)_RNA_rep3

city: Buffalo

first: Michal

last: Stachowiak

address: 3435 Main Street

department: Pathology and Anathomical Sciences

institute: State University of New York at Buffalo

description: mESC maintained in LIF

data_processing:
Raw fastq reads were mapped to the mouse mm10 genome using TopHat-2.0.8 and Bowtie2-2.1.0 software to generate SAM files.
Mapped reads were assembled into transcripts and gene expression levels were calculated and normalized using Cufflinks version 2.0.2. Cufflinks produces Fragments Per Kilobase of transcript per million fragments mapped (FPKM), which is proportional to transcript abundance in each sample. Transcript assemblies were merged together using Cuffmerge and Cuffdiff was used to determine significant differences in gene expression (FPKM) between ESCs and RA-treated NCs
Statistics were performed in R using CummeRbund
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq.csv reports abundance measurements (FPKM)

source_name: Embryonic Stem Cells

growth_protocol: mESCs were cultured in DMEM (Corning) with 4.5 g/L glucose, L-glutamine, and sodium pyruvate supplemented with 10% (v/v) ESC-screened FBS, 100U/ml penicillin/0.1 mg/ml streptomycin, 1% (v/v) nonessential amino acids and B-mercaptenal. To maintain self-renewal and pluripotency ESCs were maintained in the presence of Leukemia Inhibitory Factor (LIF),

extract_protocol:
RNA from three sets of replicate samples were processed and analyzed separately. Total RNA for each replicate sample was isolated from two 60mm plates of ESC cultures using the Qiagen RNA extraction kit according to manufacturer’s instructions.
RNA was further prepared using the Tru-Seq RNA kit and purified library cDNA was captured on an Illumina flowcell for cluster generation and sequenced on an Illumina Hisequation 2000, following the manufacturer's protocols.

treatment_protocol: To induce differentiation towards a neuronal lineage LIF-free mESC monolayers were treated with 1 µM RA for 2 days (48 hours)

value: Pluripotent mESC (E14Tg2a)

tag: growth protocol

value: Leukemia Inhibitory Factor (LIF)

tag: passage


title: mESC(RA)_miRNA_rep3

description:
mESC withdrawal of LIF and addition of Retinoic Acid for 48 hours
microRNA

data_processing:
CLC bio workbench was used to process data and align raw sequencing reads to mature miRNA database
Statistics were performed  using Deseq
Genome_build: mm10; miRBase Release 21
Supplementary_files_format_and_content: small-RNA.csv reports abundance measurements

extract_protocol:
RNA from three sets of replicate samples were processed and analyzed separately. Total RNA for each replicate sample was isolated from two 60mm plates of ESC cultures using the Qiagen RNA extraction kit according to manufacturer’s instructions.
Libraries were constructed according to Illumina Instructions

value: mESC (E14Tg2a)

tag: treatment protocol

value: 1um Retinoic Acid (RA) for 48hrs


title: mESC(RA)_RNA_rep2

description: mESC withdrawal of LIF and addition of Retinoic Acid for 48 hours


title: mESC(LIF)_RNA_rep1

description: mESC maintained in LIF


title: mESC(RA)_RNA_rep3


title: mESC(LIF)_miRNA_rep3

description:
mESC maintained in LIF
microRNA


title: mESC(RA)_RNA_rep1


title: mESC(RA)_miRNA_rep1


title: mESC(LIF)_miRNA_rep2

description:
mESC maintained in LIF
microRNA


title: FGFR1(RA)_ChIP_Seq_Exp2

data_processing:
Raw fastq reads were aligned to the mouse genome build mm10 using Bowtie 1.0 software with the following command: bowtie –m 1 –p –q –S
All peaks were called from SAM files using Model-based Analysis of ChIP-Seq (MACS) version 2.0 (p-value < 1e-5) with the following command: macs2 callpeak –p –t –f –g –n –B. MACS2 uses a dynamic Poisson distribution to calculate peaks.
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 generated peak coordinates in narrowPeak format

extract_protocol:
mESC or neuronal cells on 100mm plates were cross-linked with 1% formaldehyde for 10 min while shaking at room temperature and rinsed three times with cold phosphate-buffered saline. Cells from five plates were pooled and harvested in phosphate-buffered saline with protease inhibitors by 10 min centrifugation at 4C. All ChIP assays were performed with 112 μg of chromatin and 3 μg of FGFR1, RXR, Nur77 or H3.3 antibodies using the Invitrogen MAGnify ChIP Kit according to manufacturer’s instructions with slight modifications. Genomic DNA was precipitated with ethanol, treated with RNase A and proteinase K, and purified using the Qiagen PCR purification kit
Chromatin was further prepared using the Tru-seq ChIP Sample Preparation Kit and purified library DNA was captured on an Illumina flowcell for cluster generation and sequenced on an Illumina Hisequation 2000, following the manufacturer's protocols.

tag: chip antibody

value: FGFR1 (Abcam, ab10646)


title: mESC(LIF)_miRNA_rep1

description:
mESC maintained in LIF
microRNA


title: PolyA+_TF screening_Rluc

description: RNA-Seq

value: shRen.713 (two independent biological replicates)


title: Nur77(LIF)_ChIP_Seq

value: Nur77(Santa Cruz, SC-5569)


title: RXRα(RA)_ChIP_Seq

value: RXR (Santa Cruz, SC-774)


title: FGFR1(RA)_ChIP_Seq


title: Nur77(RA)_ChIP_Seq


title: RXRα(LIF)_ChIP_Seq


title: PolyA+_Drug screening_JQ1

description: RNA-Seq

value: JQ1 (500nM) for 6 hours


title: FGFR1(LIF)_ChIP_Seq


title: mESC(RA)_miRNA_rep2


title: mESC(LIF)_RNA_rep2

description: mESC maintained in LIF


title: ras-minus-minus-1

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the murine genome (mm9) with BOWTIE v0.12.8.
For RNAseqs, differential expression and statistical inference was done using EdgeR.
Genome_build: mm9
Supplementary_files_format_and_content: For RNAseq, the txt-files contain tables showing the differential expression (as log FoldChange, in column) of ensemble annotated genes (ensemble gene ids, in rows) between samples (=experimental conditions) and the calculated p-value and/or adjusted p-value for each FoldChange.

growth_protocol: MEFs were grown in DMEM (Sigma) supplemented with 10% FBS (Biochrom AG) and 1% penicillin/streptomycin (Sigma).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490).
Libraries for the RNA-seq samples were constructed using the NEBNext Library Prep Kit (6100) or NEBNext Ultra RNA Library Prep Kit for Illumina (E7530) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides long fragments. First and second strand cDNA synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBNext adaptors. The cDNA was size selected using agarose gels or Agencourt AMPure XP Beads (Beckman Coulter) and amplified by PCR. For the resulting RNA-seq libraries, amplicon sizes and quantities were determined using the Biorad Experion system. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacture’s instructions.

treatment_protocol: Cells were immortalized with pRetroSuper-shp19ARF. Partly, cells were transformed with pBabe-HRasG12V and infected with pWZL-USP28 or pWZL-GFP.

value: MEF

tag: developmental stage

tag: overexpression product

value: GFP

tag: ras-transformed

value: yes

tag: replicate


title: ras-plus-plus-plus-1


title: ras-plus-plus-plus-2


title: ras-plus-plus-2


title: ras-plus-minus-2


title: minus-minus-3

value: no


title: ras-plus-plus-1


title: minus-minus-1


title: ras-plus-minus-1


title: minus-minus-2


title: plus-minus-3


title: plus-plus-3


title: plus-plus-2


title: H3.3(RA)_ChIP_Seq

value: Histone H3.3 (Abcam, ab62642)


title: plus-plus-1


title: plus-minus-1


title: II_SW13_siSUZ_6_+

city: Toronto

first: Rod

last: Bremner

state: ON

address: 600 University Ave

department: Lunenfeld-Tanenbaum Research Institute

institute: Mount Sinai Hospital

data_processing:
The fast files were obtained using Illumina CASAVA v1.8
The quality of fast reads was examined by FASTQC and low quality 5' nucleotides were removed before mapping
The trimmed fast reads were mapped on human genome (hg19) using Tophat 1.4.1
The read counts were calculated using custom R scripts to obtain exon union reads
The counts were normalized by using R package DESeq before differential expression analysis by using R package NOISeq
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include counts as gene expression of all the samples in this study, with rows named by Ensemble gene identifier and columns named as sample names.

source_name: Cell lines

extract_protocol:
RNA extraction was done using Trizol according to the manufacturer
For RNAseq library construction, Oligo-dT beads were first used to isolate poly(A)+ mRNA, after randomly fragmented, RNA fragments around 300bp were selected to prepare multiplexed cDNA libraries using Illumina TruSeq RNA Sample Preparation Kit.

value: Adrenocortical carcinoma cells

tag: treatment

value: SUZ12 siRNA with 6h IFNg


title: II_SW13_siSUZ_6_-

tag: cell type

value: SUZ12 siRNA without IFNg treatment


title: II_SW13_siCtrl_+

value: control siRNA with 6h IFNg


title: II_SW13_siCtrl_-

value: control siRNA without IFNg treatment


title: I_Panc_siSUZ_6_-

value: Pancreatic adenocarcinoma epithelial cells


title: ras-minus-minus-2


title: I_Panc_siCtrl_+


title: I_Panc_siCtrl_-


title: I_Panc_siSUZ_6_+


title: II_PC3_siSUZ_6_+

value: Prostate carcinoma cells


title: PXO99A with BLS256 Tal11b replicate 2

city: Ithaca

first: Adam

last: Bogdanove

address: 334 Plant Science Building

department: Plant Pathology and Plant-Microbe Biology

institute: Cornell University

data_processing:
Adapters were trimmed using the Trimmomatic v0.22 ILLUMINACLIP function (Bolger et al., 2014) for single end reads with seedMismatches=2, palindromeClipThreshold=30, and simpleClipThreshold=7
Low quality bases at the ends of reads were trimmed using BRAT trim v2.0.1 (Harris et al., 2010) with the parameters "-q 20 -L 33"
Reads were aligned using Tophat v2.06  with command line options '--num-threads 8 --max-intron-length 10000' and with the -G option specifying that the the MSU Release 7.0 annotation downloaded from the Rice Genome Annotation Project be used to guide transcript assembly
The number of reads aligned to each gene was determined using HTSeq-count (Anders et al., 2014) from the HTSeq framework version 0.5.4p3 with the command line options ‘-i ID -t gene -s no’
Genome_build: The Oryza sativa L. ssp. japonica (cv. Nipponbare) reference genome v.7.0 was downloaded from Phytozyme 10
Supplementary_files_format_and_content: the processed files are text tab-delimited files output by HTSeq-count with locus IDs in the first column and the number of reads aligned to each locus in the second column. The last five lines in each file don't include reads aligned to specific loci, but the number of reads in the following categories: those aligned to no annotated feature (no_feature), those that cannot be unambiguously assigend to a single feature (ambiguous), reads with an alignment quality lower than ten (too_low_aQual), reads that are not aligned (not_aligned), and reads that are aligned to multiple locations (alignment_not_unique)

organism: Oryza sativa Japonica Group

source_name: leaf tissue

growth_protocol: Oryza sativa L. ssp. japonica cv. Nipponbare plants to be inoculated were grown in LC-1 soil mixture (Sungro, Bellevue, WA) in PGC15 growth chambers (Percival Scientific, Perry, IA) in trays approximately 60 cm below a combination of fluorescent and incandescent bulbs providing approximately 1,000 μmoles/m2/s measured at 15 cm, under a cycle of 12 h of light at 28 °C and 12 h of dark at 25 °C.

extract_protocol:
RNA was extracted with the Qiagen RNeasy kit and manufacturer's protocol.
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit

treatment_protocol: Plants were inoculated at four weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.9 by infiltration using a needleless syringe. A region from the leaf tip to about 5 cm from the tip was completely infiltrated with contiguous spots. Tissue was collected individually from each leaf after 48 hours.

tag: cultivar

value: Nipponbare

tag: tissue

value: leaf

tag: pathogen

value: Xanthomonas oryzae pv. oryzae strain PXO99A with BLS256 Tal11b


title: II_PC3_siSUZ_6_-

tag: cell line


title: II_PC3_siCtrl_+


title: PXO99A with BLS256 Tal11b replicate 1


title: PXO99A with dTal280 replicate 2

value: Xanthomonas oryzae pv. oryzae strain PXO99A with dTal280


title: PXO99A with dTal280 replicate 1


title: I_Beas_siSUZ_6_+

value: Bronchial epithelial cells


title: plus-minus-2

tag: strain

value: MEF


title: PXO99A with BLS256 Tal2a replicate 2

value: Xanthomonas oryzae pv. oryzae strain PXO99A with BLS256 Tal2a


title: II_PC3_siCtrl_-


title: Brd4_DMSO ChIP-Seq rep1

description: ChIP-Seq

value: Acute myeloid leukemia

tag: genotype

tag: antibody

value: Brd4 (A301-985A; Bethyl)

value: DMSO for 2 hours


title: I_Beas_siCtrl_-


title: I_MCF_siSUZ_6_+

value: Breast cancer cells


title: I_Beas_siSUZ_6_-


title: CFBP7342 replicate 3

source_name: 48 hrs after inoculation with CFBP7342

extract_protocol:
RNA was extracted using a modified hot Trizol protocol (Huang et al., 2005) followed by treatment with RNase-free DNase I (Life Technologies, Carlsbad, CA), then purified using the RNeasy MinElute Cleanup kit (Qiagen, Valencia, CA).
These libraries were prepped with the Illumina TruSeq RNA Sample Prep v2 kit

treatment_protocol: Plants were inoculated at two weeks with bacterial suspensions in 10 mM MgCl2 at approximately OD600=0.4 or with a mock inoculum of 10 mM MgCl2, by infiltration using a needleless syringe. For each inoculum, the second and third leaves of each of four plants were infiltrated at 20 contiguous spots per leaf. From each of the eight leaves inoculated with mock inoculum or a single strain, a 12 cm length of the inoculated portion was collected after 48 hours and the tissue from all eight leaves pooled together for RNA isolation.

value: cv. Nipponbare

tag: x. oryzae pv.oryzicola strain


title: MOCK replicate 2

source_name: 48 hrs after mock-inoculation

value: none (mock control)


title: CFBP7342 replicate 2


title: I_MCF_siCtrl_+

value: control siRNA with 6h IFNg


title: I_MCF_siCtrl_-

value: control siRNA without IFNg treatment


title: CFBP7342 replicate 1


title: I_BPH_siSUZ_6_+

value: Non-transformed prostatic epithelial cells

value: SUZ12 siRNA with 6h IFNg


title: I_MCF_siSUZ_6_-

value: SUZ12 siRNA without IFNg treatment


title: I_BPH_siSUZ_6_-


title: CFBP7341 replicate 2

source_name: 48 hrs after inoculation with CFBP7341

value: leaf


title: I_BPH_siCtrl_+


title: I_BPH_siCtrl_-


title: CFBP7341 replicate 1


title: CFBP7341 replicate 3


title: I_Beas_siCtrl_+


title: MOCK replicate 3


title: PXO99A with BLS256 Tal2a replicate 1

value: Nipponbare


title: I_A549_siSUZ_6_-

value: Non-small cell lung cancer cells


title: CFBP7331 replicate 3

source_name: 48 hrs after inoculation with CFBP7331


title: CFBP7331 replicate 2


title: I_A549_siCtrl_-


title: BXOR1 replicate 3

source_name: 48 hrs after inoculation with BXOR1


title: I_A549_siSUZ_6_+


title: MOCK replicate 1


title: I_184_siSUZ_6_+

value: Breast epithelial cells


title: I_A549_siCtrl_+


title: I_184_siCtrl_+


title: I_184_siSUZ_6_-


title: RS105 replicate 3

source_name: 48 hrs after inoculation with RS105


title: I_184_siCtrl_-


title: L8 replicate 2

source_name: 48 hrs after inoculation with L8


title: RS105 replicate 2


title: I_MDA_siCtrl_+


title: I_MDA_siSUZ_6_+


title: L8 replicate 3


title: BXOR1 replicate 1


title: RS105 replicate 1


title: I_MDA_siCtrl_-


title: L8 replicate 1


title: I_Hi_siSUZ_6_+

value: Cervical cancer cells

value: HeLa


title: B8-12 replicate 2

source_name: 48 hrs after inoculation with B8-12


title: CFBP7331 replicate 1


title: B8-12 replicate 3


title: I_Hi_siSUZ_6_-


title: I_Hi_siCtrl_+


title: CFBP2286 replicate 3

source_name: 48 hrs after inoculation with CFBP2286


title: B8-12 replicate 1


title: BXOR1 replicate 2


title: CFBP2286 replicate 2


title: I_AsP_siSUZ_6_+

value: Pancreatic adenocarcinoma cells


title: I_AsP_siSUZ_6_-


title: I_AsP_siCtrl_+


title: I_MDA_siSUZ_6_-


title: BLS279 replicate 1

source_name: 48 hrs after inoculation with BLS279


title: BLS279 replicate 2


title: I_AsP_siCtrl_-


title: BLS256 replicate 3

source_name: 48 hrs after inoculation with BLS256


title: BLS256 replicate 2


title: BLS256 replicate 1