title: WIBR2_6i/L/A_input

first: Rudolf

last: Jaenisch

state: MA

address: 9 Cambridge Center

department: Biology

institute: MIT/Whitehead Institute

description: Chromatin input in naive condition

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best. Seed length (-l) was set to read length for each dataset.
Genome_build: hg19
Supplementary_files_format_and_content: For all samples, aligned sequences were extended automatically by MACS and allocated into 50bp bins. Normalized read counts (Reads per million mapped reads per basepair) in 50bp are shown.

source_name: Embryonic stem cells

growth_protocol: Primed WIBR2 human ESCs were cultured on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers in primed human ESC medium (hESM) and passaged enzymatically by treatment for 20 minutes with 1 mg/mL Collagenase Type IV (Gibco) followed by sequential sedimentation steps in human ESC medium to remove single cells. Converted naive WIBR2 human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged every 5-7 days by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium. See the manuscript for composition of primed hESM and naive 5i/L/A and 6i/L/A culture media. Note that these WIBR2 naive human ESCs were initially converted from the primed state in 5i/L/A and supplemented with a JNK inhibitor (6i/L/A) (P18)

extract_protocol: Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: All samples were briefly washed in PBS, dissociated to single cells using trypsin, and 10 million naive or primed human ESCs were purified from GFP-labeled MEFs using the FACSAria (Beckton-Dickinson) prior to lysis and RNA extraction.

value: None, input


title: WIBR2_hESM_input

status: Public on Jul 16 2014

type: SRA

city: Cambridge

country: USA

description: Chromatin input in primed condition

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: chip antibody


title: Osteoblast growth on culture_Normal-Sample_NHOst5

city: Atlanta

first: Monica

middle: L.

last: Rojas-Peña

state: GA

address: 310 Ferst Dr.

department: School of Biology

institute: Georgia Institute of Technology

library_source: transcriptomic

data_processing:
The raw RNA-Seq reads for each sample were aligned to the reference human genome (hg19) using Bowtie as the short read aligner, and splice junctions were identified using TopHat
Raw sequence read depths were converted to estimated transcript abundance measures as fragments per kilobase of exons per million (FPKM) values using Cufflinks
All genes with an FPKM greater than 2 averaged across all 31 samples were retained, representing 8025 genes
FPKM values were transformed to logarithm base 2 and normalized using the supervised normalization of microarray (SNM) procedure with the R package from Bioconductor
Genome_build: hg19
Supplementary_files_format_and_content: excel file include normalize expession values matrix for all samples

molecule: total RNA

source_name: Osteoblast growth in culture from long bone

growth_protocol: Upon removal from the cranial vault, bone pieces were immediately placed in Dulbecco’s modified Eagle’s medium supplemented with 3% penicillin-streptomycin. Pieces were incubated in 0.25% trypsin-EDTA for 15 minutes to remove contaminating fibroblasts. Osteoblasts from normal bone or fused suture were cultured from 1mm2 bone pieces using the explant technique.

extract_protocol:
Total RNA was extracted from Whole peripheral blood using Tempus Spin RNA Isolation kit. Quality control was performed using Agilent's Bioanalyzer.
Illumina RNA seq kit was used for sequence library preparation using the Illumina TruSeq RNA Sample Prep Guide: Low Throughput (LT) Protocol.

tag: gender

value: Female

tag: age (months)

tag: fusion type


title: Osteoblast growth on culture_Normal-Sample_29

source_name: Osteoblast growth in culture from skull


title: Osteoblast growth on culture_Normal-Sample_21N

value: Male


title: Osteoblast growth on culture_Normal-Sample_NHOst2


title: Control_A1

city: Cork

first: Roman

middle: M

last: Stilling

address: Western Road

department: Anatomy and Neuroscience

country: Ireland

institute: University College Cork

data_processing:
Base calling was achieved through Illumina's CASAVA pipeline.
Alignment was achieved using BLAST against the miRBase database
Small RNAs were then counted and microRNAs compared using Excel
Genome_build: miRBase release 20
Supplementary_files_format_and_content: CA1_smallRNAome.xls, Excle sheet, Counted reads for each sample

organism: Mus musculus

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the suppliers manual. Following DNase1 (life Technologies) treatment for 20 min at 37 °C, RNA was again purified using phenol-chloroform extraction.
Library was constructed using standard Illumina smallRNA sequencing kits. The size of the band excised from the gel was 150bp.

tag: strain background

tag: genotype/variation

tag: age

value: 3-5 months

tag: tissue

value: dissected CA1 hippocampal subfield


title: Kat2a_cKO_novelty-exposed_D3

description:
processed data file: FilteredDifferentialExpression_min_10reads_C-D.txt
processed data file: FilteredDifferentialExpression_min_10reads_B-D.txt

data_processing:
Base calling was achieved through Illumina HiSeq2000 standard pipeline
Alignment was achieved by using STAR aligner version 2.3.0 with following non-default parameters: --outFilterMismatchNmax 2,  --outSAMstrandField intronMotif
Read counting in genes was achieved using HTSeq with the following non-default parameters:  -m intersection-nonempty, –stranded=no
Differential expression calling for pairwise comparisons was done using DESeq2 with the following non-default parameters: cooksCutoff=FALSE
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: *geneCounts.txt: tab delimited text file with read counts
Supplementary_files_format_and_content: FilteredDifferentialExpression*.txt - tab delimited text file with expression values, fold change, p-values and gene annotation

molecule: polyA RNA

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the suppliers manual. Following DNase1 (life Technologies) treatment for 20 min at 37 °C, RNA was again purified using phenol-chloroform extraction.
Library preparation and cluster generation for mRNA sequencing was performed according to Illumina standard protocols using the TruSeq RNA Sample Prep Kit v2 and the TruSeq Paired-End Cluster Generation Kit v3-cBot-HS (for PE mRNA-seq) with subsequent use of the corresponding TruSeq Cluster Generation Kit 3-cBot-HS (for SE mRNA-seq). Libraries were quality controlled and quantified using a Nanodrop 2000 (Thermo Scientific), an Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit (life Technologies).

tag: strain

value: Kat2afl/fl ; CamKII_alpha-cre+

tag: exposure

value: 15 min novetlty exposure


title: Osteoblast growth on culture_Normal-Sample_1


title: Kat2a_cKO_novelty-exposed_D5


title: Kat2a_cKO_novelty-exposed_D6


title: Osteoblast growth on culture_Normal-Sample_NHOst3


title: Osteoblast growth on culture_Normal-Sample_NHOst1


title: Osteoblast growth on culture-Sample_33

value: SAGITAL


title: Osteoblast growth on culture-Sample_32


title: Osteoblast growth on culture_Normal-Sample_NHOst6


title: Kat2a_cKO_novelty-exposed_D4


title: Osteoblast growth on culture-Sample_28


title: Osteoblast growth on culture-Sample_30


title: Kat2a_cKO_novelty-exposed_D1


title: Osteoblast growth on culture-Sample_27

value: LAMBDOID


title: Osteoblast growth on culture-Sample_25


title: Kat2a_cKO_naive_C6

description:
processed data file: FilteredDifferentialExpression_min_10reads_C-D.txt
processed data file: FilteredDifferentialExpression_min_10reads_A-C.txt


title: Kat2a_cKO_naive_C5


title: Kat2a_cKO_naive_C4


title: Osteoblast growth on culture-Sample_23-2

value: CORONAL


title: Kat2a_cKO_novelty-exposed_D2


title: Osteoblast growth on culture-Sample_21


title: Control_A2


title: Osteoblast growth on culture-Sample_18


title: Osteoblast growth on culture-Sample_19


title: Osteoblast growth on culture-Sample_20


title: Osteoblast growth on culture-Sample_16


title: Osteoblast growth on culture-Sample_13


title: Osteoblast growth on culture-Sample_10

value: METOPIC


title: Kat2a_cKO_naive_C3


title: Osteoblast growth on culture-Sample_17


title: Kat2a_cKO_naive_C1


title: Osteoblast growth on culture-Sample_9-1


title: Control_novelty-exposed_B5

description:
processed data file: FilteredDifferentialExpression_min_10reads_A-B.txt
processed data file: FilteredDifferentialExpression_min_10reads_B-D.txt


title: Control_novelty-exposed_B4


title: Kat2a_cKO_naive_C2


title: Osteoblast growth on culture-Sample_7


title: Osteoblast growth on culture-Sample_11


title: Osteoblast growth on culture-Sample_2-3


title: Osteoblast growth on culture-Sample_34


title: Osteoblast growth on culture-Sample_24


title: Control_novelty-exposed_B3


title: Osteoblast growth on culture-Sample_6


title: TARBP2_CLIP_rep2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: TARBP2 co-immunoprecipitated RNA

data_processing:
Library strategy: HITS-CLIP
After linker sequence removal and quality trimming, sequence mapping was performed using Bowtie with default parameters (build hg19).
ChIPseeqer (strand-specific) was then used to identify the TARBP2 CLIP reads (Giannopoulou et al, BMC Bioinformatics 2011, 12:277). Tags between the replicates were then overlapped between the two biological replicates.
TARBP2 binding sites were then used to generate shuffled sequences, based on a 1st order Markov model (built-in ChIPseeqer function), for further comparisons.
Genome_build: hg19
Supplementary_files_format_and_content: .bed file with the identified TARBP2 binding sites along with their shuffled controls

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
48 hours post-transfection, cells were UV cross-linked and prepared as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).
Samples were prepared for sequencing as described previously (Licatalosi D, et al. 2008, Nature 456:464-U22).

treatment_protocol: Cells were treated with a tagged TARBP2 vector (Origene) using TransIT reagent (MirusBio) per manufacturer's instructions.

tag: cell line

tag: transient transfection

value: myc-tagged TARBP2 vector

tag: rep

tag: antibody

value: anti-myc Tag, clone 4A6 (Millipore, catalog#:05-724, lot#:JBC1868960)


title: Control_novelty-exposed_B2


title: LM2_7hr_2_2_RNA-seq

description:
4sU labeled/precepitated RNA
processed data file: LM2_decay_rates.txt
processed data file: MDA-LM2_differential_stability.txt

data_processing:
Sequence mapping was performed using TopHat with default parameters (build hg18).
Cufflinks, cuffmerge and cuffcompare were used to calculate FPKMs for annotated transcripts.
For each transcript, FPKM values at every time-point were used to calculate a decay rate based on an exponential decay model.
For each transcript, four independent decay rates were measured in MDA-MB-231 cells and four in MDA-LM2 cells. A t-test based score was used to measure differential decay rates for each transcript across the two cell-lines.
Genome_build: hg18
Supplementary_files_format_and_content: Tab delimited files (linked as supplementary files on the Series record) listing the estimated decay rates along with final differential decay rate scores.

extract_protocol:
Total RNA was extracted, labeled and precipitated at 0, 2, 4 and 7 hr as described before (Dolken L, et al. 2008, RNA 14(9):1959-1972)
Samples were prepared for RNA-seq using ScriptSeq V2 (Epicentre) per manufacturers instructions.

treatment_protocol: Cells were treated with 4sU for 2-hours. After the pulse-period, the media was replaced with fresh media plus excess Uridine.

tag: time-point


title: LM2_7hr_2_1_RNA-seq


title: LM2_7hr_1_2_RNA-seq


title: LM2_7hr_1_1_RNA-seq


title: Control_naive_A6

description:
processed data file: FilteredDifferentialExpression_min_10reads_A-B.txt
processed data file: FilteredDifferentialExpression_min_10reads_A-C.txt


title: Control_novelty-exposed_B1


title: Osteoblast growth on culture-Sample_8-2


title: LM2_4hr_2_1_RNA-seq


title: TARBP2_CLIP_rep1

description: TARBP2 co-immunoprecipitated RNA


title: Control_naive_A4


title: LM2_4hr_2_2_RNA-seq


title: LM2_2hr_2_2_RNA-seq


title: LM2_2hr_1_2_RNA-seq


title: LM2_4hr_1_2_RNA-seq


title: LM2_2hr_2_1_RNA-seq


title: Control_naive_A3


title: LM2_2hr_1_1_RNA-seq


title: LM2_4hr_1_1_RNA-seq


title: LM2_0hr_2_1_RNA-seq


title: MDA_7hr_2_2_RNA-seq

description:
4sU labeled/precepitated RNA
processed data file: MDA_decay_rates.txt
processed data file: MDA-LM2_differential_stability.txt


title: LM2_0hr_2_2_RNA-seq


title: LM2_0hr_1_2_RNA-seq


title: LM2_0hr_1_1_RNA-seq


title: Control_naive_A2


title: MDA_7hr_2_1_RNA-seq


title: Control_naive_A5


title: MDA_4hr_2_1_RNA-seq


title: MDA_4hr_1_2_RNA-seq


title: MDA_7hr_1_2_RNA-seq


title: MDA_4hr_2_2_RNA-seq


title: MDA_2hr_2_2_RNA-seq


title: MDA_4hr_1_1_RNA-seq


title: MDA_2hr_2_1_RNA-seq


title: MDA_0hr_2_1_RNA-seq


title: MDA_0hr_1_2_RNA-seq


title: MDA_2hr_1_1_RNA-seq


title: MDA_0hr_2_2_RNA-seq


title: MDA_2hr_1_2_RNA-seq


title: MDA_0hr_1_1_RNA-seq


title: meDIP-seq_data_CTRL2

first: Hui

last: Shi

address: Downing Street

department: Department of Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

data_processing:
preprocessing of the raw reads were performed using FastQC and TrimGalore to remove poor quality bases and adapter sequences
reads post-QC were mapped to mouse reference genome NCBIM37/mm9 using BWA v0.6.2
mapped reads were subject to further QC by SAMtools to remove unmapped, unpaired reads and reads with mapping quality score less than 10
differentially methylated regions (DMRs) were identified using MEDIPS
DNA methylation levels across the whole genome were assessed using sliding windows (size 500bp and 200bp to shift the window)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files, scores represent methylation levels

source_name: Sperm

growth_protocol: Sperm was isolated from 2 month old male offspring of control dams or dams undernourished by 50% during the last week of gestation.

extract_protocol:
Sperm DNA was extracted by standard phenol-chloroform extraction, with an overnight proteinase K reaction at 55 degrees.
DNA was sonicated, paired end adaptors ligated and 12 cycles of whole-genome amplification employed using PhusionTM High-Fidelity Taq and paired end Illumina primers.  Libraries were electrophoresed in 2% 1x TAE agarose gels at 95V in 1x TAE buffer followed by excision of a 200bp range band either 200-400bp to 300-500bp according to the peak fragment size.  Identical size ranges were obtained for control and UN libraries.  qPCR for known methylated and unmethylated regions confirmed library quality.

treatment_protocol: Serial centrifugations were used to purify sperm from potential contaminating cells (such as epithelium or white blood cells).

value: ICR

value: anti-5methyl-cytosine antibody

value: two month

tag: treatment

value: control dams


title: Control_naive_A1


title: SVZ RNA-Seq

city: San Antonio

first: Chin-Hsing Annie

last: Lin

state: TX

address: One UTSA Circle

institute: University of Texas at San Antonio

description:
SVZ_1
Subventricular zone primary cells.

data_processing:
Basecalls were performed with Illumina RTA version 1.12.4.2.
Reads were aligned to the hg19 genome with Tophat 2.0.11.
Alignments were processed with Cufflinks 2.0.2.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited cufflink output file includes gene id, TSS id, locus genomic coordinates, and FPKM for each Sample.

organism: Papio anubis

source_name: neural progenitor cells

extract_protocol:
Total RNA was extracted from purified baboon SVZ cells using TRIzol reagent.
Sequencing libraries were generated with Illumina RNA-Seq library kit, Illumina TruSeq v2.

value: brain

tag: region

value: subventricular zone

tag: developmental stage

value: adult


title: HdhQ150_1_22wk

status: Public on Jul 15 2014

city: London

first: Michal

last: Mielcarek

state: London

address: Great Maze Pond

department: Molecular and Medical Genetics

institute: King's College London

data_processing:
Reads aligned to genome (Mouse.B37) using OSA2 algorithm
Gene models were dervived from RefGene20121217
Fragments per kilobase of exon per million fragments mapped (FPKM) were calculated as in Mortazavi, Nature Methods (2008)
Genome_build: Mouse.B37

source_name: Heart

extract_protocol:
Total RNA from whole hearts was extracted with the mini-RNA kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: (CBA x C57BL/6) F1

value: Heart

tag: genotype


title: HdhQ150_4_22wk


title: mVes

city: Sao Paulo

first: Ethel

last: Bayer-Santos

state: SP

address: 862 Botucatu

department: Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de Sao Paulo

data_processing:
Raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software, following sequencing image analysis by pipeline Firecrest module and base-calling by pipeline Bustard module.
Sequencing data analysis was performed by a proprietary pipeline script (LC Sciences).
Supplementary_files_format_and_content: fasta files with read counts

organism: Trypanosoma cruzi

source_name: metacyclic trypomastigote-derived extracellular vesicles

growth_protocol: Epimastigotes were maintained by cyclic passage in mice and axenic cultures in liver-infusion tryptose (LIT) medium containing 10% fetal bovine serum (FBS) at 28 °C. To obtain the parasite conditioned medium (CM), epimastigotes were harvested from exponentially growing cultures, washed in Dulbecco’s modified Eagle medium (DMEM)  without FBS and incubated in the same medium at a concentration of 1 × 108 cells/mL for 6 h at 28 °C. Metacyclic trypomastigote forms were obtained by induction of metacyclogenesis according to Contreras et al. (1988), purified by anionexchange chromatography and incubated in TAU3AAG medium at a concentration of 1 × 108 cells/mL for 12 h at 28 °C.

extract_protocol:
After the incubation, cells were removed by centrifugation at 3,000 × g for 10 min, and the supernatant was filtered in 0.45-µm syringe filters and ultracentrifuged at 100,000 × g for 2 h. The pellets containing extracellular vesicles were mixed with 1 mL of Tri Reagent (Sigma).
Small RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: Stage

value: metacyclic trypomastigote

value: extracellular vesicles


title: eVes

value: epimastigote


title: SVZ H3K4me3 ChIP-Seq

description:
SVZ H3K4me3
Subventricular zone primary cells.

data_processing:
Basecalls were performed with Illumina RTA version 1.12.4.2.
Reads were aligned to the Rhesus Macaque reference rheMac2 with Bowtie version 0.12.7 using the following parameters: bowtie -p 8 --mm -n 2 -m 1 --best --phred33-quals.
FDR 1% Peaks were called with the HotSpot program: http://www.uwencode.org/proj/hotspot/ using the default configuration.
Genome_build: Mmul_051212 (rheMac2)
Supplementary_files_format_and_content: Bed file containing ChIP-Seq peak calls generated from HotSpot, with FDR = 0.01.

source_name: neural progenitors cells, H3K4me3 ChIP

extract_protocol:
We manually conjugated antibody against cell type markers, such as GFAP, Nestin, Vimentin, PSA-NCAM, or Doublecortin to Dynabeads. We then used the Dynabeads-conjugated antibody to purify cells dissociated from SVZ microdissection. Briefly, cells from fresh dissected baboon SVZ were immediately dissociated with Accutase, equilibrated in binding buffer containing phosphate-buffered saline (PBS), 0.05% TritonX-100 (or saponin, detergent choice depends upon antibody), and subsequently subjected to Dynabeads-conjugated antibody purification. After elution with high salt and pH-gradient buffer, the purified populations were crosslinked in 1.1% formaldehyde before chromatin shearing by Diagenode Bioruptor. The resulting sheared chromatin fragments in a size range between 200 to 500 base pairs were incubated with H3K4me3 antibody-conjugated Protein A Dynabeads (Millipore #07-473, lot# 2289139, 1:1000; Active Motif #39160, 1:500; Life Technology Dynabeads protein A) overnight. For normalization, the aliquot of sheared chromatin fragments were incubated with antibody against total histone 3-conjugated Protein A Dynabeads (unmodified H3 antibody, Millipore #05-499; 1:1000). Subsequently, enriched chromatin fragments were eluted, subjected to de-crosslink.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina TruSeq v2.

tag: chip antibody


title: HdhQ150_2_22wk


title: WT1_22wk

value: WT


title: meDIP-seq_data_UN2

value: dams undernourished by 50% during the last week of gestation


title: SVZ Total H3 ChIP-Seq

description:
SVZ Total H3
Subventricular zone primary cells.

source_name: neural progenitors cells, total H3 ChIP

value: anti-histone H3


title: WT2_8wk


title: HdhQ150_3_22wk


title: WT3_8wk


title: HdhQ150_2_8wk


title: WT2_22wk


title: WT4_8wk


title: WT2_4wk


title: mCell

source_name: metacyclic trypomastigote parental cells

value: parental cells


title: R6_2_1_4wk


title: WT1_8wk


title: WT3_22wk


title: R6_2_4_4wk


title: MDA_7hr_1_1_RNA-seq


title: WT4_4wk


title: R6_2_3_4wk


title: HdhQ150_3_8wk


title: R6_2_2_15wk


title: WT4_15wk


title: WT2_15wk


title: R6_2_4_15wk


title: WT1_15wk


title: WT_24h_3

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: RNAseq data

data_processing:
RTA (Illumina) is used for base calling and CASAVA (version 1.8.2) for converting BCL to fastq format, coupled with adaptor trimming.
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat (version 2.0.4) infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Relative abundance (aka expression level) of genes and splice isoforms is estimated using cufflinks 2.0.2 with default settings.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: TXT files and reads

source_name: Splenic B lymphocytes

growth_protocol: 10% FBS in RPMI and anti-CD40 and anti-IgM antibodies for 24 hours.

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
poly-A pull-down were used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). For library preparation, the Illumina TruSeq RNA prep kit was used. Libraries were sequenced on the Illumina HiSeq2000 at the Columbia University Genome Center. Samples were multiplexed in each lane, which yields the targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice isolate by magnetic cell separation from splenic mononuclear cells and stimulated with anti-CD40 and anti-IgM for 24 hours.

tag: cell type

value: MACS-purified B cells

tag: stimulated

value: CD40+IgM in vitro activated (24h)


title: REL_24h_3

description: RNAseq data

tag: genotype/variation


title: REL_24h_1

description: RNAseq data


title: REL_24h_2

description: RNAseq data


title: R6_2_1_15wk

tag: tissue

tag: age


title: WT_24h_1

description: RNAseq data


title: RELA_6h_3

description: RNAseq data

growth_protocol: 10% FBS in RPMI and anti-CD40 and anti-IgM antibodies for 6 hours.

treatment_protocol: Splenic B cells from 12-week old relafl/flCD19-Cre and CD19-Cre littermate mice isolate by magnetic cell separation from splenic mononuclear cells and stimulated with anti-CD40 and anti-IgM for 6 hours.

value: CD40+IgM in vitro activated (6h)


title: WT_24h_2

description: RNAseq data


title: RELA_6h_2

description: RNAseq data


title: WT3_4wk

tag: strain


title: RELA_6h_1

description: RNAseq data


title: A WT_6h_3

description: RNAseq data


title: A WT_6h_2

description: RNAseq data


title: REL_6h_3

description: RNAseq data

treatment_protocol: Splenic B cells from 12-week old relfl/flCD19-Cre and CD19-Cre littermate mice isolate by magnetic cell separation from splenic mononuclear cells and stimulated with anti-CD40 and anti-IgM for 6 hours.


title: R6_2_3_15wk


title: A WT_6h_1

description: RNAseq data


title: WT_6h_3

description: RNAseq data


title: REL_6h_2

description: RNAseq data


title: WT_6h_2

description: RNAseq data


title: WT3_15wk


title: REL_6h_1

description: RNAseq data


title: WT1_4wk


title: WT_6h_1

description: RNAseq data


title: Undifferentiated C2C12 Si-RbFox2 (Bio-rep2)

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 3181 SW Sam Jackson Park Rd

department: Department of Biomedical Engineering

institute: Oregon Health & Science University

data_processing:
aligned to the reference genome using TopHat 2.0.5 with provided Ensembl GTF gene annotation
Calculate the coverage bedGraph file based on Aligned BAM files using tool wiggles from TopHat package
Genome_build: mm9
Supplementary_files_format_and_content: Read coverage bedGraph files

source_name: C2C12 myoblast cell line

growth_protocol: C2C12 cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM), 10% FBS with 2 mM L-Glutamine and 0.01% Penicillin and streptomycin (growth media). For differentiation, cultures at >90% confluency are placed in differentiation media (growth media with 2% horse serum replacing FBS).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SiRNAs (50-100 nM) were delivered once either by electroporation using Neon transfection system or by RNAiMax transfection reagent (Life Technologies) according to manufacturer’s protocol.

tag: cell line


title: Undifferentiated C2C12 Si-RbFox2 (Bio-rep1)


title: Undifferentiated C2C12 Si-Ctrl


title: Differentiated C2C12 Si-RbFox1 (Bio-rep1)

tag: differentiation

value: harvested 4 days following differentiation induction


title: Differentiated C2C12 Si-RbFox1 (Bio-rep2)


title: Differentiated C2C12 Si-RbFox2 (Bio-rep3)


title: Differentiated C2C12 Si-RbFox2 (Bio-rep2)


title: Differentiated C2C12 Si-RbFox2 (technical-rep)


title: Differentiated C2C12 Si-Control (Bio-rep1)


title: Differentiated C2C12 Si-RbFox2 (Bio-rep1)


title: H2B_ChIP-seq

city: Tel Aviv

first: Dror

last: Hollander

address: Ramat Aviv

department: Department of Human Molecular Genetics & Biochemistry, Sackler Faculty of Medicine

country: Israel

institute: Tel Aviv University

description: Sample 2

data_processing:
All ChIP-seq data were aligned to the hg18 human genome assembly using Bowtie (Langmead et al. 2009) while allowing for 1 mismatch per read, and only uniquely mapped reads were used for further processing.
ChIP-seq peak enrichment and annotation analyseis wereas carried out using HOMER (Heinz et al. 2010).
All other analyses were carried out using a custom PERL and R pipeline. Briefly, gene and exon annotations were derived from hg18 RefSeq gene annotations downloaded from the UCSC Genome Browser (Rhead et al. 2010). Single base pair resolution maps were constructed for each mapped ChIP-seq dataset, cast upon the examined genomic segments in each analysis, and plotted with or without applying a moving average to smooth the signal, as specified throughout the text. When scaled to fit a set size, all examined genes or introns shorter than the set size were discarded. All sequences were aligned to the plus strand.
Genome_build: hg18
Supplementary_files_format_and_content: the tsv files containing 5 data columns (chr, position, strand, No. of reads, and length of the reads)

source_name: human embryonic carcinoma cells

growth_protocol: Ntera2/D1 cells were grown in RPMI supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM Sodium Pyruvate, 0.1mM nonessential amino acid and penicillin-streptomycin antibiotics solution

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

value: human embryonic carcinoma cells

tag: chip antibody ref.

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #


title: H2Bub1_ChIP-seq

description: Sample 1

value: Minsky et al., 2008


title: HdhQ150_1_8wk


title: Hutchesen Low VPD sample 2

city: Raleigh

first: Elizabeth

middle: H

last: Scholl

state: NC

address: 1 Lampe Drive, CB 7566, Ricks Hall

department: BRC

institute: NC State University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were de-mutliplexed, screened for quality, and aligned to the reference genome using tophat2 with the Glycine max annotation file from UCSC as a guide
Fragments Per Kilobase of Exon per million fragments mapped (FPKM) was calculated using the Tuxedo pipeline. Reads were mapped to the reference genome and transcripts discovered were recorded for each of the 12 samples. Transcript annotations were merged, and count information and library size used to generate a normalized estimate of abundance. Log2 ratios were used to test for significant differences in expression levels, with p-values corrected for multiple testing.
Genome_build: Gmax_109
Supplementary_files_format_and_content: tab-delimited text files containing the fpkm, test status, p-value and q-value for each experiment are included.

organism: Glycine max

source_name: Glycine max leaf tissue

growth_protocol: Plants grown in plant growth chamber

extract_protocol:
Quiagen Column
TruSeq

treatment_protocol: Low- and High- Vapor Pressure Deficit of Detached Leaf

tag: phenotype

value: fast wilting

tag: cultivar

value: Hutchesen

tag: treatment

value: low vapor pressure


title: PI471938 High VPD sample 2

value: slow wilting

value: high vapor pressure


title: PI471938 Low VPD sample 2


title: Hutchesen Low VPD sample 1


title: PI416937 Low VPD sample 2


title: Hutchesen High VPD sample 2


title: Hutchesen High VPD sample 1


title: PI471938 High VPD sample 1


title: PI416937 High VPD sample 2


title: PI416937 Low VPD sample 1


title: mir217Tg_CD19_FasGl7_R2

city: Madrid

first: Almudena

last: Ramiro

address: Melchor Fernandez Almagro 3

department: Vascular Biology and Inflammation

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares

description: Replicate 2

data_processing:
Sequenced reads were trimmed for adaptor sequence and filtered the ones with a quality less than 20% over the 80% of nt and more than 5 Ns
Mapped to mm9 whole genome using tophat v2.0.7
Number of reads falling in the genes calculated using htseq-count version 0.5.3p9 over the mm9 gtf file from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include number of reads per gene for each Sample

source_name: GC (CD19+Fas+GL7+) B cells from miR-217TG

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen). RNA samples were first processed through the "Ovation RNA-seq system" (NuGEN) and then retrotranscribed, and cDNA was amplified by the SPIA isothermal linear amplification procedure. The resulting ds-cDNA was fragmented to a range of 150-200bp in a Covaris S2 shearing instrument
cDNA (200ng of per sample) was processed through succeeding enzymatic treatments of end-repair, dA-tailing, and ligation to indexed adapters, according to "TruSeq DNA Sample Preparation Guide" (Illumina). Ligation products were purified with AMPure XP Beads. Adapter-ligated libraries were amplified by PCR with Illumina PE primers for 10 cycles. The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation, and sequenced on the Illumina Genome Analyzer IIx with SBS TruSeq v5 reagents. Image analysis and per-cycle basecalling were performed with Illumina Real Time Analysis software (RTA1.9)

value: GC (CD19+Fas+GL7+) B cells


title: mir217Tg_CD19_FasGl7_R1

description: Replicate 1


title: mir217Tg_CD19_DN_R2

description: Replicate 2

source_name: naïve (CD19+Fas-GL7-) B cells from miR-217TG

value: naive (CD19+Fas-GL7-) B cells


title: control_CD19_FasGl7_R1

description: Replicate 1

source_name: GC (CD19+Fas+GL7+) B cells from littermate controls

value: littermate controls


title: control_CD19_FasGl7_R2

description: Replicate 2


title: Donor G, DC 14

first: Randy

last: Longman

address: 1315 York Avenue

department: Medicine

institute: Weill Cornell Medical College

data_processing:
Sequence reads were mapped to the human genome (version  hg19) by Tophat (version 2.0.6), using Bowtie2 (version 2.0.2) and Samtools (version 0.1.18).
Reads mapped per transcript served as input to DESeq (version 1.12.0), an R package that calculates differential gene expression
To improve detection of APC lineage-dependent gene-expression changes and overcome donor-dependent variability, we used the following strategy:  independently for each donor, differential gene expression, comparing CD103+ to CD14+ human myeloid cells, was estimated using the negative binomial distribution (“nbinomTest”), and then results from biological replicates were combined using Fisher’s method.
Genome_build: hg19
Supplementary_files_format_and_content: For each donor/sample, DESeq normalized counts are listed, followed by differential expression data (raw p values, adjusted p value and log (fold change) processed for each donor

source_name: Sorted from human intestinal colon

extract_protocol:
Trizol extraction for total RNA as per manufacturer's protocol
Nugen and Nextera kits

value: CD14+ myeloid cells

tag: mnp type

value: DC 14

tag: donor

value: G


title: RI-EIP1

city: Ann Arbor

first: Xiaoju

last: Wang

state: MI

address: 1500 E. Medical Center Drive

institute: University of Michigan

data_processing:
Basecalls performed using CASAVA version 1.4
Reads were aligned to HG19 using Bowtie2
Coverage files were generated using Bedtools
BigWig files were generated using bedGraphToBigWig
Genome_build: hg19

source_name: Prosate cancer cells

growth_protocol: Cells were grown in DMEM containing 10% FBS

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight followed by wash and reversal of cross-linking.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).

treatment_protocol: VCaP cells were treated with 50 µM peptide inhibitors for 12hrs.

value: vertebral metastatic lesion derived prostate cancer cells

value: VCaP

tag: chip antibody

value: ERG (Epitomics, 2805-1)

value: functional form of the peptide (*ERG inhibitory peptidomimetics*)


title: mir217Tg_CD19_DN_R1

description: Replicate 1

tag: cell type


title: PI471938 Low VPD sample 1


title: Donor H, DC 14

value: H


title: Donor H, DC 103

value: CD103+ myeloid cells


title: Donor G, DC 103


title: RI-muEIP1

value: mutational form of the peptide (*ERG inhibitory peptidomimetics*)


title: 152

city: Solna

first: Joakim

last: Lundeberg

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH-Science for Life Laboratory

description: Sample 23

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
The paired-end reads were trimmed with respect to quality and remaining adapter sequences using Trim Galore and aligned to the human genome reference hg19 (ENSEMBL v71) with TopHat version 2.0.4
The aligned reads were assembled into transcripts using Cufflinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include output from Cufflinks for each Sample 1-24

source_name: skeletal muscle

extract_protocol:
Trizol® method
RNA libraries were prepared for sequencing using standard Illumina protocols for paired end sequencing and clustered on cBot

value: skeletal muscle

tag: gender

value: female

tag: exercise status

value: untrained

tag: biopsy location

value: right leg

tag: original sample id

tag: sample id (used in publication)


title: PI416937 High VPD sample 1

value: slow wilting

value: high vapor pressure


title: 234

description: Sample 22

tag: tissue

value: male

value: left leg


title: 172

description: Sample 21


title: 224

description: Sample 24


title: control_CD19_DN_R2

description: Replicate 2

source_name: naïve (CD19+Fas-GL7-) B cells from littermate controls

value: naive (CD19+Fas-GL7-) B cells

tag: genotype/variation

value: littermate controls


title: 232

description: Sample 18


title: 157

description: Sample 19


title: 231

description: Sample 14


title: 205

description: Sample 13


title: 130

description: Sample 15


title: 228

description: Sample 12


title: 211

description: Sample 17


title: control_CD19_DN_R1

description: Replicate 1


title: 229

description: Sample 16


title: 233

description: Sample 20


title: 226

description: Sample 8


title: 169

description: Sample 9


title: 223

description: Sample 11


title: 113

description: Sample 7


title: 230

description: Sample 6


title: 135

description: Sample 5


title: 235

description: Sample 4


title: 217

description: Sample 1


title: 174

description: Sample 3


title: 225

description: Sample 2


title: 31T1B

description: Sample 21

data_processing:
Bcl to Fastq conversion was performed using bcl2Fastq v1.8.3 from the CASAVA software suite
The paired-end reads were trimmed with respect to quality and remaining adapter sequences using Trim Galore and aligned to the human genome reference hg19, ENSEMBL v71 with TopHat version 2.0.4
The aligned reads were assembled into transcripts using Cufflinks version 2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include output from Cufflinks for each Sample 1-23


title: 31U1B

description: Sample 23


title: 30U1B

description: Sample 19


title: 30U1A

description: Sample 18


title: 29U1B

description: Sample 15


title: 30T1B

description: Sample 17


title: 29T1B

description: Sample 13


title: 227

description: Sample 10


title: 30T1A

description: Sample 16


title: 29T1A

description: Sample 12


title: 10U1B

description: Sample 7


title: 17U1A

description: Sample 10


title: 10U1A

description: Sample 6


title: 17U1B

description: Sample 11


title: 10T1A

description: Sample 4


title: 17T1A

description: Sample 8


title: 10T1B

description: Sample 5


title: 17T1B

description: Sample 9


title: 29U1A

description: Sample 14


title: 6U1B

description: Sample 3


title: 6U1A

description: Sample 2


title: 6T1A

description: Sample 1


title: Differentiated C2C12 Si-Control (Bio-rep2)

tag: differentiation

value: harvested 4 days following differentiation induction

tag: cell line


title: 31U1A

description: Sample 22


title: 31T1A

description: Sample 20


title: STAT6KO-ALUM-KP

status: Public on Jul 14 2014

city: Nashville

first: Daniel

middle: E

last: Dulek

state: TN

address: D-7235 Medical Center North, 1161 21st Avenue South

department: Pediatrics

institute: Vanderbilt University Medical Center

description: KOalum6_vs_KOova6_gene_exp_significant.diff

data_processing:
TopHat 2.0.9, for reads alignment, command line with parameter is, tophat2 --segment-length 25 -r 123 -G /path_to_annotation/mm10/Mus_musculus.GRCm38.68.gtf -p 6 -o tophat_output /path_to_reference/mm10/bowtie2_index/mm10 sample_1.fastq sample_2.fastq
Cufflinks 2.0.2/cufflinks, command line with parameter is, cufflinks -p 6 -o cufflink_output path_to_each_sample_aligned.bam
Cufflinks 2.0.2/cuffmerge, command line with parameter is, cuffmerge -o merged_gtf_output -p 6 -s /path_to_reference/mm10/mm10.fa -g /path_to_annotation/Mus_musculus.GRCm38.68.gtf sample_gtf_file_list.txt
Cufflinks 2.0.2/cuffdiff, for group comparasion by FPKM value, command line with parameter is, cuffdiff -o output_folder -p 6 -L group_1,group_2 -u -b /path_to/reference/mm10/mm10.fa merged.gtf
filter for sigmificant gene expression from cuffdiff gene_exp.diff file with q_value <=0.01 and log2(fold_change) >=1.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files from Cuffdiff output including the gene_exp.diff for the FPKM based comparasions of group KOalum0hour_vs_KOova0hour, WTalum0hour_vs_WTova0hour KOalum6hour_vs_KOova6hour, and WTalum6hour_vs_WTova6hour.

source_name: Lung

extract_protocol:
For each mouse, the right lung was removed, placed in a sterile eppendorf tube, and snap frozen in liquid nitrogen.  RNA extraction was performed on each sample by TRIZOL extraction following by Qiagen RNEasy Mini kit purification and on-column DNAse digestion.
The Vanderbilt Technologies for Advanced Genomics Core Facility (VANTAGE, Nashville, TN) used the Illumina TruSeq Stranded mRNA Sample Preparation Kit to convert the mRNA in 100 ng of total RNA into a library of template molecules suitable for subsequent cluster generation and sequencing on the Illumina HiSeq 2500.  The first step was to do a quality check of the input total RNA by running an aliquot on the Agilent Bioanalyzer to confirm integrity. The Qubit RNA fluorometry assay was used to measure concentration.    The input to library prep was 50 ul of 100 ng of total RNA (2 ng/ul).  The total RNA underwent enrichment of the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads.  Following enrichment, the eluted poly(A) RNA was cleaved into small fragments of 120-210 bp using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using SuperScript II reverse transcriptase and random hexamer primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The cDNA fragments then went through an end repair process, the addition of a single ‘A’ base, and then ligation of the Illumina multiplexing adapters. The products were then purified and enriched with PCR to create the final cDNA sequencing library.  The cDNA library underwent quality control by running on the Agilent Bioanalyzer HS DNA assay to confirm the final library size and on the Agilent Mx3005P qPCR machine using the KAPA Illumina library quantification kit to determine concentration.  A 2 nM stock was created and samples pooled by molarity for multiplexing.  From the pool 12 pM was loaded into each well for the flow cell on the Illumina cBot for cluster generation.  The flow cell was then loaded onto the Illumina HiSeq 2500 for Paired-end 50 bp sequencing utilizing v3 chemistry and HTA 1.8.

tag: strain

value: BALB/c

tag: genotype

tag: intraperitoneal sensitization

value: Alum

tag: aerosol exposure

tag: infection

value: Klebsiella pneumoniae


title: STAT6KO-OVA-KP

value: OVA-Alum

value: OVA


title: STAT6KO-OVA

description: KOalum0_vs_KOova0_gene_exp_significant.diff


title: STAT6KO-ALUM


title: WT-OVA-KP

description: WTalum6_vs_WTova6_gene_exp_significant.diff

value: wild type


title: WT-OVA

description: WTalum0_vs_WTova0_gene_exp_significant.diff


title: WT-ALUM


title: CD8 Clone #2 rep1

city: Rehovot

first: Amos

last: Tanay

state: ISR

address: 234 Herzl St.

institute: Weizmann Institute of Science

data_processing:
We used Bismark (parameters –n 1 –l 20) to map reads to the appropriate genome (mm9). Mapping was done independently for the two ends of each pair. This resulted in 70-80% reads with uniquely defined genomic mapping. We next identified the distance of each mapped read to the nearest MspI site, and discarded all cases that failed to map precisely or within 1bp of such site.
We also discarded read pairs that mapped uniquely to two different fragments. In cases where one read uniquely mapped on a restriction site but the other could not be mapped uniquely or could not be mapped at all, we re-aligned the entire read pair to the fragment.
Given an aligned read pair we first searched for reads with over 1 non-converted cytosine with base quality higher than 20 and discarded them. We then extracted the methylation status of all CpGs in the MspI fragment that were covered by one or both read ends. We defined the sites on the restriction site itself, sites with conflicting methylation status on the two ends, sites with a SNP (A or G), or sites that were not covered as missing data. This resulted in the extraction of a pattern (built from 0, 1 or “*”) from each read-pair.
We discard UMI sequencing errors that are ambiguous (similar to more than one designed UMI with one mismatch). Following this conservative correction, we retain for each restriction fragment (at each strand) at most one pattern for each UMI, by random sampling.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files that include : MspI_Fragment_ID (referenced by MspI_Fragments.coords file) Strand UMI_Barcode Methylation_Pattern Number_of_reads_UMI_got Number_of_stray_barcodes

source_name: Primary CD8 cells from C57BL/6 mice

growth_protocol: Naïve T-cells were purified from C57BL/6 splenocytes, cultured in a complete RPMI 1640 medium and were stimulated by IL2 (1.2 ng/ml, R&D system) for two days followed by FACS sorting for CD8+ individual cells by anti CD3 and anti-CD28. Single cell were extended in to clonal population (2.5X104).

extract_protocol:
Genomic DNA was extracted from CD8+ clonal and non-clonal populations (Quick gDNA kit Zymo Research).
gDNA (100ng-300ng ) was digested O.N with MspI (20 units). Size selection was performed, using X0.45 SPRI beads (Agencount AMpure XP, Beckman Coulter, Inc.) in order to remove fragments that are longer than 500bp. The supernatant was separated from the beads and was cleaned by X2.5 SPRI beads in order to select for DNA fragments at size of 200-500bp. Fill in reaction, combined with addition of  3’ overhangs A was performed using Klenow. The product (10ng), was ligated in to 150ng of our T tailed UMI plasmid library and was subjected to bisulfate conversion. The bisulfate conversion protocol was performed based on the manufacturer’s instructions (EZ DNA methylation kit, Zymo Research). Bis-converted fragments were subjected to 20 cycles of amplification with the following thermocycler conditions: 95C for 10 min (95C for 20 s, 56C for 30s, and   72C for 90min), 72 for 5min, using Gotaq hot start polymerase (Promega). In order to amplify and reintroduce C at the XbaI and EcoRI sites we used primers matching the converted sequence but contain C at the right site for site direction mutagenesis. The amplification products were cut by XbaI and EcoRI, subjected to fill in reaction, combined with addition of  3’ overhangs A and were ligated in to modified illumine Truseq adapters followed by 8 cycles of amplification under the same thermocycler conditions that were mentioned above. Products were size selected on 4% 1:3 Nusieve agarose gel (Lonza) for fragments between 200 to 500bp in size and purified using QIAquick gel extraction kit (Qiagen).

value: CD8+ T cell

tag: cell divisions


title: CD8 Clone #2 rep2


title: CD8 Clone #1 rep1


title: CD8 Population

value: population

tag: passage

value: primary


title: CD8 Clone #1 rep2

tag: cell type


title: XT_500pg_rep1

city: Stockholm

first: Rickard

last: Sandberg

address: Berzelius vag 35

department: Department of Cell and Molecular Biology

institute: Karolinska Institutet

data_processing:
All reads were aligned to the human (hg19) or mouse (mm10) genomes using STAR (Dobin et al. 2013)
Non-uniquely mapped reads were removed
Rpkmforgenes (available at http://sandberg.cmb.ki.se/rnaseq/), options -readcount -fulltranscript -mRNAnorm -rmnameoverlap -u, was used to generate RPKM values and read counts. We used a file with unique positions from Storvall et al. 2013 PLOS ONE. Gene annotations used were transcripts in RefSeq (Feb 2013).
Genome_build: hg19 and mm10
Supplementary_files_format_and_content: RPKM gene expression values (tab-delimited text)

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using Nextera XT on 500pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_10pg_rep2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using Nextera XT on 10pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_1pg_rep2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using Nextera XT on 1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_500pg_rep2


title: XT_10pg_rep1


title: XT_1pg_rep1


title: XT_100pg_rep1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using Nextera XT on 100pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_10pg_rep3


title: XT_100pg_rep2


title: WT-ALUM-KP


title: XT_0.1pg_rep1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using Nextera XT on 0.1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_0.1pg_rep3


title: inhouse_low_500pg_rep3

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 (low) on 500pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_low_500pg_rep2


title: inhouse_low_500pg_rep4


title: inhouse_low_1pg_rep4

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 (low) on 1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_low_1pg_rep2


title: inhouse_low_500pg_rep1


title: inhouse_low_1pg_rep3


title: inhouse_low_1pg_rep1


title: XT_1pg_rep3


title: XT_500pg_rep3


title: inhouse_low_0.1pg_rep3

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 (low) on 0.1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_low_0.1pg_rep4


title: inhouse_low_0.1pg_rep2


title: inhouse_500pg_rep2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 on 500pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: XT_0.1pg_rep2


title: inhouse_low_0.1pg_rep1


title: inhouse_1pg_rep1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 on 1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_1pg_rep3


title: inhouse_500pg_rep3


title: inhouse_10pg_rep2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 on 10pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_500pg_rep1


title: inhouse_1pg_rep2


title: inhouse_100pg_rep1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 on 100pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: inhouse_10pg_rep3


title: R6_2_2_4wk

source_name: Heart

extract_protocol:
Total RNA from whole hearts was extracted with the mini-RNA kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: (CBA x C57BL/6) F1

value: Heart

tag: age


title: inhouse_100pg_rep3


title: inhouse_0.1pg_rep1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Tagmentation using in-house Tn5 on 0.1pg cDNA
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: generuler3

organism: synthetic construct

source_name: DNA ladder

extract_protocol:
NA
Tagmentation using in-house Tn5
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.

value: GeneRuler 100 bp DNA Ladder (Thermo Scientific)


title: GPS2_day6

city: Boston

first: Valentina

last: Perissi

address: 72 E. Concord St

department: Department of Biochemistry

institute: Boston University School of Medicine

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 by using bowtie aligner.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
The peak finding was carried by using HOMER (http://homer.salk.edu/homer/).
The motif enrichment analysis was carried by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8
Supplementary_files_format_and_content: The files with the aligned reads are in standard BED format, HOMER analysis suite (http://homer.salk.edu/homer/) generates the bedgraph files (in the standard bedgraph format), and the peak files are in standard BED format.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described (Perissi et al. 2004). Anti-GPS2 antibodies were generated in rabbit against specific peptides representing the C’terminus (aa 307-327) or N’terminus (aa 1-11).
Extracted DNA was ligated to specific adaptors followed by deep sequencing on the Illumina GAII system according to the manufacturer’s instructions.

treatment_protocol: 3T3-L1 cells were grown and induced to differentiate as previously described (Cardamone et al. 2012).

tag: chip antibody


title: generuler2


title: XT_100pg_rep3


title: GPS2_day0


title: inhouse_0.1pg_rep3


title: GATA2_TAL1_LMO2 d2

city: Madison

first: Scott

last: Swanson

state: WI

address: 330 N. Orchard St

institute: Morgridge Institute for Research

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads filtered and trimmed to eliminate low-quality reads and adapter sequences
Gene expression estimates obtained using RSEM v 1.2.3, with Bowtie 0.12.9 for alignment. Parameters to rsem-calc-expression include: "--bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 "
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files containing non-normalized "Expected Counts" and normalized "Transcripts Per Million" expression estimates calculated by RSEM.
Supplementary_files_format_and_content: 54samples.tpm.tab: normalized expression estimates
Supplementary_files_format_and_content: 54samples.ec.tab: non-normalized abundance estimates

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; cells collected 2 days after transduction

growth_protocol: H1 cells were maintained on matrigel-coated plates in a regular TeSR1 media, supplemented with 4ng of human FGF2. For lenti-viral transductions, cells were washed with PBS, dissociated to a single cell suspension by incubating with Accutase  (Invitorgen cat.#A1110501) for 5-7 minutes, collected, pelleted and resuspended in 1-2ml of mTeSR1 media. For one well of 6-well plate 0.68 x10^6 cells were mixed with concentrated viral media (MOI 1-5) in 1ml in the presence of polybrene (6ug/ml), plated on matrigel-coated plates and placed in the cell culture incubator  for 12hr. After 12hr, attached cells were maintained in a basal TeSR1 media with hFGF-20ng, SCF-100ng and TPO-50ng. Submitted RNA samples are from cells collected as indicated in “title” for the sample. Non-transduced hESCs grown in the same culture conditions were used as a control.

extract_protocol:
RNA isolation procedure was performed according to QIAGEN protocol for RNAeasy micro kit Cat# 74004
Samples were then prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit v2 (RS-122-2001), according to the manufacturer's protocol

value: ES-derived cells


title: GATA2_TAL1_LMO2 d5

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; cells collected 5 days after transduction


title: GATA2_TAL1_LMO2 d4

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; cells collected 4 days after transduction


title: GATA2_TAL1_LMO2 d3

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; cells collected 3 days after transduction


title: generuler1


title: GATA2_TAL1_LMO2 d1

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; cells collected 1 day after transduction


title: hESC d5

source_name: non-transduced Embryonic stem cells; cells collected after 5 days of culture

value: Embryonic stem cells


title: inhouse_10pg_rep1


title: P1_3

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera-Zymo-IlluminaPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.

value: MEF


title: P1_4


title: hESC d3

source_name: non-transduced Embryonic stem cells; cells collected after 3 day of culture


title: P1_2


title: hESC d1

source_name: non-transduced Embryonic stem cells; cells collected after 1 day of culture


title: M5_4

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-water-KAPAPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: GATA2_ETV2 d5

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 5 days after transduction


title: inhouse_0.1pg_rep2


title: M4_4

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-0.001%SDS-KAPAPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: GATA2_TAL1_LMO2

source_name: overexpression of GATA2, TAL1 and LMO2  in Embryonic stem cells; floating cells collected 7 days after transduction


title: M4_1


title: GATA2_ETV2 d4

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 4 days after transduction


title: GATA2_ETV2 d3

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 3 days after transduction


title: M3b_2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-0.01%SDS-KAPAPCRmix-inhouseTn5
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: M3b_4


title: GATA2_ETV2 d2

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 2 days after transduction


title: M3a_4

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-0.01%SDS-KAPAPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: M3a_3


title: GATA2_ETV2 d1

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 1 day after transduction


title: M3a_2


title: M3a_1


title: inhouse_100pg_rep2


title: P1_1


title: GATA2_TAL1 d3

source_name: overexpression of GATA2 and TAL1 in Embryonic stem cells; cells collected 3 days after transduction


title: GATA2_TAL1 d5

source_name: overexpression of GATA2 and TAL1 in Embryonic stem cells; cells collected 5 days after transduction


title: M5_1


title: M2_2

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-NTbuffer-KAPAPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: M2_3


title: M2_1


title: M2_4


title: KDM4A_siGPS2

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described (Perissi et al. 2004). The anti-KMD4A antibody (Abcam ab47984) was used.
Extracted DNA was ligated to specific adaptors followed by deep sequencing on the Illumina GAII system according to the manufacturer’s instructions.

treatment_protocol: 3T3-L1 cells were grown, transfected and induced to differentiate as previously described (Cardamone et al. 2012).  siRNAs specific for GPS2 were purchased from Invitrogen (Silencer® Select siRNAs).

tag: transfected with

value: siRNAs specific for GPS2

value: anti-KMD4A antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: M1_1

extract_protocol:
cDNA was generated using SMART-seq2 (Picelli et al. Nature Methods 2013)
Nextera20ul-NTbuffer-IlluminaPCRmix
cDNA was generated from cells according to Smart-seq2 (Picelli et al. Nature Methods 2013)
We prepared sequencing libraries from cDNA using in-house or commercial Tn5 using tagmentation conditions as outlined in the associated study.


title: M1_2


title: KDM4A_siCTL

growth_protocol: 3T3-L1 cells were grown, transfected and induced to differentiate as previously described (Cardamone et al. 2012).

value: control siRNA


title: M3b_1


title: GATA2_ERG

source_name: overexpression of GATA2 and ERG in Embryonic stem cells; cells collected 7 days after transduction


title: M3b_3


title: ETV2_1

source_name: overexpression of ETV2 in Embryonic stem cells; cells collected 5 days after transduction


title: ETV2_2


title: ERG

source_name: overexpression of ERG in Embryonic stem cells; cells collected 5 days after transduction


title: GATA1

source_name: overexpression of GATA1 in Embryonic stem cells; cells collected 5 days after transduction


title: GATA2_ETV2_2

source_name: overexpression of GATA2 and ETV2 in Embryonic stem cells; cells collected 7 days after transduction


title: RUNX1c

source_name: overexpression of RUNX1c in Embryonic stem cells; cells collected 3 days after transduction


title: GATA2_ETV2_1


title: RUNX1b

source_name: overexpression of RUNX1b in Embryonic stem cells; cells collected 3 days after transduction


title: GATA2_2

source_name: overexpression of GATA2 in Embryonic stem cells; cells collected 5 days after transduction


title: GATA3

source_name: overexpression of GATA3 in Embryonic stem cells; cells collected 5 days after transduction


title: GATA2_1


title: RUNX1a

source_name: overexpression of RUNX1a in Embryonic stem cells; cells collected 3 days after transduction


title: GATA2_TAL1

source_name: overexpression of GATA2 and TAL1 in Embryonic stem cells; cells collected 7 days after transduction


title: HHEX

source_name: overexpression of HHEX in Embryonic stem cells; cells collected 5 days after transduction


title: NFE2

source_name: overexpression of NFE2 in Embryonic stem cells; cells collected 5 days after transduction


title: SPI1

source_name: overexpression of SPI1 in Embryonic stem cells; cells collected 5 days after transduction


title: MYB

source_name: overexpression of MYB in Embryonic stem cells; cells collected 5 days after transduction


title: TAL1_1

source_name: overexpression of TAL1 in Embryonic stem cells; cells collected 5 days after transduction


title: LYL1

source_name: overexpression of LYL1 in Embryonic stem cells; cells collected 5 days after transduction


title: TAL1_2


title: GATA2_TAL1 d2

source_name: overexpression of GATA2 and TAL1 in Embryonic stem cells; cells collected 2 days after transduction


title: NAB2

source_name: overexpression of NAB2 in Embryonic stem cells; cells collected 3 days after transduction


title: CDX2

source_name: overexpression of CDX2 in Embryonic stem cells; cells collected 5 days after transduction


title: LMO2

source_name: overexpression of LMO2 in Embryonic stem cells; cells collected 5 days after transduction


title: HES1

source_name: overexpression of HES1 in Embryonic stem cells; cells collected 5 days after transduction


title: HAND1

source_name: overexpression of HAND1 in Embryonic stem cells; cells collected 5 days after transduction


title: FLI1

source_name: overexpression of FLI1 in Embryonic stem cells; cells collected 3 days after transduction


title: GFI

source_name: overexpression of GFI in Embryonic stem cells; cells collected 5 days after transduction


title: FOXF1

source_name: overexpression of FOXF1 in Embryonic stem cells; cells collected 3 days after transduction


title: EGR1

source_name: overexpression of EGR1 in Embryonic stem cells; cells collected 5 days after transduction


title: ETV6

source_name: overexpression of ETV6 in Embryonic stem cells; cells collected 5 days after transduction


title: FOXC2

source_name: overexpression of FOXC2 in Embryonic stem cells; cells collected 5 days after transduction


title: 516A ILW backfat, miRNA

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

data_processing:
Sequenced reads were pooled together with another sample's sequenced reads. After adapter removal (adapter sequence: 5'-TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAG-3'), reads without adapter and/or with N were discarded, only reads between 15 and 30 nt with base quality of at least 30 and with less than 2 nt with base quality lower than 20 were considered. Reads were mapped using Bowtie v0.12.7 (only exact matches) to hairpins sequences from miRBase v19 and to pig genome sequence (Sscrofa9). Reads belonging to unique sequences mapping to more than 5 genomic loci out of miRNA hairpins were discarded. A subsequent phase of accurate mapping of reads to extended hairpins (30 nt before and after hairpin precursor) was performed using Bowtie with -best -y -strata options. Reads alignment results were integrated with known miRNA positions to classify reads according to the number of mismatches and the relative position of known mature miRNA. The raw read counts were corrected considering the number of reference sequences showing equally good alignments with the read. Known miRNA quantification and isomiRs characterization is based on exact alignments and on alignments with at most 1 mismatch. New miRNA and moRNA discovery is based only on exact alignments.
Genome_build: miRBase v19, Sscrofa9
Supplementary_files_format_and_content: Tab-delimited text files. GSE47748_miRNA_identified_and_discovered.txt.gz, GSE47748_new_miRNA_sequences.tsv.gz, GSE47748_moRNAs.tsv.gz.

organism: Sus scrofa

source_name: backfat, male

growth_protocol: All animals were housed in the same environmental and feeding conditions.

extract_protocol: Total RNA containing the small RNA fraction was extracted with Trizol (Invitrogen) according to the manufacturer's instruction. Results of the extraction were quantified using a Nanodrop ND-1000 spectrophotometer (Nanodrop Technologies) and the quality of the extracted RNA was assayed using an Agilent 2100 BioAnalyzer (Agilent Technologies). The miRNA library was prepared using the TruSeq Small RNA kit (Illumina) and version 3 of the reagents, following the manufacturer's suggested protocol. The library was sequenced on an Illumina Genome Analyzer II as 50 bp long single-reads using half lane per sample.

treatment_protocol: Backfat sample was collected in a commercial slaughterhouse. The sample was immediately frozen in liquid nitrogen and stored at -80°C in a deep freezer until RNA isolation.

tag: breed

value: Italian Large White

tag: gender type

value: castrated male

tag: tissue

value: backfat

value: 240 days

tag: weight


title: hESC H9 CellCycle S Phase

status: Public on Jul 13 2014

data_processing:
We used Bismark (parameters –n 1 –l 20) to map reads to the appropriate genome (hg19). Mapping was done independently for the two ends of each pair. This resulted in 70-80% reads with uniquely defined genomic mapping. We next identified the distance of each mapped read to the nearest MspI site, and discarded all cases that failed to map precisely or within 1bp of such site.
We also discarded read pairs that mapped uniquely to two different fragments. In cases where one read uniquely mapped on a restriction site but the other could not be mapped uniquely or could not be mapped at all, we re-aligned the entire read pair to the fragment.
Given an aligned read pair we first searched for reads with over 1 non-converted cytosine with base quality higher than 20 and discarded them. We then extracted the methylation status of all CpGs in the MspI fragment that were covered by one or both read ends. We defined the sites on the restriction site itself, sites with conflicting methylation status on the two ends, sites with a SNP (A or G), or sites that were not covered as missing data. This resulted in the extraction of a pattern (built from 0, 1 or “*”) from each read-pair.
We discard UMI sequencing errors that are ambiguous (similar to more than one designed UMI with one mismatch). Following this conservative correction, we retain for each restriction fragment (at each strand) at most one pattern for each UMI, by random sampling.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include : MspI_Fragment_ID (referenced by MspI_Fragments.coords file) Strand UMI_Barcode Methylation_Pattern Number_of_reads_UMI_got Number_of_stray_barcodes

source_name: H9 Cell Line FACS sorted for S phase

growth_protocol: Undifferentiated human ES cells (hESCs H1/H9) are routinely cultured on mouse embryonic fibroblast feeder layers (MEFs). Single hESC (H1/H9) cells were picked using CellCelector Aviso) using a 30 micron diameter capillary into 96 well plates or 24-well plates. Individual hESC was grown on plate coated with 8x104 iMEFs cells per well and containing conditional media supplemented by hbFGF (8ng/ml, Peprotech) and Rock inhibitor (10μM, Y-27632, Calbiochem). MCF7a and K562 cells were cultured in RPMI 1640 medium supplemented with antibiotics and 10%heat-inactivated fetal calf serum. HepG2 cells was cultured in DMEM medium supplemented with antibiotics and 10%heat-inactivated fetal calf serum. WI-38 primary human embryonic lung fibroblasts were grown in MEM supplemented with 10% FCS, 1 mM sodium pyruvate, 2 mM L-glutamine and antibiotics (Biological Industries). WI-38, MCF7 HepG2 and K562 cells were first trypsinized and individual cell was picked in to 96 well plate with condition media. Cells were grown until clonal population was established, 0.05-2X106 cells (2-4 weeks). Naïve T-cells were purified from C57BL/6 splenocytes, cultured in a complete RPMI 1640 medium and were stimulated by IL2 (1.2 ng/ml, R&D system) for two days followed by FACS sorting for CD8+ individual cells by anti CD3 and anti-CD28. Single cell were extended in to clonal population (2.5X104).

extract_protocol:
Genomic DNA was extracted from WI-38, hESC (H1, H9), K562, MCF7, HepG2, CD8+ clonal and non-clonal populations (Quick gDNA kit Zymo Research).
gDNA (100ng-300ng ) was digested O.N with MspI (20 units). Size selection was performed, using X0.45 SPRI beads (Agencount AMpure XP, Beckman Coulter, Inc.) in order to remove fragments that are longer than 500bp. The supernatant was separated from the beads and was cleaned by X2.5 SPRI beads in order to select for DNA fragments at size of 200-500bp. Fill in reaction, combined with addition of  3’ overhangs A was performed using Klenow. The product (10ng), was ligated in to 150ng of our T tailed UMI plasmid library and was subjected to bisulfate conversion. The bisulfate conversion protocol was performed based on the manufacturer’s instructions (EZ DNA methylation kit, Zymo Research). Bis-converted fragments were subjected to 20 cycles of amplification with the following thermocycler conditions: 95C for 10 min (95C for 20 s, 56C for 30s, and   72C for 90min), 72 for 5min, using Gotaq hot start polymerase (Promega). In order to amplify and reintroduce C at the XbaI and EcoRI sites we used primers matching the converted sequence but contain C at the right site for site direction mutagenesis. The amplification products were cut by XbaI and EcoRI, subjected to fill in reaction, combined with addition of  3’ overhangs A and were ligated in to modified illumine Truseq adapters followed by 8 cycles of amplification under the same thermocycler conditions that were mentioned above. Products were size selected on 4% 1:3 Nusieve agarose gel (Lonza) for fragments between 200 to 500bp in size and purified using QIAquick gel extraction kit (Qiagen).

tag: cell line

value: hESC H9


title: 517A ILW backfat, miRNA

source_name: backfat, female

value: female


title: CEBPa

source_name: overexpression of CEBPa in Embryonic stem cells; cells collected 5 days after transduction


title: hESC_1

source_name: non-transduced Embryonic stem cells; cells collected after 7 days of culture


title: hESC_2


title: CBFb

source_name: overexpression of CBFb in Embryonic stem cells; cells collected 5 days after transduction


title: WI-38 CellCycle S Phase rep2

source_name: WI-38 cell culture FACS sorted for S phase

value: hTERT-immortalized WI-38 primary human lung fibroblasts. Passage 23-27

value: population


title: hESC_GFP

source_name: overexpression of GFP in Embryonic stem cells; cells collected 7 days after transduction


title: WI-38 CellCycle S Phase rep1


title: WI-38 CellCycle G Phase rep2

source_name: WI-38 cell culture FACS sorted for G phase


title: MCF7a Clone #1 rep2

source_name: MCF7 (ATCC® HTB-22™)

value: MCF7 (ATCC HTB-22)

value: MCF7a, adenocarcinoma


title: WI-38 CellCycle G Phase rep1


title: HepG2 Population rep1

source_name: Hep G2 (ATCC® HB-8065™)

value: Hep G2 (ATCC HB-8065)

value: HepG2, hepatocellular carcinoma


title: HepG2 Population rep2


title: K562 Clone #3 rep2

source_name: K-562 (ATCC® CCL-243™)

value: K562, chronic myelogenous leukemia (CML)


title: MCF7a Clone #1 rep1


title: MCF7a Population rep1


title: HepG2 Clone #1


title: MCF7a Population rep2


title: K562 Clone #3 rep1


title: K562 Clone #1 rep1


title: K562 Clone #2 rep2


title: hESC H9 CellCycle G Phase

source_name: H9 Cell Line FACS sorted for G phase


title: K562 Clone #2 rep1


title: K562 Clone #1 rep2


title: hESC H9 Clone #2 rep1

source_name: H9 Cell Line


title: hESC H9 Clone #2 rep2


title: hESC H9 Clone #1 rep1


title: hESC H9 Population rep2


title: hESC H9 Population rep1


title: hESC H1 Clone #2 rep2

source_name: H1 Cell Line

value: hESC H1


title: hESC H9 Clone #1 rep2


title: hESC H1 Clone #1 rep1


title: hESC H1 Clone #1 rep2


title: hESC H1 Clone #2 rep1


title: hESC H1 Population rep1


title: WI-38 Clone #6 rep2

source_name: WI-38 cell culture


title: WI-38 Clone #5 rep2


title: WI-38 Clone #6 rep1


title: K562 Population rep1


title: WI-38 Clone #4 rep3


title: WI-38 Clone #4 rep1


title: WI-38 Clone #3 rep1


title: WI-38 Clone #4 rep2


title: WI-38 Clone #2 rep3


title: WI-38 Clone #2 rep2


title: WI-38 Clone #3 rep2


title: WI-38 Clone #1 rep2


title: WI-38 Population rep1


title: hESC H1 Population rep2


title: WI-38 Population rep2


title: Anti-PolII-S5

city: Saint Louis

first: Takeshi

last: Egawa

state: MO

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were mapped to the mm9 mouse genome with Bowtie2-2.1.0, and further analyzed using Homer to generate bedgraph files.
Peak calling was performed using Homer with P-values of 1e-10 or 1.5e-65 for AP4 and 5e-9 for Myc
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bedgraph files for read histograms normalized to 10,000,000 reads and bed files for peak calling

source_name: In vitro activated CD8 T cells

growth_protocol: Primary WT CD8 T cells from spleen and lymph nodes were activated with anti-CD3/CD28 antibodies for 2 days before harvest

extract_protocol:
Cells were fixed with 1% paraformaldehyde for 10 minutes at room temperature. Soluble chromatin was prepared as described by Ciofani et al (Cell,2012, PubMed ID: 23021777), and immunoprecipitated with antibodies.
At least 1.5 ng of ChIP or input DNA was used for library preparation according to the Illumina ChIP-seq protocol. After end-repair and indexed adapter ligation, fragments were size-selected using Agencourt AMPure XP beads (Beckman Coulter, Brea, CA, USA) prior to amplification. The size-selected and amplified fragment libraries were verified on a 2100 Bioanalyzer (Agilent) prior to being pooled and sequenced

tag: strain

value: CD8+ T cells

tag: antibody source

tag: catalog number


title: Anti-PolII-S2

value: Abcam


title: Tra2β iCLIP 2

status: Public on Jul 12 2014

city: Newcastle upon Tyne

first: David

middle: J

last: Elliott

address: 1 Central parkway

department: Institute of Genetic Medcine

institute: Newcastle University

description:
Protocol: iCLIP-seq
Sample 8

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low quality (Q <=20) bases, first 14 bases were trimmed off for all reads,  then mapped to hg19 using tophat 2.0.8b  with parameters -p 4 --library-type fr-unstranded --read-realign-edit-dist 0 -r 50 --min-segment-intron 20 --coverage-search --microexon-search --b2-sensitive --transcriptome-index hg19_gencode.V14 -x 20 hg19
reads mapped to exons were count using bedtools 2.17.0 multicov. Ensembl 71 exons were used to define exon regions.
Differentially expressed exons were called using DESeq 1.2.1
iCLIP data analysis, crosslink site identification and quantification, randomization of iCLIP positions and pentamer enrichment analysis were performed according to published procedures ( Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13, 2498-504 (2003) )
Genome_build: hg19
Supplementary_files_format_and_content: bed, peaks of iCLIP data; txt, differentially expressed exons; raw counts of exons on Ensembl human 71, has following columns: chromosome, exonStart, exonEnd, exonID, countSample4, countSample5, countSample6, countSample1, countSample2, countSample3

source_name: MDA-MB-231 cells_Tra2B_iCLIP

extract_protocol:
iCLIP experiments were performed according to the published iCLIP protocol Konig, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., et al. iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution. J. Vis. Exp. (50), e2638, doi:10.3791/2638 (2011).
iCLIP libraries were prepared for sequencing using the TruSeq Sample Preparation kit (Illumina). mRNA libraries for RNA-seq were prepared using a TruSeq mRNA library kit (Illumina).

tag: antibody


title: WI-38 Clone #1 rep1

tag: cell divisions


title: Tra2β iCLIP 1

description:
Protocol: iCLIP-seq
Sample 7


title: Anti-Myc

value: Anti-Myc

value: Santa Cruz


title: Anti-AP4

value: in house


title: WI-38 Clone #5 rep1

tag: passage


title: Input

tag: cell type

value: none (input)


title: Tra2β iCLIP 3

description:
Protocol: iCLIP-seq
Sample 9


title: TRA2A/B siRNA treated MDA-MB-231 cells 3

description: Sample 6

source_name: MDA-MB-231 cells_TRA2A/B_siRNA


title: TKO quiescent 1

city: Stanford

first: Julien

last: Sage

address: 265 Campus Drive, SIM1 G2078

institute: Stanford University

data_processing:
Illumina HiSeq 2000 was used to run the samples.
Sequenced reads were trimmed for adapter sequences then mapped to mm10 whole genome using tophatv2.0.0 and the down stream analysis is prformed using cufflinks v1.3.0
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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: mm10
Supplementary_files_format_and_content: FPKM tracking file include FPKM values

source_name: liver

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared and sequencing was performed by Centrillion Biosciences

value: liver

tag: genotype

value: cTKO;AlbCreER/+

tag: cell cycle state

value: arrested

tag: treatment

value: 2 weeks after tamoxifen


title: TKO cycling 2

value: cycling

value: 1 week after tamoxifen


title: TKO quiescent 2


title: TKO cycling 1


title: TRA2A/B siRNA treated MDA-MB-231 cells 2

description: Sample 5


title: WI-38 Clone #2 rep1

value: hTERT-immortalized WI-38 primary human lung fibroblasts. Passage 23-27


title: control quiescent 2

value: cTKO

value: quiescent


title: negative control siRNA treated MDA-MB-231 cells 3

description: Sample 3

source_name: MDA-MB-231 cells_negative_control_siRNA


title: control cycling 2

value: 36 hrs after 2/3rd partial hepatectomy


title: control quiescent 1


title: control cycling 1

value: 48 hrs after CCl4


title: TRA2A/B siRNA treated MDA-MB-231 cells 1

description: Sample 4


title: Replicate 1

first: Eilon

last: Sharon

description: plasmidic DNA which identifies a promoter present in expression bin

data_processing:
Expression bins mean and std were estimated from the cells collected during the sorting  as described in Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205)
Mapping reads to expression bin * promoter variant by extracting both barcodes from the sequence as described in Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205).
Extracting expression mean and noise using the code attached to the manuscript
Genome_build: The reads were aligned to the synthetic promoters collection from Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205) supplementary files.
Supplementary_files_format_and_content: TableS2_Replicate1_Strains2BinsMapping_fraction.tab.txt, TableS3_Replicate2_Strains2BinsMapping_fraction.tab.txt – tabular files containing the distribution of each promoter (row) across the expression bins (columns). LibID is a unique promoter ID similar to the IDS used in Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205). TableS1_PromotersExpressionValues.tab.txt – tabular file containing for each promoter (row) the total sequencing reads in which the promoter barcode was identified, the extracted expression mean and noise (squared coefficient of variation). The table also includes an indicator of whether the promoter passed the quality filter (as described in the manuscript) . TableS4_Replicate1_ExpressionBinValues.tab.txt, TableS5_Replicate2_ExpressionBinValues.tab.txt – Tabular file containing for each bin (row) the expression mean std and edges (left edge – minimal value, right edge – maximal value).

source_name: Synthetic promoter reporter gene assay

growth_protocol: The medium used both for growing the cells and for their sorting was SC-Glu-URA (synthetic complete media with 2% glucose and without uracil) medium without amino acids, except for Histidine.

extract_protocol:
The pool of cells was sorted according to their YFP expression level into 32 expression bins according to their ratio of YFP and mCherry expression level (mCherry was used for gating one plasmid copy cells and for normalization). Each of the two extreme expression bins contained 2% of the library cells and each of the remaining 30 bins contained 3.2%. We collected a total of 10,000,000 cells. The mapping of cells to bins involves parallel sequencing of the amplified promoter regions.
Briefly, a large collection of synthetic promoter reporter gene strains was generated by a pooled ligation of 6500 fully designed DNA oligos (obtained by synthesis on a microarray(LeProust et al. 2010) by Agilent Technologies, Santa Clara, California). The oligos were ligated upstream to a yellow fluorescent protein (YFP) gene with a short (100 bp) core promoter sequence taken from HIS3 gene promoter and into a low copy plasmid which also contains a TEF2 promoter deriving red fluorescent protein (mCherry). The resulting plasmids were then transformation into yeast (S. cerevisiae). The protocol was published in Sharon et al. Nature Biotechnology 2012(doi: 10.1038/nbt.2205).

treatment_protocol: A large collection of synthetic promoter reporter gene strains was generated by a pooled ligation of 6500 fully designed DNA oligos (obtained by synthesis on a microarray(LeProust et al. 2010) by Agilent Technologies, Santa Clara, California). The oligos were ligated upstream to a yellow fluorescent protein (YFP) gene with a short (100 bp) core promoter sequence taken from HIS3 gene promoter and into a low copy plasmid which also contains a TEF2 promoter deriving red fluorescent protein (mCherry). The resulting plasmids were then transformation into yeast (S. cerevisiae).

tag: plasmid type

value: Synthetic promoter driving reporter gene


title: Day_7_Uninfected_Mouse_2

status: Public on Jul 11 2014

city: Baltimore

first: Vincent

middle: Michael

last: Bruno

state: MD

address: 801 West Baltimore Street

department: Institute for Genome Sciences

institute: University of Maryland School of Medicine

description: Sample 10b

data_processing:
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Mus musculus genome using TopHat v. 1.4.0
RPKM values were calculated for the genes present in the Mus musculus genome.
Genome_build: Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Tab-delimited files report RPKM values.

source_name: Mus musculus Day 7 Uninfected Mouse

growth_protocol: Cells from S. aureus strain SAP149 used to infect one ear of an immunocompetent mouse epicutaneously.

extract_protocol:
RNA extractions were performed using RNEasy Kit from Qiagen following manufacturer's protocols
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: ear

tag: agent


title: Day_7_Mouse_2_Left

description: Sample 8b

source_name: Mus musculus + Staphylococcus aureus Day 7 Mouse left ear

value: Staphylococcus aureus


title: Day_7_Mouse_3_Left

description: Sample 8c


title: Day_7_Mouse_2_right

description: Sample 9b

source_name: Mus musculus + Staphylococcus aureus Day 7 Mouse right ear


title: Day_7_Mouse_3_right

description: Sample 9c


title: Day_7_Uninfected_Mouse_1

description: Sample 10a


title: Day_7_Mouse_1_Right

description: Sample 9a


title: Day_7_Uninfected_Mouse_3

description: Sample 10c


title: Day_4_Uninfected_Mouse_2

description: Sample 7b

source_name: Mus musculus Day 4 Uninfected Mouse


title: Day_4_Mouse_3_Left

description: Sample 5c

source_name: Mus musculus + Staphylococcus aureus Day 4 Mouse left ear


title: Day_4_Mouse_1_Left

description: Sample 5a


title: Day_4_Mouse_2_Left

description: Sample 5b


title: Day_4_Mouse_1_Right

description: Sample 6a

source_name: Mus musculus + Staphylococcus aureus Day 4 Mouse right ear


title: Day_4_Uninfected_Mouse_3

description: Sample 7c


title: negative control siRNA treated MDA-MB-231 cells 2

description: Sample 2


title: Day_4_Mouse_3_right

description: Sample 6c


title: Day_4_Uninfected_Mouse_1

description: Sample 7a


title: Day_4_Mouse_2_right

description: Sample 6b


title: Day_1_Uninfected_Mouse_3

description: Sample 4c

source_name: Mus musculus Day 1 Uninfected Mouse


title: Replicate 2


title: Day_1_Mouse_3_right

description: Sample 3c

source_name: Mus musculus + Staphylococcus aureus Day 1 Mouse right ear


title: Day_1_Uninfected_Mouse_1

description: Sample 4a


title: Day_1_Mouse_3_Left

description: Sample 2c

source_name: Mus musculus + Staphylococcus aureus Day 1 Mouse left ear


title: Day_1_Mouse_2_right

description: Sample 3b


title: Day_1_Uninfected_Mouse_2

description: Sample 4b


title: negative control siRNA treated MDA-MB-231 cells 1

description: Sample 1


title: Day_1_Mouse_2_Left

description: Sample 2b


title: Day_1_Mouse_1_Right

description: Sample 3a


title: Day_1_Mouse_1_Left

description: Sample 2a


title: Day_7_Mouse_1_Left

description: Sample 8a


title: tet-CD45+ hDMEC-rEC-hMPP 1

city: New York

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: Sample 15

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequence reads were aligned to hg18 using TopHat with default parameters
FPKM were obtained using CuffLinks with upper-quartile and GC normalization
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited FPKM values for each Refseq transcript

source_name: tet-CD45+ hDMEC-rEC-hMPP

extract_protocol: Illumina TruSeq, PE 51x2 and SR 51

value: tet-CD45+ hDMEC-rEC-hMPP


title: tet-CD45+ hDMEC-rEC-hMPP 2

description: Sample 16


title: Day_0_Mouse_3

description: Sample 1c

source_name: Mus musculus + Staphylococcus aureus Day 0 Mouse


title: Day_0_Mouse_2

description: Sample 1b


title: CD45+ hDMEC-rEC-hMPP 3

description: Sample 14

source_name: CD45+ hDMEC-rEC-hMPP

value: CD45+ hDMEC-rEC-hMPP


title: HUVEC 2

description: Sample 9

source_name: HUVEC

value: human umbilical vein ECs (HUVECs)


title: CD45+ hDMEC-rEC-hMPP 2

description: Sample 13


title: hDMEC 1

description: Sample 5

source_name: hDMEC

value: adult human dermal microvascular ECs (hDMECs)


title: CD45+HUVEC-rEC-hMPP

description: Sample 4


title: Lin-CD34+ (CB) 2

description: Sample 2

source_name: Lin-CD34+ (CB) cells

value: Lin-CD34+ Cord blood cells


title: HUVEC CD45+CD34+ in vivo

description: Sample 11

source_name: HUVEC CD45+CD34+ in vivo

value: HUVEC CD45+CD34+ in vivo


title: Lin-CD34+ (CB) 3

description: Sample 3


title: HUVEC 1

description: Sample 8


title: hDMEC CD45+CD34+ in vivo

description: Sample 7

source_name: hDMEC CD45+CD34+ in vivo

value: hDMEC CD45+CD34+ in vivo


title: Lin-CD34+ (CB) 1

description: Sample 1


title: PC3, 24 hours, SFN, rep 1

city: Corvallis

first: Laura

last: Beaver

state: OR

address: 103 Milam, Oregon State University

department: BPHS

institute: Oregon State University

description: Sample 34

data_processing:
Illumina CASAVA 1.8.1 for base calling
TopHat v1.3.3 with parameters “--library-type fr-unstranded” was used to align reads to hg19 using the Illumina iGenome.
Cuffdiff v.1.3.0 was used to test for differential gene expression using the alignments from TopHat.
Bowtie v0.12.9 with parameter “-v 2 -f -k 50 –best” was used to align reads to hg19 using the Ensembl GRCh37 revision 65.
GENE-counter was used to test for differential gene expression using the alignments from Bowtie to GRCh37 r65.
The differential gene expression output from Cuffdiff and GENE-counter were combined using custom python scripts. Differentially expressed genes were identified based on the criteria of being in the intersect of significant genes identified using both pipelines and exceeding a threshold of an average of 2 fragments per kilobase of exon per million fragments mapped (FPKM, Tuxedo suite pipeline), and 20 normalized reads (GENE-counter) in at least one treatment group. Transcripts also had to have at least a log2 fold change greater than 0.2, or less than -0.2. Fold changes that approached infinity were reassigned as 20.  A small number of transcripts that were significantly altered in only one pipeline but not tested in the other, due to differences in underlying statistical parameters and annotation files, were also included.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated files containing differential expression data: significance, fold change, and output from both GENE-counter and Cuffdiff.

source_name: PC3_24 hrs_SFN

growth_protocol: Normal prostate epithelial cells (PREC) were obtained from Lonza and cultured as recommended with 5% CO2 and 37°C in PREC basal media supplemented with PREC growth media singleQuots. Androgen-dependent prostate cancer epithelial cells (LNCaP), and androgen-independent prostate cancer epithelial cells (PC-3), were obtained from American Type Tissue Collection. Prostate cancer cells were cultured at 5% CO2 and 37°C in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with glutamine plus 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from adherent cells using a standard Trizol protocol and was resuspended in RNA secure reagent.  Contaminating DNA was removed by Turbo DNase treatment, and RNA was purified using the RNeasy Mini Kit.
Four µg of high quality RNA was converted into an indexed cDNA library using the TruSeq RNA sample Preparation Kit v-2 according to the manufactures protocol.

treatment_protocol: Each cell line was treated at 50-70% confluency with sulforaphane dissolved in dimethylsulfoxide at a 15 µM concentration or with an equal volume of DMSO (vehicle control) that was 0.03% of the total media volume.

tag: time point

value: 24 hours

tag: treated with

value: Sulforaphane (SFN)


title: PC3, 24 hours, SFN, rep 3

description: Sample 36

value: androgen-independent prostate cancer epithelial cells (PC-3)


title: PC3, 24 hours, SFN, rep 2

description: Sample 35


title: Day_0_Mouse_1

description: Sample 1a


title: CD45+ hDMEC-rEC-hMPP 1

description: Sample 12