title: CEC-1

city: La Jolla

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

institute: University of California, San Diego

description: limbal stem cell differentiation in 3D

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to hg19 using bowtie v0.12.7
Counted the mapped reads for each genes for each samples
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw counts for each genes for each samples

source_name: limbus

growth_protocol: DMEM/F12 and DMEM (1:1) with 1/100 Pen-Strep, 10% Fetal bovine serum, 10ng/ml EGF, 5 µg/ml insulin, 0.4ug/ml  Hydrocortisone, 10-10 M cholera toxin and 2 x 10-9 M 3,3´,5-Triiodo-L-Thyronine.

extract_protocol:
Total RNA was purified by a Picropure RNA isolation kit
Briefly, 600ng of total RNA was first converted to cDNA by superscript III first strand synthesis kit with primer Biotin-B-T. The cDNA was purified by NucleoSpin Gel and PCR Clean-Up Kit column (Clontech) to remove free primers and enzyme. Then terminal transferase (NEB) was applied to block the terminal of a cDNA 3’end.  Streptavidin-coaged magnetic beads (Life Technology) were further applied to isolate cDNAs.  After RNA degradation by sodium hydroxide, second strand cDNA was synthesized by random priming with primer A-N8. The second strand cDNA was eluted from beads by heat denaturing.  The cDNA was then used as template to construct libraries by amplifies with barcode primers and primer PB. The sequencing was done on Hiseq 2000 system.

treatment_protocol: Dissociated single stem cells were embedded in Matrigel at 2x104 cells/50ul gel. 3-D structures were formed after 14-18 day culture in a differentiation medium CnT-30 (LSC differentiation) or CnT-02 (SESC differentiation).

value: WT

value: cornea epithelial cells


title: 3-D PAX6+ SESC-2

status: Public on Jul 11 2014

type: SRA

state: CA

department: Medicine

country: USA

description: skin epithelial stem cells with PAX6 transduction and differentiation in 3D

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: skin biopsy of eye lids

tag: genotype

tag: cell type

value: skin epithelial stem cells


title: SEC-2

description: skin epithelial stem cells differentiation in 3D

value: skin epithelial cells


title: 3-D PAX6+ SESC-1


title: 3-D shPAX6 LSC-1

description: limbal stem cell with PAX6 knockdown and differentiation in 3D

value: limbal stem cells


title: 3-D shPAX6 LSC-2


title: CTC-6

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: cluster of cells in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The read_counts.txt file gives the read counts described above for each sample (columns) and gene (rows).

source_name: Culture of a circulating tumor cell isolated from the blood of a patient with metastatic estrogen receptor positive breast cancer

growth_protocol: Blood specimens from 6 patients with metastatic estrogen receptor positive breast cancer were subjected to microfluidic depletion of RBCs and CD45 and CD66b-positive WBCs, leaving single CTCs and small CTC-clusters in the final product (Ozkumur et al., 2013). This was then cultured in serum-free media supplemented with growth factors (EGF and bFGF) (G. Dontu et al., Genes Dev 17, 1253 (May 15, 2003)) under hypoxic conditions (4% O2) for 2-4 months.

extract_protocol:
For each culture, a CTC-clusters was isolated from the culture manually using a pipette. The cluster was then put in a lysis buffer.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

tag: individual

value: Patient-6 (a.k.a. BRx-61)

value: circulating tumor cell from blood


title: PC3, 24 hours, DMSO, rep 1

city: Corvallis

first: Laura

last: Beaver

state: OR

address: 103 Milam, Oregon State University

department: BPHS

institute: Oregon State University

description: Sample 31

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_DMSO

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: Dimethyl sulfoxide (DMSO; vehicle control)


title: PC3, 24 hours, DMSO, rep 2

description: Sample 32

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


title: CTC-5

description: cluster of cells in lysis buffer

value: Patient-5 (a.k.a. BRx-42)


title: PC3, 24 hours, DMSO, rep 3

description: Sample 33


title: CEC-2

description: limbal stem cell differentiation in 3D


title: HUVEC 3

city: New York

first: Olivier

last: Elemento

state: NY

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description: Sample 10

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: HUVEC

extract_protocol: Illumina TruSeq, PE 51x2 and SR 51

value: human umbilical vein ECs (HUVECs)


title: SEC-1


title: hDMEC 2

description: Sample 6

source_name: hDMEC

value: adult human dermal microvascular ECs (hDMECs)


title: PC3, 6 hours, SFN, rep 3

description: Sample 30

source_name: PC3_6 hrs_SFN

value: 6 hours

value: Sulforaphane (SFN)


title: PC3, 6 hours, SFN, rep 2

description: Sample 29


title: CTC-4

description: cluster of cells in lysis buffer

value: Patient-4 (a.k.a. BRx-50)


title: PC3, 6 hours, SFN, rep 1

description: Sample 28


title: CTC-2

description: cluster of cells in lysis buffer

value: Patient-2 (a.k.a. BRx-07)


title: CTC-1

description: cluster of cells in lysis buffer

value: Patient-1 (a.k.a. BRx-33)


title: PC3, 6 hours, DMSO, rep 2

description: Sample 26

source_name: PC3_6 hrs_DMSO


title: PC3, 6 hours, DMSO, rep 3

description: Sample 27


title: CTC-3

description: cluster of cells in lysis buffer

value: Patient-3 (a.k.a. BRx-68)


title: PC3, 6 hours, DMSO, rep 1

description: Sample 25


title: LNCaP, 24 hours, SFN, rep 2

description: Sample 23

source_name: LNCaP_24 hrs_SFN

value: Androgen-dependent prostate cancer epithelial cells (LNCaP)


title: LNCaP, 24 hours, SFN, rep 3

description: Sample 24


title: LNCaP, 24 hours, DMSO, rep 3

description: Sample 21

source_name: LNCaP_24 hrs_DMSO


title: Patient#10_CL#2

description: circulating cluster of cells in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). The file platform.xls gives the genes corresponding to the row IDs in readCounts.xls.

source_name: CTCs

extract_protocol:
Blood specimens from 10 patients with metastatic breast cancer were subjected to microfluidic depletion of RBCs and CD45 and CD66b-positive WBCs, leaving single CTCs and small CTC-clusters in the final product (Ozkumur et al., 2013). Unfixed tumor cells were stained for cell surface expression of EpCAM, EGFR, HER2, MET, and the mesenchymal marker CDH11, all conjugated with an Alexa488 fluorophore, as well as stained with TexasRed-conjugated antibodies against CD45, CD14 and CD16 to identify contaminating leukocytes. Individual CTC-clusters (median of 3 cells per cluster) were isolated using a micromanipulator and compared with numerically matched pools of single CTCs from the same specimen, followed by next generation RNA sequencing (SOLiD 5500). Samples that showed high expression of contaminant leukocyte markers at the RNA level were excluded from the analysis.
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.

tag: patient

tag: single cells or cluster

value: CL

tag: also known as


title: LNCaP, 6 hours, DMSO, rep 3

description: Sample 15

source_name: LNCaP_6 hrs_DMSO


title: Patient#10_SC#1

description: circulating single cells in lysis buffer

value: SC


title: LNCaP, 6 hours, SFN, rep 2

description: Sample 17

source_name: LNCaP_6 hrs_SFN


title: Patient#3_CL#1


title: LNCaP, 24 hours, DMSO, rep 2

description: Sample 20


title: PrEC, 24 hours, SFN, rep 3

description: Sample 12

source_name: PrEC_24 hrs_SFN

value: Normal prostate epithelial cells (PrEC)


title: LNCaP, 6 hours, DMSO, rep 2

description: Sample 14


title: Patient#10_CL#1


title: LNCaP, 6 hours, SFN, rep 3

description: Sample 18


title: PrEC, 24 hours, DMSO, rep 2

description: Sample 8

source_name: PrEC_24 hrs_DMSO


title: LNCaP, 6 hours, DMSO, rep 1

description: Sample 13


title: LNCaP, 6 hours, SFN, rep 1

description: Sample 16


title: PrEC, 24 hours, SFN, rep 1

description: Sample 10


title: PrEC, 24 hours, SFN, rep 2

description: Sample 11


title: PrEC, 6 hours, SFN, rep 3

description: Sample 6

source_name: PrEC_6 hrs_SFN


title: PrEC, 24 hours, DMSO, rep 3

description: Sample 9


title: Patient#5_CL#1


title: PrEC, 6 hours, SFN, rep 2

description: Sample 5


title: PrEC, 6 hours, DMSO, rep 3

description: Sample 3

source_name: PrEC_6 hrs_DMSO


title: LNCaP, 24 hours, SFN, rep 1

description: Sample 22


title: Patient#6_CL#1


title: Patient#5_SC#2


title: PrEC, 6 hours, DMSO, rep 1

description: Sample 1


title: PrEC, 6 hours, DMSO, rep 2

description: Sample 2


title: LNCaP, 24 hours, DMSO, rep 1

description: Sample 19


title: Patient#2_SC#1


title: PrEC, 24 hours, DMSO, rep 1

description: Sample 7


title: WT_pancreatic_islets_transcriptome 9

city: Leipzig

first: Torsten

last: Schöneberg

address: Johannisallee 30

department: Medical Faculty

country: Germany

institute: Leipzig University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data was quality checked using FastQC software. It revealed low PHRED-scale scores at the 3’ end of the 101 bp long reverse reads. These reads were trimmed to a size of 80 bp. Then, reads were assigned to the individual animals using the ligated adapter indices. Further, the samples proceeded filtering to trim the adapter sequences and remove low-quality reads which were shorter than 60 bp or contained more than five bases with a quality score below 15 (PHRED-scale). The paired-end reads were mapped to the reference mouse genome (July 2007 NCBI37/mm9) with Ensembl v66 annotations using Tophat 1.3.3. with options -G -r 80 --library-type fr-unstranded and the aligner Bowtie (version 0.9.9).
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks 1.3.0 with options -G and --library-type fr-unstranded
Differential gene expression was assessed using DESeq version 1.16.0
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample, tab-delimited text file with DESeq normalized read counts for all samples

organism: Mus musculus

source_name: pancreatic islets

growth_protocol: All animals were maintained in a pathogen-free barrier facility on a 12-h light/12-h dark cycle with ad libitum access to water and food.

extract_protocol:
Mice were sacrificed by cervical dislocation and the pancreas was inflated by intraductal injection of ice cold DMEM media containing 0.2 mg/ml Liberase TL Research Grade. Distended pancreas was digested by shaking in a 37 °C water bath for 17 minutes. Isolated islets were washed and picked under a stereomicroscope and incubated overnight at 37°C and 5% CO2 in RPMI-1640 media containing fetal bovine serum.
RNA libraries were prepared for sequencing using standard Illumina protocols TruSeq RNA Sample Preparation Kits v2

value: wildtype

tag: tissue

value: pancreatic islets

tag: strain


title: WT_pancreatic_islets_transcriptome 7


title: Patient#1_SC#1


title: Patient#6_SC#1


title: WT_pancreatic_islets_transcriptome 8


title: WT_pancreatic_islets_transcriptome 4


title: P2Y14-KO_pancreatic_islets_transcriptome 6


title: WT_pancreatic_islets_transcriptome 2


title: WT_pancreatic_islets_transcriptome 3


title: WT_pancreatic_islets_transcriptome 5


title: P2Y14-KO_pancreatic_islets_transcriptome 9


title: PrEC, 6 hours, SFN, rep 1

description: Sample 4


title: P2Y14-KO_pancreatic_islets_transcriptome 10


title: P2Y14-KO_pancreatic_islets_transcriptome 4


title: P2Y14-KO_pancreatic_islets_transcriptome 3


title: WT_pancreatic_islets_transcriptome 6


title: P2Y14-KO_pancreatic_islets_transcriptome 8


title: WT_pancreatic_islets_transcriptome 1


title: P2Y14-KO_pancreatic_islets_transcriptome 5


title: P2Y14-KO_pancreatic_islets_transcriptome 7


title: P2Y14-KO_pancreatic_islets_transcriptome 1


title: P2Y14-KO_pancreatic_islets_transcriptome 2


title: Marussia sRNA

city: Daejeon

first: Jungeun

last: Kim

country: South Korea

institute: KRIBB

data_processing:
base-calling
pre-processing : removing adaptors. Small RNA sequences that did not match tRNA and rRNA sequences were selected.
genomic mapping to strawbery genome using BLAST (Ver. 2.2.26)
miRNA predicgion by modified miRDeep algorithm
normalization with total read numbers
processed file headers: id, sRNAseq, vital, marussia, sympathy, haedang

organism: Rosa hybrid cultivar

source_name: flower

extract_protocol: Illumina Small RNA Sample Preparation Kit v1

tag: cultivars

value: Marussia

value: flower


title: Vital sRNA

value: Vital


title: Haedang sRNA

organism: Rosa rugosa

value: Haedang


title: wt_chip

status: Public on Jul 10 2014

city: San Diego

first: Nicola

last: Zilio

address: 10550 N Torrey Pines Road

institute: The Scripps Research Institute

description: Sample 2

library_source: genomic

data_processing:
fastx_trimmer -f 7 -l 47 -Q33  (trim first 6 and last 47 nt of each read)
fastq_quality_filter -q 28 -p 95 -Q33 (filter - 95% of bases quality score >28)
bowtie -q -p 8 -S -n 2 -e 70 -l 40 --maxbts 800 -y -k 1--best --phred33-quals (align to reference genome and output SAM file, reads that did not align were not included in the output SAM file)
picard SortSam SORT_ORDER=coordinate (sort SAM file)
picard MarkDuplicates (mark PCR duplicates, input = 141599 reads, chip = 360672 reads)
picard DownsampleSam PROBABILITY=0.4 RANDOM_SEED=1 (downsample ChIP alignment file to 40%)
macs --gsize=12462637 --bw 600 -w (peak calling)
Genome_build: ASM294v2.22 (ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/dna/)
Supplementary_files_format_and_content: wig files were generated using MACS

molecule: genomic DNA

organism: Schizosaccharomyces pombe

source_name: yeast cells

growth_protocol: Cells were grown at 30 °C in YES to mid-logarithmic phase

extract_protocol:
700 OD600 of cells were fixed in 1% w/v formaldehyde for 25 min at room temperature. The reaction was stopped by adding glycine to a final concentration of 125 mM. After extensively washing the pellets in Tris-buffered saline solution, the cells were aliquoted into 14 equal samples. Cells were lysed by bead beating in 0.5 mL per sample of 50 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1% v/v Triton-X 100, 1 mM PMSF, 1× Complete Protease Inhibitor Cocktail. Following addition of Triton X-100 to 1% v/v, chromatin was sheared by sonication in a Misonix Sonicator 3000 (Farmingdale, NY, 15 cycles of 30 s ON at maximum intensity and 1 min OFF). The lysate was cleared by centrifugation and adjusted to 10 mL at 15 mg mL-1 of total protein, as determined by the Bradford assay. This lysate was incubated with 0.5 mL of pre-equilibrated IgG resin (GE Healthcare Life Sciences) overnight at 4 °C with rotation. Next, the resin was washed three times with 1 mL of the lysis solution described above without protease inhibitors, once with 50% the same solution and 50% of 20 mM HEPES pH 7.6, 150 mM NaCl, 0.1% v/v NP-40, 1 mM EDTA and once with 100% of the latter solution. The IgG resin was resuspended with 0.75 mL of the latter solution supplemented with 0.75 mM DTT and 500 U of TEV protease (Eton Biosciences, San Diego, CA) and incubated at room temperature for 4 h with rotation. The resin was washed three times with 0.5 mL of the same solution used for proteolysis, which were combined with the eluate, supplemented with 0.2 mL of pre-equilibrated anti-FLAG magnetic resin (M2, Sigma-Aldrich), and incubated overnight at 4 °C with rotation. The anti-FLAG resin was washed three times for 10 min with 10 mL of 50 mM HEPES pH 7.6, 140 mM NaCl, 1 mM EDTA, 1 % v/v Triton-X 100, 0.1% v/v sodium deoxycholate, twice more in the same buffer but containing 500 mM NaCL, twice in 10 mM Tris-HCl pH 8, 250 mM LiCl, 1 mM EDTA, 0.5% v/v NP-40, 0.5% v/v sodium deoxycholate and once in Tris-EDTA solution. The resin was eluted twice with 0.5 mL of 10 mM Tris pH 8, 1 mM EDTA, 1% v/v SDS for 15 min at 70 °C. The eluted DNA was de-crosslinked overnight at 65 °C, purified with Qiagen’s PCR Purification Kit (Qiagen, Germantown, MD), and eluted in 50 µL of TE.
Libraries were prepared from 10 ng of DNA using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina (NEB) following manufacturer’s recommended protocol. The libraries were amplified with 18 cycles of PCR and size selected on a 2% agarose gel to remove adapter dimer products. The purified DNA library was denatured in 0.1 N NaOH and diluted to a final concentration of 10 pM before being loaded onto an Illumina single read flow-cell.

tag: chip antibody

value: IgG (GE Healthcare, catalog# 17-0969-01, for protein A epitope) & anti-FLAG (M9, Sigma, catalog# M8823, for FLAG epitope)


title: WT_pancreatic_islets_transcriptome 10


title: wt_input

description: Sample 1


title: nts1_chip

description: Sample 2

data_processing:
fastx_trimmer -f 7 -l 47 -Q33  (trim first 6 and last 47 nt of each read)
fastq_quality_filter -q 28 -p 95 -Q33 (filter - 95% of bases quality score >28)
bowtie -q -p 8 -S -n 2 -e 70 -l 40 --maxbts 800 -y -k 1--best --phred33-quals (align to reference genome and output SAM file, reads that did not align were not included in the output SAM file)
picard SortSam SORT_ORDER=coordinate (sort SAM file)
picard MarkDuplicates (mark PCR duplicates, input = 141599 reads, chip = 360672 reads)
picard DownsampleSam PROBABILITY=0.4 RANDOM_SEED=1 (downsample ChIP alignment file to 40%)
macs --gsize=12462637 --bw 600 -w (peak calling)
Genome_build: ASM294v2.22 (ftp://ftp.ensemblgenomes.org/pub/fungi/current/fasta/schizosaccharomyces_pombe/dna/)
Supplementary_files_format_and_content: bed and wig files were generated using MACS


title: nts1_input

description: Sample 1


title: Simpas sRNA

value: Simpas


title: Sample 81a

city: Baltimore

first: David

middle: A

last: Rasko

state: MD

address: 801 W. Baltimore Street, Room 619

department: Istitute for Genome Sciences/Microbiology and Immunology

institute: University of Maryland School of Medicine

data_processing:
Base calls were performed using the bulit in Illumina basecaller.
Sequenced reads were mapped to the Acinetobacter baumannii genome using Bowtie v. 0.12.9
RPKM values were calculated for the genes present in the Acinetobacter baumannii genome.
Genome_build: Acinetobacter baumanni 1592897 ASM58231v1
Supplementary_files_format_and_content: Tab-delimted files report RPKM values.

organism: Acinetobacter sp. 983759

growth_protocol: Acinetobacter strains were inoculated 1:100 from overnight cultures and grown to an OD600 of approximately 0.4 in Mueller Hinton Broth (MHB), or MHB supplemented with 200mM NaCl, at 37˚C with shaking (225 rpm)

extract_protocol: The cells were pelleted from the media by pelleting at 5,000 x g for 5 min, and total RNA was extracted using the Ambion RiboPure Bacteria kit. The RNA was treated with the Ribopure DNase I, and the rigorous treatment using the Turbo DNA-free kit to remove contaminating DNA.

treatment_protocol: Once they reached an OD600 of 0.4, the cultures to receive antibiotic treatment were amended with 25% or 75% of the approximate MIC value of one antibiotic (meropenem, ciprofloxacin, amikacin sulfate, or polymyxin-B), then they were incubated for 15 min at 37˚C with shaking (225 rpm). The no treatment controls grown in regular MHB, and also the MHB + 200 mM NaCl treatment, were not amended with antibiotic and were incubated for an additional 15 min after reaching an OD600 of 0.4.

tag: sample name

tag: agent

value: amikacin sulfate

tag: dose

value: 25% of approximate MIC


title: Sample 76a

organism: Acinetobacter sp. 478810

value: polymyxin-B

value: 75% of approximate MIC


title: Sample 76b


title: Sample 86b


title: Sample 77a

value: meropenem


title: Sample 75b


title: Sample 77b


title: Sample 78a


title: Sample 75a


title: Sample 82a


title: Sample 86a


title: Sample 82b


title: Sample 79a

value: no treatment (Mueller Hinton Broth)


title: Sample 78b


title: Sample 85a


title: Sample 88b


title: Sample 79b


title: Sample 73b

value: ciprofloxacin


title: Sample 74b


title: Sample 72a


title: Sample 71b


title: Sample 73a


title: Sample 71a


title: Sample 81b


title: Sample 38b

organism: Acinetobacter baumannii 1457504


title: Sample 38a


title: Sample 37b


title: Sample 37a


title: Sample 74a


title: Sample 36b


title: Sample 35b


title: Sample 36a


title: Sample 34b


title: Sample 35a


title: Sample 31b


title: Sample 32b


title: Sample 31a


title: Sample 26b

organism: Acinetobacter baumannii 1428368


title: Sample 29a


title: Sample 33a


title: Sample 29b


title: Sample 22b


title: Sample 21b


title: Sample 25a


title: Sample 21a


title: Sample 34a


title: Sample 28b


title: Participant 12, Baseline

city: Durham

first: Geoffrey

middle: S

last: Ginsburg

state: NC

address: 101 Science Drive

department: Clinical Genomics Studies Unit

institute: Duke University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, more specifically, Trimmomatic version 0.25 was used, trimming trailing bases below quality 20, clipping Illumina adapters, and discarding clipped reads shorter than 25 bp.
Trimmed reads were then mapped to the hg19 genome and transcriptome using Bowtie2 version 2.0.6., and Stampy version 1.0.17. Trimmed reads were also mapped to the hg19 human genome using Tophat version 2.0.7, and GMAP (GSNAP) version 2013-03-12. Default parameters were used for all mapping methods.
Read counts for each transcript were obtained with HTSeq version 0.5.4, specifically the intersection-nonempty mode of htseq-count.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw transcript count values for each sample
Supplementary_files_format_and_content: bowtie2_trans_counts_baseline.txt: Raw Counts, Bowtie2 to Transcriptome
Supplementary_files_format_and_content: bowtie2G_trans_counts_baseline.txt: Raw Counts, Bowtie2 to Genome
Supplementary_files_format_and_content: gsnap_trans_counts_baseline.txt: Raw Counts, GSNAP to Genome
Supplementary_files_format_and_content: stampy_trans_counts_baseline.txt: Raw Counts, Stampy to Transcriptome
Supplementary_files_format_and_content: stampyG_trans_counts_baseline.txt: Raw Counts, Stampy to Genome
Supplementary_files_format_and_content: tophat_trans_counts_baseline.txt: Raw Counts, TopHat to Genome

organism: Papio cynocephalus

source_name: peripheral blood mononuclear cells

extract_protocol:
Samples were collected in PreAnalytiX PAXgene Blood RNA collection tubes, and total RNA was isolated using the PreAnalytiX PAXgene Blood RNA miRNA isolation kit.
RNA libraries were prepared for sequencing using the Illumina TruSeq protocol

tag: participant id

tag: timepoint

value: baseline

value: blood


title: Participant 10, Baseline


title: Sample 22a


title: Participant 8, Baseline


title: Sample 33b


title: Participant 11, Baseline


title: Sample 25b


title: Sample 32a


title: Sample 26a


title: Participant 7, Baseline


title: Participant 6, Baseline


title: Participant 3, Baseline


title: Participant 5, Baseline


title: Participant 4, Baseline


title: Sample 85b


title: Participant 1, Baseline


title: Participant 2, Baseline


title: Input DA

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

country: France

institute: CNRS

description: Patient cells

data_processing:
After sequencing, DNA samples were aligned against the human genome (HG19) using bowtie 1 (-v strategy, 2 mismatches). All tags aligning in multiple location were ignored and the remaining ones were processed with a custom R pipeline.
In brief, this pipeline removes the artefactual enrichments by filtering piles of reads higher than a custom threshold (nb of reads aligned/7.10^6), estimates the shift between positive and negative strand and elongates all reads according to this value. Ultimately wig files are generated by computing the pileup scores at each position on the genome and averaging these scores in 50 bp bins.
Input and IP samples were processed as described. The scores of the resulting WIG files were scaled according to the number of aligned reads and the scores from inputs were subtracted to the corresponding IP files.
Genome_build: HG19
Supplementary_files_format_and_content: WIG fixed steps - bins 50bp - Containing the enrichment scores computed by the described pipeline, before and after input subtraction for IP files.

source_name: T-ALL cancer sample_input

extract_protocol:
Chromatin Immunoprecipitation with antibodies against specific histone modifications.
Libraries were prepared according to manufacturer's instructions using Illumina TrueSeq ChIP-seq Library Preparation Kit (Ref # 15034288). At least 1ng DNA was used for each library preparation.

value: Lymphocytes

value: none (input)


title: Input Jurkat

description: Cancer derived culture cells

source_name: Jurkat culture cells_input

tag: cell line

value: Jurkat


title: H3K27me3 DA

description: Patient cells

source_name: T-ALL cancer sample_H3K27me3

tag: cell type

value: H3K27me3 (Millipore, 07-449)

tag: antibody manufacturer

value: Millipore

tag: antibody catalog number


title: H3K27ac Jurkat + sodium butirate

description: Cancer derived culture cells

value: H3K27ac (Abcam, ab4729)

value: Abcam

tag: treatment

value: Sodium butirate


title: 12hZNA30uM-rep2

city: Oklahoma City

first: Bryan

last: Welm

state: Oklahoma

address: 825 Northeast 13th Street

department: Immunobiology and Cancer

institute: Oklahoma Medical Research Foundation

data_processing:
reads were aligned to hg19 plus extended splice junctions using novoalign (2.08.01). Up to 50 alignments were reported and adapter sequences were trimmed by novoalign.
splice junction alignments were converted back to genomic space using the USeq (8.6.4) SamTranscriptomeParser application (default settings).
the final alignment files were used in the USeq (8.6.4) DefinedRegionDifferentialSeq application to generate counts per gene, variance stabilized counts, FPKM values and to determine differential expression
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files contain raw read counts, FPKM values, log2ratio (DESeq) and -10*log10(adjusted p-value) (DESeq)

source_name: MCF-7 breast cancer cell line_12hZNA30uM-rep2

extract_protocol:
RNA was isolated from cells using a Qiagen Rneasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: breast cancer

tag: treatment condition

value: 12h, ZNA, 30 uM


title: 12hZNA30uM-rep3

source_name: MCF-7 breast cancer cell line_12hZNA30uM-rep3


title: idm2_MethylC-Seq_rep1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
idm2 samples: Each raw read was first trimmed to the longest contiguous read segment with Phred quality score>=20 (using DynamicTrim from the SolexaQA software, Cox et al, 2010) and then trimmed for the adaptor sequence if exists using an inhouse perl script. We mapped paired reads and singleton reads (when read from the other end was discarded due to low quality) to the Arabidopsis genome (TAIR10) using BRAT with parameters -m 2 -i 0 -a 1000.
idm1idm2 double mutant: Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China); Clean reads were mapped to TAIR10 using BRAT-BW with parameters -m 2 -i 0 -a 1000.
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
idm2 samples: Libraries were prepared according to a published protocol (Lister et al., 2008). Briefly, Genomic DNA was extracted from 14-d-old seedlings. Sonicated DNA was end-repaired by using End Repair Enzyme Mix (NEB, #E6041A). The blunt end DNA were treated with Klenow fragment (NEB, #E6044A) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Unmethylated cytosine residues were converted to uracil by EpiTect bisulfite Kit (Qiagen, 59104) after adaptor ligation. After bisufite treated DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 250~350 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer IIx following the manufacturer's protocols in KAUST(King Abdullah University of Science and Technology)
idm1idm2 sample: Genomic DNA was extracted from 14-d-old seedlings and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype

value: idm2 mutant

tag: developmental stage

value: 14 day-old seedlings


title: idm2_MethylC-Seq_rep2

description: treated with bisulfite


title: Participant 9, Baseline

tag: tissue


title: 12h Control-rep2

source_name: MCF-7 breast cancer cell line_12h Control-rep2

value: 12h, DMSO


title: 12h Control-rep1

source_name: MCF-7 breast cancer cell line_12h Control-rep1


title: 3hZNA30uM-rep2

source_name: MCF-7 breast cancer cell line_3hZNA30uM-rep2

value: 3h, ZNA, 30 uM


title: 3hZNA30uM-rep1

source_name: MCF-7 breast cancer cell line_3hZNA30uM-rep1


title: 3hZNA30uM-rep3

source_name: MCF-7 breast cancer cell line_3hZNA30uM-rep3


title: 3hControl-rep3

source_name: MCF-7 breast cancer cell line_3hControl-rep3

value: 3h, DMSO


title: 3hControl-rep2

source_name: MCF-7 breast cancer cell line_3hControl-rep2


title: 3hControl-rep1

source_name: MCF-7 breast cancer cell line_3hControl-rep1


title: H3K27me3 Jurkat

description: Cancer derived culture cells

source_name: Jurkat culture cells_H3K27me3


title: H3K27ac Jurkat

description: Cancer derived culture cells

source_name: Jurkat culture cells_H3K27ac


title: e2f4-GFP_ChIPseq_input

first: Ian

middle: K

last: Quigley

address: 10010 North Torrey Pines Road

department: Molecular Neurobiology Lab

institute: Salk Institute

data_processing:
RNAseq reads aligned to transcriptome with RNA-STAR (PMID: 23104886)
RNAseq aligned reads counted with eXpress (PMID: 23160280)
RNAseq counts normalized and differential expression tested with DESeq (PMID: 23975260)
ChiPseq reads aligned to genome with bowtie2, http://bowtie-bio.sourceforge.ne t/bowtie2/index.shtml, mapping quality scores > 20 retained
ChiPseq aligned reads were pooled and peaks called with HOMER (PMID: 20513432)
Genome_build: Genome: JGI X. laevis v7.1
Genome_build: Transcriptome: Mayball interim models, http://daudin.icmb.utexas.edu/
Supplementary_files_format_and_content: RNAseq files are output from eXpress, ChIPseq peaks are bed files

organism: Xenopus laevis

source_name: animal cap (ectoderm)

growth_protocol: Animal caps (ectoderm) dissected from embryos at stage 10 and cultured in 0.5x MMR. 20 animal caps per condition were used for RNAseq; ~300 animal caps were used per condition for ChIPseq.

extract_protocol:
mRNAs were obtained with proteinase K digestion, phenol chloroform extraction and precipitated with ethanol, treated with Dnase, extracted with phenol chloforom, and precipitated with ethanol. For ChIPseq embryos were first fixed in 1% formaldehyde for 30 minutes and lysed in RIPA buffer prior to sonication. See our manuscript (PMID: 24934224) for a more detailed protocol.
RNAseq libraries were constructed with Illumina Truseq v2 non-stranded mRNA kits. Following IP, ChIPseq libraries were constructed with end repair mix (NEB), a-tailed (NEB), Truseq v2 adapters ligated (Illumina, NEB) and amplified with Phusion polymerase (NEB).

treatment_protocol: Animal caps containing inducible constructs (human glucocorticoid receptor fusion proteins) were induced with 20 micromolar dexamethasone at mid-stage 11.

value: animal cap (ectoderm)

tag: harvest time/stage

value: 6h @ 22 deg  after mid-11 (st 16)

tag: injected mrna


title: e2f4-GFP_MCIDAS_ChIPseq_rep1_rep2

tag: chip antibody

value: rabbit anti-GFP (Invitrogen catalog no. A11122, lot no. 1296649)


title: BRD4 siRNA E2 rep2

city: Göttingen

first: Steven

last: Johnsen

state: Niedersachsen

address: Robert-Koch-Straße 40

department: Department of General, Visceral and Pediatric Surgery

institute: University Medical Center Göttingen

data_processing:
The reads were mapped to the human reference transcriptome (UCSC HG19) using Bowtie2 2.1.0 (Langmead and Salzberg, 2012).
Read counts for each sample and each gene were aggregated using a custom Ruby script.
DESeq (version 1.14.0) was used for the measuring differential expression (Anders and Huber, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Comma-delimited text file with normalized read counts.

source_name: MCF7 breast cancer cells

growth_protocol: MCF7 cells were grown in phenol red- free high-glucose Dulbecco's Modified Eagle's Media (DMEM; Invitrogen) with 10% bovine growth serum (Thermo Scientific). For estrogen induction experiments, after one day of cell-splitting, the media was changed to DMEM containing 5% charcoal-dextran treated FBS (Sigma).

extract_protocol:
Trizol mediated RNA isolation method was used for harvesting RNA.
500 ng RNA was used for library preparation and libraries were made using the kit TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS–122–2002)

treatment_protocol: After 2 days of hormone deprivation, MCF7 cells were treated with 10 nmol/L 17-β-estradiol  (Sigma-Aldrich) for 2 hours. The cells were harvested for RNA upon Vehicle (Veh) or estrogen (E2) treatment and negative control siRNA (siCont), BRD4 siRNA (siBRD4) or JQ1 treatment. 150 nM JQ1 was pretreated to the cells 30 mins before estrogen treatment.  JQ1 treated cells were also transfected with negative control siRNA.

value: Human breast adenocarcinoma

tag: passages


title: JQ1 Veh rep1


title: JQ1 E2 rep1


title: BRD4 siRNA E2 rep1


title: JQ1 E2 rep2


title: JQ1 Veh rep2


title: BRD4 siRNA Veh rep2


title: MCIDAS_dnE2F4_9h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)

molecule: polyA RNA

value: 9h @ 22 deg  after mid-11 (st 18)


title: MCIDAS_dnE2F4_9h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)


title: e2f4-GFP_ChIPseq_rep1_rep2


title: 12hZNA30uM-rep1

source_name: MCF-7 breast cancer cell line_12hZNA30uM-rep1


title: 12h Control-rep3

source_name: MCF-7 breast cancer cell line_12h Control-rep3


title: BRD4 siRNA Veh rep1


title: MCIDAS_dnE2F4_9h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_9h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)

value: MCIDAS-HGR


title: Control siRNA E2 rep2


title: MCIDAS_9h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)


title: Control siRNA E2 rep1


title: Control siRNA Veh rep2


title: Control siRNA Veh rep1


title: MCIDAS_dnE2F4_6h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_9h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_dnE2F4_6h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_dnE2F4_6h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_6h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_6h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_6h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MEF_-OHT_pInducer-MycV394D_+Dox_RNAseq

city: Wuerzburg

first: Martin

last: Eilers

address: Am Hubland

department: Chair for Biochemistry and Molecular Biology

institute: University of Wuerzburg

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome with BOWTIE v0.12.7 or v0.12.8 using default parameters.
For ChIPseqs peak calling was performed with MACS v1.4.2 with default parameters, but depending on the sample: model fold 15 to 25, duplicates 1 to 100, p-value of 1E-5 to 1E-6 and FDR 0.1
For ChIPseqs of histone modifications SICER v1.1 with the following parameters has been used: redundancy 1, window size 200, gap size 200, fragment size 150, FDR 5E-2 to 1E-4.
For RNAseqs reads were aligned to the reference genome using BOWTIE v0.12.7 or v0.12.8
Differential expression was identified using EdgeR. For RNAseqs in MEFs reads per gene were counted.
Genome_build: hg19 for human and mm9 for murine datasets
Supplementary_files_format_and_content: txt files from ChIP-seq experiments containing peak localisation in a MACS output -bed format. txt files from ChIPseq experiments of histone modifications contain peak localisation in SICER output format.  txt files from RNA-seq experiments contain ensembl-ID, gene symbol, log2 fold change, and p(adjust).

source_name: MEFs derived from Miz1flox/flox, CreER-mice

growth_protocol: HeLa, U2OS and pancreas cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom) and penicillin/streptomycin (Sigma). MEFs were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (Biochrom), 1x non-essential amino acids (Sigma), 1% penicillin/streptamycin (Sigma) and 50µM beta-mercaptoethanol. T cells were grown in RPMI (Sigma) supplemented with 10% fetal calf serum (Biochrom), 1x non-essential amino acids (Sigma), 1% penicillin/streptamycin (Sigma) and 50µM beta-mercaptoethanol.

extract_protocol:
For ChIP-seq cells were crosslinked with 1 % formaldehyde for 10' at 37°C. After cell lysis nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-sepharose or Dyna beads and incubated with the chromatin. After sequential washing and elution with 1 % SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were contructed following manufactor's intructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired,  A tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of a agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system an quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufactor's instructions.
For RNAseq, poly-A RNA was isolated from total with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).
Library preparation was performed by using the NEBnext® mRNA Library Prep Master Mix set for Illumina (E6100S/L) following the instruction manual. Briefly, poly-A RNA was frangmented to generate 200 nucleotides fragments. First and second strand synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 12-15 cycle of PCR and the resulting library was subjected to Illumina GAIIx sequencing according to the manufacturer instructions.

treatment_protocol: U2OS cells were induced with doxycycline (1µg/ml; shMiz1: 0.05µg/ml) for 30h. Acute deletion of Miz1∆POZ was achieved with 200nM 4-OHT.

tag: antibody


title: MEF_-OHT_pInducer-MycWT_-Dox_RNAseq


title: MEF_+OHT_pInducer-MycWT_-Dox_RNAseq


title: MEF_+OHT_pInducer-MycWT_+Dox_RNAseq


title: MEF_Miz1_-OHT_ChIPseq


title: MCIDAS_dnE2F4_3h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)

value: 3h @ 22 deg  after mid-11 (st 13)


title: MEF_-OHT_pInducer-MycWT_+Dox_RNAseq


title: MEF_input_-OHT_ChIPseq


title: MEF_Myc_-OHT_ChIPseq

value: N262 (Santa Cruz, sc764)


title: MCIDAS_dnE2F4_3h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_dnE2F4_3h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)


title: U2OS_pRRL-MycV394D_replicate3_RNAseq

source_name: U2OS cells


title: MCIDAS_3h_RNAseq_rep_3

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MCIDAS_3h_RNAseq_rep_2

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MEF_-/-_pRRL-MycWT_pWZL-Miz1_RNAseq

source_name: MEFs derived from Miz1∆POZ/∆POZ-mice


title: U2OS_pRRL-MycV394D_replicate1_RNAseq


title: U2OS_pRRL-MycV394D_replicate2_RNAseq


title: U2OS_pRRL-MycWT_replicate3_RNAseq


title: MCIDAS_3h_RNAseq_rep_1

description:
Poly-A mrNA
RNAseq (non-stranded)


title: MEF_+/+_pRRL-MycWT_pWZL-Miz1_RNAseq

source_name: MEFs derived from Miz1WT-mice


title: Sample 90b

tag: sample name

tag: agent

value: no treatment (MHB + NACL)

tag: dose

value: 200 mM NaCl


title: Sample 90a


title: U2OS_pRRL-MycWT_replicate1_RNAseq


title: MEF_+/+_pRRL-MycWT_pWZL-GFP_RNAseq


title: MEF_+/+_pRRL-MycV394D_pWZL-GFP_RNAseq


title: U2OS_pRRL-MycWT_replicate2_RNAseq


title: Sample 89b

value: no treatment (Mueller Hinton Broth)


title: Sample 89a


title: MEF_+/+_pRRL-empty_pWZL-GFP_RNAseq


title: Sample 88a

value: meropenem

value: 75% of approximate MIC


title: Sample 87b

value: 25% of approximate MIC


title: MEF_-/-_pRRL-MycWT_pWZL-GFP_RNAseq


title: Sample 87a


title: U2OS_pRRL-empty_replicate1_RNAseq


title: Pancreas_Myc_ChIPseq

source_name: Pancreatic carcinoma cells derived from KrasG12D/+, p53R172H/+-mice


title: U2OS_+Dox_pLKO-shMiz1_replicate2_RNAseq


title: Pancreas_IgG_ChIPseq

value: IgG rabbit (sigma, I5006)


title: Tcell_input_-Dox_ChIPseq

source_name: T-lymphocytes


title: Pancreas_Miz1_ChIPseq


title: Sample 84b

value: ciprofloxacin


title: Tcell_IgG_-Dox_ChIPseq


title: Sample 83b


title: Tcell_input_+Dox_ChIPseq


title: Sample 84a


title: e2f4-GFP_MCIDAS_ChIPseq_input


title: Tcell_IgG_+Dox_ChIPseq


title: U2OS_-Dox_pLKO-empty_replicate1_RNAseq


title: U2OS_+Dox_pLKO-empty_replicate2_RNAseq


title: U2OS_+Dox_pLKO-empty_replicate1_RNAseq


title: Tcell_Miz1_-Dox_ChIPseq


title: Sample 80b


title: Sample 83a


title: U2OS_pRRL-empty_replicate2_RNAseq


title: U2OS_pRRL-empty_replicate3_RNAseq


title: U2OS_+Dox_pLKO-shMiz1_replicate1_RNAseq


title: Tcell_Miz1_+Dox_ChIPseq


title: Tcell_Myc_-Dox_ChIPseq


title: Sample 80a


title: Sample 72b

value: amikacin sulfate


title: U2OS_-Dox_pLKO-empty_replicate2_RNAseq


title: Tcell_Myc_+Dox_ChIPseq


title: Sample 69b

organism: Acinetobacter baumannii 34654


title: Sample 20b

organism: Acinetobacter baumannii 1207552


title: Sample 68b


title: Sample 70b


title: Sample 20a


title: Sample 40b


title: Sample 68a


title: U2OS_AcH4_-Dox_ChIPseq

description: we only used read annotated but not peak called files for our analysis

value: Acteylated Histone H4 (Upstate 06-866)


title: Sample 19b


title: U2OS_AcH4_+Dox_ChIPseq


title: Sample 67b


title: U2OS_AcH3_-Dox_ChIPseq

value: Acteylated Histone H3 (Upstate 06-599)


title: U2OS_AcH3_+Dox_ChIPseq


title: Sample 19a


title: Sample 40a


title: Sample 18b


title: Sample 39b


title: Sample 67a


title: Sample 70a


title: Sample 66b

value: polymyxin-B


title: U2OS_IgG_ChIPseq


title: U2OS_H3K4me3_ChIPseq

value: Histone H3 tri-methyl K4( Abcam, ab8580)


title: U2OS_H3K27ac_ChIPseq

value: Histone H3 acetyl K27 (Upstate, 07-360)


title: U2OS_H3K4me1_ChIPseq

value: Histone H3 mono-methyl K4( Abcam, ab8895)


title: Sample 66a


title: Sample 17b


title: Sample 69a


title: Sample 39a


title: Sample 30b


title: U2OS_-Dox_RNAseq

description: This Sample represents 3 replicates.

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome with BOWTIE v0.12.7 or v0.12.8 using default parameters.
Peak calling was performed with MACS v1.4.2 with default parameters, but: model fold 25 (HeLa-Myc) and 15 (HeLa-Miz1), duplicates 3 (U2OS-Myc) or 10 (U2OS-Miz1).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt file from RNA-seq experiments contain ensembl-ID, gene symbol, log2 fold change, and p(adjust).

source_name: U2OS cells, -Dox, RNA

growth_protocol: U2OS cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (PAA) and penicillin/streptomycin (PAA).

extract_protocol:
For RNA-seq in U2OS cells, poly-A RNA was isolated from total RNA with Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific).
Library preparation was performed by using the NEBnext® mRNA Library Prep Master Mix set for Illumina (E6100S/L) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides fragments. First and second strand synthesis were performed and the resulting cDNA was end-repaired, ligated to NEBnext Adaptor, size selected (250bps) and purified with Qiagen gel extraction kit. cDNA was then amplified with 15 cycle of PCR and the resulting library was subjected to Illumina Genome Analyzer IIx sequencing according to the manufacturer's instructions.

treatment_protocol: U2OS cells were induced with doxycycline (1µg/ml) for 30h.

tag: cell line

tag: doxycycline induction


title: U2OS_input_DNA_-Dox_ChIPseq

data_processing:
Basecalling was performed with the RTA package within the Genome Analyzer Data Collection Software (SCS2.8).
Fastq files were generated by CASAVA only considering high quality sequences (PF-cluster).
Overall sequencing quality was checked with the FastQC script.
Reads were aligned to the human genome with BOWTIE v0.12.7 or v0.12.8 using default parameters.
Peak calling was performed with MACS v1.4.2 with default parameters, but: model fold 25 (HeLa-Myc) and 15 (HeLa-Miz1), duplicates 3 (U2OS-Myc) or 10 (U2OS-Miz1).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: .txt files from ChIP-seq experiments contain peak localisation in a MACS output -bed format.

source_name: U2OS cells, -Dox, input

extract_protocol:
For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10' at 37°C. After cell lysis, nuclei were resuspended in RIPA buffer and sonicated (Bransson) until average fragment size was below 500 bps. Antibodies were bound to Protein-A/G-sepharose or Dyna beads and incubated with the chromatin. After sequential washing and elution with 1% SDS, crosslinking was reverted and DNA was purified using Qiagen PCR purification columns.
Libraries were constructed following manufacturer's instructions (NEBNext ChIP-Seq Sample Prep Kit). Briefly, ChIP DNA was end repaired,  A tailed  and Illumina adaptors were ligated. DNA fragments of about 200 bps were cut out of an agarose gel and extracted with a Qiagen PCR purification column. Afterwards, DNA was enriched with 18 PCR cycles, fragment size was controlled with Biorad Experion system and quantified using picogreen assay. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacturer's instructions.

value: none (input control)


title: Sample 65b


title: Sample 17a


title: U2OS_+Dox_RNAseq

description: This Sample represents 3 replicates.

source_name: U2OS cells, +Dox, RNA


title: Sample 30a


title: U2OS_input_DNA_+Dox_ChIPseq

source_name: U2OS cells, +Dox, input


title: U2OS_pSer2_Pol2_-Dox_ChIPseq

source_name: U2OS cells, -Dox, pSer2 Pol II ChIP

value: anti-Pol II pSer2 (phosphoS2) [Abcam, catalog# ab5095]


title: Sample 65a


title: Sample 64b


title: Sample 18a


title: Sample 27a


title: Sample 27b


title: Sample 16b


title: Sample 15b


title: U2OS_pSer2_Pol2_+Dox_ChIPseq

source_name: U2OS cells, +Dox, pSer2 Pol II ChIP


title: Sample 24b


title: Sample 63b


title: U2OS_pSer5_Pol2_+Dox_ChIPseq

source_name: U2OS cells, +Dox, pSer5 Pol II ChIP

value: anti-Pol II pSer5 (4H8) [Covance]


title: U2OS_pSer5_Pol2_-Dox_ChIPseq

source_name: U2OS cells, -Dox, pSer5 Pol II ChIP


title: Sample 15a


title: U2OS_total_Pol2_-Dox_ChIPseq

source_name: U2OS cells, -Dox, total Pol II ChIP

value: anti-Pol II (N-20) [Santa Cruz, catalog# sc899]


title: Sample 62b


title: U2OS_total_Pol2_+Dox_ChIPseq

source_name: U2OS cells, +Dox, total Pol II ChIP


title: Sample 14a


title: Sample 28a


title: Sample 13b


title: U2OS_Miz1_-Dox_ChIPseq

source_name: U2OS cells, -Dox, Miz1 ChIP

value: anti-Miz (10E2)


title: Sample 62a


title: Sample 23a


title: Sample 61b


title: U2OS_Miz1_+Dox_ChIPseq

source_name: U2OS cells, +Dox, Miz1 ChIP


title: Sample 12a


title: Sample 12b


title: Sample 13a


title: Sample 61a


title: Sample 60a

organism: Acinetobacter sp. 1592897

value: no treatment (MHB + NACL)

value: 200 mM NaCl


title: Sample 63a

value: 25% of approximate MIC


title: Sample 58a

value: meropenem

value: 75% of approximate MIC


title: Sample 64a

value: ciprofloxacin


title: Sample 24a


title: Sample 14b


title: U2OS_Myc_-Dox_ChIPseq

source_name: U2OS cells, -Dox, Myc ChIP

value: anti-c-Myc (N262) [Santa Cruz, catalog# sc764]


title: Sample 11b

value: amikacin sulfate


title: Sample 57b


title: Sample 11a


title: HeLa_input DNA_ChIPseq

source_name: HeLa cells, input

growth_protocol: HeLa cells were grown in DMEM (Sigma) supplemented with 10% fetal calf serum (PAA) and penicillin/streptomycin (PAA).

value: HeLa


title: Sample 23b


title: Sample 57a


title: HeLa_RNA Pol II_ChIPseq

source_name: HeLa cells, RNA Pol II ChIP

value: RNA Polymerase II 8WG16 Monoclonal Antibody [Covance, catalog# MMS-126R]


title: Sample 10b

organism: Acinetobacter sp. 1000160


title: U2OS_Myc_+Dox_ChIPseq

source_name: U2OS cells, +Dox, Myc ChIP


title: Sample 54b


title: Sample 10a


title: Sample 53b


title: Sample 9a

value: no treatment (Mueller Hinton Broth)


title: HeLa_Miz1_ChIPseq

source_name: HeLa cells, Miz1 ChIP

value: anti-Miz (residues 637-803) antibody [non-commercial; lab-prepared]


title: Sample 8a


title: Sample 60b


title: Sample 59b


title: Sample 8b


title: RRBS_E14

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

description: DNA was tretaed with EpiTect Bisulfite Kits (Qiagen)

data_processing:
Basecalls performed using CASAVA version 1.8
Reads for genotyping_E14 were aligned to the mouse genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1.
Reads for genotyping with the same mapping positions were collapsed into one using the rmdup tool from SAMtools. Variants calling was performed using the mpileup tool from SAMtools . Next, we used VCFtools v0.1.11 (http://vcftools.sourceforge.net/) to select only SNVs with coverage  >= 10 and a frequency  >= 0.5. Moreover, using custom Perl scripts we discarded sites with more than one variant call at the same place. These data can be found at: http://epigenetics.hugef-research.org/data.php
Reads for RRBS_E14 were aligned to the mouse genome assembly using BSMAP v2.74 using the following parameters: -r 0 -n 1
Methylation status was peformed using Methratio tool of BSMAP.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of RRBS were performed using custom perl script.

source_name: ESC E14

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
For genotyping_E14 the genomic DNA was sonicated for 17' pulse 30"ON/30"OFF high with Bioruptor Twin (Diagenode). Libraries were generated with DNA Sample Prep Kit (Illumina) and sequenced on Illumina HiScanSQ Platform.
For RRBS the genomic DNA was digested O/N with MspI (New England Biolabs). Libraries were generated with DNA Sample Prep Kit (Illumina), bisulfite converted using EpiTect Bisulfite Kits (Qiagen)  and sequenced on Illumina HiScanSQ Platform."

tag: genotype/variation

value: wt


title: Sample 6b

value: polymyxin-B


title: HeLa_Myc_ChIPseq

source_name: HeLa cells, Myc ChIP

value: c-Myc antibody (N262) [Santa Cruz,  catalog# sc764]


title: MCF7 Input Veh

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

data_processing:
The reads were mapped to the human reference genome (UCSC HG19) using Bowtie (version 1.0.0) (Langmead et al., 2009).
Peak-calling was done by Model based analysis of ChIP-seq (MACS version 1.4.2) (Zhang et al., 2008).
Coverage was normalized on the total number of mapped reads per hundred million.
Genome_build: hg19
Supplementary_files_format_and_content: WIG, normalized

source_name: MCF7 breast cancer cells

extract_protocol:
Cells were crosslinked with 1% Formaldehyde for 10 or 20 minutes and quenched with 125 mM Glycine. The nuclear pellets were sonicated to the fragment range of 200-400 bp. Sonicated extracts were incubated with specific antibodies at 4˚C overnight and ChIP-immune complexes were pulled down using Protein A sepharose.
Library preparations were done using NEBnext Ultra DNA library preparation kit according to the manufacturer’s instructions.

treatment_protocol: After 2 days of hormone deprivation, MCF7 cells were treated with 30 minutes of 150 nM JQ1 treatment prior to 10 nmol/L 17-β-estradiol  (Sigma-Aldrich) treatment for 2 hours. DMSO and vehicle were added as negative controls.

tag: cell type

value: Human breast adenocarcinoma


title: Sample 55b


title: Sample 9b


title: Sample 54a


title: Sample 53a


title: Sample 7b


title: Sample 56b


title: Sample 59a


title: Sample 51b


title: Sample 7a


title: H2Bub1 E2 rep3

tag: chip-seq antibody

value: H2Bub1 D11 (5546 from Cell signaling, 1.5 µL used)


title: Sample 58b


title: genotyping_E14

data_processing:
Basecalls performed using CASAVA version 1.8
Reads for genotyping_E14 were aligned to the mouse genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1.
Reads for genotyping with the same mapping positions were collapsed into one using the rmdup tool from SAMtools. Variants calling was performed using the mpileup tool from SAMtools . Next, we used VCFtools v0.1.11 (http://vcftools.sourceforge.net/) to select only SNVs with coverage >= 10 and a frequency >= 0.5. Moreover, using custom Perl scripts we discarded sites with more than one variant call at the same place. These data can be found at: http://epigenetics.hugef-research.org/data.php
Reads for RRBS_E14 were aligned to the mouse genome assembly using BSMAP v2.74 using the following parameters: -r 0 -n 1
Methylation status was peformed using Methratio tool of BSMAP.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of RRBS were performed using custom perl script.


title: Sample 16a


title: Sample 51a


title: Sample 6a


title: MCF7 Input E2


title: H2Bub1 E2 rep1


title: Sample 56a


title: Sample 5b


title: Sample 2a


title: Sample 50b

organism: Acinetobacter sp. 1564232

value: no treatment (MHB + NACL)


title: Sample 5a


title: H2Bub1 JQ1 E2 rep3

organism: Homo sapiens


title: H2Bub1 E2 rep2


title: Sample 4b


title: Sample 1a


title: Sample 49a


title: H2Bub1 JQ1 Veh rep1


title: Sample 55a


title: H2Bub1 JQ1 Veh rep2


title: Sample 48b


title: H2Bub1 Veh rep2


title: Sample 4a


title: H2Bub1 JQ1 E2 rep1


title: ERα JQ1 E2 rep3

value: ERα HC-20 (sc543 from Santa Cruz, 1 µg used)


title: Sample 52a


title: Sample 3a

value: 25% of approximate MIC


title: ERα JQ1 E2 rep1


title: H2Bub1 JQ1 E2 rep2


title: Sample 46a


title: Sample 52b


title: H2Bub1 JQ1 Veh rep3


title: Sample 3b


title: Sample 45a


title: Sample 50a

value: 200 mM NaCl


title: BRD4 E2 rep3

description: Cells were crosslinked with 1 % formaldehyde for 20 minutes.

value: BRD4 N-terminal antibody (Wu at al., 2006) (4 µl used)


title: ERα E2 rep1


title: Sample 1b


title: Sample 43b

value: ciprofloxacin


title: BRD4 E2 rep2


title: BRD4 E2 rep1


title: ERα JQ1 E2 rep2


title: Sample 2b

value: 75% of approximate MIC


title: Sample 49b


title: BRD4 Veh rep3


title: H2Bub1 Veh rep3


title: Sample 48a

value: meropenem


title: Sample 47b


title: H2Bub1 Veh rep1


title: BRD4 Veh rep2


title: Sample 47a


title: Sample 42b

value: amikacin sulfate


title: Sample 45b


title: Sample 46b


title: idm1idm2_MethylC-Seq

description: treated with bisulfite

source_name: Seedlings

value: idm1idm2 mutant

value: 14 day-old seedlings


title: Sample 41a


title: Sample 41b


title: ERα E2 rep3


title: BRD4 Veh rep1


title: day 4.75 total RNA, biological replicate 3

status: Public on Jul 09 2014

city: San Francisco

first: Gladstone

last: Bioinformatics

address: 1650 Owens St

department: Data Science and Biotechnology

institute: Gladstone Institutes

description:
Aligned reads from 100bp paired end FASTQ files
* Note: each replicate corresponds to cells from the same differentiation (e.g., replicate 1 in each group is from the SAME differentiation)

data_processing:
Trimming: Fastq-mcf (version 488) was used to trim off poor-quality ends of reads before alignment, with the following (default) settings:     -s N.N   Log scale for adapter minimum-length-match (2.2)       -t N     % occurance threshold before adapter clipping (0.25)       -m N     Minimum clip length, overrides scaled auto (1)       -p N     Maximum adapter difference percentage (10)       -l N     Minimum remaining sequence length (19)       -L N     Maximum remaining sequence length (none)       -D N     Remove duplicate reads : Read_1 has an identical N bases (0)       -k N     sKew percentage-less-than causing cycle removal (2)       -x N     'N' (Bad read) percentage causing cycle removal (20)       -q N     quality threshold causing base removal (10)       -w N     window-size for quality trimming (1)
Alignment to mm9 with Tophat v 2.0.10, with parameters: "--min-anchor=5 --segment-length=25 --no-coverage-search --segment-mismatches=2 --splice-mismatches=2 --num-threads=8 --mate-inner-dist=50"
Alignment: GTF annotation file used by Tophat was a combination of two files: 1) Ensembl iGenome for mouse (mm9), version NCBIM37.67, and the file 2) NONCODEv4 lincRNA annotation
Filtering: aligned reads with reported MAPQ quality of less than 30 were removed.
Differential expression and tallying of reads into each gene / feature was performed by USeq's "DefinedRegionsDifferentialSeq" version 8.6.4.
Genome_build: mm9
Supplementary_files_format_and_content: fpkm

organism: Mus musculus

source_name: embryonic stem cell

extract_protocol:
Total RNA from cells described above was harvested Qiagen RNEasy kit. Library was generated using NuGen mouse FFPE kit.
Libraries were prepared using the Illumina protocols

tag: sample group

value: total RNA, day 4.75

value: day 4.75 total = the entire population of cells, both GFP+ and GFP- at d4.75 before sorting

tag: treatment

value: From differentiation ID # 3

value: W4/129S6 ES cells (from Taconic) derived from 129S6/SvEvTac


title: day 4.75 sorted GFP positive RNA, biological replicate 2

value: day 4.75, GFP+

value: day 4.75 GFP positive = sorted GFP positive cells at d4.75, cells that have committed to the cardiac lineage.

value: From differentiation ID # 2


title: ERα E2 rep2

value: Human breast adenocarcinoma

value: ERα HC-20 (sc543 from Santa Cruz, 1 µg used)


title: day 4.75 sorted GFP negative RNA, biological replicate 1

value: day 4.75, GFP negative

value: day 4.75 GFP negative = sorted GFP negative cells at d4.75, cells that have not committed to the cardiac lineage

value: From differentiation ID # 1


title: Sample 44a

value: ciprofloxacin

value: 75% of approximate MIC


title: day 4.75 sorted GFP negative RNA, biological replicate 3


title: Sample 44b


title: day 4.75 total RNA, biological replicate 2


title: day 4.75 total RNA, biological replicate 1


title: Sample 43a

value: 25% of approximate MIC


title: Emx1-Cre-7sp animal 2

city: new york

first: Andrew

last: Pollock

state: New York

address: 1300 York Ave

department: Cell and Developmental Biology

institute: Weill Cornell Medical College

description: Emx1-Cre activated miR-7 sponge

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome and RPKM calculated using Gobyweb1.7
Genome_build: mm9
Supplementary_files_format_and_content: wig and bed files

source_name: E12.5 dorsal cortex

growth_protocol: mice were maintained using standard husbandry protocols.

extract_protocol:
embryonic cortices were removed, and total RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: brain/dorsal cortex

tag: background strain


title: Wild-type animal 3

tag: tissue


title: Emx1-Cre-7sp animal 1

description: Emx1-Cre activated miR-7 sponge


title: Wild-type animal 2


title: Wild-type animal 1


title: mRNAs from F. graminearum wild-type Z-3639 after 1 h after incubation in PDB+1 M NaCl

city: Seoul

first: Hokyoung

last: Son

address: Daehak-dong, Gwanak-gu

department: Center for Food and Bioconvergence

institute: Seoul National University

data_processing:
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads 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 was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (manually proccessed version of 'ASM24013v3' accessible at http://mips.gsf.de/genre/proj/FGDB/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample

organism: Fusarium graminearum

source_name: Fungi culture

growth_protocol: Each fungal strain was grown in potato dextrose broth (PDB) with or wihtout 1 M NaCl supplementation for an hour

extract_protocol:
Total RNA was extracted from mycelia in liquid nitrogen using the Easy-Spin Total RNA Extraction Kit (Intron Biotech, Seongnam, Korea).
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol

tag: strain background

value: wild-type

tag: cultured in

value: potato dextrose broth+ 1M NaCl for 1hr


title: Sample 42a

value: amikacin sulfate


title: RNA-seq of normal mice sperm

city: shanghai

first: Zhongdong

last: Qiao

address: NO.800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

data_processing:
The “OLB” and “CASAVA” software programs allowed the retrieval of the original fastq sequence data.
Using the fastx package, clean reads were attained.
“TOPHAT” was used after the reads and junction reads were mapped to the reference sequence.
The gene expression data estimated from the RPKM values were obtained using “Cuffinks”.
Genome_build: mm8
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample ...

source_name: spermatozoa

extract_protocol:
RNA was extracted using Trizol reagent. TruSeqTM DNA Sample Prep Kit-Set A  was used with 20 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After an adult male mouse (approximately 9-10 weeks of age) was sacrificed, the cauda of the epididymis was carefully isolated, and the spermatozoa were forced out after a nick was cut in the cauda epididymis. The isolated spermatozoa were suspended in HTF (Human Tube Fluid: 5.9 g/L NaCl, 0.35 g/L KCl, 0.049 g/L MgSO4.7H2O, 0.054 g/L KH2PO4, 0.57 g/L CaCl2, 2.1 g/L NaHCO3, 0.5 g/L Glucose, 3.4 ml/L sodium lactate, 0.037 g/L sodium pyruvate, 0.075 g/L ampicillin, 0.05 g/L streptomycin, 4 g/L BSA, 0.002g/L phenol red) for subsequent treatments.

tag: strain

value: adult


title: day 4.75 sorted GFP positive RNA, biological replicate 1

value: W4/129S6 ES cells (from Taconic) derived from 129S6/SvEvTac


title: day 4.75 sorted GFP positive RNA, biological replicate 3

value: day 4.75, GFP+

value: From differentiation ID # 3


title: day 4.75 sorted GFP negative RNA, biological replicate 2

value: From differentiation ID # 2


title: mock-transfected tRNA/rRNA-depeleted RNA-seq

status: Public on Jul 08 2014

city: Cambridge

first: Stephen

last: Eichhorn

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

data_processing:
The raw read files for all the poly(A)-selected RNA-seq samples were combined into a single file. The same was done for the raw read files for the tRNA/rRNA-depleted RNA-seq samples as well as the ribosome profiling samples.
All reads containing the 20-nt sequences representing the donor, acceptor and junction of each circRNA, respectively, were counted using a custom Perl script. The circular fraction for each circRNA was calculated based on the read counts.
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text file containing the counts and statistics for each circRNA for the poly(A)-selected RNA-seq, tRNA/rRNA-depleted RNA-seq, and ribosome profiling samples.

source_name: U2OS cells

extract_protocol:
mRNA-seq: Total mRNA was either depleted of tRNAs/rRNAs or used for poly(A)-selection. In both cases, the RNA was randomly fragmented by partial alkaline hydrolysis and then size-selected RNA fragments (25-45 nt) were used for library preparation. Ribosome profiling: Cell extracts were processed exactly as described in Guo et al., 2010 (GSE22004)
Libraries were constructed exactly as described in Guo et al., 2010 (GSE22004)

treatment_protocol: All samples were treated with cycloheximide (100ug/mL) for 8 minutes immediately prior to harvesting.

tag: transfection

value: mock

tag: time

value: 32 hours


title: miR-155-transfected poly(A)-selected RNA-seq

value: miR-155 duplex


title: miR-1-transfected poly(A)-selected RNA-seq

value: miR-1 duplex


title: mock-transfected poly(A)-selected RNA-seq


title: MNase Sperm Pellet 100 Units

city: Worcester

first: Benjamin

middle: R

last: Carone

state: Massachusetts

address: 364 Plantation St

department: BMP

institute: UMass Medical School

description: Pellet Fraction of DNA fragments resulting from Microccocal nuclease (100 Units) digestion of sperm chromatin.

data_processing:
Removal of 3' adapter sequences using eautils 1.1.2.
Alignment of trimmed sequences to genome using Bowtie v2-2.2.2.
Creation of BigWig using standard scripts in Samtools v0.1.16 and bedGraphToBigWig (available at UCSC genome).
Tab-delimited txt files representing alignment of deepseq libraries to Transcriptional Start Site (TSS) in 20bp windows upstream and downstream of TSS 2000bp using the program SeqMiner v1.3.3e.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: BigWig, tab-delimited text files.

source_name: Sperm, 100 units MNase, pellet

growth_protocol: E14 ES cells were cultured on gelatin-coated dishes without feeder cells in standard media containing serum and LIF at 37°C with 5% CO2.

extract_protocol:
Permeabilized ES and sperm nuclei were treated with 10 Units/10^6cells and 1 Unit/10^8cells of micrococcal nuclease (Worthington), respectively, for 5 min @ 37°C. Reaction was stopped with the addition of 10 mM EGTA on ice. For ES cells, nuclei were incubated for 4 hrs at 4°C with rotation, pelleted at 5000g for 5 min, and separated into supernatant and pellet (spun) or were treated the same without centrifugation and separation (unspun). After MNase digestion of sperm nuclei, digestion was centrifuged for 5000g for 5 min.
To characterize the entire range of MNase digestion products, we generated paired-end libraries of DNA fragments from both ES and sperm digestions and performed sequencing using Illumina HiSeq technology. Libraries were prepared as described in PMID: 22025700.

treatment_protocol: Sperm were isolated from the caudal epididymis and vas deferens of 10-week-old C57/6J mice by lacerating tissue in 1 mL of 37°C M2 medium (Sigma). Sperm were allowed to swim up for 1 hr, washed 1X in water, 1X PBS, crosslinked at 37°C with 1% formaldehyde for 15 min, quenched with 250mM glycine for 5 min and frozen in liquid nitrogen.

tag: strain/background

tag: age

value: 10 weeks

value: sperm

tag: chromatin preparation

value: Micrococcal Nuclease

tag: micrococcal nuclease units

tag: fraction

value: pellet

tag: antibody


title: MNase Sperm Pellet 20 Units

description: Pellet Fraction of DNA fragments resulting from Microccocal nuclease (5 Units) digestion of sperm chromatin.

source_name: Sperm, 20 units MNase, pellet


title: MNase Sperm Pellet 5 Units

description: Pellet Fraction of DNA fragments resulting from Microccocal nuclease (2 Units) digestion of sperm chromatin.

source_name: Sperm, 5 units MNase, pellet


title: MNase Sperm Supernatant 20 Units

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease (20 Units) digestion of sperm chromatin.

source_name: Sperm, 20 units MNase, supernatant

value: supernatant


title: mouse embryonic stem cell, biological replicate 2

value: mESC

tag: cell type

value: mouse embryonic stem cells

tag: cell line


title: mouse embryonic stem cell, biological replicate 3

tag: sample group

tag: treatment


title: mouse embryonic stem cell, biological replicate 1

value: From differentiation ID # 1


title: MNase Sperm Unspun 50 Units

description: Non-Separated Fraction of DNA fragments resulting from Microccocal nuclease (50 Units) digestion of sperm chromatin.

source_name: Sperm, 50 units MNase, unspun

value: non-separated


title: mRNAs from F. graminearum fss1 overexpression mutant after 1 h after incubation in PDB+1 M NaCl

tag: genotype/variation

value: fss1::gen-Pef1a-fss1; fss1 overexpression mutant

value: potato dextrose broth+ 1M NaCl for 1hr


title: Emx1-Cre-7sp animal 3

description: Emx1-Cre activated miR-7 sponge

tag: developmental stage

tag: tissue

value: brain/dorsal cortex

tag: background strain


title: mRNAs from F. graminearum fss1 deletion mutant after 1 h after incubation in PDB+1 M NaCl

tag: strain background

value: Δfss1::gen; fss1 deletion mutant

tag: cultured in


title: MNase Sperm Unspun 2 Units

description: Non-Separated Fraction of DNA fragments resulting from Microccocal nuclease (2 Units) digestion of sperm chromatin.

source_name: Sperm, 2 units MNase, unspun


title: mRNAs from F. graminearum fss1 overexpression mutant after 1 h after incubation in PDB

value: potato dextrose broth for 1hr


title: MNase Sperm Pellet 1 Unit

description: Pellet Fraction of DNA fragments resulting from Microccocal nuclease (1 Units) digestion of sperm chromatin.

source_name: Sperm, 1 unit MNase, pellet


title: Sperm PanH3 ChIP

description: ChIP with panH3 antibody in mouse sperm.

source_name: Sperm, PanH3 ChIP

value: BioRuptor sonication


title: mRNAs from F. graminearum fss1 deletion mutant after 1 h after incubation in PDB


title: Sample24_HDF_2

city: La Jolla

first: Robert

middle: E

last: Morey

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

data_processing:
RNA-Seq reads were trimmed and mapped to the hg19 reference using STAR (version 2.3.0.1)
Samtools (version 0.1.17) was then used to sort, merge, and eliminate duplicate reads
Expression levels for each gene were quantified using the python script rpkmforgenes and annotated using RefSeq (archive-2012-03-09-03-24-410). Genes that did not have at least one sample with at least ten reads were removed from the analysis.
The data was normalized using the R (version 3.0.1) package DESeq (version 1.12.0) and batch corrected using the R script ComBat. Batch correction can create negative values.
Differential expression analysis was done using ANOVA in Qlucore Omics Explorer 2.3
Transcripts with an adjusted P-Value less than 0.05 were considered differentially expressed.
All enrichment analysis was performed using GREAT (v. 2.0.2)8 with default settings.
genome build: hg19
processed data files format and content: txt file including DESeq normalized counts filtered for genes with at least 10 reads in at least one sample

source_name: Human Dermal Fibroblast

growth_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Cells were transduced by retro virus-based iPSC vectors as previously reported (Lowry, W. E. et al. Generation of human induced pluripotent stem cells from dermal fibroblasts. Proceedings of the National Academy of Sciences of the United States of America 105, 2883-2888, doi:10.1073/pnas.0711983105 (2008)). Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols (Tachibana, M. et al. Human embryonic stem cells derived by somatic cell nuclear transfer. Cell 153, 1228-1238, doi:10.1016/j.cell.2013.05.006 (2013)).

extract_protocol:
RNA was isolated (TRIzol Reagent, Life Technologies, Inc.) quantified (Qubit RNA Assay Kit, Life Technologies, Inc.) and quality controlled (RNA6000 Nano Kit and BioAnalyzer 2100, Agilent).
Approximately 500 ng was used as input for the Illumina TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, Inc.) and sequencing libraries were created according to the manufacturer’s protocol. Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented and copied into first strand cDNA using random primers and reverse transcriptase. Second strand cDNA synthesis was then done using DNA Polymerase I and RNase H. The cDNA was then ligated to adapters and enriched with PCR to create the final cDNA library. The library was then pooled and sequenced on a HiSeq 2000 (Illumina, Inc.) instrument as per manufacturer’s instructions. Sequencing was performed up to 2 X 101 cycles.

treatment_protocol: Fetal origin human dermal fibroblasts (HDF) were acquired from ScienCell Research Laboratories (catalog # 2300) and cultured in DMEM/F12 with 10% fetal bovine serum (FBS). Genetically matched iPSCs were generated by transductions of the same HDF culture with  retroviral or Sendai virus vectors carrying OCT4, SOX2, KLF4, and MYC. Sendai virus-based reprogramming was carried out according to the manufacturer’s protocol (CytoTune™-iPS Reprogramming Kit, Life Technologies, Inc). Colonies with typical morphology were isolated and manually propagated similar to NT-ESC and IVF-ESC protocols.

value: Fibroblast

value: Tissue


title: mRNAs from F. graminearum wild-type Z-3639 after 1 h after incubation in PDB

value: wild-type


title: Sample23_iPS-S3_2

source_name: induced Pluripotent Stem Cell

value: Human Pluripotent Stem Cell

value: Sendai-Virus Derived


title: miR-155-transfected tRNA/rRNA-depeleted RNA-seq

tag: transfection

value: miR-155 duplex

tag: time

value: 32 hours


title: s_1_1_bovine

city: Giessen

first: Birgit

last: Samans

address: Heinrich-Buff-Ring 26-28

institute: University of Giessen

data_processing:
Alignment: The sequencing reads were aligned to the precompiled bosTau7/hg19 genome using the short read aligner Bowtie.
Peak calling: peak calling was done using MACS with the settings: --nomodel -nolambda --shiftsize=75 --bw 140 --name s_1_1 --gsize=3e9 --tsize=50 --keep-dup=1.
The selection of common peaks in two replicate samples was done using Bedtools suite.
Genome_build: GRCh37
Genome_build: bosTau7
Supplementary_files_format_and_content: bed file: Nucleosome positions.

organism: Bos taurus

source_name: bovine sperm

growth_protocol: We used fresh ejaculates without prior freezing.

extract_protocol:
10 million sperm cells were diluted in PBS and incubated with 0.1% Lysolecithin. After 10mM DTT treatment, freed chromatin was digested with 20U micrococcal nuclease and centrifuged at 10000 rpm to separate nucleosomal (supernatant) from protamine fraction (pellet). Total DNA from nucleosomal fraction was isolated and separated on 2% agarose gel. 146 bp mono-nucleosomal DNA fragment was purified from the gel (NucleoSpin-Gel-clean-up-Kit, Macherey-Nagel).
100 ng of mono-nucleosomal DNA were applied for preparation of the DNA library. DNA samples underwent end repair, dA-tailing and adaptor ligation according to the provider's protocol (Library preparation master mix kit, New England Biolabs).

tag: breed

value: Holstein-Friesian

tag: gender

value: male

value: sperm


title: miR-155-transfected ribosome profiling


title: MNase Sperm Supernatant 100 Units

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease (100 Units) digestion of sperm chromatin.

source_name: Sperm, 100 units MNase, supernatant

tag: strain/background

tag: age

value: 10 weeks

tag: chromatin preparation

value: Micrococcal Nuclease

tag: micrococcal nuclease units

value: supernatant


title: MNase Sperm Supernatant 5 Units

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease (5 Units) digestion of sperm chromatin.

source_name: Sperm, 5 units MNase, supernatant

tag: fraction

tag: antibody


title: Sample21_iPS-S2_2

tag: cell type

tag: cell line


title: Sample22_iPS-S3_1


title: MNase Sperm Supernatant 1 Unit

description: Supernatant Fraction of DNA fragments resulting from Microccocal nuclease (1 Units) digestion of sperm chromatin.

source_name: Sperm, 1 unit MNase, supernatant


title: Sperm input

description: Non-antibody selected input used for panH3 pulldown in mouse sperm.

source_name: Sperm, input


title: mock-transfected ribosome profiling

value: mock


title: MNase Sperm Unspun 10 Units

description: Non-Separated Fraction of DNA fragments resulting from Microccocal nuclease (10 Units) digestion of sperm chromatin.

source_name: Sperm, 10 units MNase, unspun

value: non-separated


title: s_5_1_bovine


title: Sample20_iPS-S1_2


title: Sample18_iPS-R1_2

value: Retro-Virus Derived


title: Sample16_hESO7_2

source_name: Human Embryonic Stem Cell

value: IVF Derived


title: Sample13_NT2_2

source_name: Nuclear Transfer Stem Cell

value: Nuclear Transfer Derived


title: Sample19_iPS-R2_2


title: Sample12_NT1_2


title: rpoS_15min_rep1

city: Norman

first: James

last: Creecy

address: 770 Van Vleet Oval

department: Microbiology

institute: University of Oklahoma

data_processing:
The raw data output (XSEQ files) from the SOLiD 4 Genetic Analyzer System are passed through the ABI Sequence Accuracy Enhancement Tool (SAET)
For alignment of the SAET reads to the E. coli MG1655 reference genome (RefSeq NC_000913), the short read alignment tool Bowtie ver. 1.8 (Langmead, et al., PMID 19261174) was utilized in three consecutive passes for each sample dataset. For the first pass, we use paired end color space mapping with a distance cutoff of 350 bases between read mates. Bowtie parameters were set to include only perfect matches and suppress reads that map to more than one genome location, i.e., uniquely mapped reads are retained. In practice we found the efficiency of paired end mapping was between 3 and 10%. To improve the overall alignment we mapped the orphan 5’ and 3’ end reads in two additional passes with Bowtie. The output of the three passes through Bowtie was three SAM files for each sample. Overall, we achieved 40-60% mapping efficiency with this three-pass strategy.
Used SAMTOOLS (Li, et al., PMID 1950593) to sort and index the SAM files obtained from Bowtie and convert them to BAM format.
Sequence data was processed by conversion of the sample alignment (BAM) files to strand-specific base count (WIG) files. To accomplish this an in-house script was created to extract strand-specific base count data from BAM files (outputs are positive and negative strand WIG files). First, the script reads in the paired-end BAM file and counts the nucleotides spanning inserts between the mated 5’ and 3’ reads. Next, the script pulls in the orphan 5’ and 3’ reads from the respective BAM files and increments the base counts at each base location without duplicating the reads already incremented from the paired ends.
WIG files were normalized by using an in-house script that reads in the raw WIG files while excluding counts from all 22 rRNA genes. A simple global normalization approach was utilized that multiplied the count at each base location by 1 billion and divides that value by the sum of base counts at all base locations in the file. This normalization strategy is anlogous to the Total Count approach used for normalizing gene-specific read alignments. In this way, the base counts are expressed as parts per billion.
WIG files were viewed and annotated using Jbrowse and Integrated Genome Viewer.
Genome_build: ASM584v1; Reference genome for E. coli MG1655 (RefSeq NC_000913). Paper title:Escherichia coli K-12: a cooperatively developed annotation snapshot--2005
Supplementary_files_format_and_content: WIG files are provided showing uniquely mapped sequence reads (normalized).

organism: Escherichia coli K-12

growth_protocol: Wild type E. coli K-12 (strain BW38038) and BW39452(ΔrpoS) cultures were grown on MOPS glucose minimal medium with 0.2% glucose as sole carbon source in a 2L B. Braun Biostat® B fermenter with working volume of 1 L MOPS minimal medium with 0.2% glucose, at 37°C, pH was kept constant at 7.4 by the addition of 1 M NaOH, and dissolved oxygen was maintained above 40% of saturation by adjusting the agitation speeds in the range of 270–500 rpm with fixed 1.5 liter/min air flow. Culture samples were harvested by using a homemade sampling device seven times during logarithmic growth and three times following entry into stationary phase for the WT and two times during logarithmic phase and three times during stationary phase for the rpoS mutant. OD600 measurements were made on a Beckman Coulter DU 800 spectrophotometer. Samples were harvested directly into ice-cold RNAlater at a 1:1 dilution to protect RNA from degradation and cells then were pelleted by centrifugation at 8000rpm for 10 minutes. Cell pellets were stored at -80°C in an equal volume of RNAlater prior to RNA extraction.

extract_protocol:
All samples were extracted using the Qiagen Rnasey Mini Kit, following standard protocol
cDNA libraries were constructed at Purdue using an adapted SOLiD Total RNA-Seq Kit. Total RNA (DNase I digested) was fragmented by RNase III. RNA samples labeled as TEX were also subsequently digested with Terminator Exonuclease (TEX). Pyrophosphate groups were removed from the 5′ terminus using tobacco acid pyrophosphatase (TAP), and an RNA adapter was ligated to the 5′ end of the RNA. First-strand synthesis was performed using standard SOLiD 4 Total RNA-Seq protocol. RNA-seq via SOLiD 4 sequencing of libraries prepared by ligation based chemistry to provide strand-specific datasets.

treatment_protocol: Prior to total RNA extraction harvested bacterial cells were stored at -80.0°C in an equal volume of RNAlater.

tag: sub strain

tag: phase of growth

value: 15 min post stationary

tag: rna treatment

value: rRNA depleted

tag: strain


title: rpoS_30min_rep2

value: 30 min post stationary


title: rpoS_30min_rep1


title: rpoS_04_TEX

value: Log phase OD 0.4

value: rRNA depleted; Terminal Exonuclease


title: ∆vib-1 Avicel #1

city: Berkeley

first: N. Louise

last: Glass

address: 341 Koshland Hall, Univerisity of California

department: Plant and Microbial Biology

institute: UC Berkeley

data_processing:
Basecalling performed using Illumina CASAVA_v1.8.0 software
Reads were mapped to known transcripts with Tophat v2.0.4 (options: --GTF)
Fragments Per exon Kilobase per Megabase read (FPKM) were calculated with Cufflinks v2.0.2 (options: -u -b -G  --max-bundle-frags=10000000)
Differential Expression was estimated with Cuffdiff v2.0.2 (options: -u -b -G  --max-bundle-frags=10000000)
Genome_build: N. crassa: OR74A version 10 from the Broad Institute
Supplementary_files_format_and_content: FPKM

organism: Neurospora crassa

source_name: mycelia

growth_protocol: N. crassa strains were innoculated in 100mL Liquid media with 2% sucrose, grown 16 hours at 25ºC 200rpm and constant light. Mycelia were washed once in media with no carbon sourse and resuspended in fresh media with 2% Avicel PH-10 or without carbon sources, then grown an additional 4hrs at 25ºC.

extract_protocol:
Mycelia were harvested by filtration and flash frozen in liquid nitrogen. Total RNA was extracted by bead-beating in TRIZOL reagent and purified with RNeasy kit from Qiagen.
mRNA was enriched with oligo-dT magnetic beads, fragmented and reverse transcribed with Superscript II reverse polymerase from Invitrogen. Illumina adapters were added to the cDNA library with the TruSeq DNA kit v2, SetA

tag: genotype

value: ∆vib-1 a

tag: treatment

value: Avicel


title: WT_30min_TEX


title: rpoS_16_rep1

value: Late log phase OD 1.6


title: MNase Sperm Unspun .5 Units

description: Non-Separated Fraction of DNA fragments resulting from Microccocal nuclease (.5 Units) digestion of sperm chromatin.

source_name: Sperm, .5 units MNase, unspun

tag: tissue

value: sperm


title: rpoS_04_rep2


title: Sample17_hESO8_2

value: Human Pluripotent Stem Cell


title: Sample14_NT3_2


title: Sample15_NT4_2


title: 201B

city: Boston

first: Shirley

last: Liu

address: 450 Brookline Ave

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute and Harvard School of Public Health

data_processing:
Alignment: Captured bisulfite reads were mapped to the human genome (hg19) using bsmap with default parameters.
Mixing ratio determination: mappable bisulfite reads were used as input for predicting mixing ratio (alpha1) by MethylPurify with default parameters.
DMR identification: MethylPurify used mixing ratio (alpha1) and mappable bisulfite reads to calculate methylation levels of the two components within each sliding window to identify differential methylated regions (DMRs).
Genome_build: hg19

source_name: lung adenocarcinoma tissue

extract_protocol:
Genomic DNA from the tumor and corresponding adjacent tissues was prepared using the QIAamp DNA Blood Mini Kit(Qiagen) following the manufacturer’s instructions. Prior to the library construction, 3µg of genomic DNA from each sample was fragmented using a Covarias sonication system to mean sizes of approximately 200-300bp. After fragmentation, libraries were constructed according to the Illumina Paired-End protocol. Briefly, the purified, randomly fragmented DNA was treated with a mix of T4 DNA polymerase, Klenow fragments, T4 polynucleotide kinase and a nucleotide triphosphate mix to repair the ends by blunting and phosphorylation. The blunted DNA fragments were subsequently 3’-adenylated using the Klenow fragment (3’-5’exo) and ligated by T4 DNA ligase to adapters synthesized with 5’ –methyl-cytosine instead of cytosine. The adaptor-ligated library was purified using AMPure XP beads (Beckman Coulter Genomics). 500 ng of each library was hybridized to Agilent SureSelect Methyl-Seq biotinylated RNA baits (84 Mb) for 24 h at 65 C. Biotinylated target hybrids were captured on Dynal MyOne Streptavidin T1 (Invitrogen), and purified through MinElute PCR column (Qiagen). Bisulfite conversion of the purified captured library was performed using the EZ DNA Methylation Gold Kit (Zymo Research) as per manufacturer’s instructions. The bisulfite converted captured library was amplified by PCR with 14 PCR cycles, then purified by AMPure XP beads and quantified by Agilent 2100 system and qPCR. Methyl-Seq libraries were then sequenced on the HiSeq 2000 platform according to the manufacturer’s instructions, and 2 ×90bp paired-end reads were generated.
Methyl-Seq libraries were prepared for sequencing using standard Illumina protocols.

tag: patient id

tag: smoking status

value: non-smoker

value: lung adenocarcinoma tissue

value: female


title: 156B-2

tag: gender


title: rpoS_30min_TEX


title: 137C

source_name: corresponding lymph node metastasis tissue


title: 156A-2

source_name: adjacent nomal lung tissue

value: adjacent nomal lung tissue


title: rpoS_180min_rep1

value: 180 min post stationary


title: 201A


title: WT_30min_rep2


title: WT_180min_rep1

value: no RNA treatment


title: rpoS_04_rep1


title: WT_04_TEX


title: WT_30min_rep1


title: WT_30min-R_rep1


title: 137A


title: 137B


title: WT_15min_rep1


title: 109A-2

value: male


title: 109C

value: corresponding lymph node metastasis tissue


title: WT_04_rep2

value: rRNA depleted


title: 109B


title: WT_08_rep1

value: Log phase OD 0.8


title: WT_16_rep1


title: 75A-2

value: smoker


title: WT_16-R_rep1


title: WT_04_rep1

value: Log phase OD 0.4


title: WT_14_rep1

value: Log phase OD 1.4


title: Sample11_HDF

value: Fibroblast

value: Parental


title: Sample10_iPS-S2

value: Sendai-Virus Derived


title: Sample8_iPS-R2

value: Human Pluripotent Stem Cell

value: Retro-Virus Derived


title: WT_03_rep1

value: Log phase OD 0.3


title: Sample9_iPS-S1


title: Pc clr-2; ∆vib-1 No Carbon #3

value: Pc clr-2 (∆clr-2 at native locus, clr-2 under ccg-1 promoter at the his-3 locus); ∆vib-1 A

value: No Carbon


title: WT_02_rep1

value: Log phase OD 0.2


title: WT_01_rep1

value: Log phase OD 0.1

value: no RNA treatment


title: Sample7_iPS-R1


title: Sample5_hESO7

value: IVF Derived


title: Sample6_hESO8


title: Sample4_NT4

value: Nuclear Transfer Derived


title: ∆vib-1 Avicel #2

value: ∆vib-1 a

value: Avicel


title: Sample3_NT3


title: Pc clr-2; ∆vib-1 No Carbon #2


title: ∆vib-1 Avicel #3


title: miR-1-transfected tRNA/rRNA-depeleted RNA-seq

source_name: U2OS cells

tag: transfection

value: miR-1 duplex

tag: time

value: 32 hours


title: ∆vib-1 No Carbon #2


title: Sample2_NT2


title: 75B

value: smoker

value: lung adenocarcinoma tissue

value: male


title: Pc clr-2; ∆vib-1 No Carbon #1


title: Sample1_NT1

value: Human Pluripotent Stem Cell


title: miR-1-transfected ribosome profiling


title: WT_04-R_rep1

value: Log phase OD 0.4

value: rRNA depleted


title: ∆vib-1 No Carbon #1