title: heatshock_1x_CHX

description: ribosome-protected RNA fragments


title: oxidative_100x_CHX_rep1

status: Public on Aug 01 2014

type: SRA

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

country: USA

institute: Brigham and Women's Hospital

description: ribosome-protected RNA fragments

library_source: transcriptomic

data_processing:
Library strategy: Ribo-seq
Barcode and adapter sequences are deleted
Only footprints longer than 22 nt are left for analysis.
alignment was done with Bowtie 0.12.7
first nucleotide of each read was removed before alignment.
duplicated gene pairs were combined in a single virtual "gene" record
Genome_build: Saccharomyces cerevisiae S288C genome, SGD release
Series supplementary file contents: 1) Expression_Table.txt contains quantitation of gene expression as rpkm values
Series supplementary file contents: 2) Ribosome_occupancy_plots.txt contants the footprint densities over ORFs. It can se used to quickly plot all the ribosome ocupancy graphs as was done in our manuscript.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: cultured cell suspension

growth_protocol: YPD media, 30 °C

extract_protocol:
size fractionation
circ-ligation

treatment_protocol: To induce oxidative stress, cells were treated with 0.2 mM hydrogen peroxide. Concentrations of cycloheximide ranging from 1.56 to 10,000 ug/ml were used

tag: strain

tag: primer set

value: Set #2


title: oxidative_8x_CHX

description: ribosome-protected RNA fragments


title: heatshock_noCHX

description: ribosome-protected RNA fragments


title: small_subunit

description: ribosome-protected RNA fragments

value: Set #1


title: complete_SD_media

description: ribosome-protected RNA fragments


title: oxidative_1/64x_CHX

description: ribosome-protected RNA fragments


title: oxidative_1/4x_CHX

description: ribosome-protected RNA fragments


title: unstressed_100x_CHX_rep1

description: ribosome-protected RNA fragments


title: oxidative_noCHX

description: ribosome-protected RNA fragments


title: oxidative_100x_CHX_rep2

description: ribosome-protected RNA fragments


title: unstressed_1/4x_CHX

description: ribosome-protected RNA fragments


title: unstressed_100x_CHX_rep2

description: ribosome-protected RNA fragments


title: unstressed_1x_CHX

description: ribosome-protected RNA fragments


title: unstressed_1/64x_CHX

description: ribosome-protected RNA fragments


title: unstressed_noCHX

description: ribosome-protected RNA fragments


title: unstressed_1/16x_CHX

description: ribosome-protected RNA fragments


title: aurin_noCHX

description: ribosome-protected RNA fragments


title: P14 (RNA-Seq) replicate1

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Basecalling with Illumina software (OLB v1.8)
Fastx quality trimmer was used to remove low quality bases from the 3' end of the read (base quality <30)
The mouse genome was downloaded from the Ensembl ftp site (version GRCm38.70/mm10).  Reads were aligned to the mouse genome with Olego aligner with default settings.
Reads aligning to Ensembl-annotated exons with a strict mapping quality (Q≥20) were counted with BedTools and used to construct a data matrix comprising genes with an average of 10 reads or more per sample across the experiment. Differential gene expression analysis was performed using edgeR (v3.2.4).
Genome_build: GRCm38.70/mm10
Supplementary_files_format_and_content: Count matrix

organism: Mus musculus

source_name: Cardiac left ventricle - neonatal day 14

growth_protocol: Experimental Animals and Tissue Collection: All protocols were approved by The University of Queensland Animal Ethics Committee. Male C57BL/6 mice (The Jackson Laboratory, ME) were used for genome-wide DNA methylation and mRNA expression profiling during post-natal development (P1 and P14). For DNA and RNA analysis, atrial tissues were removed from ventricles (septum intact) and ventricles were blotted and weighed before snap-freezing in liquid nitrogen for storage at -80C.

extract_protocol:
Cardiac ventricles were harvested at P1 and P14 (n=9 per group) from C57BL6/J mice as described above and were homogenised in PBS. Three individual hearts were pooled per replicate. RNA was isolated by TRIzol extraction (Ambion) followed by QiaQuick MinElute cleanup including on-column DNase digestion. RNA quality was verified with MultiNA bioanalyzer (Shimadzu, Kyoto). Purified mRNA was prepared using Dynabeads® Oligo (dT)25 (Ambion) enrichment.
Libraries were generated using the NEBNext® mRNA Library Prep Reagent Set for Illumina (New England Biolabs). Libraries were validated on MultiNA bioanalyzer and sequenced at a concentration of 10 pM on Genome Analyzer IIx instrument for 36 cycles. Illumina base-calling was performed off-line with OLB v1.8.

tag: gender

value: Male

tag: age

tag: tissue

value: cardiac left ventricle


title: P14 (RNA-Seq) replicate3


title: P14 (RNA-Seq) replicate2


title: P1 (RNA-Seq) replicate3

source_name: Cardiac left ventricle - neonatal day 1


title: oxidative_1x_CHX

description: ribosome-protected RNA fragments


title: P1 (RNA-Seq) replicate2


title: P14 (MBD-Seq) replicate3

library_source: genomic

data_processing:
Basecalling with Illumina pipeline software (OLB v1.8)
Fastx quality trimmer was used to remove low quality bases from the 3' end of the read (base quality <30)
The mouse genome was downloaded from the Ensembl ftp site (version GRCm38.70/mm10).  Reads were aligned to the mouse genome with BWA (aln algorithm v0.6) with default settings. GRCm38.70
Datasets from each developmental stage were pooled and peak identification was performed using MACS peak caller with default settings. Annotation of differentially methylated regions (DMRs) with Ensembl genes was performed with BedTools intersect command. Reads aligned to DMRs with a strict mapping quality (Q≥20) were counted with BedTools and used to construct a data matrix consisting of regions with an average of 10 reads or more per sample across the experiment. Statistical significance of these regions was ascertained using edgeR (v3.2.4) with the independent replicate data.
Genome_build: GRCm38.70/mm10
Supplementary_files_format_and_content: Count matrix

molecule: genomic DNA

extract_protocol:
Genomic DNA for DNA methylation profiling was isolated using the DNeasy Blood & Tissue Kit (Qiagen). DNA was fragmented by BioRuptor sonication (Diagenode, Denville, NJ). Fragmented DNA was analyzed with bioanalyzer, and 1microgram of sonicated DNA underwent methyl-CpG enrichment using the MethylMiner™ Methylated DNA Enrichment Kit (Invitrogen).
Library preparation was undertaken using 5 ng of methyl-enriched DNA using the NEBNext DNA Library Preparation Kit for Illumina (New England Biolabs). Library DNA was quantified with MultiNA capillary electrophoresis instrument with DNA-500 kit. Libraries were sequenced at a concentration of 10 pM on Genome Analyzer IIx instrument for 36 cycles. Illumina base-calling was performed off-line with OLB v1.8.


title: oxidative_1/16x_CHX

description: ribosome-protected RNA fragments


title: P1 (RNA-Seq) replicate1


title: unstressed_8x_CHX

description: ribosome-protected RNA fragments


title: P14 (MBD-Seq) replicate1


title: P1 (MBD-Seq) replicate3


title: P1 (MBD-Seq) replicate2


title: P14 (MBD-Seq) replicate2


title: Normoxia (scrambled control) hMeDIP-seq

city: Taoyuang

first: Kou-Juey

last: Wu

state: Taiwan

address: No.15, Wenhua 1st Road, Gueishan Dist

department: Cancer Genome Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital at Linkou

data_processing:
All the 5hmc-enriched DNAs were sequenced using Illumina Hiseq2000 containing more than 2.5x107 , 50 bp single-end reads per sample. Raw sequence reads were
mapped onto the reference human genome (NCBI Build UCSC hg19) using the Bowtie v0.12.7 algorithm (-m 1 -v 3 --best --strata). Unique and monoclonal reads were used
for further analysis. The distribution of 5hmC reads at promoters or in gene body regions were analyzed by PAVIS.
Genome_build: hg19

organism: Homo sapiens

source_name: A human epithelial cell line, FaDu, from a squamous cell carcinoma of the hypopharynx

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

extract_protocol:
Extraction was performed using TriZol and routine protocol.
Genomic DNA was prepared using a genomic DNA extraction kit (QIAGEN, Germany) and sonicated with Bioruptor (Diagenode Inc. USA) to produce random fragments ranging in mean size from 300 to 1,000 bp. 2 µg of fragmented DNA was denatured for 10 min at 95°C and immunoprecipitated for 16 hr at 4°C with 5 µl of 5-methylcytidine antibody (Eurogentec, Germany) in a final volume of 250 µl IP buffer (150 mM NaCl, 1mM EDTA, 1mM EGTA, 2.5mM sodium pyrophosphate, 1mM β-glycerophosphate, 0.05% Triton X-100). The mixture was incubated with 50 µl protein A beads for another 4 hr at 4°C and washed three times with 1 ml of IP buffer. Beads were resuspended with 500 µl digestion buffer (50 mM Tris [pH 8.0], 10 mM EDTA, 1% SDS) containing 10µl proteinase K (20 mg/ml stock) overnight at 65°C. D

tag: cell line

value: FADU

tag: treatment

value: Normaxia

tag: tet1 knockdown

value: NO


title: Hypoxia (TET1-si) hMeDIP-seq

value: Hypoxia (Oxygen deprivation was carried out in an incubator with 1% O2, 5% CO2 and 94% N2 for 19 h.)

value: Yes


title: Normoxia (TET1-si) hMeDIP-seq


title: P1 (MBD-Seq) replicate1


title: Hypoxia (scrambled control) hMeDIP-seq

value: Hypoxia (Oxygen deprivation was carried out in an incubator with 1% O2, 5% CO2 and 94% N2 for 18 h.)


title: Normoxia (scrambled control)

data_processing:
The reads were aligned to the hg19 reference assembly with the TopHat/Cufflinks
alignment package using Ensembl annotations. Transcript abundance was measured
in fragments per 23 kilobase of exon per million fragments mapped (FPKM).
Genome_build: hg19

extract_protocol:
Extraction was performed using TriZol and routine protocol.
The RNA-Seq libraries were prepared according to the standard Illumina protocol with the mRNAseq Illumina TruSeq and were sequenced using Illumina Hiseq2000 to obtain 100 bp single end reads.


title: Normoxia (TET1-si)


title: Hypoxia (scrambled control)


title: Hypoxia (TET1-si)


title: RNA-seq_598-SKD_3dDox_rep2

city: South San Francisco

first: Matt

last: Grimmer

state: CA

address: 455 E Grand Ave.

department: Oncology Bioinformatics

institute: Genentech

data_processing:
Illumina Casava1.7.1a5 software used for basecalling.
For ChIP-seq, fastq files were mapped to human genome version GRCh37/hg19 using Bowtie 2.0.1 (34) with default parameters to produce SAM files. SAM files were converted to BAM files using SAMTools (35). BAM files were converted to BED files using BEDTools (36). In order to call ChIP-seq peaks, BED files were submitted individually (each with a similarly mapped MCF7 input BED file as a background reference) to the Sole-Search Tool (37) with the following parameters: permutation number, 5; average chromatin fragment size, 150; alpha value, 0.001; peak merge distance, 0; histone blur, no. Resulting GFF format peak files were sorted by peak height and truncated to the number of peaks in the smallest replicate for each set. The top 40% of peaks for each truncated replicate were tested for statistically significant overlap versus corresponding replicate total peak files using the Sole-Search GFF-overlap Tool. All 40% replicate peak files satisfied the ENCODE standard of 80% overlap with truncated corresponding replicates (http://bit.ly/ 1bAFFGp). Corresponding replicates were then submitted simultaneously as merged sets to the Sole-Search Tool for peak calling, producing sets of merged GFF peak files and SGR visualization files. Again using the Sole-Search GFF-overlap Tool, peaks for each ATF variation that overlapped with pT3-empty-vector GFF files or with regions of aneuploidy in MCF-7 cells were removed to eliminate possible artifacts not resulting from ATF binding. Remaining ATF peak sets were sorted by peak height and plotted against peak rank to select high-confidence (HC) peaks (Supplementary Figures S1A and B), along with visual inspection of SGR format visualization files. The Homer genomic suite of tools (38) was used for tag density plots (annotatePeaks.pl), scatter plots (annotatePeaks.pl), overlap analysis (mergePeaks), genomic locations (annotatePeaks.pl) and de novo motif finding (findMotifsGenome.pl). De novo motif finding for the top 4000 peaks from each HC ATF peak set was performed using all hg19 RefSeq gene promoters as a background for statistical comparison and all nucleotides within the peaks, as called by the Sole-Search tool, were subjected to the analysis. The resulting predominant motif position weight matrix files for each ATF were used to search for the presence of significant motif matches among the top 2500 HC peaks for each ATF. The predominant motif position weight matrix files were restricted to single nucleotide tolerances to represent partial target sequences in order to search the entire genome for instances of partial target sites using annotatePeaks.pl. Histone ChIP-seq enrichment values for all RefSeq promoter regions (TSS ± 1 kb) were calculated from the average tags per bp using annotatePeaks.pl within each promoter region. Tag density plots for histone enrichment at different promoter categories (downregulated, unchanged, upregulated and unbound) were calculated using the -hist 200 option of annotatePeaks.pl. H3K4me3 plots and enrichments before and after induction were compared to ENCODE datasets for H3K4me3 in MCF7 (wgEncodeEH000967) to ensure that uninduced profiles are representative of MCF7 cells.
For Bisulfite-seq, raw reads were mapped with [programs/parameters], and percent methyl-C/C was calculated for every CpG dinucleotide in the human genome. All CpG dinucleotides with a minimum sequencing coverage of 3× were used for downstream analyses. To determine the average DNA methylation surrounding a region of interest, the annotatePeaks tool of the HOMER suite was used with the ‘-ratio’ option and a bin size of 200 bp.
For RNA-seq, prealignment QA/QC and base trimming were performed in Partek Flow v3.0.14.0321 using fastqc and quality trim. Reads were mapped to the Gencode version 19 of the human hg19 reference genome using Tophat (39). Quantification to the transcriptome was performed by Partek expectation maximization (EM). The Partek Flow software suite was made available through the USC Norris Medical Library Bioinformatics Services (http://norris.usc.libguides. com/nml-bioinfo). Genes with a FDR less than 0.05 and a change in expression greater than 2-fold were counted as differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peak files in gff format, the peaks are called from the merged of all replicated samples
Supplementary_files_format_and_content: Bisulfite-seq Bed files in BED 6+2 format
Supplementary_files_format_and_content: tab-delimited text file with expression values, significance values, FDR values, and statistical model information

source_name: Human breast adenocarcinoma cell-line MCF7

growth_protocol: Thawing Cells:  1. Thaw vial immediately in 37º C water bath. Keep O ring above the water surface to prevent contamination. Thaw content with slight  shake until only small ice is left in vial. It usually takes 1 min. Spray vial with 70% ethanol all over and wipe its surface with clean tissue in the hood.  2. Open the vial and transfer the content to a 15 ml Falcon tube already containing 5 ml of fresh medium.  3. Spin down at 1000 rpm or 200g for 3 to 5 mins at 4º C. Aspirate supernatant.  4. Resuspend cells in fresh medium and transfer to 150mm x 25mm tissue culture dish.  5. Check the cells under microscope.  6. Cells are cultured in CO2 incubator and medium is changed about every 3 days.  7. It usually takes 3 days or more for cells to recovery from freezing. After cell culture reaches  80-85%  confluence, subculture is conducted. Subculture ratio is about 1:3 or 1:4.  Passaging Cells:  1. Observe cells to see how confluent they are, whether the cells are alive, whether the cells are contaminated, and whether the cells have the correct morphology. After cell culture reaches 80 to 85% confluence, subculture is conducted  2. Remove media from dish  3. Wash 1x with 10 ml of PBS  4. Add 5 ml of Trypsin and trypsinize for 3 min at 37C. Whack hard – you should see the cells coming down. (Important: never overtrypsinize the cells, so work quickly)  5. Add 5 ml of media and use it to rinse the dish to detach the cells off (4 to 5 times)  6. Spin down at 1000rpm for 3 to 5 min at room temperature. Aspirate supernatant  7. Add 15 ml of media to 15ml tube containing cell pellet, and pipette up and down to mix  8. Add 15 ml of media to each new 150mm x 25mm tissue culture dish (we split 1 dish into 3 to 4 dishes)  9. Add 5mls of cell culturecontaining media to each tissue culture dish. Make sure the media covers the entire area of the dish. Put the cells into 37C with 5% CO2.

extract_protocol:
For HA-tag ChIP-seq, stable MCF7 cell lines were induced using 100 ng/ml doxycycline (Sigma) at 0 h, doxycycline media was refreshed at 48 h, and cells were harvested at 72 h by crosslinking in a final concentration of 1% formaldehyde. Crosslinking was stopped after 5 min by adding glycine to a final concentration of 125 mM. Crosslinked cells were washed in cold phosphate buffered saline, lysed using 1 ml low-salt IP buffer (150 mM NaCl, 50 mM Tris-HCl (pH7.5), 5 mM EDTA, NP-40 (0.5%), Triton X-100 (1%) containing protease inhibitors) and aliquoted at 1 × 10∧7 cells/ml.
For Bisufite-seq, 2 microgram of genomic DNA was isolated using a QIAeasy DNA mini kit (Qiagen, Venlo, The Netherlands) and sonicated using a Covaris to an average molecular weight of 150 bp. Achievement of the desired size range was verified by Bioanalyzer (Agilent) analysis. Fragmented DNA was repaired to generate blunt ends using the END-It kit (Epicentre Biotechnologies, Madison, WI) according to manufacturer’s instructions. Following incubation, the treated DNA was purified using AmpureX beads from Agencourt. In general, magnetic beads were employed for all nucleic acid purifications in the following protocol. Following end repair, A-tailing  was performed using the NEB dA-tailing module according to manufacturer’s instructions (New England Biolabs, Ipswich, MA). Adapters with a 3′ ‘T’ overhang were then ligated to the end-modified DNA. For whole genome bisulfite sequencing, modified Illumina paired-end (PE) adapters were used in which cytosine bases in the adapter are replaced with 5-methylcytosine bases. Depending on the specific application, we utilized either Early Access Methylation Adapter Oligos that do not contain barcodes, or the adapters present in later versions of the Illumina DNA Sample Preparation kits, which contain both indices and methylated cytosines. Ligation was carried out using ultrapure, rapid T4 ligase (Enzymatics, Beverly, MA) according to manufacturer’s instructions. The final product was then purified with magnetic beads to yield an adapter-ligation mix. Prior to bisulfite conversion, bacteriophage lambda DNA that had been through the same library preparation protocol described above to generate adapter-ligation mixes was combined with the genomic sample adapter ligation mix at 0.5% w/w. Adapter-ligation mixes were then bisulfite converted using the Zymo DNA Methylation Gold kit (Zymo Research, Orange, CA) according to the manufacturer’s recommendations. Final modified product was purified by magnetic beads and eluted in a final volume of 20 µl. Amplification of one-half the adapter-ligated library was performed using Kapa HiFi-U Ready Mix for the following protocol: 98º 2′ ; then six cycles of 98º 30′ ′ , 65º 15′′, 72º 60′′; with a final 72º 10′ extension, in a 50 µl total volume reaction. The final library product was examined on the Agilent Bioanalyzer, then quantified using the Kapa Biosystems Library Quantification kit according to manufacturer’s instructions. Optimal concentrations to get the right cluster density were determined empirically but tended to be higher than for non-bisulfite libraries.
RNA was harvested using the Qiagen RNeasy kit and Illumina libraries were made with the Illumina TruSeq Stranded mRNA Sample Prep kit according to the manufacturer’s instructions.

treatment_protocol: ATF plasmids were designed and stably integrated into MCF7 cells as described in (Stolzenburg et al. 2012). Stable lines were grown at 30–80% confluency in Dulbecco’s Modified Eagle’s Medium (Corning, Corning, NY) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen, Life Technologies, Grand Island, NY) and 1% penicillin/streptomycin; cells were selected using 5 µg/ml puromycin (VWR, Radnor, PA) and 200 µg/ml G418 (VWR, Radnor, PA). ATF expression was induced by treatment with media containing 1µg/ml doxycycline (VWR, Radnor, PA) at 0 h, doxycycline media was refreshed at 48 h, and cells were harvested at 72 h. ATF expression was confirmed by hemagglutinin (HA) tag western blot prior to HA ChIP-seq, histone ChIP-seq and RNA-seq analysis.

tag: transgene

value: ZNF :598-SKD

tag: dox tx

value: 3 days


title: RNA-seq_598-SKD_0dDox_rep3

value: 0 days


title: RNA-seq_598-SKD_0dDox_rep2


title: RNA-seq_598-SKD_0dDox_rep1


title: H3K9ac_ChIP_598-SKD_3dDox

tag: chip antibody


title: WGBS_598-SKD_0dDox


title: H3K9me3_ChIP_598-SKD_3dDox


title: H3K9me3_ChIP_598-SKD_0dDox


title: H3K4me3_ChIP_598-SKD_3dDox


title: H3K9ac_ChIP_598-SKD_0dDox


title: HA_ChIP_598-SKD_rep3

value: HA


title: H3K4me3_ChIP_598-SKD_0dDox


title: HA_ChIP_598-SKD_rep1


title: E2a_MO_rep1_RNASeq_ATCACG

city: Stanford

first: Andrea

middle: E.

last: Wills

address: 300 Pasteur Drive

department: Genetics

institute: Stanford School of Medicine

data_processing:
RNA-Seq reads were aligned to the X. tropicalis genome using Bowtie.
FPKM normalization was performed, and mean normalized expression values are compared in the processed data file for each gene
Genome_build: UCSC XenTro2

organism: Xenopus tropicalis

source_name: E2a-depleted embryos

growth_protocol: Embryos were raised in 1/9 MR to stage 10.5 (Nieuwkoop and Faber staging criteria)

extract_protocol:
400ng of mRNA was used for library preparation following methods published in Tan et al. Genome Research 2013.
Total RNA was isolated by homogenizing embryos in SDS/PK buffer for 1 hr, followed by phenol/chloroform extraction and ethanol/NH4OAc precipitation.  mRNA was isolated from total RNA using Oligo-DT Dynabeads (Invitrogen).

tag: embryonic stage

value: Stage 10.5

tag: barcode

value: ATCACG


title: E2a_MO_rep2_RNASeq_CGATGT

value: CGATGT


title: Ctrl_rep2_RNASeq_TGACCA

source_name: Control embryos

value: TGACCA


title: HA_ChIP_598-SKD_rep2


title: HA_ChIP_552-SKD_rep3

value: ZNF :552-SKD


title: Ctrl_rep1_RNASeq_TAGCTT

value: TAGCTT


title: RNA-seq_598-SKD_3dDox_rep3


title: HA_ChIP_598_rep2


title: HA_ChIP_552-SKD_rep2


title: RNA-seq_598-SKD_3dDox_rep1


title: Input_Smad2_ctrl2_e2a1_e2a2_pf.fastq.gz

description: input control for samples 2, 3 and 4

data_processing:
ChIP-Seq reads are mapped to xenTro2 genome using the bwa-sw tool. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
ChIP-seq homer-output  as an excel file contains annotated peaks for Samples
Genome_build: UCSC XenTro2

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) 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. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 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 II or HiSeq following the manufacturer's protocols.
Embryos were fixed for 1hr in 1% formaldehyde, glycine treated and frozen.  Embryos were then homogenized, sonicated, and centrifuged to remove yolk and cytoplasm.  Nuclei were complexed with antibody.

tag: chip characteristics


title: HA_ChIP_552-SKD_rep1


title: HA_ChIP_552_rep2


title: HA_ChIP_598_rep1


title: HA_ChIP_552_rep1


title: E2a_MO_Smad2_Lib2


title: HA_ChIP_Empty_vector_rep1

value: empty vector


title: E2a_MO_Smad2_Lib1


title: MCF10A CDH1-/- rep2

city: Dunedin

first: Augustine

last: Chen

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

description: MCF10A with CDH1 gene deleted

data_processing:
FastQC was used to perform an initial quality check on the data
base calling software: bcl2fastq, no mismatch.
The “bowtie2” (version 2.0.0-beta5 ) and “cufflinks” (version 2.0.1) software packages were used to align the read data to human genome build GRC37, and generate read counts for each gene.
Removal of PCR duplicates was performed using the “MarkDuplicates” tool within the “picard-tools” (version 1.7.4) software.
The per gene read counts were imported into the statistical software package R (www.r-project.org), and analyzed using the functionality included in the edgeR and limma packages. Briefly, TMM (trimmed mean of M values) normalization was applied to generate normalized count data, and the the lmFit command was used to fit a liner model to the data for each gene. Normalized data were converted to log-cpm (counts per million reads) prior to analysis using the voom command in limma.
Genome_build: human genome build GRC37, Build date: May 14
Supplementary_files_format_and_content: Differential expression results for the two comparisons of interest (CDH1 vs MCF10a_0mM) were written to CSV files, viewable in Excel (limma moderated t- statistic produced for each comparison, per gene, with FDR p-value adjustment applied).
Supplementary_files_format_and_content: The per gene read counts were imported into the statistical software package R (www.r-project.org), and analyzed using the functionality included in the edgeR and limma packages. Briefly, TMM (trimmed mean of M values) normalization was applied to generate normalized count data, and the the lmFit command was used to fit a liner model to the data for each gene. Normalized data were converted to log-cpm (counts per million reads) prior to analysis using the voom command in limma.

source_name: MCF10A CDH1-/-

growth_protocol: MCF10A and MCF10A CDH1-/- cells were seeded at densities of 2.0 x 105 and 3.5 x 105 cells respectively in duplicate in a six well dish and grown until 70% confluency, with a medium change at 24 h.

extract_protocol:
Total RNA was extracted at 48 h post seeding using quick-RNA Miniprep Kit (Zymo) according to the manufacturer’s protocol. RNA yield and purity were assessed using Qubit (Invitrogen) and the Agilent 2100 Bioanalyser.
cDNA library preparation was performed by New Zealand Genomics Limited using Illumina TruSeq RNA preparation version 2.0. Each library had inserts of 200bp and sequence reads were generated from one lane of an Illumina HiSeq™ 2000 run.

tag: cell type

value: mammary epithelial cells

tag: cdh1 genotype


title: MCF10A CDH1-/- rep1

description: MCF10A with CDH1 gene deleted


title: MCF10A rep1

description: MCF10A with wildtype CDH1 gene

value: wildtype CDH1


title: MCF10A_mRNA_seq

city: Chicago

first: Kevin

last: White

institute: University of Chicago

data_processing:
Illumina Casava software (v1.5 for Hiseq2000) used for basecalling.
Sequence files were parsed and low quality reads removed using custom Perl scripts.  Reads were then aligned to hg19 using TopHat 1.4.0 default parameters with output in BAM format.  Unmapped reads were removed from further analysis.
Cufflinks (v1.3.0) was used to estimate transcript abundance using RefSeq gene models and Fragments Per Kilobase per Million mapped reads (FPKM) as output, with options -u -b --compatiable hits norm
Genome_build: hg18
Supplementary_files_format_and_content: tab delimited file include FPKM for each gene in the sample

source_name: MCF10A cells

growth_protocol: The cells were maintained in DMEM/F12 medium containing 5% horse serum, and supplemented with EGF (20 ng/ml), hydrocortisone (0.5 ng/ml), cholera toxin (100ng/ml), penicillin (100 U/ml) and 100 mg/ml streptomycin (100 mg/ml).  Cells were cultured at 37°C and in 5% CO2.

extract_protocol:
2 micrograms of RNA was extracted from MCF10A cells using the AllPrep RNA mini kit (Qiagen).
A single-end library was prepared following the protocol of Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001).  The library was indexed with one of the Illumina barcodes and sequenced in 1/4 lane on an Illumina Hiseq 2000.

tag: passages


title: kyp

city: Seattle

first: Christopher

middle: Joel

last: Hale

state: WA

address: 1959 NE Pacific St., HSC H-458

department: Pathology

institute: University of Washington

description:
Bisulfite-treated genomic DNA
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... non-multiplexed: 1 lane

data_processing:
BS-seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics), allowing up to 2 mismatches and retaining only uniquely mapping reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: Samples 1..6: Fixed step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with each line representing the methylation level (#methylated cytosines sequenced/#total cytosines sequenced) in a 50bp bin.
Supplementary_files_format_and_content: Samples 7..8: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: bp position and methylation level (#methylated cytosines sequenced/#total cytosines sequenced).
Supplementary_files_format_and_content: Sample 9: Variable step UCSC Genome Browser wiggle format files for each chromosome for each cytosine context (CG, CHG, or CHH where H=A,T,C) with each line representing the methylation level (#methylated cytosines sequenced/#total cytosines sequenced).

organism: Arabidopsis thaliana

source_name: 3-week old leaf

growth_protocol: All plants were grown at 22 degrees celsius in constant light.

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013

tag: genotype/variation

value: kyp mutant

tag: ecotype

value: Columbia

tag: sample

value: leaf

value: 3-week old


title: FLAG-KYP

value: kyp mutant carrying a FLAG-tagged wildtype KYP protein

tag: age


title: Head 1-2 day old Female small RNAs

city: Cold Spring Harbor

first: Delphine

last: Fagegaltier

state: NY

address: One Bungtown Rd

department: Genomics Division

institute: Cold Spring Harbor Lab

data_processing:
The 3' linker (CTGTAGGCACCATCAATCGTATGCCGTCTTCTGCTTG) sequence is clipped from the sequenced reads with fastx-clipper.
Only reads with a minimum length of 16nt are kept for further processing.
Sequencing artifacts (reads with all but 3 identical bases) are filtered out.
Identical reads are collapsed with fastq_collapser; Reads sequence and count are provided in Read_Count_Table processed files.
Genome_build: dm3 BDGP release 5
Supplementary_files_format_and_content: Processed data text files contain processed Read_ID, processed Read_Sequence and Read_Count

organism: Drosophila melanogaster

source_name: Head 1-2 day old Female

growth_protocol: Flies were reared on standard food at 24oC and staged according to regular procedures.

extract_protocol:
Total RNAs were prepared with Trizol reagent (Invitrogen). After 2S rRNA removal,18-30nt small RNAs were size selected on a 15% polyacrylamide, 7M urea gel.
Small RNA libraries were prepared according to Malone et al. Cold Spring Harb Protoc. 2012. In short, size selected RNAs are ligated with a 3' adaptor (Modban) with mutant T4 RNA ligase 2, truncated (home made) and ligated products extracted from a 15%  polyacrylamide, 7M urea gel. A 5’ adaptor is then added with T4 RNA ligase (Ambion) and selected ligated products reverse transcribed with Superscript lll reverse transcriptase (Invitrogen). Amplification of the cDNA using Illumina primers results in a final library sequenced on an Illumina GAIIX platform.

treatment_protocol: Tissues from wild-type flies were manually dissected in cold PBS to exclude contamination with other tissues, then quickly frozen in liquid nitrogen to preserve RNA integrity.

tag: developmental stage

value: 1-2 day old Adult

tag: strain

value: Oregon-R (wild-type)

tag: tissue

value: Head

tag: Sex

value: Female


title: Body (head removed) 1-2 day old Male  small RNAs

source_name: Body (head removed) 1-2 day old Male

value: Body (head removed)

value: Male


title: L3 salivary glands Female small RNAs

source_name: L3 salivary glands Female

value: L3 Larvae

value: Salivary glands


title: Head 1-2 day old Male  small RNAs

source_name: Head 1-2 day old Male


title: Body (head removed) 1-2 day old Female  small RNAs

source_name: Body (head removed) 1-2 day old Female


title: Y591F

description:
Bisulfite-treated genomic DNA
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/4 lane

extract_protocol:
phenol-chloroform extraction followed by bisulfite treatment
converted and fragmented genomic DNA library as described in Stroud et al., Cell 2013 with the modification that Illumina TruSeq adapters were used to allow for multiplexing.

value: kyp mutant carrying a KYP transgene with a Y591F mutation


title: FLAG-KYP (for complementation)


title: L3 salivary glands  Male small RNAs

source_name: L3 salivary glands  Male

value: L3 larvae


title: Y475F

description:
Bisulfite-treated genomic DNA
genomic DNA isolated by phenol/chloroform and bisulfite treated; quality scores in _qseq files are Phred scale with +64 ASCII offset... multiplexed: 1/7 lane

value: kyp mutant carrying a KYP transgene with a Y475F mutation


title: kyp (for complementation)


title: MCF10A rep2

description: MCF10A with wildtype CDH1 gene

value: mammary epithelial cells

tag: cell line

value: wildtype CDH1


title: 120 min replicate 2

city: Corvallis

first: Kristina

middle: M

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

description:
HTS923
mRNA profiling

data_processing:
Base-calling software was RTA 1.13.48, CASAVA v1.8.2
Reads were aligned to the Neurospora genome with TopHat v2.0.5 (-a 5 -m 1 -i 30 -I 2000 --library-type fr-unstranded).
FPKM and fold-changes were calculated using the cuffdiff command from version 2 of the Cufflinks suite (-b -u).
Genome_build: Neurospora crassa genome assembly 10, Gene annotation 10.6
Supplementary_files_format_and_content: txt file with gene name in column 1 and FPKM in column 2

organism: Neurospora crassa

source_name: mycelium

growth_protocol: 200-ml of Bird’s Medium was inoculated to a final concentration of 107 conidia/ml and grown in the dark  for 24 hrs, at 25oC with orbital shaking (150 rpm)

extract_protocol:
Total RNA was isolated from frozen mycelia using 1 g 180 °C autoclaved Zirconia/Silica Beads (Biospec Products, Inc 11079105Z) and a Mini-BeadBeater-8 with ice-cold 580 µl extraction buffer (100 mM Tris-HCl, pH 7.5; 100 mM LiCl; 20 mM DTT), 420 µL phenol, 420 µL chloroform, and 84 µL 10% SDS. Immediately after removing from -80 °C, mycelia were homogenized by 1 min beating in the bead beater. After 4 min end-over-end rotation, the homogenate was centrifuged at 12000 g at 4 °C for 1 min to separate phases. The aqueous phase was extracted with phenol/chloroform and chloroform and precipitated in 0.3 M NaOAc/ethanol. The pellet was washed twice with 70% ethanol (prepared with DEPC-treated water), briefly air-dried, and then was dissolved in filter-sterilized DEPC-treated water. Poly(A) mRNA was purified from total RNA using oligo-dT cellulose (SACHS and YANOFSKY 1991) for replicate 1 or Ambion Poly(A)Purist MAG kit of replicate 2, and further treated with Ambion Turbo DNase kit and Epicentre mRNA-Only kit.
cDNA was suspended in 300 µl TE in a 1.5 ml TPX micro tube (Diagenode) and sheared using the low energy cycle for 15 min (15 sec on/15 sec off) with a Diagenode Bioruptor whose water bath was maintained at 4°C with a recirculating chiller. Sheared cDNA was transferred to a 1.7 ml polypropylene microcentrifuge tube and precipitated in 0.3 M NaOAc/ethanol.The pellet was washed once with 70% ethanol, air-dried, and dissolved in 15 µl sterile water and stored at -20°C. RNA-Seq library was prepared from 1 µg of sheared DNA using Illumina TruSeq Sample Prep kit. Each sample was ligated to an indexing adapter and selectively enriched through a 10-cycle amplification.

treatment_protocol: Cultures were exposed to white-light using cool white fluorescent bulbs (1200 lux) and cells were harvested in a darkroom at time 0 (dark), 15, 60, 120 and 240 min after light exposure.

tag: strain number

tag: light induction time point

value: 120 min

value: WT

value: mycelia


title: 15 min replicate 2

description:
HTS921
mRNA profiling

value: 15 min


title: 60 min replicate 2

description:
HTS922
mRNA profiling

value: 60 min


title: 240 min replicate 2

description:
HTS924
mRNA profiling

value: 240 min


title: P4 RV Single Cell RNA-Seq-cell 4

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

data_processing:
Processing step: Samples were aligned to the mm9 genome using TopHat v1.4.1. Known junctions from the RefSeq database were provided to TopHat with the -G option. The generation of RPKM data was carried out using GeneSpring 12.6.1-GX-NGS-RV (Agilent Technologies). Read density (nRPKM) in GeneSpring NGS is computed as the normalized read count (DESeq) per kilo base of exon model per Million reads. This is similar to the standard RPKM used in the literature except that it is computed on the normalized read count rather than on the raw read count.
Genome build: mm9
data file format and content: Excel spreadsheet including RPKM values for each Sample in Series.

source_name: Analysis of single cells from P4 renal vesicles

extract_protocol:
The single cell suspension was loaded into the Fluidigm C1 machine. The cell capture, wash and lysis were carried out according to standard Fluidigm protocols. Following capture individual capture sites were examined microscopically to record which chambers received single cells.
The reverse transcription and amplification reactions were carried out using standard Fluidigm (C1 Single-Cell Auto Prep System) methods with the SMARTer Ultra Low Input RNA for Illumina Sequencing Kit (Clontech) and the Advantage 2 PCR Kit (Clontech).   The libraries were prepared with the Nextera XT DNA Sample Preparation Kit (Illumina Technologies).  1ng cDNA was suspended in Tagment DNA Buffer, and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme).  Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research).  The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail, 2 Nextera Indexes (Index 1 (i7) N701-N712 & Index 2(i5) N501-N508) and barcoded according to the following program: one cycle 98C for 30s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min.  The purified DNA was captured on an Illumina flow cell for cluster generation.  Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocols.

treatment_protocol: Kidneys from Tg(Crym-EGFP)GF82Gsat mice were isolated in ice-cold PBS, bisected and minced into pieces <1mm.  The minced kidneys were placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The tubes were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and isolated by FACS.

tag: genotype

value: Tg(Crym-EGFP)82Gsat / MGI:4846969

tag: component sampled

value: renal vesicle

tag: theiler stage

value: mixed background

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: 2 kidneys


title: P4 RV Single Cell RNA-Seq-cell 12


title: Ctrl_Smad2_Lib2

tag: embryonic stage

value: Stage 10.5

tag: chip characteristics

tag: barcode


title: 240 min replicate 1

description:
HTS764
mRNA profiling

tag: genotype/variation


title: P4 RV Single Cell RNA-Seq-cell 44

tag: age


title: Dark replicate 2

description:
HTS920
mRNA profiling

value: 0 min


title: HA_ChIP_Empty_vector_rep2

tag: transgene

value: empty vector

tag: dox tx

value: 3 days

tag: chip antibody

value: HA


title: 120 min replicate 1

description:
HTS763
mRNA profiling

value: 120 min

tag: tissue


title: TAB-Seq: H1 Cell Line treated with BMP4 (r1); 2013_02_22_FISH_SR_flowcell-B/lane4.fastq.gz

status: Public on Aug 02 2014

city: La Jolla

first: UCSD AND

last: SALK

address: Health Sciences Drive

institute: University of California, San Diego

description:
sample_term_id: UBERON_0000088
assay_term_id: NTR_0002490
nucleic_acid_term_id: SO_0000352
Library strategy: TAB-Seq
Library name: GH259B_L4.2013_02_22
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.19753
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.3377
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing: Various levels of processed data files will be made available as this project proceeds.

source_name: H1 Cell Line treated with BMP4, biological replicate 1 (r1); 2013_02_22_FISH_SR_flowcell-B/fastq_files/lane4.fastq.gz

extract_protocol: Library construction protocol: See http://www.nature.com/nprot/journal/v7/n12/full/nprot.2012.137.html

tag: sra sample accession

tag: disease

value: Thomson Laboratory

value: Cell Line

tag: line

tag: lineage

value: embryonic stem cell differentiated by treatment with BMP4

value: H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days

tag: passage

value: 27, including 16 passages in TeSR

tag: medium

value: TeSR

tag: Sex

value: Male

tag: batch

value: Replicate 1

value: DNA Methylation

value: Covaris

value: Sonicate the genomic DNA in 120 µl of EB buffer to the desired size range. We typically sonicate for 55 s using a Covaris system, with a 10% duty cycle, intensity set at 4 and cycle per burst set at 200 in order to achieve the size range of 200-500bp.

value: Standard Illumina adaptor sequence

value: TruSeq

value: Convert 450 ng of adapter -ligated DNA as per MethylCode Kit instructions (InvitrogenMECOV-50)

value: not measured

value: PfuTurbo Cx Hotstart DNA Polymerase, catalog #600410

value: standard Illumina TruSeq

value: undiluted Illumina TruSeq kit PCR primers

value: 2% high-resolution (APEX) agarose gel purification. Excise 250-600bp fragment, followed by MinElute-QG purification.


title: 60 min replicate 1

description:
HTS762
mRNA profiling

tag: strain number

tag: light induction time point

value: 60 min

value: WT

value: mycelia


title: Y593F

value: kyp mutant carrying a KYP transgene with a Y593F mutation

tag: ecotype

value: Columbia

tag: sample

value: leaf

value: 3-week old


title: P4 RV Single Cell RNA-Seq-cell 51

tag: genotype

value: Tg(Crym-EGFP)82Gsat / MGI:4846969

tag: component sampled

value: renal vesicle

tag: theiler stage

tag: age

tag: strain

value: mixed background

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: 2 kidneys


title: Col (for complementation)

tag: genotype/variation

value: wildtype

tag: tissue


title: 15 min replicate 1

description:
HTS761
mRNA profiling

value: 15 min


title: P4 RV Single Cell RNA-Seq-cell 35


title: Dark replicate 1

description:
HTS760
mRNA profiling

value: 0 min


title: P4 RV Single Cell RNA-Seq-cell 27


title: P4 RV Single Cell RNA-Seq-cell 43


title: P4 RV Single Cell RNA-Seq-cell 11


title: P4 RV Single Cell RNA-Seq-cell 58


title: NOK cl1 AkataBX-1 cl4 p31 EBV+

city: Shreveport

first: Rona

middle: S.

last: Scott

state: LA

address: 1501 Kings Highway

department: Microbiology and Immunology

institute: Louisiana State University Health Sciences Center-Shreveport

data_processing:
Sequence reads from bisulphite-treated EpiQuest libraries were identified using standard Illumina base-calling (bcl2fastq version 1.8.3).
Sequence reads from bisulphite-treated EpiQuest libraries were identified using standard Illumina base-calling (bcl2fastq version 1.8.3). Bismark version 0.7 was used for alignment and data was analyzed using a proprietary (Zymo) pipeline implemented in Python (version 2.7) for methylation calling and further downstream analysis. Residual cytosines (Cs) in each read were first converted to thymines (Ts), with each such conversion noted for subsequent analysis. A reference sequence database was constructed from the 50-bp ends of each computationally predicted MspI-TaqI fragment in the 40–350 bp size range. All Cs in each fragment end were then converted to Ts (only the C-poor strands are sequenced in the RRBS process; the converted reads were aligned to the converted reference by Bowtie.  The number of mismatches in the induced alignment was then counted between the unconverted read and reference, ignoring cases in which a T in the unconverted read is matched to a C in the unconverted reference.  For a given read, the best alignment was kept if the second-best alignment had 2 more mismatches, otherwise the read was discarded as non-unique.  The methylation level of each sampled cytosine was estimated as the number of reads reporting a C, divided by the total number of reads reporting a C or T.  Fisher’s exact test or t-test were performed for each CpG site which has at least 5 reads covered.  CpG were classified as hypermethylation or hypomethylated (meth ratio 0.01 – 0.33) based on methylation difference in the uninfected sample compared to all other samples.  Thus, a hypomethylated CpG refers to its state in the uninfected cell line.  Strongly hyper and hypomethylated CpGs had a meth ratio between 0.33 – 1.00).  Also, promoter, gene body and CpG island annotations were added to each CpG.
Data were filtered using the following specifications:  * pvalue <= 0.05
Second filtering of data based on * Site position is not part of the vector sample (ie, vector and uninfected had same methylation call)       * classification is the same across ebv+ and all ebv- samples. (e.g., if a record is ebv+ stronglyHypermeth, then all ebv- values must also be stronglyHypermeth)
For the EBV+ sample, reads that did not align to EBV were aligned to the Akata EBV strain (KC207813).
Genome_build: hg19
Supplementary_files_format_and_content: 6 Bed files are provided for visualization of CpG methylation calls (human) in uninfected, vector, EBVpositive, and three EBV-negative clones (cl1 ,cl3, cl4). 5 CSV files are included with CpG methylation data filtered by  p<= 0.05  for vector, EBVpos, and three EBV-negative clones (cl1, cl3, cl4) as CSV files. This data is compared to the uninfected sample.  1 CSV files with final processed data  p<= 0.05  with methylation differences being unique for EBV pos and three EBV negative, transiently infected clones compared to uninfected and vector controls, EBV_CpG_methylation data (CSV file).

source_name: NOK EBV+

growth_protocol: Human telomerase (hTERT)-immortalized normal oral keratinocytes (NOK, kindly gifted by Dr. Karl Munger) were grown in keratinocyte serum free media (KSFM) supplemented with human epidermal growth factor and bovine pituitary extract (Life Technologies) in a humidified CO2 incubator at 37oC. Cells were passaged once a week using trypsinization at a 1:4 split.

extract_protocol:
DNA was extracted from cells by DNA lysis buffer (100mM NaCl, 10mM Tris pH 8, 25mM EDTA,  0.5% SDS, 0.1mg/ml proteinase K).  DNA extracts were incubated overnight at 56oC.  DNA was purified by   2 rounds of phenol/chloroform  and precipitated with 2 volumes of ethanol and 1/10 volume of 3M sodium acetate solution.
Libraries were prepared by the Zymo Epiquest service. RRBS libraries were prepared from 200-500 ng genomic DNA digested with 60 units of TaqI and 30 units of MspI (NEB) sequentially. Size-selected TaqI-MspI fragments (40–120 bp and 120–350 bp) were filled in and 3’-terminal-A extended, extracted with Zymo Research DNA Clean & Concentrator™ kit. Ligation to pre-annealed adapters containing 5’- methyl-cytosine instead of cytosine (Illumina) was performed using the Illumina DNA preparation kit and protocol. Purified, adaptor ligated fragments were bisulphite-treated using the EZ DNA Methylation-Direct™ Kit (Zymo Research). Preparative-scale PCR was performed and DNA Clean & Concentrator™ -purified PCR products were subjected to a final size selection on a 4% NuSieve 3:1 agarose gel. SYBR-green-stained gel slices containing adaptor-ligated fragments of 130–210 bp or 210–460 bp in size were excised. Library material was recovered from the gel (Zymoclean™ Gel DNA Recovery Kit) and sequenced on the Illumina HiSeq platform.

treatment_protocol: Uninfected parental cells, vector control (pTVRF=PTURF), EBV-infected, and EBV-negative  transiently-infected clones were seeded at 1x10^6 cells in a T75 flask.  DNA was harvested 3 days after seeding in using phenol/chloroform extraction, followed by ethanol precipitaiton of the DNA.

value: gingiva

tag: cell type

value: hTert immortalized normal oral keratinocytes derived from gingiva

tag: infection state

value: EBV+

tag: passage


title: NOK cl1 AkataBX-1 cl4 p28 EBV-

source_name: NOK EBV-

value: Transiently-infected, EBV-negative


title: P4 RV Single Cell RNA-Seq-cell 50

tag: Sex


title: P4 RV Single Cell RNA-Seq-cell 34


title: NOK cl1 pTURF transfected p22

source_name: NOK vector transfected

value: Vector transfected


title: P4 RV Single Cell RNA-Seq-cell 18


title: P4 RV Single Cell RNA-Seq-cell 10


title: 1221 cell line

middle: A

last: French

address: 77 Avenue Louis Pasteur 630G

institute: Brigham and Women's Hospita

data_processing:
TopHat-Fusion (v2.0.8b bundled with TopHat2) was run with default parameters (as described at http://tophat.cbcb.umd.edu/fusion_tutorial.html#toph but with -r 50 and --max-intron-length 1000000) to identify novel fusion transcripts from paired-end 50 base reads.
Genome_build: Hg19
Supplementary_files_format_and_content: .txt file of fusion results; .txt file of fusion reads

growth_protocol: The 1221 cells were grown in basic WIT medium is supplemented with insulin (20 μg/ml), EGF (10 ng/ml), hydrocortisone (0.5 μg/ml), and cholera toxin (100 ng/ml).

extract_protocol:
Live cultured 1221 cells were lysed and total RNA was extracted with Qiagen RNEasy Mini kit.  Elim Biopharmaceuticals (Hayward, CA) performed library preperation and sequencing. First, rRNA was removed using the Ribo-Zero kit (Epicentre, Madison, WI).  The library was prepared using standard Illumina protocols with proprietary modifications and sequenced using HiSeq2500 (Illumina, San Diego, CA).
The library was prepared using standard Illumina protocols with proprietary modifications by Elim Biopharmaceuticals (Hayward, CA).

tag: cell line

value: NUT-variant NUT Midline Carcinoma

tag: gender

value: Female


title: Sth1-ChIP

city: London

first: Lidia

last: Lopez-Serra

address: 44 Lincoln's Inn Fields

department: Chromosome segregation

institute: Canser Research UK

description: DNA inmunoprecipitated with anti-Pk

data_processing:
The data sets were aligned using Eland (version 1.4) to the Saccharomyces cerevisiae genome (version sacCer2)
To identify protein enriched regions, the genomic distance between every pair of forward and reverse strand mapped reads was calculated and the average fragment size was taken to be the median of these distances. Half of this value was used with MACS version 1.3.7.1 in NOMODEL mode to identify regions enriched in the aligned data over a whole genome input DNA sample that was processed and sequenced in parallel
Default settings were used apart from 'model fold=32' and an effective genome size of 1.2x10e8.
Genome-wide wig files were generated normalised to 20 million reads.
Genome_build: Saccharomyces cerevisiae genome (version sacCer2)
Supplementary_files_format_and_content: Genome-wide wig files

source_name: Inmunoprecipitated DNA

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0,6

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed as described (Lengronne et al. 2004) followed byhigh throughput sequencing on a Genome Analyzer IIx (Illumina).
Sequencing libraries were prepared according to the manufacturer's protocol (11257047 Rev. A). The kit used for these preps was the IP-102-1001.

treatment_protocol: Cells were cross-linked with 1% Formaldehide for 30 minutes at room temperature. The reaction was stopped with 0.125 M Glycine for 10 minutes.

value: MATα, Sth1-Pk9::TRP1

tag: chip antibody

value: PK, clone SV5-Pk1

tag: chip antibody vendor

value: Serotec

tag: chip antibody cat. #

tag: chip antibody batch #


title: P4 RV Single Cell RNA-Seq-cell 26

tag: genotype

value: Tg(Crym-EGFP)82Gsat / MGI:4846969

tag: component sampled

value: renal vesicle

tag: theiler stage

value: mixed background


title: P4 RV Single Cell RNA-Seq-cell 41

tag: age

tag: strain

value: unknown

tag: pooled sample

value: yes

value: 2 kidneys


title: Scc2-UB-ChIP

description: Input DNA

source_name: Supernatant DNA

tag: genotype/variation

value: MATa, Scc2-Pk9::TRP1


title: P4 RV Single Cell RNA-Seq-cell 42

tag: pool size


title: Scc4-ChIP

description: DNA inmunoprecipitated with anti-Pk

value: MATa, Scc4-Pk9::TRP1


title: Scc2-ChIP

description: DNA inmunoprecipitated with anti-Pk


title: P4 RV Single Cell RNA-Seq-cell 3


title: NOK cl1 AkataBX-1 cl3 p28 EBV-

tag: tissue

value: gingiva

tag: cell type

value: hTert immortalized normal oral keratinocytes derived from gingiva

tag: infection state


title: P4 RV Single Cell RNA-Seq-cell 49

tag: Sex


title: P4 RV Single Cell RNA-Seq-cell 57


title: P4 RV Single Cell RNA-Seq-cell 33


title: P4 RV Single Cell RNA-Seq-cell 25


title: NOK cl1 AkataBX-1 cl1 p28 EBV-

value: Transiently-infected EBV-

tag: passage


title: NOK cl1 uninfected p30

source_name: NOK uninfected

value: Uninfected


title: P4 RV Single Cell RNA-Seq-cell 17


title: Sth1-3 25°C  Mnase-Seq

description: Genomic DNA obtained after digestion with MNase to isolate mono-nucleosomal DNA

data_processing:
Read alignment was performed using the Burrows-Wheeler Aligner, bwa (version 0.5.9-r16). If required, prior to alignment, the sacCer2 release of the budding yeast genome was modified to reflect genome alterations that were introduced for the experiment.
Discordantly mapped read-pairs were removed, leaving only those that were paired, had a maximum of 2 mismatches in any given read and an insert size between 140 and 170 bp.
Genome-wide wig files were generated by treating each pair of reads as a single fragment.
Genome_build: Saccharomyces cerevisiae genome (version sacCer2)
Supplementary_files_format_and_content: Genome-wide wig files were generated at 1bp resolution by treating each pair of reads as a single fragment, including the inferred insert portion. A total library size of 25 million read pairs was used to normalise the coverage for cross-sample comparison.

source_name: Mono-nucleosomal DNA

growth_protocol: Cells were grown in YP + 2% Glucose to an OD600 of 0,4. Then the cells were incubated for two more hours at the indicated temperature.

extract_protocol:
Preparation of mono-nucleosomal DNA was performed as described (Lantermann et al. 2009) followed by high throughput sequencing on Illumina GAIIx and HiSeq 2500. Briefly, cells were grown under the specified conditions and then fixed with 1% formaldehyde. Spheroblasts were obtained and the chromatin digested with 30u/ml of Mnase (Fermentas) at 37°C for 20 minutes. The samples were then treated with RNase and Proteinase K to isolate the undigested, mono-nucleosomal DNA. The DNA was then size selected and purified in a 1.5% agarose gel and precipitated with ethanol.
Sequencing libraries were prepared according to the manufacturer's protocol (15005180 Rev. A and 15026486 Rev. B).

value: MATα, sth1-3ts, Scc2-Pk9::TRP1


title: Sth1-3 37°C  Mnase-Seq


title: P4 RV Single Cell RNA-Seq-cell 1


title: Scc2-4 37°C  Mnase-Seq

value: MATa, scc2-4, Scc1-Pk9::TRP1, Sth1-9myc::URA3


title: P4 RV Single Cell RNA-Seq-cell 9


title: P4 RV Single Cell RNA-Seq-cell 40

treatment_protocol: Kidneys from Tg(Crym-EGFP)GF82Gsat mice were isolated in ice-cold PBS, bisected and minced into pieces <1mm. The minced kidneys were placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added. The tubes were incubated at 37C for 5 minutes. After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added. The samples were centrifuged at 1800rpm for 5 minutes. The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes. The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and isolated by FACS.


title: Scc2-4 25°C  Mnase-Seq


title: P4 RV Single Cell RNA-Seq-cell 32


title: P4 RV Single Cell RNA-Seq-cell 24


title: WT 25°C Mnase-Seq


title: WT 37°C  Mnase-Seq


title: P4 RV Single Cell RNA-Seq-cell 16


title: P4 RV Single Cell RNA-Seq-cell 8


title: TATA∆  Mnase-Seq

value: MATa, TATA box between positions 559322 and 559330 on chromosome V deleted (the cloning strategy leaves a 142 bp direct repeat inserted between coordinates 559330 and 559331), Scc2-Pk9::TRP1


title: a2/MCM1  Mnase-Seq

value: MATα, Poly(dA:dT)∆::TGTAATTACCTAATAGGGAAATTTACA-142 bp direct repeat between positions 167978 and 167993 on chromosome II, Scc2-Pk9::TRP1


title: P4 RV Single Cell RNA-Seq-cell 55


title: TATAC  Mnase-Seq

value: MATa, 142 bp direct repeat cloned between positions 559330 and 559331 on chromosome V, Scc2-Pk9::TRP1


title: P4 RV Single Cell RNA-Seq-cell 56

value: Tg(Crym-EGFP)82Gsat / MGI:4846969


title: P4 RV Single Cell RNA-Seq-cell 39

value: renal vesicle


title: P4 RV Single Cell RNA-Seq-cell 31

value: mixed background


title: P4 RV Single Cell RNA-Seq-cell 23

value: unknown


title: P4 RV Single Cell RNA-Seq-cell 2

value: yes


title: P4 RV Single Cell RNA-Seq-cell 38

value: both

value: 2 kidneys


title: P4 RV Single Cell RNA-Seq-cell 30


title: P4 RV Single Cell RNA-Seq-cell 47


title: P4 RV Single Cell RNA-Seq-cell 48


title: P4 RV Single Cell RNA-Seq-cell 54


title: P4 RV Single Cell RNA-Seq-cell 15


title: P4 RV Single Cell RNA-Seq-cell 5


title: P4 RV Single Cell RNA-Seq-cell 53


title: P4 RV Single Cell RNA-Seq-cell 21


title: P4 RV Single Cell RNA-Seq-cell 29


title: P4 RV Single Cell RNA-Seq-cell 13


title: P4 RV Single Cell RNA-Seq-cell 22


title: P4 RV Single Cell RNA-Seq-cell 37


title: P4 RV Single Cell RNA-Seq-cell 6


title: P4 RV Single Cell RNA-Seq-cell 7


title: P4 RV Single Cell RNA-Seq-cell 46


title: P4 RV Single Cell RNA-Seq-cell 52


title: P4 RV Single Cell RNA-Seq-cell 20

source_name: Analysis from single cell P4 renal vesicles


title: P4 RV Single Cell RNA-Seq-cell 45


title: E11.5 MM Single Cell RNA-Seq-cell 35

source_name: Analysis of single cells from E11.5 metanephric mesenchyme

treatment_protocol: E11.5 kidneys of Crym-GFP mice were visualized with GFP fluorescence and microdissected to include the cells surrounding the ureteric bud and a few cells beyond the Crym boundary (Crym expression is the same as Six2 in the E11.5 kidney). Cells were rapidly dissociated with trypsin to single cell state, visualized under a microscope. The cells were adjusted to around 250/microliter and introduced into the Fluidigm C1 instrument for capture, wash, lysis and amplification with Clontech SMARTer technology according to Fludigm protocols. Samples were harvested, tagmented and barcoded, again according to Fluidigm protocols.

value: metanephric mesenchyme

value: no


title: E11.5 MM Single Cell RNA-Seq-cell 20


title: E11.5 MM Single Cell RNA-Seq-cell 30


title: E11.5 MM Single Cell RNA-Seq-cell 5


title: E11.5 MM Single Cell RNA-Seq-cell 40


title: E11.5 MM Single Cell RNA-Seq-cell 15


title: E11.5 MM Single Cell RNA-Seq-cell 45


title: E11.5 MM Single Cell RNA-Seq-cell 10


title: P4 RV Single Cell RNA-Seq-cell 14


title: P4 RV Single Cell RNA-Seq-cell 28


title: P4 RV Single Cell RNA-Seq-cell 36


title: E11.5 MM Single Cell RNA-Seq-cell 24


title: E11.5 MM Single Cell RNA-Seq-cell 25


title: E11.5 MM Single Cell RNA-Seq-cell 50


title: E11.5 MM Single Cell RNA-Seq-cell 4


title: E11.5 MM Single Cell RNA-Seq-cell 23


title: E11.5 MM Single Cell RNA-Seq-cell 14


title: E11.5 MM Single Cell RNA-Seq-cell 39


title: E11.5 MM Single Cell RNA-Seq-cell 29


title: E11.5 MM Single Cell RNA-Seq-cell 33


title: E11.5 MM Single Cell RNA-Seq-cell 8


title: E11.5 MM Single Cell RNA-Seq-cell 44


title: E11.5 MM Single Cell RNA-Seq-cell 43


title: E11.5 MM Single Cell RNA-Seq-cell 34


title: E11.5 MM Single Cell RNA-Seq-cell 18


title: E11.5 MM Single Cell RNA-Seq-cell 38


title: E11.5 MM Single Cell RNA-Seq-cell 12


title: E11.5 MM Single Cell RNA-Seq-cell 48


title: E11.5 MM Single Cell RNA-Seq-cell 19


title: E11.5 MM Single Cell RNA-Seq-cell 32


title: E11.5 MM Single Cell RNA-Seq-cell 13


title: E11.5 MM Single Cell RNA-Seq-cell 49


title: E11.5 MM Single Cell RNA-Seq-cell 28


title: E11.5 MM Single Cell RNA-Seq-cell 22


title: E11.5 MM Single Cell RNA-Seq-cell 47


title: E11.5 MM Single Cell RNA-Seq-cell 42


title: E11.5 MM Single Cell RNA-Seq-cell 7


title: E11.5 MM Single Cell RNA-Seq-cell 27


title: E11.5 MM Single Cell RNA-Seq-cell 17


title: E11.5 MM Single Cell RNA-Seq-cell 3


title: E11.5 MM Single Cell RNA-Seq-cell 2


title: E11.5 MM Single Cell RNA-Seq-cell 37


title: E11.5 MM Single Cell RNA-Seq-cell 36


title: E11.5 MM Single Cell RNA-Seq-cell 41


title: E11.5 MM Single Cell RNA-Seq-cell 31


title: E11.5 MM Single Cell RNA-Seq-cell 6


title: E11.5 MM Single Cell RNA-Seq-cell 11


title: E11.5 MM Single Cell RNA-Seq-cell 51


title: E11.5 MM  Single Cell RNA-Seq-cell 1


title: E11.5 MM Single Cell RNA-Seq-cell 26


title: E11.5 MM Single Cell RNA-Seq-cell 16


title: E12.5 Kidney Single Cell RNA-Seq-cell 40

source_name: Analysis of single cells from E12.5 kidneys

treatment_protocol: 1. E12.5 embryonic kidneys are dissected in ice-cold PBS and pooled into a 1.5ml nuclease-free tube.  2. Dissociate with 200ul Trypsin 0.5% at 37C for 5 minutes with trituration.  3. Add 1ml ice-cold 10% FBS/PBS.  4. Spin down at 2300rpm for 5 minutes.  5. Re-suspend in 1ml ice-cold 1% FBS/PBS.    6. Filter using 20um mesh filter - rinse with 4ml 1% FBS/PBS to remove clumps and debris.   7. Centrifuge at 2300rpm for 5 minutes and re-suspend in appropriate volume 1% FBS/PBS to yield a concentration of 300,000 cells/ml.  Verify cell concentration using haemocytometer.  8. Load into Fluidigm for single cell analysis.

value: wild type

value: metanephros

value: pooled male and female

value: unspecified


title: E11.5 MM Single Cell RNA-Seq-cell 21


title: E12.5 Kidney Single Cell RNA-Seq-cell 24


title: E12.5 Kidney Single Cell RNA-Seq-cell 8


title: E12.5 Kidney Single Cell RNA-Seq-cell 16


title: E12.5 Kidney Single Cell RNA-Seq-cell 55


title: E12.5 Kidney Single Cell RNA-Seq-cell 79


title: E12.5 Kidney Single Cell RNA-Seq-cell 87


title: E12.5 Kidney Single Cell RNA-Seq-cell 54


title: E12.5 Kidney Single Cell RNA-Seq-cell 47


title: E12.5 Kidney Single Cell RNA-Seq-cell 31


title: E12.5 Kidney Single Cell RNA-Seq-cell 39


title: E12.5 Kidney Single Cell RNA-Seq-cell 63


title: E12.5 Kidney Single Cell RNA-Seq-cell 32


title: E12.5 Kidney Single Cell RNA-Seq-cell 23


title: E12.5 Kidney Single Cell RNA-Seq-cell 15


title: E12.5 Kidney Single Cell RNA-Seq-cell 7


title: E12.5 Kidney Single Cell RNA-Seq-cell 46


title: E12.5 Kidney Single Cell RNA-Seq-cell 86


title: E12.5 Kidney Single Cell RNA-Seq-cell 70


title: E12.5 Kidney Single Cell RNA-Seq-cell 78


title: E12.5 Kidney Single Cell RNA-Seq-cell 62


title: E12.5 Kidney Single Cell RNA-Seq-cell 38


title: E12.5 Kidney Single Cell RNA-Seq-cell 71


title: E12.5 Kidney Single Cell RNA-Seq-cell 30


title: E12.5 Kidney Single Cell RNA-Seq-cell 14


title: E12.5 Kidney Single Cell RNA-Seq-cell 22


title: E12.5 Kidney Single Cell RNA-Seq-cell 45


title: E12.5 Kidney Single Cell RNA-Seq-cell 77


title: E12.5 Kidney Single Cell RNA-Seq-cell 85


title: E12.5 Kidney Single Cell RNA-Seq-cell 52


title: E12.5 Kidney Single Cell RNA-Seq-cell 69


title: E12.5 Kidney Single Cell RNA-Seq-cell 29


title: E12.5 Kidney Single Cell RNA-Seq-cell 60


title: E12.5 Kidney Single Cell RNA-Seq-cell 68


title: E12.5 Kidney Single Cell RNA-Seq-cell 44


title: E12.5 Kidney Single Cell RNA-Seq-cell 13


title: E12.5 Kidney Single Cell RNA-Seq-cell 5


title: E12.5 Kidney Single Cell RNA-Seq-cell 21


title: E12.5 Kidney Single Cell RNA-Seq-cell 75


title: E12.5 Kidney Single Cell RNA-Seq-cell 84


title: E12.5 Kidney Single Cell RNA-Seq-cell 59


title: E12.5 Kidney Single Cell RNA-Seq-cell 67


title: E12.5 Kidney Single Cell RNA-Seq-cell 20


title: E12.5 Kidney Single Cell RNA-Seq-cell 36


title: E12.5 Kidney Single Cell RNA-Seq-cell 53


title: E12.5 Kidney Single Cell RNA-Seq-cell 61


title: E12.5 Kidney Single Cell RNA-Seq-cell 51


title: E12.5 Kidney Single Cell RNA-Seq-cell 76


title: E12.5 Kidney Single Cell RNA-Seq-cell 91


title: E12.5 Kidney Single Cell RNA-Seq-cell 43


title: E12.5 Kidney Single Cell RNA-Seq-cell 37


title: E12.5 Kidney Single Cell RNA-Seq-cell 82


title: E12.5 Kidney Single Cell RNA-Seq-cell 74


title: E12.5 Kidney Single Cell RNA-Seq-cell 58


title: E12.5 Kidney Single Cell RNA-Seq-cell 83


title: E12.5 Kidney Single Cell RNA-Seq-cell 27


title: E12.5 Kidney Single Cell RNA-Seq-cell 35


title: E12.5 Kidney Single Cell RNA-Seq-cell 3


title: E12.5 Kidney Single Cell RNA-Seq-cell 89


title: E12.5 Kidney Single Cell RNA-Seq-cell 81


title: E12.5 Kidney Single Cell RNA-Seq-cell 73


title: E12.5 Kidney Single Cell RNA-Seq-cell 65


title: E12.5 Kidney Single Cell RNA-Seq-cell 57


title: E12.5 Kidney Single Cell RNA-Seq-cell 4


title: E12.5 Kidney Single Cell RNA-Seq-cell 49


title: E12.5 Kidney Single Cell RNA-Seq-cell 26


title: E12.5 Kidney Single Cell RNA-Seq-cell 34


title: E12.5 Kidney Single Cell RNA-Seq-cell 2


title: E12.5 Kidney Single Cell RNA-Seq-cell 10


title: E12.5 Kidney Single Cell RNA-Seq-cell 18


title: E12.5 Kidney Single Cell RNA-Seq-cell 72


title: E12.5 Kidney Single Cell RNA-Seq-cell 80


title: E12.5 Kidney Single Cell RNA-Seq-cell 41


title: E12.5 Kidney Single Cell RNA-Seq-cell 50


title: E12.5 Kidney Single Cell RNA-Seq-cell 64


title: E12.5 Kidney Single Cell RNA-Seq-cell 48


title: E12.5 Kidney Single Cell RNA-Seq-cell 11


title: E12.5 Kidney Single Cell RNA-Seq-cell 19


title: E12.5 Kidney Single Cell RNA-Seq-cell 25


title: E12.5 Kidney Single Cell RNA-Seq-cell 17


title: E12.5 Kidney Single Cell RNA-Seq-cell 33


title: E12.5 Kidney Single Cell RNA-Seq-cell 90


title: E12.5 Kidney Single Cell RNA-Seq-cell 42


title: E12.5 Kidney Single Cell RNA-Seq-cell 9


title: E12.5 Kidney Single Cell RNA-Seq-cell 1


title: CD8-TGFb

city: Würzburg

first: Anoop

last: Chandran P

address: Josef-schneiderstrasse

country: Germany

institute: University of Würzburg

description:
Small RNA-Seq.
CD8+ T cells treated fo 24 h with 5ng/ml TGF-b.

data_processing:
To process sequences, Perl scripts were used (available upon request).
Raw sequences were filtered and converted to FASTA format. Sequences were truncated at the first 7-mer of A's. Sequences shorter than 16 bases were omitted.
Adapter sequences were then removed.
Each sequence was aligned against all sequences in the miRbase. Sequences that did not hit any miRNA were computed further. Multiple sequences that mapped to one miRNA (due to sequencing errors) were then merged to build final number of read counts.
Different groups were then compared by normalizing the number of reads to 10000 reads in each group and in reads per million (RPM).
Genome_build: miRBase 15
Supplementary_files_format_and_content: File format: .txt. Contains the normalized number of reads (per 10000 and RPM) for each miRNA for respective groups in each column.

source_name: CD8+ T cells, TGF-b

growth_protocol: Cells were cultured in X-VIVO15 medium (Lonza).

extract_protocol:
Total RNA was extracted with mirVana miRNA isolation kit (Ambion); subsequent fractionation of miRNAs was done by means of PAA gel electrophoresis.
Poly-A-tailing of the miRNAs; ligation of an RNA-adapter to the 5'-end; first-strand cDNA-synthesis using poly(T)-adapter; addition ot the complete flanking sequences while PCR-amplification; final purification of the PCR-product by means of agarose gel electrophoresis.

treatment_protocol: Cells were activated using T cell activation beads (Miltenyi) overnight and then treated for 24 h with 5ng/ml TGF-b, with 1µM SD-208 or left untreated.

value: CD8+ T cells

value: peripheral blood

tag: disease status

value: healthy

value: 25-40 years

tag: treatment

value: TGF-b


title: CD8-SD208

description:
Small RNA-Seq.
CD8+ T cells treated fo 24 h with 1µM SD-208.

source_name: CD8+ T cells, SD208


title: CD8-control

description:
Small RNA-Seq.
CD8+ T cells untreated.

source_name: CD8+ T cells, untreated


title: corn_S3_rep2

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

data_processing:
Basecalls performed using CASAVA version 1.8.2
RNA-Seq reads were aligned to the draft Zea Mays genome assembly (B73_RefGen_v2) using tophat version 0.12.8 with default parameters.
Digital gene expression files were generated using cuffdiff version v2.0.2 (3522) with default parameters, and results were further annotated and summarised via in-house perl scripts.
Genome_build: B73_RefGen_v2
Supplementary_files_format_and_content: Tab delimited file containing FPKM gene-level values for each sample, as well as a cuffdiff generated, merged, and further annotated tab-delimited file containing fold-changes and q-values of S1 versus water and S3 versus S1 (GeneExpression.tsv on Series record).

organism: Zea mays

source_name: leaves

growth_protocol: Zea Mays seedlings were grown in potting soil in growth rooms at 22 °C with a 12-h light photoperiod and light intensity of 180 μmol m− 2 s−1.

extract_protocol:
Total RNA was isolated from materials by using TRIzol Reagent (Invitrogen cat#: P/N 15596-018), followed by further purification by Qiagen RNeasy Mini Kit (P/N 74104). RNA qualities were assessed using an Agilent BioAnalyzer 2100 system (Agilent Technologies).
RNA libraries were prepared from 4ug total RNA using the Illumina TruSeq RNA Sample Prep Kit-V2 set A (RS-122-2002 ) according to the manufacturer’s instructions. Libraries were analyzed and measured by gel electrophoresis and Nanodrop 1000 Spectrophotometer to a concentration of 10nM each.

treatment_protocol: Repeated dehydration stresses were performed by air-drying for 2 h followed by a 22 h period of full re-hydration recovery. S1 sample taken at first dehydration, S3 at third dehydration.

value: leaves

value: Third drought stress


title: corn_S3_rep1


title: Input_Smad2_ctrl1_e2a3pf.fastq.gz

description: input control for samples 1 and 5

source_name: Control embryos

tag: embryonic stage

value: Stage 10.5

tag: chip characteristics

tag: barcode


title: corn_S1_rep2

value: First drought stress


title: C2C12_GM_Ago2_CLIP-Seq_myoblast

city: Wuhan

first: Bo

last: Yang

state: Hubei

address: Luo-jia-shan, Wuchang

department: Biochemistry and Molecular Biology

country: China

institute: College of Life Sciences, Wuhan University

description:
library from Ago2-RNA complex in C2C12 myoblasts
two replicates were combined to make one bedGraph file for the plus strand and one bedGraph file for the minus strand

data_processing:
CLIP-seq: After removing 5' barcode (NNNT) and 3' adaptor sequence (CTCGTATGCCGTCT), the tags longer than 20 nt were mapped to the reference mouse genome (mm10) with Bowtie2 (version 2.0.0-beta7 with parameters --very-sensitive -rdg 5,2 --score-min L, -0.6, -0.7)
Genome_build: mm10

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were maintained in Dulbecco’s minimal essential medium (DMEM; Life Technology) supplemented with 10% FBS (Life Technology).

extract_protocol:
C2C12 Cells (GM or DM) were UV-irradiated at 400 mj and collected by scraping the cells from 15-cm plates. Ago2 immunoprecipitation was done in 1% NP-40 wash buffer.
3' adaptor was first added to the immunoprecipitated Ago2 complex on beads, then the eluted protein-RNA complex was subject to 10% Novex NUPAGE gel. After transfering to NC membrane, the corresponding band was cut and RNA was extracted. After 5' adaptor liagtion, RT-PCR was performed by using Super Script III and Ex taq polymerase.

treatment_protocol: To induce C2C12 cell differentiation, cells were first grown to reach 80-90% confluency and the growth medium GM was subsequently replaced with the differentiation media DM (DMEM plus 2% horse serum) and continually cultured for 4 days.

tag: cell line

value: myoblast

tag: antibody

value: monoclonal anti-EIF2C2 antibody (M01)

tag: antibody source

value: Abnova catalog number H00027161-M01

tag: antibody lot number


title: C2C12_DM_Ago2_CLIP-Seq_myotubes

description:
library from Ago2-RNA complex in C2C12 myotubes
two replicates were combined to make one bedGraph file for the plus strand and one bedGraph file for the minus strand

source_name: C2C12 myotubes

value: myotubes


title: corn_water_rep1

value: Watered condition


title: corn_water_rep2


title: Patient 2 RNA-Seq rep1

city: Santa Barbara

first: Kenneth

last: Kosik

address: 552 University Rd

department: Neuroscience Research Institute

institute: University of California Santa Barbara

description: Sample 3 D3-1

data_processing:
Base-calling performed by Torrent Suite Software 4.0.2
Reads were first aligned to UCSC hg19 with TopHat v2.0.10, default settings
The unmapped reads were subsequently mapped with bowtie2 (v2.1.0) --local --very-sensitive-local -p 8 --mm
Reads mapped by tophat and bowtie were merged
Reads mapping to CDS (excluding UTR) were counted using coverageBed (v2.10.0)
Genome_build: hg19
Supplementary_files_format_and_content: Counts for the CDS of each transcript is provided for each replicate in genecounts.tsv files.  These files can be read directly into edgeR

molecule: polyA RNA

source_name: Patient 2_induced neuron_RNA-Seq

growth_protocol: iPSCs colonies were detached from the feeder layer with collagenase (1 mg/ml) treatment for 1 hr and suspended in EB medium, consisting of FGF-2-free iPSC medium supplemented with Dorsomorphin (2 µM) and A-83 (2 µM), in non-treated polystyrene plates for 4 days with a daily medium change. After 4 days, EB medium was replaced by neural induction medium (hNPC medium) consisting of DMEM/F12, N2 supplement, NEAA, heparin (2 µg/ml) and cyclopamine (2 µM). The floating EBs were then transferred to matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with hNPC medium change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates (Corning) in hNPC medium containing B27. For neuronal differentiation, resuspended neural progenitor spheres were dissociated with Accutase at 37⁰C for 10 min and placed onto Poly-D-Lysine/laminin-coated coverslips in the neuronal culture medium, consisting of Neurobasal medium supplemented with 2 mM L-glutamine, B27, BDNF (10 ng/ml) and GDNF (10 ng/ml). Half of the medium was replaced once a week during continuous culturing.

extract_protocol:
Total RNA was isolated using mirVana kit (Invitrogen) according to manufacturer’s instructions, polyA selected
Ion Total RNA-Seq Kit v2 for Whole Transcriptome sequencing following the protocol provided by the manufacturer (Life Technologies, Carlsbad, CA).

value: iPSC-derived neurons

tag: differentiation time

value: 4 weeks

value: carrying heterozygous 4bp deletion in DISC1 gene


title: Patient 2 RNA-Seq rep2

description: Sample 3 D3-2

tag: genotype/variation


title: Patient 2 RNA-Seq rep3

description: Sample 3 D3-3


title: Patient 1 RNA-Seq rep3

description: Sample 2 D2-3

source_name: Patient 1_induced neuron_RNA-Seq


title: Control 1 RNA-Seq rep3

description: Sample 1 C3-3

source_name: Control 1_induced neuron_RNA-Seq

value: control


title: Patient 1 RNA-Seq rep1

description: Sample 2 D2-1


title: Control 1 RNA-Seq rep2

description: Sample 1 C3-2


title: Patient 1 RNA-Seq rep2

description: Sample 2 D2-2


title: Control 1 RNA-Seq rep1

description: Sample 1 C3-1


title: Dnmt3a CKO rep3

status: Public on Jul 31 2014

city: New York

first: Seungyeul

last: Yoo

address: 1425 Madison Avenue

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequence reads are mapped and aligned to mouse genome assembly mm10 and then quantified in terms of FPKM using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including FPKM values of each gene for each Sample ...

source_name: Cortex

growth_protocol: All of the mice used in this study were handled in accordance with IACUC-approved protocols. Dnmt1flox/flox (Fan et al, 2001; Jackson-Grusby et al, 2001) and Dnmt3aflox/flox (Nguyen et al, 2007) mice were backcrossed onto a C57BL/6 background and crossed with Olig1-cre mice to generate Dnmt1 conditional knockout (Olig1cre/+;Dnmt1flox/flox) and littermate control (Olig1+/+;Dnmt1flox/flox) mice, and Dnmt3a conditional knockout (Olig1cre/+;Dnmt3aflox/flox) and littermate control (Olig1+/+;Dnmt3aflox/flox) mice.

extract_protocol:
Cortices were dissected from Dnmt1 conditional knockout (CKO), Dnmt3a CKO, and respective littermate control mice at postnatal day 16. RNA was isolated from three biological replicates for each genotype using TRIzol (Invitrogen) extraction and isopropanol precipitation. RNA samples were resuspended in water and further purified with RNeasy columns with on-column DNase treatment (Qiagen). RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument according to the manufacturer's instructions.

tag: strain

value: Cortex

tag: age

value: post natal day 16

tag: genotype


title: Ctrl_Smad2_Lib1

data_processing:
ChIP-Seq reads are mapped to xenTro2 genome using the bwa-sw tool. Aligned ChIP-Seq files are used to call peaks with the MACS2.08 software at a stringent q value of 0.00001.
Called peaks are annotated using HOMER software to the closest gene
ChIP-seq homer-output  as an excel file contains annotated peaks for Samples
Genome_build: UCSC XenTro2

extract_protocol:
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Catalog # FC-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) 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. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of 200~400 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 II or HiSeq following the manufacturer's protocols.
Embryos were fixed for 1hr in 1% formaldehyde, glycine treated and frozen.  Embryos were then homogenized, sonicated, and centrifuged to remove yolk and cytoplasm.  Nuclei were complexed with antibody.


title: Dnmt3a CKO rep2

tag: tissue


title: 35S:NGA 3

city: Milan

first: Vicente

last: Balanza

state: Lombardia

address: Via Celoria 26

department: Bioscienze

country: Italy

institute: University of Milan

description: Sample 8

data_processing:
Quality control on the raw sequence data was done using FastQC (Babraham Bioinformatics)
Reads were aligned to whole genome sequences from the TAIR10 A. thaliana database (www.arabidopsis.org) and analyzed using the CLC Genomics workbench (www.clcbio.com)
RPKM was considered as expression values
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include gene model,short description, RPKM values for each Sample ...

source_name: carpel

growth_protocol: seed were sow on soil, and plant were grown under long day condition

extract_protocol:
Arabidopsis carpels between stages 8-13 from wt, nga mutant and NGA overexpression were collected manually from 15 developing inflorescences and storage transiently in cold extraction buffer of the Kiagen RNA extraction kit.The RNA extraction was made with the Kiagen RNA extraction kit. RNA was analyzed for yield and quality on a Bioanalyzer 2100 (Agilent 2100).
Libraries for sequencing were prepared from 2–4 µg total RNA using Illumina TruSeq RNA kits and sequenced with Illumina HiSeq2000

tag: ecotype

value: Columbia

value: 35S:NGA overexpression

tag: developmental stage

value: carpels (collected manually from 15 developing inflorescences)


title: nga 2

description: Sample 4


title: nga 3

description: Sample 5


title: 35S:NGA 1

description: Sample 6


title: Dnmt3a Control rep3


title: E12.5 Kidney Single Cell RNA-Seq-cell 56

value: wild type

tag: component sampled

value: metanephros

tag: theiler stage

value: mixed background

tag: Sex

value: pooled male and female

tag: pooled sample

value: unspecified


title: Dnmt3a CKO rep1


title: corn_S1_rep1

value: leaves

tag: treatment

value: First drought stress


title: WT 2

description: Sample 2


title: nga 1

description: Sample 3


title: WT 1

description: Sample 1


title: Dnmt1 CKO rep2


title: Dnmt3a Control rep2


title: Dnmt1 Control rep3


title: Dnmt1 CKO rep3


title: Dnmt1 CKO rep1


title: Dnmt1 Control rep1


title: 35S:NGA 2

description: Sample 7


title: TZM-bl ami BaL Day 3 RISC PAR-CLIP

city: Durham

first: Adam

middle: Wesley

last: Whisnant

state: NC

address: 213 Research Drive 427 CARL Bldg

department: Molecular Genetics and Microbiology

institute: Duke University

description: RISC-associated RNAs isolated from RISC PAR-CLIP

data_processing:
Casava1.8.2 software used for basecalling.
Reads <15nt were discarded, adaptors trimmed, and low quality reads discarded using the FastX tool kit and the following pipeline: fastq_quality_filter -Q33| fastq_to_fasta -Q33 | fastx_clipper -a TruSeq-Index#  -l 15 –c | fastx_collapser
Bowtie v.0.12.7, with the following options: –a --best --strata –m 25, was used to remove adapters and size-fractionation markers with no variant nucleotides for all libraries but the PAR-CLIP libraries.  The aforementioned parameters were kept throughout the pipline
Total small RNA and RISC RIP-Seq reads were sequentially filtered by aligning to the viral genome (1mismatch, negative sense alignments allowed), then human pre-miRNAs from miRbasev19 (1mismatch), EnsemblncRNAv70 Homo sapiens (1mismatch), fRNAdbv3.4 Homo sapiens (1mismatch), then human genome 19 (2mismatches, negative sense alignments allowed)
PAR-CLIP reads were aligned to a reference of the human genome combined with either the near-full length viral genome or the 3'LTR of each virus to avoid ambiguous alignments occuring with both annotated LTRs on the same sequence.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data are in a tab-delineated BED format presented as chromosome/gene, starting location for aligned read relative to the start of the gene beginning at 1, ending position of the aligned read, aligned reads per million of total library reads, and the strand (+ or -) that the read aligns to.  Processed data files include alignemnts to HIV,  miRbase human pre-miRNAs v19,  Ensembl human ncRNAs v70, fRNAdb human ncRNAs v3.4,  human genome 19 alignments,  human+viral genome PARCLIP alignments and human+viral genome Nef+U3 PARCLIP alignments.

source_name: TZM-bl Cell Line

growth_protocol: Dulbecco’s modified Eagle medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
TRI-zol, PAGE fractionation ~15-40nt
RNA libraries were prepared according to standard Illumina Truseq protocols

treatment_protocol: Forty-eight hours postinfection, cells were labeled with 100 µM 4-thiouridine (Sigma) for 16 h. Cells were washed with PBS and cross-linked using a Stratagene UV Stratalinker 2400 at 365 nm. The samples were then processed as previously described (Gottwein et al, 2011, Cell Host Microbe 10:515-526). RISC cross-linked RNAs were isolated using anti-Ago2 antibody (Abcam AB57113). (This antibody also recognizes Ago1 and Ago3 [data not shown].) Cloning of isolated small RNAs was performed using the TruSeq small RNA cloning kit (Illumina).

tag: cell line

value: TZM-bl

tag: hiv-1 strain

value: WT/BaL

tag: cell type

value: Cervical Epithelial Cell Line, HeLa derivative transduced with shRNAs against HIV-1

tag: length of infection (days)

tag: rip antibody

value: Abcam AB57113

tag: illumina truseq index number


title: TZM-bl BaL Day 3 RISC PAR-CLIP

value: Cervical Epithelial Cell Line, HeLa derivative


title: Dnmt1 Control rep2

tag: strain

value: Cortex


title: C8166 NL4-3 Day 3 RISC PAR-CLIP

description: RISC-associated RNAs isolated from RISC PAR-CLIP.  Two separate PCR amplifications were sequenced on separate lanes. Sequencing data from both lanes were combined for analysis after initial read trimming and processing.

source_name: C8166 Cell Line

growth_protocol: Roswell Park Memorial Institute (RPMI) 1640 medium (Sigma) supplemented with 10% FBS

value: CD4+ T-cell Line


title: Macrophage ADA Day 27 Small RNA Deep Sequencing

description: Total size fractionated small RNA deep sequencing with protocol from Umbach et al J Virol 84:695-703

source_name: Primary cells isolated from peripheral blood

growth_protocol: Peripheral blood monocytes were obtained by elutriation and cultured for 4 days in DMEM containing 10% human serum, 1% l-glutamine, and 6 ng/ml monocyte colony-stimulating factor (MCSF) to activate macrophages

treatment_protocol: otal RNA was isolated using TRIzol. The RNA fraction containing ~15- to 30-nt-long RNAs was isolated by polyacrylamide gel electrophoresis (PAGE) purification on 15% Tris-borate-EDTA (TBE)-urea gels (Bio-Rad), electroeluted from the excised gel slice (gel eluter; Hoefer), and cloned as previously described (Umbach & Cullen, 2010.  J. Virol. 84:695-703). Adapter-ligated small RNAs were reverse transcribed using SuperScript III, amplified using GoTaq green PCR master mix (Promega) with the Tru-Seq 3′ indices (Illumina), and sequenced on an Illumina HiSeq 2000.

value: NLHXADA

value: Monocyte-derived macrophage


title: Macrophage Uninfected Day 5 Small RNA Deep Sequencing


title: CD4+ BaL Day 3 Small RNA Deep Sequencing

growth_protocol: Isolated from total blood by density gradient centrifugation (lymphocyte separation medium; Cellgro number 25-072-CV), and CD4+ T cells were then isolated using the Dynabead CD4 positive isolation kit from Invitrogen (number 1131 D). Cells were activated by incubation in phytohemagglutinin (PHA) and mouse monoclonal antibodies specific for human CD28 and CD49d (BD Biosciences number 347690) for three days. Activation of the CD4+ T cells was confirmed by fluorescence-activated cell sorting (FACS) by using an anti-CD69 antibody, and the cells were then cultured in RPMI supplemented with 10% FBS and interleukin-2

value: BaL

value: CD4+ T-cells


title: Dnmt3a Control rep1

tag: age

value: post natal day 16


title: C8166 NL4-3 Day 3 Small RNA Deep Sequencing


title: TZM-bl BaL Day 3 RISC RIP-Seq

description: RISC-associated size fractionated small RNA deep sequencing with the TruSeq kit

treatment_protocol: RISC-bound miRNAs from uninfected and WT/BaL-infected TZM-bl cells at 72 h postinfection were isolated by immunoprecipitation using a monoclonal antibody specific for Ago1, Ago2, and Ago3 (Abcam: AB 57113), and proteins were removed by digestion with proteinase K. Recovered small RNAs were then isolated using an miRVana kit (Ambion). The immunoprecipitated RNA (RIP-Seq) cDNA library was constructed using an Illumina TruSeq small RNA kit, prior to sequencing using an Illumina HiSeq 2000.


title: C8166 Uninfected Day 3 Small RNA Deep Sequencing


title: TZM-bl Uninfected Day 3 RISC RIP-Seq


title: TTF.2

city: Boston

first: Robert

middle: E

last: Kingston

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

description: protocol specific to mouse samples: Cells were pretreated with mild detergents (0.2% Tween-20 and 0.2% Triton X-100) for 5 minutes followed by crosslinking, mononucleosome sized DNA fragments were agarose gel extracted and pooled

data_processing:
50 bp reads aligned with Bowtie aligner v. 0.12.7
tag processing and filtering with the SPP workflow (Kharchenko 2008)
GC-correction coefficient for each read was computed in such a way that the resulting genome-wide distributions of GC-content become similar to the target 50%  GC-content distribution
Genome_build: mm9, hg19
Supplementary_files_format_and_content: space delimited text files containing locus and coverage

source_name: cell line

extract_protocol:
Cells underwent a 1.1% formaldehyde treatment for 10 minutes to preserve chromatin structure. Nuclei were then prepared from the crosslinked cells and the chromatin treated with multiple micrococcal nuclease (MNase) concentrations for 15 minutes at room temperature. Nucleosome-sized fragments were isolated and sequenced
Illumina, limited rounds of PCR, as in PMID: 23837789

value: tail tip fibroblasts

tag: sample type

value: Mnase-digested DNA


title: TZM-bl BaL Day 3 Small RNA Deep Sequencing

description: Total size fractionated small RNA deep sequencing with the TruSeq kit

treatment_protocol: Total RNA was isolated using TRIzol. The RNA fraction containing ~15- to 30-nt-long RNAs was isolated by polyacrylamide gel electrophoresis (PAGE) purification on 15% Tris-borate-EDTA (TBE)-urea gels (Bio-Rad), electroeluted from the excised gel slice (gel eluter; Hoefer), and cloned with the Illumina small RNA Truseq kit. Adapter-ligated small RNAs were reverse transcribed using SuperScript III, amplified using GoTaq green PCR master mix (Promega) with the Tru-Seq 3′ indices (Illumina), and sequenced on an Illumina HiSeq 2000.


title: TTF.1


title: Liv.1

value: liver primary culture


title: iPSC.TTF.1

value: induced pluripotent stem cells


title: T47D_HIF1β ChIP-Seq

city: Chapel Hill

first: Qing

last: Zhang

address: 450 West Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie with the following configurations. bowtie -p 1 -S -m 1 /mnt/Storage/data/Bowtie/hg19 *.fastq *.sam
peaks were called using MACS2 with the following setting. macs2 callpeak -t *.bam -B --nomodel --shiftsize 73 --SPMR -g hs
Genome_build: hg19
Supplementary_files_format_and_content: BED format with peak positions

source_name: T47D breast cancer cells

growth_protocol: T47D breast cancer cells were grown in RPMI supplemented with 10%FBS+1% Pen-Strep

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed by using Illumina ChIP-Seq library preparation kit as instructed

treatment_protocol: Cells were treated with Hypoxia (1%O2) and DMOG (1 mM) for a period of 16 hours

tag: antibody

tag: antibody manufacturer

value: Abcam

tag: antibody catalog number


title: iPSC.TTF.2


title: T47D_EglN2 ChIP-Seq

value: HA antibody, Clone 7

value: Santa Cruz


title: T47D_Ctrl_ChIP_Seq


title: T47D_HIF1α ChIP-seq


title: T47D_NRF1 ChIP_Seq

value: NRF1 antibody


title: Liv.2


title: NTC RNA-seq

city: Stanford

first: Andrew

last: Gentles

address: 1201 Welch Road

institute: Stanford University

description: Non-tumorigenic cells

data_processing:
Bases were called using RTA 1.13.48, and reads were de-multiplexed using Casava 1.8.2
Reads were trimmed by 9bp at 5' end to remove Nugen primers using fastx-trimmer from the FastX toolkit
Alignment was performed to the mouse genome (UCSC mm9 assembly) using Tophat 1.4.0 with default parameters
Expression values (FPKM) were generated using Cufflinks and Cuffdiff with igenomes GTF gene models
Genome_build: UCSC mm9 Mus musculus
Supplementary_files_format_and_content: tab-delimited text file with FPKM values for each gene

source_name: non-tumorigenic cells (NTCs)

growth_protocol: Cells dissociated from tumors and immediately purified by FACS

extract_protocol:
Total RNA was extracted using RNeasy kit according to manufacturer's instruction (Qiagen, cat# 74004)
15 ng total RNA was amplified using the Ovation RNA-Seq System V2 (Nugen). 1 mg of resulting cDNA was fragmented (average size of 150-200 bases) and used to construct DNA libraries for sequencing using NEBNext DNA sample Prep Master Mix Set 1 (New England Biolabs, #E6040S).

value: FVB

value: non-tumorigenic cells (NTCs)


title: CD4+ Uninfected Day 3 Small RNA Deep Sequencing