title: Human rep 3 neurons 0hr post-KCl stim


title: Mouse rep 1 cortical neurons 1hr post-KCl stim

status: Public on Nov 02 2016

type: SRA

city: Boston

first: Bulent

last: Ataman

state: MA

address: 220 Longwood Ave. GB405

department: Neurobiology

country: USA

institute: Harvard Medical School

library_source: transcriptomic

data_processing:
For RNA-Seq of mouse and rat cortical cultures, strand-specific single-end reads of length 75 bp or shorter were trimmed at their 3' ends to 70 bp; those shorter than 70 bp (<0.2%) were discarded.  The remaining 70-bp reads were mapped to the mm10 (mouse) or rn6 (rat) genome using BWA (v.0.7.8) allowing up to 2 mismatches.  For mouse and rat respectively, the usual 20 and 21 chromosomal alignment targets were supplemented with their mitochondrial genomes plus ~8 and ~6 million short sequences.  The latter targets represent all possible intragenic exonic sets from their respective RefSeq annotations whose junctions are spannable by 70-bp reads.  Typically 80% of all reads in each mouse library (90% in rat) were mappable and ~50-80% of these aligned uniquely; nonuniquely mapped reads were discarded.
The exons for all transcripts assigned to a gene based on the RefSeq annotation for mouse (GRCm38/mm10; Dec. 2011) or for rat (RGSC 6.0/rn6; July 2014) were merged (unioned); along with the constructed library of exon-exon splice-junction sequences, these defined each gene's mature-RNA target region.  The total number of bases of all reads that overlapped a gene's exonic region were divided by the total length of the region to yield an average read Density (coverage).  Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/70), where R is the total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements (RPKM units are proportional to Normalized Density units via  RPKM = Density/0.35).
Genome_build: mm10
Genome_build: rn6
Supplementary_files_format_and_content: Standard bigWig-formatted files (.bw) for both mouse and rat RNA-seq samples represent bwa-aligned trimmed 70-bp reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.  Each sample has its own pair of separate tracks for POS & NEG strands.

molecule: total RNA

organism: Mus musculus

growth_protocol: Mouse and rat neuronal cultures from three independent dissections were grown for RNA-seq experiments as outlined in the Methods section.

extract_protocol:
The libraries for RNA-Seq were constructed using the NEBNext Ultra Directional RNA library prep kit (for Illumina).
Strand-specific and single-end for RNA-Seq.

treatment_protocol: For KCl depolarization of neurons, neuronal cultures were first silenced overnight in culture media with 1 μM Tetrodotoxin (TTX) and 100 μM D-AP5.  The following day samples were incubated for 0, 1 or 6 hours in 55 mM KCl prior to harvest.

tag: strain

tag: tissue

value: E16.5 cortex, cultured, DIV7

tag: time post-kcl stimulation

tag: replicate


title: DOHH2 CUDC-907 2nM_6hr

city: Lexington

first: Kaiming

last: Sun

address: 4 Maguire Rd.

department: Translational Science

institute: Curis

data_processing:
mapped the sequencing reads to the  hg19) and gencode v19 using the software RNA STAR (v2.4.0j), which can align reads across splice junctions with or without gene annotations
did transcript abundance estimation with featureCounts (v1.4.6), using gene annotations from the database gencode v19. And FPKM values were calculated with R package edgeR (v3.8.5)
Most annotated genes can’t be detected in one given sample. So we removed genes whose mean FPKM values across all samples were less than 1, before the gene expression densities were plotted.
Genome_build: hg19 and gencode v19

organism: Homo sapiens

growth_protocol: Cell lines were purchased from the German Collection of Microorganisms and Cell Cultures and were maintained as recommended by the source. Growth media was changed every 2 to 3 days and cells were maintained at a density of 2 x 10^6 to 4 x 10^6 cells/mL. Cells at exponential growth stage were used for the experiment

extract_protocol:
Cells were pelleted by centrifugation at 10,000 x g at 4°C for 10 min, and immediately lysed in buffer RLT Plus (QIAGEN). RNA was purified from lysed cells using RNeasy columns (QIAGEN) following the manufacturer instructions.
Total RNA input was used to construct RNASeq libraries using the TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer instructions.

treatment_protocol: Cells were seeded at densities of 3 x 10^5 per mL in 24-well plates with the recommended culture medium and incubated with CUDC-907 at various concentrations for 6 or 12 hours.

tag: cell type

value: B cell lymphoma

tag: cell line

tag: treatment

value: CUDC-907 2nM 6hr


title: DOHH2 CUDC-907 20nM_12hr

value: CUDC-907 20nM 12hr


title: Mouse rep 1 cortical neurons 0hr post-KCl stim


title: WSUDLCL2 CUDC-907 50nM_12hr

value: CUDC-907 50nM 12hr


title: BM.MDP 1

city: La Jolla

first: Graham

middle: David

last: Thomas

state: CA

address: 9420 Athena Circle

department: Inflammation Biology

institute: La Jolla Institute for Allergy and Immunology

data_processing:
Illumina BCL to FASTQ conversion using bcl2fastq v1.8.4
Reads mapped to mm10 reference genome compiled with ensembl v73 gene models using RNA-STAR v2.3.0
Reads in ensembl v73 annotations counted using featureCounts v1.4.3
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file containing read counts for Ensembl v73 annotations at the gene level

source_name: Bone Marrow

extract_protocol:
RNA stored in Trizol was extracted using DirectZol mini columns (Zymo Research) without DNAse treatment to preserve RNA integrity. RNA was quantitated and integrity analyzed using an Agilent Bioanalyzer. Only RNA samples with a RIN > 8 were used for library preparation.
100ng total mRNA per library was prepared for sequencing using Illumina TruSeq v2 library kit in accordance with the manufacturer's instructions.

treatment_protocol: Bone marrow cells were obtained from hip bones, femurs and tibias of male C57BL/6 mice aged 10 weeks obtained from the Jackson Laboratory. Following  2 minute red blood cell lysis cells were blocked in FC receptor block (anti-CD16/32) for 20 minutes on ice. Surface stain (Live/Dead Yellow, Lineage (CD3/ CD19/ Ly6G/ NK1.1 / Ter119 - APC), CD115 - BV421, CD117 - PE-Cy7, Ly6C APC-Cy7, CD135 - PE, CD11c - FITC) was directly added to blocking antibody mix and incubated on ice for 30 minutes. Cells were washed in 5ml FACS buffer and subject to lineage depletion using anti_APC beads prior to sorting on a FACS Aria. Cell pellets were spun at 150g for 5 minutes, supernatants discarded and stored at -80oC in Trizol until RNA extraction.

value: MDP

value: Bone Marrow

tag: facs gating strategy


title: BM.MDP 2


title: WSUDLCL2 CUDC-907 5nM_12hr

value: CUDC-907 5nM 12hr


title: WSUDLCL2 control_12hr

value: control 12hr


title: WSUDLCL2 CUDC-907 50nM_6hr

value: CUDC-907 50nM 6hr


title: DOHH2 control_6hr

value: control 6hr


title: BM Ly6C.hi Mono Pos 3


title: Mouse rep 1 cortical neurons 6hr post-KCl stim


title: BM Ly6C.hi Mono Pos 1


title: WSUDLCL2 Control_6hr


title: Mouse neurons 6hr post-KCl stim

data_processing:
For RNA-Seq of human fetal brain cultures, strand-specific paired-end 76-bp reads were mapped to the hg19 genome using BWA (v.0.6.2) allowing up to 5 mismatches; only #1 ends of fragment pairs were used in subsequent analyses.  The usual 24 chromosomal alignment targets were supplemented with ~7 million short sequences representing all possible intragenic exonic sets from the hg19 RefSeq annotation whose junctions are spannable by 76-bp reads.  Typically 75-95% of all reads in each library were mappable and ~90% of these aligned uniquely; nonuniquely mapped reads were discarded.
The exons for all transcripts assigned to a gene based on the RefSeq annotation for human 37.1 (12 March 2009) were merged (unioned); along with the constructed library of splice-junction sequences these defined each gene's mature-RNA target region.  The total number of bases of all reads that overlapped a gene's exonic region were divided by the total length of the region to yield an average read Density (coverage).  Normalization of Densities to a standard of 10M 35-bp reads was effected by multiplying the raw Density by (10M/R)*(35/76), where R is the total number of uniquely mapped reads in a sample that did not overlap any RepeatMasker rRNA elements (RPKM units proportional to Normalized Density units via  RPKM = Density/0.35).
Note:  Some of the human samples derived from distinct sequencing runs using reads of different length.  For consistency, reads longer than 76 bp (100 bp and 101 bp) were truncated to 76bp at their 3' ends before .fastq files from different runs were concatenated together.
For RNA-Seq of cultured mouse cortical cells, strand-specific 76-bp paired-end were mapped to the mm9 genome using BWA, with subsequent analyses the same as described for human but based on the RefSeq annotation for mouse 37.1 (5 July 2007).
genome build: mm9
processed data files format and content: Standard bigWig-formatted files (.bw) for both human and mouse RNA-seq samples represent bwa-aligned reads piled up with single-base-pair resolution and then averaged over tiles of width 20bp.  Each set of fragment-end (#1 or #2) reads for a sample have their own pair of tracks for POS & NEG strands, i.e., so there are 4 tracks per sample.

growth_protocol: Human neuronal cultures from five and two different individuals were grown for RNA-seq and ChIP-seq experiments, respectively, according to the supplier’s instructions (ScienCell).

extract_protocol:
The mini-ChIP assays were performed (as described in Adli and Bernstein, 2011) on human neuronal cells that had been cultured for around two weeks.  Cells were cross-linked, lysed, sonicated for 3.5 minutes using a Branson 250, and the fragmented chromatin was immunoprecipated overnight with 1ug of H3K27Ac (abcam Cat# ab4728) and H3K27me3 (Millipore Cat# 074490) antibodies.  After samples were incubated with Protein A-Sepharose beads for 2 hours they were collected and washed; the DNA was eluted from the beads twice at 65°C for 10 minutes; the eluted chromatin and the "input" samples were reverse cross-linked at 65°C for 5 hours, then Proteinase K digested at 37°C for 2 hours.  The ChIP DNA was recovered by standard phenol-chloroform-isoamyl alcohol extraction, then precipitated overnight with ethanol.
The libraries for RNA-Seq were constructed using the PE RNAseq library kit (Illumina).

value: cerebral cortex

tag: background strain

tag: Sex

value: female


title: WSUDLCL2 CUDC-907 5nM_6hr

value: CUDC-907 5nM 6hr


title: BM Ly6C.low Mono Neg 1


title: BM Ly6C.low Mono Neg 2


title: BM Ly6C.hi Mono Pos 2


title: Mouse neurons 0hr post-KCl stim


title: DOHH2 CUDC-907 20nM_6hr

value: CUDC-907 20nM 6hr


title: Bl Ly6C.hi Mono Pos 1

source_name: Blood

value: Blood


title: Bl Ly6C.low Mono Neg 1


title: BM.cMoP 2

value: cMoP


title: 5448_earlystationary-planktonic_3

city: Nashville

first: Eric

middle: P

last: Skaar

state: Tennessee

address: 1161 21st Avenue South, A5303B MCN

institute: Vanderbilt University Medical Center

data_processing:
Illumina base-calling software
Reads were trimmed and Illumina adapters were clipped using Trimmomatic v0.32 with a leading and trailing minimum score of 3 and a 4-base sliding window minimum score of 15
Reads were mapped to the GAS MGAS5005 genome (NC_007297, NCBI) using Bowtie2 v2.2.4 run in end-to-end mode with default settings
Transcript abundances were calculated in Reads Per kilobase per Million mapped reads (RPKM) using Cufflinks v2.2.1 with a ribosomal masking file for all 5S, 16S, 23S, and tRNA loci, (NC_007297.gff, NCBI). Cuffdiff, a program within the Cufflinks package, was used to calculate differential expression values for genes with a false discovery rate adjusted p-value (q-value) less than 0.05.
Operon structure was predicted from the resulting Bowtie2 alignment files using Rockhopper v2.03 with the following relevant references: McClure R, Balasubramanian D, Sun Y, Bobrovskyy M, Sumby P, Genco CA, Vanderpool CK, Tjaden B. 2013. Computational analysis of bacterial RNA-Seq data. Nucleic Acids Res 41:e140. andTjaden B. 2015. De novo assembly of bacterial transcriptomes from RNA-seq data. Genome Biol 16:1.
Genome_build: NC_007297.1
Supplementary_files_format_and_content: All_samples_gene_exp_diff.txt; cuffdiff differential gene expression
Supplementary_files_format_and_content: All_samples_fpkm_values.txt; cufflinks FPKM values
Supplementary_files_format_and_content: NC_007297_Rockhopper_operons.txt; rockhopper operon prediction

organism: Streptococcus pyogenes

growth_protocol: Grown in Todd Hewitt Broth + 0.2% yeast extract diluted to 1/5 strength

extract_protocol:
RNA was isolated from frozen cell pellets using the Direct-zol RNA Miniprep kit (Zymo Research) following the manufacturer’s instructions with the addition of an extra step for cell disruption using glass beads. Genomic DNA was removed using the TURBO DNA-free kit (Ambion) according to the manufacturer’s instructions. Ribosomal RNA (rRNA) was removed using the Ribo-Zero™ Gram Positive Bacteria rRNA Removal Kit (Epicentre Technologies) and remaining RNA was purified with the Agencourt RNAClean XP kit (Beckman Coulter) according to the manufacturers’ instructions.
cDNA libraries were prepared from the purified RNA using the Epicentre ScriptSeq v2 RNA-seq library preparation kit (Epicentre Technologies) and purified using the Agencourt AMPure XP system (Beckman Coulter) according to the manufacturer’s instructions.

treatment_protocol: Cells were stored in RNAprotect Bacteria Reagent (QIAGEN) prior to RNA extraction

tag: growth phase

value: early stationary planktonic

tag: sample type

value: Whole bacterial cell


title: Mouse neurons 1hr post-KCl stim


title: BM.cMoP 1


title: Logarithmic phase -Nitrogen_wild type

city: Auckland

first: Justin

middle: M.

last: O'Sullivan

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

description: proximity ligation (Genome conformation capture) library

library_source: genomic

data_processing:
Sequences were intercalated
Network assembly was performed using the Topography suite v1.19. GCC networks were constructed from 36bp (P. aeruginosa) paired end Illumina Genome Analyser sequence reads. Topography uses the SOAP algorithm to position PE tags and single ends which contain a SacII restriction site onto the  P. aeruginosa (NC_002516) reference genome. The reference genome also contained the pUC19 (SYNPUC19CV) sequence. No mismatches or unassigned bases (N) were allowed during positioning.
Except where indicated, bioinformatics and statistical analyses were performed on interactions in which the sequence reads were able to be mapped uniquely onto the reference genome and were above the FDR cut-off value.
Genome_build: NC_002516
Supplementary_files_format_and_content: Processed files contain the uniquely mappable interactions for each condition.

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

growth_protocol: Pseudomonas aeruginosa strains were stored (-80°C) and cultured (37°C) on/in mineral salts medium (MM) with either 0.05% (w/v) or 0.2% (w/v) NH4Cl. NH4Cl was used as nitrogen source. The cells were cultivated with 2% (w/v) sodium gluconate. For GCC analyses, P. aeruginosa strains were recovered from -80°C on LB-plates for 24 hours prior to starter culture inoculation. Starter cultures were cultured (37°C, 160rpm, O/N) in MM medium (gluconate 2% w/v) with or without nitrogen, as indicated. Test cultures were inoculated, from the starter cultures, in MM media gluconate (2% w/v) with or without nitrogen, grown (37°C, 160rpm) and harvested at an OD600 = 0.6-8 (log phase) or OD600 = 4-5 (stationary phase).

extract_protocol:
P. aeruginosa chromatin was prepared according to Rodley et al. (2009) with the following modifications. Chromatin was prepared from a total of 6.6 x 10^10 formaldehyde cross-linked cells, treated with lysozyme (5mg ml-1) supplemented FA-lysis buffer (15min, 4°C), prior to sonication (5 x 10sec pulse, 20-28 watt, 30sec pause in between pulses, 4°C).(modified from (2)) Chromatin samples were aliquoted into 15 sets of 4 x 10^9 cells. Samples were digested with SacII (100U, New England Biolabs) and ligated with T4 DNA ligase (20U, Invitrogen). Cross-links were reversed in the presence of Proteinase K (7-11μg, Roche) before pUC19 (149 x 106 molecules) was added, to control for ligation events during preparation for sequencing. RNA was removed and the samples purified by three Phenol:Chloroform (1:1) extractions. Samples were subsequently column purified (Zymo, DNA clean and concentratorTM-5 kit), eluted in milliQ H2O and combined for sequencing. Paired-end sequencing (36bp) was performed on 5μg DNA using the Illumina Genome Analyser platform (Allan Wilson Centre, Massey University, New Zealand).
Sequences were fragmented to 200 bp fragments. End filled and primers ligated on, following standard Illumina protocols.

tag: genotype/variation

value: wild type


title: Stationary phase -Nitrogen_ΔphaC1-Z-C22

source_name: P. aeruginosa PAO1 ΔphaC1-Z-C22


title: Stationary phase +Nitrogen_ΔphaC1-Z-C22


title: 5448_earlystationary-planktonic_2


title: 5448_earlystationary-planktonic_1


title: Stationary phase -Nitrogen_wild type


title: Logarithmic phase -Nitrogen_ΔphaC1-Z-C22


title: Ly6Clow_Cebpb

description: 3ug Santa Cruz sc-150x/IP

data_processing:
Illumina BCL to FASTQ conversion using bcl2fastq v1.8.4
Reads mapped to mm10 reference genome compiled with ensembl v73 gene models using Bowtie
Mapped reads converted into tag directories and bigWig files generated using HOMER
Genome_build: mm10

extract_protocol:
ChIP assays for histone modifications were performed as previously described (Gilfillan et al., 2012). For each ChIP assay 500,000 FACS isolated cells were immediately washed with PBS and resuspended in MNase digestion buffer (50mM Tris pH 8.0, 1mM CaCl2, 0.2% Triton X-100). Cells were then digested in to mononucleosomal fragments using micrococcal nuclease (MNase, Affymetrix, CA). Enzymatic digestion was quenched by addition of 1/10 volume stop buffer (110mM Tris pH 8.0, 55mM EDTA), samples briefly sonicated using a Bioruptor (Diagenode, Belgium) and then adjusted to RIPA buffer conditions by adding an equal volume of 2x RIPA buffer (280mM NaCl, 1.8% Triton x100, 0.2% SDS, 0.2% Sodium Deoxycholate, 5mM EGTA). Immunoprecipitations were performed in a final volume of 100 μl. 2 μg of anti-H3K4me2 (Millipore 07-030) or 2μg of anti-H3K27ac (Diagenode C15410196) were added and incubated overnight with rotation at 4 °C. Antibody-antigen-DNA complexes were recovered by incubating for 2 hours with 10 μl Protein A Dynabeads previously washed in RIPA buffer (10mM Tris pH 8.0, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.2% SDS, 0.2% Sodium Deoxycholate). Complexes were then washed 5x in ice cold RIPA buffer and 1x in LiCl wash buffer (10mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0.5% Igepal CA-630, 0.5% Sodium deoxycholate,), each wash was performed in 200 μl at 4 °C for 5 minutes with rotation. All above buffers were supplemented with 1x Protease inhibitor Cocktail, 1mM PMSF and 5mM Sodium Butyrate (Sigma). Beads were subject to a final wash in 200 μl ice cold TE buffer (Invitrogen) without protease inhibitors and eluted in 100 μl 1% SDS-TE buffer at 37 °C for 20 minutes. Finally, protein was treated with 2 μl proteinase K (Ambion) for 1h at 55 °C and DNA purified using a ChIP Clean & Concentrate column (Zymo, Irvine, CA) eluting in 30 μl final volume.      ChIP for PU.1 and C/EBPb were performed as previously described (Gosselin et al., 2014). 500,000 sorted cells were washed in PBS and immediately fixated for 9 minutes at room temperature in 1% methanol free formaldehyde in PBS (ThermoFisher Scientific). Fixation was quenched by addition of 1/20 volume 2.625M glycine solution and cells were washed twice with PBS. Cell pellets were then snap frozen in a dry ice/methanol bath and stored at -80oC until needed. Nuclei were enriched by resuspending cell pellets in 10mM HEPES pH 7.9, 85mM KCl, 1mM EDTA, 0.5% Igepal CA-630 and incubating on ice for 10 minutes. Nuclei were harvested by spinning at 3000 g for 10 minutes, and lysed in 130 μl lysis buffer (10mM Tris pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Sodium Deoxycholate, 0.5% N-lauroylsarcosine). DNA was transferred in to Covaris micro tubes (Covaris, MA) sheared into 150-600bp fragments using a Covaris E220 (14 mins, duty cycle 3%, 100 cycles per burst). Final volume was adjusted to 200 μl and 22 μl 10% Triton X-100 added, cell debris was then cleared by spinning at maximum speed for 5 minutes. 20 μl of protein A dynabeads pre-conjugated to 3ug anti PU.1 or C/EBPb (sc-352x and sc-150x respectively, Santa Cruz Biotechnology, CA) were added to each chromatin preparation and incubated with rotation for 2h at 4 °C. Antibody-antigen-DNA complexes were then washed in 3x WBI (20mM Tris pH 7.4, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA, ), 3x LiCl WB (10mM Tris Ph 7.4, 250mM LiCl,, 1% Triton X-100, 0.7% Sodium Deoxycholate, 1% Igepal CA-630) and 1x TET (TE, 0.2% Tween-20) buffer. All wassh volumes were 200 μl. DNA was eluted in 1% SDS-TE for 30 minutes at 37 °C, NaCl was added to a final concentration of 300mM and corsslinking reversed overnight at 65 °C. Finally, protein was treated with 2 μl proteinase K (Ambion) for 1h at 55 °C and DNA purified using a ChIP Clean & Concentrate column (Zymo, Irvine, CA) eluting in 30 μl final volume.
ChIP-Seq libraries were prepared using an initial 0.3 - 5 ng DNA using the ThruPlex-FD kit (Rubicon Genomics, MI) in accordance with the manufacturer's guidelines. RNA-Seq libraries were prepared using the Tru-Seq v2 library preparation kit (Illumina, La Jolla, CA) in accordance with the manufacturer's instructions.

value: Ly6Clo monocytes

tag: antibody

value: Cebpb

tag: antibody volume/vendor/catalog

value: 3ug Santa Cruz sc-150x/IP


title: 5448_latelog-planktonic_3

value: late log planktonic


title: Stationary phase +Nitrogen_wild type


title: 5448_latelog-planktonic_2


title: Ly6Clo_PU1

description: 3ug Santa Cruz sc-352x/IP

value: Bone Marrow

value: 3ug Santa Cruz sc-352x/IP


title: Ly6Chi_PU1

description: 3ug Santa Cruz sc-352x/IP

value: Ly6Chi monocytes


title: Logarithmic phase + Nitrogen_wild type


title: 5448_latelog-planktonic_1


title: 5448_earlylog-planktonic_2

value: early log planktonic


title: 5448_earlylog-planktonic_3


title: MNase_input

description: Micrococcal nuclease treated input DNA control


title: 5448_10day-biofilm_3

value: 10 day biofilm


title: 5448_earlylog-planktonic_1


title: Input_CH2O

description: Formaldehyde treated input control


title: Ly6Clo_H3K27ac

description: 2ug Diagenode C15410196/IP

value: 2ug Diagenode C15410196/IP


title: Ly6Chi_H3K27ac

description: 2ug Diagenode C15410196/IP


title: cMoP_H3K27ac

description: 2ug Diagenode C15410196/IP


title: 5448_10day-biofilm_1


title: 5448_10day-biofilm_2


title: 5448_6day-biofilm_3

value: 6 day biofilm


title: Ly6Clo_H3K4me2

description: 2ug Millipore 07-030/IP

value: 2ug Millipore 07-030/IP


title: MDP_H3K4me2

description: 2ug Millipore 07-030/IP

value: MDP


title: sac3b-7_mRNA-Seq_rep2

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: mRNA

data_processing:
mRNA-Seq: Clean reads were mapped to TAIR10 by TopHat2, allowing up to two mismatches.
genome build: TAIR10
processed data files format and content: For sRNA-Seq and mRNA-Seq: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Seeds were sowed on half-strength Murashige and Skoog (MS) media containing 1.5% sucrose with 0.7%  agar. After stratification at 4◦C for 2 days, plants were grown under a long day photoperiod (16 h light/8 h dark) at 22◦C.

extract_protocol:
Total RNA were extracted from 12-day-old seedlings of Col-0 and sac3b-7 using Trizol reagent (Ambion, 15596) and treated with DNase (Turbo) to remove any genomic DNA contaminants. Each sample has two biological replicates.
Library construction and deep sequencing were performed by the Core Facility of Genomics in Shanghai Plant Stress Biology Center, China.

tag: genotype

value: seedlings


title: cMoP_H3K4me2

description: 2ug Millipore 07-030/IP

value: cMoP


title: 5448_16hr-biofilm_3

value: 16 hr biofilm

value: Whole bacterial cell


title: sac3b-7_mRNA-Seq_rep1

description: mRNA


title: 5448_6day-biofilm_2


title: 5448_6day-biofilm_1


title: Col-0_WT_mRNA-Seq_rep2

description: mRNA

value: WT


title: Ly6Chi_H3K4me2

description: 2ug Millipore 07-030/IP


title: 5448_16hr-biofilm_1


title: Col-0_WT_mRNA-Seq_rep1

description: mRNA


title: 5448_8hr-biofilm_3

value: 8 hr biofilm


title: sac3b-3_sRNA-Seq

description: small RNA

data_processing:
sRNA-Seq: We get clean reads from BGI. Clean reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie with parameter -v 0. Reads that can be mapped to annotated structural RNAs were removed. Only uniquely mapped reads were retained.
genome build: TAIR10
processed data files format and content: For sRNA-Seq and mRNA-Seq: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

extract_protocol:
Total RNA was extracted from 12-day-old seedlings of Col-0, sac3b-7 and sac3b-3 mutants using Trizol reagent.
Library construction and deep sequencing were performed by the Beijing Genomics Institute in Shenzhen, China.


title: 5448_16hr-biofilm_2


title: 5448_8hr-biofilm_2


title: MDP_H3K27ac

description: 2ug Diagenode C15410196/IP


title: 5448_8hr-biofilm_1


title: sac3b-3_MethylC-Seq

description:
genomic DNA
treated with bisulfite

data_processing:
MethylC-Seq:Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000. Copy-duplicates were remove using remove-dupl command of BRAT-BW. acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
genome build: TAIR10
processed data files format and content: For MethylC-Seq: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol:
Genomic DNA was extracted from 12-day-old seedlings and sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for bisulfite treatment, library preparation, and sequencing.
Bisulfite sequencing libraries were prepared using standard Illumina protocols.


title: Col-0_WT_sRNA-Seq

description: small RNA


title: sac3b-7_MethylC-Seq

description:
genomic DNA
treated with bisulfite


title: Hyphal cells and spores

city: Beijing

first: xiaoling

last: zhang

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of microbiology chinese academy of sciences

data_processing:
Illumina Casava software was used for base calling.
Sequenced reads were trimmed for adaptor sequences, masked for low-complexity or low-quality sequences, and then mapped to Pestalotiopsi fici W106-1 mitochondrial genome data using HISAT2
Fragments Per Kilobase of exon per Million mapped reads (FPKM) were calculated.
Genome_build: Pestalotiop fici W106-1 mitochondrial
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

organism: Pestalotiopsis fici

source_name: Hyphal cells and spores

extract_protocol:
Mycelia were collected after 20 days, and the total RNA was extracted with TriZol®.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Col-0_WT_MethylC-Seq

description:
genomic DNA
treated with bisulfite


title: Hyphal cells

source_name: Hyphal cells


title: ros1_rep1_sRNA-Seq

status: Public on Nov 01 2016

data_processing:
Briefly, after adapter sequences were trimmed, clean reads of size 18-31 nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameter -v 0 -k 10. Reads that can mapped to annotated structural RNAs were removed.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bedGraph files were generated using genomeCoverageBed from bedtools with parameter  -bga -split

extract_protocol:
Total RNAs were isolated from 14-d-old seedlings by Trizol reagent (Invitrogen).
Small RNAs were precipitated by PEG 8000 solution (20% PEG, 1 M NaCl). Small RNAs were sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for library preparation and Illumina sequencing.

value: ros1 mutant

tag: age

value: 14 days


title: C24_nrpd1_methyl-Seq

description: treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done by BGI (Shenzhen, China)
A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome with C24 variants  (http://1001genomes.org/data/ MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Clean reads were mapped to the pseudo-C24 genome using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each  cytosine of forward and reverse strands of the reference
Genome_build: A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome (TAIR10) with C24 variants  (http://1001genomes.org/data/ MPI/MPISchneeberger2011/releases/current//C24/Marker/C24.SNPs.TAIR9.txt)
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol:
The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq 2500.
And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq 2500.

tag: background

value: nrpd1 mutant


title: ros1nrpd1_rep1_sRNA-Seq

value: ros1/nrpd1 double mutant

tag: tissue


title: Col_rep1_sRNA-Seq


title: Microvesicle treated, rep s2

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

data_processing:
Alignment: tophat 2.0.7
Quantitation: featureCounts 1.5.0
Normalization & Differential Expression: DESeq2 1.10.1
Genome_build: hg19
Supplementary_files_format_and_content: han-rawcounts.txt: contains raw gene-level counts against UCSC hg19 genes using featureCounts 1.5.0. han-normalizedcounts.csv contains DESeq-normalized expression values, normalized by library size.

source_name: BEAS-2B cells

extract_protocol:
Total RNA was extracted from cells using Quick-RNA Miniprep Kit (Zymo Research) or RNeasy Mini Kit (Qiagen) and cDNA was synthesized using QuantiTect Reverse Transcription Kit (Qiagen) according to manufacturers' instructions.
Total RNA was extracted and an mRNA library was prepared using Illumina TruSeq platform and followed by transcriptome sequencing using an Illumina NextSeq 500 cartridge.

treatment_protocol: BEAS-2B cells were treated with HDM and alveolar macrophage-derived microvesicles for 3 hours.

tag: condition

value: Microvesicle treated


title: Control, rep s2

value: Control


title: HDM+Microvesicle treated, rep s2

value: HDM+Microvesicle treated


title: nrpd1_rep2_sRNA-Seq


title: HDM treated, rep s2

value: HDM treated


title: HDM+Microvesicle treated, rep s21


title: nrpd1_rep1_sRNA-Seq


title: Microvesicle treated, rep s28


title: sac3b-7_sRNA-Seq

description: small RNA


title: Col_rep2_sRNA-Seq


title: HDM+Microvesicle treated, rep s28


title: Control, rep s20


title: HDM treated, rep s21


title: HDM+Microvesicle treated, rep s20


title: Microvesicle treated, rep s20


title: HDM treated, rep s20


title: Pax6KO_rep2_RNASeq

city: Jerusalem

first: Yuval

last: Dor

address: Ein Kerem

department: Department of Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to mouse genome mm9 and Refseq transcriptome and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
genome_build: mm9
supplementary_files_format_and_content: Tab delimited file of transcript raw read counts.

source_name: Pancreatic beta cell

extract_protocol:
RNA-Seq: Pancreatic islets were isolated from transgenic MIP-CreER; Pax6lox/lox; Rosa26-LSL-YFP and from their control littermates  (MIP-CreER; Rosa26-LSL-YFP), one week after tamoxifen injection. Beta cells were than sorted by YFP. RNA was extracted using Qiagen RNA extraction Mini Kit.
RNA-Seq:Total RNA was amplified and converted to cDNA using NuGen Ovation amplification kit. Libraries were constructed using Illumina's TruSeq RNA sample prep kit using manufacturer's protocols.

value: mouse pancreatic beta cells

value: 6-8 weeks

value: MIP-CreER; Pax6lox/lox; Rosa26-LSL-YFP


title: Pax6KO_rep1_RNASeq


title: Pax6KO_rep3_RNASeq


title: ros1_rep2_sRNA-Seq

value: seedlings


title: Pax6CTRL_rep4_RNASeq

value: WT (MIP-CreER; Rosa26-LSL-YFP)


title: ros1nrpd1_rep2_sRNA-Seq


title: Pax6CTRL_rep3_RNASeq


title: Pax6CTRL_rep1_RNASeq


title: Control, rep s28


title: Min6_Input2

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
ChIP-Seq -Reads were aligned to mm9 or hg19 genome using Bowtie-1.0.0 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating BedGraph profiles.
Peak calling was done using HOMER software in factor mode for Pax6 ChIP with default setting for fold-change and FDR=0.01. For H3K9Ac histone mode was used at FDR=0.01 and fold change set to 2 over Input.
genome_build: mm9
supplementary_files_format_and_content: Peak files are HOMER output files including header information.Significant regions with respective scores and p-values are listed.

source_name: Min6 cells

extract_protocol:
ChIP-Seq: Sonicated chromatin from Min6 cells or EndoC cells was immunoprecipitated with rabbit anti Pax6 (Biolegend) and that of sorted pancreatic beta cells using anti-H3K9Ac antibody.
ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.

value: mouse beta cell line Min6

tag: chip antibody


title: Control, rep s21


title: HDM treated, rep s28


title: Min6_Input1


title: Microvesicle treated, rep s21


title: Pax6_ChIP_Min6_rep2

value: Rabbit anti-Pax6 (Biolegend,  901301)


title: Pax6_ChIP_Min6_rep3

value: WT


title: Pax6CTRL_rep2_RNASeq


title: Pax6_ChIP_Min6_rep1


title: F1

city: Bethesda

first: Koray Dogan

last: Kaya

state: MD

address: 6 CENTER DR

department: NEI

institute: NIH

description: MEFs generated from Macf1flox/+ mice

data_processing:
Trimming Illumina adapters, defined in TrueSeq3-PE-2.fa file, by Trimmomatic (version 0.36) from paired end data.
Transcript level abundance was quantified against Ensemble release 84 cDNA FASTA file by Kallisto (version 0.42.5).
The effective counts were converted to FPKM values via edgeR. The transcripts below 1 FPKM in every sample of both groups were eliminated.
Final FPKM values were calculated based on those normalized counts
Differentially Expressed transcripts were identified by exact test of edgeR
Genome_build: GRCm38.p4/Ensembl 84
Supplementary_files_format_and_content:
raw_counts.csv: Raw transcript level abundance count
normalized_fpkms.csv: Normalized fragments per kilobase per million mapped reads (FPKM)
de.csv: Differential Expression analysis results per transcript.

molecule: polyA RNA

source_name: MEFs generated from Macf1flox/+ mice

growth_protocol: Cells were grown to 75% confluency and treated with AAV8-CMV-Cre (1.2x10e13vg/ml) overnight. Single cell colonies were generated for the Macf1 knockout allele (Macf1-/-) and heterozygous control (Macf1-/+)

extract_protocol:
RNA was extracted using TriPure reagent.
Illumina Stranded mRNA Library Prep Kit

tag: cell type

value: mouse embryonic fibroblasts (MEFs)


title: C6

description: MEFs generated from Macf1flox/+ mice


title: B5

description: MEFs generated from Macf1flox/+ mice


title: A5

description: MEFs generated from Macf1flox/flox mice

source_name: MEFs generated from Macf1flox/flox mice


title: A4

description: MEFs generated from Macf1flox/flox mice


title: PEGAF2

city: Lausanne

first: Nikolce

last: Gjorevski

address: Station 15 AI 1106

department: SV-IBI

country: Switzerland

institute: EPFL

description: ISCs grown in non-degradable PEG replicate 2

data_processing:
Sequencing data was processed using the Illumina Pipeline Software version 1.82.
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3, Martin 2011) and filtered for low complexity with seq_crumbs (v. 0.1.8).
Reads were aligned against Mus musculus genome (version GRCm38) using STAR (v. 2.4.2a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Mus musculus (Ensembl v. GRCm38.82) gene annotation.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: Tab-delimited text files include gene counts for each Sample.

source_name: Intestinal stem cells

growth_protocol: Dissociated ISCs were embedded in the three different matrices, allowed to form colonies and expanded in the presence of R-spondin, noggin, EGF, CHIR99021 and valproic acid

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen)
RNA-seq libraries were prepared using the Illumina Truseq Stranded mRNA protocol

tag: protocol

value: non-degradable PEG


title: PEGW2

description: ISCs grown in degradable PEG replicate 2

value: degradable PEG


title: PEGW3

description: ISCs grown in degradable PEG replicate 3


title: MATR3

description: ISCs grown in Matrigel replicate 3

value: Matrigel


title: MATR2

description: ISCs grown in Matrigel replicate 2


title: PEGAF1

description: ISCs grown in non-degradable PEG replicate 1


title: MATR1

description: ISCs grown in Matrigel replicate 1


title: ∆Liz_Input

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
Single-end 100bp reads were mapped onto the Mouse reference genome mm10 using Bowtie2 v2.1.0 allowing one mismatch in a 22bp-long seed.
Tracks were created using HOMER software v4.7 (Heinz et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: E14 mouse embryonic stem cells

growth_protocol: Feeder-free ESCs were grown on gelatin-coated flasks. 2i+vitC culture conditions were as follows: N2B27 medium (50% neurobasal medium (Gibco), 50% DMEM/F12 (Gibco), 2mM L-glutamine (Gibco), 0.1mM β- mercaptoethanol, NDiff Neuro2 supplement (Millipore), B27 serum-free supplement (Gibco)) supplemented with 1000U/ml LIF, 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901), and vitamin C (Sigma) at a final concentration of 100 µg/ml.

extract_protocol: Lysates were obtained from cross-linked nuclei, and chromatin was immunopreciptated with antibodies against H3K27me3

treatment_protocol: To induce differentiation towards EpiLCs, cells were plated at a density of 104 cells/cm2 on Fibronectin (10 µg/ml) coated plates in ground state medium. After one day, cells were gently washed with 1xPBS, and cultured in N2B27 medium supplemented with 12 ng/ml Fgf2 (R&D) and 20ng/ml Activin A (R&D). EpiLCs were passaged with Accutase at day 4 of differentiation.

tag: cell-type

value: delta-Liz ground-state ESC


title: E14_Input

value: wild-type ground-state ESC


title: ∆Liz_D7_H3K27me3

value: delta-Liz Epiblast-like

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9738

value: Day 7 of Activin/FGF2 treatment


title: ∆Liz_D4_H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9737

value: Day 4 of Activin/FGF2 treatment


title: E14_D7_H3K27me3

value: wild-type Epiblast-like

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9735


title: A6

description: MEFs generated from Macf1flox/flox mice


title: E14_D4_H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9734


title: ∆Liz_D0_H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9736

value: Cultured in 2i+vitc


title: RNA_cre_4h

first: Kai

last: Ge

address: 50 South Dr Rm 4154

department: NIDDK

data_processing:
Basecalls performed using Illumina's CASAVA package v1.8.2 with default parameters
ChIP-seq reads and RNA-seq were aligned to the mm9 genome assembly using Illumina's CASAVA package v1.8.2 with default parameters
Peaks of ChIP-seq were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3); For ChIP-seq of others: Windows (50), Gaps (50), FDR (1e-10).
Aligned reads on exonic regions from RNA-Seq were used to calculate RPKM to measure the gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: For ChIP-seq data, wig files were generated using in-house script and the scores represent RPKM; For RNA-seq data, tab-delimited text files were generated to include RPKM values for each gene.

source_name: Brown preadipocyte cell

growth_protocol: Primary preadipocytes were isolated from interscapular BAT of new born GRf/f (Jackson No. 021021) pups and immortalized by SV40T

extract_protocol:
Total RNA was harvested using Trizol reagent. mRNA wasfurther  purified using Invitrogen Dynabeads® mRNA DIRECT™ Kit  (Cat. 610-11).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After immortalization with SV40T, cells were infected with retroviral Vec or Cre to generate WT or GR KO cells. For adipogenesis assay, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 4 days before induction of adipogenesis. The confluent cells (0h) were induced with 0.02 μM insulin, 1 nM T3, 0.5 mM 3-isobutyl-1-methyl-xanthine (IBMX), 2 μg/ml dexamethasone, and 0.125mM indomethacin for 4 hour.

tag: strain

value: immortalized GR-flox/flox brown preadipocytes

tag: stage of adipogenesis


title: E14_D0_H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb #9733


title: RNA_vec_4h


title: RNA_vec_D2

value: day 2


title: RNA_vec_D0

value: day 0 (0h)


title: RNA_vec_D7

value: day 7


title: RNA_cre_D7


title: RNA_cre_D2


title: PEGW1

description: ISCs grown in degradable PEG replicate 1

value: degradable PEG


title: PEGAF3

description: ISCs grown in non-degradable PEG replicate 3

value: non-degradable PEG


title: H3K4me1_ChIPSeq_cre_4h

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 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 15-18 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 following the manufacturer's protocols.

value: H3K4me1 Antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot/batch #


title: input_ChIPSeq_cre_4h


title: H3K27ac_ChIPSeq_vec-2_4h

value: H3K27ac Antibody


title: input_ChIPSeq_vec_4h


title: H3K27ac_ChIPSeq_cre_4h


title: input_ChIPSeq_vec_0h


title: CBP_ChIPSeq_vec_4h

value: CBP (D6C5) Rabbit mAb

value: Cell Signaling Technology


title: CBP_ChIPSeq_cre_4h


title: H3K4me1_ChIPSeq_vec_4h


title: input_ChIPSeq_cre_0h


title: H3K27ac_ChIPSeq_vec_4h


title: RNA_cre_D0


title: PCREB_ChIPSeq_vec_4h

value: p-CREB Antibody

value: Millipore


title: PCREB_ChIPSeq_cre_4h


title: C/EBPβ_ChIPSeq_cre_4h

value: C/EBP β Antibody (C-19)

value: Santa Cruz Biotechnology


title: C/EBPβ_ChIPSeq_vec-2_4h


title: C/EBPβ_ChIPSeq_vec_4h


title: GR_ChIPSeq_vec-2_4h

value: GR Antibody


title: PCREB_ChIPSeq_vec-2_4h

value: immortalized GR-flox/flox brown preadipocytes


title: input_ChIPSeq_vec-2_4h


title: GR_ChIPSeq_vec_4h


title: GR_ChIPSeq_vec_0h


title: GR_ChIPSeq_cre_0h


title: CAF-7 Triptolide 6h

city: Minneapolis

first: Xianda

last: Zhao

state: Minnesota

address: 515 Delaware St SE

department: Surgery

institute: University of Minnesota

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat v2.0.5 with settings --library-type fr-unstranded --fusion-search -r 200 --mate-std-dev 100 -a 5 --no-coverage-search
The resulting TopHat data served as input to other Cufflinks tools 2.2.0. Transcripts were also assembled using Cufflinks, with stipulating the reference transcriptome Mus_musculus.GRCm38.74.  All cufflinks assemblies were merged with Cuffmerge.
Differentially expressed genes (DEGs) were calculated with Cuffdiff and presented the data in terms of fragments per kilobase of transcript per million mapped reads (FPKMs).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Pancreatic Cancer Tissue

growth_protocol: Cancer associated fibroblasts were kept in DMEM media with 10% FBS.

extract_protocol:
Cells were harvested by scratching and washed with 1X PBS twice. Total RNA isolation was made by Rneasy Mini Kit (QIAGEN). All steps were same as manufacturer's instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100nM triptolide was used to treat cancer associated fibroblasts for either 6 or 24h.

value: Fibroblasts

value: KrasG12D; Trp53R172H; Pdx-1 Cre (KPC)


title: CAF-1 Triptolide 24h


title: CAF-5 Triptolide 24h


title: CAF-5 Control


title: CAF-1 Triptolide 6h


title: CAF-1 Control


title: AB15

city: Cambridge

first: Cory

middle: Haley

last: White

address: 320 Bent St

department: DAGS

institute: Merck

data_processing:
CASAVA
Sequenced reads were trimmed for adaptor sequence and filtered for low quality sequences, then mapped to hg38 whole genome using TopHat v2.0.13 with parameters --bowtie1 --transcriptome-index --no-coverage-search --library-type fr-firststrand
Read counts were calculated with HTSeq (htseq-count) using the following parameters:  --stranded=reverse.  Mapped files were counted against the Gencode v21 database with all level 3 annotations removed.
Data filtering was performed for both genes and ERCCs before differential expression analysis with EdgeR.  Any gene which did not achieve 1 count per million in at least 4 samples or any ERCC that did not achieve at least 5 total reads in at least 4 samples was removed from future analysis.  Data was upper quartile normalized and ERCCs were used in conjunction with the program RUVSeq to create a variable to remove unwanted variation.  That variable was then used as a blocking factor in general linear modeling tests within EdgeR.  Significance was determined at an FDR corrected p-value < 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file for read counts in each sample.

source_name: CD4 T-cell RNA extract

extract_protocol:
Total RNA was extracted from cell samples using the Rneasy Plus Mini Kit (QIAGEN, Cat. No. 74134) with the addition of an on-column DNase treatment (Rnase-free Dnase Set, QIAGEN, Cat. No. 79254)
Paired end RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD4 T cell

tag: cd4 t cell subtype

value: Central Memory T Cell (TCM)

value: 17 days post extraction from host

tag: treatment state

value: Resting Latently Infected


title: AB16

value: 19 days post extraction from host

value: Activated Latently Infected


title: CAF-7 Triptolide 24h


title: AB14

value: Activated Uninfected


title: CAF-5 Triptolide 6h


title: AB06


title: AB11


title: AB09

value: Resting Uninfected


title: AB08


title: AB05


title: AB13


title: AB03


title: AB01


title: AB02


title: AB07


title: AB10


title: AB04


title: A13-Lg_rep2 [BS-Seq]

city: Guangzhou

first: Xin

last: Li

state: Guangdong

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned by BSmooth bisulfite alignment pipeline (version 0.7.1) as previously described in detail. Briefly, reads were aligned by Bowtie2 (version 2.0.1) against human genome (hg19) as well as the lambda phage genome.
After alignment, methylation measurements for each CpG were extracted from aligned reads. We filtered out measurements with mapping quality < 20 or nucleotide base quality on cytosine position < 10 and we also removed measurements from the 5’ most 10 nucleotides of both mates.
bsseq package in BSmooth was used to identify small and large differentially methylated regions (DMRs).
Genome_build: hg19
Supplementary_files_format_and_content: text file, methylated read count and total read count at each CpG site and each sample

source_name: Patient A13

growth_protocol: Unless otherwise stated, cells were grown to 70% (A38-Lg) or 100% (A38-Per) confluence in DMEM with 10% Fetal Bovine Serum (FBS)

extract_protocol:
DNA was extracted with MasterPure kits
Whole genome bisulfite sequencing libraries were generated using TruSeq DNA Sample preparation protocol (Illumina) with modifications. Bisulfate conversion was done after gel size selection using EZ DNA Methylation-Gold Kit (Zymo Research). To amplify bisulfate converted library Kapa Hifi Uracil+ (Kapa Biosystems) polymerase was used.

tag: patient

value: Patient A13

value: lung metastasis


title: 38-Lg_6AN_2_INP_batch5

description: for 38-Lg_6AN_2 K27Me3

data_processing:
Basecalls performed using CASAVA version 1.8.2
For 46 bp paired-end Illumina HiSeq2000 sequencing data, reads were aligned against human genome (hg19) using BWA with default parameters. After alignment, duplicate reads were removed and only uniquely aligned reads were kept for further analysis. For 48 bp single-end Solid sequencing data, reads were aligned using Bowtie with default parameters and only uniquely aligned reads were kept for further analysis.
For narrow histone modification peaks including H3K4Me3, H3K9Ac, H3K16Ac and H3K27ac, MACS2 were used for peak calling with default parameters. While for broad histone modifications peaks in including H3K36Me3, H3K27me3, H3K9Me2/3, and yH2AX, peak calling were performed using RSEG which is based on hidden Markov model (HMM) and specifically designed for identifying broad histone peaks.
Genome_build: hg19
Supplementary_files_format_and_content: bed files, called peaks by MACS2 and called domains by RSEG

source_name: Patient A38

extract_protocol:
For ChIP-seq, input and IP DNA were extracted with Phenol:Chloroform.
Libraries were prepared from 10-20 ng of IP ChIP DNA and 100-150 ng of input DNA according to Illumina’s instructions along with the ChIP-seq DNA Sample Prep Kit (IP-102-1001). Briefly, samples were checked for quality and concentration from 150-250 bp on a bioanalyzer. DNA was end-repaired using Klenow polymerase in 58 μL of reaction buffer. For IP DNA, Klenow was diluted 1:5. Samples were incubated at 20°C for 30 minutes and subsequently purified on QIAquick PCR purification columns. A-tails were then added to the DNA with Klenow and dATP in NEB buffer 2 at 37°C for 30 minutes and cleaned with Qiagen MiniElute PCR purification columns. Sequencing adapters were then ligated onto the DNA for 15 minutes at room temperature followed by cleaning with MiniElute columns. Samples were then run on 2% agarose gels and DNA from 216-366 bp (DNA plus adapters) were cut from the gel and purified with a Qiagen QIAquickGel Extraction kit. Concentrations were then checked on a bioanalyzer and 8 ng were PCR amplified with Phusion polymerase (Fisher) for 15 cycles (10 sec 98°C, 30 sec 65°C, 30 sec 72°C) followed by 5 minutes at 72°C. Samples were then cleaned with Ampure kits (Illumina) and washed with 80% ethanol. DNA samples were resuspended at the end of the cleanup into 17.5 μL buffer EB (Qiagen) and subjected to next generation sequencing on Illumina HiSeq platform according to manufacturers instructions.

treatment_protocol: For ChIP-seq, cells were crosslinked with 1% formaldehyde for 10 min at 37 degrees. Isolated chromatin was sonicated to avg length of 200-600bp.

tag: antibody

value: input

tag: treatment

value: 6AN treated


title: 38-Lv_rep1 [BS-Seq]

value: Patient A38

value: liver metastasis


title: A13-Pr1_rep2 [BS-Seq]

value: primary tumor


title: A13-Pr2_rep2 [BS-Seq]


title: A13-Pr1_rep1 [BS-Seq]


title: A13-Pr2_rep1 [BS-Seq]


title: A13-Lg_rep1 [BS-Seq]


title: AB12

tag: age


title: 38-Lv_rep2 [BS-Seq]

tag: tissue


title: 38-Lg_6AN_1_INP_batch5

description: for 38-Lg_6AN_1 K27Me3


title: 38-Lg_6AN_2_INP_batch4

description: for 38-Lg_6AN_2 K9Me3 and K9Me2


title: 38-Lg_6AN_1_INP_batch4

description: for 38-Lg_6AN_1 K9Me3 and K9Me2


title: 38-Lg_6AN_2_INP_batch3

description: for 38-Lg_6AN_2 K36Me3 and K27Ac


title: 38-Lg_6AN_1_K27Ac


title: 38-Lg_6AN_1_K27Me3


title: 38-Lg_DMSO_1_INP_batch5

description: for 38-Lg_DMSO_1 K27Me3

value: DMSO control


title: 38-Lg_DMSO_1_INP_batch3

description: for 38-Lg_DMSO_1 K36Me3 and K27Ac


title: 38-Lg_6AN_1_K9Me2


title: 38-Lg_6AN_2_K27Me3


title: 38-Lg_6AN_1_INP_batch3

description: for 38-Lg_6AN_1 K36Me3 and K27Ac


title: 38-Lg_DMSO_2_INP_batch3

description: for 38-Lg_DMSO_2 K36Me3 and K27Ac


title: 38-Lg_6AN_2_K27Ac


title: 38-Lg_DMSO_1_INP_batch4

description: for 38-Lg_DMSO_1 K9Me3 and K9Me2


title: 38-Lg_DMSO_2_INP_batch5

description: for 38-Lg_DMSO_2 K27Me3


title: 38-Lg_DMSO_1_K9Me2


title: 38-Lg_DMSO_2_INP_batch4

description: for 38-Lg_DMSO_2 K9Me3 and K9Me2


title: 38-Lg_DMSO_2_K27Ac


title: HPDE_2_INP_batch5

description: for HPDE_2 K27Me3 and K4Me3

source_name: HPDE (Human Pancreatic Duct Epithelial Cell Lines

tag: cell line


title: 38-Lg_DMSO_1_K27Ac


title: 38-Lg_DMSO_2_K27Me3


title: HPDE_2_INP_batch3

description: for HPDE_2 K36Me3 and K27Ac

value: Human Pancreatic Duct Epithelial Cell Lines


title: HPDE_1_INP_batch4

description: for HPDE_1 K9Me3 and K9Me2


title: HPDE_2_K9Me3


title: 38-Lg_DMSO_1_K27Me3


title: HPDE_1_INP_batch5

description: for HPDE_1 K27Me3 and K4Me3


title: HPDE_1_K9Me3


title: CAF-7 Control

value: Fibroblasts

tag: genotype

value: KrasG12D; Trp53R172H; Pdx-1 Cre (KPC)


title: A13-Lg_2_INP_batch1

description: for A13-Lg_2 K36Me3


title: A13-Lg_1_INP_batch2

description: for A13-Lg_1 K27Me3 and K9Me3


title: A13-Lg_2_INP_batch5

description: for A13-Lg_2 K27Ac and K9Me2


title: A13-Lg_1_INP_batch1

description: for A13-Lg_1 K36Me3


title: HPDE_2_INP_batch4

description: for HPDE_2 K9Me3 and K9Me2


title: A13-Lg_1_INP_batch5

description: for A13-Lg_1 K27Ac and K9Me2


title: HPDE_1_INP_batch3

description: for HPDE_1 K36Me3 and K27Ac


title: A13-Lg_2_K9Me2


title: A13-Lg_2_K9Me3


title: A13-Lg_2_K27Me3


title: A13-Lg_1_K36Me3


title: A13-Lg_1_K27Ac


title: A13-Lg_2_K27Ac


title: A13-Lg_1_K9Me3


title: A13-Lg_1_K9Me2


title: A13-Lg_2_K36Me3


title: A13-Lg_1_K27Me3


title: A13-Pr1_1_INP_batch5

description: for A13-Pr1_1 K27Me3 and K4Me3


title: A13-Pr1_2_INP_batch3

description: for A13-Pr1_2 K36Me3 and K27Ac


title: A13-Pr1_2_INP_batch4

description: for A13-Pr1_2 K9Me3 and K9Me2


title: A13-Pr1_1_K4Me3


title: A13-Lg_2_INP_batch2

description: for A13-Lg_2 K27Me3 and K9Me3


title: A13-Pr1_2_K4Me3


title: A13-Pr1_1_INP_batch4

description: for A13-Pr1_1 K9Me3 and K9Me2


title: A13-Pr1_2_K9Me2


title: A13-Pr1_1_K9Me2


title: A13-Pr1_1_INP_batch3

description: for A13-Pr1_1 K36Me3 and K27Ac


title: A13-Pr1_2_K9Me3


title: A13-Pr1_1_K9Me3


title: A13-Pr1_1_K27Ac


title: A13-Pr1_2_K27Ac


title: A13-Pr1_2_K36Me3


title: A13-Pr1_1_K36Me3


title: A13-Pr1_2_INP_batch5

description: for A13-Pr1_2 K27Me3 and K4Me3


title: A13-Pr1_1_K27Me3


title: A13-Pr1_2_K27Me3


title: A13-Pr2_1_INP_batch2

description: for A13-Pr2_1 K27Me3 and K9Me3


title: A13-Pr2_2_INP_batch2

description: for A13-Pr2_2 K27Me3 and K9Me3


title: A13-Pr2_1_INP_batch1

description: for A13-Pr2_1 K36Me3


title: A13-Pr2_1_INP_batch5

description: for A13-Pr2_1 K27Ac and K9Me2


title: A13-Pr2_2_INP_batch5

description: for A13-Pr2_2 K27Ac and K9me2


title: A13-Pr2_2_K9Me2


title: A13-Pr2_1_K9Me2


title: A13-Pr2_2_K27Ac


title: A13-Pr2_2_K36Me3


title: A13-Pr2_1_K27Ac


title: A13-Pr2_2_K9Me3


title: A13-Pr2_rep1 [RNA-Seq]

description:
primary tumor
all_gene_raw_readcounts2.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Paired-end HiSeq2000 sequencing reads were aligned against human genome (hg19) by OSA (version 2.0.1) with default parameters. After alignment, only uniquely aligned reads were kept for further analysis.
Reads count for each gene of all samples were estimated using HTSeq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html) and then were used to identify differentially expressed (DE) genes using DESeq package. Genes with adjusted p-value < 0.01 and fold-change > 2 between A38-41 and A38-5 were considered as DE genes.
Genome_build: hg19
Supplementary_files_format_and_content: text file, raw read counts of each gene for all samples

extract_protocol:
For RNA-seq, RNA was extracted with Trizol reagent.
RNA-Seq libraries were generated using TruSeq Stranded mRNA protacol (Illumina). 2ug of total RNA was used for library generation and 6 minutes of fragmentation. For enrichment of cDNA fragments 11 PCR cycles were used.

value: 10% FBS


title: A13-Pr2_rep2 [RNA-Seq]


title: A13-Pr2_1_K27Me3


title: A13-Lg_rep2 [RNA-Seq]

description:
lung metastasis
all_gene_raw_readcounts2.txt


title: A13-Pr2_1_K36Me3


title: A13-Pr1_rep2 [RNA-Seq]


title: A13-Lg_rep1 [RNA-Seq]


title: A13-Pr2_2_K27Me3


title: 38-Lg_DMSO_rep2 [RNA-Seq]

description:
lung metastasis, DMSO control
all_gene_raw_readcounts2.txt

value: lung metastasis, DMSO control

value: DMSO


title: 38-Lg_DMSO_rep1 [RNA-Seq]


title: A13-Pr1_rep1 [RNA-Seq]


title: 38-Lg_6AN_rep2 [RNA-Seq]

description:
lung metastasis, 6AN treated
all_gene_raw_readcounts2.txt

value: lung metastasis, 6AN treated


title: 38-Lv_rep2 [RNA-Seq]

description:
liver metastasis
all_gene_raw_readcounts2.txt


title: A13-Pr2_2_INP_batch1

description: for A13-Pr2_2 K36Me3


title: HKC_MNase_High_Salt_Rep1

city: New York

first: Nicholas

last: Gomez

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Paired reads were filtered using TagDust and aligned to the human genome (hg19) using bowtie with max insertion size of 1000 and Maq rounding disabled. Two peaks clearly shown, indicating the co-existence of mono-nucleosomes and di-nucleosomes. A wiggle file was created using DANPOS v2.1.3 (Chen et al., 2013).  DANPOS is designed mainly for mono-nucleosome MNase-Seq data, so we preprocessed our sequencing data to account for DANPOS center-weighted mapping for reads from di-nucleosomes. According to the fragment size distribution fragments greater than 266 bp were considered from di-nucleosomes and others were from mono-nucleosomes. The empirical distribution of mono-nucleosomes was estimated and used to simulate the fragment length when splitting di-nucleosomes into mononucleosomes in silico.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Cultured Kidney Cell

extract_protocol: TruSeq libraries were constructed per manufacturer's instructions

tag: cell type

value: Kidney Cell

tag: growth protocol

value: Cells were maintained in DMEM high glucose supplemented with 10% serum, 1% NEAA, and 1% L-Glutamine

tag: extract protocol

value: Nuclei were Mnase-treated and extracted with varying concentrations of NaCl


title: HKC_MNase_High_Salt_Rep2


title: 38-Lv_rep1 [RNA-Seq]

tag: protocol


title: HKC_MNase_Low_Salt_Rep1


title: A13-Pr2_1_K9Me3


title: 38-Lg_6AN_rep1 [RNA-Seq]


title: H1-ESC_MNase_High_Salt_Rep1

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell

value: Cells were maintained undifferentiated onplates coated with growth factor-reduced Matrigel in mTeSR1 media changed daily. Cells were passaged every three days.


title: H1-ESC_MNase_High_Salt_Rep2


title: H1-MSC_FAIRE

data_processing:
Reads were filtered using TagDust (Lassmann et al. 2009). Reads were aligned to the reference human genome (hg19) with bowtie, allowing two mismatches and extended to 134bp. Reads aligning to more than four locations or overlapped blacklisted regions of the human genome were removed. Available Replicates were pooled for final analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Mesnechymal progenitor

value: ES-derived-mesenchymal progenitor

value: Cells were maintained in Mesencult Proliferation Kit (StemCell Technologies) according to the manufacturer's instructions

value: Fixed Cells were lysed, sonicated, and extracted with phenol-choloroform (Simon 2012)


title: H9-ESC_FAIRE


title: H1-ESC_FAIRE_Rep2


title: H1-ESC_FAIRE_Rep1


title: ED123 mRNA-Seq

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
All the RNA-seq reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
Paired end fastq files were mapped to refenrence genome by using Tophat 2.0.10 with default parameters.
The output mapping files from the TopHat2 alignment, along with the GTF file from ENSEMBL (http://uswest.ensembl.org/) bovine gene annotation v75.30, were used in the htseq-count (http://www-huber.embl.de/users/anders/HTSeq/) to count the total number of reads mapped to each gene.
The expression level of mRNAs in each library was obtained by normalizing reads number to counts per million reads (CPM): CPM = (gene reads number / total mapped reads number per library) × 1,000,000.
All the small RNA reads were demultiplexed according to their index sequences using CASAVA version 1.8 (Illumina)
The small RNAs sequencing reads with good quality were subjected to 3’ adaptor sequence trimming by miRDeep2
The miRNA expression (CPM) were identified by miRDeep2, while piRNA expression (CPM) were identified by costumised Perl program based on method descibed by other studies (Liu et al., 2012.PLoS ONE 7(4): e34770).
Genome_build: UMD3.1
Supplementary_files_format_and_content: Tab-delimited text files include CPM values for each Sample

organism: Bos taurus

source_name: Ileal tissue

extract_protocol:
The tissue samples were frozen on liquid nitrogen, and RNA was extracted using Trizol reagent. Illumina TruSeq small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of small RNA sequencing libraries.  Illumina TruSeq RNA Sample Prep Kit (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of RNA sequencing libraries.
RNA-seq libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample name

tag: post-treatment

tag: allicin dose


title: ED121 mRNA-Seq


title: ED122 mRNA-Seq


title: ED033 mRNA-Seq


title: hlh-30(tm1978)-Cry5B

city: Tainan

first: Huan-Da

last: Chen

address: No.1, University Road

country: Taiwan

institute: National Cheng Kung University

description:
30Cvs30P_score.xlsx
30CvsN2C_score.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: worm base
Supplementary_files_format_and_content: xlsx files include RPKM values, Fold change values and P-values for each Sample.

organism: Caenorhabditis elegans

source_name: whole body

growth_protocol: All worms were fed with E. coli OP50 for 44 hours to reached L4 stage, and ready for Cry5B treatment.

extract_protocol:
All worms were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were treated with control(pQE9 in E. coli OP50) or Cry5B(pQE9-Cry5B in E. coli OP50) for 3 hours.

tag: strain

tag: bacteria strain

value: pQE9-Cry5B in E. coli OP50

value: Cry5B (pQE9-Cry5B in E. coli OP50) for 3 hours


title: N2-Cry5B

description:
N2CvsN2P_score.xlsx
30CvsN2C_score.xlsx

value: wild type


title: N2-control

description:
N2CvsN2P_score.xlsx
30PvsN2P_score.xlsx

value: pQE9 in E. coli OP50

value: control (pQE9 in E. coli OP50) for 3 hours


title: hlh-30(tm1978)-control

description:
30Cvs30P_score.xlsx
30PvsN2P_score.xlsx


title: H7-ESC_FAIRE


title: ED032 mRNA-Seq


title: H1-ESC_MNase_Low_Salt_Rep2


title: DD122 mRNA-Seq


title: ED013 mRNA-Seq


title: DD123 mRNA-Seq


title: DD121 mRNA-Seq


title: ED012 mRNA-Seq


title: ED011 mRNA-Seq


title: DD033 mRNA-Seq


title: H1-ESC_MNase_Low_Salt_Rep1


title: DD031 mRNA-Seq


title: DD011 mRNA-Seq


title: CD122 mRNA-Seq


title: DD032 mRNA-Seq


title: CD123 mRNA-Seq


title: CD121 mRNA-Seq


title: CD033 mRNA-Seq


title: CD012 mRNA-Seq


title: CD032 mRNA-Seq


title: CD031 mRNA-Seq


title: CD013 mRNA-Seq


title: ED031 mRNA-Seq


title: CD011 mRNA-Seq


title: DD012 mRNA-Seq


title: BD122 mRNA-Seq


title: BD123 mRNA-Seq


title: BD033 mRNA-Seq


title: BD121 mRNA-Seq


title: DD013 mRNA-Seq


title: BD032 mRNA-Seq


title: BD013 mRNA-Seq


title: BD012 mRNA-Seq


title: BD011 mRNA-Seq


title: BD031 mRNA-Seq


title: AD122 mRNA-Seq


title: AD033 mRNA-Seq


title: AD121 mRNA-Seq


title: ED033 miRNA-Seq


title: ED122 miRNA-Seq


title: AD031 mRNA-Seq


title: AD032 mRNA-Seq


title: AD011 mRNA-Seq


title: ED123 miRNA-Seq


title: AD012 mRNA-Seq


title: AD013 mRNA-Seq


title: ED012 miRNA-Seq


title: ED032 miRNA-Seq


title: ED031 miRNA-Seq


title: ED121 miRNA-Seq


title: ED011 miRNA-Seq


title: ED013 miRNA-Seq


title: DD123 miRNA-Seq


title: DD121 miRNA-Seq


title: DD122 miRNA-Seq


title: DD033 miRNA-Seq


title: DD031 miRNA-Seq


title: DD032 miRNA-Seq


title: AD123 mRNA-Seq


title: DD013 miRNA-Seq


title: DD012 miRNA-Seq


title: DD011 miRNA-Seq


title: CD123 miRNA-Seq


title: CD122 miRNA-Seq


title: CD121 miRNA-Seq


title: CD033 miRNA-Seq


title: CD032 miRNA-Seq


title: CD031 miRNA-Seq


title: CD011 miRNA-Seq


title: BD123 miRNA-Seq


title: BD032 miRNA-Seq


title: BD033 miRNA-Seq


title: BD031 miRNA-Seq


title: BD121 miRNA-Seq


title: BD013 miRNA-Seq


title: CD013 miRNA-Seq


title: AD123 miRNA-Seq


title: AD033 miRNA-Seq


title: BD012 miRNA-Seq


title: CD012 miRNA-Seq


title: AD122 miRNA-Seq


title: BD011 miRNA-Seq


title: AD012 miRNA-Seq


title: AD011 miRNA-Seq


title: AD031 miRNA-Seq


title: old_beta_Input

source_name: Pancreatic beta cell

value: mouse pancreatic beta cells

value: 16 months

value: WT

tag: chip antibody


title: AD032 miRNA-Seq


title: old_H3K9Ac-1_ChIP

value: ab8898 (Abcam)


title: AD121 miRNA-Seq


title: WT_CHF-INF

city: Oslo

first: Gunn

middle: Annette

last: Hildrestrand

state: Oslo

address: Sognsvannsveien 20

department: Microbiology

country: Norway

institute: Oslo University Hospital and University of Oslo

description: infarcted left ventricle, 3 days post myocardial infarction

data_processing:
Libray preparation: mRNA is enriched by using the oligo(dT) magnetic beads, followed by fragmentation into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification.
Sequencing: The library products are sequenced using Illumina HiSeqTM 2000.
Sequenced reads were trimmed by removing adaptor sequences, and masked for low-complexity or low-quality sequences. The clean reads were mapped to mouse reference sequences (Li R., Yu C., Li Y., et al . 2009, Bioinformatics).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Left ventricle

extract_protocol:
Total RNA was isolated from mouse left ventricle using TRIzol (Invitrogen,Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s instructions. RNA quality and concentration were examined using the Agilent RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA) in combination with a 2100 Bioanalyzer (Agilent Technologies) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were subjected to experimental myocardial infarction three days prior to RNA extraction

value: heart

value: 8 weeks


title: Neil3_KO_CHF-INF


title: WT_CHF-LV

description: non-infarcted left ventricle, 3 days post myocardial infarction


title: AD013 miRNA-Seq


title: Neil3_KO_CHF-LV


title: BD122 miRNA-Seq


title: H3K4me3 hypoxia 8 hours

city: Maastricht

first: Michiel

last: Adriaens

address: Universiteitssingel 60

department: Maastricht Centre for Systems Biology - MaCSBio

country: Netherlands

institute: Maastricht University

description: Sample name: 10

data_processing:
Image processing and base calling was performed using Illumina software tools provided by the manufacturer.
Subsequent paired-end genome alignment was performed using Novoalign with Human Genome 18 (HG18) used as a reference genome.  Only uniquely aligned reads were used for further analysis.
To remove PCR artifacts all data were collapsed prior to peak calling.
To identify H3K4me3 and H3K27me3 marked regions the peak caller Findpeaks (version 4.0) was used using standard settings.
Genome_build: HG18
Supplementary_files_format_and_content: WIG files containing H3K4me3 and H3K27me3 marked regions

growth_protocol: MCF7 (human mammary adenocarcinoma) were cultured at 37°C, 5% CO2, 100% humidity in Dulbecco's Modified Eagle Medium:Nutrient Mixture F-12 (DMEM/F12 1:1; MCF7) and DMEM McCoy’s 5A medium (DU145). The culture medium was supplemented with 10% fetal calf serum (FCS), 200 mM L-glutamine and antibiotics.

extract_protocol:
MCF7 cells were transferred to hypoxic culturing conditions for the indicated durations and immediately fixed to avoid reoxygenation. After 24 hours of hypoxia, cells were reoxygenated for 8 hours. Cells were disrupted by sonication, yielding genomic DNA fragments ranging from 200-1000 bp, with a bulk size of 200-500bp. For each immunoprecipitation 10-20 million cells were used. ChIPs were performed and analyzed using standard protocols (antibody: H3K4me3 and H3K27me3 (07-449; Upstate)).
ChIP-seq libraries were prepared for sequencing using standard 36 bp paired-end protocol for the Illumina Genome Analyser IIx (GAIIx). Two lanes were used per sample for sufficient coverage.

treatment_protocol: For hypoxic exposure, cells were transferred to a MACS VA500 microaerophilic workstation (Don Whitley Scientific, Shipley, UK) for the indicated duration. The atmosphere in the chamber consisted of <0.02% O2, 5% H2, 5% CO2, and 74% N2.

tag: oxygen state

value: hypoxia

tag: timepoint

value: 8 hours

tag: oxygen concentration

value: anti-H3K4me3 (Abcam, catalog# Ab8580, lot# 1054726)


title: H3K27me3 reoxygenation 8 hours

description: Sample name: 23

value: normoxia

value: 32 hours

value: anti-H3K27me3 (Upstate, catalog# 07-449, lot# DAM1514011)


title: H3K4me3 hypoxia 24 hours

description: Sample name: 16

value: 24 hours


title: H3K4me3 normoxia

description: Sample name: 4

value: 0 hours


title: H3K27me3 normoxia

description: Sample name: 5


title: H3K4me3 reoxygenation 8 hours

description: Sample name: 24


title: MCF7L-P cells

city: Houston

first: Xiaoyong

last: Fu

state: Tx

address: 1 Baylor Plaza

department: Breast Center

institute: Baylor College of Medicine

description: Tamoxifen-sensitive

data_processing:
Analysis was performed with the ALEXA-seq software package (http://www.alexaplatform.org/alexa_seq/) as previously described by Griffith et al, in Nature Methods, 2010.
Creation of a database of expression and alternative expression sequence “features” (genes, transcripts, exons, junctions, boundaries, introns, and intergenic sequences) based on Ensembl (53_36o) gene models
Alignment of short paired-end sequence reads to these features using BWA (0.5.8a) and BLAST (2.2.18)
Identification of features that are expressed above background while taking into account locus-by-locus noise
Assignment of FPKM-like values for each feature type, normalized to feature size and total library coverage
Identification of differentially expressed genes and sequence features between samples
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include UCSC transcript id, hg19 gene symbol, gene FPKM values, log2 and computed fold change, and false discovery rate (q).

source_name: human breast cancer cells

growth_protocol: Cells were maintained in RPMI/1640 medium, supplemented with 10% heat inactivated fetal bovine serum (FBS) and 1% penicillin/streptomycin/glutamine (PSG).

extract_protocol:
Total RNA was isolated using an RNeasy Mini Kit (Qiagen), using manufacturer's protocol.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) and Agilent Automation NGS system according to manufacturers’ instructions.

treatment_protocol: The TamR cells were kept in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped-FBS and 1% PSG, with the addition of 100 nM 4HT.


title: TR_TAM_Input

description: Tamoxifen resistant cells grown in 4OH-Tam-FOXA1 input

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using Tophat2 (version 0.6) with parameters -r 300. UCSC known transcripts were supplied in GTF format file.
Peak calling was done using MACS 2
Genome_build: hg19
Supplementary_files_format_and_content: Peaks based on MACS 2 peak calleing

source_name: MCF7L breast cancer cell line

extract_protocol:
chromatin from approximately 1 × 107 fixed cells was sonicated to a size range of 200-300 bp.  Solubilized chromatin was subjected to immunoprecipitation with the FOXA1 antibody  bound to protein A and protein G beads.  A fraction of the sample was not exposed to antibody to be used as control (input).  The samples were reversed crosslinked, treated with proteinase K, and DNA was extracted.  DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics).  Libraries were sequenced using 50-bp reads on the Illumina platform
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Rubicon Genomics per manual).  Libraries were sequenced using Illumina platform

tag: antibody


title: MCF7L-TamR-siIL8

description: tamoxifen resistant cell line derived from MCF7L cells after transfection with a siIL8

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to Hg19 whole genome using Bowtie aligner.
Cufflinks was used to generate expression value (RPKM) for each gene
Genome_build: Hg19
Supplementary_files_format_and_content: Processed files include RPKM values for each gene symbol in TXT files.

extract_protocol:
Qiagen Rneasy kit, using manufacturer's protocol.
TruSeq RNA Sample Preparation Kit


title: MCF7L-TamR-siFoxA1-Seq1

description:
tamoxifen resistant cell line derived from MCF7L cells after transfection with a siFOXA1
RJ2_TR_SiFOXA1.txt


title: TR_TAM

description: Tamoxifen resistant cells grown in 4OH-Tam-FOXA1 ChIP


title: MCF7L-FoxA1-Dox

description: MCF7L cells with DOX-inducible expression of FOXA1-without DOX treatment


title: MCF7L-TamR-siFoxA1-Seq2

source_name: tamoxifen resistant cell line derived from MCF7L cells after transfection with a siFOXA1


title: MCF7L-P-siER

description: MCF7L cells after treatment with a siER

source_name: MCF7L cells after treatment with a siER


title: MCF7L-P-siFoxA1-Seq2

description:
MCF7L cells after treatment with a siFOXA1
RJ7_TR_siFOXA1.txt


title: MCF7L-TamR-siER

description: tamoxifen resistant cell line derived from MCF7L cells after transfection with a siER


title: K23_ros1nrpd1_MethylC-Seq

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

source_name: Seedlings

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facility of Shanghai Center for Plant Stress Biology for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: tissue

value: seedling

tag: age

value: 14 days old


title: MCF7_TAM

description: Parental cells after 45 minutes treatment with 4OH-Tam -FOXA1 ChIP


title: H3K27me3 hypoxia 24 hours

description: Sample name: 17

tag: cell line


title: K22_nrpe1_MethylC-Seq

description: treated with bisulfite

tag: genotype


title: MCF7L-P-siFoxA1-Seq1

source_name: MCF7L cells after treatment with a siFOXA1


title: H3K27me3 hypoxia 8 hours

description: Sample name: 11


title: MCF_TAM_Input

description: Parental cells after 45 minutes treatment with 4OH-Tam -input


title: ros1-1 mutant_methyl-Seq

description:
ros1-1_methyl-Seq
treated with bisulfite

data_processing:
Basecalling, trimming for low quality reads and adaptor sequence were done byBiosciences Core Laboratory of KAUST.
A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome with C24 variants (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current/C24/Marker/C24.SNPs.TAIR9.txt)
Clean reads were mapped to the pseudo-C24 genome using BRAT-BW with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: A pseudo-C24 genome was generated through the replacement of SNPs in the Col-0 genome (TAIR10) with C24 variants (http://1001genomes.org/data/MPI/MPISchneeberger2011/releases/current/C24/Marker/C24.SNPs.TAIR9.txt)
Supplementary_files_format_and_content: The wig files give methylation level for all Cs (three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position (converted_C / ( converted_C+ unconverted_C ) ).

source_name: seedlings

extract_protocol: The bisulfite treatment, library preparation, and sequencing was done in Biosciences Core Laboratory of King Abdullah University of Science & Technology (KAUST) . Bisulfite sequencing libraries were prepared using standard Illumina protocols.

tag: genotype/variation

value: ros1-1 mutant


title: C24_wildtype_methyl-Seq

description:
C24_WT_methyl-Seq
treated with bisulfite


title: MCF7L-TamR cells

description: Tamoxifen-resistant


title: Endo_Input

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
ChIP-Seq -Reads were aligned to mm9 or hg19 genome using Bowtie-1.0.0 with parameters -v 3 -k 1 -m 1 --best --strata. Redundant reads were discarded before creating BedGraph profiles.
Peak calling was done using HOMER software in factor mode for Pax6 ChIP with default setting for fold-change and FDR=0.01. For H3K9Ac histone mode was used at FDR=0.01 and fold change set to 2 over Input.
genome_build: hg19
supplementary_files_format_and_content: Peak files are HOMER output files including header information.Significant regions with respective scores and p-values are listed.

source_name: EndoC cells

extract_protocol:
ChIP-Seq: Sonicated chromatin from Min6 cells or EndoC cells was immunoprecipitated with rabbit anti Pax6 (Biolegend) and that of sorted pancreatic beta cells using anti-H3K9Ac antibody.
ChIP-Seq: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Prep Kit.

value: human beta cell line EndoC


title: K21_nrpd1_MethylC-Seq

description: treated with bisulfite


title: MCF7L-P-siControl

description: MCF7L cells after treatment with a siCONTROL


title: MCF7L-FoxA1+Dox

description: MCF7L cells with DOX-inducible expression of FOXA1-with DOX treatment


title: K19_Col0_MethylC-Seq

description: treated with bisulfite

value: WT control


title: K20_ros1_MethylC-Seq

description: treated with bisulfite


title: MCF7L-TamR-siControl

description: tamoxifen resistant cell line derived from MCF7L cells after transfection with a sicontrol


title: Pax6_ChIP_Endo_rep1

value: WT

value: Rabbit anti-Pax6 (Biolegend,  901301)


title: RNase H8

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: HG19
Supplementary_files_format_and_content: HTSeq Read Count Table

source_name: Breast Tissue

extract_protocol:
RNA was extracted and purified using the Qiagen’s miRNeasy FFPE Kit, a kit specifically designed for purification of total RNA and microRNA from FFPE tissue sections.
Ribo-Zero and RNase H kits were used to prepare RNA library following manufacture protocols

value: breast cancer FFPE specimen

tag: extract protocol

value: RNase H


title: RNase H5


title: RNase H1


title: RNase H2


title: RNase H6


title: RNase H4


title: RNase H3


title: Ribo-zero8

value: Ribo-Zero


title: Ribo-zero7


title: Ribo-zero5


title: Ribo-zero3


title: Ribo-zero4


title: Ribo-zero6


title: Ribo-zero2


title: Ribo-zero1


title: Pax6_ChIP_Endo_rep2


title: H3K27me3_ChIP-seq_clf_Col/C24

first: Mei

last: Yang

address: No.5 Yiheyuan Road, Haidian District

institute: PKU

description: Chromatin IP against H3K27me3

data_processing:
RNA-sequencing reads for Col and C24 were mapped to TAIR10 genome and SNP corrected C24 genome using Tophat software. For hybrid RNA sequencing data analysis, we aligned the reads to both of the TAIR10 genome and SNP corrected C24 genome. Reads were assigned to an allele based upon the highest quality alignment and were further used to calculated allelic expression divergence. ChIP-seq data was mapped to Arabidopsis genome using the similar methods as in RNA-seq. The only difference is that we use bowtie to map our ChIP-seq reads. MACS software with default parameters  was used to call peaks representing enriched binding sites.llele based upon the highest quality alignment and were further used to calculated allelic expression divergence.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for mRNA seq samples,  read counts for ChIP-seq samples

source_name: seedling shoot

growth_protocol: Wild-type hybrid was generated by crossing Arabidopsis thaliana ecotype Col and C24. clf hybrid was generated by crossing clf mutant in Col background (SALK_139371) and clf mutant in C24 background which was identified from our ethyl methanesulfonate mutant library. The mutation in clfC24 contained a G-to-A substitution at position 4196 of CDS, which generated a D-to-N amino acid substitution in the SET domain of CLF protein. Plants were grown on Murashige and Skoog plates containing 1% Sucrose. The shoots of 14-day-old seedlings were used for ChIP-seq and RNA-seq. All seedlings were grown under short-day condition (8 hours light at 22℃ and 16 hours dark at 18℃), unless otherwise indicated.

extract_protocol:
Chromatin immunoprecipitation experiment was performed following previously published procedure (Gendrel et al. 2005). Briefly, 1.5 g of shoots of 14-day-old plants were cross-linked by 1% formaldehyde in a vacuum, and then the samples were ground to fine powder in liquid nitrogen. Chromatin was immunoprecipitated with antibody against H3K27me3 (Millipore).Total RNA was extracted from shoots of 14-day-old Arabidopsis seedling using the Rneasy plant mini kit (Qiagen). mRNAs were extracted from the total RNAs by Dynabeads oligo(dT) (Invitrogen Dynal). First- and second-strand cDNAs were obtained using random hexamer primers and SuperScript II reverse transcriptase (Invitrogen).
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: 14 day old

value: seedling shoot

tag: cultivar

value: F1 Col X C24

value: clf

value: H3K27me3 (Millipore)


title: H3K27me3_ChIP-seq_WT_Col_Rep2

description: Chromatin IP against H3K27me3

value: Col

value: wildtype


title: H3K27me3_ChIP-seq_WT_Col/C24_Rep2

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-seq_WT_C24_Rep1

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-seq_WT_Col/C24_Rep1

description: Chromatin IP against H3K27me3


title: H3K27me3_ChIP-seq_WT_Col_Rep1

description: Chromatin IP against H3K27me3


title: mRNA-seq_Col/C24_clf_Rep3

description: polyA RNA isolated


title: H3K27me3_ChIP-seq_WT_C24_Rep2

description: Chromatin IP against H3K27me3


title: RNase H7


title: mRNA-seq_Col/C24_clf_Rep2

description: polyA RNA isolated


title: mRNA-seq_Col/C24_clf_Rep1

description: polyA RNA isolated


title: H3K27me3_ChIP-seq_clf_C24

description: Chromatin IP against H3K27me3


title: SC5314-Glutamate, replicate 2

first: Michael

middle: C

last: Lorenz

state: TX

address: 6431 Fannin

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to C. albicans genome assembly 21 using TopHat v2.0.9 and Bowtie v2.1.0.0.
Fragments per kilobase of gene length per million mapped reads (FPKM) were calculated from the mapped reads using Cufflinks 2.2.0.
Replicates were combined and binary comparisons were in all possible combinations were generated with Cuffcompare 2.1.1.
Genome_build: Assembly 21
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for all named features.  Separate files are provided for each replicate

organism: Candida albicans

source_name: In vitro

growth_protocol: Cells were grown in the indicated media (standard Yeast Nitrogen Base containing ammonium sulfate and the indicated carbon source at 2% (w/v) for about 5 hours (until the pH of the casamino acid culture reached 5.5) at 37°C with aeration.

extract_protocol:
RNA was prepared from flash-frozen cultures using the SV40 total RNA isolation kit (Promega) with a zymolyase digestion step.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: In vitro

value: ~5 hours

value: wild type

tag: media

value: glutamate


title: mRNA-seq_C24_clf_Rep2

description: polyA RNA isolated


title: mRNA-seq_Col_clf_Rep2

description: polyA RNA isolated


title: mRNA-seq_Col_clf_Rep3

description: polyA RNA isolated


title: mRNA-seq_C24_clf_Rep3

description: polyA RNA isolated


title: SC5314-a-Ketoglutarate, replicate 1

value: a-Ketoglutarate


title: H3K27me3_ChIP-seq_clf_Col

description: Chromatin IP against H3K27me3


title: SC5314-Casamino acids, replicate 1

value: 2% casamino acids


title: SC5314-Glutamate, replicate 1


title: SC5314-Casamino acids, replicate 2


title: SC5314-Glucose, replicate 2

value: 2% glucose


title: SC5314-Glucose, replicate 1


title: flo11D batch 2 rep3

city: Seattle

first: Aimee

last: Dudley

state: Washington

address: 720 Broadway

institute: PNDRI

data_processing:
Read-pair alignment was carried out using Bowtie2 (version 2.1.0) with the parameters [-N 1 -I 50 -X 450 -p 6 --reorder -x -S] and allowing 1 mismatch per read
Read alignments were converted to gene counts using featureCounts (version 1.4.0) in the Subread package , with the parameters [-a -o -t gene –g ID –s 2 -T 1 -p -P -d 50 -D 450]
Genome_build: R64-1-1, extended with non-reference contigs
Supplementary_files_format_and_content: Tab-delimited text files include aligned read counts per gene for each Sample

organism: Saccharomyces cerevisiae

source_name: Whole colony

extract_protocol:
Hot acid phenol extraction
RNA libraries were prepared for sequencing using the Illumina Tru-Seq stranded mRNA kit and protocol


title: flo11D batch 2 rep2


title: flo11D batch 2 rep4


title: cis3D batch 2 rep1


title: cis3D batch 2 rep4


title: cis3D batch 2 rep2


title: WT batch 2 rep3


title: flo11D batch 2 rep1


title: cis3D batch 2 rep3


title: SC5314-a-Ketoglutarate, replicate 2


title: MUT_rep2

city: Karlsruhe

first: Raphael

last: Wild

address: Fritz-Haber-Weg 2

department: Zoology

country: Germany

institute: Karlsruhe Institute of Technology

data_processing:
RNA-seq reads were aligned to the Danio rerio genome DanRer7 (Zv9) using tophat-2.0.10 (bowtie2-2.1.0)
Transcripts were assambled using cufflinks-2.1.1
Differentially expressed genes were identified using Cuffdiff and CummeRbund (Trapnell et al., 2012, Nature Protocols) or HTSeq-0.6.1 and DESeq, cutoff p<0.05
Genome_build: zv9
Supplementary_files_format_and_content: tab-delimited text file with HTSeq count numbers WT_vs_flt1ka601_4dpf_htseqCountTable.txt
Supplementary_files_format_and_content: .csv file containing differentially expressed genes with fold change >2, p<0.05,  WT_vs_flt1ka601_4dpf_DEseq_2fold_p005.csv
Supplementary_files_format_and_content: .csv file containing differentially expressed genes with fold change >2, p<0.05,  WT_vs_flt1ka601_4dpf_CuffDiff_2fold_p005.csv

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Zebrafish were grown at standard conditions and flash frozen in liquid nitrogen at 4dpf, RNA was harvested using Trizol reagent. rRNA was depleted from 20µg total RNA using RiboMinus™ Eukaryote Kit v2 A15020 (Ambion/Life Technologies).
TruSeqIllumina RNA sample prepv2 kit  Part # 15026495 was used for RNA library preperation using standard Illumina protocols

tag: developmental stage

value: flt1ka601 (flt1-/-), Tg(kdrl:eGFP)s843


title: MUT_rep1


title: mRNA-seq_C24_clf_Rep1

city: Beijing

description: polyA RNA isolated


title: mRNA-seq_Col_clf_Rep1

description: polyA RNA isolated


title: WT_rep3

value: wildtype AB, Tg(kdrl:eGFP)s843


title: WT batch 2 rep2


title: WT_rep1


title: WT_rep2


title: S49GT

city: South Bend

first: Reginald

last: Hill

state: Indiana

address: 1234 North Notre Dame Ave.

department: Biological Sciences

institute: University of Notre Dame

description: microRNA

data_processing:
Processing of miRNA sequences, including adapter trimming, mapping, and statistical analysis was performed in iMir.  iMir utilizes Cutadapt for adapter trimming, Bowtie for read mapping, and the DESeq bioconductor package for differential expression analysis of replicated samples.  Processed reads were assessed for quality with FastQC.
Data were filtered using the following specifications: MicroRNAs that showed a log2 fold change of at least 2 or -2 in all gemcitabine-treated CAFs were included in subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: csv files containing base mean value for each miR for untreated (baseMean A) and gemctiabine treated (baseMean B) conditions. Fold change, log fold change, and p-vlaues included.

source_name: cancer associated fibroblasts

growth_protocol: Cells were grown in culture according to standard procedures and protocols with DMEM (Sigma) or RPMI (Sigma) supplemented with 10% FBS (RMBI) and 1% Pen-Strep (Life Technologies).  L3.6 and fibroblast cells were grown in DMEM with 10% FBS and 1% Pen-Strep.  Cells were tested throughout studies for mycoplasma using the MycoAlert™ kit (Lonza).

extract_protocol:
RNA was collected using TRIzol® according to standard protocol: Initial RNA concentration and integrity was assessed using the Qubit 2.0 Fluorometer (Life Technologies Corp., Carlsbad, CA) and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
The sequencing library was constructed using the NEBNext Small RNA Library Prep Set and protocol companion (New England Biolabs, Ipswich, MA). Briefly, starting with 1 µg of total RNA, a 3’-tagging sequence (the 3’ Adaptor Oligo) is ligated to the 3’ end of the RNA. Small RNA with 3’ ends containing either a 2’,3’-OH or 2’-O-Me,3’-OH are efficiently tagged in the reaction. Excess 3’ Adaptor is removed using a reverse transcription primer. A 5’-tagging sequence (the 5’ Adaptor Oligo) is ligated to the 5’ end of 5’-monophosphorylated RNA. cDNA was synthesized using reverse transcriptase. The cDNA is then amplified by PCR using a standard forward primer and an indexing reverse primer. The library was then cleaned up using a Zymo DNA Clean & Concentrator-5 (Zymo Research, Irvine, CA). Size selection is performed on the library using the BluePippin (Sage Science, Inc., Beverly, MA) and the 3% agarose gel cassette (Sage Science, Inc.). To calculate final library concentration the quantity and average fragment length for each library was measured using the Agilent DNA 7500 Assay (Agilent Technologies, Santa Clara, CA), and Qubit High Sensitivity DNA Assay (Life Technologies Corp.) Libraries were normalized to 2nM in buffer EB (Qiagen, Santa Clarita, CA) and combined in equal molar amounts. Single read sequencing of 51bp was performed using the Illumina MiSeq platform and MiSeq Reagent Kit v2 (50 cycles) (Illumina, Inc.).  A total of 11.7 million single reads passing filter were attained.

treatment_protocol: Three separate patient-derived PDAC CAF cell lines (CAF1-3) were left untreated as a control baseline or were treated with 1µM gemcitabine for 6 days.

tag: cell type

value: immortalized cancer associated fibroblasts

tag: passages

value: 2 through 10

tag: treatment status

value: Gemcitabine treated


title: WT batch 2 rep1

tag: strain