title: 16E7-3512

city: Huntsville

first: Nripesh

last: Prasad

state: Alabama

address: 601 Genome way

institute: Hudson Alpha Institute for Biotechnology

description:
population 1 (replicate 1)
small RNA (<200 nt)
16E7-3512

data_processing:
miRNAseq Data Analysis: Post-processing of the miRNAseq reads from each sample was performed according to the HudsonAlpha Genomic Services Laboratory unique in-house pipeline. Briefly, quality control checks on raw sequence data from each sample was performed using FastQC (Babraham Bioinformatics).  Raw reads were then imported into the commercial data analysis platform Avadis NGS (Strand Scientifics).  Adapter trimming was performed to remove the ligated adapter sequence from the 3' end of the sequenced reads with only one mismatch allowed.  Poorly aligned 3' ends were also trimmed.  Sequences shorter than 15 nucleotides length were excluded from further analysis.  Additionally, trimmed reads with low quality control scores (base quality score less than 30, alignment score less than 95, mapping quality less than 40) were removed.  Filtered reads were then used to extract and count the small RNAs, which were annotated using miRBase release 21.  The quantification operation carries out measurements at both the RNA and active region level.  Active region quantification only considers reads whose 5' end matches the 5' end of the mature miRNA annotation. Samples were then grouped as identifiers and the differential expression of miRNAs was calculated on the basis of their fold change (default cut-off ≥ ±3.0) observed between different groups (control HFKs versus HFKs + HPV16 E6/E7).  The p-value of differentially expressed miRNAs was estimated via z-score calculations using the Benjamini Hochberg FDR corrections of 0.05.
Analysis of RNAseq: Downstream analysis of the sequenced reads from each sample was performed per a unique in-house pipeline designed by HudsonAlpha.  Briefly, quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics).  Raw reads were then mapped to the reference human genome hg19 using TopHat v2.0  with two mismatches allowed and other default parameters.  The alignment metrics of the mapped reads was estimated using SAMtools.  Aligned reads were then imported into the commercial data analysis platform, Avadis NGS (Strand Scientifics).  After quality inspection, the aligned reads were filtered on the basis of read quality metrics where reads with a base quality score less than 30, alignment score less than 95 and mapping quality less than 40 were removed.  Remaining reads were then filtered on the basis of read statistics, where missing mates, translocated, unaligned and flipped reads were removed.  The reads list was then filtered to remove duplicates.  Samples were grouped and quantification of transcript abundance was performed on this final read list using Trimmed Means of M-values (TMM) as the normalization method.  Differential expression of RNAs was calculated on the basis of fold change (using a cut-off ≥ ±3.0) observed between defined conditions.  The p-value of the differentially expressed RNAs was estimated by z-score calculations utilizing the Benjamini Hochberg FDR correction of 0.05.  Ingenuity Pathway Analysis (Qiagen) software was used to analyze the unique canonical pathways, biological functions and networks affected.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file with Normalized expression values for each sample

source_name: human foreskin

extract_protocol:
small and large RNA samples were extracted using the mirVana miRNA isolation kit from Ambion
rRNA Reduction RNA-seq libraries were prepared for sequencing using standard Illumina protocols. Small RNA libraries were prepared from small RNA utilizing the TruSeq®Small  RNA Library Preparation Kit (Illumina) as described in the manufacturer’s sample preparation guide.

treatment_protocol: Human foreskin keratinocytes (HFKs) were isolated from a pool of de-identified newborn foreskin samples and transduced with LXSN based recombinant retroviruses encoding HPV16 E6 or E7 or both oncogenes or a control LXSN vector as previously described in Halbert et al. J Virol. 1991. 65(1):473-8.

tag: transduced with

value: vector expressing HPV16 E7

value: human foreskin keratinocytes


title: 16E6E7-72612

status: Public on Jan 17 2017

type: SRA

country: USA

description:
population 2 (replicate 2)
small RNA (<200 nt)
16E6E7-72612

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: vector expressing HPV16 E6/E7

tag: cell type


title: 16E6E7-3512

description:
population 1 (replicate 1)
small RNA (<200 nt)
16E6E7-3512


title: 16E6-3512

description:
population 1 (replicate 1)
small RNA (<200 nt)
16E6-3512

value: vector expressing HPV16 E6


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_2-1

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description: processed data file: miR19.totalnorm.txt

library_source: genomic

data_processing:
Library strategy: Genome-scale CRISPR-Cas9 Screen (GeCKO)
Raw reads were trimmed using inhouse scripts to extract the exact sgRNA sequence
Trimmed reads were mapping to library using bowtie 1.0.1, require perfect, unique match
Summarize bowtie results to sgRNA count using inhouse script
Normalize each sample to total reads, and combine library A and library B
Call significant gene using RIGER
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized reads. A key to the sample names used in the processed data files is provided on the series record.

molecule: genomic DNA

source_name: HCT116 cells

growth_protocol: Cell lines used in this study were obtained from ATCC and cultured under standard conditions.

extract_protocol:
gDNA was extracted from the unsorted cells using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.  Extractions were performed on 4x10^7 cells using 5x10^6 cells per column to ensure enough gDNA for 300X coverage of the library.  DNA was eluted by adding 125 µL of water to each column.  The same eluate was added back to the column for a second elution.  The DNA concentration in the final eluate was assessed using the Qubit dsDNA BR assay kit (Thermo Fisher).  To facilitate maximum recovery of gDNA from the sorted cells, a previously described method (Largaespada, et al., 2008) was used  with the following modifications:  Sorted cell pellets were resuspended in 500 µL of tissue lysis buffer, consisting of 460 µL of STE buffer [1 mM EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), 100 mM NaCl] supplemented with 10 µL of 0.5 M EDTA, 10 µL of proteinase K [10 mg/mL in TE buffer containing 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA], and 20 µL of 10% SDS.  Pellets were digested overnight at 55°C while shaking at 1000 rpm on a Thermomixer (Eppendorf).  The following day, 5 µL of 2 mg/mL RNase A was added to each tube and incubated at 37°C for 1 hr while shaking at 1000 rpm.  Extractions were performed with an equal volume of pH 7.9-buffer saturated phenol, followed by phenol:chloroform:isoamyl alcohol (25:24:1), followed by chloroform.  20 µg of glycogen (Roche) and 1.5 mL of 100% ethanol was added to each tube and DNA was precipitated at -80°C for 1 hr followed by centrifugation at 18,000 g for 10 min at 4°C.  Pellets were washed with 1 mL of 75% ethanol, dried, and resuspended in 21 µL of water by incubating at 37°C for a minimum of 4 hrs. DNA concentration was determined with the Qubit dsDNA BR assay kit.
Methods to prepare PCR amplicon libraries for deep sequencing were adapted from a previously published protocol (Shalem, et al., 2014).  All primer sequences are provided in Supplementary Table 8.  For unsorted cells, an initial round of PCR (PCR I) was performed using 6.6 µg of gDNA per 100 µL PCR reaction.  To maintain 300X coverage, 20 reactions were assembled for each sample.  For sorted cells, all extracted gDNA for a given sample was distributed into two 100 µL reactions.  In both cases, 18 cycles of amplification were performed using Herculase II Fusion polymerase (Agilent).  All reactions for a given sample from PCR I were then pooled together and a second round of PCR (PCR II) was performed to add the necessary adapters for Illumina sequencing.  Due to variable PCR efficiency between samples, the cycle number for PCR II was adjusted so that each library was amplified in a 50 µL reaction to a common endpoint with respect to DNA quantity (approximately 50 ng of DNA library in a 50 µL PCR sample).  DNA was purified for sequencing using AMPure XP beads (Agencourt) according to the manufacturer’s instructions with the following modifications:  Each 50 uL PCR II reaction was mixed with 25 uL of beads and incubated for 5 minutes.  Magnetic separation was used to collect the supernatant.  The supernatant was mixed with 90 µL of beads and incubated for 5 minutes.  The supernatant was collected and discarded.  Beads were washed twice with 200 µL of 70% ethanol and then dried for approximately 12 minutes.  Bound DNA was eluted from the beads using 40 µL of water.

treatment_protocol: Two days prior to sorting, ten 15 cm dishes with 1.2x10^7 cells per dish were seeded for each library-reporter pair.

value: Human colorectal carcinoma

tag: cell line


title: LXSN-72612

description:
population 2 (replicate 2)
small RNA (<200 nt)
LXSN-72612

value: control vector


title: 16E6-72612

description:
population 2 (replicate 2)
small RNA (<200 nt)
16E6-72612


title: HCT116_EGFP_miR19_Unsorted_LibraryB_Replicate_2-2


title: HCT116_EGFP_miR19_Unsorted_LibraryB_Replicate_2-1


title: LXSN-3512

description:
population 1 (replicate 1)
small RNA (<200 nt)
LXSN-3512


title: HCT116_EGFP_miR19_Unsorted_LibraryA_Replicate_2-2


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_2-2


title: D20F-E

city: Victoria

first: Stephanie

middle: M.

last: Willerth

state: BC

address: 3800 Finnerty Rd.

department: Department of Mechanical Engineering/Division of Medical Science

country: Canada

institute: University of Victoria

data_processing:
Basecalls by MiSeq Control Software
Read alignment by MiSeq Reporter software
TargetHitsBySample imported into R (v3.2.2) for analysis using DESeq2 (v1.10.0) (http://doi.org/10.1186/s13059-014-0550-8)
Data prefiltered in DESeq2 to remove genes with 0 reads in all samples before differential analysis
Differential expression calculated using DESeq2 (Negative bionomial generalized linear model and Wald statistics). Normalized abundance measures by total reads/sample
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of counts for each target for each sample (not normalized)

molecule: polyA RNA

source_name: hiPSC_day20 FIBRIN

growth_protocol: Neural aggregates (NAs) were formed from hiPSCs over 5 days in an Aggrewell plate (Stem Cell Technologies). NAs were then passaged to PLO/laminin-coated tissue culture plastic surfaces or 3D fibrin hydrogels and cultured for 15 additional days (20 days from undifferentiated hiPSCs). NAs in/on each substrate were treated with 1µM retinoic acid and purmorphamine to induce motor neuron differentiation. Samples were collected for sequencing on day 0, 5, 12, and 20.

extract_protocol:
RNA purification using Norgen Single Cell RNA Purification Kit according to manufacturers protocol.
Library was constructed using Illumina TruSeq Targeted RNA Expression Stem Cell Panel with additional 132 gene Supplemental Panel according to TruSeq Targeted RNA Expression Guide (#15034665 Rev. C)

tag: substrate

value: Fibrin hydrogel

tag: time

value: day 20

value: iPS (Foreskin)-1, Lot 1-DL-01, WiCell


title: D20F-F


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_2-1


title: HCT116_EGFP_miR19_Unsorted_LibraryA_Replicate_2-1


title: 1_0_DAT_Rep_1_Control

city: Ottawa

first: Sylvie

last: Cloutier

state: Ontario

address: 960 Carling Avenue

institute: Agriculture and Agri-Food Canada

data_processing:
Adapter sequences were trimmed using a custom Perl script and quality assessment was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads ranging from 18 to 24 bp were filtered and exported as fasta files using Geneious (Biomatters Ltd, Auckland, New Zealand)
Redundant reads from each dataset were grouped as distinct tags and were used to query the Rfam (version 11) and wheat chloroplast (http://www.ncbi.nlm.nih.gov/nuccore/NC_002762.1) databases to remove rRNAs, tRNAs, snRNAs, snoRNAs, other long non-coding RNAs and chloroplast sequences
Distinct tags represented by ≥10 reads per million (RPM) in at least one library were mapped to miRNA coding loci previously identified from the hexaploid bread wheat assembly (International Wheat Genome Sequencing Consortium, Science 2014) using Bowtie2. These tag sequences were then matched to another set of high confidence precursor sequences (Kurtoglu et al. Funct Integr Genomics 2014). Distinct tags with 0 mismatch were extracted for hairpin structure prediction using RNAfold (Lorenz et al. Algorithms Mol Biol 2011).
The distinct tags with secondary hairpin structure with <-0.2 kcal/mol/nt were filtered for prediction of star sequence in the opposite strand with a 2bp offset on the 3’-strand of the hairpin.
The read counts of miRNAs annotated with strong evidence for biosynthesis were chossen for differential expression ananysis.
Genome_build: GCA_000818885.1 - International Wheat Genome Sequencing Consortium (IWGSC) Science 2014
Supplementary_files_format_and_content: Conserved miRNA families and their coresponding read counts.xls

organism: Triticum aestivum

source_name: Leaf tissues

growth_protocol: Wheat (Triticum aestivum L.) cv Glenlea plants, obtained from a single self-fertilized homozygous line, were grown in a PG-40 growth chamber under long-day conditions of 16h light at 18°C and 8h darkness at 16°C

extract_protocol:
Leaf tissue was collected from individual plants at six time points: 0, 1, 2, 3, 7 and 10 DAT where 0 DAT corresponded to tissue sampled immediately at the end of the 5-day stress exposure period, prior to their return to the non-stressful growth conditions. Leaf tissue pieces, approximately 2.5 cm in length, were pooled from the eight plants that represented each treatment and replicate. The harvested leaf tissue pools were flash-frozen and stored in liquid nitrogen until RNA extraction. For the latter, tissue samples were ground to a fine powder with liquid nitrogen in a mortar and pestle. Total RNA was isolated from homogenized tissue samples using TRI-reagent as per manufacturer’s instructions (Ambion, Naugatuck, CT). Total RNA quality and quantity were assessed on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano chip (Agilent Technologies, Santa Clara, CA). A total of 72 high-quality total RNA samples, corresponding to three biological replicates, four treatments and six sampling time points, were produced.
Small RNA libraries were constructed for each of the 72 samples from 5 µg of total RNA using a plate-based method developed at the BC Cancer Agency Genome Sciences Centre (Vancouver, BC, Canada). Briefly, total RNA samples were mixed with oligo-dT microbeads and loaded into a 96-well MACS column (Miltenyi Biotec, Germany). The sRNA fractions were recovered from the flow-through and precipitated with ethanol. Quality was assessed for a subset of 12 samples using an Agilent Bioanalyzer RNA 6000 Nano chip (Agilent Technologies). An adenylated 3’-adapter (5’/5rApp/ ATCTCGTATGCCGTCTTCTGCTTGT /3ddC/3’) was ligated using a truncated T4 RNA ligase (New England BioLabs, Ipswich, MA) by incubating at 22°C for 1 hour. An RNA 5’-adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUCUGGUCAA-3’) was then added using a T4 RNA ligase (Ambion) by incubating at 37°C for 1h. The first strand cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and RT primer (5'-CAAGCAGAAGACGGCATACGAGAT-3’). The cDNA was used as template for PCR amplification where unique index sequences were introduced to enable identification of the pooled libraries. PCR cycling conditions were 98°C for 30 sec, followed by 15 cycles at 98°C for 15 sec, 62°C for 30 sec and 72°C for 15 sec and a final incubation at 72°C for 5 min. The quality of the libraries was assessed using a Caliper LabChipGX DNA chip (PerkinElmer, Waltham, MA). Three pools of randomly assigned sRNA libraries were created, resolved on a gel and, the 145-160 bp fractions were size-selected. Pooled libraries were ethanol precipitated and quality checked using an Agilent Bioanalyzer DNA1000 chip (Agilent Technologies). Each pooled library was diluted for cluster generation on a HiSeq 2000 flow cell according to manufacturer’s instructions. Small RNA sequencing was performed using a 50 cycle HiSeq SBS v4 kit

treatment_protocol: At the boot stage, three sets of 24 plants each were exposed to one of three stress conditions for five consecutive days. The first set was exposed to continuous light. The second set was exposed to UV light for two min every day of the 5-day period. The third set, called heat-stressed, was transferred to a growth chambers where the temperature was kept constant at 37°C day and night. These plants were well watered twice per day during the 5-day stress exposure to avoid a confounding drought stress. The remaining 24 control plants were kept in the growth chamber at 16h/8h day/night at 18/16°C. After the 5-day stress exposure treatment, all plants were returned to the original growth chamber under control conditions. The experiment was conducted as a completely randomized block design with three biological replicates where each treatment and replicate corresponded to a group of eight plants.

tag: stress

value: Control

tag: sampling time

value: 0 day after treatment (DAT)

tag: cultivar

value: Glenlea


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_2-2


title: D20F-C


title: D20F-A


title: D20L-F

source_name: hiPSC_day20 PLO/LAMININ

value: PLO/laminin-coated tissue culture plastic


title: HCT116_EGFP_Bright_LibraryA_Replicate_2-2


title: D20L-D


title: HCT116_EGFP_Bright_LibraryB_Replicate_2-1


title: 16E7-72612

description:
population 2 (replicate 2)
small RNA (<200 nt)
16E7-72612


title: D20L-C


title: D20F-D


title: HCT116_EGFP_Bright_LibraryB_Replicate_2-2


title: HCT116_EGFP_Bright_LibraryA_Replicate_2-1


title: HCT116_EGFP_miR19_Bright_LibraryB_Replicate_2-2


title: D12F-J

source_name: hiPSC_day12 FIBRIN

value: day 12


title: D12F-I


title: D20L-A


title: D12F-H


title: D20L-B


title: HCT116_EGFP_miR19_Bright_LibraryB_Replicate_2-1


title: D12F-F


title: D12F-E


title: D20F-B


title: HCT116_EGFP_miR19_Bright_LibraryA_Replicate_2-2


title: HCT116_EGFP_miR19_Bright_LibraryA_Replicate_2-1


title: D20L-E


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_1-4


title: D12F-B


title: D12F-C


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_1-3


title: D12L-F

source_name: hiPSC_day12 PLO/LAMININ


title: D12F-A


title: D12L-B


title: D12L-C


title: SL120909

description:
population 2 (replicate 2)
large RNA (>200 nt)
3317-KM-0003


title: SL120910

description:
population 2 (replicate 2)
large RNA (>200 nt)
3317-KM-0004


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_1-2


title: D12L-A


title: SL120908

description:
population 1 (replicate 1)
large RNA (>200 nt)
3317-KM-0002


title: D12F-G


title: HCT116_EGFP_Unsorted_LibraryB_Replicate_1-1


title: SL120907

description:
population 1 (replicate 1)
large RNA (>200 nt)
3317-KM-0001


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_1-4


title: D12F-D


title: D5-G

value: day 5


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_1-3


title: D5-H


title: D5-E


title: WT_3

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

data_processing:
Raw reads were trimmed using Trimmomatic v0.32 .Low quality reads, sequencing adapters and over-represented K-mers were removed.
Trimmed PE reads were assembled to a reference genome (Ensembl release 82-GRCm38) using v2.1.0.with default parameteres
calculate transcript abundances, we used Cufflinks v2.2.
Differential expression analysis was performed using Cuffdiff2
Raw count was obtained using htseq-coun v0.6.1p1
Genome_build: GRCm38.82

organism: Mus musculus

extract_protocol:
Primary mouse enamel organ (EO) cells from the lower incisors were isolated and placed directly into RLT buffer (RNeasy Micro Kit (Qiagen). Cells were homogenized with a pestle and processed for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer's instructions.
RNA quality and quantity was analyzed on a Nanodrop2000 (Fisher Scientific) and RNAseq libraries were prepared using the TruSeq RNA sample prep v2 kit (Illumina), starting from 500 ng of DNAse I (Qiagen) treated total RNA, following the manufacturer’s protocol. The amplified libraries (12 PCR cycles) were purified using AMPure beads (Beckman Coulter), quantified by Qubit 2.0 fluorometer (Life Technologies), and visualized in an Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on the HiSeq 4000 Sequencing System (Illumina) and run as paired-end 150 nucleotide reads generating about 50 million reads per sample.

tag: strain

tag: genotype

value: Wild Type

tag: tissue

value: Primary mouse enamel organ (EO) cells


title: D5-F


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_1-2


title: D12L-E


title: D12L-D


title: D5-D


title: WT_2

source_name: Primary mouse enamel organ (EO) cells from the lower incisors


title: HCT116_EGFP_Unsorted_LibraryA_Replicate_1-1


title: D5-B


title: WT_1


title: D5-C


title: DKO_4

value: Stim1/2 Knock out


title: HCT116_EGFP_Bright_LibraryB_Replicate_1-3


title: DKO_1


title: D5-A


title: HCT116_EGFP_Bright_LibraryB_Replicate_1-2


title: HCT116_EGFP_Bright_LibraryB_Replicate_1-1


title: HCT116_EGFP_Bright_LibraryA_Replicate_1-4


title: HCT116_EGFP_Bright_LibraryB_Replicate_1-4


title: D0-G

value: day 0


title: HCT116_EGFP_Bright_LibraryA_Replicate_1-3


title: D0-E


title: HCT116_EGFP_Bright_LibraryA_Replicate_1-2


title: Vegetal Pole 3

city: Miami

first: Mary

middle: Lou

last: King

state: Fl

address: 1600 nw 10th ave

department: Cell Biology

institute: University of Miami: Miller school of Medicine

data_processing:
BCL conversion was done with Casava 1.8 pipeline
Read QC was checked using FastQC v 0.10.1
Alignment of reads was done using Tophat 2.0.11
Differential Expression was calculated using Cufflinks 2.0.2
Genome_build: Xenbase 7.1 J-Strain
Supplementary_files_format_and_content: cufflinks fpkm files

organism: Xenopus laevis

source_name: Stage VI Oocyte

extract_protocol:
Oocyte-paired animal and vegtal pole tip samples were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. 1 ug of total RNA was used for sequencing library construction using standard Illumina protocols..
RiboZero ScriptSeq V2, Truseq small RNA. RNA libraries were prepared for sequencing using standard Illumina protocols

value: Stage VI Oocyte


title: Vegetal Pole 2


title: Animal Pole 2


title: Animal Pole 3


title: HCT116_EGFP_Bright_LibraryA_Replicate_1-1


title: Vegetal Pole 1


title: D0-D


title: HCT116_EGFP_miR19_Unsorted_LibraryB_Replicate_1


title: Animal Pole 1


title: in vivo mRNA

city: Stanford

first: Shigeki

last: Nagai

state: CA

address: 299 Campus Dr

department: Structural Biology

institute: Stanford University

data_processing:
For analysis, paired-ends were separated and each end treated as a single read.
Reads that began precisely at the 5’ end with the RLM-RACE adaptor (5’– CGCGGATCCGAACACTGCGTTTGCTGGCTTTGATGAAA–3’) were identified, the adaptor removed, and, after trimming, only reads 25 bp or longer were retained.
Reads were then mapped to the S. cerevisiae genome (April 2011/sacCer3 assembly) with bowtie.
The number of reads with identical 5’ ends was determined and the 5’ most base was identified as the transcription start site.
Data was normalized to the number of reads per base per thousands of aligned reads per sample.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab-delimited text file (bed format) of transcription start sites.  Column 1: chromosome, column 2: bp start, column 3: bp end, column 4: normalized counts.

organism: Saccharomyces cerevisiae

source_name: S.cereviase mRNA

extract_protocol:
in vitro RNA transcripts were purified by QUAGEN Rneasy plus micro kit, RNA samples were subsequently subjected to 5' RACE.
After nested PCR of 5’-RACE samples, DNA was prepared for next- generation sequencing using a NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs) except the end prep step was omitted and in the final purification step 17 μL of 0.1X TE buffer was used to elute the DNA from the AMPure XP beads and 15 μL was reclaimed as the purified RACE library. DNA concentration was determined using a Qubit dsDNA HS Assay Kit (Life Technologies) and DNA integrity determined by running an aliquot on a Bioanalyzer High Sensitivity DNA Chip (Agilent). The library was accurately quantified using a KAPA Library Quantification Kit (KAPA)

value: ySH141 (yeast strain)


title: D0-C


title: DKO_3


title: D0-H


title: D0-B


title: HCT116_EGFP_miR19_Bright_LibraryB_Replicate_1

value: Human colorectal carcinoma


title: chromatin transcribed with complete factors

source_name: in vitro transcription from chromatin

value: YS13 (yeast strain)


title: D0-I


title: HCT116_EGFP_miR19_Bright_LibraryA_Replicate_1


title: D0-A


title: DNA transcribed with complete factors

source_name: in vitro transcription from DNA


title: D0-F


title: siSRSF2 Huh7 cells

city: Shanghai

first: Chunling

last: Luo

address: yueyang road,number 320

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Illumina GA Pipeline v1.3 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
The stat of mapped reads was list in siNC.gene.MapReadsStat.xls and siSRSF2.gene.MapReadsStat.xls
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Mortazavi, 2008.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Huh7 cells two days after tranfection

extract_protocol:
Huh7 cells two days after tranfected with siRNA were collected , and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

tag: tissue type

value: HCC


title: AC_FLI_Nfu_49

status: Public on Jan 16 2017

city: Jena

first: JenAge

last: Project

address: Beutenbergstr. 11

country: Germany

institute: Leibniz Institute for Age Research - Fritz Lipmann Institute

description:
RNA_49
total RNA from Nfu brain

data_processing:
Sequence information was extracted in FastQ format using Illumina's bcl2fastq software v1.8.4.
Reads were mapped using Tophat (v2.0.6)
Reads per gene were counted using featureCounts v1.4.3-p1
Counts were normalized to RPKM values as described in Mortazavi et al. (2008)
Genome_build: genome v20150522 and annotation v20140422 can be downloaded from the Nothobranchius furzeri Information Network Genome Browser (http://nfingb.fli-leibniz.de/)
Supplementary_files_format_and_content: Counts.txt and RPKMs.txt include raw counts and RPKM values of all genes for each sample.

organism: Nothobranchius furzeri

source_name: kif5a::miR-29sponge, brain

extract_protocol:
Extraction was done as described in Baumgart et al. 2012. (PMID:22487494)
Library preparation was done using Illumina's Tru seq RNA library preparation kit v2 following the manufacturer's instruction

value: brain

tag: age

value: 12 weeks


title: siNC Huh7 cells

value: control


title: AC_FLI_Nfu_48

description:
RNA_48
total RNA from Nfu brain


title: DNA transcribed with pol II and GTFs


title: AC_FLI_Nfu_46

description:
RNA_46
total RNA from Nfu brain


title: AC_FLI_Nfu_45

description:
RNA_45
total RNA from Nfu brain

source_name: MZM-04/10p, brain

value: MZM-04/10p (control)


title: AC_FLI_Nfu_47

description:
RNA_47
total RNA from Nfu brain


title: adult males

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

institute: McGill University

data_processing:
basecall using illumina bcl2fastq v1.8.4
The 3' adaptor is removed from raw reads and reads with the length between 18 to 25 nt constitute the mappable reads.
The mappable reads were aligned against dog genome and miRbase using Bowtie.
Genome_build: Dirofilaria immitis 2.2; miRbase v21; Canis familiaris 3.1;
Supplementary_files_format_and_content: TableS1_miRNAs_found_in_culture_media.xls: read counts and values after normalization of miRNAs identified in Dirofilaria immitis

organism: Dirofilaria immitis

source_name: Worm secretions, culture media

growth_protocol: Live whole worms in culture

extract_protocol:
RNA extraction kit (Norgen Biotek #23000) from concentrated culture media.
Illumina Truseq Small RNA Preparation
small RNA

value: live worms


title: AC_FLI_Nfu_42

description:
RNA_42
total RNA from Nfu brain


title: Protamine1_ChIPSeq_replicate2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

description: chormatin IP against Protamine1

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bowtie 0.12.7 for ChIP-seq. Duplicates were removed using Samtools.  For generating wiggle files, we combined each replicates.
Genome_build: mm9

source_name: Sperm

extract_protocol:
For ChIP-seq of crosslink samples, sperm were crosslinked with 1% formaldehyde in 1x PBS for 10 min at RT, and the reaction was quenched with 125 mM glycine for 10 min at RT. After washing with PBS, crosslinked sperm were lysed with 5 mM PIPES, 85 mM KCl, 0.5% NP40 and 1x proteinase inhibitor on ice for 10 min. Then we performed a second fixation step by directly adding 1% formaldehyde to the lysis buffer on ice. After 10 min sperm were homogenized with a glass dounce homogenizer. Following quenching and washing, sperm cells were resuspended in RIPA buffer (1x PBS; 1% NP40; 0.5% sodium deoxycholate; 0.1% SDS; 1x proteinase inhibitor) and incubated on ice for 20 min. The purified sperm chromatin was sonicated to 300-1000 bp using a Diagenode Bioruptor at 25 cycles of 30 sec on and 30 sec off and the supernatant was collected. Immunoprecipitation was performed overnight at 4°C with antibodies. For ChIP-seq of Mnase samples, lysate was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were constructed using the following standard protocol. The fragment end were repaired using the NEBNext End Repair Module, and adenosine was added at the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA and input DNA were incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers.

tag: strain background

tag: chip antibody

value: sc-30174, Santa Cruz


title: AC_FLI_Nfu_43

description:
RNA_43
total RNA from Nfu brain


title: HCT116_EGFP_miR19_Unsorted_LibraryA_Replicate_1


title: fourth-stage larvae (L4)


title: third-stage larvae (L3)


title: adult females


title: microfilariae


title: MAC3

city: Ischia

first: Amit

last: Kumar

address: Villa Dohrn

department: Department of Integrative Ecology

country: Italy

institute: Stazione Zoologica Anton Dohrn

description:
Tissues from S. vulgare growing under acidified conditions at coast of Castello Aragonese, ischia, Italy
MAC_FPKM

data_processing:
Raw reads were filtered by removing sequences with more than 10% of indetermined bases (N) or with more than 50 bases with a basecall quality score lower than 7. Adapter sequences were clipped from raw reads using Scythe (version 0.98; https://github.com/najoshi/scythe) and were quality trimmed using Sickle using a Q score minimum threshold of 20 calculated in a window of 10 nucleotides (version 0.94; https://github.com/najoshi/sickle).
Filtered reads were de novo assembled with Trinity assembler (version 2.0) using default parameters and were mapped to assembled putative transcripts using bowtie 2. Putative transcripts covered by less than 100 reads were removed. Redundancy among assembled sequences was removed using cd-hit-est with a threshold of 90% sequence identity.
The expression analysis was performed using RSEM (version 1.1.21) with default parameters and expression values converted to FPKM (Fragments Per Kilobase of exon per Million fragments mapped)
Only those transcripts with expression values FPKM ≥ 0.1 in at least 2 replicates from either of the two conditions were considered for downstream analysis.
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample

organism: Sargassum vulgare

extract_protocol:
Apical tissues of the Sargassum vulgare thalli were collected from natural acidified and control sites off Ischia Island. The tissues were cleaned for visible epiphytes and flash frozen in liquid nitrogen and RNA was extracted using CTAB extraction method. A total of 2.5 μg of total RNA per sample with high purity and high integrity were used for construction of sequencing libraries using TruSeq Stranded Total RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissues

value: Apical tissues

tag: locations

value: Acidified site


title: MAC2

source_name: Tissues from S. vulgare growing under acidified conditions at coast of Castello Aragonese, ischia, Italy


title: MAC1


title: MLA 1

description:
Tissues from S. vulgare growing under control conditions at coast of Lacco Ameno, ischia, Italy
MLA_FPKM

value: Control site


title: MLA3

source_name: Tissues from S. vulgare growing under control conditions at coast of Lacco Ameno, ischia, Italy


title: Crypt EedKO

city: Milan

first: Sri Ganesh

last: Jammula

address: Via Adamello 16

institute: IFOM-IEO

description: total RNA extracted with miRNeasy Mini Kit Qiagen processed for mRNA library preparation

data_processing:
Sequencing data is aligned to mouse (mm9) genome in a reference guided manner by tophat.
Differentially expressed genes were identified using DESeq.
Genome_build: mm9
Supplementary_files_format_and_content: list of genes with normalized read count, fold change and p-value.

source_name: Crypt

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying theTruSeq RNA Sample Preparation Kit v2 ( RS-122-2001 )

treatment_protocol:
The mice were treated with 3 injection of ß-naphthoflavone and sacrified at 15 days post injection. The small intestine crypts of the mice were isolated and used for Rna purification.
total RNA was extracted with miRNeasy Mini Kit Qiagen

value: AhCreEedfl/fl mice


title: Crypt Input

description: Input.

data_processing:
Alignment: Short reads were mapped onto the mouse July, 2007 genome release (mm9) using Bowtie allowing to retain only reads with unique alignment.
Peaks: Peak calling was performed with the Model-based Analysis of ChIP-Seq (MACS2) algorithm
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing locus of of enriched regions for target of interest

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol:
The small intestine crypts of the mice were isolated
Crypt cells were cross-linked with 1% formaldehyde and chromatin sonicated to an average size of 200-300 bp. Chromatin was precipitated with specific antibody, which was further purified using magnetic protein A coupled beads, and recovered DNA was used for high-throughput sequencing.

tag: antibody


title: Crypt Suz12

description: Immuno-precipitation of chromatin using a specific antibody against Suz12.


title: Crypt H3K27me3

description: Immuno-precipitation of chromatin using a specific antibody against H3K27me3.


title: Crypt WT

value: AhCre


title: AC_FLI_Nfu_44

description:
RNA_44
total RNA from Nfu brain


title: sample bi43651, brain region #3, population:E

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: brain region #3, population:E

data_processing:
Illumina bcl2fastq 1.8.3 software used for basecalling and FASTQ file generation.
Sequenced reads in FASTQ files were mapped to mm10 whole genome using Tophat (Galaxy tool version 0.9) with parameters -r 100. UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0) with parameters -r 100.  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: mouse brain cells

extract_protocol:
NucleoSpin RNA Kit from Macherey-Nagel, using manufacturer's protocol.
Total RNA samples were made into cDNA using the NuGEN Ovation® RNA‑Seq System V2 kit (using both random priming and poly d(T) priming). cDNA from the NuGEN kit were taken into the Illumina TruSeq DNA Sample Prep Kit for library construction. Completed libraries were sequenced on the Illumina HiSeq 2500.

tag: brain region

value: Brainstem

tag: cell type

value: astrocyte


title: sample bi43648, brain region #2, population:E

description: brain region #2, population:E

value: Cortex


title: sample bi43650, brain region #3, population:E

description: brain region #3, population:E


title: sample bi43649, brain region #2, population:E

description: brain region #2, population:E


title: sample bi43647, brain region #1, population:E

description: brain region #1, population:E

value: olfactory bulb


title: sample bi43646, brain region #1, population:E

description: brain region #1, population:E


title: sample bi43645, brain region #3, population:D

description: brain region #3, population:D


title: sample bi43644, brain region #3, population:D

description: brain region #3, population:D


title: RIP WT 2

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

country: Spain

institute: IRB Barcelona

description: RIP mRNA

data_processing:
Illumina Hi-Seq 100bp single end reads were aligned against the mm10 genome using Tophat2 with default options
Duplicated reads potentially arising from amplification artifacts were detected and removed with the filterDuplReads function of the htSeqTools R package (Planet et al., 2012) using a False Discovery Rate of 0.05.
Genomic coordinates for mouse mm10 3’UTR regions were retrieved using the biomaRt package (Smedley et al., 2015), using the February 2014 archive.
Afterwards, significantly enriched regions between Cpeb4KO against pooled WT RIP samples were detected using the enrichedRegions function of the htSeqTools package using default settings and a Benjamini-Hochberg adjusted p-value of 0.05. Only regions overlapping known mm10 3’UTRs were reported for downstream analysis.
Target regions were defined as those enriched regions wider than 200bp and with a log 2 Foldchange WT-KO greater than 2
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include chromosome, start, end, BH adjusted pvalue and log2FC IP/WT for defined target regions in BED format

source_name: Primary hepatocytes

growth_protocol: Collagenase perfusion (0.5 U/mL) via the inferior cava vein was used to isolate hepatocytes from fed 12-week-old male mice. Cells were suspended in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10 mM glucose, 10% fetal bovine serum (FBS), 100 nM insulin, and 100 nM dexamethasone and then seeded onto plates treated with 0.01% (w/v) collagen solution (Sigma). After 3 h, cells were washed with phosphate-buffered saline (PBS), and the media were replaced with fresh serum-free DMEM without glucose for 16 h.

extract_protocol:
RNP-complexes were crosslinked with 0.5% PFA for 5 min, then CPEB4 was immunoprecipitated with anti-CPEB4 specific antibodies and associated-mRNAs were extracted with phenol-chlorophorm.
Inputs and IPs samples from a RIP experiment were quantified by Qubit RNA HS (Life Technologies) when it was possible, and fragment size distribution was checked by Bioanalyzer Pico Chip (Agilent). Library generation was done with the kit NEBNext Ultra RNA Library Prep Kit (New England Biolabs), following manufacturer´s instructions and 14-15 cycles of library amplification. Previous Poly A purification was only performance on Input samples in only one step of purification. Size selection of the libraries and purification were done by magnetic beads (Agencourt AMPure XP, Beckman Coulter). Finally, library quantification was performance with Qubit DNA HS (Life Technologies) and fragment size distribution with Bioanalyzer DNA HS (Agilent)

treatment_protocol: No specific treatment was used.

value: Hepatocytes

value: Wild-type

tag: rip antibody

value: anti-CPEB4 (ab83009)

tag: sample name


title: sample bi43641, brain region #1, population:D

description: brain region #1, population:D

value: brain


title: RIP CPEB4 KO 1

description: RIP mRNA

value: Cpeb4 KO


title: WT LV 2

description: RNA LV 9

data_processing:
FastQ files were aligned against the Mus musculus mm10 reference genome using STAR 2.3.0e, using a mismatch FDR setting of 0.05 and a minimum of 25 aligned bases per read
Aligned BAM files were sorted and indexed using Sambamba 0.5.1
Per-gene counts (mm10 genome, Biomart July 2015 annotation) were generated with summarizeOverlaps function (Union mode, single-end) from the GenomicAlignments v1.1.30 R package
DESeq2 1.6.3 was used to perform the differential expression analysis between KO and WT samples in Liver-purified ER and Liver tissue respectively. Significant genes were those with |FC|>1.25 and BH adjusted pvalue < 0.1
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include DESeq2 output results with Ensembl mouse gene ID, baseMean, log2FoldChange, lfcSE, stat, pvalue and BH adjusted pvalue for CPEB4 KO vs WT in Liver-purified ER and Liver respectively

source_name: Liver

growth_protocol: tissue sample (no growth protocol)

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen) from flash-frozen livers. The endoplasmic reticulum was purified from whole livers of overnight-fasted mice using the Endoplasmic Reticulum Isolation Kit (ER0100-1KT, Sigma) and following the manufacturer's protocol. Then, RNA was extracted by TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: sample bi43642, brain region #2, population:D

description: brain region #2, population:D


title: CPEB4 KO LV 2

description: RNA LV 8


title: MLA2


title: sample bi43640, brain region #1, population:D

description: brain region #1, population:D


title: sample bi43369, brain region #3, population:C

description: brain region #3, population:C


title: CPEB KO ER 2

description: RNA ER 8

source_name: Liver-purified ER


title: WT LV 1

description: RNA LV 7


title: sample bi43368, brain region #3, population:C

description: brain region #3, population:C


title: RIP WT 1

description: RIP mRNA

data_processing:
Illumina Hi-Seq 100bp single end reads were aligned against the mm10 genome using Tophat2 with default options
Duplicated reads potentially arising from amplification artifacts were detected and removed with the filterDuplReads function of the htSeqTools R package (Planet et al., 2012) using a False Discovery Rate of 0.05.
Genomic coordinates for mouse mm10 3’UTR regions were retrieved using the biomaRt package (Smedley et al., 2015), using the February 2014 archive.
Afterwards, significantly enriched regions between pooled WT RIP samples against Cpeb4KO were detected using the enrichedRegions function of the htSeqTools package using default settings and a Benjamini-Hochberg adjusted p-value of 0.05. Only regions overlapping known mm10 3’UTRs were reported for downstream analysis.
Target regions were defined as those enriched regions wider than 200bp and with a log 2 Foldchange WT-KO greater than 2
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include chromosome, start, end, BH adjusted pvalue and log2FC WT/KO for defined target regions in BED format


title: sample bi43364, brain region #2, population:C

description: brain region #2, population:C


title: sample bi43358, brain region #1, population:C

description: brain region #1, population:C


title: sample bi43363, brain region #2, population:C

description: brain region #2, population:C


title: CPEB4 KO LV 1

description: RNA LV 6


title: sample bi43357, brain region #1, population:C

description: brain region #1, population:C


title: WT ER 2

description: RNA ER 9


title: sample bi43643, brain region #2, population:D

description: brain region #2, population:D


title: sample bi43352, brain region #3, population:B

description: brain region #3, population:B


title: sample bi43349, brain region #2, population:B

description: brain region #2, population:B


title: sample bi43344, brain region #1, population:B

description: brain region #1, population:B


title: IMR90-4 R2

city: Vilnius

first: Saulius

last: Klimašauskas

address: Sauletekio al. 7

department: Department of Biological DNA Modification, Institute of Biotechnology

country: Lithuania

institute: Vilnius University

description:
processed data file:
uDensity_IMR90_4.bedGraph.gz
mEstimate_IMR90_high2.bedGraph.gz
mEstimate_IMR90_all.bedGraph.gz

data_processing:
library strategy: TOP-seq
Select reads with length >= 80 nt
Select reads with 5' adapter ("cutadapt" with arguments: adapter GTTACATCTGGTAGTCAGTCTCCAATAAATATATAAAA; error 0.1; minimum overlap length 10 )
Trim 3' read ends ("FASTX" fastx_trimmer with arguments: N nucleotides 33)
Trim nucleotides from ends with low quality ("FASTX" fastq_quality_trimmer with arguments: quality threshold 20; minimum length 16)
Trim nucleotides from ends specifying maximum length ("FASTX" fastx_trimmer with arguments: last base to keep 165; discard reads shorter than 16)
Align reads ("bwa" with arguments: bwa mem -t 4 -v 3)
Filter aligned reads ("samtools" with arguments: samtools view -b -@ 1 -q 30 -F 4)
Remove PCR duplicates, an in house script.
Calculate coverage per CG, an in house script.
Calculate weighted coverage and CG density, an in house script.
Calculate u-density, an in house script.
Estimate methylation values, an in house script.
Genome_build: hg19
Supplementary_files_format_and_content: "uDensity" bedGraph files contain TOP-seq u-density values for each CG in autosomes per cell type and replicate.  "mEstimate" bedGraph files contain estimated methylation values (m-Estimate) for IMR90 samples.

extract_protocol:
IMR90, N and S-type DNA were purchased from the European Collection of Cell Cultures (ECACC), UK (https://www.phe-culturecollections.org.uk/); DNA from post mortem human brain (the prefrontal brain cortex, Brodmann area 10) of 50-year old healthy men was kindly provided by A.Petronis lab (CAMH, Toronto). DNA was extracted with phenol-chloroform extraction method.
Libraries were constructed according to the TOP-seq (Tethered Oligonucleotide-Primed sequencing) protocol (Stasevskij et al., under revision). Briefly, sonicated genomic DNA was mTAG-labeled (Kriukiene et al., 2013) at unmodified CG sites, than  azide-tagged DNA was end-filled, a 3’-dA mononucleotide extension was added and DNA was ligated to  adapters. Ligated DNA was then subjected to Cu(I)-catalyzed cycloaddition reaction in which the priming oligodeoxyribonucleotide was attached to the azide moiety of the modified DNA. The TOP DNA synthesis was primed from the attached priming oligodeoxyribonucleotide, the products were amplified and subjected to Ion Proton sequencing.

tag: tissue source

value: Lung

tag: cell line

tag: tissue/cell type

value: lung fibroblast cells


title: sample bi43343, brain region #1, population:B

description: brain region #1, population:B

tag: strain


title: sample bi43348, brain region #2, population:B

description: brain region #2, population:B

tag: tissue


title: N-R1

source_name: Neuroblastoma specific LA1-55n

value: Cell line

value: Neuroblastoma-specific cells


title: IMR90-4 R3


title: S-R3

source_name: Non-neuronal progenitor LA1-5s

value: Non-neuronal progenitor cells


title: N-R3


title: S-R1


title: N-R2


title: S-R2


title: IMR90-4 R1


title: CPEB4 KO ER 1

description: RNA ER 6

tag: genotype


title: WT ER 1

description: RNA ER 7


title: IMR90-3 R3

description:
processed data file:
uDensity_IMR90_3.bedGraph.gz
mEstimate_IMR90_high1.bedGraph.gz
mEstimate_IMR90_all.bedGraph.gz


title: sample bi43638, brain region #3, population:A

description: brain region #3, population:A


title: sample bi43637, brain region #2, population:A

description: brain region #2, population:A


title: sample bi43333, brain region #2, population:A

description: brain region #2, population:A


title: sample bi43337, brain region #3, population:A

description: brain region #3, population:A


title: IMR90-3 R2


title: IMR90-2 R1

description:
processed data file:
mEstimate_IMR90_all.bedGraph.gz


title: sample bi43328, brain region #1, population:A

description: brain region #1, population:A


title: sample bi43327, brain region #1, population:A

description: brain region #1, population:A


title: sample bi43639, brain region #3, population:B

description: brain region #3, population:B


title: sample bi43323, brain region #3, population:Neg

description: brain region #3, population:Neg


title: IMR90-1 R2


title: sample bi43322, brain region #3, population:Neg

description: brain region #3, population:Neg


title: IMR90-1 R1


title: sample bi43317, brain region #2, population:Neg

description: brain region #2, population:Neg


title: Brain-2 R2

source_name: Prefrontal brain cortex

value: Brain

value: Prefrontal brain cortex


title: WT_T2_rep2

status: Public on Jan 15 2017

city: los angeles

first: matteo

last: pellegrini

address: 610 charles young drive east

institute: UCLA

description:
DRJKmmWTT2.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt

data_processing:
We first filtered out reads with low quality and reads containing sequencing adapters and then mapped raw reads to the mouse reference genome (UCSC mm10) with the gapped aligner Tophat allowing up to two mismatches.
In total for all libraries sequenced, 365,022,996 reads were uniquely mapped (corresponding to an overall mappability of 91.7%) and used for further analysis. Transcript expression levels were quantified using RPKM units (Reads Per Kilobase of exon per Million reads mapped) using customized scripts written in Perl.
Differential expression analysis was performed using both DESeq and edgeR in R (http://www.R-project.org). Raw read counts were used and modeled based on a negative binomial distribution. The multiple testing errors were corrected by the false discovery rate (FDR).
We considered genes as differentially expressed if (1) the FDR was less than 0.05, (2) the expression ratio between two time points was >2x, (3) the maximal RPKM value for at least one group in the comparison was >1, and (4) there was agreement between DESeq and edgeR.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: all_rpkm.txt: Tab-delimited text file includes RPKMs.

source_name: Primary transitional-2 B-cells, Wild-type

extract_protocol:
Total RNA was extracted from WT and Mir146a-/- B-cell subsets with Qiazol using the Qiagen miRNeasy mini kit with additional on-column DNase I digestion.
cDNA libraries were constructed using the Illumina TruSeq RNA Sample Preparation kit V2 (RS-122-2001). An Agilent Bioanalyzer was used to determine RNA quality (RIN >8) prior to sequencing.

tag: strain/background

tag: genotype/variation

value: Spleen

value: B-cells

tag: developmental stage

value: Transitional-2 (T2)


title: WT_T2_rep1

description:
DRJKmmWTT2.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt


title: Brain-2 R1


title: sample bi43315, brain region #1, population:Neg

description: brain region #1, population:Neg

value: astrocyte


title: Brain-1 R1


title: sample bi43321, brain region #2, population:Neg

description: brain region #2, population:Neg

value: Cortex


title: sample bi43314, brain region #1, population:Neg

description: brain region #1, population:Neg

value: olfactory bulb


title: WT_MZ_rep2

description:
DRJKmmWTMZ.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt

source_name: Primary marginal zone B-cells, Wild-type

value: Wild-type

value: Marginal zone


title: WT_T1_rep2

description:
DRJKmmWTT1.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt

source_name: Primary transitional-1 B-cells, Wild-type

value: Transitional-1 (T1)


title: WT_T1_rep1

description:
DRJKmmWTT1.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt


title: KO_T2_rep1

description:
DRJKmmKOT2.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt

source_name: Primary transitional-2 B-cells, Mir-146a-/-


title: WT_MZ_rep1

description:
DRJKmmWTMZ.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt


title: Brain-1 R2


title: WT_FO_rep2

description:
DRJKmmWTFO.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt

source_name: Primary follicular B-cells, Wild-type

value: Follicular


title: WT_FO_rep1

description:
DRJKmmWTFO.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt


title: KO_T2_rep2

description:
DRJKmmKOT2.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt


title: KO_T1_rep1

description:
DRJKmmKOT1.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt

source_name: Primary transitional-1 B-cells, Mir-146a-/-


title: IMR90-3 R1

value: Lung


title: KO_MZ_rep1

description:
DRJKmmKOMZ.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt

source_name: Primary marginal zone B-cells, Mir-146a-/-


title: KO_FO_rep2

description:
DRJKmmKOFO.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt

source_name: Primary follicular B-cells, Mir-146a-/-


title: KO_MZ_rep2

description:
DRJKmmKOMZ.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt


title: KO_T1_rep2

description:
DRJKmmKOT1.2
mRNA
Replicate 2
Processed data file: all_rpkm.txt


title: KO_FO_rep1

description:
DRJKmmKOFO.1
mRNA
Replicate 1
Processed data file: all_rpkm.txt


title: DBbMBF1_OS

city: Hangzhou

first: Shenghua

last: Ying

state: Zhejiang

address: Yu-hang-tang Road 688

institute: Zhejiang University

description: Experiment of library DBbMBF1

data_processing:
Illumina HiSeq™ 2000 used for sequencing
The sequenced tags were filtered to remove low-quality tags, empty tags and tags with a copy number of <2. All the clean tags vectoring the CATG and 49 bp tag fragments were mapped to the sequenced genome of Beauveria bassiana ARSEF2860 with the precision of no more than two nucleotide mismatch.
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.
Screening of differentially expressed genes in paired library of WT_OS/BbMBF1_OS. FDR (False Discovery Rate) is a method to determine the threshold of P-value in multiple tests (Benjamini, Y. and Yekutieli D. The Annals of Statistics. 2001, 29: 1165-1188).
Genome_build: ASM28067v1, Beauveria bassiana ARSEF 2860
Supplementary_files_format_and_content: Excel files, including Gene ID, gene length, RPKM values, log2(fold change) and FDR-value for the paired sample.

organism: Beauveria bassiana ARSEF 2860

growth_protocol: Conidia of WT and ΔBbMBF1 of Beauveria bassiana were individually  inoculated into SDB medium at the final concentration of 105 conidia/ml, and incubated at 25 °C for 2 days with shaking.

extract_protocol:
Resultant mycelia of each strain were ground into powder in liquid nitrogen. Total RNA was isolated from mycelial powder using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA).
The double-stranded cDNA were prepared with the Illumina gene expression sample prep kit for Illumina arrays.

treatment_protocol: Resultant mycelia of each strain were resespended fresh SDB media and stressed with 2 mM menadione for 1 h.

tag: culture time

value: 2 days

value: mycelia


title: WT_OS

description: Experiment of library WT

source_name: WT

value: WT


title: P. gingivalis plus S. gordonii biofilm 360 minutes sample 3

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

data_processing:
The Genbank files were combined and converted to a GFF file suitable for use with htseq-count tool from HTSeq (Anders, Pyl et al. 2015) with BioPerl’s (Stajich, Block et al. 2002) bp_genbank2gff3.pl tool.
The raw reads were aligned to the combined genomes at the same time using BWA (Li, Handsaker et al. 2009, Li and Durbin 2010) version 0.7.4-r385 using the aln/samse mode under default options.
The alignments were post-processed, sorted into BAM files, and indexed with SAMTools version 0.1.19-44428cd (Li, Handsaker et al. 2009).
Reads per gene was computed from the alignments with htseq-count version 0.5.4p5 in the ‘intersection-nonempty’ mode.
Normalized read counts and p-values for differential abundance were computed for each organism separately using DESeq2 (Anders and Huber 2010).
The p-values were subsequently corrected for multiple testing using q-value method of Storey.
Genome_build: The genomes for P. gingivalis ATCC 33277 and S. gordonii CH1 were retrieved from Genbank (loci AP009380 [ASM1050v1] and NC_009785 [ASM1700v1] respectively).
Supplementary_files_format_and_content: .dat file reports raw counts

organism: Porphyromonas gingivalis

source_name: sessile Porphyromonas gingivalis plus S. gordonii

growth_protocol: Porphyromonas gingivalis ATCC 33277 was grown anaerobically (85% N2, 10% H2, 5% CO2) at 37°C in trypticase soy broth supplemented with 1 mg/ml yeast extract, 1 μg/ml menadione and 5 μg/ml hemin. S. gordonii DL1 was grown anaerobically at 37°C in Todd-Hewitt broth.  Bacteria were cultured to mid-log phase, harvested by centrifugation and resuspended in pre-reduced PBS (rPBS), pH 7.2. 1 x 109 cells of S. gordonii were mixed with an equal number of P. gingivalis, pelleted an held anaerobically at 37°C for the times indicated.  P. gingivalis cells alone were used as a control

extract_protocol:
RNA was extracted from the cells using the Ambion mirVana miRNA Isolation Kit AM1561 (ThermoFisher Scientific, Waltham, Ma).
Library construction was done using the Illumina TruSeq Stranded mRNA library prep kit RS-122-2101 (Illumina, San Diego, CA).  Fragmented RNA were converted to cDNA and enriched and purified by PCR to create the library without rRNA depletion.  The high throughput sequencing was done on a HiSeq2500-v4 sequencer (Illumina, San Diego, CA).

treatment_protocol: Mid-log phase cells of P. gingivalis alone or mixed with an equal number of S. gordonii cells were centrifuged at 3000g for 5 min and pellets held in 1 mL pre-reduced PBS in an anaerobic chamber for 5, 30, 120, 240, or 360 minutes before harvesting. Time 0 control cells were harvested from mid-log phase cells of P. gingivalis.

tag: phenotype

value: sessile

tag: sample composition

value: P. gingivalis plus S. gordonii

tag: time

value: 360 minutes

tag: condition

value: model biofilm


title: planktonic P. gingivalis 0 minute control sample 1

source_name: planktonic Porphyromonas gingivalis

value: planktonic

value: P. gingivalis alone

value: time 0 control

value: planktonic cells


title: P. gingivalis plus S. gordonii biofilm 360 minutes sample 1


title: P. gingivalis plus S. gordonii biofilm 360 minutes sample 2


title: P. gingivalis plus S. gordonii biofilm 240 minutes sample 3

value: 240 minutes


title: P. gingivalis plus S. gordonii biofilm 240 minutes sample 1


title: P. gingivalis plus S. gordonii biofilm 240 minutes sample 2


title: P. gingivalis plus S. gordonii biofilm 30 minutes sample 3

value: 30 minutes


title: P. gingivalis plus S. gordonii biofilm 5 minutes sample 1

value: 5 minutes


title: P. gingivalis biofilm 360 minutes sample 3

source_name: sessile Porphyromonas gingivalis


title: P. gingivalis plus S. gordonii biofilm 120 minutes sample 2

value: 120 minutes


title: P. gingivalis biofilm 240 minutes sample 3


title: P. gingivalis plus S. gordonii biofilm 30 minutes sample 2


title: P. gingivalis biofilm 120 minutes sample 3


title: P. gingivalis biofilm 360 minutes sample 2


title: planktonic P. gingivalis 0 minute control sample 2


title: P. gingivalis biofilm 120 minutes sample 1


title: P. gingivalis biofilm 240 minutes sample 2


title: P. gingivalis biofilm 360 minutes sample 1


title: P. gingivalis biofilm 30 minutes sample 2


title: P. gingivalis plus S. gordonii biofilm 120 minutes sample 1


title: P. gingivalis biofilm 30 minutes sample 3


title: P. gingivalis plus S. gordonii biofilm 5 minutes sample 3


title: P. gingivalis biofilm 240 minutes sample 1


title: P. gingivalis biofilm 5 minutes sample 3


title: P. gingivalis biofilm 30 minutes sample 1


title: P. gingivalis plus S. gordonii biofilm 120 minutes sample 3


title: P. gingivalis biofilm 120 minutes sample 2


title: P. gingivalis plus S. gordonii biofilm 30 minutes sample 1


title: P. gingivalis biofilm 5 minutes sample 1


title: P. gingivalis biofilm 5 minutes sample 2


title: P. gingivalis plus S. gordonii biofilm 5 minutes sample 2


title: H3K4me3 IP

city: Vancouver

first: Benjamin

last: Martin

address: 2350 Health Sciences Mall

department: Biochemistry

institute: UBC

data_processing:
library strategy: Paired-end MNase ChIP-seq
Fastq files were aligned to saccer3 using BWA
Samtools was used to filter for mapped reads with a mapping quality score of at least 10
Bedtools and AWK were used to convert the BAM files into bed files of mapped DNA fragments
Fragments smaller than 500bp were selected for using AWK
Read coverage wig files were generated using the java-genomics-toolkit base.align.count function
Genome_build: saccer3
Supplementary_files_format_and_content: wig files, coverage in 1bp intervals

source_name: yeast_H3K4me3 IP

growth_protocol:
Yeast strains were grown to midlog and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

extract_protocol:
Cell pellets were resuspended in lysis buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF) and bead beat for 25 minutes. Cell lysates were spun down at 15,000g for 30 minutes. The chromatin pellets were re-suspended in 1000 μl of NP-S buffer (0.5 mM spermidine, 1 mM β-ME, 0.075% NP-40, 50 mM NaCl, 10 mM Tris pH 7.4, 5 mM MgCl2, 1 mM CaCl2) and digested with microccocal nuclease at 37°C for 10 minutes to obtain predominantly mono-nucleosomal DNA. Reactions were stopped with the addition of 10 mM EDTA and digested lysates were clarified by centrifugation at 9000g for 10 minutes. To extract insoluble chromatin, pellets were re-suspended in 300 μl of lysis buffer with 0.2% SDS, and sonicated in a Diagenode Bioruptor at high output for 30 seconds on/30 seconds off four cycles. Extracts were then re-clarified by centrifugation at 9000g for 10 minutes, and the supernatant pooled with the pre-existing extract. The buffer composition of the lysate was adjusted to that of the original lysate buffer (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate, 1X roche protease inhibitor cocktail, 1mM PMSF), and 10% was set aside as input. The supernatant was pre-cleared by incubation with magnetic protein-G Dynabeads (Life Technologies) for 1 hour at 4°C. Pre-cleared lysates were incubated with αHA (Roche, cat no. 12013819001), αH3K4me3 (Abcam, cat no. ab1012), αH3K23ac (Active Motif, cat no. 39131), or αIgG (Millipore, cat no. PP64) antibodies at 4°C overnight. Immune complexes were precipitated by incubation with magnetic protein-G Dynabeads for one hour at 4°C. Beads were washed twice with lysis buffer, high salt wash buffer (50mM HEPES pH 7.5, 640mM NaCl, 1mM EDTA, 2% Tritox X-100, 0.2% Na-deoxycholate), LiCl was buffer (10mM Tris-HCL pH 8.0, 250mM LiCl, 0.6% NP-40, 0.5% Na-deoxycholate, 1mM EDTA), and once with TE. The immunoprecipitated DNA was subjected to Illumina HiSeq paired-end sequencing.
Library construction for the Illumina platform was performed using a custom procedure for paired-end sequencing. Briefly, 2–10 ng of ChIP material was end-repaired and A-tailed before being ligated to TruSeq PE adaptors. In between each reaction, the material was purified using phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation. The resulting material was then amplified in the Phusion HF master mix (NEB) using TruSeq PE PCR primer 1.0 and custom indexed multiplexing primers [5′ AAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC 3′, where “NNNNNN” corresponds to unique hexamer barcodes]. PCR amplification was performed as follows: denaturation at 98 °C for 60 s; eight cycles of (98 °C, 30 s; 65 °C, 30 s; 72 °C, 30 s), and a final extension at 72 °C for 5 min. Amplified libraries were purified using 0.8 (vol) Agencourt AMPure XP solid phase reversible immobilization paramagnetic beads and eluted in 10 mM Tris⋅HCl pH 8.5. An aliquot of each library was run on an Agilent High Sensitivity chip to check the size distribution and molarity of the PCR products. Equimolar amounts of indexed, amplified libraries were pooled, and fragments in the 200–600 bp size range were selected on an 8% (wt/vol) Novex TBE PAGE gel (Invitrogen). An aliquot (1 μL) of the library pool was run on an Agilent High Sensitivity chip to confirm proper size selection and measure DNA concentration. The pooled libraries were diluted to 15 nM and their concentration was confirmed using the Quant-iT dsDNA HS assay kit and Qubit fluorometer (Invitrogen).

treatment_protocol: 1% formaldehyde crosslinking

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63

tag: chip antibody

value: H3K4me3 (Abcam, mAbcam1012, lot 1152779)

tag: growth stage

value: Log growth


title: Mock input

source_name: yeast_Mock input


title: H4K4me3 Input

source_name: yeast_H4K4me3 Input


title: H3K23ac IgG Control rep2

source_name: yeast_H3K23ac IgG Control

growth_protocol:
Yeast strains were arrested in G1 with alpha factor, and crosslinked with 1% formaldehyde for 15 minutes
Cells were grown in YPD

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

value: IgG (Millipore PP64, lot 1602263)


title: ALS_Female_blood_G

city: Darlinghurst

first: Paul

middle: E

last: Young

state: NSW

address: 405 Liverpool Street

country: Australia

institute: Victor Chang Cardiac Research Institute

description: TwinG

data_processing:
methylated and unmethylated Msp1 site + 3'adapter trimming
Bismark/bowtie1 genomic alignment
methylation extraction
Twin pair specific outlier analysis
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: bed files contain coverage and percent methylation for the listed CpG site.

source_name: blood

extract_protocol:
Genomic DNA extraction protocol not provided.
MSP1 enriched fragmentation. TrueSeq adapter ligation and Bisulfite conversion.

value: blood

tag: gender

value: Female

tag: disease state

value: ALS

tag: age (years)

tag: twin pair


title: ALS_Male_blood_C

description: TwinC

value: Male


title: Sas3-6HA input

source_name: yeast_Sas3-6HA input

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 SAS3-6HA::TRP


title: ALS_Female_blood_E

description: TwinE


title: control_Male_blood_B

description: TwinB

value: healthy


title: Mock HA IP

source_name: yeast_Mock HA IP

value: HA (Roche, cat no. 12CA5)


title: Xmult_Ohio.11_M_B_BC_2015.10.22 HJQE

city: San Marcos

first: Yuan

last: Lu

address: university drive

institute: Xiphophorus Genetic Stock Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adaptor seuqence were trimmed off, then low qualtiy basecall was trimmed off, at last, low qualtiy sequence reads were filtered out.
Short sequencing reads were aligned to X. multilineatus reference cDNA (https://viewer.xgsc.txstate.edu/data/transcriptomes/Xmulti_cdna_kmer73.fa), gene expression value is quantified as raw read using custom perl script (Molecular genetic response of Xiphophorus maculatus-X. couchianus interspecies hybrid skin to UVB exposure).
Genome_build: Xmulti_cdna_kmer73.fa (viewer.xgsc.txstate.edu/data/transcriptomes/Xmulti_cdna_kmer73.fa)
Supplementary_files_format_and_content: csv, raw gene expression read

organism: Xiphophorus multilineatus

source_name: brain

growth_protocol: The X. multilineatus used in the nutritional/behavioral study were F2 laboratory reared from wild-caught females, collected from the Rio Tambaque, San Luis Potosi, MX.

extract_protocol:
Entire brains were dissected from these four animals. Total RNA from these tissue samples was isolated as previously detailed using TRI-Reagent (Sigma Inc., St. Louis, MO, USA). Tissue samples were homogenized in TRI-Reagent followed by addition of 200 µl/ml chloroform and the samples vigorously shaken and subjected to centrifugation at 12,000 g for 5min at 4 ºC. Total RNA was further purified using RNeasy mini RNA isolation kit (Qiagen, Valencia, CA, USA). Residual DNA was eliminated by performing column DNase digestion at 25 oC for 15 min. Total RNA concentration was determined using a Qubit 2.0 fluorometer (Life Technologies, Grand Island, NY, USA). RNA quality was verified on an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA) to confirm that RIN scores were above 8.0 prior to sequencing.
RNA sequencing was performed upon libraries constructed using the Illumina TruSeq library preparation system (Illumina, Inc., San Diego, CA, USA)

treatment_protocol: Low quality juvenile environment fish were housed in group tanks as juveniles (densities > 6 fish per liter, N = 23). Fish in this group were fed Tetramin once a day; High quality juvenile environment fish were housed individually after 14 days of age, and were fed Tetramin and brine shrimp, ad libitum.

value: brain

value: male


title: control_Female_blood_J

description: TwinJ


title: ALS_Female_blood_I

description: TwinI


title: Cell 2

city: Münster

first: Nina

last: Neuhaus

address: Albert-Schweitzer-Campus 1, D11

department: Centre of Reproductive Medicine and Andrology

institute: University Hospital of Münster

data_processing:
TorrentSuite software (version 3.2, Ion Torrent/Life Technologies) was used for mapping the reads to the reference genome version hg19.
Resulting BAM files were used for plot coverage analysis.
Splus software was used to create coverage plots
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Splus software.The number of reads falling in the exons of the gene were counted and normalized by the size of the gene and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

source_name: Spermatogonia

growth_protocol: For establishment of germ cell enriched cultures, testicular biopsies were enzymatically digested as previously published (Kossack et al. Hum Reprod. 2013). For enrichment of the germ cell population, cells in the supernatant were transferred to a separate cell culture dish, 18 hrs following plating of the initial cell suspension. Following 3-4 days of culture somatic and germ cells could be distinguished based on morphological characteristics, so that micromanipulation of selected spermatogonia could be performed.

extract_protocol:
Libraries were made from 20 ng of double standed cDNA according to previous methods (Tang et al., Nat Methods, 2011).
Samples were barcoded and sequenced on an IonTorrent/Life Technologies Personal Genome Machine (PGM) 1.0 gig, 316 chip following manufacturer's protocols.

treatment_protocol: Cells picked from the sample were bathed in an additional rinse well containing cold PVS-BSA. Each cell was drawn into and expelled out of the microcapillary tube approximately three times before final capture. Finally, single cells were transferred to a sterile 0,2 ml thin-walled PCR tube in a 1,0 ul  droplet of cold PBS-BSA. Cells were then either immediately processed for cDNA synthesis using previously published protocols (Tang et al., Nat Methods, 2011) or flash frozen in liquid nitrogen.

tag: cell type

value: human spermatogonia


title: control_Female_blood_H

description: TwinH

tag: tissue


title: Xmult_Ohio.17_M_B_BC_2015.10.22 LJQE


title: Cell 1


title: Sas3-6HA IP

source_name: yeast_Sas3-6HA IP


title: dme_old_ZT20_RNASeq_r1

status: Public on Jan 14 2017

city: Corvallis

middle: Anthony

last: Hendrix

state: OR

address: 2011 Ag & Life Sciences Bldg

department: Biochemistry and Biophysics/EECS

institute: Oregon State University

data_processing:
reads were quality trimmed with skewer using -q 30 and -Q 30
reads were aligned using tophat2 and the dm6/BDGP6 assembly of the Drosophila melangaster genome
Differentially expressed genes were computed using cuffdiff, resulting in the provided "diff" files.
rhtymicity was determined with ARSER using a pvalue of < 0.05
Genome_build: dm6/BDGP Realse 6
Supplementary_files_format_and_content: diff files are the output of cuffdiff

organism: Drosophila melanogaster

source_name: heads of old flies

growth_protocol: Drosophila melanogaster were raised on a standard yeast (35g/L), cornmeal (50g/L) and molasses (5%) diet at 25±1°C, under a 12 h light/12 h dark regimen.

extract_protocol:
RNA was extracted from TRIzol reagent (Thermo Fisher), treated with rDNAse I (Takara), followed by ethanol/sodium acetate precipitation. Quality control was performed with Agilent Bioanalyser.
Illumina TruSeq Stranded mRNA kit

tag: strain

value: heads

tag: age

value: 55 day old

tag: time point

value: 20 hours post sunrise


title: control_Female_blood_F

description: TwinF


title: control_Male_blood_D

description: TwinD


title: dme_old_ZT12_RNASeq_r2

value: 12 hours post sunrise


title: dme_old_ZT12_RNASeq_r1


title: Xmult_Ohio.15_M_B_BC_2015.10.22 HJQE


title: ALS_Male_blood_A

description: TwinA


title: dme_old_ZT20_RNASeq_r2


title: Xmult_Ohio.18_M_B_BC_2015.10.22 LJQE


title: dme_old_ZT8_RNASeq_r1

value: 8 hours post sunrise


title: dme_old_ZT16_RNASeq_r2

value: 16 hours post sunrise


title: dme_old_ZT0_RNASeq_r2

value: 0 hours post sunrise


title: dme_old_ZT16_RNASeq_r1


title: H3K23ac IgG Control rep1

tag: genotype/variation

value: his3D200 leu2D1 lys2-128d ura3-52 trp1D63 bar1::KAN

value: IgG (Millipore PP64, lot 1602263)


title: dme_young_ZT12_RNASeq_r2

source_name: heads of young flies

value: 5 day old


title: dme_old_ZT8_RNASeq_r2


title: dme_old_ZT4_RNASeq_r1

value: 4 hours post sunrise


title: dme_old_ZT4_RNASeq_r2


title: dme_young_ZT20_RNASeq_r2


title: dme_young_ZT20_RNASeq_r1


title: dme_young_ZT16_RNASeq_r1


title: dme_young_ZT8_RNASeq_r1


title: dme_young_ZT16_RNASeq_r2


title: dme_young_ZT4_RNASeq_r1


title: dme_young_ZT8_RNASeq_r2


title: dme_young_ZT0_RNASeq_r2


title: dme_young_ZT4_RNASeq_r2


title: 20 min of infection with TEX treatment

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

data_processing:
FastQ quality trimming: cut-off value of 20 (FastX 0.0.13)
Adaptor trimming (cutadapt 1.10)
Read mapping (READemption 0.3.0 and segemehl version 0.1.7)
Wiggle generation and gene quantification (READemption 0.4.2)
Genome_build: NC_000964; KU878088
Supplementary_files_format_and_content: wiggle format with coverages normalized by total number of aligned reads

organism:
Bacillus subtilis
Bacillus phage AR9

source_name: bacterial cells with phage infection_20 min

growth_protocol: Bacillus subtilis cells were grown in LB medium to OD595 of 0.6 and infected with AR9 at MOI of 10. At various time points (5, 20 and 40 min), an aliquots of infected cultures were withdrawn and chilled on ice.

extract_protocol:
Total RNA was purified with hot-phenol method (Sambrook & Russell 2006). RNA samples were treated by RNase-free DNaze I in presence of RiboLock, then samples were extracted with phenol:isoamyl:chloroform, ethanol precipitated and re-suspended in DEPC-treated water.
RNA libraries were prepared for sequencing using standard Illumina protocols. The 20 min RNA sample was treated with TEX as described in Sharma et al. 2010

tag: bacterial strain

value: Bacillus subtilis subsp. subtilis str.168

tag: phage strain

tag: genotype

value: wild type


title: dme_young_ZT0_RNASeq_r1


title: HT-29-MTX, untreated #2

city: Ithaca

first: Caitlin

middle: M

last: Feather

state: NY

address: Riley-Robb Hall, Wing Dr

department: Biological and Environmental Engineering

institute: Cornell University

description:
gene_exp.diff : Ctl
genes.read_group_tracking : Ctl_1

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the Human hg19 reference genome (UCSC).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the Human hg19 reference transcriptome (UCSC).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the Human hg19 reference transcriptome (UCSC).
Genome_build: Human hg19 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: HT-29-MTX cells from Dr. Thécla Lesuffleur, INSERM U560, Lille France

growth_protocol: 7 days post-confluency (21 days total), 37°C, 5% CO2

extract_protocol:
Total RNA from the samples was purified using Trizol (Thermo Fisher).  The purification procedure deviated from the commercial Trizol protocol in the following regards: 1) after the first phase separation, an additional chloroform extraction step of the aqueous layer was performed using Phase-lock Gel tubes (5 prime), 2) 1 µL of GlycoBlue (Thermo Fisher) was added immediately prior to the isopropanol precipitation, and 3) the RNA was washed twice with 75% ethanol.  RNA sample quality was confirmed by spectrophotometry (NanoDrop) and with a fragment analyzer (AATI Fragment Analyzer).  For each sample, 1 µg of total RNA was used for further analysis.  PolyA+ RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Directional RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), with initial polyA+ isolation.

treatment_protocol: 24 hours, 37°C, 5% CO2, +/- A.ceylanicum iL3 larvae

tag: cell line

value: Intestinal epithelium

tag: disease

value: Colorectal carcinoma

tag: treatment

value: untreated


title: 40 min of infection

source_name: bacterial cells with phage infection_40 min


title: 20 min of infection


title: HT-29-MTX, untreated #1

description:
gene_exp.diff : Ctl
genes.read_group_tracking : Ctl_0


title: HT-29-MTX, A. ceylanicum treated #2

description:
gene_exp.diff : ACE
genes.read_group_tracking : ACE_1

value: treated for 24 hours with A. ceylanicum iL3 larvae


title: dme_old_ZT0_RNASeq_r1

value: heads


title: 5 min of infection

source_name: bacterial cells with phage infection_5 min


title: HT-29-MTX, A. ceylanicum treated #1

description:
gene_exp.diff : ACE
genes.read_group_tracking : ACE_0


title: RNA130812RH_14

status: Public on Jan 13 2017

city: Portland

first: Priscila

last: Darakjian

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

description: Binge Drinker (BD): ethanol consumption of >= 2 g/kg for >= 55% of days AND a recorded BEC >= 80 mg/dl at least once per year

data_processing:
Base Calling was done through Illumina CASAVA software
FASTQC was run for data inspection
Alignment: Reads were aligned to MacaM assembly (Zimin et al., 2014) using STAR v.2.3.0e (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax=3,outFilterScoreMinOverLread=0.33,outFilterMismatchNoverLmax=0.03, outFilterMultimapNmax=1.
Upper-Quartile normalization was performed using the edgeR Bioconductor package. Genes with at least 100 average reads per sample and exons with more than 10 average reads were retained for further analysis.
Genome_build: MacaM
Supplementary_files_format_and_content: [RNA130812RH_exon_reads_UQNormalized_for_GEO.csv] first column has the exon ID (a combination of chromosome number, start, and end location of exon, and gene symbol). subsequent 30 columns provide the normalized reads for each sample for each exon
Supplementary_files_format_and_content: [RNA130812RH_gene_reads_UQNormalized_for_GEO.csv] first column has the Gene Symbol, and subsequent 30 columns provide the normalized reads for each sample for each gene

organism: Macaca mulatta

source_name: Dissected Tissue (Brain) - Central Nucleus of the Amygdala (CeA)

extract_protocol:
Monkeys were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session. Preparation of brain tissue was described previously (Davenport et al., 2014) and the tissues were collected as part of the MATRR. Necropsy occurred at the time when they would normally begin their drinking session; monkeys were anesthetized with ketamine (10 mg/kg) and maintained on isoflurane. The brains were perfused with ice-cold oxygenated artificial cerebral spinal fluid, removed (< 5 min post-mortem) and sectioned according to each monkey’s individual MRI (Daunais et al., 2010). The CeA was identified by visible landmarks, lateral of the optic tract and ventral of the globus pallidus (Watson et al., 2010: -4.5 mm to -9.9 mm). The block of tissue that contained the CeA was dissected and placed into sterile tubes maintained at –80 degrees.
Library formation (TruSeq Stranded RNA-Seq with RiboZero Gold rRNA depletion) and sequencing on a HiSeq 2000 were all performed according to Illumina’s specifications at the OHSU Massively Parallel Sequencing Shared Resource. Libraries were multiplexed 4 per lane, yielding approximately 50 million total reads per sample.

treatment_protocol: Male rhesus monkeys that were experimentally naïve at the onset of alcohol induction (Macaca mulatta, n = 30, 4-11 years-old, 6-8 kg) were used. They were first induced to drink 4% (w/v) ethanol and then allowed to self-administer ethanol for over 12 months under open access conditions (22h/d, 7d/wk) with concurrent meals and continuous access to water. They were trained in awake blood draws as described (Porcu et al., 2006) and approximately every fifth day, blood-ethanol concentration (BEC) samples were collected 7 h after the onset of the 22-h/d session.The monkeys were from four cohorts, referred to as cohorts 4, 5, 7a and 7b in the Monkey Alcohol Tissue Research Resource (www.MATRR.com). These cohorts where selected because they all had approximately 90 days of induction followed by approximately two 6-month periods of alcohol open access. All monkeys were individually housed (quadrant cages, 0.8 m x 0.8 m x 0.9 m) in a room with controlled light cycle (11 hours lights on, 13 hours lights off), temperature (20-22oC) and humidity (65%). The monkeys had visual, auditory and olfactory contact with other monkeys. They were weighed weekly.

tag: matrr (monkey alcohol tissue research resource) id

tag: cohort

value: COHORT 7b

tag: avg age at beginning of 1.5 g/kg etoh induction

tag: avg age after second 6 months of open access

tag: Sex

value: Male

tag: drinking category

value: Binge Drinker (BD)


title: RNA130812RH_20

description: Low Drinker (LD): not BD, not HD, and not VHD

value: Low Drinker (LD)


title: dme_young_ZT12_RNASeq_r1

tag: tissue

value: 12 hours post sunrise


title: RNA130812RH_29


title: RNA130812RH_6

description: Heavy Drinker (HD): ethanol consumption of >= 3 g/kg for >= 20% of days

value: Heavy Drinker (HD)


title: RNA130812RH_5

description: Very Heavy Drinker (VHD): average daily ethanol intake exceeding 3 g/kg AND have >= 10% of open access days with an ethanol intake exceeding 4 g/kg

value: COHORT 7a

value: Very Heavy Drinker (VHD)


title: RNA130812RH_13


title: RNA130812RH_26


title: RNA130812RH_24


title: RNA130812RH_7


title: RNA130812RH_18


title: RNA130812RH_4


title: RNA130812RH_22


title: RNA130812RH_17

value: COHORT 5


title: RNA130812RH_2


title: RNA130812RH_30


title: RNA130812RH_1


title: RNA130812RH_10

value: COHORT 4


title: RNA130812RH_9


title: RNA130812RH_16


title: RNA130812RH_28


title: RNA130812RH_15


title: RNA130812RH_19


title: RNA130812RH_8


title: RNA130812RH_21


title: RNA130812RH_27


title: vsc09_zn13

city: Santa Cruz

first: Alan

last: Zahler

address: Sinsheimer Labs

department: MCD Biology

institute: UC Santa Cruz

data_processing:
Raw sequencing results in the form of FASTQ files were used as input for alignment of the sequencing data to the Oxytricha trifallax macronuclear genome reference RNA database (Swart et al., 2013).
Alignments were performed with Tophat2, which produced BAM alignment files (Kim et al., 2013).
Tophat BAM files were used directly as input into Cuffdiff2 to generate normalized FPKM values (Trapnell et al., 2013).
Genome_build: The reference RNA GTF and macronuclear genome sequence files were retrieved from the Oxytricha genome website (oxy.ciliate.org).
Supplementary_files_format_and_content: tab delimitted table showing the fpkm coverage for each library on each annotated Oxytricha trifallax gene

organism: Oxytricha trifallax

source_name: Strains ALXC2 x ALXC9

growth_protocol: Oxytricha trifallax strains ALXC2 and ALXC9 (Zahler et al., 2012) were grown vegetatively in Pyrex dishes in inorganic salts media (Chang et al., 2004) using the food source Chlorogonium elongatum (UTEX collection strain B203). Typical daily feedings consisted of 10 mL of washed algae per 300 mL Pyrex dish of Oxytricha trifallax, depending on culture density.

extract_protocol:
Pyrex dishes of mating cells were cotton filtered to remove cellular debri and concentrated onto 10 mM Nitex and transferred into microcentrifuge tubes. Cells were gently pelleted for 2 minutes at 500 x g in a microcentrifuge and supernatants were removed leaving 50 mL of pelleted cells. 200 mL of mirVana Lysis/Binding Buffer from the mirVana miRNA Isolation Kit (Ambion) was added to each tube. Total RNA was purified using the kit’s protocol for total RNA purification. Total RNA yields from a single 300mL Pyrex dish of cells (~450,000 cells) were typically between 100 and 300mg.
mRNA cDNA libraries were prepared using the TruSeq RNA Sample Preparation v2 Kit (Illumina) following the manufacturer’s LT protocol. Library preparation started with 3mg of total RNA from each of the control and mating cell timepoints. Poly-A containing mRNA molecules were selected for using poly-T oligo attached beads with two rounds of purification. Individual libraries were analyzed on a Bioanalyzer (Agilent) for cDNA quality and bar-coded libraries were pooled into one sample for sequencing.

treatment_protocol: Mating competent strains ALXC2 and ALXC9 were grown vegetatively to high density, fed lightly the day before a mating and allowed to completely exhaust their food supply. Cells were then cotton filtered to remove any residual algae and were concentrated on 10mM Nitex membranes into Pringhsheim salts media (Fang et al., 2012). Each individual mating strain was counted and cells were then mixed at equal numbers to a total concentration of 1,500 cells per mL in Pyrex dishes. These mating cells were then fed 1 mL of unwashed Klebsiella pneumonia stationary phase culture as a food source. Aggregates of 10-30 cells were observed by 2 hours after mixing mating types, with the first mating pairs visible by 4 hours post mixing. Typical mating efficiency when mixing ALXC2 and ALXC9 strains is ~70%, with visible anlage present by 48 hours.

tag: strain

value: Strains ALXC2 x ALXC9

tag: developmental stage

value: 0 hours after mixing mating strains


title: vsc09_zn14


title: veg09_zn12

source_name: Strain ALXC2

value: Strain ALXC2

value: vegetatively growing strain


title: mat12_zn07

value: 12 hours after mixing mating strains


title: mat48_zn09

value: 48 hours after mixing mating strains


title: mat06_zn01

value: 6 hours after mixing mating strains


title: mat12_zn02


title: mat48_zn04


title: mat72_zn05

value: 72 hours after mixing mating strains


title: mat06_zn06


title: veg09_zn11


title: RNA130812RH_11

value: Male


title: mat24_zn03

value: 24 hours after mixing mating strains


title: mat72_zn10


title: Lur_ChemSeq

city: Illkirch

first: Tao

last: YE

address: 1 rue Laurent Fries

country: France

institute: IGBMC (CNRS/INSERM/UDS)

data_processing:
Raw data were analyzed by the Illumina CASAVA 1.8.2
Alignment : Reads were mapped to hg19 assembly of human genome using Bowtie aligner release<=1.0.0, with principle parameters: -m 1 --strata --best
Peak detection was performed using the MACS (version 1.4.2) software under settings where an input DNA was used as a negative control
Peaks overlapping with the ENCODE blacklist  have been dropped
Genome_build: hg19
Supplementary_files_format_and_content: MACS 1.4.2 peak calling file with the following collumns: chr, start,end,length,summit,tags,-10*LOG10(pvalue),fold_enrichment,FDR(%),peak name.

source_name: Lung cancer cell line A549

extract_protocol:
A549 cells treated with 300nM of Biotin-Lurbinectedin during 4h were cross-linked with 1% formaldehyde at room temperature for 10 min. After sonication, the soluble chromatin was incubated with 80ul of Streptavidin beads (Life technologies) over-night. After wash the captured DNA was eluted, de-cross-linked and purified by QiAquick Spin columns (Qiagen). The DNA was used to construct a library and sequenced on a Illumina HiSeq 2500 system.
ChIP-seq (Chem-seq)
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, around 10 ng of ChIP enriched DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881,Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads. Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Hiseq2500 as single-end 50 base reads following Illumina’s instructions.

tag: affinity purification

value: Magnetic streptavidin beads(M-280) Invitrogen11206D


title: DON2531A98

city: Oxford

first: Eshita

last: Sharma

state: Oxfordshire

address: Roosevelt Drive, Headington

department: Bioinformatics

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics

data_processing:
Adapter trimming: RNA-seq reads were trimmed for Nextera and Illumina  adapter sequences using skewer-v0.1.125
Alignment: Reads in gzipped fastq format were aligned using Hisat2 version-2.0.0-beta with default parameters to a modified reference genome comprising the human genome, Homo sapiens GRCh37 - human_g1k_v37, and fasta sequences for ERCC spike-ins
Mark Duplicates: Duplicate reads were marked using MarkDuplicates.jar implemented in Picard tools v1.92
Read counts: Reads mapping uniquely to genes annotated in ENSEMBL release 75 were counted using featureCounts implemented in subread-v1.5.0
Genome_build: GRCh37
Supplementary_files_format_and_content: Count_table.txt: raw read counts for all 63677 ENSEMBL annotated genes
Supplementary_files_format_and_content: additional_file_2.xlsx:  Contains multiple excel sheets with Sheet1= tpm table (subset for 13873 expressed genes);
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet2= cell metadata with information regarding chip, sequencing batch, imaging, and QC metrics;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet3= wildtype differential expression;
Supplementary_files_format_and_content: additional_file_2.xlsx: Sheet4= knockout differential expression

source_name: HUES2 Embryonic stem cell line

growth_protocol:
Macrophages grown on fibronectin coated polaris chip in XVIVO 15 + MCSF + FCS + PS
LPS 100ng/ml in either XVIVO 15 + FCS + MCSF or from previously cultured Macrophages exposed to same batch of LPS

extract_protocol:
FluidigmC1 RNAseq protocol: cDNA was generated using SMARTer Ultra Low RNA Kit (Clontech)
Nextera XT DNA Library Preparation Kit (Illumina); Illumina RNAseq HiSeq4000 75bp PE

tag: cell type

value: embryonic stem cell derived macrophage

tag: macrophage batch

value: KOC

tag: macrophage samhd1

value: dNTPase knockout

tag: macrophage culture time in hours

tag: macrophage culture media

value: standard media


title: DON2531A891

tag: cell line

value: WTB

value: wildtype

value: conditioned media


title: DON2531A903


title: mat24_zn08

value: Strains ALXC2 x ALXC9


title: DON2531A890

value: conditioned media with LPS


title: DON2531A9


title: RNA130812RH_12

value: COHORT 5

value: Very Heavy Drinker (VHD)


title: DON2531A896


title: input_DNA


title: DON2531A886

value: standard media with LPS


title: DON2531A877


title: DON2531A876


title: DON2531A875


title: DON2531A887


title: DON2531A874


title: DON2531A872


title: DON2531A902


title: DON2531A867


title: DON2531A873


title: DON2531A87

value: WTA


title: DON2531A866


title: DON2531A900


title: DON2531A898


title: DON2531A864


title: DON2531A895


title: DON2531A862


title: DON2531A860


title: DON2531A86


title: DON2531A856


title: DON2531A857

value: KOF

value: knockout


title: DON2531A850


title: DON2531A854


title: DON2531A855


title: DON2531A85


title: DON2531A848


title: DON2531A847


title: DON2531A859


title: DON2531A846


title: DON2531A845


title: DON2531A844


title: DON2531A869


title: DON2531A849


title: DON2531A841


title: DON2531A838


title: DON2531A840


title: DON2531A839


title: DON2531A84


title: DON2531A842


title: DON2531A863


title: RNA130812RH_3

value: Male

value: Heavy Drinker (HD)


title: DON2531A833

value: embryonic stem cell derived macrophage


title: DON2531A858


title: DON2531A832


title: DON2531A835


title: DON2531A831


title: DON2531A830


title: DON2531A821


title: DON2531A827


title: DON2531A826


title: DON2531A83

value: KOE


title: DON2531A82


title: DON2531A816


title: DON2531A817


title: DON2531A815


title: DON2531A810


title: DON2531A809


title: DON2531A80


title: DON2531A800


title: DON2531A824


title: DON2531A796


title: DON2531A795


title: DON2531A801


title: DON2531A814


title: DON2531A794


title: DON2531A79


title: DON2531A793


title: DON2531A789


title: DON2531A823


title: DON2531A792


title: DON2531A822


title: DON2531A782


title: DON2531A777


title: DON2531A787


title: DON2531A773


title: DON2531A778


title: DON2531A77


title: DON2531A770


title: DON2531A797


title: DON2531A767

value: WTG


title: DON2531A768


title: DON2531A765


title: DON2531A764

value: KOC

value: dNTPase knockout

value: standard media


title: DON2531A758

value: WTB

value: wildtype


title: DON2531A808


title: DON2531A759

value: conditioned media


title: DON2531A790


title: DON2531A763


title: DON2531A757

value: conditioned media with LPS


title: DON2531A761


title: DON2531A756


title: DON2531A843


title: DON2531A75


title: DON2531A755


title: DON2531A776


title: DON2531A749


title: DON2531A748


title: DON2531A753


title: DON2531A746


title: DON2531A745


title: DON2531A771


title: DON2531A752


title: DON2531A742


title: DON2531A738

value: KOD


title: DON2531A74


title: DON2531A736

value: standard media with LPS


title: DON2531A729


title: DON2531A728


title: DON2531A730


title: DON2531A726


title: DON2531A837

value: WTA


title: DON2531A734


title: DON2531A731


title: DON2531A732


title: DON2531A727


title: DON2531A725


title: DON2531A72


title: DON2531A715


title: DON2531A716


title: DON2531A721


title: DON2531A711


title: DON2531A701


title: DON2531A710


title: DON2531A71


title: DON2531A696


title: DON2531A70


title: DON2531A702


title: DON2531A704


title: DON2531A713


title: DON2531A694


title: DON2531A692


title: DON2531A689


title: DON2531A691


title: DON2531A703


title: DON2531A695


title: DON2531A709


title: DON2531A690


title: DON2531A680


title: DON2531A682


title: DON2531A686


title: DON2531A717


title: DON2531A683


title: DON2531A688


title: DON2531A69


title: DON2531A675


title: DON2531A687


title: DON2531A674


title: DON2531A678


title: DON2531A714


title: DON2531A7


title: DON2531A663


title: DON2531A660


title: DON2531A662


title: DON2531A652


title: DON2531A653


title: DON2531A66


title: DON2531A658


title: DON2531A648


title: DON2531A651


title: DON2531A639


title: DON2531A647


title: DON2531A640


title: DON2531A635


title: DON2531A644


title: DON2531A64


title: DON2531A638


title: DON2531A625


title: DON2531A642


title: DON2531A621


title: DON2531A622


title: DON2531A634


title: DON2531A629


title: DON2531A62