title: Day 7 control

city: Lexington

first: Gregg

middle: Brooks

last: Whitworth

address: 204 West Washington St

department: Biology

institute: Washington and Lee Unversity

description:
d7.c
TRAP RNA

data_processing:
Raw sequencing reads in FASTQ format were filtered for quality and adapter sequences removed using Trimmomatic (v. 0.33) with the following parameters: a 4-base sliding window with average quality cutoff of 15, removal of 3 leading and trailing low quality bases and a minimum read length of 36 bases.
Surviving reads were aligned to the Xenopus laevis genome using the JGI gene models version 9.1, retrieved from xenbase.org on 11/21/2015, using Bowtie2 (v. 2.2.5) with ‘sensitive’ alignment presets augmented with a minimum acceptable alignment score of -0.1.
Gene expression estimation, expressed as fragments per killibase per million reads (FPKM), was performed using RSEM (v. 1.2.21) with default options.
Genome_build: XENLAv9.1 (X. laevis 9.1, xenbase.org)
Supplementary_files_format_and_content: .csv files represent TPMs and FPKMs

organism: Xenopus laevis

source_name: RGC TRAP

growth_protocol: Restriction enzyme mediated integration was used to create lines of Xenopus laevis that stably express TRAP transgenes in RGCs .  Biologically independent experiments were each carried out using F1 progeny from single tg(islet2b:EGFP-RPL10a) female founder lines. These progeny were screened for presence of the EGFP-rpl10a transgene using a fluorescent dissecting microscope.  eGFP positive progeny were then grown to post-metamorphic stage (> 6 months) under 12L:12D photoperiod at 22 oC. All animal experiments were carried out using procedures approved by the Washington and Lee University and Johns Hopkins University School of Medicine’s IACUCs.

extract_protocol:
Both left and right eyes were harvested separately.  Retinas were isolated by removing the lens, then peeling off and discarding the retinal pigment epithelial layer. Freshly dissected retinas were immersed in ice-cold lysis buffer (20 mM HEPES KOH, pH 7.4, 5 mM MgCl2, 150 mM KCl) to which was added freshly prepared 100 μg/ml cycloheximide, 0.5 mM DTT, protease inhibitors (Roche Mini Complete, EDTA-Free) and 40 U/ml recombinant Rnasin (Promega).  We isolated total RNA from the retina or used the translation ribosomal affinity purification (TRAP) protocol to isolate and purify the RNAs specific to the RGCs (described in Watson et al., 2012; DOI 10.1002/dvdy.23880).  To immunoprecipitate ribosomes and associated RNAs, we used equal amounts of anti-eGFP antibodies (19C8 and 19F7; Memorial Sloan-Kettering Monoclonal Antibody Facility) at a concentration of 100 µg of total anti-eGFP antibody per 375 µl of Dynal Protein G-magnetic beads (Life Technologies).
To obtain a minimum of 120 ng/sample of purified TRAP-isolated mRNAs, equal quantities from each of the three independent biological replicates were combined to generate a single pooled sample.  RNA samples were then sent to the JHMI Deep Sequencing Core for RNA-Seq cDNA library construction using poly(A) selection, with standard Illumina protocols for HiSeq 2000.

treatment_protocol: The retinas from each of 10 post-metamorphic transgenic Tg(Islet2b:EGFP-RPL10a) Xenopus laevis frogs, 3.5 - 5.0 cm in length, were either left untreated (naïve) or received a surgery (operated).  Operated individuals were anesthetized with 0.05% tricaine methanesulfonate and received either a sham surgery (sham) or a crush injury to the right optic nerve (crush), and no treatment the left optic nerve (control). To avoid the surrounding vasculature, an initial surgical incision was made in the right medial roof of the buccal cavity, the muscles were then gently teased apart and the optic nerve was exposed from at a 45o angle. The exposed nerve was gently separated from the adjacent ophthalmic artery and a pair of #55 forceps were used to perform a five second crush located 5 mm from the optic nerve head. Crush injuries were verified by visual inspection by observing a region of clear sheath flanked by a more opaque area. Frogs with excessive bleeding were excluded from further study.  Following the surgery, frogs were allowed to recover in a shallow bath of 0.1X MMR (10 mM NaCl, 0.2 mM KCl, 0.1 mM MgCl2, 0.2 mM CaCl2, 0.5 mM HEPES; pH 7.5), transferred to individual tanks, and immersed in fresh 0.1 X MMR.  Ten untreated (naïve) frogs were also moved to individual tanks for a day. At 24 hours post-surgery, frogs were transferred to 18.25" x 12" x 6.25"communal tanks with a maximum of ten frogs per tank.   The surgically manipulated frogs were allowed to recover for 1, 3, 7, or 11 days post optic nerve crush.  Following the crush surgery at these discreet time periods, the frogs were immersed in 0.5% tricaine methanesulfonate, decapitated and exsanguinated.

value: left eye

tag: time (days post-surgery)

tag: treatment

value: control

value: RGC


title: Day 7 crush

status: Public on Nov 01 2016

type: SRA

state: VA

country: USA

description:
d7.x
TRAP RNA

library_source: transcriptomic

molecule: total RNA

tag: tissue

value: right eye

value: optic nerve crush

tag: cell type


title: S49

city: South Bend

first: Reginald

last: Hill

state: Indiana

address: 1234 North Notre Dame Ave.

department: Biological Sciences

institute: University of Notre Dame

description: microRNA

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

organism: Homo sapiens

source_name: cancer associated fibroblasts

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

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

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

value: immortalized cancer associated fibroblasts

tag: passages

value: 2 through 10

tag: treatment status

value: untreated


title: S02GT

description: microRNA

value: Gemcitabine treated


title: Day 3 crush

description:
d3.x
TRAP RNA


title: S02

description: microRNA


title: Day 11 crush

description:
d11.x
TRAP RNA


title: MUT_rep3

city: Karlsruhe

first: Raphael

last: Wild

address: Fritz-Haber-Weg 2

department: Zoology

country: Germany

institute: Karlsruhe Institute of Technology

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

organism: Danio rerio

source_name: whole embryo

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

tag: developmental stage

tag: genotype

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


title: Day 3 control

description:
d3.c
TRAP RNA


title: S63

description: microRNA


title: S63GT

description: microRNA


title: Day 1 crush

description:
d1.x
TRAP RNA


title: Sham surgery crush

description:
d1.shx
TRAP RNA

value: no optic nerve crush (sham surgery)


title: 704_SHAPEmap_rep1

city: Chapel Hill

first: Alain

last: Laederach

state: NC

address: Coker Hall

institute: University of North Carolina Chapel Hill

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_001127704.1
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

molecule: polyA RNA

source_name: SERPINA1, transcript variant 8

extract_protocol:
NA
Library construction protocol: Nextera DNA Library Prep Kit (Illumina).

treatment_protocol:
1M7 (SHAPE reagent) in DMSO.
Transcripts were folded at 37 C for 10-15 minutes in vitro.

tag: transcript variant


title: 700_SHAPEmap_rep2

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_001127700.1
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: SERPINA1, transcript variant 4


title: 700_SHAPEmap_rep1

description:
mRNA
in vitro


title: 705_SHAPEmap_rep1

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_001127705.1
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: SERPINA1, transcript variant 9


title: Sham surgery control

description:
d1.shc
TRAP RNA

value: control (sham surgery)


title: Naïve (non-surgical)

description:
ip.naive
TRAP RNA

value: both eyes

value: control (no surgery)


title: 705_SHAPEmap_rep2

description:
mRNA
in vitro


title: 295_SHAPEmap_rep2

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_000295.4
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: SERPINA1, transcript variant 1


title: Total retina RNA

description:
tot.ret
total RNA

source_name: Retina

value: retina


title: Day 11 control

description:
d11.c
TRAP RNA


title: 704_SHAPEmap_rep2

description:
mRNA
in vitro


title: 236_SHAPEmap_rep1

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_001002236.2
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: SERPINA1, transcript variant 2


title: HKC_MNase_Low_Salt_Rep2

city: New York

first: Nicholas

last: Gomez

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: genomic

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

molecule: genomic DNA

source_name: Cultured Kidney Cell

extract_protocol: TruSeq libraries were constructed per manufacturer's instructions

value: Kidney Cell

tag: growth protocol

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

tag: extract protocol

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


title: 235_SHAPEmap_rep1

description:
mRNA
in vitro

data_processing:
Library strategy: SHAPE-MaP
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper pipeline version 1.2:
1. Reads from 'p', 'm' and 'd' samples are mapped to the reference transcripts with Bowtie2.
2. Mutation frequencies are calculated for each base in the samples.
3. SHAPE reactivities are calculated from 'p', 'm' and 'd' mutation frequencies and normalized.
Genome_build: NM_001002235.2
Supplementary_files_format_and_content: .tab.txt files include the read depths, standard errors and SHAPE reactivity of each base. Column "Normalized reactivity" is the SHAPE reactivity.

source_name: SERPINA1, transcript variant 3


title: Empty plasmid control batch 1 rep3

city: Seattle

first: Aimee

last: Dudley

state: Washington

address: 720 Broadway

institute: PNDRI

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

organism: Saccharomyces cerevisiae

source_name: Whole colony

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

tag: strain


title: Empty plasmid control batch 1 rep4


title: Empty plasmid control batch 1 rep2


title: 295_SHAPEmap_rep1

description:
mRNA
in vitro


title: Empty plasmid control batch 1 rep1


title: Chr 16 disome batch 1 rep4


title: Chr 16 disome dig1D hemizygous batch 1 rep3


title: Chr 16 disome dig1D hemizygous batch 1 rep1


title: Chr 16 disome dig1D hemizygous batch 1 rep2


title: Chr 16 disome batch 1 rep3


title: Day 1 control

description:
d1.c
TRAP RNA

value: left eye

value: control


title: Chr 15 disome batch 1 rep4


title: Chr 16 disome dig1D hemizygous batch 1 rep4


title: Chr 16 disome batch 1 rep1


title: Chr 15 disome batch 1 rep3


title: Chr 15 disome batch 1 rep1


title: DIG1 overexpression plasmid batch 1 rep4


title: 236_SHAPEmap_rep2

description:
mRNA
in vitro


title: DIG1 overexpression plasmid batch 1 rep2


title: Chr 15 disome batch 1 rep2


title: Chr 16 disome batch 1 rep2


title: WT batch 1 rep1


title: WT batch 1 rep2


title: DIG1 overexpression plasmid batch 1 rep3


title: DIG1 overexpression plasmid batch 1 rep1


title: Uhrf1_cKO_2

city: Planegg-Martinsried

first: Gunnar

last: Schotta

address: Grosshaderner Strasse 9

department: Biomedical Center

institute: LMU Munich

data_processing:
Image analysis and base calling resulted in .bcl files, which were converted into .fastq files by the CASAVA1.8.2 software
Fastq files were imported to the commercially available Genomatix mining station with the data import and validation tool ver. 2.2.2
Reads were mapped to the mouse genome version GRCm38 with the commercially available Genomatix mapper ver. 3.7.6.3 allowing no mismatch
Methylation per CpG was calculated  with the commercially available Genomatix mining station
CpGs were filtered for a minimal coverage > 5 with the free software R ver 3.2.1
Merging of the individual files and further analyzes were performed with the R package methylkit
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited .txt file with methylation per CpG, columns are column1: chr.base column2: chromosome column3: base column 4: strand column5: coverage column6: frequency C column7: frequency T

organism: Mus musculus

source_name: E16 full cortex

growth_protocol: dissection of the entire cortex in E16 mice

extract_protocol:
Samples were prepared according to the protocol from the NextFlex kit from Bioo Scientific. An oxidation step was added to remoce 5-hydroxymethylcytosine. Briefly 1 µg of mouse DNA was digested with MSPI (NEB Biolabs) in Buffer 4 at 37°C O/N. Then, the digested DNA was cleaned up with the MinElute® Reaction Cleanup Kit (Qiagen) according to the manufacturer´s instructions. Briefly, 300 µl buffer ERC were added to the MSPI digest, applied to a spin column provided in the kit and centrifugation was performed for 1 minute at 17,900 x g. Then, the column was washed with 750 µl buffer PE, dried by centrifugation for 1 minute at 17,900 x g and the DNA was eluted with 18 µl buffer EB.  DNA concentration was determined with a NanoDrop 2000 spectrophotometer (peqlab). 500 ng of digested and purified DNA were used for the library preparation procedure with the NEXTflex™ Bisulfite Library Prep Kit (BIOO Scientific). Library preparation was performed according to the manufacturer´s instructions with some modifications. Specifically, to avoid any false positives through changes in hydroxymethylation, a DNA oxidation step was included. Briefly, end repair was performed with 500 ng digested, purified DNA in end repair buffer mix and end repair enzyme mix in a total volume of 50 µl. The reaction was incubated at 22°C for 30 minutes and then cleaned up with the MinElute® Reaction Cleanup Kit as described above. Then, 16.5 µl of the eluate were mixed with 4.5 µl of adenylation mix and the reaction was incubated for 30 minutes at 37 °C. Afterwards, 31.5 µl ligation mix and 2.5 µl of individual adapters (diluted 1:2) were added, and adapter ligation was performed for 15´ at 22°C. All control PCR products were ligated to a separate adapter, to avoid any mix up between samples and controls.  Then, a gel free size selection was performed. 44 µl of Agencourt AMPure XP Beads    (Beckman Coulter) were added to the reaction and DNA was allowed to bind to the beads for 5 minutes at RT. Then, the reaction tubes were placed on a magnetic stand and the beads were allowed to be separated from the solution for 5 minutes. Afterwards, the supernatant was discarded and two washes with 200 µl 80 % Ethanol were performed. Then, the beads were allowed to dry for 3 minutes and resuspended in 52 µl resuspension buffer. The beads were incubated for 2 minutes at RT. Then, the reaction tubes were placed on a magnetic stand and the beads were allowed to be separated from the solution for 5 minutes. Then, 50 µl of the supernatant containing the DNA was transferred into a new well, 25 µl Agencourt AMPure XP Beads were added to the reaction and incubated for 5 minutes at RT. Then, the reaction tubes were placed on a magnetic stand and the beads were allowed to be separated from the solution for 5 minutes. Afterwards, 73 µl of the supernatant containing the DNA of interest was transferred into a new well and again 14 µl Agencourt AMPure XP Beads were added to the reaction and incubated for 5 minutes at RT. Then, the reaction tubes were placed on a magnetic stand and the beads were allowed to be separated from the solution for 5 minutes. The supernatant was discarded and two washes with 200 µl 80% Ethanol were performed. Afterwards, the beads were dried for 15 minutes at RT, to ensure that all ethanol had been removed. Then, the beads were resuspended in 25 µl sterile water (Carl Roth) and incubated for 15 minutes at RT. Then, the reaction tubes were placed on a magnetic stand and the beads were allowed to be separated from the solution for 5 minutes.  Afterwards the DNA was prepurified with Micro-Bio-Spin P-6 SCC columns (Bio-Rad) as has been described in [3]. Briefly, 24 µl sample were transferred to a spin column that had been washed with 500 µl sterile water four times. The DNA was purified by centrifugation through the spin column for 8 minutes at 1000 x g at RT. Oxidation was performed as with KRuO4 (Sigma-Aldrich) [4] as has been described by others [3]. First, 21.75 µl DNA were mixed with 1.25 µl extra pure NaOH (Carl Roth) and incubated at 37°C and 300 rpm on a shaking incubator. Then, the DNA was snap cooled on ice for 5 minutes and 20 µl KRuO4 solution (15mM in 0.05 M NaOH) was added. The DNA was oxidized for 1 h on ice, and purified again with Micro-Bio-Spin P-6 SCC columns as described above.  Then, bisulfite conversion of the DNA was performed with the EZ Methylation Gold Kit (Zymo Research) according to the manufacturer´s instructions. Briefly, 130 µl conversion reagent were added to 20 µl oxidized and purified DNA. The reaction was incubated for 10 minutes at  98°C and for 2.5 hours at 64°C. Then, the samples were loaded on spin columns containing 600 µl M-Binding buffer and mixed by inverting. The DNA was bound to the column by centrifugation for 30 seconds at 18620 x g. Then, the column was wahed with 100 µl wash buffer, and 200 µl desulphonation buffer were added. The desulphonation buffer was incubated for 17 minutes at RT, and then removed by centrifugation. The column was washed twice with 200 µl wash buffer, and dried by centrifugation for 10 seconds. Finally, 17 µl elution buffer were added to the column, incubated for 1 minute and  the DNA was eluted by centrifugation.  Afterwards, PCR amplification of the oxidized and bisulfite converted libraries was performed with PfuCx Hot Start (Agilent). 15 µl DNA were amplified with the NEXTflex™ Primer Mix. Cycling conditions were: Initial denaturation for five minutes at 95°C. Then 18 cycles of 95°C for 30 seconds, 65°C for 30 seconds and 72°C for 45 seconds. Afterwards a final extension at 72°C for 7 minutes. The libraries were purified again using AMPure  XP beads (Beckmann Coulter). Finally, quality control with a Bioanalyzer® (Agilent) and sequencing with a HiSeq 1500 sequencer (Illumina Inc.)
RRBS including an oxidation step to remove 5-hydroxymethylcytosine

value: Uhrf1 -/-

tag: age

value: full cortex


title: Uhrf1_Heterozygous_1

value: Uhrf1 +/-


title: Uhrf1_cKO_3


title: Uhrf1_cKO_1


title: MG7 VR_p5_238

data_processing:
Paired end RNA-seq reads were mapped to the mouse genome (mm10) using tophat2 (Kim et al., 2013). Expression of genes in FPKM was calculated with cuffdiff and cummerbund (Trapnell et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Uhrf1_P5_repFpkmMatrix.txt file

source_name: Postnatal  P5 full cortex

growth_protocol: dissection of the entire cortex in P5 mice

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research), Ribozero gold (Illumina MRZG126)
NEB Ultradirectional RNA library prep kit (E7530S)


title: MG6 VR_p5_272


title: MG8 VR_p5_268


title: Uhrf1_Heterozygous_2


title: 235_SHAPEmap_rep2

description:
mRNA
in vitro


title: MG2 VR_p5_230


title: Uhrf1_Heterozygous_3


title: MG5 VR_p5_260


title: MG13_VR_E16_401

data_processing:
Trimming of 3 bases from the 5' end of each read using FastqFilter (Galaxy); Paired end RNA-seq reads were mapped to the mouse genome (mm10) using tophat2 (Kim et al., 2013). Expression of genes in FPKM was calculated with cuffdiff and cummerbund (Trapnell et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Uhrf1_E16VZ_repFpkmMatrix.txt file

source_name: E16 germinal zone of cortex

growth_protocol: dissection of the entire cortex in E16 embryos; further microdissection of the germinal zones:  this involved using a tissue cutter to slice the cortex into several slices and micro dissecting each slice for the germinal zone

extract_protocol:
Trizol and RNA clean and concentrator kit (Zymo research), Clontech -  RiboGone-Mammalian(634846 )
Clontech- SMARTer Stranded RNA-Seq Kit-(634837)

value: germinal zone of cortex


title: WT batch 1 rep3


title: MG14_VR_E16_402


title: MG12_VR_E16_314


title: MG11_VR_E16_303


title: MG10_VR_E16_308


title: MG18_VR_E16_510

data_processing:
Paired end RNA-seq reads were mapped to the mouse genome (mm10) using tophat2 (Kim et al., 2013). Expression of genes in FPKM was calculated with cuffdiff and cummerbund (Trapnell et al., 2013).
Genome_build: mm10
Supplementary_files_format_and_content: Uhrf1_E16_repFpkmMatrix.txt file


title: MG19_VR_E16_514


title: MG9_VR_E16_310


title: MG17_VR_E16_506


title: MG15_VR_E16_468


title: GS26-Homo_prog_5hmC

data_processing:
reads were mapped to the mouse genome (mm10) using bowtie (Langmead et al., 2009)
bedgraph files were generated from homer tag directories using makeUCSCfile
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph file

growth_protocol: dissection of the ventricular zone in E16 embryos

extract_protocol:
Isolation of genomic DNA
NEBNext Ultra DNA library preparation kit


title: WT batch 1 rep4


title: GS23-Het_prog_5hmC


title: GS24-Homo_prog_input


title: GS21-Het_prog_input


title: MG1 VR_p5_231


title: Replacement tooth rep5

city: Los Angeles

first: Ping

last: Wu

state: CA

address: 2011 Zonal Ave HMR313A

department: Pathology

institute: University of Southern California

data_processing:
Read alignment was performed using Partek Flow version 3
We used Tophat2 2.1.0 to perform alignment
Partek Genomic Suite (version 6.6) was used for RNA-seq read quantification, normalization and differentially expressed analysis
Genome_build: American alligator genome allMis1
Supplementary_files_format_and_content: RPMK

organism: Alligator mississippiensis

source_name: Replacement tooth

growth_protocol: Lab raised animal at 30 degree

extract_protocol:
Dissected tissue were extracted in Trizol reagent
Libraries were prepared using Illumina TruSeq RNA Sample Preparation V2

treatment_protocol: untreated

value: one year old

tag: tooth cycle stage

value: Pre-initiation stage

tag: number of replicates


title: 10DAG-CKX rep2

city: Olomouc

first: Veronique

last: Bergougnoux

address: Slechtitelu 27

department: Molecular Biology

country: Czech Republic

institute: CRH/UPOL

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Hordeum vulgare v.25 (Ensembl) barley genome using TopHat with default parameters
Reads were quantified by HTSeq v.0.6.0; Differential expression was determined using DESeq2 package in R.
Genome_build: Hordeum vulgare v.25 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include count of reads mapped on each genes for each Sample.

organism: Hordeum vulgare

growth_protocol: sterilization of grains: 30 sec in 70%EtOH; 3 rinses in H2O; 3 min in 5% sodium hypochloride; extensive washes in H2O. Sowing on wet filter paper. Incubation for 2 days at 4C in the dark. Germination in long photoperiod. Growth in hydropony for 10 days.

extract_protocol:
stem bases (2 mm) were excised from the rest of the seedling, frozen in liquid nitrogen. Total RNA was extracted using ZR Plant RNA kit (Zymo Research). Illumina TruSeq RNA sanple prep kit was used with 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: AtCKX1-overexpressing line

tag: development stage

value: 10 days after germination

value: stem base (crown)


title: 10DAG-CKX rep3


title: Replacement tooth rep4


title: 10DAG-CKX rep1


title: Replacement tooth rep3


title: 1DAG-CKX rep3

value: 1 day after germination


title: MG16_VR_E16_466


title: 1DAG-CKX rep2


title: Replacement tooth rep2


title: BY4741_Control_1

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description: rRNA depleted total RNA

data_processing:
Library strategy: ChemModSeq
Base calling was performed using the software provided by Illumina
Adapter sequences (AGATCGGAAGAGCACACG) were trimmed using flexbar version 2.5. Following trimming, one nucleotide was removed from the 5' end of the forward read and the reads were collapsed by pyFastqDuplicate remover from the pyCRAC package (Webb et all, Genome Biology 2014) using the random barcode information present in the 5' adapter sequences.
Collapsed reads were mapped to the yeast genome version R64 (ENSEMBL) using novoalign. To generate the processed sgr data files, pyReadCounters was used count the number of reads overlapping with genomic features followed by conversion of the resulting GTF files to sgr files using pyGTF2sgr (using the --count and --zeros flags)
The sgr files with posterior probabilities were generated using the BUM_HMM pipeline. The R code can be downloaded from: https://sgrann@bitbucket.org/aselega/pipeline.git
Genome_build: R64
Supplementary_files_format_and_content: All files are in sgr format which contains at least three colomns with (1) chromosome name, (2) location on chromosome and (3) number of reads / RT dropoff-counts mapping that position. The merged.sgr data contain the counts for all samples.

source_name: rRNA depleted RNA isolated from culture_BY4741_control

growth_protocol: S.cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) or YPG/R (YP with 2% Galactose and 2% Raffinose) at 30ºC.

extract_protocol:
Cells were pelleted and total RNA was extracted using Gunanidium thiocyanate and phenol-chloroform method as previously described (Tollervey 1987, EMBO Journal). Ribosomal RNA was depleted usign the Illumina RiboZero kit for yeast, according to the manufactuer's procedures.
cDNA libraries were generated from purified ribosomal RNA using an RT oligonucteotide containing random hexamers (SuperScript III, Invitrogen). 5' adapters were ligated on (CircLigase II, EpiCentre) and 3' adaptors generated during PCR amplification.
Random primer used: 5’- CGTGTGCTCTTCCGATCT NNN NNN-3’
reverse transcription primer: 5'-AGATCGGAAGAGCACACG-3'
Adapters ligated to cDNAs: P5_RAND_Barcode_IDX1_phospho_adapter: 5’P-N  cgt gat NNN NNN AGA TCG GAA GAG CGT CGT GTA GGG -ddC-3’
Adapters ligated to cDNAs: P5_RAND_Barcode_IDX2_phospho_adapter: 5’P-N aca tcg NNN NNN AGA TCG GAA GAG CGT CGT GTA GGG -ddC -3’
Adapters ligated to cDNAs: P5_RAND_Barcode_IDX3_phospho_adapter: 5’P-N gcc taa NNN NNN AGA TCG GAA GAG CGT CGT GTA GGG -ddC -3’
Adapters ligated to cDNAs: P5_RAND_Barcode_IDX4_phospho_adapter: 5’P-N tgg tca NNN NNN AGA TCG GAA GAG CGT CGT GTA GGG -ddC -3’
PCR oligonucleotides: P5_Forward: 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’
PCR oligonucleotides: BC1: 5′-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3'
PCR oligonucleotides: BC6: 5′-CAAGCAGAAGACGGCATACGAGATATTGGCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′
All libraries were 50bp paired-end sequenced on a HiSeq 2500

treatment_protocol: Cells were harvested, washed with phosphate buffer saline (PBS), resuspended in 1 volume PBS and incubated with NAI (100 mM final concentration) or solvent (DMSO; 5% final) for ten minutes at room temperature with constant agitation.


title: BY4741_NAI_1

description: rRNA depleted total RNA

source_name: rRNA depleted RNA isolated from culture_BY4741_NAI


title: BY4741_NAI_2

description: rRNA depleted total RNA


title: BY4741_Control_2

description: rRNA depleted total RNA


title: csoR_1

city: Madison

first: Adel

middle: M

last: Talaat

state: WI

address: 1656 Linden Dr.

department: Pathobiological Sciences

institute: UW-Madison

description: rRNA depleted RNA

data_processing:
Base-calling was done with CASAVA-1.8.2
Reads were trimmed and filtered for quality using FASTX-Toolkit in Galaxy
Filtered reads were mapped to the M. tuberculosis H37Rv genome using Bowtie in the web-based Galaxy platform.  Parameters were n = 2; l = 50; v = 2; m = 1; s = 15 with all others left as default.
Raw counts were generated from the mapped files using BedTools in Galaxy requiring a 51% overlap for mapping reads to be counted.
Raw counts were then normalized to TMM and differential expression levels were determined using edgeR.
Genome_build: Mycobacterium tuberculosis H37Rv, complete genome VERSION NC_000962.2
Supplementary_files_format_and_content: csoR_DGE.txt, tab delimited: C1-locus tags; C2-H37Rv wild type biological replicate 1 counts per million (CPM); C3-H37Rv wild type biological replicate 2 CPM; C4-ΔcsoR biological replicate 1 CPM; C5-ΔcsoR biological replicate 2 CPM; C5-log fold change; C6-log CPM; C7-P-value; C8-False discovery rate

organism: Mycobacterium tuberculosis

source_name: Bacterial culture

growth_protocol: Cultures were grown in 30ml Sauton's medium with 0.05% Tween at 37C until cultures reached late log phase (OD600 ~ 1.0)

extract_protocol:
Cultures were pelleted and resuspended in cold Trizol before mechanical lysis using a bead beater followed by standard Trizol based extraction. Samples were treated with Turbo DNAse (Ambion) and rRNA depleted using the Ribo-Zero™ Magnetic Kit for bacteria (Epicentre)
Final RNA samples were submited to the UW-Madison Biotechnology Center DNA Sequencing Facility where libraries were constructed following a standard Illumina protocol with the TruSeq RNA Sample Preparation Kit

treatment_protocol: Before inoculation into copper free Sauton's media, all inoculums were washed 2x with copper free Sauton's media to remove traces of copper present in the previous growth medium (7H9).

value: H37Rv delta-csoR

tag: culture conditions

value: Copper depleted Sauton's medium


title: H37Rv_2

description: rRNA depleted RNA


title: H37Rv_1

description: rRNA depleted RNA


title: 1DAG-CKX rep1


title: Dental lamina Early Growth stage rep4

source_name: dental lamina


title: 10DAG-GP rep3

value: wild-type cv. Golden Promise


title: 10DAG-GP rep2


title: csoR_2

description: rRNA depleted RNA


title: Dental lamina Early Growth stage rep3


title: Dental lamina Early Growth stage rep2


title: 10DAG-GP rep1


title: 1DAG-GP rep3


title: Dental lamina Early Growth stage rep1


title: 1DAG-GP rep2


title: Dental lamina Initiation stage rep2


title: 1DAG-GP rep1


title: Dental lamina Initiation stage rep1


title: Dental lamina Pre-initiation stage rep5


title: P1-2

city: Guangzhou

first: OuYang

last: Hongjia

state: Guangdong

address: Wushan street 483

department: College of Animal Science

country: China

institute: South China Agricultural University

description: RNase R treated and ribo- RNAs

data_processing: Sequenced reads were assemblyed by Cufflinks, and mapped to chicken genome using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml) and Tophat (Trapnell et al., Bioinformatics, 2009).

organism: Gallus gallus

source_name: leg muscle

extract_protocol:
Total RNAs were isolated by Trizol reagent (Invitrogen) and then treated with DNase (Promega) following the manufacturer’s instructions.
Total RNA samples (5 μg) were treated with the ribo-zero-magnetic-kit (Epicenter) to remove rRNA, and then digested with 20 U of RNase R (RNR07250, Epicenter). RNA-seq libraries were prepared using the TruSeq® RNA LT Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions.

value: 1 days post hatch

tag: breeds

value: Xinghua chicken

tag: Sex

value: female


title: P1-1

description: RNase R treated and ribo- RNAs


title: Dental lamina Pre-initiation stage rep4


title: Dental lamina Pre-initiation stage rep3


title: E16-1

description: RNase R treated and ribo- RNAs

value: 16 embryo age


title: Dental lamina Pre-initiation stage rep2


title: E16-2

description: RNase R treated and ribo- RNAs


title: E11-2

description: RNase R treated and ribo- RNAs

value: 11 embryo age


title: HH23-R

status: Public on Oct 31 2016

city: Montpellier cedex 5

first: Elsa

last: Ballini

address: UMR BGPI – TA A-54/K – Equipe ICAP campus International de Baillarguet

department: Biology and ecology

country: France

institute: SupAgro Montpellier

data_processing:
Quality control of raw sequence
Alignment with reference genome (Kasalath or Magnaporthe v8) using SOAPAligner and SOAP2
Read count and RPKM per gene was measured with NOIseq
Data were filtered for low expressed genes (<5reads in threee repetition)
Genome_build: Rice reference genome Kasalath http://rice50ks.dna.affrc.go.jp/, Magnaporthe reference genome vMG8 http://fungi.ensembl.org/Magnaporthe_oryzae/Info/Index
Supplementary_files_format_and_content: There are 5 columns in each txt file and meanings of each column as follows: GeneID (in genome reference), Uniq_reads_num (number of reads which aligned to just one position on gene,  Length (length of gene coverage calculating :the base number of all Uniq_reads in the gene/the base number of gene),  rpkm (expression analysis using NOIseq)
Supplementary_files_format_and_content: See supplementary files (Official_Kasalath_database.txt, kasalath_cuffmerge.gff) for rice gene mapping details.

organism: Oryza sativa

source_name: Shoot tissues

growth_protocol: Seeds of Oryza sativa, cv. Kasalath were sown in Neuhaus S soil in which poudzolane was added (2L/70L1N). A routine fertilization solution containing nitrogen source and corresponding to a ratio of 75% NO3-/25% NH4+ (1N condition) was supplied every Monday for 3 weeks; 28 days after sowing, we supplied on Monday either our routine fertilization solution (NO3-/NH4+) 1N or the same solution without nitrogen source and corresponding to the 0N condition. This fourth fertilization was done 1 day before inoculation.

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer's instructions. It was treated with RNase-free DNase according to manufacturers's instructions (Promega) to remove residual DNA.
cDNA library construction and paired-end sequencing was performed by BGI using an Illumina HiSeq™ 2000 platform according to the manufacturer’s instructions

treatment_protocol: Plants were inoculated either with Magnaporthe oryzae isolate Guy11 spore suspensions at 150000 spore/ml or with a mock solution corresponding to the solution into which spores are re-suspended (ie 0,5% gelatin solution).

tag: nitrogen treatment

tag: magnaporthe inoculation

value: Guy11 inoculated

tag: timing

value: 2 dpi

tag: sequencing depth


title: HH20-R


title: HH21-R


title: HH19-R

value: Mock inoculated


title: HH13-R


title: Dental lamina Initiation stage rep3

value: one year old


title: HH17-R


title: HH14-R


title: HH12-R


title: Replacement tooth rep1

value: Pre-initiation stage


title: HH11-R


title: HH08-R


title: HH10-R


title: SirA - ChIP-exo

city: Gainesville

first: Anastasia

middle: Haley

last: Potts

state: FL

address: 1355 Museum Drive, Bldg. 981

department: Department of Microbiology and Cell Science

institute: University of Florida

data_processing:
Library strategy: ChIP-exo
Peconic LLC performed data processing
ChIP-exo reads were aligned using BWA with  default parameters
Peaks were called with GeneTrack 1.0.3 (s=5, e=10)
Peaks on opposing strands were paired with Genetrack (u=0, d=80, b=2, m=mode)
Singleton peaks (standard deviation =0) and peaks without matched peaks on the opposing strand where discarded
Genome_build: NC_000913.3
Genome_build: NC_016856.1
Supplementary_files_format_and_content: Bedgraphs files representing the extracted peak data
Supplementary_files_format_and_content: chromosome chromosomeStartPosition chromosomeStopPosition readCoverage(positive values on + strand, negative on - strand)

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: SirA (Response regulator of the BarA/SirA two-component system)

growth_protocol:
E. coli cells were grown in Kornberg medium (1.1% [wt/vol] K2HPO4, 0.85% [wt/vol] KH2PO4, 0.6% [wt/vol] yeast extract containing 0.5% [wt/vol] glucose) to mid-exponential phase (OD600 = ~0.6) at 37C and shaking 250rpm
S. Typhimurium cells were grown in LB (supplemented with 10mM glucose) to mid-exponential phase (OD600 = ~0.6) at 37C and shaking 250rpm

extract_protocol:
E. coli and S. Typhimurium cells (at mid-exponential growth phase) were fixed with formaldehyde (1% final concentration) for  20 min at 30°C with shaking. The crosslinking reaction was then quenched by the addition of glycine (0.33M final concentrationg) for 5 minutes at room temperature with gentle mixing.  Cells where then lysed on ice with lysozyme and sonication.
Samples were used for on-bead enzymatic reactions of the ChIP-exo procedure and Illumina Tru-seq sequencing libraries were construction as described in Rhee and Pugh, 2012

tag: chip antibody

value: Monoclonal anti-FLAG antibody, Murine IgG

tag: chip antibody manufacturer/lot#

value: Sigma-Aldrich, M8823-1ML, Lot #  SLBD7244V


title: HH06-R

value: Before inoculation

value: 0 dpi


title: HH03-R


title: HH04-R


title: HH02-R


title: HH05-R


title: Dental lamina Pre-initiation stage rep1


title: HH01-R


title: E11-1

description: RNase R treated and ribo- RNAs


title: HH18-R


title: Pi9.ZH10.24.1-RNAseq

city: Beijing

first: Mengdi

last: Liu

address: No.38 Xueqing Road, Haidian District

institute: Novogene institute

data_processing:
For mRNA RNA-Seq data, TopHat for mapping, HTSeq for estimating their abundances
Genome_build: Reference genome sequences and annotations were downloaded from the rice genome website .(ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/pseudomolecules/version_7.0/).
Supplementary_files_format_and_content: The rpkm.txt.gz files include abundance measurements (RPKM values) for each mRNA RNA-Seq sample.

source_name: leaf

growth_protocol: Rice seedlings were grown in 32°C day 16 hours and 28°C night 8 hours in greenhouse. Four-week seedlings were used for pathogen inoculation.

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Life Technologies) and treated with RNase-free DNase I (Takara) to remove any contaminating genomic DNA.
mRNA extraction was performed using Dynabeads oligo(dT) (Dynal; Invitrogen Corp.). Double-stranded cDNAs were synthesized using reverse transcriptase (Superscript II; Invitrogen Corp.) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries.

treatment_protocol: Four-week seedlings were subjected to spray inoculation with conidial suspensions (for each strain) of 2.5 × 105 conidia/ml (suspended in 0.25% gelatin solution). For the mock control, the conidial suspensions were replaced with 0.25% gelatin solution. The inoculation was carried out under controlled conditions at 28℃ and 100% relative humidity for 24 h in darkness, then shifted to a 16/8 h light/dark regime.

tag: tissue

value: leaf

value: 4 weeks old

tag: inoculation type

value: Zhong inoculation

tag: phenotype

value: resistant

tag: interaction

value: incompatible


title: Pi9.mock.24.2-RNAseq

tag: age

value: inoculation without pathogen

value: no change

value: no interaction


title: Pi9.ZH10.24.2-RNAseq


title: Pi9.mock.24.1-RNAseq


title: Pi9.ZB13.24.2-RNAseq

value: ZB13 inoculation


title: Pid3.ZH10.24.2-RNAseq


title: Pid3.mock.24.1-RNAseq


title: Pid3.ZB13.24.1-RNAseq

value: susceptible

value: compatible


title: Pid3.mock.24.2-RNAseq


title: Pid3.ZB13.24.2-RNAseq


title: Pi9.ZH10.16.1-RNAseq


title: Pi9.ZH10.16.2-RNAseq


title: Pid3.ZH10.16.2-RNAseq


title: Pi9.mock.16.2-RNAseq


title: Pi9.mock.16.1-RNAseq


title: Pid3.ZH10.24.1-RNAseq


title: Pi9.ZB13.16.1-RNAseq


title: Pid3.ZH10.16.1-RNAseq


title: Pi9.ZB13.16.2-RNAseq


title: Pid3.ZB13.16.1-RNAseq


title: Pid3.mock.16.2-RNAseq


title: Pid3.mock.16.1-RNAseq


title: Pi9.ZH10.8.2-RNAseq


title: Pi9.ZB13.24.1-RNAseq


title: Pi9.ZH10.8.1-RNAseq


title: Pi9.ZB13.8.1-RNAseq


title: Pi9.ZB13.8.2-RNAseq


title: Pi9.mock.8.2-RNAseq


title: Pi9.mock.8.1-RNAseq


title: Pid3.ZH10.8.2-RNAseq


title: Pid3.ZB13.8.1-RNAseq


title: Pid3.mock.8.1-RNAseq


title: Pi9.ZH10.0.2-RNAseq


title: Pid3.ZB13.8.2-RNAseq


title: Pid3.mock.8.2-RNAseq


title: B2 SINE-seq replicate 1

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

description: B2 SINE RNA

data_processing:
Sequenced on Miseq, base called with CASAVA 1.9
Alignment was done using bwa against mouse mm10 reference genome
Reads mapping to known B2 SINEs in repeatmasker track were counted and normalized RPKM values were computed using BamUtil
Genome_build: mm10
Supplementary_files_format_and_content: text file with counts and normalized RPKM values.

source_name: NIH 3T3_MHV68

extract_protocol:
Total RNA was isolated with Trizol.
200 μg total RNA was primer extended using an oligonucleotide specific for B2 SINEs. Primer extension products were resolved on 8% polyacrylamide–7 M urea gels. For isolation of B2 products, the region of the gel corresponding to 130bp – 180 bp was isolated and placed in a 10 mL polypropylene tube containing 5 mL of G50 buffer (20 mM Tris-HCl, 300 mM NaCl, 2 mM EDTA, 0.2% SDS), flash frozen in liquid N2, and allowed to incubate overnight at RT. The following day the G50 buffer containing the isolated B2 products was phenol-chloroform extracted and ethanol precipitated. The B2 extension products were further 3’ poly dG-tailed using 20 U of terminal deoxynucleotidyl transferase (TDT, Fermentas) and 0.25 mM dGTP. After 3’ poly dG-tailing, the cDNAs were used as templates for 10 cycles of PCR amplification using an oligoC and B2 extension oligo that contained barcoded sequencing adapters.

treatment_protocol: Cells were infected with MHV68 at an MOI of 5 for 1 hr. Following infection cells were washed with 1X PBS and then growth media was replaced and cells were allowed to grow for an additional 24 hr.

tag: cell line

value: NIH 3T3


title: Pid3.ZB13.0.2-RNAseq


title: Pi9.ZH10.0.1-RNAseq


title: Pid3.mock.0.2-RNAseq


title: Pid3.ZH10.0.2-RNAseq


title: Pi9.ZB13.0.2-RNAseq


title: Pid3.mock.0.1-RNAseq


title: Pi9.mock.0.1-RNAseq


title: Pi9.ZB13.0.1-RNAseq


title: Pid3.ZH10.0.1-RNAseq


title: Pid3.ZB13.0.1-RNAseq


title: B2 SINE-seq replicate 2

description: B2 SINE RNA


title: Pi9.mock.0.2-RNAseq


title: 3658-A-0

city: beltsvill

first: jiajie

last: sun

state: MD

address: 10300 BALTIMORE AVENUE

department: Agriculture research sevice

institute: U.S. department of agriculture

description: Control 4

data_processing:
Eight libraries were subjected to single-end sequencing in 36 nt reads using an Illumina Genome Analyzer II. Preliminary quality control analysis of the 8 fastq files was carried out with FASTQC software v0.10.0 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Subsequently, a Perl script (Adapter_trim.pl, http://122.228.158.106/mr2_dev/start_filter.php) was used to filter low quality short reads, remove polyA, trim 3'/5' adapter, and format into a non-redundant fasta file. The occurrence of each unique sequence read was counted as sequence tag and the number of reads for each tag reflected its relative expression level. All unique sequence tags that passed through above filtering criteria were mapped onto the bovine genome assembly (ftp://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/bigZips/bosTau6.fa.gz) using the SOAP program. Then, these uniquely mappable reference genome tags were also aligned against Rfam v11.0, miRBase v19.0, repeat database produced by RepeatMasker (http://www.repeatmasker.org) and the coding genes of the reference genome (http://hgdownload.cse.ucsc.edu/goldenPath/bosTau6/ bigZips/refMrna.fa.gz). In this way, the unique sequence tags can be classified into the following categories: degradation fragments of non-coding RNA, known miRNA, genomic repeats and mRNA. Sequences that were assigned to none of these annotations but can be mapped to the reference genome were classified as ‘unknown’. This approach will hereafter be referred to as ‘BGI-method’. We also used a second method named ‘miRDeep2-method’ for data processing as previously described, with some improvements. Firstly, Cutadapt v1.3 (http://code.google.com/p/cutadapt/) was used to trim 3'/5' adaptor sequences, and reads less than 18 nt were thrown out. Trimmed reads were then further filtered using Sickle (https://github.com/najoshi/sickle/) to remove low quality sequences had a quality value < 20. Finally, Reads which successfully passed filtering were aligned to the bovine miRBase v19.0 using miRDeep v2.0.0.5 with a Perl script ‘quantifier.pl’.
Genome_build: bosTau6
Supplementary_files_format_and_content: Text files include count values for each identified miRNAs

organism: Bos taurus

source_name: bovine breast milk_prior to infection

extract_protocol:
Total RNA and small RNA were extracted from each of the 8 exosomal samples using the mirVanaTM miRNA Isolation Kit (Life Technologies, Carlsbad, CA, USA).  Procedures were performed according to the manufacturer’s protocol.
Then 8 indexed small RNA libraries were prepared using the ScriptMinerTM Small RNAseq Library Preparation Kit (Epicentre, Madison, WI, USA).

tag: breed

value: US Holstein

value: mid-lactation cows

tag: infected with

value: none (control)

tag: time point

value: prior to infection

value: bovine breast milk

tag: molecule subtype

value: exosomal small RNA


title: 3504-A-0

description: Control 3


title: 3658-A-2

description: Infection 4

source_name: bovine breast milk_S aureus_2 dpi

value: Staphylococcus aureus

value: 2 days post-infection


title: 3206-A-2

description: Infection 1


title: 3207-A-2

description: Infection 2


title: 3504-A-2

description: Infection 3


title: 3206-A-0

description: Control 1


title: 3207-A-0

description: Control 2


title: Pid3.ZH10.8.1-RNAseq

value: leaf

value: 4 weeks old

value: Zhong inoculation

value: resistant


title: Sample_UHRR3

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

institute: University of Pennsylvania

data_processing:
For bulk samples and those generated with C1 SMARTer, BaseSpace Fastq generation algorithm was used for base calling (Illumina). For aRNA and Nugen Ovation samples,  Casava 1.8.2 was used.
For diluted HBR and UHR samples: Low confidence nucleotides (with Phred score less than 20) were treated as unknown and replaced with Ns. Unknown nucleotides (Ns) at the ends of reads were trimmed. Poly-A and method-specific adapter sequences were trimmed from the 3’ end of reads using in-house software. Reads were aligned to the human reference genome, build hg19, and to ERCC spike-in transcript sequences using STAR (Spliced Transcripts Alignment to a Reference) aligner version 2.4.0. We provided STAR with GENCODE18 annotations to generate a splice-junction loci database for use in alignment. We retained reads that aligned to at least 40% (paired-end) or 60% (single-end) of trimmed length or 30bp, whichever was greater. In addition, we discarded reads with greater than 30% mismatched positions in trimmed length.
For diluted HBR and UHR samples: Uniquely aligned reads were assigned to GENCODE18 gene annotations and to ERCC transcripts using HTSeq and htseq-counts. Reads overlapping multiple annotations were assigned to a single gene or discarded using the intersection non-empty method.
For bulk HBR and UHR samples: raw sequencing data from all three ribosome-depleted bulk HBR or UHR replicates were pooled resulting in a single sample for each HBR and UHR. Sequencing characteristics of bulk RNA sequencing are relatively well known and we used a model theoretic method to estimate reference gene expression, as implemented in RSEM (RNA-seq by Expectation-Maximization, version 1.2.18, using Bowtie version 1.1.1) strand-specific quantification. Poly-A tails were not added to transcripts. RSEM gene abundances were normalized to transcripts per million (TPM).
Genome_build: hg19
Supplementary_files_format_and_content: [txt.gz] htseq abundance measurements: tab-delimited text files with raw counts
Supplementary_files_format_and_content: [RSEM.gz] RSEM abundance measurements: tab delimited text files including gene abundance estimates as generated by RSEM

source_name: Universal Human Reference

extract_protocol: Illumina TruSeq stranded Total RNA

tag: amount of starting rna

value: Bulk

tag: ercc spike-in dilution used

tag: single-cell amplification protocol used


title: Sample_UHRR2


title: Sample_UHRR1


title: Sample_BRAIN2

source_name: Human Brain Reference


title: Sample_BRAIN1


title: SIOD-Kidney-RNA

city: Vancouver

first: Cornelius

middle: F.

last: Boerkoel

state: British Columbia

address: 950 West 28th Avenue

department: Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
Base-calling was performed using SAMtools v0.1.18 (default option)
RNA-seq reads were aligned to the hg19 genome assembly using TopHat v1.3.3 (default option)
Transcript assembly and generation of normalized abundance measurements were performed by Cufflinks v2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes FPKM values for both samples

source_name: Kidney

extract_protocol:
Total RNA was extracted from flash frozen kidney pulverized with a Bessman tissue pulverizer (Spectrum Laboratories) by using the RNeasy Mini Kit (Qiagen). Genomic DNA was removed by on-column DNase I digestion (Qiagen).
cDNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA Library Prep Kit using standard Illumina protocols.

tag: siod disease status

value: Affected

value: 5.4 years

tag: Sex

value: Male


title: Control-Kidney-RNA

value: Unaffected

value: 3.0 years


title: HH23-M

organism: Pyricularia oryzae

tag: nitrogen treatment

tag: magnaporthe inoculation

value: Guy11 inoculated

tag: timing

value: 2 dpi

tag: sequencing depth


title: BM clone_3

city: Boston

first: Aldo

last: Roccaro

state: MA

address: 450 Brookline Av

institute: Dana-Farber Cancer Institute

description: bone marrow clone obtained after in vivo selection

data_processing:
We used Bcbio_nextgen (https://github.com/chapmanb/bcbio-nextgen/) to process the RNA-seq data. Briefly, cutadapt (https://github.com/marcelm/cutadapt/) was used to trim adapters; trimmed reads were aligned to Human reference genome (GRCh37) with tophat2; read count for each gene was calculated by HT-seq. Genes with low expression (FPKM < 1 across all samples) were filtered out. GSEA was used to identify differentially expressed mRNA signatures, with false discovery rate (FDR) <0.25 and P value <0.05.
Genome_build: GRCh37
Supplementary_files_format_and_content: RPKM files

source_name: Bone marrow prone clone

growth_protocol: BM-prone and EMD-prone MM cell lines were developed by serial in vivo selection.

extract_protocol:
Total RNA was isolated from EMD-prone and BM-prone cell lines using RNeasy Mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols
poly-A selection and cDNA synthesis were performed, followed by library preparation using Illumina TruSeq RNA Sample Prep Kit, sequencing (75bp paired reads), and sample identification for quality control.

tag: cell type

value: multiple myeloma bone marrow prone clone


title: HH20-M


title: HH13-M


title: HH21-M


title: parental_1

description: parental cell line

source_name: MM cells parental

value: multiple myeloma


title: EMD clone_2

description: extra medullary clone obtained after in vivo selection

source_name: Extra medullary prone clone

value: multiple myeloma extra medullary prone clone


title: parental_3

description: parental cell line


title: BM clone_2


title: parental_2

description: parental cell line


title: BM clone_1


title: EMD clone_3


title: HH12-M


title: Ct M1570 15 g/L xylose-4

city: Oak Ridge

first: Dawn

middle: Marie

last: Klingeman

address: 1 Bethel Valley Rd building 15056 Rm 366  MS 6038

department: Biosciences Division

institute: Oak Ridge National Lab

data_processing:
Basecall files and fastq files were created on the MiSeq instrument during the sequencing run using  MiSeq Real Time Analysis (RTA v 1.18.54.0) software and the MiSeq Reporter (MSR v 2.5.1.3).
RNAseq reads were aligned to the C. thermocellum DSM1313 (NC_017304.1) genome assembly using Fastq files imported into the CLCBio RNA-sequencing pipeline. Default settings were used for mismatch, insertion, and deletion costs.
Total gene counts from the CLCBio mapping were used for DESeq2 analysis to normalise and determine significant gene expression differences
Genome_build: ASM18492v1
Supplementary_files_format_and_content: Tab deliminated file includes read counts for each gene across the 8 samples used in this study
Supplementary_files_format_and_content: DESeq2 with 5%FDR. Data provided as log2(15g/L - 0 g/L)

organism: Acetivibrio thermocellus

source_name: CtM1570 growth in bottles

growth_protocol: Anaerobic, sterile MTC medium containing 5 g/L cellobiose was prepared either without (control) or with (experimental) 15 g/L xylose. A mid-exponential phase (OD600=0.467) culture of Clostridium thermocellum M1570 was used to inoculate (5%; v/v) replicate serum bottles for each condition. Forty mL cultures in quadruplicate were grown at 55°C without shaking. Upon reaching an average OD600 of 0.494 ± 0.028 or 0.324 ± 0.006, representative of mid-point exponential growth for the control and experimental condition respectively, cell pellets were harvested for RNA-Seq analyses.

extract_protocol:
Cells pelleted from a 40 mL sample from each bottle were resuspended in 2 mL of TRIzol (Invitrogen, CA). A 1 ml aliquot of the TRIzol cell suspension was used for cell lysis by bead beating with 0.8 g of 0.1mm glass beads (Biospec Products) with 3 X 20 s bead beating treatments at 6,500 rpm in a Precellys 24 high-throughput tissue homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France). The RNA from each cell lysate was purified and DNaseI treated using the Qiagen RNeasy kit. The RNA quantity and quality assessed by Nanodrop and Bioanalyzer respectively. Purified RNA was depleted of rRNA using the Ribo-Zero rRNA Removal kit for Gram Positive Bacteria (Epicentre/Illumina). The sample was then concentrated with RNA Clean & Concentrate-5 (Zymo Research, CA) following the manufacturer’s protocol.
Depleted RNA was used as the starting material for the Epicentre ScriptSeq™ mRNA-Seq Library preparation kit (Illumina compatible) utilising Epicentres Fail Safe PCR Enzyme mix (Epicentre, WI) and following the manufacturer’s protocol. cDNA, tagged with ScriptSeq adaptors (1-12), was eluted with 20 µl of Buffer EB provided in the Min-Elute PCR purification kit (Qiagen) according to the ScriptSeq™ mRNA-Seq Library preparation kit protocol. Twelve PCR cycles were used during library amplification and samples were purified using the Min-Elute PCR purification kit and eluted with 20 µl of buffer EB. The final mRNA Seq library was quantified with a Qubit Fluorometer (Invitrogen, CA) and library quality was assessed with an Agilent Bioanalyzer DNA Chip (Agilent, CA). Samples were pooled to make a stock of 6 nM.  The Library pool was further diluted and then denatured according to manufactures protocols.  Paired end sequencing was completed (2 x 251 + 6 bp barcode(508 cycles in total)) on an Illuimina MiSeq instrument.

treatment_protocol: Cultures were grown in the absence (control condition) or presence of 15 g/L xylose (experimental condition).

tag: treatment

value: 15 g/L xylose

tag: strain


title: Sample_BRAIN3


title: Ct M1570 15 g/L xylose-1


title: Ct M1570 0 g/L xylose-3

value: 0 g/L xylose


title: Ct M1570 15 g/L xylose-2


title: Ct M1570 0 g/L xylose-4


title: Ct M1570 0 g/L xylose-2


title: Sample_HBR10pg-10

description: optimizationCounts.txt.gz

extract_protocol: Illumina TruSeq stranded, modified to begin with amplified aRNA (15 PCR rounds, input all amplified product)

value: 10 pg

value: aRNA (first round:use 0.691mM dNTPs in 2nd strand rxn. & no minelute; 2 rounds only)


title: Sample_HBR10pg-9

description: optimizationCounts.txt.gz


title: Ct M1570 0 g/L xylose-1


title: EMD clone_1


title: Sample_HBR10pg-8

description: optimizationCounts.txt.gz


title: Sample_HBR10pg-6

description: optimizationCounts.txt.gz


title: Sample_HBR10pg-7

description: optimizationCounts.txt.gz


title: Ct M1570 15 g/L xylose-3


title: Sample_TPM5b

description: optimizationCounts.txt.gz

extract_protocol: Illumina TruSeq stranded, modified to begin with amplified aRNA (15 PCR rounds)

value: aRNA


title: Sample_TPM6b

description: optimizationCounts.txt.gz


title: Sample_TPM1b

description: optimizationCounts.txt.gz

value: aRNA (first round:use 0.691mM dNTPs in 2nd strand rxn. & no minelute)


title: Sample_TPM8b

description: optimizationCounts.txt.gz

extract_protocol: Illumina TruSeq stranded, modified to begin with amplified aRNA (10 PCR rounds)


title: Sample_TPM1

description: optimizationCounts.txt.gz

extract_protocol: Illumina TruSeq stranded, modified to begin with amplified aRNA


title: Sample_TPM2

description: optimizationCounts.txt.gz


title: Sample_TPM2b

description: optimizationCounts.txt.gz


title: Sample_RD-NRW24T10-H100-2

description: counts.txt.gz

extract_protocol: Nugen Ovation Rapid (100ng input)

value: Nugen Ovation RNASeq V2 (0.25X volume, +10 min.)


title: Sample_TPM7b

description: optimizationCounts.txt.gz


title: Sample_RD_NRW24T10_H100_7

description: counts.txt.gz


title: Sample_RD-NRW24T10-H100-1

description: counts.txt.gz


title: Sample_TPM7a

description: optimizationCounts.txt.gz

extract_protocol: Illumina TruSeq stranded, modified to begin with amplified aRNA (8 PCR rounds)


title: Cell__number_1

city: Heidelberg

first: Ana

last: Martin-Villalba

state: Deutschland

address: Im Neuenheimer Feld 280

department: Molekulare Neurobiologie (A290)

institute: German Cancer Research Center (DKFZ)

data_processing:
Basecalls performed using RTA 1.18.64
Before alignment, adapter sequences in raw reads were trimmed by Btrim64 (http://graphics.med.yale.edu/trim)
Trimmed reads were mapped to mouse genome (ENSEMBL Release 80) using STAR_2.4.2a.
Expression level of each gene was quantified in unites by transcript per million (TPM) and fragments per kilobase of transcript per million fragments mapped (FPKM) using RSEM 1.2.21 with default parameters.To compare expression levels of different genes across samples, we performed an additional TMM (trimmed mean of M-values) normalization on TPM using Trinity9 (http://trinityRNA-seq.github.io/) based on edgeR (abbreviated TMM-TPM). The purpose of this normalization is to account for differences in total cellular RNA production across all cells.
We developed custom R scripts based on FactoMineR library (http://factominer.free.fr/) performing PCA analysis on gene expression matrices.PCA analysis was performed on cells passed quality control using all genes expressed in more than two cells and with a variance in log2 (TMM-TPM+1) across all single cells greater than 0.5. Subsequently, genes with the highest correlation coefficient with one of the first three or four principal components were identified using dimdesc function in FactoMineR. Hierarchical clustering was performed on cells and on the genes identified by PCA using Euclidean distance or correlation metric.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression matrices (TPM value) of each gene in each cells in CSV format

growth_protocol: C57BL/6 male mice used for this experiments were 12 weeks of age. Mice were purchased from Charles River or bred in house at the DKFZ Center for Preclinical Research facility. Animals were housed under standard conditions and fed ad libitum. All procedures were in accordance to the DKFZ guidelines and approved by the Regierungpräsidium Karlsruhe.

extract_protocol:
Mice were perfused with 20ml HBSS (Gibco), the pancreas was extracted and adipose tissue removed. Four solutions were prepared, including D solution: 1mg/ml Collagenase Type CLS IV supplemented with 0.25% BSA (Sigma-Aldrich), R solution: 1% BSA dissolved in PBS, C solution: 4% BSA in PBS and I solution: 0.1% BSA in PBS. The tissue was chopped into small pieces and incubated in 10ml of D solution at 37°C for 30 minutes. The digestion product was filtered through a 70μm cell strainer (Islets of Langerhans were thereby removed). 10ml of R solution was pipetted on the cell strainer. A quarter of the filtered cell suspension was gently transferred on top of 6ml C solution to achieve layer separation of the liquids. Acini were spun down at 50g for 2 minutes and washed with C solution and I solution successively. Purified acini were treated with 2ml Accutase (Sigma-Aldrich) for 5min to acquire acinar cell suspension containing single cells and clusters of acinar cells
Single cell RNA seq library preparation protocol was based on the SMART seq2 protocol by Picelli et al., 2014 with following modifications: Acinar cells were isolated as described in the section “Acinar Cell Isolation and Culture” and resuspended in DPBS without Ca2+ and Mg2+ (Beckman Coulter). Cells were collected in a volume of 0.5µl and transferred to a reaction tube containing 4µl of 6M Guanidine-HCl (Sigma-Aldrich) and 0.1% (vol/vol) Triton X-100 (Sigma-Aldrich). The tube was immediately transferred into liquid nitrogen and kept there for the duration of cell collection. Next, 2.2x RNA SPRI beads (Beckman Coulter) was added directly to the lysis buffer and incubated for 5 min at room temperature. The beads were washed twice with 70% Ethanol. Air-dried beads were resuspended in a solution containing 2µl H20, 1 µl oligo-dT primer and 1µl dNTP mix (primer and nucleotides used as in 4). 24 cells contained ERCC Spike-In RNAs (1:10 000 – Mix2, Ambion) Mix in addition to primer and nucleotides. Beads were incubated for 3 min at 72°C and reverse transcription and PCR (19 cycles) were performed as described in Picelli et al., 2014. PCR product was cleaned up using 0.8x DNA SPRI beads (Beckman Coulter) and air dried beads were resuspended in 15µl H2O. Quality of cDNA library was assessed for each cell on a high sensitivity DNA Bioanalyzer chip. Subsequent steps (tagmentation, amplification, multiplexing) were done as previously described in Llorens-Bobadilla et al., 2015

treatment_protocol: All mice used in this study were untreated

value: acinar

tag: age

tag: tissue

value: pancreas

tag: gender


title: Sample_RD-NRW21-100-1

description: counts.txt.gz


title: Sample_RD-NRW21-100-2

description: counts.txt.gz


title: Cell__number_100

value: Male


title: Cell__number_101


title: Sample_RD_NRW24T10_H100_4

description: counts.txt.gz


title: Sample_RD_NRW24T10_H100_6

description: counts.txt.gz


title: Sample_NRW22-H100-1

description: counts.txt.gz

extract_protocol: Lucigen NxSeq (0.1X volume, 10ng input)

value: Nugen Ovation RNASeq V2 (0.25X volume)


title: Sample_TPM4b

description: optimizationCounts.txt.gz


title: Cell__number_102


title: Cell__number_103


title: Sample_TPM3b

description: optimizationCounts.txt.gz


title: Sample_TPM3

description: optimizationCounts.txt.gz


title: Sample_TPM8a

description: optimizationCounts.txt.gz


title: LG10A0-1-NGS4-H100-2

description: counts.txt.gz


title: Cell__number_104


title: Cell__number_105


title: LG10A0-1-NGS4-H100-1

description: counts.txt.gz


title: 20-UHRR-100pg-rep5_S20

description: counts.txt.gz

extract_protocol: Nextera XT (C1 protocol)

value: C1 SMARTer


title: Cell__number_10


title: Cell__number_106


title: Cell__number_107


title: HH14-M

extract_protocol:
Total RNA was isolated with TRIzol (Invitrogen) from each sample according to the manufacturer's instructions. It was treated with RNase-free DNase according to manufacturers's instructions (Promega) to remove residual DNA.
cDNA library construction and paired-end sequencing was performed by BGI using an Illumina HiSeq™ 2000 platform according to the manufacturer’s instructions

value: Guy11 inoculated


title: 19-UHRR-100pg-rep4_S19

description: counts.txt.gz


title: 17-UHRR-100pg-rep2_S17

description: counts.txt.gz


title: Cell__number_108


title: Cell__number_109


title: Sample_100G

description: counts.txt.gz

extract_protocol: Illumina TruSeq stranded mRNA, modified to begin with amplified aRNA


title: Cell__number_11


title: Cell__number_110


title: Sample_100F

description: counts.txt.gz


title: LG10A0-1-NGS4-H100-3

description: counts.txt.gz


title: Sample_100E

description: counts.txt.gz


title: Cell__number_113


title: Sample_100D

description: counts.txt.gz


title: Sample_100pC

description: counts.txt.gz


title: Sample_100pB

description: counts.txt.gz


title: Cell__number_13


title: Cell__number_12


title: Sample_100pA

description: counts.txt.gz


title: Cell__number_14


title: Sample_RD-NRW24T10-H10-2

description: counts.txt.gz


title: Cell__number_15


title: 18-UHRR-100pg-rep3_S18

description: counts.txt.gz


title: Cell__number_16


title: Sample_RD_NRW24T10_H10_7

description: counts.txt.gz


title: Cell__number_18


title: kin28-AA_minusrap_Srb10

first: Natalia

last: Petrenko

address: 240 Longwood Ave

department: BCMP

institute: Harvard Medical School

description: Chip-seq of Myc-tagged Mediator subunit

data_processing:
map using Bowtie in Galaxy (Penn State).  Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 .
Sam-to-Bam using Galaxy
Bam-to-Bed using Galaxy (Concatenate the two  kin28-AA_minusrap_Gal11 files).
MACS using Galaxy to create a shifted raw tag count at every bp in a wiggle file and save as bigwig.  All libraries have an average fragment size of 200-300, except the Srb4 libraries, which are 80-200
for plotting, normalize to # of sequenced reads
Genome_build: sacCer3
Supplementary_files_format_and_content: every processed file contains a shifted raw tag count at every bp in a bigwig file

source_name: Saccharomyces cerevisiae_KHW333

extract_protocol:
Genomic DNA extraction protocol as described in Fan, X., Lamarre-Vincent, N., Wang, Q., and Struhl, K. (2008). Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucl. Acids Res. 36, e125. Antibodies used in this study include 9E10 anti-Myc antibodies from Santa Cruz and 8WG16 antibodies from Covance.
Library construction as described in Wong, K.-H., Jin, Y., and Moqtaderi, Z. (2013). Multiplex Illumina sequencing using DNA barcoding. Curr Protoc Mol Biol Chapter 7, Unit 7.11.


title: 16-UHRR-100pg-rep1_S16

description: counts.txt.gz


title: kin28-AA_plusrap_Srb10

description: Chip-seq of Myc-tagged Mediator subunit


title: Cell__number_19


title: Sample_RD_NRW24T10_H10_6

description: counts.txt.gz


title: Cell__number_111


title: Cell__number_2


title: Sample_RD_NRW24T10_H10_5

description: counts.txt.gz


title: kin28-AA_minusrap_Med7

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_KHW329


title: Sample_RD_NRW24T10_H10_4

description: counts.txt.gz


title: Sample_RD_NRW24T10_H10_10

description: counts.txt.gz


title: kin28-AA_plusrap_Med7

description: Chip-seq of Myc-tagged Mediator subunit


title: kin28-AA_minusrap_Srb6

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_KHW332


title: Sample_NRW22-T10-H10-3

description: counts.txt.gz


title: kin28-AA_plusrap_Srb6

description: Chip-seq of Myc-tagged Mediator subunit


title: LG10A0-1-NGS4-H10-7

description: counts.txt.gz


title: kin28-AA_plusrap_Srb7

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_YJ147


title: Sample_RD-NRW24T10-H10-1

description: counts.txt.gz


title: LG10A0-1-NGS4-H10-5

description: counts.txt.gz


title: LG10A0-1-NGS4-H10-4

description: counts.txt.gz


title: LG10A0-1-NGS4-H10-6

description: counts.txt.gz


title: Cell__number_24


title: Cell__number_20


title: Cell__number_23


title: Cell__number_22


title: Cell__number_27


title: LG10A0-1-NGS4-H10-3

description: counts.txt.gz


title: Cell__number_28


title: Cell__number_29


title: LG10A0-1-NGS4-H10-2

description: counts.txt.gz


title: kin28-AA_plusrap_Gal11

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_KHW328


title: kin28-AA_minusrap_Srb7

description: Chip-seq of Myc-tagged Mediator subunit


title: kin28-AA_minusrap_Gal11

description: Chip-seq of Myc-tagged Mediator subunit


title: kin28-AA_minusrap_Med8

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_YJ141


title: kin28-AA_plusrap_Srb2

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_YJ146


title: 9-UHRR-10pg-rep9_S9

description: counts.txt.gz


title: kin28-AA_plusrap_Rgr1

description: Chip-seq of Myc-tagged Mediator subunit

source_name: Saccharomyces cerevisiae_KHW330


title: Cell__number_25


title: kin28-AA_minusrap_Srb2

description: Chip-seq of Myc-tagged Mediator subunit


title: kin28-AA_plusrap_Med8

description: Chip-seq of Myc-tagged Mediator subunit


title: 8-UHRR-10pg-rep8_S8

description: counts.txt.gz


title: 7-UHRR-10pg-rep7_S7

description: counts.txt.gz


title: 11_L436_Mvex_miRNA

city: Rochester

first: Sneha

last: Nishtala

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Adapter trimmed reads were obtained from raw reads using Cutadapt v0.9.5
Bowtie v0.12.7 was used to align the reads.
mirDeep2 along with miRBase v20 was used to identify novel miRNAs.
Genome_build: susScr3, miRBase v20
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each miRNA per sample

organism: Sus scrofa

source_name: MSC-derived extracellular vesicles (Evs)

growth_protocol: Primary MSCs were isolated from abdominal fat (5-10g) of 3 female domestic pigs using collagenase-H, cultured for 3 weeks in advanced MEM medium (Gibco/Invitrogen) supplemented with platelet lysate (PLTmax, Mill Creek Life Sciences, Rochester, MN), and used at the third passage. MSC cultures did not include any animal products with the exception of porcine MSCs. Cells were characterized in vitro by positive immuno-fluorescent staining and fluorescence activated cell sorting analysis for CD44, CD73, CD90, and CD105, and consistent with our observations in human MSCs. EVs were isolated from MSC supernatants (10x106 cells) by ultracentrifugation at 2,000g and 100,000g for 1h at 4°C. Transmission electron microscopy was performed to investigate size and structure of MSC-derived EVs using digital electron microscopy (JEOL 1200 EXII, Mayo Clinic’s electron microscopy core). EVs were then characterized based on the expression of both EV (CD9, CD29, and CD63) and MSC (CD73 and CD105) surface markers by western blot (AbD Serotec cat#: MCA1189 and AA120-175, and Abcam cat#: ab61873, ab115289, and ab135528). In addition, EV concentration and size distribution were assessed by nanoparticle tracking analysis (NTA) using NanoSight NS300.

extract_protocol:
Total RNA were extracted from 0.5 x 10^6 MSCs or EVs isolated from 10^6-10^7 MSCs, using 350ul of ice cold lysis buffer supplied by mirVana PARIS total RNA isolation kit (Life Technologies, Cat# AM1556).
1ug of RNA was used for construction of sequencing libraries by TruSeq stranded total RNA method.

value: extracellular vesicles

tag: passages

value: 3 months

tag: pig id


title: Cell__number_31


title: Mvex4_miRNA


title: 6-UHRR-10pg-rep6_S6

description: counts.txt.gz

tag: amount of starting rna


title: 5-UHRR-10pg-rep5_S5

description: counts.txt.gz

tag: ercc spike-in dilution used


title: Cell__number_33


title: Mvex3_miRNA


title: Cell__number_21


title: Cell__number_26


title: MSC4_miRNA

source_name: Adipose tissue derived-mesenchymal stromal/stem cells (MSC)

value: mesenchymal stromal/stem cells


title: 3-UHRR-10pg-rep3_S3

description: counts.txt.gz

source_name: Universal Human Reference

tag: single-cell amplification protocol used


title: MSC3_miRNA


title: Cell__number_36


title: Cell__number_30


title: 15-UHRR-10pg-rep15_S15

description: counts.txt.gz


title: Cell__number_37


title: 2-UHRR-10pg-rep2_S2

description: counts.txt.gz


title: Cell__number_35


title: Mvex3_mRNA


title: Cell__number_38


title: 14-UHRR-10pg-rep14_S14

description: counts.txt.gz


title: Cell__number_34


title: Mvex2_mRNA


title: Cell__number_32


title: 12-UHRR-10pg-rep12_S12

description: counts.txt.gz


title: 13-UHRR-10pg-rep13_S13

description: counts.txt.gz


title: Cell__number_39


title: Cell__number_40


title: 4__L436_MSC_miRNA


title: MSC3_mRNA


title: Cell__number_4


title: 11-UHRR-10pg-rep11_S11

description: counts.txt.gz


title: 10-UHRR-10pg-rep10_S10

description: counts.txt.gz


title: 1-UHRR-10pg-rep1_S1

description: counts.txt.gz


title: Cell__number_41


title: Sample_10J

description: counts.txt.gz


title: Sample_10K

description: counts.txt.gz


title: Cell__number_43


title: MSC1_mRNA


title: Cell__number_42


title: Sample_10L

description: counts.txt.gz


title: Cell__number_44


title: Cell__number_45


title: Mvex1_mRNA


title: Cell__number_46


title: Sample_10H

description: counts.txt.gz


title: Pid3.ZB13.16.2-RNAseq

source_name: leaf

extract_protocol:
Total RNAs were isolated using TRIzol reagent (Life Technologies) and treated with RNase-free DNase I (Takara) to remove any contaminating genomic DNA.
mRNA extraction was performed using Dynabeads oligo(dT) (Dynal; Invitrogen Corp.). Double-stranded cDNAs were synthesized using reverse transcriptase (Superscript II; Invitrogen Corp.) and random hexamer primers. The cDNAs were then fragmented by nebulization, and the standard Illumina protocol was followed thereafter to create the mRNA-seq libraries.

value: leaf

value: 4 weeks old

tag: inoculation type

value: ZB13 inoculation

tag: phenotype

value: susceptible

tag: interaction

value: compatible


title: Cell__number_47


title: Sample_10G

description: counts.txt.gz

value: 10 pg

value: aRNA


title: Cell__number_48


title: MSC2_mRNA


title: Sample_UHRR_10pF

description: counts.txt.gz


title: Input_Rb_arrested_KO

city: London

first: Fred

last: Dick

state: ON

address: Cancer Research Labs 790 Commissioners Road East

institute: Western University

description:
antibody: NA
P4 MEFs EGS and formalin fixed prior to chromatin harvest

data_processing:
Basecalls were performed using the Illumina pipeline 1.8.1
ChIP-seq reads aligned using Bowtie2 using options -t -p 24 -D 15 -R 2 -L 32 -i S,1,0.75, -x mm9 -U sequence.fastq -S output.sam
MACS2 ChIP-seq peaks were called using options MACS2 callpeak -t treat.sam -c control.sam -g mm -q 0.01 --broad --keep-dup all -B
Overall peak genomic distribution determined using HOMER options annotatePeaks.pl peaks.bed mm9 > peaks.txt
Peak overlap assessed using BEDintersect options bedtools intersect -bed -sorted -wa -wb -f 0.05 -a sample2.bed -b sample1_index_intersect.bed | sortBed -i > Sample1-2-index_intersect.sorted.bed
Genome_build: mm9
Supplementary_files_format_and_content: sam files

source_name: embryonic fibroblast chromatin

growth_protocol: MEFs grown in DMEM supplimented with 10% FBS until passage 4

extract_protocol:
Chromatin was isolated from passage 4 MEFs cross-linked with ethylene glycol bissuccinimidylsuccinate and formaldehyde, then sonicated to ≤ 400 bp. DNA fragments were immunoprecipitated using different antibodies, washed, then purified. DNA was prepared for sequencing according to the Illumina TruSeq protocol.
Illumina TruSeq manufacturers protocol

treatment_protocol: Cytostasis achieved with 0.1% FBS for 72 hours

tag: passage

value: E13.5 MEFs

tag: growth condition

value: arrested


title: Cell__number_49

value: acinar

value: pancreas


title: Sample_UHRR_10pE

description: counts.txt.gz


title: Input_Rb_proliferating_KO

value: asynchronously proliferating


title: Cell__number_5

value: Male


title: Cell__number_51


title: Cell__number_3


title: Sample_10pD

description: counts.txt.gz


title: Sample_10pC

description: counts.txt.gz


title: Sample_10pB

description: counts.txt.gz


title: kin28-AA_minusrap_Rgr1

description: Chip-seq of Myc-tagged Mediator subunit


title: Cell__number_53


title: ChIP_H3K27me3_proliferating_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 26

data_processing:
Basecalls were performed using the Illumina pipeline 1.8.1
ChIP-seq reads aligned using Bowtie2 using options -t -p 24 -D 15 -R 2 -L 32 -i S,1,0.75, -x mm9 -U sequence.fastq -S output.sam
MACS2 ChIP-seq peaks were called using options MACS2 callpeak -t treat.sam -c control.sam -g mm -q 0.01 --broad --keep-dup all -B
Overall peak genomic distribution determined using HOMER options annotatePeaks.pl peaks.bed mm9 > peaks.txt
Peak overlap assessed using BEDintersect options bedtools intersect -bed -sorted -wa -wb -f 0.05 -a sample2.bed -b sample1_index_intersect.bed | sortBed -i > Sample1-2-index_intersect.sorted.bed
Genome_build: mm9
Supplementary_files_format_and_content: bed files: the first column indicates chrID followed by Chr start, and chr end. Beyond these first three columns are peak name, scores, etc.

tag: developmental stage

value: mouse embryonic fibroblast (MEF)

tag: chip antibody

value: H3K27me3 (EMD Millipore, 07-449)


title: ChIP_Ezh2_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 28

tag: cell type

value: quiescence via serum-deprivation

value: Ezh2 (Cell signalling, 5264)


title: ChIP_Ezh2_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 27

tag: strain


title: ChIP_Rb_arrested_KO

description:
antibody: pRb: M153 (Santa Cruz, sc-7905), C15 (Santa Cruz, sc-50), S855 (in-house, affinity-purified rabbit Ab), M136 (in-house, affinity-purified sheep Ab), Hyb4.1 (Developmental Studies Hybridoma Bank)
P4 MEFs EGS and formalin fixed prior to chromatin harvest


title: Sample_10pA

description: counts.txt.gz


title: ChIP_H3K27me3_proliferating_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 25


title: Cell__number_52

tag: age


title: Sample_10I

description: counts.txt.gz


title: Cell__number_55

tag: tissue


title: ChIP_Rb_proliferating_KO


title: ChIP_H3K27me3_arrested_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 24


title: LG10A0-1-NGS4-R100-4

description: counts.txt.gz

source_name: Human Brain Reference

value: Nugen Ovation RNASeq V2 (0.25X volume)


title: Cell__number_56

tag: gender


title: Cell__number_54


title: LG10A0-1-NGS4-R100-3

description: counts.txt.gz


title: ChIP_H3K27me3_arrested_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 23


title: ChIP_Rb_proliferating_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 20

value: pRb; M153 (Santa Cruz, sc-7905), C15 (Santa Cruz, sc-50), S855 (in-house, affinity-purified rabbit Ab), M136 (in-house, affinity-purified sheep Ab), Hyb4.1 (Developmental Studies Hybridoma Bank)


title: LG10A0-1-NGS4-R100-2

description: counts.txt.gz


title: LG10A0-1-NGS4-R100-1

description: counts.txt.gz


title: Cell__number_59


title: Cell__number_6


title: ChIP_Rb_arrested_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 16

value: confluence arrested


title: Cell__number_60


title: 20140312-HBR-100-pg-rep5_S35

description: counts.txt.gz

value: C1 SMARTer


title: 20140312-HBR-100-pg-rep4_S34

description: counts.txt.gz


title: ChIP_Rb_arrested_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 15


title: Cell__number_61


title: 20140312-HBR-100-pg-rep3_S33

description: counts.txt.gz


title: Cell__number_62


title: Cell__number_63


title: Input_Ezh2_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 13


title: Input_H3K27me3_proliferating_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 12


title: 20140312-HBR-100-pg-rep2_S32

description: counts.txt.gz


title: Input_H3K27me3_proliferating_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 11


title: 20140312-HBR-100-pg-rep1_S31

description: counts.txt.gz


title: Cell__number_66


title: Cell__number_64


title: Input_H3K27me3_arrested_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 10


title: Cell__number_58


title: Sample_HBR_100pA

description: counts.txt.gz


title: ChIP_Rb_proliferating_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 19


title: Cell__number_67


title: Cell__number_68


title: Sample_HBR_100pB

description: counts.txt.gz


title: LG10A0-1-NGS4-R10-6

description: counts.txt.gz


title: Input_Rb_proliferating_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 6


title: Input_Rb_proliferating_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 5


title: Cell__number_69


title: Cell__number_7


title: LG10A0-1-NGS4-R10-3

description: counts.txt.gz


title: Input_H3K27me3_arrested_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 9


title: Input_Ezh2_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 14


title: LG10A0-1-NGS4-R10-13

description: counts.txt.gz


title: Sample_HBR_100pC

description: counts.txt.gz


title: Input_Rb_arrested_SS

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 2


title: LG10A0-1-NGS4-R10-12

description: counts.txt.gz


title: Cell__number_70


title: Cell__number_71


title: 20140312-HBR-10-pg-rep9_S9

description: counts.txt.gz


title: 20140312-HBR-10-pg-rep8_S8

description: counts.txt.gz


title: Cell__number_72


title: Cell__number_73


title: Input_Rb_arrested_WT

description:
P4 MEFs EGS and formalin fixed prior to chromatin harvest
Sample 1


title: 20140312-HBR-10-pg-rep7_S7

description: counts.txt.gz


title: 20140312-HBR-10-pg-rep6_S6

description: counts.txt.gz


title: Cell__number_74


title: Rb1+/+ - 4 - rRNA-depleted RNA

data_processing:
Basecalls were performed using the Illumina Off-Line Basecaller (OLB) pipeline v1.8.
RNA-seq differential expression analysis of Rb1+/+ and Rb1∆S/∆S MEFS at unique targets was conducted using the Tuxedo protocol
TopHat v2.0.9 was used to align paired-ends sequence reads for each biological replicate to the mouse genome (mm9; UCSC) using the default parameters of TopHat v2.0.9
The resulting read alignments generated by TopHat were provided to Cufflinks v2.1.1 to generate a transcriptome assembly for each condition using Cufflinks v2.1.1 default parameters.
The transcriptome assembly for each condition and the reference transcripts for the mm9 genome were merged by Cuffmerge to produce a single annotation file for differential expression analysis.
Cuffdiff carried out the differential expression analysis between Rb1+/+ and Rb1∆S/∆S, and reported differential expression using a LOG2 ratio
CummeRbund was finally used to manage and visualize the data generated by Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: gene_exp.diff file from Cuffdiff which contains gene differential FPKM. This was done through tests for differences between samples (all replicates merged) in the summed FPKM of transcripts sharing each gene ID

source_name: MEF_Rb1+/+_rRNA-depleted RNA

growth_protocol: Primary mouse embryonic fibroblasts were prepared and cultured using previously reported methods (Hurford et al. 1997).

extract_protocol:
Total RNA extracted according to TRIzol manufacturer protocol. rRNA was depleted from total RNA using the RiboMinus Euk System V2 protocol according to manufacturer’s procotol
Ths library was built using the Illumina TruSeq RNA library prep kit (Sample Preparation v2 Guide), following Illumina's low sample protocol. Through the use of Illumina v3 chemistry, sequencing of the library was then performed on a lane of an Illumina HiSeq 2500 instrument using the multiplex paired end protocol (2x100-bases).

treatment_protocol: Serum starvation performed as previously escribed (Isaac et al. 2006)

tag: strain background

value: Mouse embryonic fibroblasts (MEFs)

value: Passage 4

tag: growth state

value: Serum starved

tag: molecule subtype

value: rRNA-depleted total RNA


title: Rb1ΔS/ΔS - 2 - rRNA-depleted RNA

source_name: MEF_Rb1ΔS/ΔS_rRNA-depleted RNA


title: Rb1ΔS/ΔS - 4 - rRNA-depleted RNA


title: Rb1ΔS/ΔS - 1 - rRNA-depleted RNA


title: 20140312-HBR-10-pg-rep5_S5

description: counts.txt.gz

tag: amount of starting rna

value: 10 pg

tag: ercc spike-in dilution used


title: Rb1+/+ - 3 - rRNA-depleted RNA


title: Cell__number_76

value: acinar


title: Cell__number_77

value: pancreas


title: Rb1+/+ - 1 - rRNA-depleted RNA


title: 20140312-HBR-10-pg-rep4_S4

description: counts.txt.gz

tag: single-cell amplification protocol used


title: Cell__number_78


title: 20140312-HBR-10-pg-rep3_S3

description: counts.txt.gz


title: 20140312-HBR-10-pg-rep2_S2

description: counts.txt.gz


title: 2014_001_028 [non pathological renal tissue]

city: Bonnn

first: Jörg

last: Ellinger

state: NRW

address: Sigmund-Freud-Straße 25

department: Urologie

institute: Universitätsklinikum Bonn

description: Gene expression in non pathological renal tissue

data_processing:
After adapter trimming, reads were collapsed and mapped to the genome using Bowtie (Langmead et al., 2009)
Mapped reads were subsequently annotated to different contaminants (tRNA, rRNA, sn(o)RNA, piRNA, ...) and mature miRNAs using genome annotation data from Ensembl, UCSC and miRBase v20.
Prior to normalization, data were filtered using a cutoff of 4 reads. miRNA expression data were normalized based on the total read count per sample. Read count for each miRNA was divided by the total read count in that sample and multiplied by the median total read count across all samples. After normalization, data were log2-transformed.
The expression level of each miRNA unit is measured by the number of sequenced fragments that map to the transcript and represent count data. This measure is different from gene probe-based methods, such as microarrays or RT-qPCR.
Genome_build: Ensembl, UCSC and miRBase v20
Supplementary_files_format_and_content: abundance measurements; annex_*_phase1_*.txt contains processed data for GSM1891367-74; annex_*_phase2_*.txt contains processed data for GSM1891375-402; A brief description of each file is included in the 'readme.txt'

source_name: non pathological renal tissue

extract_protocol:
Fresh-frozen tissue samples (approximately 50 mg) were cut on liquid nitrogen and homogenized with Yttrium stabilized Zirkonoxid-Beads (Silibeads, Sigmund-Lindner, Warmensteinach, Germany) using a Precellys24 tissue homogenizer. Total RNA was isolated using the mirVana miRNA Isolation Kit (Ambion, Foster City, CA, USA) according to the manufacturers recommendation. To remove residual DNA fragments, we treated the isolate twice with DNase (DNA-free Kit, Ambion).
Libraries for small RNA sequencing were prepared using the TruSeq small RNA library kit (Illumina) according to the manufacturer’s instructions. 500 ng of total RNA was used as input for RNA adapter ligation, followed by reverse transcription and PCR amplification with bar-coded primers. Small RNA libraries were sequenced on a NextSeq500 (Illumina).

value: female

tag: age (yrs)

tag: tissue type

value: non pathological renal tissue

tag: pt-stage

value: CTRL

tag: lymph node metastasis

tag: distand metastasis

tag: grading

tag: ajcc stage

tag: tumor size (cm)


title: 2014_001_029 [ccRCC]

description: Gene expression in ccRCC tissue

source_name: ccRCC

value: ccRCC


title: 20140312-HBR-10-pg-rep15_S15

department: Biology

description: counts.txt.gz


title: Cell__number_8

tag: strain

tag: cell type

tag: age

value: Male


title: Cell__number_79

tag: tissue

tag: gender


title: 20140312-HBR-10-pg-rep13_S13

description: counts.txt.gz


title: 20140312-HBR-10-pg-rep14_S14

description: counts.txt.gz


title: 2014_001_024 [non pathological renal tissue]

value: male


title: 2014_001_025 [ccRCC]

description: Gene expression in ccRCC tissue


title: Cell__number_81


title: 20140312-HBR-10-pg-rep12_S12

description: counts.txt.gz


title: 2014_001_023 [ccRCC]

description: Gene expression in ccRCC tissue


title: Cell__number_75


title: Cell__number_83


title: 2014_001_022 [non pathological renal tissue]


title: Cell__number_82


title: 20140312-HBR-10-pg-rep11_S11

description: counts.txt.gz


title: 20140312-HBR-10-pg-rep10_S10

description: counts.txt.gz


title: Cell__number_84


title: 2014_001_021 [ccRCC]

description: Gene expression in ccRCC tissue


title: Cell__number_85


title: 20140312-HBR-10-pg-rep1_S1

description: counts.txt.gz


title: 2014_001_020 [non pathological renal tissue]


title: Sample_NRW22-T10-H10-1

description: counts.txt.gz

value: Nugen Ovation RNASeq V2 (0.25X volume, +10 min.)


title: Cell__number_80


title: 2014_001_026 [non pathological renal tissue]


title: 2014_001_019 [ccRCC]

description: Gene expression in ccRCC tissue


title: Sample_TPM6

description: counts.txt.gz

value: aRNA


title: Cell__number_87


title: Cell__number_86


title: Sample_TPM5

description: counts.txt.gz


title: 2014_001_018 [non pathological renal tissue]


title: Cell__number_88


title: 2014_001_017 [ccRCC]

description: Gene expression in ccRCC tissue


title: Sample_TPM4

description: counts.txt.gz


title: 2014_001_016 [non pathological renal tissue]


title: Cell__number_89


title: Sample_ERCC_9

description: counts.txt.gz


title: Sample_ERCC_8

description: counts.txt.gz


title: 2014_001_015 [ccRCC]

description: Gene expression in ccRCC tissue


title: Cell__number_9


title: Sample_ERCC_7

description: counts.txt.gz


title: Cell__number_90


title: Cell__number_91


title: 2014_001_013 [ccRCC]

description: Gene expression in ccRCC tissue


title: 2014_001_014 [non pathological renal tissue]


title: Sample_ERCC_5

description: counts.txt.gz


title: 4-UHRR-10pg-rep4_S4

description: counts.txt.gz


title: Sample_ERCC_4

description: counts.txt.gz


title: 2014_001_012 [non pathological renal tissue]


title: Sample_ERCC_2

description: counts.txt.gz


title: Sample_ERCC_3

description: counts.txt.gz


title: 2014_001_010 [non pathological renal tissue]


title: 2013_024_012 [non pathological renal tissue]


title: 2014_001_009 [ccRCC]

description: Gene expression in ccRCC tissue


title: Cell__number_96