title: R_H3K27me3S28p

city: Copenhagen N

first: Mads

last: Lerdrup

address: Blegdamsvej 3C

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

data_processing:
High quality reads (Chastity score .= 0.6) were aligned to the mouse genome (mm9) using Bowtie allowing up to two mismatches within the first 32 bases. Reads not aligning uniquely to the mouse genome were removed.
Aligned datasets were filtered for multiple reads at the same position occurring after PCR amplication. Where more than one read mapped to the same position and at the same strand duplicates were removed.
The reads were extended to 250 bp length, and the number of reads at a given position was counted and saved as a fixedStep wig file with 100 bp resolution. Values are denominated in fragments pr. Mreads pr. kbp.
Genome_build: mm9
Supplementary_files_format_and_content: wig: fixedStep Wiggle file containing densities with 100 bp resolution of aligned and filtered reads.

source_name: 6-OHDA lesioned striatum, L-DOPA injected

extract_protocol:
Mice were killed by decapitation 1h after L-DOPA injection, the heads of the animals were cooled in liquid nitrogen for 6 s and the brains were removed. Coronal slices of 1 mm thickness were obtained from a mouse brain dissection matrix, and three striatal punches of 2 mm diameter from sequential slices were dissected out on an ice-cold surface. The tissue was fixed in 1% PFA for 12 min, washed with PBS and snap frozen for later chromatin extraction.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Mice were anesthetized with a mixture of fentanyl citrate (0.315 mg/ml), fluanisone (10 mg/ml) (VetaPharma, Leeds, UK), midazolam (5 mg/ml) (Hameln Pharmaceuticals, Gloucester, UK), and water (1:1:2 in a volume of 10 ml/kg) and mounted in a stereotaxic frame (David Kopf Instruments, Tujunga, CA) equipped with a mouse adaptor. 6-OHDA-HCl (Sigma-Aldrich Sweden AB) was dissolved in 0.02% ascorbic acid in saline at a concentration of 3 µg of free-base 6-OHDA per microliter.  Each mouse received one unilateral (right hemisphere) injection of 6-OHDA of 1 µl (0.5 µl /min) into the medial forebrain bundle according to the following coordinates (mm): anteroposterior (AP), -1.2; mediolateral (ML), –1.2; dorsoventral (DV), –4.8 (all millimeters relative to bregma) [40].  Noradrenergic neurons were protected by injection of 25 mg/kg desipramine (Sigma) thirty minutes prior to 6-OHDA injection. This procedure leads to a decrease in striatal tyrosine hydroxylase immunoreactivity ≥80% and to a marked akinesia affecting the side of the body contralateral to the lesioned striatum. Animals were allowed to recover for 2 weeks before experimentation. L-DOPA (10 mg/kg in combination with 7.5 mg/kg benserazide; purchased from Sigma) was dissolved in saline (0.9% NaCl), and injected intraperitoneally in a volume of 10 ml per kilogram of body weight. Mice were injected with a single dose of L-DOPA.

value: striatum

value: H3K27me3S28p (Hansen lab)


title: L_H3K4me3

status: Public on Oct 01 2014

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: unlesioned striatum, L-DOPA injected

tag: strain

tag: tissue

tag: chip antibody

value: H3K4me3 (9751, Cell Signaling)


title: L_H3K27me3

value: H3K27me3 (9756, Cell Signaling)


title: ChL_R3

description:
transcripts.txt
ChL_R_vs_ChL_L.diff_expressed_transcripts.tsv
ChL_R_vs_AL_R.diff_expressed_transcripts.tsv

library_source: transcriptomic

data_processing:
Sequenced reads were processed by the Genomatix GMBH pipeline, and differential expression was computed by using their integration of DeSeq.
Genome_build: mm9
Supplementary_files_format_and_content: transcripts.txt: Tab separated text file containing read counts and normalized expression from all samples
Supplementary_files_format_and_content: *.diff_expressed_transcripts.tsv: Tab separated text file containing read counts and normalized expression, log2fd, and p-values

molecule: total RNA

source_name: 6-OHDA lesioned striatum, chronic L-DOPA injected, L-DOPA challanged

extract_protocol:
Mice were killed by decapitation 1h after a single dose of L-DOPA (AL samples) or 1h after the last dose after 9 days of daily L-DOPA injections (ChL samples). The heads of the animals were cooled in liquid nitrogen for 6 s and the brains were removed. Coronal slices of 1 mm thickness were obtained from a mouse brain dissection matrix, and three striatal punches of 2 mm diameter from sequential slices were dissected out on an ice-cold surface. The tissue was incubated in RNAlater for storage. RNA was extracted using RNease plus universal kit (Qiagen).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were anesthetized with a mixture of fentanyl citrate (0.315 mg/ml), fluanisone (10 mg/ml) (VetaPharma, Leeds, UK), midazolam (5 mg/ml) (Hameln Pharmaceuticals, Gloucester, UK), and water (1:1:2 in a volume of 10 ml/kg) and mounted in a stereotaxic frame (David Kopf Instruments, Tujunga, CA) equipped with a mouse adaptor. 6-OHDA-HCl (Sigma-Aldrich Sweden AB) was dissolved in 0.02% ascorbic acid in saline at a concentration of 3 µg of free-base 6-OHDA per microliter.  Each mouse received one unilateral (right hemisphere) injection of 6-OHDA of 1 µl (0.5 µl /min) into the medial forebrain bundle according to the following coordinates (mm): anteroposterior (AP), -1.2; mediolateral (ML), –1.2; dorsoventral (DV), –4.8 (all millimeters relative to bregma) [40].  Noradrenergic neurons were protected by injection of 25 mg/kg desipramine (Sigma) thirty minutes prior to 6-OHDA injection. This procedure leads to a decrease in striatal tyrosine hydroxylase immunoreactivity ≥80% and to a marked akinesia affecting the side of the body contralateral to the lesioned striatum. Animals were allowed to recover for 2 weeks before experimentation. L-DOPA (10 mg/kg in combination with 7.5 mg/kg benserazide; purchased from Sigma) was dissolved in saline (0.9% NaCl), and injected intraperitoneally in a volume of 10 ml per kilogram of body weight. Mice were injected with either a single dose or daily for 9 days.


title: R_H3K27me3


title: R_H3K4me3


title: R_input


title: L_input


title: G1E_Mitotic_Dnase rep1

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

country: USA

institute: Pennsylvania State University

description: processed data file: G1E_Mitotic_pooled_peaks.bed.gz; G1E_Mitotic_pooled.bigWig

data_processing:
Raw reads from DNase-seq libraries were first groomed using FASTQ Groomer on Galaxy Giardine (2005); Blankenberg et al. (2001);Goecks et al. (2010). This program verifies that each base call has a corresponding quality value, and that the quality value is in the Sanger, Phred+33 format. Groomed reads were then trimmed as only the first twenty bases of each read are genomic DNA. The trimmed reads were then mapped to mouse mm9 genome using Bowtie Langmead et al. (2009) using the parameters -m = 4 , -k = 1, and -best, thus allowing the 20 basepair reads to map to at most 4 locations, but reporting only the single, best alignment. This option was chosen to allow reads to map in duplicated regions, while still excluding reads to highly repetitive DNA. The mapped reads from Bowtie were then filtered to retain only those reads successfully mapped to the mm9 genome.
Using DNase2Hotspots as described in Baek et al., 2011, we initially called hotspots using mapped reads pooled from biological triplicates for each experimental condition. After testing a range of z-score thresholds, we decided on a final stringent threshold of 0% FDR that still captured many mildly DNase-sensitive areas. From within hotspots that meet the 0% FDR threshold, we called DNase peaks further enriched from the surrounding hotspot, using a thresholded at a z-score >20.
Reads pooled from biological triplicates for each experimental condition were converted to bed files that were used as input to F-seq (Boyle et al., 2008), which generates smoothed signals based on library-size normalized density of reads. From these pooled reads we used F-seq to identify a set of top 100,000 read-enriched regions. For visualization in browser tracks, genome-wide signal track produced by F-seq for individual replicates as well as the reads pooled from replicates are available as bigwig files at https://mery.genome-browser.bx.psu.edu/cgi-bin/ hgTrackUi?hgsid=187170_w5iejxXAHeIanNii3mA1Otjcfthv&c=chr17&g=chopDnase2. Note that F-seq signal is linearly proportional to RPKM.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain genome wide DNase signals calculated by F-seq as described above.  Bed files contain the chromosone, start, and end positions of the peak signal regions called by F-seq.

growth_protocol: G1E and G1E-ER4 cells were grown as described in Weiss et al., 1997.

extract_protocol:
At harvest, nocodazole-treated and asynchronous cells were cross-linked with 0.1% formaldehyde at room temperature for 10 minutes, then quenched with 1 M glycine. Fixed cells were washed with PBS and resuspended in 1X Cell Lysis Buffer (60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 10 mM Tris pH 7.4, 300 mM sucrose, 0.1 mM EGTA, 0.5 mM PMSF, 0.1% NP40, and 2 μL/mL protease inhibitor cocktail (Sigma)). For mitotic samples, cells were then stained with anti-H3S10Phos antibody (Millipore 04-817) and Dy488 F(ab’)2 anti-rabbit IgG secondary antibody (Jackson 711-485-152), and sorted by FACS for H3S10Phos-positive cells as shown in Fig. 1. DNase I digestion was performed based on protocol from (Cockerill, 1999), with details outlined as follows. 2-10 million asynchronous cells (in Cell Lysis Buffer) or 2 million mitotic cells (collected from the FACS machine in PBS) were resuspended in 50 μL Nuclei Lysis Buffer (300 mM sodium acetate, 5mM EDTA pH 7.4, 0.5% SDS), added to 5 μL of 100 mM CaCl2, equilibrated at room temperature for 10minutes. A range of units of DNase I were added (see DNase-seq library preparation below for the range of units selected for sequencing) and the digestion reaction proceeded for 10 minutes at room temperature, then terminated by adding 350 μL of 0.1 mg/mL proteinase K in Nuclei Lysis Buffer. Samples were gently mixed by inversion, then incubated at 55◦Cfor 5 minutes, then overnight at 65◦Cfor reversal of formaldehyde crosslinks. Additional proteinase K was added to a final concentration of 0.1 mg/mL and incubated at 55◦Cfor 1h. DNA fragments were isolated by phenol-chloroform extraction and ethanol precipitation.
DNase-seq library construction was performed as described in (Song and Crawford, 2010), with the following modifications. Standard 0.8% agarose gels were run for 2h at 80V with 5 μL of each sample and stained with ethidium bromide to check extent of chromatin digestion. A range of 3 different DNase I concentrations were chosen for each condition that best matched digestion patterns between conditions. For mitotic samples, this was 2U, 4U, and 8U of DNase. For asynchronous samples, this was between 4U to 40U, adjusted proportionally to the number of cells in the sample. 70 μL of each sample (for each DNase I concentration) were subjected to blunt-end reaction containing 20 μL NEB Buffer 2, 7 μL 10 mM dNTP’s, 6 μL T4 DNA polymerase (NEB M0203), 2 μL BSA (100x), 4 μL 50mMMgCl2, and 95 μL dH2O, incubated at room temperature for 3.25h. 200 μL TE buffer was added and samples placed at 65◦Cfor 15 minutes to deactivate enzyme. Reactions were cleaned up by phenol-chloroform extraction and DNA resuspended in 30 μL 10 mM Tris-Cl. The samples corresponding to the three chosen DNase I concentrations chosen for each condition were measured by nano drop and pooled at equimolar concentrations into a single tube for overnight ligations to the first DNase-seq linker, as per (Song and Crawford, 2010). The one modification from (Song and Crawford, 2010) is that we added a 5’ phosphate to linker 1 to increase ligation efficiency.

treatment_protocol: G1E-ER4 cells were treated with 100 nM estradiol for 22h prior to harvest. Then, for mitotic arrest, both G1E and G1E-ER4 cells were treated with nocodazole (200 ng/ml) for 7h prior to harvest.

tag: strain background

tag: cell line

tag: cell line source

value: targeted disruption of GATA-1 in strain 129 embryonic stem cells

tag: cell type

value: GATA-1 (null) cell line

tag: cell markers

tag: treated with


title: ChL_R1


title: ChL_L3

description:
transcripts.txt
ChL_R_vs_ChL_L.diff_expressed_transcripts.tsv

source_name: unlesioned striatum, chronic L-DOPA injected, L-DOPA challanged


title: RNA-seq (Ribo-)

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

description: Ribo-depleted total RNA

data_processing:
Reads were mapped to mm9 genome assembly (UCSC) using Bowtie v1. Mapped BED6 file presents 6 columns: 1. Chromosome, 2. Start mapping position of the read (0-based), 3. End mapping position of the read (0-based), 4. Illumina read's ID, 5. Score (0), 6. Strand. Attached Wiggle file: RNA-seq_E14_mm9.wig (RNA-seq data track, generated using Wiggles).
Prior to mapping, the reads quality was estimated using the FastQC tool v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads nucleotide positions with a quality score behind 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). After low-quality positions trimming, reads in which sequencing continued through the 3’ adapter sequence were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and reads shorter than 35nt were discarded. Reads mapping was performed using TopHat v2.0.6 (http://tophat.cbcb.umd.edu/). Wiggle track was generated using the Wiggles v1.2.0 tool from the TopHat suite.
Genome_build: mm9

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells E14 were grown on 0.1% gelatin-coated plates and maintained in DMEM (4.5g/L D-Glucose), supplemented with 15% heat-inactivated FBS, 0.1mM NEAA, 1mM Sodium Pyruvate, 0.1mM 2-Mercaptoethanol, 25U/ml penicillin, 25 μg/ml streptomycin and 1,500U/ml LIF

extract_protocol:
Approximately 10^7 cells were lysed directly on plate with 1 ml TRIzol (Invitrogen). RNA extraction was performed following manufacturer protocol.
For RNA-seq library preparation, approximately 1 μg of TRIzol (Invitrogen) isolated total RNA from mESC cells was subjected to ribosomal RNAs depletion using Ribo-Zero Gold kit (Epicentre). rRNAs-depleted RNA was used as input for RNA-seq library preparation using the TruSeq RNA Sample Prep Kit (Illumina), following manufacturer instructions

value: E14 mESC


title: rat pancreatic primary beta cell batch 2 under control condition

city: Bruxelles

first: Olatz

last: Villate

address: Route de Lennik 808 CP618

department: Faculty of Medecine

country: Belgium

institute: Universite Libre de Bruxelles

description: control

data_processing:
Sequencing reads were mapped to the Rattus norvegicus genome (version Rnor_5.0) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options and Ensembl 71 rat annotation. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify transcripts from the RefSeq reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: Rnor_5.0
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

organism: Rattus norvegicus

growth_protocol: rat pancreatic primary beta cells FACS-purified (FACSAria; BD Bioscience, San Jose, CA, USA) and cultured as described Cunha, D.A et al. 2008 J. Cell Sci., 121, 2308-2318.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) which favors purification of RNA molecules longer than 200 nucleotides, and sample preparation was done as described by the manufacturer (Illumina, Eindhoven, The Netherlands).
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2000 system

treatment_protocol: Cells were transfected with siRNA (30nM) using the Lipofectamine RNAiMAX lipid reagent (Invitrogen). Allstars Negative Control siRNA (Qiagen, Venlo, The Netherlands) was used as negative control (siCTL). This siCTL does not affect beta cell gene expression or insulin release, as compared with non-transfected cells. After 16h of transfection, cells were cultured for 48h recovery period before RNA-seqencing

value: pancreas

value: beta cell


title: rat pancreatic primary beta cell batch 1 with Nova1 knock-down

description: Nova1 knockdown


title: ChL_R2


title: CIRS-seq (Dimethyl sulfate, Replicate #2)

description:
library strategy: CIRS-seq
Ribo-depleted total RNA

data_processing:
Transcriptome reference was built from ENSEMBL (release 65) and sequences were extracted from a modified mm9 assembly with annotated SNVs  from mESC E14 cells (http://www.ncbi.nlm.nih.gov/pubmed/25004115). Supplementary analysis data/tools (transcripts annotations, sequences, Bowtie v1 index, IGV genome file) are available from: http://epigenetics.hugef-research.org/cirs.php. Raw counts BED6 files present 6 columns: 1. Official ENSEMBL ID (release 65), 2. Transcript's position (0-based), 3. Transcript's position + 1 (0-based), 4. ENSEMBL Gene Symbol, 5. RT-stops at this position, 6. Strand (+). Attached Wiggle files: 1. CIRS-seq_Reactivity_rep1.wig (Normalized reactivity for biological replicate #1), 2. CIRS-Seq_Reactivity_Combined.wig (Normalized reactivity for pooled biological replicates #1 and #2).
For reads mapping, we used a recently published mm9 reference genome assembly variant that incorporates E14 mESCs (PMID: 25004115). Prior to mapping, the reads quality was estimated using the FastQC tool v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The nucleotide positions with a quality score below 20 (Phred33 scale) were trimmed using the fastx_trimmer tool from the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). After low-quality position trimming, the reads in which sequencing continued through the 3’ adapter sequence (TGGAATTCTCGGGTGCCAAGG) were subjected to adapter clipping using the fastx_clipper tool from the FASTX Toolkit, and the reads shorter than 35 nt were discarded. The reads were then subjected to two mapping rounds on the E14 mm9 genome reference. In the first round, the reads were mapped using Bowtie v1.0.0, allowing for a maximum of 2 mismatches in the seed and allowing multiple mappings (parameters: -n 2 -a -y --best). In the second round, the unmapped reads were truncated to 35 nucleotides and mapped again with the same parameters used in the first round, except for the maximum allowed number of mismatches that was reduced to 1 (parameters: -n 1 -a -y --best).  For transcriptome analysis, the full Ensembl mouse gene annotation was downloaded from UCSC (http://genome.ucsc.edu/cgi-bin/hgTables, Table: ensGene) in the BED format, and the transcript sequences were extracted from the reference E14 genome using the fastaFromBed utility from the BEDTools v2.17.0 suite (http://code.google.com/p/bedtools/). Genome mappings corresponding to Ensembl annotated transcripts were extracted using custom Perl scripts, and converted to Ensembl transcriptome-based coordinates.
Genome_build: mm9

extract_protocol:
DMS reaction was quenched by placing samples on ice and adding 0.7M final ice-cold 2-Mercaptoethanol and 1ml ice-cold TRIzol (Invitrogen). After chloroform addition and centrifugation, one volume of 100% ethanol was added to the upper aqueous phase, and sample was purified using RNEasy Mini Spin Columns (Qiagen) to allow complete removal of 2-Mercaptoethanol and DMS. CMCT reaction was stopped by addition of 1ml ice-cold TRIzol. Samples corresponding to 0mM DMS/CMCT (NT condition), were extracted in 1ml ice-cold TRIzol.
For CIRS-seq library preparation, we first prepared pools of each treatment. The DMS sample was obtained by pooling the 50-100-150-200mM treated conditions, while the CMCT sample was obtained by pooling the 10-20-25-50mM treated conditions (~1.25 μg each). The samples obtained by treating with 0mM DMS and 0mM CMCT were pooled in equal amounts (~2.5 μg each), and constituted the Not treated (NT) control. Ribosomal RNA was depleted using Ribo-Zero Gold Kit (Epicentre). One-third of each sample (corresponding approximately to 100ng of Ribo- RNA) was subjected to reverse transcription with random hexamers using SuperScript II Reverse Transcriptase (Invitrogen). Reverse transcription reaction was carried out in 1 hour at 42°C, followed by 10 minutes at 70°C to inactivate the reverse transcriptase. Template RNA was then degraded by adding 10U of Ribonuclease H (Ambion) and incubating for 20 minutes at 37°C. After ethanol precipitation of cDNA, an adapter modified with a 5’-P group and a 3’-C3 spacer, corresponding to the reverse complement of the standard Illumina TruSeq Small RNA 5’ adapter (RC5), was ligated to cDNA 3’-OH termini using 200U of CircLigase II for 4 hours at 68°C. This approach allowed us to keep the strand-specificity of the library, so that each read will start 1nt downstream of the RT stopping point. Then, to enable ligation of a 5’ adapter, cDNA was treated with T4 Polynucleotide Kinase (NEB) in T4 DNA Ligase Buffer (NEB) for 1 hour at 37°C. After ethanol precipitation cDNA was loaded on a TBE-Urea 5% PAGE gel. A gel slice corresponding to 70-200nt was cut and cDNA was recovered by passive diffusion into diffusion buffer (500mM Ammonium acetate, 1mM EDTA, 10mM Magnesium acetate, 0.1% SDS) for 16 hours at 37°C, followed by ethanol precipitation. cDNA 5’ termini was then ligated to a second adapter, corresponding to the reverse complement of the standard Illumina TruSeq Small RNA 3’ adapter (RC3), using 200U of CircLigase II for 4 hours at 68°C. Adapter-ligated cDNA was then subjected to 15-18 cycles of PCR using standard Illumina TruSeq primers. To remove adapter dimers, library was loaded on a 3% (w/v) TBE-Agarose gel, and slice corresponding to 150-300nt was cut and purified using NucleoSpin Gel and PCR Clean-up kit (Macherey-Nagel).

treatment_protocol: Approximately 10^7 cells were harvested and lysed in 1ml of ice-cold Structure Buffer D (10mM Hepes-KOH pH 7.9, 100mM KCl, 10mM MgCl2, and 0.5% NP-40) for DMS probing, or Structure Buffer C (50mM Potassium Borate pH 8.0, 100mM KCl, 10mM MgCl2, and 0.5% NP-40) for CMCT probing, supplemented with 100U/ml RNAse Inhibitor (Ambion), 100U/ml RNAse OUT (Invitrogen), and 100U/ml Superase IN (Invitrogen). After lysis, the extract was treated with 100 μg/ml of Proteinase K (Sigma) for 15 minutes at 30°C, and reaction was stopped by adding 20 μl of Protease Inhibitor Cocktail (Sigma). Sample was then splitted in 5 x 200 μl aliquots. For DMS treatment, DMS (Sigma) was added to final concentrations of 0, 50, 100, 150, and 200mM to each aliquot, and samples were incubated at 30°C for 2 minutes with moderate shaking. For CMCT treatment, CMCT (Sigma) was added to final concentrations of 0, 10, 20, 25, and 50mM to each aliquot, and samples were incubated at 30°C for 20 minutes with moderate shaking.

tag: treatment

value: Dimethyl sulfate


title: G1E_Async_Dnase rep1

description: processed data file: G1E_Async_pooled_peaks.bed.gz; G1E_Async_pooled.bigWig


title: AL_R3

description:
transcripts.txt
AL_R_vs_AL_L.diff_expressed_transcripts.tsv
ChL_R_vs_AL_R.diff_expressed_transcripts.tsv

source_name: 6-OHDA lesioned striatum, acute L-DOPA injected


title: CIRS-seq (Not treated, Replicate #2)


title: L_H3K27me3S28p


title: CIRS-seq (N-Cyclohexyl-  N’-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate, Replicate #2)


title: CIRS-seq (Dimethyl sulfate, Replicate #1)


title: CIRS-seq (N-Cyclohexyl-  N’-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate, Replicate #1)


title: CIRS-seq (Not treated, Replicate #1)


title: AL_L3

description:
transcripts.txt
AL_R_vs_AL_L.diff_expressed_transcripts.tsv

source_name: unlesioned striatum, acute L-DOPA injected


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT spleen replicate 2

city: NEW YORK

first: Panagiotis

last: Ntziachristos

address: 522 FIRST AVENUE

department: PATHOLOGY

institute: NYU MEDICAL SCHOOL

data_processing:
Basecalls performed using CASAVA
RNA-seq reads were aligned to the mm9 genome assembly using Tophat
Differential gene expression analysis was performed for knockout vs wildtype. Analysis was performed using DEGseq.
Genome_build: mm9
Supplementary_files_format_and_content: TAB-delimited text, Degexp output containing normalized expression values

source_name: UTXWT_spleen T-ALL blasts

growth_protocol: in vivo (intravenous transplantation)

extract_protocol:
RNeasy kit (Qiagen)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina HiSeq 2000 using 50bp single-read method.

treatment_protocol: cells were isolated as cKit hematopoietic progenitors from knockout and wildtype Utx background, tansduced in vitro with Notch1-IC-expressing retroviruses and transplanted into mice

tag: genotype/variation

value: Utx wild-type (Utx+/+ or Utx+/Y)

value: spleen

value: mouse T cell leukemia cells


title: Growing

city: New York

first: Zichen

last: Wang

state: NY

address: 1468 Madison Ave

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: IMR90 cells expressing empty vector pBabe

data_processing:
The mRNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's protocol (Illumina, CA, USA).
TopHat v2.0.3 and Bowtie2 used for reads alignment with default parameters
Cufflinks v2.1.1 used for transcriptome assembly with default parameters
fragments per kilo-base per million reads (FPKM) were calculated to measure the expression for each genes
log2 fold change of FPKM values for all samples pair-wise combinations were used to call differentially expressed genes with a cutoff 1.6
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Primary fibroblast

growth_protocol: Commercially available IMR90 cells (ATCC CCL-186) were grown in DMEM supplemented with 10% FBS and penicillin/streptomycin

extract_protocol:
Cells were harvested after treatment with trypsin. Total RNA samples were isolated folowing the RNeasy kit (Qiagen) protocol
The sequencing library was prepared with the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, total RNA was poly-A-selected and then fragmented. The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina recommended 6 bp barcode bases are introduced at one end of the adaptors during PCR amplification step. The size and concentration of the RNAseq libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer.

treatment_protocol: For oncogene-induced senescence samples, IMR90s carrying a tamoxifen-inducible H-RasV12 retroviral construct were induced to senesce by addition of 10nM tamoxifen to the media for 8 days. Finally, IMR90s were infected with a retroviral construct expressing the cleaved form of H3.3 with a C-terminal Flag tag. RNA samples form this group were isolated at days 3 (early) and 13 (late) post-infection

value: Lung

tag: passage


title: H3.3cs1-induced senescence early time point

description: IMR90 cells expressing Flag-tagged cleaved H3.3. Samples harvested 3 days post-infection


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT spleen replicate 1


title: ChL_L1


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT spleen replicate 3


title: ChL_L2


title: AL_L2


title: SCCA2KO SAL Rep 3

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: SAL-treated Serpinb3a-transgenic mice Rep 3

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of read counts was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: skin tissue

growth_protocol: All mice were maintained under pathogen-free conditions in the Veterinary Biosciences Department at Cincinnati Children's Hospital Medical Center

extract_protocol:
Total RNA was extracted with the RNeasy MinElute kit  (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Day 0-  shave a 2x2 cm2 patch on the back of all the mice. Day 1 - apply 200ug ASP extract on a gauze patch and tape onto the shaved back. Day-4 remove ASP patch. Day 5- sacrifice mice, collect skin from the patched area, place in 1 ml Trizol, homogenize and isolate RNA.

value: BALB/C

value: skin

value: SAL


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT spleen rerun replicate 1


title: AL_L1

value: striatum


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT bone marrow rerun replicate 1

source_name: UTXWT_bone marrow T-ALL blasts

value: bone marrow


title: SCCA2KO SAL Rep 2

description: SAL-treated Serpinb3a-transgenic mice Rep 2


title: BALB/C WT SAL Rep 3

description: SAL-treated BALB/C wide type mice Rep 3

value: wild type


title: SCCA2KO SAL Rep 1

description: SAL-treated Serpinb3a-transgenic mice Rep 1


title: BALB/C WT SAL Rep 1

description: SAL-treated BALB/C wide type mice Rep 1


title: RNA-Seq analysis in mouse T-ALL tumors UTXKO spleen replicate 3

source_name: UTXKO_spleen T-ALL blasts

value: Utx knockout (Utx-/Y)


title: RNA-Seq analysis in mouse T-ALL tumors UTXWT bone marrow replicate 1


title: AL_R1


title: SCCA2KO ASP Rep 3

description: ASP-treated Serpinb3a-transgenic mice Rep 3

value: 200ug of Aspergillus fumigatus


title: RNA-Seq analysis in mouse T-ALL tumors UTXKO spleen replicate 2


title: SCCA2KO ASP Rep 2

description: ASP-treated Serpinb3a-transgenic mice Rep 2


title: RNA-Seq analysis in mouse T-ALL tumors UTXKO bone marrow rerun replicate 1

source_name: UTXKO_bone marrow T-ALL blasts


title: RNA-Seq analysis in mouse T-ALL tumors UTXKO bone marrow replicate 1


title: BALB/C WT ASP Rep 3

description: ASP-treated BALB/C wide type mice Rep 3


title: SCCA2KO ASP Rep 1

description: ASP-treated Serpinb3a-transgenic mice Rep 1


title: BALB/C WT ASP Rep 1

description: ASP-treated BALB/C wide type mice Rep 1


title: BALB/C WT ASP Rep 2

description: ASP-treated BALB/C wide type mice Rep 2


title: PJ-2 (Day 1)

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
MNase-seq reads were aligned to reference genome with bowtie2 while using no-unal to exclude reads that didn't align.
BAM files were converted to BED files using bamToBed.
Histone peaks were determined using DANPOS (v2.1.3) using quantile normalization; all other parameters were default.
DANTOOLS (v0.2.1) was used for the wig analysis to determine histone occupancy at TSS sites.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are the native output of DANPOS which is a table for each sample that contains information on each peak that was detected by the software.  The information in the tables include the chromosome, start, end, summit position, summit value, fuzziness score, and fuzziness p-value.

source_name: in vitro cultured mouse fetal liver erythroblasts, day 1

growth_protocol: Ter119 negative mouse fetal liver erythroblasts were cultured in IMDM containing 10% fetal bovine serum, 2 U/ml erythropoietin, 1% BSA, and insulin.

extract_protocol:
Mouse fetal liver erythroblasts obtained from 6 fetuses were cultured and purified on different days (day 0, 1, and 2). Chromatins were extracted from the purified cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue type

value: liver

value: erythroblasts


title: ASCL1_526_1

city: Dallas

first: Tao

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center

description: control.wig

data_processing:
All samples were ran on a Illumina GAIIX and basecalls were performed using CASAVA
Mapping using bowtie with parameters "-S -n 2 -e 70 -l 20 -m 3 --time -p 12 --chunkmbs 512"
Replicates were mapped individually and pooled together. Multi-mapped reads were removed in order to reduce ambiguity
Peaks called with MACS1.4.0 with parameters "-f 'SAM' -g 'hs' --keep-dup=1 --nomodel -wig -S". Reads from H524 and H526 cell lines were pooled as control. The shift size for H1184 is 74, H128 86, H1755 89, H2107 89 and HCC4018 71.
Called peaks are screened by a fold change cutoff between 11 and 19 that is specific for each dataset and chosen by manual inspection.
A hierarchical clustering algorithm is used to identify consensus peaks in the ASCL1(+) cell lines
Genome_build: hg19
Supplementary_files_format_and_content: The wiggle files are generated with span=10bp by MACS1.4.0 using parameters "-wig -S"

source_name: Tumor

growth_protocol: Cells were grown in RPMI 1640 supplemented with 10% FBS

extract_protocol:
For full ChIP protocol see Borromeo et al. Development. 2014. For extraction, nuclei were liberated from cells by dounce homogenization in PBS and then fixed in 1% formaldehyde for 10 minutes at room. temperature. Fixation was terminated by adding glycine to a final concentration of 0.125M. Chromatin was sheared by using a Diagenode Bioruptor for 30 minutes on high power with 30s:30s on:off cycles. 100 μg chromatin was immunoprecipitated with 5 μg affinity-purified mouse anti-ASCL1 antibody (BD Biosciences) followed by anti-mouse Dyna beads (Invitrogen).
All libraries were made according to Illumina’s ChIP-seq DNA sample prep protocol

treatment_protocol: No treatment performed

tag: classification

value: SCLC

tag: ascl1 expression

tag: antibody

value: mouse anti-ASCL1,BD Pharmigen, cat# 556604


title: ASCL1_4018_1

value: NE-NSCLC


title: ASCL1_4018_2


title: PJ-1 (Day 0)

source_name: in vitro cultured mouse fetal liver erythroblasts, day 0


title: ASCL1_2107_2


title: ASCL1_2107_1


title: PJ-3 (Day 2)

source_name: in vitro cultured mouse fetal liver erythroblasts, day 2


title: ASCL1_526_2

description: control.wig


title: ASCL1_524_1

description: control.wig


title: RNA-Seq analysis in mouse T-ALL tumors UTXKO spleen replicate 1


title: NoTag

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description: strain info listed in Supplemental Table S1

data_processing:
Raw reads were aligned to the sacCer2 genome assembly using Bowtie1 with options "--best --strata --chunkmbs 512 -Sam 20"
Data were filtered to retain only the mapped reads with at most 5 hits in the reference
Genome_build: sacCer2
Supplementary_files_format_and_content: Signal density in bigwig format

organism: Saccharomyces cerevisiae

source_name: whole organism

extract_protocol:
Sample preparation and DNA analysis for ChIP-seq (Preti et al. 2010) were carried out as described.
Chromatin for MNase digestion was prepared essentially as described (Kent and Mellor 1995). Spheroplasts derived from 100-mL cultures were treated with either 0.5 U (underdigested) or 2 U (overdigested) of MNase (Sigma) for 45 min at 37°C. Samples were then decrosslinked and DNA was precipitated.
Purified and precipitated DNA was sequenced using the modified paired-end TruSeq protocol (Illumina) (Henikoff et al., 2011).


title: Input


title: Hmo1

value: Anti-Flag from Sigma (#F1804)

value: Flag-tagged Hmo1


title: ASCL1_4018_3


title: ASCL1_1755_1


title: ASCL1_128_1


title: dme_Embryo_6h

city: Seoul

first: Yeon

last: Choi

address: Building 504 Room 501, School of Biological Sciences, Seoul National University, 1 Gwanangno, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
small RNA-Seq
processed data file: dme_miRNA-TMM.csv

data_processing:
The base calling was done by Illumina Pipeline (CASAVA) v1.8.2.
The 3′ adaptor sequences starting with “TGGAATTC” were removed, and the sequence reads with short length (<16 nt) or artifacts (e.g. long homopolymer) or low quality (Phred quality <30 in >15% of nucleotides) were filtered out using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Filtered sequence reads from Drosophila melanogaster and Danio rerio were aligned to dm3 and danRer7 reference genomes from UCSC, respectively. The BWA short-read aligner (Li and Durbin, 2009) version 0.7.5a-r405 was used for the alignment, with options of ‘18nt long seed length’ and ‘no allowed mismatches in the seed region.
Each aligned read was classified using intersectBed in Bedtools (Quinlan and Hall, 2010) with annotations retrieved from RefSeq, GtRNAdb, FlyBase, RepeatMasker, Rfam, and miRBase.
We collected reads that perfectly match to the mature miRNA sequences annotated in miRBase as well as those that have 3’ additions to the perfectly matching sequences. Sample-wise normalization of miRNA read counts was done by TMM normalization (Robinson and Oshlack, 2010) using edgR package (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html).
Genome_build: dm3 (GCF_000001215.2); danRer7 (GCA_000002035.2)
Supplementary_files_format_and_content: *.classcount.csv : comma separated files containing sequencing statistics. Column class indicates each class of RNA. Column reads indicates number of sequence reads mapped on each class of RNA. Column proportion indicates the read count proportion to the total pre-processed reads of each class of RNA; dme_miRNA-TMM.csv : comma separated files containing expression level of miRNAs normalized by TMM. Column hairpin indicates name of each mature miRNA.  Rest of the columns indicates the normalized expression levels of each mature miRNA in each sample.

organism: Drosophila melanogaster

source_name: embryo

extract_protocol:
Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit (Illumina) according to manufacturer’s guide. For each library, 10 ug of total RNA was separated on 15% urea-PAGE. RNA of 15-29 nt was gel-purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated (NEB). After gel purification of 3’ adaptor-ligated RNA, the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse-transcribed by SuperScript II (Life Technologies) and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by HiSeq 2000 or HiSeq 2500.
Total RNA was extracted using TRIzol reagent for each experimental condition.

tag: developmental stage

value: embryo 4h-6h


title: ASCL1_1184_1


title: dme_Embryo_4h

value: embryo 3h-4h


title: dme_Embryo_3h

value: embryo 2h30m-3h


title: dme_Embryo_2h30m

value: embryo 2h-2h30m


title: dme_Embryo_2h

value: embryo 1h30m-2h


title: dme_Embryo_60m

value: embryo 45-60m


title: dme_Embryo_1h30m

value: embryo 60m-1h30m


title: dme_Embryo_45m

value: embryo 30-45m


title: dme_Embryo_15m

value: embryo 0-15m


title: dme_wispy_0_2h

source_name: egg

value: wispKG5287 (wispy knockout)

value: unfertilized egg 0-2h


title: MNase_over_digested


title: dme_w1118_0_2h


title: dme_Embryo_30m

value: embryo 15-30m


title: MNase_under_digested


title: Fhl1_myc

value: Custom mouse monoclonal anti-myc

value: myc-tagged Fhl1


title: Fhl1_DeltaFH_FLAG

value: Flag-tagged Fhl1 with deletion of forkhead domain


title: BALB/C WT SAL Rep 2

description: SAL-treated BALB/C wide type mice Rep 2

tag: strain

value: BALB/C

value: wild type

value: skin

value: SAL


title: Fhl1_FLAG

value: Anti-Flag from Sigma (#F1804)

value: Flag-tagged Fhl1


title: dme_w1118_0_3h

description: small RNA-Seq

value: unfertilized egg 0-3h


title: Rap1

value: Custom rabbit polyclonal anti-Rap1


title: Ifh1

value: myc-tagged Ifh1


title: Fhl1_DeltaFH_myc

value: myc-tagged Fhl1 with deletion of forkhead domain


title: HC

city: Qingdao

first: Xuelin

last: Zhao

address: Yushan Road 5

department: Fisheries College

country: China

institute: Ocean University of China

data_processing:
Basecalls performed using Off-line Base Caller version 1.8
Raw data were preprocessed to remove nonsense sequences and was assembled as contigs by Velvet (version 1.0.15) and Oases (version 0.1.18) software.
Sequenced reads were masked for low-complexity or low-quality sequence, then mapped to contigs assembled using Bowtie version 0.12.5
Reads Per Kilo bases per Million reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. In short, The number of reads falling in the contigs assembled were counted and normalized by the size of the two libraries, respectively.
Genome_build: contigs by assembling two libraries
Supplementary_files_format_and_content: List files were generated using Newbler version 2.7, including sequences that were aligned the same ones and the occurrence of each sequence.

organism: Magallana hongkongensis

source_name: Gill

extract_protocol:
Gills were removed and kept in RNA store. The total RNA was harvested using TRIzol reagent. Poly-A RNA was extracted from each total RNA sample using MicroPoly(A)PuristTM Kit (Part# AM1919M) according to manufacturer’s instructions and pooled for cDNA synthesis. cDNA samples were prepared following the protocol from Ng et al., Nat Methods, 2009. Briefly, first-strand cDNA was synthesized using SuperScript II reverse transcriptase (Cat#18064-014) with Gsul-oligo-dT primer. The second-strand cDNA was synthesized using Ex Taq polymerase (Cat# RR001A).
Construct cDNA library. Methods is as followed: the synthetic cDNA was mode to 300-500 bp by a UTR200 sonication device, The fragments were amplified with TruSeq PE cluster kit v3-cBot-HS (Cat# PE-401-3001) and used to construct libraries with TruSeqTM DNA sample prep kit-set A (Cat#FC-121-1001) according to the manufacturer’s instructions.

treatment_protocol: Twenty four oysters were devided evenly into two groups, one was exposed in optimal salinity seawater (25‰) and the other was exposed in low salinity seawater (8‰) for 8 hours.

tag: tissue

value: Gill

tag: handing time

value: 8 hours

tag: condition

value: in optimal salinity seawater

tag: development stage

value: adult


title: Seedlings

city: Bet Dagan

first: Tzahi

last: Arazi

state: ISRAEL

address: Institute of Plant Sciences, ARO the Volcani Center

department: Institute of Plant Sciences

country: Israel

institute: ARO - Volcani Center

description: deep sequencing

data_processing:
Raw sequencing data were processed with the ACGT-miR-v3.5 package (LC Sciences) to filter out adaptors, technical impurities, repetitive sequences, and low-quantity reads (<3) while applying length-cutoff values (15–26 nt), resulting in a nonredundant sequence list
Genome_build: http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Egrandis
Supplementary_files_format_and_content: Tab delimited file including small RNA sequence and reads per milion (RPM)

organism: Eucalyptus grandis

source_name: whole seedlings

growth_protocol: growth chamber with a 16 h light period and 8 h dark period 24 °C

extract_protocol:
RNA purification kit (Norgen Biotek, Thorold, Ontario, Canada)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Germination on MS medium

tag: age

tag: genotype

value: a pool of seedlings

value: roots stems leaves


title: RhpR-HA-1

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
ChIP-seq reads were mapped to the P. syringae pv. phaseolicola genomes, using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (CK vs RhpR-HA) (version 2.0.0)
RhpR binding motif was identified by MEME.
Genome_build: Pseudomonas syringae pv. Phaseolicola
Supplementary_files_format_and_content: rhpr_peaks.xls

organism: Pseudomonas savastanoi pv. phaseolicola

source_name: liquid culture in minimal medium

growth_protocol: King's B medium and minimal medium

extract_protocol:
P. syringae was cultured in KB medium supplemented with spectinomycin until the mid-log phase (OD=0.6), before transfered to MM for 4h. Pellet was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol: grow until mid-log phase in KB, then transfer to MM for 4h

tag: antibody manufacturer

value: Sigma

tag: antibody name

value: EZview Red Anti-HA Affinity Gel

tag: antibody catalog number

tag: antibody lot/batch number


title: CK-1

tag: genotype/variation


title: CK-2


title: S3_caIBDV_12hpi

first: Raymond

last: Hui

address: 5N01, Kadoorie Biological Sciences Building, The University of Hong Kong, Pokfulam

department: School of Biological Science

institute: The University of Hong Kong

data_processing:
Raw reads generated from the run were demultiplexed and underwent quality trimming prior to the downstream analytical pipelines. Only reads with Q Score >/30, and aligned with corresponding paired reads were retained for the differential expression analysis.
The paired-end sequence reads of individual sample were aligned and mapped to the chicken reference genome (Gallus gallus reference genome Galgal4.73) with STAR RNA-Seq aligner 2.3.0 in default setups.
The mapped reads were then converted to binary BAM files with SAMtools 1.0.2 for transcript expression levels comparison.
The expression levels at the isoform and gene level were calculated with Cuffdiff package in Cufflink transcript assembly tool.
Genome_build: Gallus_gallus-4.0 (Galgal4)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Gallus gallus

source_name: Chicken embryonic fibroblast cells DF-1, caIBDV infected, 12 hpi

extract_protocol:
Total RNAs were extracted from cell lysates with SV96 Total RNA Isolation System (Promega, WI) according to manufacturer's protocol.
Four micrograms of each total RNA were used for cDNA library construction using TruSeq RNA Sample Prep Kits v2 (Illumina, CA) according to the Low Sample (LS) Protocol of the TruSeq RNA Sample Preparation v2 Guide (Part# 15026495 Rev. D September 2012, Illumina, CA). The libraries were indexed with individual adaptor and normalized with Library Quantification Kit - Illumina/ Universal (Kapa Biosystems, MA) according to manufacturer's instructions.

treatment_protocol: Chicken embryo fibroblast DF-1 cells were infected with cell-adapted Infectious Bursal Disease Virus (caIBDV) or mock infected, and cells were analyzed 0, 6 and 12 hpi.

tag: cell line

tag: cell type

value: embryonic fibroblast cell line

tag: treatment

value: infected with 10 m.o.i cell-adapted Infectious Bursal Disease Virus

tag: time point

value: 12 hpi


title: S2_caIBDV_6hpi

source_name: Chicken embryonic fibroblast cells DF-1, caIBDV infected, 6 hpi

value: 6 hpi


title: HT

value: in low salinity seawater


title: S1_caIBDV_0hpi

source_name: Chicken embryonic fibroblast cells DF-1, caIBDV infected, 0 hpi

value: 0 hpi


title: S3_NIC_12hpi

source_name: Chicken embryonic fibroblast cells DF-1, mock infected, 12 hpi

value: mock infected


title: Glc rep2

city: Madison

first: Dan

last: Cullen

state: WI

address: One Gifford Pinchot Dr

institute: UW/FPL

description: run254.G2_GTGAAA_L008_R1 - Glc rep2  RPKM

data_processing:
Cluster generation was performed using a TruSeq Single Read Cluster Kit (v3) and the Illumina cBot, with libraries multiplexed in a single HiSeq2000 lane.
Images were analyzed using CASAVA version 1.8.2 and FASTQ files generated.
RPKM generated. DNAStar Inc (Madison, WI) modules SeqNGen and Qseq were used for mapping reads and statistical analysis.
Final fastq files processed using DNASTAR modules SeqNGen and Qseq
Genome_build: DoE JGI models (http://genome.jgi.doe.gov/Phlgi1/Phlgi1.home.html)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Phlebiopsis gigantea

growth_protocol: Mycelium was derived from triplicate cultures of 250 ml basal salts containing: 1. 2.5 g freshly-harvested, ground (1mm mesh) loblolly pine that had been ‘spiked’ with acetone and thoroughly dried (NELP); or 2. The same material following extended soxhlet extraction and drying (ELP).  Duplicate cultures of basal salts medium with glucose as sole carbon source also served as a reference. After 5 days incubation, total RNA was purified from frozen mycelium

extract_protocol:
Total RNA was purified using the RNeasy Maxi kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol for RNA cleanup.
The Illumina TruSeq protocol was used to prepare samples for multiplexed HiSeq2000 sequencing. Briefly, total RNA samples were tested at the University of Wisconsin-Madison Biotechnology Center for quality control (NanoDrop Spectrophotometer and Agilent 2100 BioAnalyzer for purity and integrity verification, respectively). For RNA-Seq library preparation, each library was generated using Illumina’s “TruSeq RNA Sample Preparation Guide” (Illumina Part # 15008136, Rev. A, August 2011) and the Illumina TruSeq RNA Sample Preparation Kit (Illumina Inc., San Diego, California, USA). Messenger RNA was purified from 1μg total RNA using poly-T oligo-attached magnetic beads. Double-stranded cDNAs were synthesized using SuperScript II (Invitrogen, Carlsbad, California, USA) and random primers for first strand cDNA synthesis followed by second strand synthesis using DNA polymerase I and RNAse H for removal of mRNA. Double-stranded cDNA was purified using Agencourt AMPure XP beads (Qiagen, Valencia, California, USA) as recommended in the TruSeq RNA Sample Prep Guide. cDNAs were end-repaired by T4 DNA polymerase and Klenow DNA polymerase and phosphorylated with T4 polynucleotide kinase. The blunt ended cDNA was purified using Agencourt AMPure XP beads. The cDNA products were incubated with Klenow DNA polymerase to add an ‘A’ base (Adenine) to the 3’ end of the blunt phosphorylated DNA fragments and then purified using Agencourt AMPure XP beads. DNA fragments were ligated to Illumina adapters having a single ‘T’ base (Thymine) overhang at their 3’end. The adapter-ligated products were purified using Agencourt AMPure XP beads.  Adapter ligated DNA was amplified in a Linker Mediated PCR reaction (LM-PCR) for 15 cycles using PhusionTM DNA polymerase and Illumina's PE genomic DNA primer set, then purified using Agencourt AMPure XP beads. Quality and quantity of the finished libraries were assessed using an Agilent DNA1000 series chip assay (Agilent Technologies, Santa Clara, CA) and Invitrogen Qubit HS Kit (Invitrogen, Carlsbad, California, USA), respectively, and libraries standardized to 2 μM.  Cluster generation was performed using a TruSeq Single Read Cluster Kit (v3) and the Illumina cBot, with libraries multiplexed in a single HiSeq2000 lane. Images were analyzed using CASAVA version 1.8.2 and FASTQ files generated. DNAStar Inc (Madison, WI) modules SeqNGen and Qseq were used for mapping reads and statistical analysis.

value: mycelia

tag: carbon source substrate

value: Glucose (reference)


title: RhpR-HA-2


title: S2_NIC_6hpi

source_name: Chicken embryonic fibroblast cells DF-1, mock infected, 6 hpi


title: Zeb_fish_Emb_t_24h

description: small RNA-Seq

organism: Danio rerio

value: WT

tag: developmental stage

value: embryo 24h


title: S1_NIC_0hpi

source_name: Chicken embryonic fibroblast cells DF-1, mock infected, 0 hpi


title: ELP rep1

description: run254.E1_AGTTCC_L008_R1 -ELP rep1 RPKM

source_name: mycelia_acetone extracted lobollly pine

tag: tissue

value: Extracted loblolly pine (ELP)


title: ELP rep2

description: run254.E2_ATGTCA_L008_R1 -ELP rep2 RPKM


title: Zeb_fish_Emb_t_30m

description: small RNA-Seq

value: embryo 30m


title: ELP rep 3

description: run254.E3_CCGTCC_L008_R1 -ELP rep3 RPKM


title: Glc rep1

description: run254.G1_GTCCGC_L008_R1 -Glc rep1 RPKM


title: cassava_stems_+TALE1Xam_5dpi_2

city: Montpellier

first: Alvaro

middle: Luis

last: Pérez-Quintero

state: Montpellier

address: 911 Avenue Agropolis

department: RBP

country: France

institute: IRD

data_processing:
Quality of the libraries was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reads with more than 80% of bases with Phred quality values lower than 20 were excluded.
Reads were mapped against the cassava genome Cassava4 using tophat (default parameters) (Trapnell et al. 2012) and FPKM (fragments per kilobase of exon per million fragments mapped) values for annotated cassava genes were obtained with cufflinks (Trapnell et al. 2012).
Genome_build: Cassava4 available from http://www.phytozome.net/cassava.php
Supplementary_files_format_and_content: Cassava_FPKMs.txt containing FPKM values for annotated genes in the version 4 of the cassava genome, FPKM values obtained with the Tuxedo suite

molecule: polyA RNA

organism: Manihot esculenta

source_name: Cassava stems incoulated with Xam strain ORST4+TALE1Xam, collected at 5dpi

growth_protocol: Cassava plants from variety MCOL1522 (susceptible to Xam)  were obtained from CIAT germplasm collection. Plants were propagated, multiplied and maintained in greenhouse conditions (day/night temperature 28/19°C, photoperiod 12h, and relative humidity = 80%). 8-weeks-old plants were used for all assays. Xam strain ORST4 (CFBP1851Δp44 in (Castiblanco et al. 2013)) is a spontaneous non-pathogenic mutant lacking TALE1Xam due to a deletion in the plasmid that contains the effector  (Castiblanco et al. 2013). For functional studies this strain was previously complemented with TALE1Xam (+TALE1Xam\). Both strains were streaked onto YPGA medium (5% yeast extract, 5% peptone, 5% glucose and 15% agar) and incubated at 28°C for growth.

extract_protocol:
Samples collected were immediately submerged in liquid nitrogen and then stored at -80°C. 100mg of grounded tissue was incubated in lysis buffer (b-mercaptoethanol 2%, PVP, 2%, SDS 1%, EDTA 25mM, NaCl 100mM and tris HCl pH 7.5 100mM). RNA extraction was carried out with acid phenol:cloroform:isoamylic 25:24:1 and precipitated using  NaCl 5M and ethanol. RNA was treated with DNAse I following the instructions of commercial manufacturer (Ambion). Once the DNA-free total RNA was obtained it was visualized by agarose gel electrophoresis and quantify in NanoDrop (Thermo Scientific).
Protocol for library constriction was adapted from (Zhong et al. 2011). Six RNAseq libraries were constructed from 7ug of DNA-free mRNA purified by oligo dT25 Dynabeads (invitrogen).  cDNA was synthesized employing Superscript III Reverse Transcriptase (Life technologies). cDNA quality and quantification was done using an Agilent Bioanalyzer on a High sensitivity DNA chip (Agilent Technologies) and an equal amount (20-50 ng) of index libraries were pooled together. The libraries were sequenced in two different lanes of Illumina Sequence (technical replicates). Each library was Paired End (PE) sequenced.

treatment_protocol: For inoculations, one colony was grown onto YPG medium and incubated at 28°C for 18h. Liquid inoculums were calibrated at OD600nm= 0.02, corresponding to 108 colony forming units (CFU). For stem inoculation, a puncturing with a sterile toothpick was made on the third internode from the apical region. 10ul of calibrated inoculum was placed on the puncture.Three cms (2 cms above and one below the inoculation point) were collected at 0, 5 and 7 days post inoculation (dpi).

tag: host

value: cassava (Manihot esculenta)

tag: host variety

tag: inoculation

value: Xam (Xanthomonas axonopodis pv. manihotis)

tag: xam strain

value: ORST4+TALE1Xam (pathogenic)

tag: time

value: stem


title: NELP rep3

description: run254.T3_AGTCAA_L008_R1 - NELP rep3 RPKM

source_name: mycelia_ freshly harvested loblolly pine

value: Non-extracted loblolly pine (NELP)


title: NELP rep2

description: run254.T2_CTTGTA_L008_R1 -NELP rep2 RPKM


title: cassava_stems_+TALE1Xam_0dpi_2

source_name: Cassava stems incoulated with Xam strain ORST4+TALE1Xam, collected at 0dpi


title: cassava_stems_+TALE1Xam_7dpi_2

source_name: Cassava stems incoulated with Xam strain ORST4+TALE1Xam, collected at 7dpi


title: cassava_stems_ORST4_7dpi_2

source_name: Cassava stems incoulated with Xam strain ORST4, collected at 7dpi

value: ORST4 (non-pathogenic)


title: Zeb_fish_Emb_t_10m

description: small RNA-Seq

source_name: embryo

value: embryo 10m


title: Zeb_fish_Emb_t_0m

description: small RNA-Seq

source_name: egg

value: embryo 0m


title: AL_R2

first: Mads

address: Blegdamsvej 3C

institute: University of Copenhagen

data_processing:
Sequenced reads were processed by the Genomatix GMBH pipeline, and differential expression was computed by using their integration of DeSeq.
Genome_build: mm9
Supplementary_files_format_and_content: transcripts.txt: Tab separated text file containing read counts and normalized expression from all samples
Supplementary_files_format_and_content: *.diff_expressed_transcripts.tsv: Tab separated text file containing read counts and normalized expression, log2fd, and p-values

source_name: 6-OHDA lesioned striatum, acute L-DOPA injected

extract_protocol:
Mice were killed by decapitation 1h after a single dose of L-DOPA (AL samples) or 1h after the last dose after 9 days of daily L-DOPA injections (ChL samples). The heads of the animals were cooled in liquid nitrogen for 6 s and the brains were removed. Coronal slices of 1 mm thickness were obtained from a mouse brain dissection matrix, and three striatal punches of 2 mm diameter from sequential slices were dissected out on an ice-cold surface. The tissue was incubated in RNAlater for storage. RNA was extracted using RNease plus universal kit (Qiagen).  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: striatum


title: ZFL

city: Dunedin

first: Aniruddha

last: Chatterjee

state: Otago

address: 270 Great king Street

department: Pathology

country: New Zealand

institute: University of Otago

data_processing:
DNA from the RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Single CpG site methylation calculation was perfromed using the R package methylKit.
UNIX scripts and our in house developed tool DMAP (Stockwell et al 2014, Bioinformatics) was used for post processing of the data
Genome_build: Zv9
Supplementary_files_format_and_content: .txt files describing methylation status of each filtered CpG sites.

source_name: Liver

extract_protocol:
The liver methylome was a pool of 5 male and 5 female liver harvested by dissection. Required DNA for RRBS library preparation was used from this pooled samples.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 100bp run.

value: Liver


title: Hela_RASL-seq_si-NC+pcDNA3.0_rep3

status: Public on Oct 08 2014

city: Wuhan

first: Bo

last: Yang

state: Hubei

address: Luo-jia-shan, Wuchang

department: Biochemistry and Molecular Biology

institute: College of Life Sciences, Wuhan University

description:
RASL-seq library from cells of transfection of NC siRNA and pcDNA3.0
Library strategy: RASL-Seq

data_processing:
The sequences were mapped to the oligo pool sequences by Bowtie. The processed data file contain both the genomic location (the first 6 columns) and counts for the short and long isoforms (last 2 columns) of each alternative splicing event.
Genome_build: hg18
Supplementary_files_format_and_content: bedGraph and bed files

source_name: Hela Cells

growth_protocol: Hela cells were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM, Gibico) supplemented with 10% fetal bovine serum (FBS) at 37 degress Centigrade and 5% CO2.

extract_protocol:
Total RNAs were extracted by Trizol from treated HeLa cells.
1 µg of Hela total RNA was mixed with 100 fmol of human RASL oligos, 2 pmol of biotinylated-oligo-dT and 5 µl of streptavidin magenetic beads. Followed by one hour of annealing at 45ºC, magnetic beads were washed 3 times by washing buffer. Then ligation was achieved by adding 5U of T4 DNA ligase for 1 hour at 37ºC. After 3 times of wash, ligated oligos were eluted to water by heating at 65ºC for 5 minutes, and then PCR amplified using primers containing sequencing adaptor and barcode sequences. PCR products were purified and sequenced.

treatment_protocol: Transfection of NC siRNA and pcDNA3.0

value: Hela

tag: transfection

value: NC siRNA and pcDNA3.0


title: cassava_stems_ORST4_5dpi_2

source_name: Cassava stems incoulated with Xam strain ORST4, collected at 5dpi


title: Female2

data_processing:
DNA from 4 RRBS were sequenced in Illumina HiSeq Machines, Base-calling perfromed using RTA software and demultiplexed to obtain individual Fastq files.
Single CpG site methylation calculation was perfromed using the R package methylKit.
UNIX scripts and our in house developed tool DMAP (Stockwell et al 2014, Bioinformatics) was used for post processing of the data
Genome_build: Zv9
Supplementary_files_format_and_content: .txt files describing methylation status of each filtered CpG sites.

source_name: Brain

extract_protocol:
Brains were dissected from 12 male and 12 female zebrafish and were halved through the sagittal plane. 2 male and 2 female RRBS library was prepared with each library containing a pool of six halved zebrafish brain.  A total of four RRBS libraries were prepared from 2 pooled male brain and 2 pooled female brain library each containing 6 halved zebrafish brain.
Genomic DNA was digested with MspI (New England Biolabs, Ipswich, MA) followed by end repair and addition of 30 A overhangs. Methylated adaptors (Illumina, San Diego, CA) with a 30 T overhang were then ligated with the generated fragments. Following adaptor ligation, DNA fragments ranging from 40 to 220 bp (preligation size) were cut from a 3% (w/v) NuSieve GTG agarose gel (Lonza, Basel, Switzerland) and subsequently bisulphite modified using the EZ DNA methylation kit (Zymo Research, Irvine, CA). The final library was amplified by PCR. The resulting library was sequenced on an Illumina platform with a single-ended, 49bp run.

value: Whole Brain


title: NELP rep 1

description: run254.T1_GGCTAC_L008_R1 - NELP rep1 RPKM

value: mycelia


title: Male2


title: cassava_stems_ORST4_0dpi_2

source_name: Cassava stems incoulated with Xam strain ORST4, collected at 0dpi


title: Female1


title: cassava_stems_+TALE1Xam_7dpi_1


title: cassava_stems_+TALE1Xam_5dpi_1


title: Male1


title: dme_Embryo_11-12h_spike-in

description: small RNA-Seq

extract_protocol:
Small RNA cDNA libraries were generated using TruSeq small RNA sample preparation kit (Illumina) according to manufacturer’s guide.   Four synthetic RNA oligos were used for spike-ins, after 5’end phosphorylation by T4 PNK. Four different amount of spike-ins (0.5, 2,4,8 fmole) were added to 10ug total RNA of each sample. For each library, 10 ug of total RNA was separated on 15% urea-PAGE. RNA of 17-29 nt was gel-purified and then ligated to the 3’ adaptor with T4 RNA ligase2 truncated (NEB). After gel purification of 3’ adaptor-ligated RNA, the 5’ adaptor ligation was performed using T4 RNA ligase1. The ligation product was reverse-transcribed by SuperScript II (Life Technologies) and amplified by PCR with Phusion DNA polymerase. The cDNA libraries were sequenced by MiSeq.
Total RNA was extracted using TRIzol reagent for each experimental condition.

value: embryo 11-12h


title: cassava_stems_+TALE1Xam_0dpi_1


title: cassava_stems_ORST4_7dpi_1


title: dme_Embryo_2-3h_spike-in

description: small RNA-Seq

value: embryo 2-3h


title: cassava_stems_ORST4_0dpi_1


title: dme_Embryo_0-1h_spike-in

description: small RNA-Seq

value: embryo 0-1h


title: cassava_stems_ORST4_5dpi_1

value: cassava (Manihot esculenta)


title: F. graminearum 96h

status: Public on Sep 30 2014

city: East Lansing

first: Frances

last: Trail

state: MI

address: 612 Wilson Road

department: Plant Biology; Plant, Soil and Microbial Sciences

institute: Michigan State University

data_processing:
The libraries were run on six lanes of an Illumina Genome Analyzer II, generating an average of 30 million single-end reads of 36 bases each.
The program Tophat v1.2.0 was used to perform spliced alignments of the tags against the F. graminearum genome, strain PH-1, obtained from the Broad Institute (http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html).
We scored results only for tags that mapped to a single unique location in the genome (--max-multihits option was set to 1) with less than three mismatches (--splice-mismatches option was set to 2). We used the default settings for all other Tophat options. We tallied tags aligning to exons of genes with the program HTSeq v0.4.5p6
The data was normalized and differential expression was calculated by fragments per kilobase per million mapped reads (FPKM) using Cufflinks and Cuffdiff v.1.0.3
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html
Supplementary_files_format_and_content: Tables of FPKM values for all predicted genes at each time-point. Text file with LOX  output.

organism: Fusarium graminearum

source_name: perithecia

growth_protocol: Carrot agar (60 mm diam. Petri dish) was center-inoculated with 10 μl of F. graminearum strain PH-1 conidial stock solution and incubated under continuous light at room temperature (22–24 °C) until the mycelium reached the edge of the plate. Sexual development was induced by gently removing the surface mycelium and applying 900 μl of 2.5% Tween-60 to the surface of the plates. Development at each time-point was examined prior to sample collection to confirm that the cultures reached the appropriate stage of development. For later stages, where individual perithecia were visible, the representative cultures were checked by performing squash mounts of individually harvested perithecia.

extract_protocol:
RNA was isolated from homogenized material with TRIzol reagent (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen).
Standard Illumina protocol

treatment_protocol: Material was flash frozen on dry ice, lyophilized and stored at -80 °C.

tag: timepoints

value: 96h after induction of sexual development

value: perithecia


title: F. graminearum 144h

value: 144h  induction of sexual development


title: SVZ H3K9me3 ChIP-Seq

city: San Antonio

first: Chin-Hsing Annie

last: Lin

address: One UTSA Circle

department: Biology

institute: University of Texas at San Antonio

data_processing:
Basecalls performed with Illumina RTA version 1.12.4.2
Reads were aligned to the Rhesus Macaque reference rheMac with Bowtie version 0.12.7 using the following parameters: bowtie -p 8 --mm -n 2 -m 1 --best --phred33-quals
FDR 5% Peaks were called with the MACS2 program, using -q 0.05
Genome_build: rheMac2
Supplementary_files_format_and_content: xls file containing ChIP-Seq peak calls generated from MACS2, with FDR = 0.05

organism: Papio anubis

source_name: neural progenitors cells

extract_protocol:
We manually conjugated antibody against cell type markers, such as GFAP, Nestin, Vimentin, PSA-NCAM, or Doublecortin to Dynabeads. We then used the Dynabeads-conjugated antibody to purify cells dissociated from SVZ microdissection. Briefly, cells from fresh dissected baboon SVZ were immediately dissociated with Accutase, equilibrated in binding buffer containing phosphate-buffered saline (PBS), 0.05% TritonX-100 (or saponin, detergent choice depends upon antibody), and subsequently subjected to Dynabeads-conjugated antibody purification. After elution with high salt and pH-gradient buffer, the purified populations were crosslinked in 1.1% formaldehyde before chromatin shearing by Diagenode Bioruptor. The resulting sheared chromatin fragments in a size range between 200 to 500 base pairs were incubated with H3K9me3 antibody-conjugated Protein A Dynabeads (Millipore #07-473, Upstate #07-442; Active Motif #39162; Life Technology Dynabeads protein A) overnight. For normalization, the aliquot of sheared chromatin fragments were incubated with antibody against total histone 3-conjugated Protein A Dynabeads (unmodifiedH3 antibody, Millipore #05- 499; 1:1000). Subsequently, enriched chromatin fragments were eluted, subjected to de-crosslink, purified for library preparation (Illumina Library Kit) and sequenced with 200millinon tags through Illumina HiSeq2000 sequencer.
Libraries were prepared according to instructions for Illumina Library Kit, Illumina  TruSeq v2. Total H3 reads are maintained in GEO Sample GSM1413005.

value: brain

tag: region

value: subventricular zone

value: neural progenitors cells

tag: chip antibody

value: H3K9me3 antibody

tag: chip antibody info


title: F. graminearum 48h

value: 48h after induction of sexual development

tag: cell type


title: F. verticillioides 144h

data_processing:
The libraries were run on six lanes of an Illumina Genome Analyzer II, generating an average of 29 million single-end reads of 36 bases each.
The program Tophat v1.2.0 was used to perform spliced alignments of the tags against the F. verticillioides genome, from strain 7600, obtained from the Broad Institute (http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html).
We scored results only for tags that mapped to a single unique location in the genome (--max-multihits option was set to 1) with less than three mismatches (--splice-mismatches option was set to 2). We used the default settings for all other Tophat options. We tallied tags aligning to exons of genes with the program HTSeq v0.4.5p6
The data was normalized and differential expression was calculated by fragments per kilobase per million mapped reads (FPKM) using Cufflinks and Cuffdiff v.1.0.3
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: http://www.broadinstitute.org/annotation/genome/fusarium_group/GenomesIndex.html
Supplementary_files_format_and_content: Tables of FPKM values for all predicted genes at each time-point. Text file with LOX  output.

organism: Fusarium verticillioides

growth_protocol: Fusarium verticillioides strain Fv999 was grown on carrot agar. When the mycelia reached the edge of the plate (5–6 days), sexual development was induced by scraping off the surface mycelium and conidia and applying 900 μl of 2.5% Tween-60 along with the 5 μl of conidial stock of the strain of the opposite mating type, Fv149. Development at each time-point was examined prior to sample collection to confirm that the cultures reached the appropriate stage of development. For later stages, where individual perithecia were visible, the representative cultures were checked by performing squash mounts of individually harvested perithecia.


title: F. graminearum 2h

source_name: hyphae

value: 2h after induction of sexual development

value: monokaryotic


title: F. verticillioides 48h


title: F. verticillioides 72h

value: 72h after induction of sexual development


title: F. verticillioides 24h

source_name: protoperithecia

value: 24h after induction of sexual development

value: dikaryotic cells and perithecium initials


title: C- rep 3

city: Vancouver

first: David

middle: Christopher

last: Tack

state: B. C.

address: 3529-6720 University Boulevard

department: Botany

country: Canada

institute: Universtiy of British Columbia

description: Pooled first true leaf

data_processing:
CASAVA version 1.8.2
GSNAP version 2014-01-21.
gsnap -d thaliana --pairmax-rna=10000 --localsplicedist=10000 --clip-overlap -N 1 --nthreads=6 --quality-protocol=sanger --ordered --format=sam --nofails R1.fastq R2.fastq
Custom Python Scripts
Genome_build: TAIR 10
Supplementary_files_format_and_content: .tsv of counts of alternatively and constitutively spliced reads for each junction where an alternative splicing event was found

organism: Arabidopsis thaliana

source_name: first true leaf

growth_protocol: Arabidopsis thaliana (Col-0) was grown at 20ºC with a 16h/8h light/dark cycle and 70% humidity in a growth chamber.

extract_protocol:
RNA-Aqueous
Turbo DNAase
Illumina TruSeq

treatment_protocol: No special treatment

value: first true leaf

tag: ecotype


title: B- rep 2

description: Pooled first true leaf


title: F. verticillioides 2h


title: A- rep 1

description: Pooled first true leaf


title: F. graminearum 72h


title: F. graminearum 24h


title: F. verticillioides 96h


title: dme_Embryo_5-6h_spike-in

description: small RNA-Seq

tag: genotype/variation

value: embryo 5-6h


title: pSMAD_Input_HFSC

first: Maria

last: Genander

address: 1130 York Avenue

department: Laboratory of Mammalian Cell Biology and Development

institute: Rockefeller University

data_processing:
Reads were aligned to the mouse genome (mm9) using bowtie (Langmead et al., 2009)
Peaks were called using MACS 1.4 (Zhang et al., 2008).
Peaks at a false discovery cutoff of 2% were used.
The .tdf files contain the peaks and can be easily accessed through any genome browser.
Genome_build: mm9

source_name: Mouse hair follicle stem cells

extract_protocol:
Samples were prepared in accordance with previous publications (Lien et al 2011)
Library was constructed in accordance with previous publications (Lien et al 2011)

value: Hair follicle bulge stem cells


title: pSMAD_ChIP_HFSC

value: Cell Signal pSmad1/5/8 no 9511


title: Wild-type AB strain rep1

city: Dublin

first: Breandan

last: Kennedy

address: Belfield

department: UCD School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute, University College Dublin

data_processing:
Due to low sequencing quality at 3’ ends, RNA-seq reads were trimmed at 40 bp. Reads were mapped to the zebrafish genome version 9 using TopHat. Novel transcripts were assembled by Cufflinks using mapped reads. Novel transcripts less than 300 bp were discarded. RNA-seq reads were counted using HTSeq.
Genome_build: Zv9
Supplementary_files_format_and_content: counts.txt: Tab-delimited text files include gene symbol, chromosome location and No. of mapped reads and RPKM for each sample.

source_name: Whole embryo

growth_protocol: Zebrafish were handled according to standard protocols and animals studies were approved by the UCD Animal Research Ethics Committee (AREC-P-08-54). Heterozygous carriers of a recessive rx3 mutation (chkw29 allele) were mated. These fish originate from mutagenesis screens performed in AB zebrafish. Offspring were grown to the 13 hpf stage in embryo medium containing methylene blue at 28.5°C in 10 hour dark: 14 hour light cycle conditions. The eyeless mutant (rx3-/-) and eyed sibling (wild-type rx3+/+ and heterozygous rx3+/- carriers) samples were distinguished based on their morphology using a dissecting light microscope at the 8-somite stage.

extract_protocol:
Three biological replicates were collected for each sample and one replicate of wild-type (AB strain) embryos at the same developmental stage was collected. Each replicate contained pools of 10 whole embryos. Samples were collected in RNAlater (Qiagen, Hilden, Germany) and stored at 4°C until processing. The RNeasy mini RNA extraction kit was used to isolate RNA, on-column DNaseI digestion was performed and RNA was collected in RNase-free water, as per manufacturer’s instructions (Qiagen, Hilden, Germany). A Nanodrop spectrophotometer (Beckman, USA) was used to determine the concentration of RNA and a Bioanalyser (Agilent, Santa Clara, USA) was used to confirm the RNA Integrity Number (RIN) of the samples as 8 or higher.
Using 1 μg of total RNA, cDNA libraries were prepared using the mRNA-seq 8-Sample Prep Kit as per manufacturer’s instructions (Illumina, RS-100-0801). Briefly, poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, mRNA was fragmented and cDNA generated with ligated adaptors. These products were purified and PCR enriched to create the final cDNA library.

value: AB

value: Whole embryo

tag: age

value: 13 hpf

tag: genotype

value: Wild-type AB strain


title: pSMAD_ChIP_TACs

city: New York

source_name: Mouse hair follicle TACs

value: Hair follicle TACs

tag: developmental stage


title: Wild-type siblings rep3

tag: tissue

value: Wild-type siblings


title: Zn excess  Condition

city: Beijing

first: Jian

last: Wu

address: Zhongguancun Nan Da Jie 12

institute: Institute of Vegetables and Flowers, CAAS

data_processing:
Hiseq Control Software (HCS), Real-Time Analysis (RTA) and OLB V1.9.4  used for basecalling
All sequences were filtered to remove the adaptor sequences, low quality sequences (tags with unknown nucleotides), empty tags (no tag sequence between the adaptors) and singletons (tags occurring only once that might result from sequencing errors).
Then, the clean tags mapped to Brassica rapa genome using SOAP V2.20 with default parameters, allowing no more than one nucleotide mismatch; The unmapped tags were then mapped to the B. rapa genome sequence by SOAP allowing no more than one nucleotide mismatch on the sense and antisense strands.
The tags mapped to the reference database were defined as unambiguous tags. For expression analysis, the number of unambiguous tags for each gene was normalized to TPM (number of transcripts per million clean tags).
The mean TPM value of three biological replicates under the same condition was used for identification of differentially expressed genes.A statistical analysis of the frequencies of tags in each library was performed to compare the expression levels of genes under different trace metal element supply conditions according to the method described by Audic and Claverie (1997). The false discovery rate (FDR) was used to determine the threshold P-value in multiple tests. We used an absolute value of the log2(TPMtreatment/TPMcontrol) ratio ≥1 and FDR ≤ 0.001 as the threshold to judge the significance of differentially expressed genes.
Genome_build: AENI01000000
Supplementary_files_format_and_content: tab-delimited text files include number of Tags and TPM values for each condition (gene IDs from brassicadb.org)

organism: Brassica rapa

source_name: leaves

growth_protocol: Plants of B. rapa accession R-o-18 were grown in a hydroponic system with 0.5 × Hoagland’s nutrient solution in a climate-controlled growth chamber set at 70% humidity with a 20/15°C (12h/12h) day/night temperature regime. The plants were grown in normal nutrient solution (2 µM Zn, 3µM Fe, without Cd) for 14 days.

extract_protocol:
Total RNA was extracted from the harvested leaves of B. rapa using the RNeasy Plant Mini Kit (Qiagen) and DNase treated with RNase-free DNase set (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The plants were subjected to Fe deficiency (FeD; 0.05µM), Zn deficiency (ZnD; 0.005 µM), Zn excess (ZnE; 50µM), or Cd exposure (CdE; 1 µM) treatments. Plants kept under normal nutrient conditions were used as a control. Three replicates were used for each treatment, with three plants for each replicate. Zn was added into nutrient solutions as ZnSO4·7H2O, Fe was supplied as Fe(Na)EDTA and Cd was applied as 3CdSO4·8H2O. After 7 days exposure to the treatments, the first pair of expanded leaves of each plant was harvested for RNA extraction. The nutrient solutions were refreshed every 4 days.

tag: treatment

value: 50µM Zn

value: leaves


title: Cd exposure Condition

value: 1 µM Cd


title: Zn deficiency Condition


title: rx3-/- rep3


title: Wild-type siblings rep1


title: AA

city: Hangzhou

first: Muhammad Awais

last: Ghani

state: Zhejiang

address: Room# 517, Buliding A, College of agriculture and biotechnology, Zhejiang university

department: Horticulture

institute: Zhejiang University

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

source_name: Leaves

growth_protocol: All of the plants were grown in vermiculite mixed with 30% soil in a growth chamber under growth conditions of 22/18°C (day/night) and 16 h of illumination per day.

extract_protocol:
The total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions and was sent to Beijing Genomics Institute (BGI) for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaves

value: 45 days after seed germination

tag: generation

value: female parent


title: pSMAD_Input_TACs

organism: Mus musculus


title: Fe deficiency Condition

value: 0.05µM Fe


title: Synthetic - bisSeq 1

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

description: Synthetic library: E.coli transformation of mouse fragments (selected)

data_processing:
150bp long reads were splited in three instances (40-70-40bp). Short reads were used directly.
Bismark/ Bowtie 0.12.7 were used to align bisulfite reads against an in silico converted reference genome (C>T and G>A) and call methylation state for each CG. (mouse-mm9; Ecoli-NC_010473.1)
CGs covered by at least 10 reads were used for analysis. Strain specific SNPs were masked.  Methylation was called per CG and fragment averages were derived using the previously established reference set of regions for the library. Only fragments where >50% of the CG and a minimum of 4 CGs were covered were considered in the analysis.
Genome_build: mm9/NC_010473.1
Supplementary_files_format_and_content: tab delimited fragment report : Fragment level average methylation call

organism: synthetic construct

source_name: synthetic

growth_protocol: Wild type embryonic stem cells derived from pure 129S6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA (2μg) of ES cells carrying the libraries was bisulfite converted with the EpiTec Bisulfite Kit (QIAGEN). Libraries were amplified by PCR (AmpliTaq Gold-Invitrogen) using bisulfite compatible primers (5’-AACCTAACTATAATAAACAACC-3’; 5’-GGTATATGTATTTTTTTAGGGT-3’) annealing to the universal priming region flanking the fragments cloning site. PCR product was gel purified and fragmented by sonication (Covaris S220). The sonicated material was used to construct sequencing libraries following Illumina’s recommendations. Samples were sequenced as barcoded pools on Illumina GAII or MiSeq instruments.
http://www.illumina.com/products/chip-seq_dna_sample_prep_kit.ilmn

treatment_protocol: The Recombinase-mediated Cassette Exchange (RMCE) insertion protocol was adapted from Lienert et al to scale the needs of inserting large number of fragments in paralell. Briefly, TC-1 ES cells were selected under hygromycin (250μg/ml, Roche) for 10 days. Next, 12x106 cells were electroporated (Amaxa nucleofection, Amaxa) with 75 μg of L1-library-1L plasmid and 45 μg of pIC-Cre. Negative selection with 3 μM Ganciclovir (Roche) was started 2 d after transfection and continued for 10 days. Pools of selected cells were tested for successful insertion of DNA libraries by PCR using primers recognizing the universal priming region flanking the insertion site.

tag: library type

value: synthetic fragments

tag: replicate type

value: biological replicate


title: Synthetic - bisSeq 2


title: rx3-/- rep1

tag: strain


title: zfp blastema b

city: Cambridge

first: Josien

middle: C

last: van Wolfswinkel

state: MA

address: 9 Cambridge Center

department: Planarian regeneration

institute: Whitehead Institute

data_processing:
low quality reads were removed and remaining reads were mapped to the transcriptome using bowtie version 1.0.1 with the parameters --best -S -5 5 to trim remaining adaptor sequence
SAMtools was used to view, sort, index and output raw read counts.
DESeq was used to compute fold changes and statistical significance
Genome_build: Transcriptome submitted as part of this bioproject (PRJNA248468)
Supplementary_files_format_and_content: tab-delimited file containing raw read counts per transcript

organism: Schmidtea mediterranea

source_name: blastema

growth_protocol: standard growth conditions

extract_protocol:
For X1 and X2 samples, worms were macerated into single cell suspensions, stained with Ho33342, and cell populations were separated by FACS. For blastema samples, worms were amputated prepharyngeally and 5d blastemas were harvested by surgical dissection. For all samples, RNA was isolated by Trizol according to the manufacturer's instructions. Libraries were constructed using the Truseq kit v2 according to manufacturer's instructions.
Truseq

treatment_protocol: RNAi by feeding

value: 5 day blastema

tag: RNAi


title: zfp X1 b

source_name: X1 cells

value: X1 cells


title: zfp X2 b

source_name: X2 cells

value: X2 cells


title: zfp X1


title: control blastema b

value: control


title: control blastema


title: Wild-type siblings rep2

value: AB

value: Whole embryo

value: 13 hpf


title: control X2 b


title: control X1 b


title: control X2


title: control X1


title: Sample_94_AEG1_MYC

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat v2.0.7
gene count measurements were obtained using HTSeq-count
Genome_build: mm9
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: AEG1 & MYC  transgenic

growth_protocol: Mouse liver tissues were derived from adult WT, Alb/AEG-1 and Alb/c-Myc and Alb/AEG-1/c-Myc mice. Heterozygote Alb/AEG-1 and Alb/c-Myc mice were crossed to obtain the 4 genotypes

extract_protocol:
Total RNA is extracted using Qiagen miRNAeasy mini kit (Qiagen, Valencia, CA) from livers
RNASeq library was prepared using Illumina TruSeq RNA sample preparation kit and were pooled together to aim about 25-40M read passed filtered reads per sample

value: AEG1 & MYC  transgenic

value: liver


title: Sample_48_AEG1_MYC


title: Sample_87_MYC

source_name: MYC transgenic

value: MYC transgenic


title: Sample_68_AEG1_MYC


title: Sample_31_MYC


title: Sample_27_AEG1

source_name: AEG1 transgenic

value: AEG1 transgenic


title: rx3-/- rep2


title: zfp blastema


title: Sample_26_AEG1


title: Sample_120_AEG1


title: Sample_75_MYC


title: Oncogene-induced senescence

first: Zichen

last: Wang

address: 1468 Madison Ave

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

description: IMR90 cells carrying ER:RasV12 induced to senesce with 10nM tamoxifen for 8 days

data_processing:
The mRNA libraries were sequenced on the Illumina HiSeq 2500 System with 100 nucleotide single-end reads, according to the standard manufacturer's protocol (Illumina, CA, USA).
TopHat v2.0.3 and Bowtie2 used for reads alignment with default parameters
Cufflinks v2.1.1 used for transcriptome assembly with default parameters
fragments per kilo-base per million reads (FPKM) were calculated to measure the expression for each genes
log2 fold change of FPKM values for all samples pair-wise combinations were used to call differentially expressed genes with a cutoff 1.6
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

source_name: Primary fibroblast

growth_protocol: Commercially available IMR90 cells (ATCC CCL-186) were grown in DMEM supplemented with 10% FBS and penicillin/streptomycin

extract_protocol:
Cells were harvested after treatment with trypsin. Total RNA samples were isolated folowing the RNeasy kit (Qiagen) protocol
The sequencing library was prepared with the standard TruSeq RNA Sample Prep Kit v2 protocol (Illumina, CA, USA). Briefly, total RNA was poly-A-selected and then fragmented. The cDNA was synthesized using random hexamers, end-repaired and ligated with appropriate adaptors for sequencing. The library then underwent size selection and purification using AMPure XP beads (Beckman Coulter, CA, USA). The appropriate Illumina recommended 6 bp barcode bases are introduced at one end of the adaptors during PCR amplification step. The size and concentration of the RNAseq libraries was measured by Bioanalyzer and Qubit fluorometry (Life Technologies, NY, USA) before loading onto the sequencer.

value: Lung

tag: cell line

tag: passage


title: Sample_93_WT

source_name: wild type

value: wild type


title: Normal Condition

value: 2 µM Zn, 3µM Fe, without Cd

value: leaves


title: Sample_54_WT


title: zfp X2


title: H3.3cs1-induced senescence late time point

description: IMR90 cells expressing Flag-tagged cleaved H3.3. Samples harvested 13 days post-infection


title: Hairbulb_KO_84

data_processing:
The raw reads were aligned using Tophat to the mm9 build of the mouse genome.
Cufflinks was used to assemble transcripts and determine differential expression with the Ensemble mRNA transcripts reference as a guide.
CummeRbund was used to analyze the data.
Genome_build: mm9

extract_protocol:
RNA Samples were prepared using Zymed RNA extractio kit
Library was prepared at the Cornell Genomic Core Facility

value: Hair follicle transit amplifying cells (TACs)

value: mix


title: Hairbulb_con_52


title: Sample_72_WT


title: Sample_Shh_Het


title: Sample_HOM1

value: Hair follicle bulge stem cells


title: Hairbulb_con_57


title: Sample_Shh_CKO


title: Hairbulb_KO_64


title: Sample_HET2


title: N8_ESC_1

city: Portland

first: Gail

last: Mandel

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Vollum Institute

institute: Oregon Health & Science Universtiy

data_processing:
Sequenced reads were trimmed of first 9 bases to eliminate high Kmer content, then mapped to the mouse mm9 genome using Subread
Raw gene-level counts were calculated using FeatureCounts
Genome_build: mm9
Supplementary_files_format_and_content: raw read counts for each gene in comma-separated values (.csv) format

source_name: embryonic stem cells

growth_protocol: Mouse ESC cultures, N6 (WT) and N8 (REST -/-) (Jorgensen et al., 2009), were cultured in DMEM supplemented with 1000 units/ml Leukemia Inhibitory Factor (LIF, ESGRO from Millipore), 15% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1X non-essential amino acids (NEAA), 1X nucleoside mixture (adenosine, guanosine, uridine, cytidine, and thymidine), and 1X penicillin/streptomycin. ESCs were cultured on feeder layers of irradiated mouse embryonic fibroblasts and passaged three times on plates coated with 0.1% gelatin to eliminate MEFs before harvesting cells for mRNA extraction.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) followed by on-column DNAse treatment with RNase-free DNase and RNesay mini kit (Qiagen). 2μg total RNA was used to make one sequencing library. Two biological replicates were made for each condition: WT ESC, REST-/- ESC, WT NP, and REST-/- NP.
Indexed libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (San Diego, CA). Four libraries of ESC or NP were mixed at equal concentration and sequenced by an Illumina HiSeq 2000 sequencer at the OHSU Massively Parallel Sequencing Shared Resource (MPSSR).

value: ESC

value: REST -/-


title: N8_ESC_2


title: N6_ESC_2

value: WT


title: N6_ESC_1


title: WFat_CT46

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

institute: University of Pennsylvania

data_processing:
Align raw data to mm9 genome using STAR (v2.3.0e) with default parameters. STAR also generated files containing junction data.
Normalize read counts with DESeq2, using default parameters.
Quantify normalized read counts by running HTSeq (v0.5.4p1) in stranded mode, with default parameters. Use Ensembl gene quantifications.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain normalized, gene-level read counts and are located at series level
Supplementary_files_format_and_content: SJ.out.tab files contain splice  junction data generated by STAR

source_name: white adipose

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness prior to collection. Collection began at CT18. Mice were housed in light-tight boxes for the duration of the experiment.

extract_protocol:
Organ samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, then pooled from three mice for each organ and time point.
Prepared using Illumina TruSeq Stranded mRNA HT Sample Preparation Kit as per manufacturer’s protocol. Briefly, 1 ug of total RNA was polyA-selected, fragmented by metal-ion hydrolysis, and converted into double-stranded cDNA using Invitrogen Superscript II. The cDNA fragments were subjected to end-repair, adenylation, ligation of Illumina sequencing adapters, and PCR amplification.

tag: mouse strain

value: white adipose


title: WFat_CT40


title: WFat_CT28


title: Mus_CT52

source_name: skeletal muscle

value: muscle


title: Mus_CT64


title: WFat_CT34


title: Mus_CT58


title: WFat_CT22


title: WFat_CT64


title: Mus_CT46


title: Mus_CT40


title: Mus_CT34


title: Mus_CT28


title: Mus_CT22


title: Lun_CT64

source_name: lung

value: lung


title: Lun_CT58


title: Lun_CT52


title: Lun_CT40


title: Lun_CT34


title: Liv_CT64

source_name: liver