title: E17epi_miRNAseq

description:
Sample 9
small RNA library made from total RNA

value: embryonic skin epithelia

value: Integrin A6+, B1+


title: MiSeq_HepG2_H3K27ac

status: Public on Oct 08 2015

type: SRA

city: Emeryville

first: Philipp

last: Tropberger

address: 4560 Horton Street

country: USA

institute: Novartis Institutes for BioMedical Research

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
paired reads were aligned to the hbv genome (ayw, GenBank V01460.1, or de novo assembled from sequencing data with samtools mpileup) using Bowtie2  ( parameters: --no-unal --no-discordant --no-mixed -I 120 -X 200 (or  -I 30 -X 300 for Polymerase2)
Midpoint of each aligned paired-end reads was determined with a self-written python script
SAM files with midpostion of each aligned paired-end read were converted with SAMtools into .BAM format and sorted
sorted BAM files with midpostion of each aligned paired-end read were converted with bedtools into .bedgraph file format.
Genome_build: HBV
Supplementary_files_format_and_content: genome coverage in bedgraph formal

molecule: genomic DNA

organism: Homo sapiens

source_name: liver

extract_protocol:
Cells for chromatin immunoprecipitation (ChIP) were harvested with Accutase (Millipore) and crosslinked in PBS with 1% freshly cracked formaldehyde (Pierce) for 5 min. Fixation was quenched by adding 125mM glycine final concentration for 2 min. Next cells were washed with 10ml ice cold PBS with 0.1% Triton-X 100, 0.1% NP-40, 1mM DTT 10mM sodium butyrate, 1x protease inhibitor (Roche), resuspended in 1ml of the same buffer and incubated on ice for 10min with occasional mixing. Crude nuclei were pelleted and resuspended in Mnase digestion buffer (50mM Tris pH 7.5, 4mM MgCl2, 1mM CaCl2, 10% glycerol, 10mM sodium butyrate, 1x protease inhibitor) with 600U/ml Mnase (Fermentas). Chromatin was digested for 10 min at 37°C to mainly mononucleosomes before digestion was quenched with 10mM EGTA on ice for 30min. The digested nuclei were spun at 10,000 rpm for 5min and the supernatant (S1) saved into a fresh tube. The pellet was resuspended in Mnase buffer with 10mM EGTA and 300mM NaCl and mildly sonicated on ice 4x for 10 pulses in Heat Systems W-375 sonicator at 50% duty cycle and power setting 3. The sample was spun at 10,000 rpm for 5min and the supernatant (S2) combined with the S1 fraction. S1 and S2 fraction were mixed with an equal volume of 0% sucrose buffer (50mM Tris pH 7.5, 50mM NaCl, 5mM EDTA pH 8.0, 0.01% NP-40, 10mM sodium butyrate, 1x protease inhibitor) and concentrated in a Vivaspin 4 spin column (Sartorius) with 100K cutoff membrane to ~250ul. The concentrated sample was applied to a 5-30% sucrose gradient and centrifuged in a SW41TI at 40,000rpm at 4°C for 4h. Mononucleosome-containing fractions were pooled, concentrated to ~500ul and 100ng/ul BSA added. For ChIP antibodies were prebound to 20-30ul Protein G Dynabeads (Life Technologies) on a rotator at 4°C for 2h. The following antibodies were used: 0.5ug H3K4me3 (Abcam ab8580), 2ug H3K9me3 (Abcam ab8898), 1ug H3K27me3 (Millipore 07-449), 2ug H3K36me3 (Millipore ABE435), 0.6ug H3K27ac (Abcam ab4729), 1.2ug H3K122ac (Abcam ab33309), 2ug RNA Polymerase 2 (Abcam ab817). 1ug purified mononucleosomes (for histone modifications) or 20ug of Mnase-digested chromatin (for Polymerase 2 ChIP) were diluted in 400ul ChIP dilution buffer (20mM Tris pH 8.0, 150mM NaCl, 2mM EDTA pH 8.0, 1% Triton X-100, 10mM sodium butyrate, 1x protease inhibitor), added to the bead-antibody complex and incubated on a rotator at 4°C overnight. Samples were washed in LiCl was buffer (500mM LiCl, 50mM Tris pH 8.0, 1mM EDTA pH 8.0, 1% NP-40, 0.7% sodium deoxycholate) five times and eluted in elution buffer (1% SDS, 100mM NaHCO3). The samples were decrosslinked at 65°C for 5-6h in the presence of Proteinase K (Ambion) and purified with Qiagen PCR purification columns. ChIP DNA yield was quantified using QuBit Fluorometric Quantitation (Life Technologies).
1-2ng of DNA was used to prepare sequencing libraries with the KAPA Hyper Prep Kit (KAPA Biosystems) according to the manufacturer's instructions. For indexing, 2ul of adaptors from a TruSeq ChIP Sample Preparation Kit (Illumina) were used. Libraries were amplified with 13 PCR cycles and sequenced on a HiSeq2500 instrument (Illumina) in rapid run mode with 2x33bp paired end reads. Custom designed xGen Lockdown probes (Integrated DNA Technology) of 60bp each tiling the entire HBV genome with two-fold coverage were designed and equal amounts of libraries were pooled (500-1000ng DNA total amount) and enriched for HBV DNA according to the manufacturer's xGen rapid capture protocol v2 with slight modifications: Hybridization was performed at 50°C, and 50ul Dynabeads MyOne Streptavidin C1 (Life Technologies) were used per capture reaction. Target enriched libraries were amplified with 8 PCR cycles (KAPA HIFI HotStart ReadyMix) and sequenced on a MiSeq (Illumina) with 2x33bp paired end reads.

tag: cell type

value: hepatoblastoma cells

tag: infection

value: HBV (ayw)

tag: cell line

tag: chip antibody

value: H3K27ac (Abcam ab4729)


title: 419_L_9

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

description: liver by percutaneuos punch (PMID: 12545545)

library_source: transcriptomic

data_processing:
Basecalls using CASAVA 1.8
Trimming; Trimmomtatic sliding window from end 30 or below removed; Alignment; STAR, Dobin et al doi:10.1093/bioinformatics/bts635, version 2.2.0; default run except ‘--outFilterMismatchNoverLmax’ set to 0.02 (i.e. 2 mismatches per 100bp)
Count generation; featureCounts, flags -p, -P, -C, and with a maximum insert size of 590 kb flag –D
Filtering by FPKM following TMM normalisation of the library using edgeR, retained 18,000 genes
Genome_build: UMD3.1.70 (close to Bos_taurus_UMD_3.1 with the ENsembl build version 70)
Supplementary_files_format_and_content: Format: tab separated; content: column1=bovine gene ID, column2=number of sequence reads overlapping bovine gene ID as defined by GTF
Supplementary_files_format_and_content: The *1-48.count.txt files contain all 48 counts files from each tissue group.

molecule: polyA RNA

organism: Bos taurus

source_name: Liver_Mid Lactation_Fert-

extract_protocol:
Standard trizol extraction [PMID:2440339]
Illumina TruSeq v2 kit

treatment_protocol: Percutaneuos punch [PMID: 22365213]

tag: breed

value: Holstein

tag: tissue

value: Liver

tag: timepoint

value: Mid Lactation

tag: fertility group

value: Fert-


title: PR-Set7_RNAi_γ-H2Av_rep1

city: Durham

first: Jason

middle: Alan

last: Belsky

state: NC

address: LSRC Room C333

department: Pharmacology and Cancer Biology

institute: Duke University

data_processing:
Single-end sequencing reads were aligned with Bowtie 0.12.7 with the following parameters: -n 2 -l 30 -m 1 --best --strata -y.
RPKM (reads per thousand kb, per million mappable reads) was determined with RSamtools and GenomicRanges packages in R. For early origin and H4K20me1 experiments, genome is divided into 10 kb bins stepping every 1 kb. For γ-H2Av experiment, genome is divided into nonoverlapping 5 kb bins.
Genome_build: BDGP R5/dm3
Supplementary_files_format_and_content: csv files with columns chr, start,end,RPKM.

organism: Drosophila melanogaster

growth_protocol: Drosophila Kc167 cells were cultured at 25℃ in Schneider’s Insect Cell Medium (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (Gemini) and 1% penicillin/streptomycin/glutamine (Invitrogen).

extract_protocol:
In early origin experiments, chromatin was isolated and BrdU was immunoprecipted as described in (Ryba et al., Nat Protoc, 2011). H4K20me1 and γ-H2Av ChIP were performed as described in (MacAlpine et al., Genome Research, 2010).
Sequencing libraries were prepared using Illumina's TruSeq protocols

tag: experiment

value: Mouse anti-γ-H2Av (DSHB UNC93-5.2.1-s)

tag: RNAi treatment


title: 419_L_8

source_name: Liver_Early Lactation_Fert-

value: Early Lactation


title: control_RNAi_γ-H2Av_rep1

value: control


title: sort_S2_H4K20me1

value: Rabbi anti-H4K20me1 (Abcam, Egelhofer 2011)


title: 164_L_6


title: 419_L_7

source_name: Liver_Late Pregnancy_Fert-

value: Late Pregnancy


title: 430_L_14

source_name: Liver_Early Lactation_Fert+

value: Fert+


title: 164_L_5


title: sort_G1_H4K20me1


title: HU_arrest_H4K20me1


title: 33_L_2


title: 33_L_3

source_name: Liver_Mid Lactation_Fert+


title: HU_release_H4K20me1


title: PR-Set7_oe

value: early origin

value: Mouse anti-BrdU (BD Biosciences #555627)

tag: overexpression


title: 426_L_10


title: 164_L_4


title: Suv4-20_RNAi


title: PR-Set7_oe+Suv4-20_RNAi


title: control_RNAi


title: HiSeq_HepG2_H3K27ac


title: PR-Set7_Suv4-20_RNAi

value: PR-Set7 & Suv4-20


title: 33_L_1

source_name: Liver_Late Pregnancy_Fert+


title: ATR_PR-Set7_RNAi_rep1

value: ATR & PR-Set7


title: HiSeq_HepG2_Nuc

description: Nucleosome input for Sample 2-4

value: hepatoblastoma cells


title: no_treatment


title: ATR_RNAi_rep1

value: ATR


title: AtMYB12_fruit_breaker_input

status: Public on Oct 07 2015

city: Norwich

first: Ghanasyam

last: Rallapalli

address: Norwich Research Park

country: United Kingdom

institute: The Sainsbury Laboratory

data_processing:
The data we have received from BGI, has adapter reads deleted and the low quality reads (quality value <=20 is no less than 50% or the rate of “N” in a read is no less than 10%) were removed.
The quality filtered library was aligned to the Solanum lycopersicum chromosome sequences (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_genomic.fasta) using soap2.21. Only the aligments within 2 mismathches were considered in peak calling.
Whole genome peak scanning was performed using MACS-1.4.0. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads and the region with p-value <1e-5 were defined as a peak.
Genome_build: Tomato ITAG2.3
Supplementary_files_format_and_content: wig files were generated using MACS-1.4.0

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: Tomato plants were grown in glasshouse under natural light. Temperature were maintained between 20-25 °C.

extract_protocol:
Chromatin isolation was performed using Honda buffer as previously described. ChIP was performed using anti-AtMYB12 polyclonal antibody (prepared in rabbit against peptide sequence:  CLLDGDDEATIGNSN; GenScript USA Inc). DNA was recovered after immunoprecipitation.
Library construction was done using an Illumina ChIP-seq Sample Prep Kit following the manufacturer’s instructions and sequencing was undertaken on Illumina’s HiSeq platform (Beijing Genomics Institute (BGI), China)

treatment_protocol: ChIP experiments were done using WT and AtMYB12 tomato fruit at 3-4 days after breaker (when the expression of AtMYB12 is strongly induced). To cross-link protein and DNA, fruit were sliced into small pieces and immersed in cross-linking buffer (0.4M Sucrose, 10 mM Tris- HCl pH8.0, 0.1% β-mercaptoethanol, 100μM PMSF, 1% formaldehyde and 1x protease inhibitor cocktail (Roche, http://www.roche.com/index.htm) and vacuum infiltrated two times, for 10 minutes each time. To terminate cross-linking, glycine was added to a final concentration of 0.125 M and samples were vacuum infiltrated for an additional 5 min. After cross-linking, samples were washed in ice-cold water and ground in liquid nitrogen.

value: input

tag: ecotype

value: MicroTom

tag: genotype

value: pericarp

tag: time point

value: 3-4 days after breaker


title: wt small RNA seq

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

data_processing:
All samples were sequenced (together with other libraries) on one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the TruSeq barcode. Illumina software Casava v 1.8 was used.  The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Alignments to the S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) were performed for the minus strand by the software bowtie (version 0.9.9.1) ( Langmead et al., 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Alignments were normalized for the size of the each library, transformed into log2 scale and corrected with a pseudocount of 3. Annotations were used as described in Woolcock et al., Genes Devc 2012, PMID: 22431512
Genomic read coverage plots were made created separately for the plus (wiggle files with _p_) and minus (wiggle files with _m_) strand, transformed into log2 scale and normalized for the size of each library based on weights of the alignments
Genome_build: May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: wt S. pombe cells

growth_protocol: Fission Yeast strains were grown in standard YES medium in shaking flasks to OD ~0.5

extract_protocol:
Cells were pelleted by centrifugation, washed with PBS and then total RNA was isolated using the hot phenol method. This was followed by enrichment and gel purification of small RNAs as described in Keller et al. (Nat. Struct. Mol. Biol., 2013 vol. 20 (8) pp. 994-1000)
Libraries were constructed using the Illumina TruSeq Small RNA Library Prep Kit starting with 1ug total RNA as input.

tag: strain

tag: genotype/variation

value: wt

tag: stain details

value: h90 mat3M(EcoRV)::gfp+::natMX ura4-DS/E leu1-32 ade6-M210

tag: molecule subtype

value: small RNA (18 - 28 nt)


title: control_RNAi_rep1

value: control


title: HiSeq_HepG2_Pol2

tag: cell type

tag: infection

value: HBV (ayw)

value: RNA Polymerase 2 (Abcam ab817)


title: PR-Set7_RNAi_rep1

tag: chip antibody


title: HiSeq_HepG2_H3K4me3

tag: cell line

value: H3K4me3 (Abcam ab8580)


title: 72_VentricleAHR_WT_100_Female

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

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 for RNA-Seq samples
For RNA-Seq samples, number of reads 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 for RNA-Seq samples

organism: Mus musculus

source_name: mouse heart tissue

growth_protocol: Mouse C57BL6J trited by gavage at embryonic days 13.5, 15.5, and 18.5, total RNA extracted from heart tissue at 9 month of age

extract_protocol:
mRNA was extracted by TirReagent. Cell debris were removed by micro-centrifugation and male and female tissues were processed and thereafter analyzed separately.
Libraries were prepared for sequencing using standard Illumina protocols.

value: cardiomyocytes

tag: tissue

value: Ventricle

tag: gender

value: female

value: WT

tag: treatment

value: TCDD AHR WT 100


title: 71_VentricleAHR_WT_100_Male

treatment_protocol: Mouse C57BL6J trited by gavage at embryonic days 13.5, 15.5, and 18.5

value: male


title: 66_VentricleAHR_WT_1000_Female

value: TCDD AHR WT 1000


title: 43_VentricleAHR_WT_1000_Female


title: 45_VentricleAHR_WT_100_Male


title: 65_VentricleAHR_WT_1000_Male


title: AtMYB12_fruit_breaker_ChIP

value: MicroTom


title: 44_VentricleAHR_WT_1000_Female


title: Swi6D_H3K9me2_ChIPSEQ_rep1

description: GTGCGCT

data_processing:
Samples were barcoded at the 3'end of the 5'adapter using a hamming distance two code with a 3' CT (b3 = GTGCGCT, b4 = GCCACCT) and sequenced (with other samples) in one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the first 7 nucleotides containing the barcode. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Genome_build: Reads were aligned against "pombe_160807.fasta". Initial identification of elements is based on the features described in the GFF file “pombe_09052011.gff”. Both files were originally downloaded from ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF.
Supplementary_files_format_and_content: wig file for multiple tracks

source_name: yeast cells

growth_protocol: S.pombe strain was grown in YES media. ~150x10^7 cells were harvested from o/n cultures and processed for ChIP

extract_protocol:
Lysates were clarified from sonicated S. pombe cells and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were generated using an Illumina-based protocol using custom reagents and barcoded adapters. Briefly, immunoprecipitated 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 fragments were size selected to remove excess adapters and adapter modified DNA fragments were enriched by PCR amplification with Illumina primers for 18 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified ChIP-seq libraries thus generated were validated and subsequently captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2000 system following the manufacturer's protocols.


title: Swi6D_H3K9me2_ChIPSEQ_rep2

description: GCCACCT


title: 46_VentricleAHR_WT_100_Male


title: swi6∆ small RNA seq

source_name: swi6∆ S. pombe cells

value: swi6 deletant

value: h90 mat3M(EcoRV)::gfp+::natMX ura4-DS/E leu1-32 ade6-M210 swi6Δ::ura3+


title: 47_VentricleAHR_WT_100_Female


title: 48_VentricleAHR_WT_100_Female


title: 40_VentricleAHR_KO_Female

value: KO

value: TCDD AHR KO


title: 38_VentricleAHR_KO_Male


title: 41_VentricleAHR_WT_1000_Male


title: 37_VentricleAHR_KO_Male


title: 60_VentricleAHR_KO_Female


title: 39_VentricleAHR_KO_Female


title: 59_VentricleAHR_KO_Male


title: 54_VentricleAHR_WT_CTRL_Female

value: TCDD AHR WT CTRL


title: 34_VentricleAHR_WT_CTRL_Male


title: 70_LeftAtriumAHR_WT_100_Female

value: Left Atrium


title: 33_VentricleAHR_WT_CTRL_Male


title: 36_VentricleAHR_WT_CTRL_Female


title: 31_LeftAtriumAHR_WT_100_Female


title: 69_LeftAtriumAHR_WT_100_Male


title: 32_LeftAtriumAHR_WT_100_Female


title: 53_VentricleAHR_WT_CTRL_Male


title: 29_LeftAtriumAHR_WT_100_Male


title: 30_LeftAtriumAHR_WT_100_Male


title: 64_LeftAtriumAHR_WT_1000_Female


title: 27_LeftAtriumAHR_WT_1000_Female


title: 24_LeftAtriumAHR_KO_Female


title: 28_LeftAtriumAHR_WT_1000_Female


title: 22_LeftAtriumAHR_KO_Male


title: 63_LeftAtriumAHR_WT_1000_Male


title: 20_LeftAtriumAHR_WT_CTRL_Female


title: 25_LeftAtriumAHR_WT_1000_Male


title: 23_LeftAtriumAHR_KO_Female


title: 26_LeftAtriumAHR_WT_1000_Male


title: 35_VentricleAHR_WT_CTRL_Female


title: 19_LeftAtriumAHR_WT_CTRL_Female


title: 58_LeftAtriumAHR_KO_Female


title: CTL2

city: Smithville

first: Jeesun

last: Kim

state: Texas

address: 1808 Park Road 1C

department: Department of Epigenetics and Molecular Carcinogenesis

institute: UT MD Anderson Cancer Center

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm9) by TopHat (version 2.0.7).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on March 9, 2012) was enumerated using htseq-count from HTSeq package (version 0.5.3p9).
Genome_build: mm9
Supplementary_files_format_and_content: Number of fragments in each gene (raw counts)

source_name: Oocytes

extract_protocol:
Fully-grown GV oocytes were obtained from the ovaries of 4-6-week-old female mice 48 hours after intraperitoneal injection of 5 IU of pregnant mare’s serum gonadotrophin. GV oocytes were released by puncturing antral follicles with a fine needle on the stage of a dissecting microscope. Each sample, which contained 100 oocytes, was lysed directly in 1 μl of prelude direct lysis buffer (Nugen).
RNA was subject to amplification using the ovation RNA-seq system v2 (Nugen). Amplified cDNA was fragmented using Covaris and paired-end libraries were then constructed using the TruSeq RNA Sample Preparation Kit v2 (Illumina) starting from end repair.

value: Mixed C57BL/6-129

value: oocyte

tag: cell stage

value: GV

value: Control


title: CTL1


title: 18_LeftAtriumAHR_WT_CTRL_Male

value: cardiomyocytes


title: 51_LeftAtriumAHR_WT_CTRL_Male


title: 17_LeftAtriumAHR_WT_CTRL_Male


title: CKO3

value: Lsd1 KO


title: 42_VentricleAHR_WT_1000_Male

value: Ventricle

value: WT


title: CKO2


title: 68_RightAtriumAHR_WT_100_Female

value: Right Atrium

value: female

value: TCDD AHR WT 100


title: 15_RightAtriumAHR_WT_100_Female


title: 16_RightAtriumAHR_WT_100_Female


title: CKO1


title: 14_RightAtriumAHR_WT_100_Male

value: male


title: CTL3


title: RNA-seq primary culture

city: Seoul

first: Jun

last: Cho

address: Building 504 Room 509, School of Biological Sciences, Seoul National University, 1 Gwanangno, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description:
RNA-seq
PrimaryCulture_RPF_RNA-seq.csv

data_processing:
Basecalls performed using Illumina Pipeline CASAVA v1.8.2
The first few steps in the sequence analysis were done using Assaf Gordon's FASTX-Toolkit. The reads was trimmed from the 3'-end so that the remaining reads were 27-nt in length. After trimming, the reads were collapsed to generate a set of unique sequences.
The collapsed reads were aligned to were aligned to non-redundant RefSeq transcript sequences (constructed from UCSC mm9 assembly) using Bowtie version 1.1.1 with options for unique mapping that allows a maximum 1-nt of mismatch.
To quantify translation and mRNA abundance of individual genes, the number of the RPF and RNA-seq tags aligned to each individual mRNA transcript were counted. The transcripts with low read counts in RPF and RNA-seq (i.e., < 50 raw reads in all of the libraries) were excluded to reduce noise.
Each read count per individual mRNA transcript was normalized by the median values of the read counts in the RPF or RNA-seq libraries ("ncount" in PrimaryCulture_RPF_RNA-seq.csv).
Genome_build: mm9
Supplementary_files_format_and_content: The .csv files report read counts for individual genes/transcripts.

source_name: Hippocampal primary culture

extract_protocol:
The homogenized tissues and primary cultured cells were lysed with the buffer of 10 mM Tris-HCl at pH 7.4, 100 mM KCl, 5 mM MgCl2, 2mM DTT,  1% Triton X-100, 100 µg/mL cycloheximide with 1 µL protease inhibitor cocktail (Calbiochem), 2 µL RNasin (Promega) and 2 µL SUPERase In (Ambion) to maintain bindings between the ribosomes and mRNAs. the ribosome-mRNA complexes were purified by using Sephacryl S-400 columns
The preparation method of libraries were based on the standard protocol of Illumina Truseq small RNA library prep.

treatment_protocol: All single-caged mice were handled for 3 min every day for 4 days and then subjected to contextual fear conditioning. Each of them was allowed to explore the Coulbourn fear conditioning chamber for 148 s and then given a 2-s electric foot shock and returned to the home cage 30 s later. The hippocampi were collected and rapidly frozen in liquid nitrogen at the given time points after the conditioning.

tag: stress

tag: cell culture

value: hippocampal primary culture


title: 57_LeftAtriumAHR_KO_Male

value: KO


title: RPF primary culture

description:
ribosome profiling
PrimaryCulture_RPF_RNA-seq.csv


title: 21_LeftAtriumAHR_KO_Male

value: TCDD AHR KO


title: 13_RightAtriumAHR_WT_100_Male


title: 62_RightAtriumAHR_WT_1000_Female

value: TCDD AHR WT 1000


title: RNA-seq 4hr rep3

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

source_name: Hippocampal tissue

value: contextual fear conditioning

tag: time

value: 4 hr

value: hippocampus


title: RNA-seq 30min rep3

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 30 min


title: 9_RightAtriumAHR_WT_1000_Male


title: 11_RightAtriumAHR_WT_1000_Female


title: RNA-seq 10min rep3

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 10 min


title: 56_RightAtriumAHR_KO_Female

value: cardiomyocytes


title: 61_RightAtriumAHR_WT_1000_Male


title: 12_RightAtriumAHR_WT_1000_Female


title: 10_RightAtriumAHR_WT_1000_Male


title: RNA-seq 5min rep3

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 5 min


title: RNA-seq control rep3

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: control (without stimulus)

value: control


title: 67_RightAtriumAHR_WT_100_Male

value: Right Atrium

value: WT


title: 7_RightAtriumAHR_KO_Female

value: female


title: 8_RightAtriumAHR_KO_Female


title: 6_RightAtriumAHR_KO_Male

value: male


title: 55_RightAtriumAHR_KO_Male


title: 50_RightAtriumAHR_WT_CTRL_Female

value: TCDD AHR WT CTRL


title: 5_RightAtriumAHR_KO_Male

value: KO


title: 49_RightAtriumAHR_WT_CTRL_Male


title: 2_RightAtriumAHR_WT_CTRL_Male


title: 4_RightAtriumAHR_WT_CTRL_Female


title: RPF 5min rep3

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: 1_RightAtriumAHR_WT_CTRL_Male


title: RPF 10min rep3

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: H3A_shBPTF_rep3

city: Illkirch

first: Patrick

last: Laurette

address: 1 Rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Illumina Casava v1.8 software was used for basecalling.
Sequence reads were mapped onto the hg19 assembly of the human  using Tophat v1.4.1 and the bowtie v0.12.7 aligner.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file corresponding to abundance measurements (raw read counts for each ensembl gene id) for each sample

source_name: Hermes 3A

extract_protocol:
Total RNA isolation from 501M or Hermes3A cells was performed according to standard procedure (Qiagen kit). 1.5 μg of RNA was reverse transcribed using a mix 1/1 of SuperScript II RNase H-reverse transcriptase (Invitrogen) and AMV retrotranscriptase (Roche) with 500 ng of oligodT22 primer, hexanucleotides or specific primers according to the manufacter’s instructions
Total RNA-seq libraries were prepared following the Illumina protocol with some modifications. Briefly, 2 µg of total RNA was hybridized with rRNA sequence-specific 5’biotin labeled oligonucleotide probes to selectively deplete ribosomal RNA. The rRNA/5’biotin labeled probe was removed from the sample with streptavidin-coated magnetic beads. (Ribominus Eukaryote kit for RNA-seq, #A10837-08, Invitrogen Corporation). The rRNA depleted RNAs were then fragmented using divalent cations at 95°C for 5 minutes and used to generate a reverse transcribed cDNA library. 100 ng of each DNA library was then denatured at 98°C for 2 minutes, incubated at 68°C for 5 hours and then incubated in the presence Duplex-Specific thermostable Nuclease enzyme (DSN, #EA001, Evrogen) for DSN normalization following the Illumina protocol. DSN treated libraries were purified using Agencourt AMPure XP beads, enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 6 cycles; 5 min at 72°C) and purified again using Agencourt AMPure XP beads.

value: Hermes 3A

value: melanocyte


title: H3A_shBPTF_rep2


title: RNA-seq 30min rep2

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: contextual fear conditioning


title: RNA-seq 4hr rep2

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 4 hr


title: RPF 4hr rep3

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: hippocampus


title: 501_shBPTF_rep2

value: melanoma


title: RNA-seq 10min rep2

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 10 min


title: 501_shBPTF_rep1


title: Indigo_4week_rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
EXPRSS sub-libraries are separated using perfect match to the barcode (at 5' end). Individual library is quality filtered using FASTX Toolkit 0.0.13 with parameters -q20 and -p50 and reads containing “N” are discarded.
The quality filtered library was aligned to the Solanum lycopersicum cDNA sequences (ITAG2.3 ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_cdna.fasta) using Bowtie version 0.12.8. Unaligned reads were aligned to the tomato genome sequence (ftp://ftp.solgenomics.net/tomato_genome/annotation/ITAG2.3_release/ITAG2.3_genomic.fasta) using Bowtie. Tag to gene association was carried out using following considerations: reads aligning to each gene limits were assigned to that gene, reads aligning to genes with overlapping gene limits were split equally between them, reads aligning to more than 10 genes were discarded. Differential expression analysis was performed using the R statistical language version 2.11.1 with the Bioconductor package edgeR version 1.6.15 with the exact negative binomial test using tagwise dispersions.
Genome_build: Tomato ITAG2.3
Supplementary_files_format_and_content: tab-delimited text files containing each genes tag counts for individual samples

extract_protocol:
Total RNA was extracted using the TRI reagent (Sigma) and 1-Bromo-3-chloropropane (Sigma), as per manufacturer’s guidelines. RNA was precipitated with half volume of isopropanol and half volume of high salt precipitation buffer (0.8 M sodium citrate and 1.2 M sodium chloride). RNA samples were treated with DNaseI (Roche) according to the manufacturer’s recommendation and phenol/chloroform extracted and ethanol precipitated.
Typically 3 µg of total RNA was used to generate first strand cDNA using a oligo(dT) primer comprising P7 sequence of Ilumina flowcell. Double strand cDNA is synthesized as described previously [Okayama & Berg, Molecular and cellular biology 1982, 2:161-170]. Purified cDNA is subjected to Covaris shearing to a target size of 200bp (parameters: Intensity – 5, Duty cycle – 20%, Cycles/Burst – 200, Duration – 90seconds). End repairing and A-tailing of sheared cDNA is carried out as described by Illumina. Y-shaped adapters are ligated to A-tailed DNA and subjected to size selection on 1X TAE agarose gel. The gel-extracted library is PCR enriched and quantified using qPCR with previously sequenced similar size range Illumina library

treatment_protocol: Fruit were labelled at breaker stage and harvested at either one week or four weeks after breaker. Seeds were removed and the pericarp was ground into fine powder in liquid nitrogen. Samples were stored at -80°C before RNA isolation.

tag: ecotype

value: MicroTom

tag: genotype

value: Indigo (MYB12 X Del/Ros1)

value: pericarp

value: 4 weeks after breaker

tag: barcode sequence

value: AACAGAGT

tag: barcode position

value: 5' end of the read


title: 3_RightAtriumAHR_WT_CTRL_Female

value: cardiomyocytes

value: Right Atrium

value: female

tag: genotype/variation

value: WT


title: Indigo_1week_rep2

tag: time point

value: 1 week after breaker

value: ATCCT


title: Del-Ros_4week_rep2

value: CAGAGT


title: RNA-seq control rep2

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

tag: strain

value: control (without stimulus)

value: control


title: Del-Ros_1week_rep2

value: GCAT


title: Indigo_1week_rep1

value: ACTGT


title: RNA-seq 5min rep2

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: contextual fear conditioning

value: 5 min

value: hippocampus


title: Unassigned Reads

description: All RNA samples were sequenced in one individual Illumina flowcell lane. nobarcode-sequences.TomatoRNAseq.fq is the file containing sequences unassigned to any of 16 barcodes.

value: pericarp


title: RPF 30min rep2

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: 30 min


title: RPF 4hr rep2

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: 4 hr


title: RPF control rep3

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: Del-Ros_4week_rep1

value: MicroTom

value: 4 weeks after breaker

value: GACACT

value: 5' end of the read


title: Del-Ros_1week_rep1

value: 1 week after breaker

value: CGGT


title: AtMYB12_1week_rep2

value: GTACT


title: AtMYB12_4week_rep2

value: TTGCGCT


title: RPF 10min rep2

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: 10 min


title: RPF 30min rep3

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: AtMYB12_1week_rep1

value: GCTCT


title: MicroTom_4week_rep2

value: Wild type

value: CGAGAT


title: H3A_shBPTF_rep1

value: Hermes 3A

tag: cell type

value: melanocyte


title: Indigo_4week_rep2

value: Indigo (MYB12 X Del/Ros1)

value: pericarp

value: TGTGCGAT


title: RPF 5min rep2

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: contextual fear conditioning

value: 5 min

value: hippocampus


title: MicroTom_1week_rep2

value: MicroTom

value: TCGT

value: 5' end of the read


title: MicroTom_4week_rep1

value: 4 weeks after breaker

value: TTGGAT


title: MicroTom_1week_rep1

value: 1 week after breaker

value: AGCT


title: RNA-seq 30min rep1

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 30 min


title: RNA-seq 5min rep1

description:
RNA-seq
Tissue_RNA-seq_CFC.csv


title: RNA-seq 10min rep1

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 10 min


title: RNA-seq control rep1

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: control (without stimulus)

value: control


title: RNA-seq 4hr rep1

description:
RNA-seq
Tissue_RNA-seq_CFC.csv

value: 4 hr


title: RPF 5min rep1

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: RPF 30min rep1

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: AtMYB12_4week_rep1

value: pericarp

value: CATACGT


title: RPF 10min rep1

description:
ribosome profiling
Tissue_RPF_CFC.csv

value: contextual fear conditioning


title: RPF 4hr rep1

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: RPF control rep1

description:
ribosome profiling
Tissue_RPF_CFC.csv


title: uremic monocytes

city: Frankfurt am Main

first: GenXPro

last: GenXPro

address: Altenhöferallee 3

country: Germany

institute: GenXPro GmbH

description:
DNA from 5 experiments was matched
Meth-Seq_Patient_Control_1-550000.xlsx, Meth-Seq_Patient_Control_550001-1155950.xlsx

data_processing:
PCR-duplicates identified by TrueQuant technology (GenXPro GmbH)
Reads starting with the HpaII-specific recognition sequence (CCGG) were quality-trimmed
Mapping to the human genome (hg19) using novoalign (http://www.novocraft.com/products/novoalign/). For each genomic HpaII site, reads starting at this position were quantified in each library
The RefSeq track as well as the CpG island track from the UCSC table browser (https://genome.ucsc.edu/cgi-bin/hgTables) were used to annotate genomic restriction sites. Regions up to 2 kb upstream of the transcription start site (TSS) of genes contained in the RefSeq track were considered potential promoter regions. Accordingly, downstream regions were defined as genomic regions up to 2 kb downstream of the 3'UTR. In order to annotate miRNA promoter regions, miRNA TSS information was retrieved from the miRStart web service (http://mirstart.mbc.nctu.edu.tw/).
To test for differential CpG methylation, quantification results for all restriction sites were normalized to tags per million (NML) and a statistical test was carried out using NOISeq
Genome_build: hg19
Supplementary_files_format_and_content: XLSX Microsoft Excel table

source_name: differentiated monocytes under uremic conditions

growth_protocol: Monocyte subsets were isolated from blood of healthy donors; Hematopoetic stem cells were differentiated to monocytes according established protocols (Rogacev et al., Nephrol Dial Transplant. 2015 Jan;30(1):143-53.)

extract_protocol:
DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany)
HpaII was used as the methylation-sensitive enzyme, recognizing non-CpG-methylated CCGG sites. After digestion by HpaII, DNA was size selected (300-500 bp including adaptors) and ligated to Illumina’s p5 primer for sequencing (Illumina HiSeq2000)

treatment_protocol: Hematopoetic stem cells were treated with 10% serum of healthy donors (control monocytes) or with serum of hemodialysis patients (uremic monocytes).

value: monocytes

tag: state of health

value: uremic


title: control monocytes

source_name: differentiated monocytes under control conditions

value: healthy


title: Mesenchymal-like prostate tumor cells, rep 2

city: Los Angeles

first: Yu-Ting

last: Tseng

state: California

address: 650 Charles E. Young Drive South

department: Department of Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

data_processing:
Paired-end sequencing data with read lengths of 100 bp were generated using the Illumina HiSeq2000 system. An average of 75.5 million read pairs per replicate were generated.
The NEBNext Poly(A) mRNA kit was then used to isolate mRNA, and the KAPA stranded RNA-Seq library preparation kit for library preparation.
Reads were mapped to the reference genome mm9 by TopHat (v.2.0.4), allowing 2 mismatches per seed.
Fragments Per Kilobase of exon per Million fragments mapped (FPKM) were calculated using cufflinks v2.0.2 with uniquely and properly mapped pairs. The differentially expressed genes were calculated using Cuffdiff (v2.2.0), with a false discovery rate less than 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: Mesenchymal-like prostate tumor cells FACS sorted from Pb-Cre+/-;PtenL/L;KrasG12D/+;Vim-GFP (CPKV) mice

extract_protocol:
Total RNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit per the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prostate

tag: age

value: Mesenchymal-like prostate tumor cell


title: CD14++CD16-

description:
DNA from 7 volunteers was matched
Mo1_Mo2_Mo3_merged.xlsx

source_name: isolated monocyte subset


title: CD14++CD16+


title: CD14+CD16++


title: Epithelial prostate tumor cells, rep 2

source_name: Epithelial prostate tumor cells FACS sorted from Pb-Cre+/-;PtenL/L;KrasG12D/+;Vim-GFP (CPKV) mice

tag: tissue

value: Epithelial prostate tumor cell


title: Epithelial prostate tumor cells, rep 1


title: EMT prostate tumor cells, rep 2

source_name: EMT prostate tumor cells FACS sorted from Pb-Cre+/-;PtenL/L;KrasG12D/+;Vim-GFP (CPKV) mice

value: EMT prostate tumor cell


title: EMT prostate tumor cells, rep 1


title: OCI-AML5

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

data_processing:
Illumina Casava1.7 software used for basecalling
Read mapping: Two reference sequences were prepared based on the HG19 reference
The alignment was performed using the bowtie alignment software version  0.12.8
Methylation calls files for C's in the bowtie alignment files were generated using Bismark software
Genome_build: HG19
Supplementary_files_format_and_content: Methylation calls files. Headers: chromosome, position, methylated C's, unmethylated C's

source_name: Cancer cell line

growth_protocol: Cells were cultured in DMEM at 10% FBS, 5% CO2.

extract_protocol:
DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)
We spiked genomic DNA (1 or 2 μg) with unmethylated λ DNA (5 ng of λ DNA per μg of genomic DNA) (Promega). We sheared DNA by sonication to 50–500 bp with a Covaris E220 and selected 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience Corp.). We constructed genomic DNA libraries using the TruSeq Sample Preparation kit (Illumina Inc.) following Illumina’s standard protocol. After adaptor ligation, we treated DNA with sodium bisulfite using the EpiTect Bisulfite kit (Qiagen) following the manufacturer's instructions for formalin-fixed and paraffin-embedded (FFPE) tissue samples. We performed two rounds of conversion to achieve >99% conversion. We enriched adaptor-ligated DNA through seven cycles of PCR using the PfuTurboCx Hotstart DNA polymerase (Stratagene). We monitored library quality using the Agilent 2100 BioAnalyzer (Agilent) and determined the concentration of viable sequencing fragments (molecules carrying adapters at both extremities) by quantitative PCR using the Library Quantification Kit from KAPA Biosystems. We performed paired-end DNA sequencing (two reads of 100 bp each) using the Illumina Hi-Seq 2000.

tag: dnmt3a mutation status

value: wild type

tag: cell line

value: AML


title: OCI-AML3

value: mutant


title: Sample 383

status: Public on Oct 06 2015

city: Bar Harbor

first: Steven

middle: C

last: Munger

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

data_processing:
Basecalls were performed with CASAVA version 1.8.0
Fragmented fastq files from CASAVA were concatenated together, and then reads that did not pass quality filtering were removed with fastq_illumina_filter (http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/)
Read Alignment and Gene Abundance Quantitation - We aligned raw reads against pooled transcriptomes of eight founder strains and quantified expected read counts expressed from each of transcript alleles. We repeated the same process for liver RNA-seq data from the eight founder strains to assess how specifically each founder read aligns back to their origin strain when exposed to all other founder alleles simultaneously in the alignment pool. We then evaluated the genotype probability of each transcript using a hidden Markov Model (HMM), where we bring those read counts together and calculate (1) how likely allele-specific read counts are generated from a specific genotype and (2) how much those likelihoods comply within the context of neighboring transcripts. Finally, we re-quantified total and allele specific expression by repeating the similar process but this time using individualized diploid transcriptomes reconstructed along our genotype calls.
Normalization - For each sample, gene-level count estimates were normalized to the upper quartile value (after trimming zeros).
Genome_build: Mouse GRCm38/mm10
SNP/inel file used to build individualized transcriptomes: Sanger Mouse Genomes Project Release-1410
annotation version: Ensembl version 75
Supplementary_files_format_and_content: Tab-delimited text file includes upper quartile normalized gene-level count values, with genes (Ensembl gene ids) as rows and samples as columns.

source_name: Liver

growth_protocol: Male and female Diversity Outbred mice (J:DO Stock# 009376) were obtained from The Jackson Laboratory (Bar Harbor, ME). Animals were received at 3 weeks of age, housed at The Jackson Laboratory, and given free access to either standard rodent chow containing 6% fat by weight (LabDiet 5K52, LabDiet, Scott Distributing, Hudson, NH) or high-fat chow containing 22% fat by weight (TD.08811, Harlan Laboratories, Madison, WI) from wean age throughout the study. Animals were phenotyped for multiple metabolic and hematological parameters as described in Svenson et al. (2012), and then sacrificed at 26 weeks of age. Liver samples were collected from each animal and stored in RNAlater solution (Life Technologies) at -80C.

extract_protocol:
Livers were dissected and stored in RNAlater at -80C (DO samples). Total RNA was isolated using the Trizol Plus RNA extraction kit (Life Technologies) with on-column DNase digestion.
Following the Illumina TruSeq standard protocol, indexed mRNA-seq libraries were generated from 1ug total RNA followed by QC and quantitation on the Agilent Bioanalyzer and the Kapa Biosystems qPCR library quantitation method.

value: Diversity Outbred (JAX#009376)

value: liver

value: post natal 26 weeks

tag: Sex

value: Male

tag: diet

value: High Fat Diet

tag: outbreeding generation

tag: coat color

value: agouti


title: Sample 384


title: Sample 381


title: Sample 382


title: Sample 380


title: Sample 376

value: black


title: Sample 373


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title: Sample 377

value: buff


title: Sample 369


title: Sample 378


title: Sample 368


title: 52_LeftAtriumAHR_WT_CTRL_Female

value: cardiomyocytes

value: Left Atrium

tag: gender

value: female

value: WT

tag: treatment

value: TCDD AHR WT CTRL


title: Sample 362

value: white

tag: genotype


title: Sample 364

value: wild type


title: Sample 366


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title: Sample 342

value: Standard Chow


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title: Sample 326


title: RPF control rep2

description:
ribosome profiling
Tissue_RPF_CFC.csv

tag: stress

value: control (without stimulus)

tag: time

value: control

value: hippocampus


title: Mesenchymal-like prostate tumor cells, rep 1

value: prostate

value: Mesenchymal-like prostate tumor cell


title: Sample 324

value: Diversity Outbred (JAX#009376)

value: liver

value: post natal 26 weeks

value: Male


title: Sample 320

value: agouti


title: Sample 315


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value: black


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value: agouti blaze


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value: High Fat Diet


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value: Female


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value: Standard Chow


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title: 4-NQO and ethanol treated mice (4-NQO/EtOH) 1

city: New York

first: Alison

last: Urvalek

state: NY

address: 1300 York Ave

institute: Weill Cornell Medical College

data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the GSNAP aligner version 2011.11.17 (with support Goby file format)   Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.  GobyWeb's Plugin GSNAP_GOBY version 1.1; Goby version 1.9.8.3 (20120216154520); GobyWeb version 1.7
differential expression analysis was performed using EdgeR plugin
Compression of structured high-throughput sequencing data, Campagne F, Dorff KC,  Chambwe N,  Robinson JT, Mesirov JP, Plos One, in press [see also our pre-print of this manuscript at http://arxiv.org/abs/1211.6664]
Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien Campagne. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 10.1371/journal.pone.0069666.
Genome_build: mm9
grp1 V.C. and untr. treated mice (V.C./Untr.)
grp2 V.C. and ethanol treated mice (V.C./EtOH)
grp3 4-NQO and Untr. mice (4-NQO/Untr.)
grp4 4-NQO and ethanol treated mice (4-NQO/EtOH)

extract_protocol:
RNA was extracted with QIAGEN RNeasy mini kit and cleaned up wiith DNAse I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
RNA sequencing was performed using Illumina TruSeqRNA technology, following the manufacturer’s protocol. Briefly, mRNA is purified using poly-T oligo-attached magnetic beads and subsequently fragmented. The cleaved RNA fragments are reverse transcribed into first strand cDNA using random primers. Next, second strand cDNA is synthesized using DNA Polymerase I and RNase H. The second strand cDNA fragments are subject to an end repair, the addition of a single ‘A’ base, and ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: tongue

value: 31 weeks


title: 4-NQO and ethanol treated mice (4-NQO/EtOH) 3


title: 4-NQO and Untr. mice (4-NQO/Untr.) 3

source_name: 4-NQO and Untr. mice (4-NQO/Untr.)


title: 4-NQO and ethanol treated mice (4-NQO/EtOH) 2


title: sakA.4b

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

institute: Max-Delbrück-centrum

description: Deletion of the gene Afu1g12940 in the CEA17 background

data_processing:
FASTQ files were receiven from GATC, Konstanz, Germany
repeated runs concatenated
Mapping of read pairs using TopHat (v1.4.1; --GTF GTF from CADRE; -maxintronlength 4000, -g 1)
Read counting using R-package easyRNASeq, annotation from BioMart (fungi_mart_19)
Normalisation using R-package DESeq
Genome_build: Aspergillus fumigatusa1163 A1163 (CADRE)
Supplementary_files_format_and_content: comma seperated values (csv) with the normalised read counts

organism: Aspergillus fumigatus

source_name: fungal cells

growth_protocol: 10^6 spores / ml were inoculated in AMM media supplemented with Glucose (1% w/v), MgSO4 (1% w/v), and Hunter’s trace elements

extract_protocol:
Total RNA was prepared using the RNeasy Plant Mini kit (Qiagen, Germany) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols; 50 bp single end

treatment_protocol: After 16 hours incubation (37 °C, 200 rpm shaking), 0,1 mg / L Caspofungin was added to the media and samples collected 30 min (T0.5), 1 hour (T1), 4 hours (T4), and 8 hours (T8) after induction

tag: mutant

value: akuB, sakA knock-out mutant

tag: time point


title: sakA.4c-2

tag: strain

tag: repeated run

value: repeated due to lack of reads


title: sakA.1b


title: sakA.4a


title: V.C. and ethanol treated mice (V.C./EtOH) 3

tag: age


title: 4-NQO and Untr. mice (4-NQO/Untr.) 1

tag: tissue


title: sakA.1c


title: V.C. and ethanol treated mice (V.C./EtOH) 2


title: sakA.0c


title: sakA.1a


title: 4-NQO and Untr. mice (4-NQO/Untr.) 2


title: Sample 3

value: Diversity Outbred (JAX#009376)

value: liver


title: sakA.4c-1


title: sakA.0a


title: mpkA.4c

description: Deletion of the gene Afu4g13720 in the CEA17 background

value: akuB, mpkA knock-out mutant


title: mpkA.1c


title: mpkA.4a-1


title: V.C. and ethanol treated mice (V.C./EtOH) 1


title: sakA.0b


title: mpkA.4a-2


title: mpkA.4b-2


title: V.C. and untr. treated mice (V.C./Untr.) 1


title: V.C. and untr. treated mice (V.C./Untr.) 2


title: mpkA.1b-2


title: mpkA.1b-1


title: mpkA.0b


title: V.C. and untr. treated mice (V.C./Untr.) 3


title: mpkA.0c


title: akuB.8b

description: Strain CEA17 (deletion of the gene Afu2g02620 in the CEA10 background)

value: akuB knock-out mutant


title: akuB.4a_2


title: akuB.8a-1


title: akuB.8c


title: akuB.1b


title: mpkA.0a


title: mpkA.4b-1


title: akuB.4c_2


title: akuB.4b_2


title: akuB.1a


title: akuB.0.5c


title: akuB.0.5a


title: wt.8c

description: strain CEA10


title: wt.8a

description: strain CEA10


title: wt.4c

description: strain CEA10


title: mpkA.1a


title: akuB.0b_2


title: wt.4b

description: strain CEA10


title: akuB.0.5b


title: akuB.8a-2


title: akuB.1c


title: wt.0.5b

description: strain CEA10


title: wt.4a

description: strain CEA10


title: wt.0.5c

description: strain CEA10


title: wt.1b

description: strain CEA10


title: wt.0c

description: strain CEA10


title: wt.1a

description: strain CEA10


title: wt.1c

description: strain CEA10


title: wt.0b

description: strain CEA10


title: wt.0a

description: strain CEA10


title: akuB.0a_2


title: Seedling

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

country: China

institute: South China Agricultural University

data_processing:
Fastx toolkit was used for data pre-processing. Original .fastq files were converted to .fasta files using fastq_to_fasta command (fastq_to_fasta -v -r -i INPUT_FILE.fastq -o OUTPUT_FILE.fasta -Q 33);
Adaptor was trimmed using the fastx_clipper (fastx_clipper -a "CTTGGCACCCGAGAATTCCA" -c -v -i INPUT_FILE.fasta -o OUTPUT_FILE -l 15);
Trimmed read file was collapsed into tag_count file using fastx_collapser (fastx_collapser -i INPUT_FILE -o OUTPUT_FILE);
Collapsed reads were mapped to reference genome by bowtie 1.0;
miRNA annotation, target identification and PHAS FBX annotation were conducted with customized pipelines.
Genome_build: fvesca_v1.0(scaffolds, http://www.rosaceae.org/species/fragaria/fragaria_vesca/genome_v1.0)
Supplementary_files_format_and_content: trimmed and collapsed read file in a tag_count formate. In the .txt file, each row has two columns. The first column is a small RNA sequence, and the second column the read count of the sequence.

organism: Fragaria vesca

source_name: Seedling

growth_protocol: A seventh generation inbred line of Fragaria vesca, Yellow Wonder 5AF7 was grown in soil in growth chambers under 12 hr light as previously described (Hollender et al. 2012).

extract_protocol:
For small RNA sequencing, total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen, Germantown, MD) with certain modifications. Specifically, the supernatant passing through Qiashedder spin column was precipitated in 1.5 volumes of ethanol and then centrifuge for 2 min at 12000 rpm. The pellet was dissolved in 50 µl of water, mixed with 500 µl Qiazol, and then 140 μl chloroform. After centrifuge, the supernatant was transferred to RNeasy mini spin column for further purification following the instruction from RNeasy Plant Mini Kit. The quality of total RNA was checked by Experion Automated Electrophoresis System (Bio-Rad, Hercules, CA).
10-20 µg total RNA per sample with RIN (RNA integrity number) above 7.8 were sent to the Weill Cornell Medical College’s Genomics Resources Core Facility for library preparation following the Illumina® TruSeq™ Small RNA Sample Preparation protocol. The libraries were sequenced on the Illumina Hiseq 2000 platform.

value: Seedling

tag: plant stage

value: 6 months old

tag: organ stage

value: 4 weeks old

tag: line

value: Yellow Wonder 5AF7


title: akuB.0c_2


title: Vegetative PARE

source_name: Leaf and seedling

value: Leaf and seedling

value: mixed tissues


title: Fruit PARE

source_name: Achene and receptacle

value: Achene and receptacle


title: Leaf

source_name: Leaf

value: Leaf

value: unexpanded leaf


title: Receptacle

source_name: Receptacle

value: Receptacle

value: 10 days post anthesis


title: wt.8b

description: strain CEA10

value: wild type


title: 4D ovary wall

source_name: Ovary wall

value: Ovary wall

value: 4 days post anthesis


title: 4D seed

source_name: Seed

value: Seed


title: 10D ovary wall


title: 10D seed


title: Flower PARE

source_name: Open flower and flower bud

value: Open flower and flower bud


title: wt.0.5a

description: strain CEA10


title: DMSO_virus_minus

city: Tokushima

first: Takashi

last: Kuzuhara

address: Nishihama, Yamashiro-cho

country: Japan

institute: Tokushima Bunri University

data_processing:
Illumina bcl2fastq-1.8.4 software used for basecalling.
Sequenced reads were aligned to the canFam3 reference genome using ELAND v2 software (Illumina).
Unmapped or redundantly mapped sequences were removed from the data set, and only uniquely mapped sequences with two or less mismatches were used for further analyses. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using in-house Perl script.
Genome_build: danFam3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Canis lupus familiaris

source_name: MDCK cells

extract_protocol:
Total RNA was extracted from cell lysates in each well at 24 hrs post incubation.
For analysis of NGS, each mRNA sequencing library was constructed from extracted total RNAs by using SureSelectXT RNA Target Enrichment for Illumina Multiplexed Sequencing (Agilent technologies, CA, USA) according to the manufacturer’s instructions.

tag: cell line

value: MDCK

value: DMSO


title: DMSO_virus_plus

value: DMSO and influenza A virus (A/Puerto Rico/8/34 (H1N1))


title: Bakuchiol_un-natvirus_minus

value: (-)-(R)-bakuchiol


title: Bakuchiol_natvirus_plus

value: (+)-(S)-bakuchiol and influenza A virus (A/Puerto Rico/8/34 (H1N1))


title: Bakuchiol_natvirus_minus

value: (+)-(S)-bakuchiol


title: HpSC_FL651

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006 Vet Research Tower

institute: Cornell University

data_processing:
Sequencing quality was assessed using fastqc/0.11.3
Reads were aligned using Mapsplice/2.1.4 to the UCSC hg19 reference genome and BOWTIE index. The --fusion parameter was used to search for both canonical and semi-canonical splice junctions.
Alignments were quantified and used to generate gene level counts tables using RSEM/1.2.9
Gene level counts were read into R version 3.1.1 (2014-07-10). DESeq/1.16.0 was used to normalize counts and conduct differential gene expression analysis. A table of normalized counts for each gene and sample is included as processed data.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text files include normalized (using DESeq) count values for each sample

source_name: Hepatic stem cells

extract_protocol:
RNA was isolated from purified cell populations of FL-HCCs, biliary tree stem cells, hepatic stem cells, hepatoblasts, and adult hepatocytes using the Qiagen RNeasy Kit
Libraries were prepared using Tru-seq Stranded mRNA as per the manufacturer's instructions by the UNC High Throughput Sequencing Core Facility. The samples were sequenced on an Illumina HiSeq 2500, paired-end, 48bp reads.

tag: cell type

value: Hepatic stem cells


title: HpSC_FL552


title: HB_FL634

source_name: Hepatoblasts

value: Hepatoblasts


title: HB_FL627


title: HpSC_FL614


title: Cerebellum_E60

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

country: Denmark

institute: Omiics ApS

description:
cerebellum_E60_index06
other_tissues.genes.fpkm_tracking

data_processing:
Basecalling performed with Illumina Casava1.7 at BGI-Shenzhen
Quality (Phred score: 20) and adapter trimmed using Trim Galore.
Gene expression was evaluated using Tophat2/Cufflinks
Circular RNA detection was done with the find_circ pipeline (http://circbase.org/cgi-bin/downloads.cgi)
Genome_build: Sscrofa10.2/SusScr3
Supplementary_files_format_and_content: Excel file with detected circular RNAs (.xls) and standard cuffdiff (cufflinks) output file with gene expression in FPKM (.fpkm_tracking)

organism: Sus scrofa

source_name: Embryonic brain

extract_protocol:
Dissected porcine fetal brain samples were transferred to dry ice. High molecular weight RNA, above 200 nt, was purified using the MirVana kit (Ambion).
RNA was then rRNA depleted using the Ribo-Zero Magnetic Kit (Human/Mouse/Rat) (Epicentre). Sequencing libraries were generated using the ScriptSeq v2 kit (Epicentre).

tag: brain region

value: Cerebellum

tag: embryonic day


title: Cerebellum_E115

description:
cerebellum_E115_index10
other_tissues.genes.fpkm_tracking


title: HB_FL626


title: Hippocampus_E115

description:
hippocampus_E115_index11
other_tissues.genes.fpkm_tracking

value: Hippocampus


title: Bakuchiol_un-natvirus_plus

tag: treatment

value: (-)-(R)-bakuchiol and  influenza A virus (A/Puerto Rico/8/34 (H1N1))


title: Brain_stem_E60

description:
brain_stem_E60_index08
other_tissues.genes.fpkm_tracking

value: Brain stem


title: Brain_stem_E115

description:
brain_stem_E115_index04
other_tissues.genes.fpkm_tracking


title: Flower bud

source_name: Flower bud

value: Flower bud

value: 6 months old

value: unopen flowers

value: Yellow Wonder 5AF7


title: FLHCC_469

source_name: Fibrolamellar hepatocellular carcinoma

value: Fibrolamellar hepatocellular carcinoma


title: FLHCC_470


title: Basal_ganglia_E115

description:
basal_ganglia_E115_index09
other_tissues.genes.fpkm_tracking

value: Basal ganglia


title: Basal_ganglia_E60

description:
basal_ganglia_E60_index05
other_tissues.genes.fpkm_tracking


title: FLHCC_4628


title: Hippocampus_E60

description:
hippocampus_E60_index07
other_tissues.genes.fpkm_tracking


title: Cortex_E42

description:
cortex_E42_Index4
cortex.genes.fpkm_tracking

value: Cortex


title: Cortex_E60

description:
cortex_E60_Index5
cortex.genes.fpkm_tracking


title: Cortex_E80

description:
cortex_E80_Index6
cortex.genes.fpkm_tracking


title: Cortex_E115

description:
cortex_E115_Index12
cortex.genes.fpkm_tracking


title: BAP1 KO GMP 3

status: Public on Oct 05 2015

first: Barbara

last: Spitzer

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
BAM converted back to FASTQ using PICARD Sam2Fastq.
Reads mapped to mm9 (junctions from ENSEMBL, Mus_musculus.NCBIM37.67) using STAR RNA-seq aligner, using read overhang of 49
Unmapped reads were mapped to mm9 using BWA MEM (version 0.7.5a).
The two mapped BAM files were merged and sorted.
Gene level counts computed using htseq-count (options -s y -m intersection-strict).
Differential expression analysis was performed with the R Bioconductor DESeq2 package using default parameters.
Genome_build: mm9, ENSEMBL Mus_musculus.NCBIM37.67
Supplementary_files_format_and_content: Normalized count tables provided as computed by DESeq2.

source_name: bone marrow

extract_protocol:
Bone marrow was extracted and red cell lysed, cells were stained for GMP markers (Lineage-c-Kit+Sca1-CD34+Fcϒ), and sorted using a FACS Aria. RNA was harvested using Trizol reagent. Smart Clontech RNA Kit (Cat# 635001) was used with 20 ng RNA for library construction.
10ng of high quality total RNA was amplified using the SMARTer Universal Low Input RNA Kit for Sequencing (Clontech Laboratory, cat# 634940) according to manufacturer instructions. Amplified material underwent whole transcriptome library preparation according to the Ion Total RNA-Seq Kit v2 protocol (Life Technologies), with 16 cycles of PCR.

value: granulocyte macrophage progenitors (GMP)

tag: genotype

value: MX1+ Cre Bap1 f/f

value: 65 days (pIpC at 42 days)


title: BAP1 KO GMP 1


title: Forebrain_E23

description:
forebrain_E23_Index2
cortex.genes.fpkm_tracking

value: Forebrain


title: Cortex_E100

description:
cortex_E100_Index7
cortex.genes.fpkm_tracking


title: CON GMP 2

value: Bap1 f/f


title: FLHCC_460


title: AHEP_H0173

source_name: Adult hepatocytes

value: Adult hepatocytes


title: AHEP_H0965


title: BTSC_FL693

source_name: Biliary tree stem cells

value: Biliary tree stem cells


title: BTSC_AL703


title: CON GMP 3


title: AHEP_H0301


title: BTSC_NN692


title: BAP1 KO GMP 2


title: CON GMP 1


title: RX136_Thymus_Treg

first: Alexander

middle: Y

last: Rudensky

department: Immunology

data_processing:
In order to precisely represent the abundance of individual TCR transcript, we introduced random barcodes to label each mRNA molecule during reverse transcription. Analysis of these data requires the identification of unique barcodes, translation of coding regions, alignment with different Variable and Junction segments, and extraction of CDR3 etc.
Step 1: From read1, extract unique barcodes that represent individual cDNA molecules. Random barcodes are introduced during reverse transcription by 5’ RACE to label individual TCR alpha mRNA, which is represented by 12 random nucleotides in read1 separated to 3 groups by thymidines (T). Reads with the same barcodes are grouped to generate consensus sequences of the sense strands.
Step 2: From the consensus sequences identify the isoforms of V segments by aligning the sequences to mouse genome with tools available from http://www.imgt.org or http://mitcr.milaboratory.com.
Step 3: The corresponding sequences from read2 for each unique barcode identified in Step 1 are grouped to generate consensus sequences of the anti-sense strands.
Step 4: Isoforms of J segments and CDR3 sequences are extracted from the consensus sequences of the anti-sense strands with tools available from http://www.imgt.org or http://mitcr.milaboratory.com.
Step 5: Numbers of unique barcodes for the same CDR3 with identical V and J isoforms representing the relative abundance TCR clones are counted and used for further statistical analysis.
Processed data has not been included in the GEO submission because of the numerous parameters and variables. Instead, with the provided raw sequence data and a detailed explanation of our library preparation and data processing algorithm in the manuscript, readers will be able to reanalyze the data in a similar manner or with their own modified procedures.

growth_protocol: Treg and conventional CD4+ T cells were sorted, lysed with TRIzol and kept at -80°C until RNA extraction and library preparation (within one month).

extract_protocol:
RNA extraction from TRIzol cell lysate was performed according to the manufacturer’s manual.
mRNA purified from extracted total RNA with Dynabeads mRNA DIRECT Kit (Life Technologies) was used for reverse transcription, during which the 5’end of TCRα mRNA was tagged with a synthesized oligo bearing random barcodes AAGCAGTGGTATCAACGCAGAGUNNNNUNNNNUNNNNUCTTrGrGrGrGrG (N for random nucleotides, r for RNA) via template switch. Sample indices and sequencing adaptors were introduced during the PCR amplification of the cDNA.
Libraries were quantified with KAPA Library Quantification Kits. Indexed samples were mixed and sequenced with Illumina MiSeq Reagent Kit V3 for paired-end 200 + 200 cycles.

value: Treg

value: Thymus


title: RX78_Thymus_Treg


title: RX78_Spleen_Treg

value: Spleen


title: Pcon18_DD36_c

city: Bochum

first: Minou

last: Nowrousian

address: Universitaetsstr. 150

department: Molecular and Cellular Botany

institute: Ruhr-University Bochum

data_processing:
Illumina Casava 1.8.2 used for base calling.
reads were trimmed for low quality bases, and reads with undefined bases ("N") were removed as described in Teichert et al. 2012, BMC Genomics 13: 511
read counts and expression ratios for annotated gene models were determined with DESeq (Anders S, Huber W 2010, Genome Biol 11: R106) and LOX 1.8 (Zhang et al. 2010, Bioinf 26: 1918-1919) as described in Teichert et al. 2012, BMC Genomics 13:511.
Genome_build: P. confluens genome version 01 (acc. no. CATG01000000, BioProject acc. PRJNA65573)
Supplementary_files_format_and_content: tab-delimited text file includes read counts and expression ratios (from LOX and DESeq) for all annotated genes as well as additional information (e.g. predicted function, length of transcript, peptide etc.)

organism: Pyronema omphalodes CBS 100304

source_name: vegetative mycelium

growth_protocol: Samples were grown for at least 24 hours in constant light and afterwards shifted to constant darkness. Shifts for DD24 and DD36 were staggered so that harvest of the samples was at the same overall growth time to exclude differences in mycelial mass/development. Growth was in WPC medium at 25 °C and 100 rpm.

extract_protocol:
Total RNA was extracted with the Qiagen RNeasy lipid tissue mini kit with some modifications as described in Nowrousian and Kück 2006, FEMS Microbiol Lett 257: 328-335
RNA libraries were prepared for sequencing using standard Illumina protocols (TrueSeq Chemistry)

treatment_protocol: Samples were harvested under red light and flash frozen in liquid nitrogen.

value: DD

tag: treatment time

value: 36 hours

value: vegetative mycelium


title: Pcon13_DD24_a

value: 24 hours


title: Pcon14_DD24_b


title: RX141_Spleen_Treg


title: Pcon16_DD36_a


title: Pcon17_DD36_b


title: RX78_LN_Treg

value: Lymph nodes


title: RX136_Spleen_Treg


title: RX141_LN_Treg


title: RX136_LN_Treg


title: RX141_Thymus_Tn

value: naive CD4+ T


title: RX136_Spleen_Tn


title: RX78_Thymus_Tn


title: Pcon15_DD24_c


title: RX136_LN_Tn


title: RX141_LN_Tn


title: RX78_Spleen_Te

value: effector CD4+T


title: RX141_Spleen_Te


title: RX78_LN_Te


title: RX141_LN_Te


title: RX78_Spleen_Tn


title: RX78_LN_Tn


title: RX141_Thymus_Treg


title: RX136_Spleen_Te


title: RX136_LN_Te


title: RX79_Thymus_Treg


title: RX67_Thymus_Treg


title: RX164_Thymus_Treg


title: RX67_Spleen_Treg


title: RX142_Thymus_Treg


title: RX79_Spleen_Treg


title: RX164_Spleen_Treg


title: RX161_Spleen_Treg


title: RX67_LN_Treg


title: RX161_Thymus_Treg


title: RX79_LN_Treg


title: RX164_LN_Treg


title: RX142_Spleen_Treg


title: RX136_Thymus_Tn


title: RX141_Spleen_Tn


title: RX67_Spleen_Tn


title: RX79_Spleen_Tn


title: RX164_Thymus_Tn


title: RX161_Thymus_Tn


title: RX67_Thymus_Tn


title: RX142_Spleen_Tn


title: RX79_LN_Tn


title: RX164_LN_Tn


title: RX67_LN_Tn


title: RX161_LN_Tn


title: RX142_LN_Tn


title: RX164_Spleen_Tn


title: RX67_Spleen_Te


title: RX79_Spleen_Te


title: RX161_LN_Treg


title: RX161_Spleen_Te


title: RX164_Spleen_Te


title: RX161_LN_Te


title: RX142_LN_Te


title: RX142_Spleen_Te


title: RX164_LN_Te


title: Nanog ChIP-seq

city: Salt Lake City

first: Edward

middle: J

last: Grow

state: UT

address: 2000 Circle of Hope Drive

department: Oncology

institute: University of Utah

description: ChIP DNA

data_processing:
Sequence reads were aligned with bowtie and peaks were called using QuEST software (v2.4)
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: H9 hESC

growth_protocol: hESCs (H9 line, Wi-Cell) were expanded in feeder free, serum free medium, mTESR-1 from StemCell technologies. Cells were passaged 1:7 every 5-6 days by incubation with accutase (Invitrogen) long and resultant small cell clusters were subsequently re-plated on tissue culture dishes coated overnight with growth factor reduced matrigel (BD biosciences). hESCs quality was regularly tested by evaluating the expression of a panel of hESC markers (e.g. Alkaline phosphatase, OCT4) and the capacity to differentiate into cell types derived from the three germ layers.

extract_protocol:
Anti-Nanog antibody (R&D AF1997) was used.  Lysates were clarified from sonicated nuclei and ChIP-DNA complexes were isolated with antibody. 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 3â end. After adapter ligation, DNA was size selected on agarose gel from 200-700 bp. Then isolated DNA was PCR amplified with Illumina primers for 18 cycles. 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.
NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7370L)

treatment_protocol: cells were crosslinked with 1% formaldehyde for 10 min at room temperature, then quenched with 0.125M glycine for 10 min at room temperature.

value: H9 ESC

tag: chip antibody

value: Anti-Nanog antibody (R&D AF1997)


title: input control for ChIP-seq

description: input DNA


title: RX142_LN_Treg


title: RX79_LN_Te


title: rTreg_D304_batch4

first: Aaron

last: Arvey

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
Reads were aligned using BWA. Peak calling was performed by MACSv2.  Reads were aligned to peaks and normalized as reads per million (RPM)
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Numeric matrix of reads per million in each organism

source_name: CD4+ T cells

extract_protocol:
ChIP-seq DNA sample prep kit from Illumina
Standard Illumina library prep

treatment_protocol: Human cells were isolated ex vivo and untreated.  Murine cells were isolated day 13 after Foxp3GFP-DTR mice were treated with PBS or DT.

tag: antibody

value: H3K27ac, Abcam, ab4729

tag: cell source

value: Primary Human T cells isolated from buffy coat preparations and sorted

value: resting Treg cells (CD4+ CD25+ CD45RA+) from donor 304


title: RX142_Thymus_Tn


title: Tn_D54_batch4

value: naive T conventional cells (CD4+ CD25- CD45RA+) from donor 54


title: rTreg_D204_batch4

value: resting Treg cells (CD4+ CD25+ CD45RA+) from donor 204


title: Teff_D60_batch3

value: activated T conventional cells (CD4+ CD25mid CD45RO+) from donor 60


title: Tmem_D60_batch3

value: memory T conventional cells (CD4+ CD25- CD45RO+) from donor 60


title: RX67_LN_Te


title: rTreg_rep1_batch2

value: Primary Mouse T cells isolated ex-vivo and sorted

value: resting CD4+ Regulatory T cells


title: Tn_rep2_batch2

value: naive CD4+ T conventional cells


title: aTreg_D60_batch3

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 60


title: Tmem_D24_batch3

value: memory T conventional cells (CD4+ CD25- CD45RO+) from donor 24


title: rTreg_D60_batch3

value: resting Treg cells (CD4+ CD25+ CD45RA+) from donor 60


title: Tn_rep1_batch2


title: Teff_D24_batch3

value: activated T conventional cells (CD4+ CD25mid CD45RO+) from donor 24


title: rTreg_D24_batch3

value: resting Treg cells (CD4+ CD25+ CD45RA+) from donor 24


title: MALE_GFPKO_rep2_batch2

value: GFP+ CD4+ T cells from Foxp3GFPKO male mice


title: aTreg_D24_batch3

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 24


title: aTreg_D563_batch4

value: H3K27ac, Abcam, ab4729

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 563


title: RX79_Thymus_Tn

value: naive CD4+ T

value: Thymus


title: aTreg_D21_batch4

value: Primary Human T cells isolated from buffy coat preparations and sorted

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 21


title: MALE_GFPKO_rep1_batch2


title: GFPKO_rep2_batch2

value: GFP+ CD4+ T cells from Foxp3GFPKO/WT mice


title: aTreg_D304_batch4

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 304


title: GFPKO_rep1_batch2

value: Primary Mouse T cells isolated ex-vivo and sorted


title: aTreg_D204_batch4

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 204


title: Teff_rep1_batch2

value: activated CD4+ T conventional cells (Foxp3-negative CD4+ T cells from DT-treated Foxp3DTR mice)


title: JB1

city: Durham

first: Jennifer

middle: Yunyan

last: Zhang

address: 3 Genome Ct, rm4130

department: Dermatology

institute: Duke University

data_processing:
The analysis pipeline includes the initial QC to remove sequencing adaptors and low quality bases to facilitate mapping using fastx toolkit
High quality reads were mapped to the human reference genome (hg19) using tophat
The gene differential expression analysis was performed between control and treatment using cuffdiff with upper quartile normalization, multi-hit correction and 0.5% FDR
Three biological replicates were used for statistical analysis of differential expression for each comparison
Pathway analyses were performed using WEB-based GEne SeT AnaLysis Toolkit
Genome_build: hg19
Supplementary_files_format_and_content: JB_gene_exp_diff_all.xlsx  include RPKM values for average of 3 Samples

source_name: keratinocytes_JunB siRNA

growth_protocol: Primary human keratinocytes isolated from foreskin samples were grown with keratinocyte serum free media. At passage 3, cells were transfected with 100nM siCon or siJunB oligonucelotides.

extract_protocol:
total RNA was isolated from triplicate sets of human keratinocytes at 48h after transfection using RNAeasy column purification (Qiagen, Germantown, MD).
cDNA library was prepared via oligo-dT-directed reverse transcription (Ambion, Grand Island, NY)

value: foreskin skin

value: human neonatal keratincoytes

tag: passage

value: Passage 3

tag: transfected with

value: siRNA oligonucleotides targeting JunB


title: Input con

data_processing:
The analysis pipeline includes the initial QC to remove sequencing adaptors and low quality bases to facilitate mapping using fastx toolkit 48.
High quality reads were mapped to the human reference genome (hg19) using bwa
The list of genes is from the Ensemble Gene database (http://www.ensemble.org) and The RefSeq (www.ncbi.nlm.nih.gov/RefSeq). Distal promoter and terminator regions of the genes were defined as those sequences that mapped +/-2 kb upstream or +/- 50 kb from transcription “start” and “end” sites, respectively
Peak detection, annotation, de novo motif discovery and pathway analysis were performed with treatment and control and comparison between different chips using ChIPseeqer tool. The read density was generated using ChIPseeqer and visualized by UCSC genome browser
Motif analysis was performed with FIRESeq as described in Mathelier, A. & Wasserman, W.W. The Next Generation of Transcription Factor Binding Site Prediction. Plos Computational Biology 9(2013).
Genome_build: hg19
Supplementary_files_format_and_content: peak density  using ChIPseeqer and visualized by UCSC genome browser

source_name: keratinocytes

growth_protocol: Primary human keratinocytes isolated from foreskin samples were grown with keratinocyte serum free media.

extract_protocol:
primary keratinocytes cultured in eight 30-cm plates were scraped off the dish with PBS at about 60-80% confluence, and cross-linked with sequentially with 1% formaldehyde for 8 mins, then treated with 1.25M glycine for 5 min to stop crosslink. Cells were pelleted by centrifuging 5 min at 1500 rpm, and washed twice with PBS (1mM PMSF). Cell nuclei was isolated following cell lysis with ChIP lysis buffer and resuspended with complete RIPA buffer (Santa Cruz Biotechnology, Santa CruZ, CA) for DNA fragmentation by sonication with Branson Sonifier. The fragmented DNA underwent IP with the antibody against JunB (Cell Signaling Technology) followed by purification with MinElute DNA kit (Qiagen).
10 ng of the purified DNA was used for library construction with - the NEBNext® DNA library preparation kit (New England BioLabs).

value: none (input DNA)


title: BAP1 KO input

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

extract_protocol: Bone marrow cells were extracted, red cell lysed and sorted for Lin-c-Kit+Sca1-CD34+CD16/32+ cells using a BD FACSAria. Lysates were isolated from sonicated nuclei and immunoprecipitation was done with an H3K27me3 antibody.

tag: strain

value: Kit enriched bone marrow cells

value: MX1+ Cre Bap1 f/f

tag: age

value: 65 days (pIpC at 42 days)


title: JunB KC

value: JunB

tag: chip antibody vendor

value: Cell signaling

tag: chip antibody cat. #


title: rTreg_rep1_batch1

value: H3K27ac, Abcam, ab4729

value: resting CD4+ Regulatory T cells


title: rTreg_rep2_batch2


title: CO1

tag: tissue

value: non-silencing siRNA control


title: CO3


title: Tn_rep2_batch1

value: naive CD4+ T conventional cells


title: JB2


title: aTreg_rep1_batch2

value: Primary Mouse T cells isolated ex-vivo and sorted

value: activated CD4+ Treg cells (Foxp3-positive CD4+ T cells from DT-treated Foxp3DTR mice)


title: BAP1 KO 4

value: H3K27me3 (abcam, ab6002)


title: aTreg_rep2_batch2


title: JB3

value: foreskin skin


title: rTreg_rep2_batch1


title: GFPKO_rep1_batch1

value: GFP+ CD4+ T cells from Foxp3GFPKO/WT mice


title: Tn_rep1_batch1


title: CON Input

value: Bap1 f/f


title: BAP1 KO 3


title: CO2

value: human neonatal keratincoytes

value: Passage 3


title: GFPKO_rep2_batch1


title: BAP1 KO 2

value: Kit enriched bone marrow cells


title: aTreg_D54_batch4

value: Primary Human T cells isolated from buffy coat preparations and sorted

value: activated Treg cells (CD4+ CD25hi CD45RO+) from donor 54


title: CON 5

value: 65 days (pIpC at 42 days)


title: BAP1 KO 1

value: MX1+ Cre Bap1 f/f


title: CON 3


title: CON 4


title: CON 2


title: CON 1


title: ST111_K3

status: Public on Oct 04 2015

city: Charlotte

first: Kevin

middle: Chad

last: Lambirth

address: 9201 University City Blvd

department: Biological Sciences

institute: University of North Carolina at Charlotte

data_processing:
Sequence reads were trimmed of adapters, mapped to ver. 2.75 G. max reference genome using Tophat 2.0.10 with parameter -I 5000
Mapped reads were quantified using cufflinks 2.2.1 and parameters -u -b

organism: Glycine max

source_name: Ground half-seed

growth_protocol: Soybean parental seeds were geminated in Miracle Grow potting soil mix and transferred to quart and gallon-sized pots during growth.  Light conditions and humidity conditions were kept constant for all plants, and watering was kept as consistant as possible.

extract_protocol:
Seeds were cut in half along the cotyledonary axis.  One half was frozen in liquid nitrogen and ground to a powder, then seed total RNA was extracted using the Qiagen Rneasy plant kit (catalog # 74904) and digested on column with Invitrogen Dnase 1 (catalog # 18068-015).
cDNA libraries were constructed as described in the Illumina TruSeq RNA Sample Prep version 2 protocol utilizing Superscript II Reverse Transcriptase from Invitrogen (catalog # 18064-014). Illumina unique adapters were ligated to each library and quality control was performed on the agilent 2100 bioanalyzer before sequencing.

treatment_protocol: Three of the sample groups, ST77, ST111, and 764, were transformed by Agrobacterium to express the recombinant protein listed above in the samples list.  Each was carried forward multiple generations and sample seeds were chosen from respective generations listed.

tag: transgene

value: myelin-basic protein sigma conjugate

tag: generation

tag: cultivar

value: Williams 82


title: WT_B1


title: WT_B3


title: WT_B2


title: WT_L3


title: WT_H3


title: ST111_K2


title: ST111_B3


title: WT_L2


title: 5hmc-MeDIP-MCF7-hypoxia

city: La Jolla

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

description: hMeDIP-Seq in MCF7 cells under hypoxia conditions

data_processing:
Basecalls performed using CASAVA version 1.8.2
hMeDIP-Seq reads were aligned to the human genome (hg19) using bowtie2 (v2.1.0), keeping only reads that mapped to a unique genomic location (MAPQ > 10).
HOMER (v4.6) was used to process alignment files to generate normalized bedGraphs and bigwigs for the UCSC Genome Browser and quantify 5hmC levels at promoters.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format.  Initial reads were extended to approximately 150 bp and normalized coverage bedGraphs were generated using HOMER.  The bedGraphToBigWig utility from the UCSC Genome Browser was then used to generate the bigwig files.

source_name: MCF7 (human breast cancer cell line)

growth_protocol: MCF7  cells were cultured in the DMEM medium supplemented with 10% FBS at 37℃ in the presence of 5% CO2.

extract_protocol:
genomic DNA was prepared with genomic DNA extraction kit (Promega) and sonicated into fragments ranging ~500bp.
Libraries were prepared according to Illumina's instructions.  Illumina barcode adapters were ligated before hMeDIP. Adaptor-ligated DNA was denatured, followed by incubation with 5-hmC antibody (Active Motif). The immunoprecipitated DNA was purified and sequenced followed by standard Illumina protocols.

treatment_protocol: For hypoxia treatment, cells were cultured in hypoxia chamber (1% oxygen tension) for 24 hr.

value: 5hmC (#39769, Active Motif, Lot No:1031001)

value: hypoxia


title: ST111_B2


title: WT_H2


title: ST111_K1


title: ST111_B1


title: WT_H1


title: ST77_J1

value: human thyroglobulin


title: ST77_J3


title: ST111_I3


title: WT_L1


title: 5hmc-MeDIP-MCF7-normoxia

description: hMeDIP-Seq in MCF7 cells under normoxia conditions

value: normoxia


title: ST111_I1


title: ST77_F2


title: ST77_F3


title: ST77_F1


title: Teff_rep2_batch2

value: H3K27ac, Abcam, ab4729

value: Primary Mouse T cells isolated ex-vivo and sorted

tag: cell type

value: activated CD4+ T conventional cells (Foxp3-negative CD4+ T cells from DT-treated Foxp3DTR mice)


title: ST77_D3


title: ST77_D1


title: ST77_J2


title: 764_K3

value: non-toxic Staphylococcus enterotoxin B


title: 764_K2


title: 764_K1


title: 764_H2


title: ChIP-Seq analysis for WSTF (Williams syndrome transcription factor)

city: Abu Dhabi

first: Piergiorgio

last: Percipalle

state: Abu Dhabi

address: Saadiyat Campus, Abu Dhabi

department: Biology Department, Science Division

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
For sequencing data alignment and analysis, the current assembly of mouse reference genome is missing the ribosomal rDNA repeats, of which there are approximately 400, located on chromosomes 12, 14 and 15. To compensate for this we utilized the procedure of Zentner et al (2011) and constructed a custom reference sequence that contained a non-masked rDNA repeat, taken from BK000964, which was added to the end of chromosome 12 of the MM9 assembly.
The analysis procedure involved the use of the SOAP2 program to map the reads to the constructed reference genome. Sequences with more than two mismatches were discarded from further analysis. The resulting individual sequences were remapped back to the annotated UCSC MM9 reference sequence which allows for the identification of peaks corresponding to the levels of association of the ChIP target with those loci.
Sequence data was filtered to obtain clean data which was then mapped to the reference genome. Only cleanly mapped sequences were used in further analysis.
The distribution of sequence hits along each chromosome is shown in the WIG file output.
Supplementary_files_format_and_content: WIG (Wiggle) format file, that allows the mapping of sequence hits to the reference genome, for example using the UCSC genomic browser.

source_name: Mouse embryonic fibroblasts, WSTF ChIP

growth_protocol: Mouse embryonic fibroblasts cells were grown in DMEM medium (Gibco), supplemented with 10% foetal bovine serum (Gibco) and a 1% penicillin/streptomycin cocktail.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the indicated antibody.
5 ng of precipitated DNA was used to prepare sequencing libraries at the Bejing Genome Institute (Hong Kong) using the Illumina HiSeq 2000 platform. Briefly, ChIP DNA was fragmented to 100-500bp by sonication. DNA-end was repaired to overhang a 3’-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification. Finally we got qualified library for sequencing.

value: mouse embryonic fibroblasts

tag: passages

value: anti-WSTF (Abcam ab50850)


title: 764_H3


title: 764_H1


title: NL3

city: Waco

first: Tamarah

middle: L

last: Adair

state: Tx

address: One Bear Place 97388

department: Biology

institute: Baylor University

description: treatment: no light during incubation for 2 hours

data_processing:
The Illumina miSeq Next Generation Sequencer software was used.
Illumina files were loaded into GeneSifter (PerkinElmer) for quality analysis.
GeneSifter was used to perform Pairwise analysis on quality reads.
EdgeR statistics including a Benjamini and Hochberg false discovery rate correction were performed using GeneSifter.
The combined results of both independent experiments were analyzed using the Pairwise Analysis tools in GeneSifter®.  In order to identify statistically different expression levels of individual genes we applied the following criteria to the pairwise analysis: (i) Quality must have a minimum number of 10 reads, (ii) the transcript level must change by at least 5-fold, and (iii) the P value for the t test must be 0.05 or less.
Genome_build: NC_002952 was used to align sequnce reads
Supplementary_files_format_and_content: These include the gid, count, rpm, NC accession numbers, gene ID, title, and gene type.

organism: Staphylococcus aureus

source_name: Broth culture

growth_protocol: BUSA2288 was grown overnight in 5mL of Brain Heart Infusion (BHI) broth at 37 °C. Broth cultures were  inoculated from a single colony on a TSA plate. The contents of this overnight culture were added to 45mL BHI broth, resulting in a concentration of 1 x 108 CFU/ml as measured by colony counts. One mL aliquots of this diluted overnight culture were transferred to each well of two BD Falcon™ non-treated 24-well plates.

extract_protocol:
Total RNA was extracted from the NL and BL samples using a modified phenol chloroform extraction method as follows.  The pelleted cells were resuspended in RNAse free water and incubated with an equal volume of 1:1 phenol/chloroform.  Phases were separated after centrifugation, and RNA solution was centrifuged at 12,000 x g for 10 minutes. Two times the volume of isopropanol was added to the aqueous layer. The RNA was pelleted, and the pellet was washed with ethanol on ice and resuspended in Elution Solution (Ambion).  Both samples were treated with DNAse Inactivation Reagent (Ambion).  Enrichment of the RNA was performed using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion) which involves using a modified capture hybridization involving magnetic beads to remove 16S and 23S ribosomal RNAs.  RNA was analyzed at the University of Oklahoma Science Center’s lab for Molecular Biology and Cytometry Research using Agilent Bioanalyzer 2100 to verify the concentration and purity of the mRNA.
Illumina MiSeq RNA library Building (TruSeq)

treatment_protocol: 1.5 mm Blue (465nm) LED lights were attached to the lid of a 24 well culture dish 0.5 mm above the broth cultures. The lights were operated at a forward current of 20mA for 2 hours resulting in a total light dosage of 250 J/cm2.

tag: source

value: human nasal isolate

tag: antibiotic sensitivity

value: MRSA


title: BL4

description: treatment: blue light illumination with 2 hour incubation


title: ChIP-Seq analysis for the chromatin remodeller SNF2h

source_name: Mouse embryonic fibroblasts, SNF2h ChIP

tag: chip antibody

value: anti-SNF2h (Abcam ab3749)


title: 764_B2


title: ChIP-Seq analysis for beta-actin

source_name: Mouse embryonic fibroblasts, beta-actin ChIP

value: anti-beta-actin, clone AC74 (Sigma Aldrich)