title: D. shibae 5 h in the light after 24 days in coculture with the dinoflagellate P. Minimum, replicate 2

city: Třeboň

first: Jürgen

last: Tomasch

address: Novohradská 237

country: Czech Republic

institute: Center Algatech, Institute of Microbiology of the Czech Academy of Science

data_processing:
Sequencing was done on the Genome Analyzer IIx (Illumina, San Diego, CA, USA) following a standard protocol. The fluorescent images were processed to sequences and transformed to FastQ format using the Genome Analyzer Pipeline Analysis software 1.8 (Illumina, San Diego, CA, USA).
The sequencing output (50 bp single end short reads) of the Genome Analyzer IIx was controlled for general quality features using the fastq-mcf tool of ea-utils (http://code.google.com/p/ea-utils) and was mapped against the genome sequence of D.shibae (NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1) using BWA v 0.5.9-r16.
Genome_build: NC_009952.1, NC_009955.1 NC_009956.1, NC_009957.1, NC_009958.1 and NC_009959.1
Supplementary_files_format_and_content: tab-delimited text files include unique and total mapped reads and RPKM values for each gene of one sample

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: Co-culture of D. shibae with P. minimum

extract_protocol:
RNA isolation: For RNA extraction, the sample was thawed at room temperature and then transferred to a cryotube filled with 0.3 g acid washed glass beads. The cells were homogenized using the FastPrep-24 instrument (MP Biomedicals, California, USA) at 6.0 m/s for 3 min and then incubated for 5 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C and the supernatants were transferred to fresh tubes, followed by the addition of 100 µl of 1-bromo-3-chloropropane (BCP, Sigma, Germany) and incubation for 10 min at room temperature. Samples were centrifuged at 12,000 g for 10 min at 4°C, after which the aqueous phase was transferred to new tubes and mixed with 500 µl of absolute ethanol. Extracts were applied to RNeasy spin columns (RNeasy mini kit, Qiagen, Hilden, Germany) and processed according to the manufacturer’s instructions. In addition, samples were treated with DNAse I (Qiagen, Hilden, Germany). Removal of genomic DNA was verified via PCR using total RNA as template. The concentration of the RNA was quantified using a NanoDrop spectrophotometer (Peqlab, Erlangen, Germany) and the RNA integrity was assessed using Bioanalyzer 2100 (Agilent, Santa Clara, USA). PolyATract System IV (Promega, Madsion, WI, USA) was used for isolation of algal mRNA according to the manufacturer’s instructions. For isolation of the bacterial mRNA Ribo-Zero Magnetic Kit for both plant leaf and gram-negative bacteria (Epicentre, Madsion, WI, USA) were used according to the manufacturer’s instructions. The final purification of the eluted mRNA was performed using ethanol precipitation.
Libraries of 300 bp for RNA sequencing were prepared using the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA) according the manufacturer’s instructions. Quality control of the prepared libraries was validated using the Agilent Bioanalyzer (Agilent Technologies, Santa Clara, USA). Cluster generation was performed using the Illumina cluster station.

tag: single/co-culture

value: co-culture

tag: light/dark

value: 5 h light

tag: day of co-culture


title: D. shibae 5 h in the light after 30 days in coculture with the dinoflagellate P. Minimum, replicate 1

status: Public on May 01 2014

type: SRA

library_source: transcriptomic

molecule: total RNA


title: D. shibae 5 h in the light after 24 days in coculture with the dinoflagellate P. Minimum, replicate 1


title: D. shibae 5 h in the light after 30 days in coculture with the dinoflagellate P. Minimum, replicate 2


title: Embryo

city: Beijing

first: Bin

last: Liu

state: Beijing

address: Hai Dian

department: School of Life Sciences

country: China

institute: Tsinghua University

description: Small RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to Tetranychus urticae whole genome using SOAP software.
Normalize the expression of miRNA in two samples (control and treatment; embryo and adult were regarded as controls, larva and nymph were regarded as treatments) to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads*1000000
Genome_build: Tetranychus_urticae.main_genome_200909.scaffolds.fasta.gz (Sep 29 2009 03:46:56 PM; http://bioinformatics.psb.ugent.be/orcae/overview/Tetur).
Supplementary_files_format_and_content: Tab-delimited text files containing the identified known miRNAs and their expression levels. The first column contains the name of each identified miRNA, the second column indicates the expression level (unnormalized value), the third column contains the sequence, and the fourth column indicates the normalized expression level.

organism: Panonychus citri

source_name: Whole body, embryo

extract_protocol:
More than 3000 embryos, 2500 larvae, 1500 nymphs (a mixture of protonymphs and deutonymphs) and 1000 adults were gathered into four centrifuge tubes, respectively, and stored at -80 °C for RNA extraction. Total RNA from the four samples was extracted using the TriZol reagent (TransGen Biotech, Beijing, China), according to the manufacturer's instructions.
For each library, small RNAs of 18 to 30 bp in length were separated by 15% polyacrylamide gel electrophoresis (PAGE). The ligation between these small RNAs and 5' and 3' adaptors was performed using T4 RNA Ligase (Takara:D2050). The 5'- and 3'-ligated RNA products were purified and then reverse transcribed for the first-strand cDNA using a SuperScript® II Reverse Transcriptase kit (InvitrogenTM: 18064-014) with the complementary sequence of the 3' adaptor. Thereafter, the cDNAs were used as templates for double-stranded cDNA synthesis using PCR amplification in a Veriti Thermal Cycler (Applied Biosystems), using primers that anneal to the adapters. After second-strand cDNA synthesis, the adaptor sequence primers were used to amplify the PCR products as a small RNA library for deep sequencing.

tag: tissue

value: whole body

tag: developmental stage

value: embryo


title: C2

city: Utrecht

first: Erik

last: Bathoorn

address: Heidelberglaan 100

department: MMB

country: Netherlands

institute: UMC Utrecht

data_processing:
Dirty raw reads were removed by the following filter steps: remove reads with adaptor, reads in which unknown bases are more than 10%, and low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read).
Clean reads were mapped to reference sequences using SOAPaligner/soap2. No more than 2 mismatches bases were allowed in the alignment.
An RNA fragment based library was used to evaluate the randomness of distribution of reads on reference genes.
The reference AF293 gene and genome was assessed from http://www.ncbi.nlm.nih.gov/genome/assembly/284548, GenBank Assembly ID: GCA_000002655.1, RefSeq Assembly ID:GCF_000002655.1.
Genome_build: ASM265v1
Supplementary_files_format_and_content: Sample-level .txt files represent RPKM expression.  Series-level .txt file represents analysis of mean difference in RPKM expression over 3 experiments corrected for gene length and total gene reads per condition.

organism: Aspergillus fumigatus Af293

source_name: experiment 2 control

growth_protocol: Spores were isolated from minimal medium (MM) [775] plates containing 2% glucose. Liquid cultures were grown at 37°C at 200 rpm for 8 hours. To this end, 100 mL TM (MM supplemented with 0.5% yeast extracts, 0.2% casamino acids, and 2% glucose [776]) at 200 rpm in 500 ml Erlenmeyers, incubated with a final concentration of 8 x 106 spores/ml.

extract_protocol:
After washing the mycelium with 0.8% NaCl, the material was snap-frozen in liquid nitrogen in a 2 ml Eppendorf tube, containing two metal bullets (4.76 mm in diameter). Samples were ground with a precooled adapter set of the tissue lyser (Qiagen) for 2 min at 20 Hz. The frozen material was taken up in 1 ml TRIzol® Reagent (Invitrogen) by vortexing. After removing the metal bullets, 200 μl chloroform was added. After mixing well, samples were centrifuged at 10.000 g for 10 min. RNA was purified following further instructions of the Trizol provided instructions. The purified RNA was eluted using RNAse free water. RNA absorbance ratios and integrity were checked by Agilent 2100 bioanalyser™.
After extracting the total RNA from the samples, mRNA was enriched with oligo (dT) magnetic beads (Illumina). Fragmentation buffer was added to break the mRNA into short fragments (about 200 bp).  The first cDNA strand was synthesized by random hexamer-primer using the mRNA fragments as templates. The second strand was synthesized by adding dNTPs, RNase H, and DNA polymerase I. The double strand cDNA was purified with QiaQuick PCR extraction kit (Qiagen) and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments. The required fragments was purified by agrose gel electrophoresis and enriched by PCR amplification. The library products were analysed via Illumina HiSeq™ 2000. The original image data was transferred into sequence data by base calling, which is defined as .raw data or raw reads and saved as .fastq files.

treatment_protocol: Control or addition of   0.5 µM MP (Santa-Cruz biotechnology)

tag: agent

value: control

value: mycelia


title: Nymph

description: Small RNA

source_name: Whole body, nymph

value: nymph


title: C3

source_name: experiment 3 control


title: Adult

description: Small RNA

source_name: Whole body, adult

value: adult


title: Larvae

description: Small RNA

source_name: Whole body, larvae

value: larva


title: TBS-seq for 10ng repeat2

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

description: tagmentation-based whole genome bisulfite sequencing

library_source: genomic

data_processing:
After sequencing, adapters were first removed using cutadapt-1.2.1 software (http://code.google.com/p/cutadapt/), only reads with minimally 45 bp length were remained. After removing adapters, low quality reads that contained more than 10% N’s or more than 50% of the sequence with low quality value (quality value <5) per read were filtered out. Read mapping was done on the rice reference genome (IRGSP_build5) using BS-MAP (version 2.73) alignment software that combines genome hashing and bitwise masking to achieve fast and accurate bisulfite mapping, allowing for maximally 5 mismatches or 1 small insertion or deletion.
After mapping, PCR duplicates were removed using Samtools software. Then, we separated the reads into two categories, depending on whether they are from the top (C changed to T, C-T) and bottom (G changed to A, G-A) strands. By simulating the methylation proportion across each possible read position, the 12 bps from the 3’ ends of C-T reads and the 5’ ends of G-A reads were then removed as which were affected by the 5-methyl-dCTPs incorporated during the gap-repair and strand displacement step.
Methylation level was defined as the fraction of read counts of ‘C’ in the total read counts of both ‘C’ and ‘T’ for each covered C site, and herein average percentage methylation of all cytosine residues for any genomic region covered was computed as the fraction of read counts of ‘C’ in the total read counts of both ‘C’ and ‘T’ for each genomic region. Based on such read fraction, methylated cytosines were called using a binomial distribution as in the method described by Lister et al. (2009), whereby a probability mass function is calculated for each methylation context (CpG, CHG, CHH). The non-conversion rate and sequencing error rate were taken into account, for which the total error rate was determined by unmethylated lambda DNA spike-ins
We comprehensively assessed the repeatability, sensitivity as well as specificity and characterized both global and genic methylation patterns of a rice strain by this new T-WGBS, proving its consistency in comparison with LC-WGBS.
Genome_build: IRGSP_build5
Supplementary_files_format_and_content: *.cout.gz files contain 8 columns. The format is that: (1)Chromosome ID, (2)Cytosine position, (3)+/- Watson/Crick chain, (4)Type (CG/CHH/CHG), (5)Base pattern, (6)Methylation Ratio, (7)Methylated reads num, (8)Un-methylated reads num.

molecule: genomic DNA

organism: Oryza sativa

source_name: rice leaf

extract_protocol:
Genomic DNA prepared from a rice strain was quantified by QuantiT dsDNA HS assay kit (0.2-100ng; Invitrogen, Q32854, Carlsbad, CA, USA).
10ng ( each aliquot was spiked with 10pg of unmethylated lambda DNA), 1ng and 0.5ng aliquots of genomic DNA were prepared by gradient dilution and then subjected to fragmentation reaction (regardless of the quantity of DNA used ) by incubating with 4 µL Nextera HMW Buffer (Epicentre-Illumina), nuclease-free water (Ambion) to 16 uL and 4 µL prepared Tn5mC transposomes for 12 min at 55°C followed by purification using 36 µl (1.8X) Agencourt AMPure XP magnetic beads with elution in 14 µL EB buffer. An extension step was then performed by adding 2 µL of 10X Thermopol reation buffer (NEB), 2 µL 10mM 5-Methylcytosine dNTP Mix (Zymo Research, D1030), 1 µl of Bst DNA Polymerase Large Fragment (NEB, M0275s) to each reaction and incubating for 20 min at 65°C. Each reaction was spiked with 200ng of sonicated unmethylated lambda DNA (200-400 bp) and then subjected to bisulfite conversion using a Zymo EZ DNA Methylation Kit (D5100) according to recommended protocols with a 14h 50°C dark incubation and 22 µL (2 x11 µL) elution. The purified DNAs were then amplified using 25 µL Kapa 2G Robust Hot Start Ready Mix (Kapa Biosystems), 1 µL 50X Nextera Primer Cocktail (Illumina - compatible) and 1 µL barcoded Illumina-compatible Adaptor 2 (8-bp index) on the thermocycler with the following parameters: 1 min at 95°C; (20 sec at 95°C; 30 sec at 60°C; 45 sec at 72°C) X (10-15) cycles. The prepared libraries were analyzed by Agilent 2100 Bioanalyzer (Agilent Technologies) and quantified by qPCR and then used for cluster generation and pair-end sequencing with 90 bp reads (PE90) on Illumina Hiseq 2000 using the following sequencing primers: read 1, 5’-GCCTCCCTCGCGCCATCAGAGATGTGTATAAGAGA-3’; read 2, 5’-GCCTTGCCAGCCCGCTCAGAGATGTGTATAAGAGA-3; and index read, 5’-TCTCTTATACACATCTCTGAGCGGGCTGGCAAGGCAGACCG-3.  We generated two chemistry ligation based WGBS libraries from 1000 ng of genomic DNA prepared from Rice (each library was spiked with 1ng of unmethylated lambda DNA) according to methods described previously [10]. Libraries were sequenced in a strategy with pair-end 90 bp read (PE90) on Illumina Hiseq 2000 according to the standard Illumina protocol.

value: leaf

tag: input(ng)


title: MP1

source_name: experiment 1 test

value: methylprednisolone


title: MP2

source_name: experiment 2 test


title: LCBS-seq

description: Chemistry ligation based WGBS library construction


title: C1

source_name: experiment 1 control


title: 400.68

status: Public on Apr 30 2014

city: Pacific Grove

first: Stephen

last: Palumbi

state: CA

address: 120 Ocean View Blvd

department: Biology

country: USA

institute: Stanford University

description: transplanted Aug 3, 2010. Sampled in situ Aug 30, 2011

data_processing:
Mapped using bwa (fraction missing alignments = 0.005)
assembly as in Barshis et al. 2013
Normalization was performed with DESeq using default parameters
filtered so mean # mapped reads>5
Genome_build: de novo built assembly described in Barshis et al. 2013
Supplementary_files_format_and_content: Text file containing normalized mapped read counts

organism: Acropora aff. hyacinthus sp. E JTL-2012

source_name: polyp

extract_protocol:
Ambion RNAqueous Kit
Illumina TruSeq kits, Illumina barcoded: 12 per lane

treatment_protocol: All colonies were sampled within 10 minutes of noon on August 30, 2011

tag: pool of origin

tag: pool transplanted into


title: 400.70


title: TBS-seq for 10ng repeat1


title: 400.40


title: MP3

source_name: experiment 3 test


title: 300.70


title: 300.40


title: 300.68


title: D. shibae 5 h in the light after 18 days in coculture with the dinoflagellate P. Minimum, replicate 2


title: D. shibae 5 h in the light after 18 days in coculture with the dinoflagellate P. Minimum, replicate 1


title: TBS-seq for 0.5ng repeat1


title: TBS-seq for 1ng repeat1


title: 400.75


title: 300.7


title: 400.7


title: 300.75


title: 300.2


title: 400.2


title: Nuc/MNase-Seq-WT ctrl- S2 Cells

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

description: MNase digestion followed by library prep (TruSeq)

data_processing:
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
Positive and negative reads were mapped separately (average distance ~82.5 bp) followed by Gaussian smoothing to generate genome-wide profiles. The average fragment size and variance was calculated using the spatial correlation function between the + and – reads (25 bp reads from either the 5’ (+) or 3’ (-) end of each fragment) by making a histogram of the distances between all + and – reads across the genome.
Each read’s contribution was obtained by shifting (~ 41bp) +/- by +/- half the average fragment size providing a Gaussian density with a fixed standard deviation (50bp) for genome-wide profiles (the total score at a given location is the sum of all the read densities).
Genome_build: Flybase release 5.41
Supplementary_files_format_and_content: tab-delimited text files

organism: Drosophila melanogaster

source_name: wild-type control

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/ (GIBCO, Invitrogen).

extract_protocol:
Chromatin was digested with MNase as described (Cuddapah et al., 2009)
Library preparation was from total nucleosomes or purified H3K27me3 nucleosomes (following  ChIP using anti-H3K27me3 antibodies).
ChIP samples were prepared for sequencing using standard Illumina protocols of ChIP sample prep kits from 12 ng of starting precipitated DNA to generate sequencing libraries

treatment_protocol: S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 or luc  were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.

tag: cell type

value: Late embryonic derived S2 cells

tag: cell line

value: S2 Schneider cells


title: H3K27me3_Beaf_KD

description: MNase digestion followed by ChIP-Seq with anti-H3K27me3 antibodies (Upstate #07-449)

source_name: Beaf32-depleted - anti-H3K27me3


title: RNASeq-Beaf-KD- S2 Cells

description: RNA extraction in trizol

data_processing:
Basecalls performed using CASAVA version 1.8
Burrows Wheeler Alignment tool (BWA) software (default parameters) was used for base-calling
DEGSeq package (Wang et al., 2010) was then used to identify differentially expressed genes (p-value<0.001)
Genome_build: Flybase release 5.41
Supplementary_files_format_and_content: tab-delimited text files

source_name: Late embryonic derived S2 cells

extract_protocol:
RNA were purified into Trizol.
Libraries were prepared by the MGX platform (http://mgx-project.igf.cnrs.fr) for Digital Gene expression by Tag-sequencing.


title: Nuc/MNase-Seq-BEAF-KD- S2 Cells


title: H3K27me3_WT

source_name: wild-type control - anti-H3K27me3


title: RNASeq-dMes4-KD1- S2 Cells

description: RNA extraction in trizol


title: RNASeq-dMes4-KD2- S2 Cells

description: RNA extraction in trizol


title: RNASeq-WT ctrl 2- S2 Cells

description: RNA extraction in trizol


title: RNASeq-WT ctrl 1- S2 Cells

description: RNA extraction in trizol


title: S2-H3K36me3-dm3

description: ChIP-Seq with anti-H3K36me3 antibodies (Abcam, ab9050)

data_processing:
S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/ (GIBCO, Invitrogen).
S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for beaf32 or luc  were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 5 days and cells were then harvested.
Chromatin was sonicated (Bioruptor) followed by immunoprecipitations with anti-H3K36-me2 or me3 specific antibodies or anti- RNA Polymerase II specific antibodies
Illumina library preparation by TruSeq.
ChIP-Seq
Genome_build: Flybase release 5.41
Supplementary_files_format_and_content: tab-delimited text files

source_name: wild-type cells - anti-H3K36me3

growth_protocol: S2 cells were grown in Schneider’s Drosophila medium (SDM, GIBCO,Invitrogen) supplemented with 10% Fetal Bovine Serum (FBS, Sigma) and 1% penicillin/streptomycin (GIBCO, Invitrogen).

extract_protocol:
Standard chromatin extraction procedures were utilized for  ChIP analysis using anti-Beaf32 or anti-IgG control antibodies
ChIP samples were prepared for sequencing using standard Illumina protocols of ChIP sample prep kits from 12 ng of starting precipitated DNA to generate sequencing libraries

treatment_protocol: S2 cells were treated with formaldehyde followed by standard sonication procedures


title: S2-H3K36me2-dm3

description: ChIP-Seq with anti-H3K36me2 antibodies (Upstate #07-369)

source_name: wild-type cells - anti-H3K36me2


title: Pol2_WT

description: ChIP-Seq with anti-RNAPII antibodies (Covance)

source_name: wild-type cells - anti-RNAPII


title: sample:71; strain:K; Day:28; Con - 15C

city: Hagerman

first: Nathan

middle: Reed

last: Campbell

state: Idaho

address: 3059F National Fish Hatchery Rd

department: Genetics Lab

institute: Columbia River Inter-Tribal Fish Commission

description: K cpm all

data_processing:
Base calls, demultiplexing, and fastq conversion: CASAVA 1.8
Read alignments to reference transcriptome: Bowtie (options: -v 3 -3 30 -5 10)
Bowtie alignment counts: perl
Data formatting: Linux and perl
Data normalization and analysis: edgeR Bioconductor package
Genome_build: n/a
Supplementary_files_format_and_content: contigs described in O. mykiss stress response transcriptome: Sanchez CC, Weber GM, Gao G, Cleveland BM, Yao J, Rexroad III CE. 2011  Generation of a reference transcriptome for evaluating rainbow trout responses to various stressors.  BMC Genomics 12:626-640.
Supplementary_files_format_and_content: contig sequences available at http://www.ars.usda.gov/Research/docs.htm?docid=8033
Supplementary_files_format_and_content: edgeR output files containing normalized read counts per sample for each strain

organism: Oncorhynchus mykiss

source_name: Gill tissue

extract_protocol:
Qiagen Rneasy Kits; Epicentre Ribo-Zero rRNA depletion kit
Epicentre Script-Seq library preparation kit

value: gill

tag: strain

value: Keithly Creek

tag: treatment

value: 15 degrees C

tag: time

value: Day 28


title: sample:72; strain:K; Day:28; Con - 15C

description: K cpm all


title: sample:70; strain:K; Day:28; Con - 15C

description: K cpm all


title: sample:68; strain:LJ x K; Day:28; Con - 15C

description: LJxK cpm all

value: Little Jacks x Keithly F1 cross


title: sample:66; strain:LJ; Day:28; Con - 15C

description: LJ cpm all

value: Little Jacks Creek


title: sample:64; strain:LJ; Day:28; Con - 15C

description: LJ cpm all


title: sample:67; strain:LJ x K; Day:28; Con - 15C

description: LJxK cpm all


title: sample:69; strain:LJ x K; Day:28; Con - 15C

description: LJxK cpm all


title: sample:63; strain:K; Day:7; Con - 15C

description: K cpm all

value: Day 7


title: sample:61; strain:K; Day:7; Con - 15C

description: K cpm all


title: sample:65; strain:LJ; Day:28; Con - 15C

description: LJ cpm all


title: sample:62; strain:K; Day:7; Con - 15C

description: K cpm all


title: sample:59; strain:LJ x K; Day:7; Con - 15C

description: LJxK cpm all


title: sample:60; strain:LJ x K; Day:7; Con - 15C

description: LJxK cpm all


title: sample:58; strain:LJ x K; Day:7; Con - 15C

description: LJxK cpm all


title: sample:57; strain:LJ; Day:7; Con - 15C

description: LJ cpm all


title: sample:56; strain:LJ; Day:7; Con - 15C

description: LJ cpm all


title: sample:54; strain:K; Day:3; Con - 15C

description: K cpm all

value: Day 3


title: sample:53; strain:K; Day:3; Con - 15C

description: K cpm all


title: sample:51; strain:LJ x K; Day:3; Con - 15C

description: LJxK cpm all


title: sample:50; strain:LJ x K; Day:3; Con - 15C

description: LJxK cpm all


title: sample:49; strain:LJ x K; Day:3; Con - 15C

description: LJxK cpm all


title: sample:46; strain:LJ; Day:3; Con - 15C

description: LJ cpm all


title: sample:48; strain:LJ; Day:3; Con - 15C

description: LJ cpm all


title: sample:47; strain:LJ; Day:3; Con - 15C

description: LJ cpm all


title: sample:44; strain:K; Day:1; Con - 15C

description: K cpm all

value: Day 1


title: sample:45; strain:K; Day:1; Con - 15C

description: K cpm all


title: sample:42; strain:LJ x K; Day:1; Con - 15C

description: LJxK cpm all


title: sample:43; strain:K; Day:1; Con - 15C

description: K cpm all


title: sample:41; strain:LJ x K; Day:1; Con - 15C

description: LJxK cpm all


title: sample:39; strain:LJ; Day:1; Con - 15C

description: LJ cpm all


title: sample:40; strain:LJ x K; Day:1; Con - 15C

description: LJxK cpm all


title: sample:37; strain:LJ; Day:1; Con - 15C

description: LJ cpm all


title: sample:38; strain:LJ; Day:1; Con - 15C

description: LJ cpm all


title: sample:36; strain:K; Day:28; Trt - 28C

description: K cpm all

value: 28 degrees C


title: sample:55; strain:LJ; Day:7; Con - 15C

description: LJ cpm all


title: m24_hsc_l4 RNA-Seq

city: Houston

first: deqiang

last: sun

state: TX

address: 2121 W Holcombe Blvd

institute: Texas A&M University

description: technical replicate of old biological replicate 14

data_processing:
RUM to make alignments; Customized script to count fragments on gene; DESEQ to do differential expression test;
Genome_build: mm9
Supplementary_files_format_and_content: Tab separated text file for gene's count and fpkm for each sample; deg.m04_hsc_vs_m24_hsc.txt file for two sample comparison testing if a gene is differentially expressed;

organism: Mus musculus

source_name: 24 month Hematopoietic Stem Cells

growth_protocol: Freshly forted 4 month and 24 month-old mouse HSCs (SP-KSL-CD150+)

extract_protocol:
Extract RNA using Qiagen Rneasy Micro kit.
Tru-Seq RNA sample prep kit

treatment_protocol: PolyA selection

value: Murine bone marrow derived primary HSCs

tag: cell surface marker


title: m24_hsc_l1 RNA-Seq

description: technical replicate of old biological replicate 13


title: m04_hsc_l2 RNA-Seq

description: technical replicate of young biological replicate 13

source_name: 4 month Hematopoietic Stem Cells


title: m24_hsc_l2 RNA-Seq


title: m04_hsc_l4 RNA-Seq

description: technical replicate of young biological replicate 14


title: m04_hsc_l1 RNA-Seq


title: m04_hsc_l3 RNA-Seq


title: sample:52; strain:K; Day:3; Con - 15C

description: K cpm all


title: nAtf6-Cherry #1

city: Oakland

first: Ravi

last: Sachidanandam

address: 2945 Webster St

institute: Girihlet Inc.

data_processing:
Illumina CASAVA version 1.7 used for basecalling (?)
Mapped to the Danio rerio genome build Zv9/danRer7
Genome annotation from UCSC was used to identify exon expression and expression values for each gene were assigned by normalizing to the median of the coverage at each position of genes with non-zero expression
Values were quantile-normalized allowing comparisons of the two sets using custom-built software and algorithms as described (Aravin et al., 2008; Olson et al., 2008; Tam et al., 2008)
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: Tab-delimted text file includes reads and their frequencies.

organism: Danio rerio

source_name: Zebrafish 5 dpf liver

extract_protocol: Total small RNA from livers of 5 dpf larval zebrafish were collected: 2 batches of Tg(fabp10:nls-mCherry) control larvae, 2 batches of ethanol-treated Tg(fabp10:nls-mCherry) larvae, and 1 batch of Tg(fabp10:nAtf6-cherry; cmlc2:GFP). Each batch was purified for preparation of high-throughput sequencing libraries.

tag: tissue type

value: liver

tag: genotype

value: Tg(fabp10:nAtf6-cherry; cmlc2:GFP)

value: 5 dpf


title: m24_hsc_l3 RNA-Seq


title: m24_b6l1

description: technical replicate of old biological replicate 12

data_processing:
The bisulfite sequencing data is processed by a newly developed program MOABS: MOdel based Analysis of Bisulfite Sequencing (Sun et al.
http://code.google.com/p/MOABS/). It seamlessly integrates alignment, methylation calling, identification of hypomethylation for one sample and differential methylation for multiple samples, and other downstream analysis integrating histone modification ChIP-Seq data and gene expression RNA-Seq data.
Genome_build: mm9
Supplementary_files_format_and_content: text; chromosome, start, end, methylation ratio, total reads, methylated reads, strand, next nucletide of cytosine, plus_strand, total reads from plus strand, methylated reads from plus strand, minus strand, total reads from minus strand, methylated reads from minus strand

extract_protocol:
Extract genomic DNA using Invitrogen PureLink Genomic DNA kits
Tru-Seq DNA sample prep kit

treatment_protocol: Adapter-ligated fragments were treated with sodium bisulfite (Qiagen)


title: m24_b3

description: technical replicate of old biological replicate 10


title: m24_b6l2


title: m24_b4l1


title: sample:34; strain:K; Day:28; Trt - 28C

description: K cpm all


title: sample:35; strain:K; Day:28; Trt - 28C

description: K cpm all


title: m04_b6l3

description: technical replicate of young biological replicate 12


title: m24_b5


title: m04_b6l2


title: m04_b6l1


title: sample:33; strain:LJ x K; Day:28; Trt - 28C

description: LJxK cpm all


title: sample:32; strain:LJ x K; Day:28; Trt - 28C

description: LJxK cpm all


title: m04_b4l2

description: technical replicate of young biological replicate 10


title: sample:30; strain:LJ; Day:28; Trt - 28C

description: LJ cpm all


title: sample:31; strain:LJ x K; Day:28; Trt - 28C

description: LJxK cpm all


title: m04_b5


title: m04_b4l1


title: sample:29; strain:LJ; Day:28; Trt - 28C

description: LJ cpm all


title: sample:28; strain:LJ; Day:28; Trt - 28C

description: LJ cpm all


title: m04_b3


title: sample:27; strain:K; Day:7; Trt - 28C

description: K cpm all


title: m24_b4l2


title: sample:26; strain:K; Day:7; Trt - 28C

description: K cpm all


title: H3K4me3_m24_b18

description: technical replicate of old biological replicate 7

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using SOAP with 2 mismatches allowed; H3K4me3 and H3K36me3 are processed by MACS and H3K27me3 are processed by SICER for peak calling
genome build: mm9
processed data files format and content: BED format with 1-3 columns as chromosome, start, end. The 4th column for sicer.bed is read count. The 4th and 5th columns for peaks.bed are MACS peak id and pvalue.

source_name: Hematopoietic stem cells (HSC)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipittaion with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)

tag: chip antibody

value: Millipore 07-473

tag: age

value: 24 month

tag: ChIP


title: H3K4me3_m04_b21

description: technical replicate of young biological replicate 8

value: 4 month


title: H3K4me3_m24_b19

description: technical replicate of old biological replicate 8


title: H3K4me3_m04_b18

description: technical replicate of young biological replicate 7


title: sample:24; strain:LJ x K; Day:7; Trt - 28C

description: LJxK cpm all

tag: tissue

value: gill


title: H3K36me3_m24_b18

description: technical replicate of old biological replicate 6

value: Abcam ab9050


title: H3K36me3_m24_b16

description: technical replicate of old biological replicate 4


title: sample:22; strain:LJ x K; Day:7; Trt - 28C

description: LJxK cpm all


title: sample:21; strain:LJ; Day:7; Trt - 28C

description: LJ cpm all


title: sample:23; strain:LJ x K; Day:7; Trt - 28C

description: LJxK cpm all


title: sample:20; strain:LJ; Day:7; Trt - 28C

description: LJ cpm all


title: H3K36me3_m04_b20

description: technical replicate of young biological replicate 6


title: sample:19; strain:LJ; Day:7; Trt - 28C

description: LJ cpm all


title: H3K36me3_m04_b16

description: technical replicate of young biological replicate 4


title: sample:18; strain:K; Day:3; Trt - 28C

description: K cpm all

value: Keithly Creek


title: H3K27me3_m24_b20

description: technical replicate of old biological replicate 3

value: Millipore 07-449


title: sample:16; strain:K; Day:3; Trt - 28C

description: K cpm all


title: H3K27me3_m24_b18

description: technical replicate of old biological replicate 2


title: H3K27me3_m24_b17

description: technical replicate of old biological replicate 1


title: sample:15; strain:LJ x K; Day:3; Trt - 28C

description: LJxK cpm all

value: Little Jacks x Keithly F1 cross


title: H3K27me3_m04_b20

description: technical replicate of young biological replicate 3


title: sample:25; strain:K; Day:7; Trt - 28C

description: K cpm all


title: H3K36me3_m24_b17

description: technical replicate of old biological replicate 5


title: H3K27me3_m04_b18

description: technical replicate of young biological replicate 2


title: sample:14; strain:LJ x K; Day:3; Trt - 28C

description: LJxK cpm all


title: sample:13; strain:LJ x K; Day:3; Trt - 28C

description: LJxK cpm all


title: H3K27me3_m04_b16

description: technical replicate of young biological replicate 1


title: sample:9; strain:K; Day:1; Trt - 28C

description: K cpm all


title: sample:12; strain:LJ; Day:3; Trt - 28C

description: LJ cpm all

value: Little Jacks Creek


title: H3K36me3_m04_b18

description: technical replicate of young biological replicate 5


title: sample:10; strain:LJ; Day:3; Trt - 28C

description: LJ cpm all


title: sample:8; strain:K; Day:1; Trt - 28C

description: K cpm all


title: sample:6; strain:LJ x K; Day:1; Trt - 28C

description: LJ cpm all


title: sample:11; strain:LJ; Day:3; Trt - 28C

description: LJ cpm all


title: sample:7; strain:K; Day:1; Trt - 28C

description: K cpm all


title: sample:3; strain:LJ; Day:1; Trt - 28C

description: LJ cpm all


title: sample:5; strain:LJ x K; Day:1; Trt - 28C

description: LJ cpm all


title: sample:4; strain:LJ x K; Day:1; Trt - 28C

description: LJ cpm all


title: Total RNA 1

city: Pasadena

first: Frederick

middle: E

last: Tan

address: 1200 E. California Blvd, M/C 114-96

department: Biology and Applied Physics

institute: California Institute of Technology

data_processing:
Basecaller software: RTA 1.13.48.0, Pipeline and conversion to FASTQ format: CASAVA 1.8.2
Sequencing reads were trimmed of first 13nts to remove random hexamer priming bias
Trimmed reads were aligned to a mm9 transcript annotation containing only protein coding genes using Bowtie (v. 1.1.2) using default paramters
FPKM measurements were generated by eXpress (v. 1.1.1) using default parameters (see Roberts A. and Pachter L., in submission)
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and other abundance statistics for each transcript annotation

source_name: E14 mESCs

growth_protocol: E14 mESCs were cultured in 15% FBS, DMEM + 1000U/ml LIF.

extract_protocol: Cytoplasmic extracts were prepared via cold hypotonic lysis, and RNA/RNA binding protein complexes were immunoprecipitated (RIP) followed by extraction of co-isolated RNAs. As a control, RIP procedure was conducted using a non-specific rabbit IgG. Two E14 Total RNA preparations were sequenced to gauge gene expression levels prior to RIP. Isolated RNAs were processed according to manufacturer's instructions for Illumina's TruSeq RNA Prep kit. Briefly, RNA is fragmented at 94C to generate lengths of approximately 200nts. The fragments are reverse transcribed to double stranded DNA using random hexamer primers. Ends were blunted, adenylated and ligated to Illumina adapters. Fragments were gel separated and bands corresponding to 350bps were isolated for sequencing.

tag: genetic background

value: wt

tag: sample type

value: Total RNA

tag: antibody

value: E14 mESCs


title: Total RNA 2


title: Control IgG 1

value: control

value: rabbit IgG


title: Sample immunoprecipitate 2

value: Brf1 and Brf2 immunoprecipitated complexes

value: anti-Brf1/2 antibody

tag: antibody manufacturer

value: Cell Signaling Technologies

tag: antibody catalog #


title: Control IgG 2

tag: cell type


title: 72_control_bs2

status: Public on Apr 29 2014

city: London

first: Michael

last: Lovett

state: London

address: Dovehouse St

department: NHLI

country: United Kingdom

institute: Imperial College

description: control

data_processing:
Sequences were mapped to gga3 using Tophat v1.4.0 with defaul settings
Alignment files (.bam) were inputed to Partek Genomics Suite v6.6 to calculate RPKM
Genome_build: gga3
Supplementary_files_format_and_content: tab-delimited text files include RPKM values of individual sample

organism: Gallus gallus

source_name: Utricle

extract_protocol:
Chicken utricles were dissected and treated with streptomycin for 24 hours and recovered for specific time period. Total RNA was harvested with  Trizol.
RNA libraries were prepared following Illumina protocols

tag: time point (in hours)

value: utricle


title: 72_treated_bs2

description: treated


title: 144_treated

description: treated


title: sample:1; strain:LJ; Day:1; Trt - 28C

description: LJ cpm all

tag: strain

value: 28 degrees C

value: Day 1


title: 144_control

description: control


title: 0_control_bs1.2

description: control


title: 168_control_bs2

description: control


title: 0_treated_bs1.2

description: treated


title: 24_control_bs3

description: control


title: 168_treated_bs2

description: treated


title: 24_treated_bs3

description: treated


title: Sample immunoprecipitate 1


title: 120_control_bs2.2

description: control


title: 96_treated_bs2

description: treated


title: 120_control_bs2

description: control


title: 96_control_bs2

description: control


title: 120_treated_bs2

description: treated


title: 168_control

description: control


title: 168_treated

description: treated


title: sample:2; strain:LJ; Day:1; Trt - 28C

description: LJ cpm all

value: gill

tag: treatment


title: 120_treated_bs2.2

description: treated


title: 24_treated_bs2

description: treated


title: 120_control

description: control


title: 120_treated

description: treated


title: 96_control

description: control


title: 24_control_bs2

description: control


title: 48_treated

description: treated


title: 96_treated

description: treated


title: 48_control

description: control


title: 72_control

description: control


title: 0_control

description: control


title: 72_treated

description: treated


title: 0_treated

description: treated


title: 24_control

description: control


title: 24_treated

description: treated


title: 54_control_bs2

description: control


title: 60_treated_bs3

description: treated


title: 66_control_bs2

description: control


title: 60_control_bs3

description: control


title: 66_treated_bs2

description: treated


title: 66_treated

description: treated


title: 54_treated

description: treated


title: 54_treated_bs2

description: treated


title: 60_treated_bs2

description: treated


title: 72_control_bs3

description: control


title: 48_control_bs2

description: control


title: 72_treated_bs3

description: treated


title: 144_control_bs2

description: control


title: sample:17; strain:K; Day:3; Trt - 28C

description: K cpm all

tag: time

value: Day 3


title: 144_treated_bs2

description: treated


title: 120_control_bs3

description: control


title: 60_control_bs2

description: control


title: 96_control_bs3

description: control


title: 168_treated_bs3

description: treated


title: 120_treated_bs3

description: treated


title: 168_control_bs3

description: control


title: 24_treated_bs4

description: treated


title: 24_control_bs4

description: control


title: 0_control_bs2

description: control


title: 66_control

description: control


title: 0_treated_bs2

description: treated


title: 54_control

description: control


title: ACA28_miRNASeq

city: Paris

first: Nabila

last: Elarouci

address: 14 rue Corvisart

department: Recherche

institute: Ligue Nationale contre le Cancer

data_processing:
image analysis, base calling and bcl conversion. Evaluation of quality based on Qphred (average score of 20, i.e. e=0.01)
CASAVA demultiplexes multiplexed samples during the bcl conversion step, and converts *bcl files into compressed FASTQ files. It also trim the sequence adaptor
Fastqc software is used to perform quality control checks on raw sequence data
the script "Trim_adapter", provided by mirExpress (http://mirexpress.mbc.nctu.edu.tw/usage.php), handles the sequence files with or without adaptor sequence.
Genome_build: hg19
Supplementary_files_format_and_content: miRanalyzer 0.3 standalone version (http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php)

organism: Homo sapiens

source_name: Adrenocortical adenoma

growth_protocol: ES cell–derived NS cells were routinely generated by re-plating d 7 adherent neural differentiation cultures (typically 2–3 × 106 cells into a T75 flask) on uncoated plastic in NS-A medium (Euroclone, Milan, Italy) supplemented with modified N2 and 10 ng/ml of both EGF and FGF-2 (NS expansion medium).

extract_protocol:
miRNA-Seq libraries are performed from at least 1µg of extracted total RNA with a RIN greater than 7. Before starting, total RNAs are purified with miRNeasy kit wich allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to the protocol published by François Vigneault : Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. "High-throughput multiplex sequencing of miRNA"; Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G.
miRNA-Seq libraries are performed from at least 1ug of extracted total RNA with a RIN greater than 7. Before starting, total RNAs are purified with miRNeasy kit wich allows the selection of the small RNA fraction less than 100b. From these samples enriched in small RNAs, libraries are performed according to the protocol published by François Vigneault : Curr Protoc Hum Genet. 2012 Apr;Chapter 11:Unit 11.12.1-10. High-throughput multiplex sequencing of miRNA; Vigneault F, Ter-Ovanesyan D, Alon S, Eminaga S, C Christodoulou D, Seidman JG, Eisenberg E, M Church G. Extraction with Qiacube-miRNeasy 96 Mini (Qiagen) kits; 1 to 10 ug per sample, concentration in range 70-500 ng/uL, volume range 15 to 50 uL, BioAnalyzer profile RIN > 7; Ligation, amplification , quantification and purification according to manufacturer's instructions, with the following details: First, a 3 prime adenylated DNA adaptor is ligated to the enriched sample in the absence of ATP preventing the self-ligation of miRNAs.Then a 5 prime RNA adaptor is ligated in the presence of ATP at the other end of the miRNAs.The RT primer complementary of the 3 prime adaptor is added at this stage with which it will form a duplex thereby reducing the ligation between adaptors. A reverse transcription is therefore perfomed from the RT primer and finally these captured miRNAs are amplified by PCR with primers complementary to the 3 prime and 5 prime adaptors. During this PCR a specific barcode is incorporated allowing individualisation of each library.Each PCR is loaded on the Fragment Analyzer (AATI) for a precise quantification of each miRNA peak of interest.Based on these results a equimolar pool of about ten of different samples are performed. Finally the pooled PCR product is loaded on PAGE in order to excise the band of miRNA that is extracted and purified on a Qiagen MinElute column. Pool Concentration between 0.97 and 4.84 nM per uL; purification quantity is 3500 ng

tag: gender

value: F

tag: age (years)

value: Adrenocortical adenoma


title: ACC43_miRNASeq

source_name: Adrenocortical carcinoma

value: M

value: Adrenocortical carcinoma


title: ACC45_miRNASeq


title: ACC44_miRNASeq


title: ACA29_miRNASeq


title: 48_treated_bs2

description: treated


title: 96_treated_bs3

description: treated


title: ACC50_miRNASeq


title: ACA27_miRNASeq


title: ACC42_miRNASeq


title: ACA25_miRNASeq


title: ACA24_miRNASeq


title: ACA22_miRNASeq


title: ACA23_miRNASeq


title: ACA21_miRNASeq


title: ACA20_miRNASeq


title: ACC49_miRNASeq


title: ACC40_miRNASeq


title: ACA30_miRNASeq


title: ACC39_miRNASeq


title: ACC37_miRNASeq


title: ACC48_miRNASeq


title: ACA17_miRNASeq


title: ACC47_miRNASeq


title: ACC35_miRNASeq


title: ACA16_miRNASeq


title: ACA26_miRNASeq


title: ACC33_miRNASeq


title: ACC32_miRNASeq


title: ACC29_miRNASeq


title: ACA12_miRNASeq


title: ACA15_miRNASeq


title: ACA14_miRNASeq


title: ACA13_miRNASeq


title: ACC28_miRNASeq


title: ACC27_miRNASeq


title: ACA18_miRNASeq


title: ACC26_miRNASeq


title: ACC38_miRNASeq


title: ACA19_miRNASeq


title: ACC25_miRNASeq


title: ACA11_miRNASeq


title: ACC24_miRNASeq


title: ACC51_miRNASeq


title: ACC23_miRNASeq


title: ACA8_miRNASeq


title: ACC36_miRNASeq


title: ACC22_miRNASeq


title: Norm3_miRNASeq

source_name: Normal adrenal tissue

value: Normal adrenal


title: ACC46_miRNASeq


title: ACA7_miRNASeq


title: ACC21_miRNASeq


title: ACA6_miRNASeq


title: ACC20_miRNASeq


title: ACC18_miRNASeq


title: Norm2_miRNASeq


title: ACC16_miRNASeq


title: ACA9_miRNASeq


title: ACC15_miRNASeq


title: ACC14_miRNASeq


title: ACA5_miRNASeq


title: ACC13_miRNASeq


title: ACC17_miRNASeq


title: ACC19_miRNASeq


title: ACA3_miRNASeq


title: ACC11_miRNASeq


title: ACA10_miRNASeq


title: ACC8_miRNASeq


title: ACC10_miRNASeq


title: ACA4_miRNASeq


title: ACC6_miRNASeq


title: ACC5_miRNASeq


title: ACC4_miRNASeq


title: Norm1_miRNASeq


title: ACA2_miRNASeq


title: ACC2_miRNASeq


title: ACA1_miRNASeq


title: CTRL8

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

data_processing:
Fastq files were aligned to human genome (Hg19) using novocraft novoalign application version 2.08.02
SAM files were converted to binary BAM files using USeq SamTranscriptomeParser application version 8.2.6
Data normalization, differential gene expression and statistical analyses were performed using USeq OverDispersedDefinedRegionScanSeqs application version 8.2.6
Visualization tracks for the Integrated Genome Browser were created using Useq Sam2USeq application version 8.2.6
Genome_build: Hg19
Supplementary_files_format_and_content: Tab-delimited text file with false discovery rate (FDR), fold change (polyp/control), mean RPKM (reads per kilobase gene length per million reads) for each gene, and individual reads for each sample

source_name: Colon

extract_protocol:
Colon biopsy samples were stored in RNAlater at 4°C overnight and RNA extracted with TRIzol
Illumina TruSeq RNA Sample Prep Kit

tag: location

value: Ascending colon

tag: disease

value: normal colon (patient with no polyps)

tag: Sex

value: Male


title: CTRL7


title: ACC12_miRNASeq


title: ACC9_miRNASeq


title: CTRL6

value: patient matched uninvolved colon

value: Female


title: CTRL5

value: Cecum


title: CTRL2


title: CTRL4


title: CTRL1


title: SSP4

value: sessile serrated polyp


title: SSP6


title: CTRL3


title: SSP2


title: SSP5


title: SSP3


title: SSP1


title: ACC1_miRNASeq


title: SSP7


title: YY1 ChIP-seq

city: Piscataway

middle: P

last: Verzi

state: NJ

address: 145 Bevier Road

department: Genetics

institute: Rutgers, the State University of New Jersey

description: Sample 1

data_processing:
Illumina CASAVA 1.8.2 for basecalling
ELAND mapping
Genome_build: mm9
Supplementary_files_format_and_content: Wig files and bed file were generated using MACS version 1.4.2. p-value cutoff was set to 1e-4. Tag size was set to 50, all other conditions were default.

source_name: jejunal crypt intestinal  epithelial cells

growth_protocol: wt adult mice, 2-4 months old

extract_protocol:
Crypt epithelial isolation using 3mM EDTA and excluding tissue fragments retained above 70um in size
Tru-seq Illumina Kit according to manufacturer's instructions

value: C57BL/6J enriched

value: crypt epithelium

tag: chip antibody

value: anti-YY1 (Santa Cruz, catalog# SC-1703, lot# E0511)


title: T161 pooled RNA from guts of three 7d old workers

status: Public on Apr 28 2014

city: Zürich

first: Seth

last: Barribeau

state: Canton of Zurich

address: Universitatstrasse 16

department: Institute of Integrative Biology

country: Switzerland

institute: ETH Zürich

data_processing:
remove reads with adaptors, remove reads with unknown nucleotides larger than 5%, remove reads with low quality (more than half of the bases' qualities are less than 5)
Obtain clean reads
SOAP2 mapping to genome
Analysis- Genome Mapping -SOAPsplice, SOAP
Software-  TopHat, Release 1.9, Release 2.21, -s 40 -l 32 -v 3 -r 2
Genome_build: Bter_1.1

organism: Bombus terrestris

source_name: Gut

extract_protocol:
qiagen Rneasy RNA extraction
Beads with oligo(dT) were used to isolate poly(A) mRNA after total RNA was collected from eukaryote (prokaryocyte can be treated with kit to remove rRNA before next step). Fragmentation buffer was added for interrupting mRNA to short fragments. Taking these short fragments as templates, Random hexamer-primer were used to synthesize the first-strand cDNA. The second-strand cDNA was synthesized using buffer, dNTPs, RNase H and DNA polymerase I, respectively. Short fragments were purified with QiaQuick PCR extraction kit and resolved with EB buffer for end reparation and adding poly(A). After that, the short fragments were connected with sequencing adaptors. And, for amplification with PCR, we selected suitable fragments, as templates, with respect to the result of agarose gel electrophoresis. At last, the library could be sequencing using Illumina HiSeq™ 2000.

tag: colony

value: T

value: 161 (Crithidia bombi genotype)


title: TC pooled RNA from guts of three 7d old workers

value: CONTROL


title: T75 pooled RNA from guts of three 7d old workers

value: 075 (Crithidia bombi genotype)


title: L75 pooled RNA from guts of three 7d old workers

value: L


title: L161 pooled RNA from guts of three 7d old workers


title: S161 pooled RNA from guts of three 7d old workers

value: S


title: SC pooled RNA from guts of three 7d old workers


title: S68 pooled RNA from guts of three 7d old workers

value: 068 (Crithidia bombi genotype)


title: LC pooled RNA from guts of three 7d old workers


title: K75 pooled RNA from guts of three 7d old workers

value: K


title: K68 pooled RNA from guts of three 7d old workers


title: KC pooled RNA from guts of three 7d old workers


title: T68 pooled RNA from guts of three 7d old workers


title: EpiSC_3_FT_9.73_p11_MethylCap-Seq

city: Nijmegen

first: Hendrik

last: Marks

address: Geert Grooteplein 26/28

department: Molecular Biology

institute: Radboud University Nijmegen, RIMLS

data_processing:
Initial data processing, base calling, and alignment to the mouse reference genome was performed using the Illumina Analysis Pipeline allowing one mismatch. Only tags aligning to one position on the genome were considered for further analysis.
For RNA-seq, further analysis was performed with the 36 bp aligned sequence.
For MethylCap-seq, the uniquely mapped sequence reads were directionally extended to 300 bp, the estimated median length of the original DNA library. If multiple tags mapped on the same genomic position, only one was included for further analysis. Mapped reads from the initial 600 mM and 800 mM NaCl eluate libraries were combined.
For both RNA-seq and MethylCap-seq data was converted to Browser Extensible Data (BED) files for downstream analysis. To compensate for differences in sequencing depth and mapping efficiency among samples, the total number of unique reads of each sample was uniformly equalized relative to the sample with the lowest number of sequence reads, allowing quantitative comparisons.
Wiggle (WIG) files for viewing the data in the UCSC Genome Browser were generated from the normalized files.
Genome_build: mm9
Supplementary_files_format_and_content: Bed files were generated according to general instructions and were used for analysis; Wig files can be directly uploaded to the UCSC genome browser.

source_name: EpiStem Cells (EpiSC)

growth_protocol: EpiSCs and cEpiSCs were grown in serum-free medium (CDM) with FGF2 (12ng/mL, R&D) and Activin A (20ng/ml, R&D) on serum coated dishes as described (Brons et al., 2007).

extract_protocol:
Genomic DNA was purified using DNA extraction kit (Promega) according to the manufacturer’s instructions. DNA was extracted pools of seven E6.5 epiblasts or pools of three E7 epiblasts. After proteinase K digestion in lysis saline buffer DNA was extracted using NaCl/EtOH precipitation.Genomic DNA was sonicated to generate 300 bp fragments on average. MethylCap was performed using the IP-STAR robot (Diagenode) as described before (Bock et al., 2010).  In short, 1 μg DNA was incubated with paramagnetic beads coated with the MBD domain of MeCP2 fused to GST. After washing with 200 mM, 400 mM and 500 mM NaCl, the bound methylated DNA was eluted in two fractions using 600 mM and 800 mM NaCl, respectively. 20 ng of DNA eluates was prepared for sequencing. For RNA-Seq, Total RNA was isolated with Trizol (Invitrogen) according to the manufacturer’s recommendations. 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN). 100–200 ng mRNA was fragmented by hydrolysis (5x fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized using 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Double-strand cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer’s recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). 20 ng was used for sequencing.
DNA or cDNA samples were prepared for sequencing by end repair of 20 ng DNA as measured by Qubit (Invitrogen). Adaptors were ligated to DNA fragments, followed by size selection (~300 bp) and 14 cycles of PCR amplification. Integrity of DNA libraries was confirmed by running the products on a Bioanalyzer (BioRad). Cluster generation and sequencing (36 bp) was performed with the Illumina Genome Analyzer IIx (GAIIx) (MethylCap-seq) or HiSeq (RNA-seq) platform according to standard Illumina protocols.

value: EpiSC

tag: measurement

value: DNA Methylome

tag: passage


title: cDNA_Dana_OSC_rep2

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

description:
STARR-Seq
PCR amplified cDNA (STARR-seq transcript)

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
STARR-seq
Reads were mapped to the respective genomes ( droYak2, droAna3, dp4, droWil1) using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Fragments mapped in the respective genomes were translated to dm3 coordinates using the liftover tool. Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
RNA-seq
Reads were mapped to the dm3 genome and transcriptome using bowtie (bowtie -f -v 3 -m 1 --best --strata --quiet -S INDEX -).. We estimated RPKM values for each gene based on the number of reads falling over each exon merging exons from a all genes' isoforms into one meta-transcript. Reads counts were normalized by the total reads per library and the merged meta-gene exons lengths. All data was evaluted on D. melanogaster gene models.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

molecule: polyA RNA

organism: Drosophila ananassae

source_name: OSC cells

extract_protocol: Genomic DNA (source: https://stockcenter.ucsd.edu) was isolated for all Drosophila species listed above, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated. See also Arnold et al. Science 2013.

value: OSC cells

tag: experimental procedure

value: STARR-Seq


title: cDNA_Dana_OSC_rep1


title: cDNA_Dpse_rep1

data_processing:
Basecall where performed using Real-Time Analysis (RTA) version > 1.12.4.2 or CASAVA 1.9.1
Reads were mapped to the respective genomes ( droYak2, droAna3, dp4, droWil1) using bowtie (bowtie -p 12 -f -X 2000 -v 3 -m 1 --best --strata --quiet INDEX -1 reads_1.fa -2 reads_2.fa). For all subsequently analysis we used only reads collapsed on chromosome, start, end, strand (fragments). Fragments mapped in the respective genomes were translated to dm3 coordinates using the liftover tool. Significantly enriched regions (peaks) were called with an in-house pipeline using read density profiles of cDNA and input and an hypergeometric test to assign a p-value to each peak. Enrichment values were corrected within a 95% confidence interval taking into account the number of independent fragments at a single peak summit position.
Genome_build: dm3
Supplementary_files_format_and_content: All processed data files are in plain text. For STARR-seq we report for each peak the chromosome, the summit position, the enrichment over input at the summit, and the p-value.

organism: Drosophila pseudoobscura

source_name: S2 cells

extract_protocol:
Genomic DNA (source: https://stockcenter.ucsd.edu) was isolated for all Drosophila species listed above, sheared and size selected (~500bp). Following the instructions of NEBNext® DNA Library Prep Reagent Set for Illumina® (NEB; cat. no. E6000L), Illumina Multiplexing Adapters (Illumina Inc; cat. no. PE-400-1001) were ligated and homology arms for In-Fusion® recombination were added by PCR, followed by recombination into the STARR-seq vector (pGL3-Promotor backbone (Promega; cat. no. E1751) with the sequence between BglII and FseI replaced with the following sequence, containing a Drosophila Synthetic Core Promoter (DSCP) (1), an ORF (sgGFP, Qbiogene, Inc), a ccdB suicide gene flanked by homology arms (used for cloning the genomic enhancer candidates during library generation), and the pGL3’s SV40 late polyA-signal.). The In-Fusion® reactions were transformed (MegaX DH10B; Invitrogen), grown in liquid culture and plasmids were isolated. See also Arnold et al. Science 2013.
STARR-Seq (Arnold et al. Science 2013)

value: S2 cells


title: cDNA_Dpse_rep2


title: Input_Dana

description:
sequenced strained (https://stockcenter.ucsd.edu)
STARR-Seq
PCR amplified Plasmid library, used for S2 STARR-seq

source_name: whole genome library (in STARR-seq vector)


title: Input_Dpse


title: EpiSC_1_FT_8.73_p15_MethylCap-Seq


title: cDNA_Dwil_rep1

organism: Drosophila willistoni


title: L68 pooled RNA from guts of three 7d old workers


title: cDNA_Dwil_rep2


title: S75 pooled RNA from guts of three 7d old workers


title: 4C_E10.5LST_Hoxd9

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

institute: EPFL

data_processing:
De-multiplexing, mapping and 4C-seq were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009 Genome Biology) with parameters -n 2 --best -strata -m 5.
Mapped reads were translated to restriction fragments using the HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
4C figures were made using a running mean algorithm with a window size of eleven fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Signal/restriction fragment (bedGraph) and smoothed (bedGraph), one per viewpoint, per tissue

source_name: Lumbo-sacral trunk E10.5

extract_protocol:
Multiplexed samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Illumina adapters (single end reads) were included in the inverse 4C PCR primers used for 4C-seq library preparation
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. Tissue sample were further made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Chromatin was crosslinked in the presence of 2% formaldehyde.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq2000)

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 143 E10.5 lumbo-sacral trunk samples. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.

tag: tissue

value: Lumbo-sacral trunk cells

tag: age

tag: genotype

value: WT


title: 4C_E10.5LST_Hoxd4


title: cDNA_Dana_rep1

tag: cell type


title: cDNA_Dana_rep2


title: Input_Dwil


title: K161 pooled RNA from guts of three 7d old workers


title: 4C_E10.5LST_Hoxd13

tag: strain


title: 4C_E10.5AT_Hoxd4

source_name: Anterior trunk E10.5

extract_protocol:
Multiplexed samples were sequenced on the Illumina Genome Analyzer IIx system using 76 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Illumina adapters (single end reads) were included in the inverse 4C PCR primers used for 4C-seq library preparation
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. Tissue sample were further made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Chromatin was crosslinked in the presence of 2% formaldehyde.
PCR amplification using primers with included adapter sequences (for Illumina HiSeq2000)

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 12 E10.5 anterior trunk samples. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences. Multiplexed samples were sequenced on the Illumina Genome Analyzer IIx system using 76 bp single-end reads according to the manufacturer’s specifications. 4C-seq reads were sorted, aligned, and translated to restriction fragments using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.

value: Anterior trunk cells


title: Dilated rep10

city: Valencia

first: Estefanía

middle: Tarazón

last: Melguizo

state: Valencia

address: Avenida Fernando Abril Martorell, 106

country: Spain

institute: Health Research Institute La Fe

description: total RNA

data_processing:
Bioscope mapping software version 1.3
Hg19 Homo Sapiens genome. Low quality sequences filter
Htseq-count algorithms for gene counts (Htseq software version 0.5.4p3)
Differential expression using EdgeR method version 3.2.4
Genome_build: Hg19 Homo Sapiens

source_name: Heart

extract_protocol:
Heart samples were homogenized with TRIzol® agent in a TissueLysser LT (Qiagen, UK). All RNA extractions were performed using a PureLink™ Kit according to the manufacturer’s instructions (Ambion Life Technologies, CA). RNA was quantified using a NanoDrop1000 spectrophotometer (Thermo Fisher Scientific, UK) and the purity and integrity of RNA samples was measured using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip kit (Agilent Technologies, Spain). All samples displayed a 260/280 ratio greater than 2.0 and RNA integrity numbers ≥ 9.
Total PolyA-RNA samples were used to generate whole transcriptome libraries for sequencing on the SOLiD 5500XL platform, following the manufacturer’s recommendation (Life Technologies, CA). No RNA-spike in controls was used. Amplified cDNA quality was analyzed by the Bioanalyzer 2100 DNA 1000 kit (Agilent Technologies, Spain) and quantified using the Qubit 2.0 Fluorometer (Invitrogen, UK). The whole transcriptome libraries were used for making SOLiD templated beads following the SOLiD Templated Bead Preparation guide. Bead quality was estimated based on WFA (workflow analysis) parameters. The samples were sequenced using the 50625 paired-end protocol, generating 75 nt + 35 nt (Paired-End) + 5 nt (Barcode) sequences. Quality data were measured using software SETS parameters (SOLiD Experimental Tracking System).

treatment_protocol: Transmural samples were taken from near the apex of the left ventricle and stored at 4°C for a maximum of 6 h from the time of coronary circulation loss. Samples were stored at -80°C until the RNA and protein extractions were performed.

value: Left ventricular tissue

tag: disease state

value: dilated


title: Dilated rep8

description: total RNA


title: Dilated rep9

description: total RNA


title: EpiSC_2_FT_3.83_p24_MethylCap-Seq


title: Ischemic rep13

description: total RNA

value: ischemic


title: Dilated rep12

description: total RNA


title: Dilated rep13

description: total RNA


title: 4C_E10.5AT_Hoxd9


title: Dilated rep6

description: total RNA


title: Dilated rep11

description: total RNA


title: 4C_E10.5AT_Hoxd11


title: Dilated rep7

description: total RNA


title: Control rep9

description: total RNA

value: healthy


title: Control rep8

description: total RNA


title: Ischemic rep12

description: total RNA


title: 4C_E10.5AT_Hoxd13


title: Control rep10

description: total RNA


title: Dilated rep5

description: total RNA


title: 4C_E10.5LST_Hoxd11


title: 4C_E10.5TB_Hoxd9

source_name: Tail bud E10.5

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 143 E10.5 tail bud samples. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.

value: Tail bud cells


title: Ischemic rep11

description: total RNA


title: Dilated rep4

description: total RNA


title: Dilated rep3

description: total RNA


title: 4C_E10.5TB_Hoxd11


title: Ischemic rep10

description: total RNA


title: 4C_E10.5TB_Hoxd4


title: 4C_E9.5TB_Hoxd4

source_name: Tail bud E9.5

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 196 E9.5 tail bud samples. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.


title: Ischemic rep7

description: total RNA


title: Control rep7

description: total RNA


title: Dilated rep2

description: total RNA


title: Ischemic rep6

description: total RNA


title: Ischemic rep8

description: total RNA


title: Ischemic rep9

description: total RNA


title: 4C_E9.5TB_Hoxd9


title: Ischemic rep5

description: total RNA


title: Control rep4

description: total RNA


title: Ischemic rep4

description: total RNA


title: 4C_E10.5TB_Hoxd13


title: Control rep5

description: total RNA


title: Control rep3

description: total RNA


title: Control rep6

description: total RNA


title: 4C_E9.5TB_Hoxd13


title: Ischemic rep3

description: total RNA


title: Control rep1

description: total RNA


title: Ischemic rep1

description: total RNA


title: Dilated rep1

description: total RNA


title: 4C_E8.5PSM_Hoxb13

source_name: Pre-somitic mesoderm E8.5

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 129 E8.5 pre-somatic mesoderm samples. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.

value: Pre-somitic mesoderm cells


title: 4C_E8.5PSM_Hoxc13


title: Ischemic rep2

description: total RNA


title: Control rep2

description: total RNA


title: mRNA_Dyak_follicle_cells

description:
RNA-Seq
PCR amplified cDNA (cellular polyA+ RNA)

organism: Drosophila yakuba

source_name: follicle cells

extract_protocol: RNA was isolated using QIAShredder (QIAGEN; cat.no. 79654) and RNeasy Mini Kit (QIAGEN; cat.no. 74106; including DNase I on column digestion) from 5-10 x 10^6 cells. 5ug total RNA was then processed as described before (S. Zhong et al., High-throughput illumina strand-specific RNA sequencing library preparation., Cold Spring Harbor protocols 2011, 940-9 (2011)) with minor adjustments. End-repair, dA-tailing and adapter ligation were performed with the NEBNext DNA Library Prep Reagent Set for Illumina (NEB, cat.no. E6000L) with proportionally reduced enzyme amounts to account for low RNA concentrations. Indexed library amplification was carried out using KAPA Library Amp Real Time (KAPA biosystems: cat.no. KK2701).

value: follicle cells

value: RNA-Seq


title: cDNA_Dyak_OSC_rep1


title: 4C_E8.5PSM_Hoxa13


title: 4C_E9.5TB_Hoxd11


title: 4C_E8.5PSM_Hoxd9


title: cDNA_Dyak_rep1


title: cDNA_Dyak_rep2


title: cDNA_Dyak_OSC_rep2


title: Input_Dyak


title: 4C_E8.5PSM_Hoxd11


title: 4C_E8.5PSM_Hoxd13


title: 4C_E8.5PSM_Hoxb9


title: ChIP-seq_Escells_H3K4me3

data_processing:
Mapping and generation of density files was done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009 Genome Biology) with parameters -n 2 --best -strata -m 5.
If read length was shorter than 100 bp, reads were extended to 100 bp. Reads mapping to top and bottom strand were shifted 50 bp to compensate for average fragment length. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
Genome_build: mm9
Supplementary_files_format_and_content: density file (bedGraph) per cell type and antibody target

source_name: ES cells

extract_protocol:
Samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications. ChIP-seq reads were sorted and aligned using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Libraries (single end reads) were prepared according to the manufacturers description
Cells were isolated in PBS supplemented with 10% Fetal Calf Serum. Tissue sample were further made single cell by collagenase treatment and applying a cell-strainer cap (BD Biosciences). Chromatin was crosslinked in the presence of 2% formaldehyde. Nuclei were sonicated to generate fragments with average length around 300 bp.
Immuno-precipitated DNA was prepared using the TruSeq ChIP Sample Preparation Kit (Illumina)

treatment_protocol:
ChIP-seq libraries were constructed as described before (Noordermeer et al. 2011, Science). Libraries were prepared from samples consisting of 20 million cells. Nuclei were sonicated to generate fragments with average length around 300 bp. For each ChIP, 10 ug of sonicated nuclei were lysed and histone-DNA complexes were isolated with indicated antibody.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 (#17-614, Millipore) or H3K27me3 (#17-622, Millipore) antibody.

value: Embryonic stem cells

tag: antibody

value: H3K4me3 (#17-614, Millipore)


title: EpiSC_3_FT_9.73_p15_RNA_Seq

value: EpiSC

value: RNA


title: 4C_E10.5FB_Hoxb9

source_name: Forebrain E10.5

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). 4C-seq libraries were prepared from 12 E10.5 forebrains. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.

value: Forebrain cells


title: ChIP-seq_Escells_H3K27me3


title: ChIP-seq_E8.5PSM_H3K4me3

treatment_protocol:
ChIP-seq libraries were constructed as described before (Noordermeer et al. 2011, Science). Libraries were prepared from 750 E8.5 pre-somatic mesoderm samples. Nuclei were sonicated to generate fragments with average length around 300 bp. For each ChIP, 10 ug of sonicated nuclei were lysed and histone-DNA complexes were isolated with indicated antibody.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3 (#17-614, Millipore) or H3K27me3 (#17-622, Millipore) antibody.


title: 4C_E10.5FB_Hoxb13


title: 4C_E8.5PSM_Hoxd4


title: EpiSC_1_FT_8.73_p19_RNA_Seq


title: ChIP-seq_E8.5PSM_H3K27me3


title: RNA-seq_E10.5FB

data_processing:
Mapping and RNA-seq analyses were done through HTSstation (David et al, 2014 PLoS ONE and http://htsstation.epfl.ch/).
Reads were mapped to the mm9 (NCBIM37) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009 Genome Biology) with parameters -n 2 --best -strata -m 5.
Reads Per Kilobase per Million reads (RPKM) for each gene were calculated from the number of reads for all the exons and normalized by the total length of the exons and by then total number of reads mapped.
Genome_build: mm9
Supplementary_files_format_and_content: One density file (bigWig) and one tab-delimited text file with RPKM per transcript and per cell type

extract_protocol:
Samples were sequenced on the Illumina HiSeq system using 100 bp single-end reads according to the manufacturer’s specifications. RNA-seq reads were sorted and aligned using the 4C-seq pipeline of the BBCF HTSstation (David et al. 2014, Plos ONE and available at http://htsstation.epfl.ch). Samples were mapped to the ENSEMBL Mouse assembly NCBIM37 (mm9).
Samples were ribo-depleted and strand specific libraries (single end reads) were prepared according to the manufacturers description
ES cells were isolated in Trizol and embryonic E10.5 forebrain cells were isolared in Trizol LS.
After ribodepletion, total RNA was prepared using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina)

treatment_protocol:
Total RNA was isolated from 1 million cells and isolated using Trizol LS reagent (Invitrogen).
Total RNA was extracted according to the manufacturers instructions (Life Technologies).


title: RNA-seq_Escells

treatment_protocol:
Total RNA was isolated from 1 million cells and isolated using Trizol reagent (Invitrogen).
Total RNA was extracted according to the manufacturers instructions (Life Technologies).


title: 4C_E10.5FB_Hoxd9


title: 4C_E10.5FB_Hoxc13


title: 4C_E10.5FB_Hoxd13


title: 4C_E10.5FB_Hoxd11


title: EpiSC_2_FT_3.83_p14_RNA_Seq


title: 4C_EScells_CNS(39)

treatment_protocol:
4C–seq libraries were constructed as described before (Noordermeer et al. 2011, Science). ES cell 4C-seq libraries were prepared from samples consisting of 20 million cells. The primary restriction enzyme used was NlaIII (New England Biolabs, R0125L) and the secondary restriction enzyme was DpnII (New England Biolabs, R0543M). For each viewpoint approximately 1 μg of the 4C-seq library was amplified using 16 individual PCR reactions with inverse primers containing Illumina Solexa adapter sequences.
Circular Chromosome Conformation Capture (4C) technique was performed as described (Noordermeer et al, 2011 Science). Cross-linked chromatin was digested with NlaIII, ligated under diluted conditions, cross links were reversed and DNA was further digested by DpnII and again ligated under diluted conditions.


title: 4C_EScells_Hoxa13


title: 4C_EScells_Hoxc13


title: 4C_EScells_Hoxb9


title: 4C_EScells_Hoxd9


title: RLN-infected plant Inf1

city: Changsha

first: Touming

last: Liu

address: NO.348, western road of xianjia lake

department: Institute of Bast Fiber Crops

institute: Chinese Academy of Agricultural Sciences

data_processing:
RNA-seq: the cDNA library with a fragment length range of 200 bp (±25 bp) was consturcted and the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000).
Filtering: the trimming adapter sequences were removed and low-quality reads (less than 13 bp or reads with unknown nucleotides larger than 5%) were filtered with the software
Gene annotation: for annotation of unigenes using various bioinformatics approaches, the unigenes were firstly searched against the Nr, COG, KEGG and Swiss-Prot protein database using local BLASTx with E value cutoff of 10-5.
Gene Expression Analysis: Gene expression levels were measured in the RNA-Seq analysis as reads per kilobase of exon model per million mapped reads (RPKM). The DEseq software was used to identify differentially expressed genes in pair-wise comparison, and the results of all statistical tests were corrected for multiple testing with the Benjamini–Hochberg false discovery rate (FDR < 0.01).
Supplementary_files_format_and_content: the files contain the gene name, gene length, RPKM value, the number of total reads and the number of unique reads

organism: Boehmeria nivea

source_name: Zhongzhu 1

extract_protocol:
After seven days the ramie infected, the whole plant excluding root of four potted ramie were individually sampled. The sampled tissues were immediately frozen in liquid nitrogen and stored at -80° until use. The sample of tissue of CO1, CO2, Inf1 and Inf2 were individually extracted RNA by using TRIzol reagent (Transgene Company, Illkirch Graffenstaden Cedex, France) according to the manufacturer’s protocol. The RNA was stored at -80° for cDNA library preparation.
RNA of four samples were separately used to construct the cDNA library with a fragment length range of 200 bp (±25 bp). Then, the paired-end sequencing was performed by using the Illumina sequencing platform (HiSeqTM 2000) according to the manufacturer’s instructions (Illumina, San Diego, CA).

treatment_protocol: The four potted 60-day-old plants were used for experiment. Two potted ramie were set as infection plant (Inf) which were inoculated 200 RLN of P. coffeae every plant, whereas the other two potted plant were set as control (CO). The CO and Inf respectively contained two replicates which were named as CO1, CO2 and Inf1 and Inf2, respectively. After seven days the ramie infected, the whole plant excluding root of four potted ramie were individually sampled.

value: the whole plant excluding root

tag: developmental stage

tag: cultivar

value: Zhongzhu 1


title: RLN-infected plant Inf2


title: 4C_E10.5FB_Hoxa13

value: WT


title: mRNA_Dmel_follicle_cells


title: control plant CO1


title: 4C_EScells_Hoxd11


title: control plant CO2


title: 4C_EScells_Hoxd13


title: 4C_E10.5FB_Hoxd4


title: Spleen DX5+ rep2

status: Public on Apr 26 2014

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Data were sequenced on HiSeq 2500 instrument (Illumina, San Diego, CA) using 50bpX25bp pair-end! 10 sequencing. Second mate was used for sample demultiplexing, at which point individual single-end fastqs were aligned to mm9 genome using TopHat with following options -G mm9.mrna.10.31.gtf --prefilter-multihits --segment-length 20 --max-multihits 15. Geneexpression was obtained using ESAT software tool(http://garberlab.umassmed.edu/software/esat/) focused on analysis of 3’end targetedRNA-Seq. The following parameters were used: -task "score3P" –normalizedOutput -window 1000 -maxExtension 3000 -maxIntoGene 2000 -stranded –collapseIsoforms.
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file that includes normalized count data for each sample

source_name: spleen

extract_protocol:
Spleen, liver and bone marrow cells were isolated from Rag1-/- mice and sorted for CD3-CD19-NK1.1+CD49a+DX5- or CD3-CD19-NK1.1+CD49a-DX5+ which were lysed.
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen). For cDNA synthesis, we used custom oligo-dT primer with a barcode and adapter-linker sequence (CCTACACGACGCTCTTCCGATCT—XXXXXXXX-T15). After first strand synthesis samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded using consecutive acid-alkali treatment. Then, second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated using T4 ligase (New EnglandBiolabs, Ipswich, MA) and after SPRI clean-up, mixture was PCR enriched 14 cycles andSPRI purified to yield final strand specific 3'end RNA-seq libraries

value: spleen

value: Spleen DX5+ NK cells


title: Liver DX5+ rep1

source_name: liver

value: liver

value: Liver DX5+ NK cells


title: Spleen NK1.1+ CD49- rep3

value: Spleen NK1.1+ CD49-


title: Spleen NK1.1+ CD49- rep2


title: Spleen NK1.1+ CD49- rep4


title: Liver DX5-CD49+ rep2

value: Liver DX5-CD49+ NK cells


title: Liver NK1.1+ CD49+ rep2

value: Liver NK1.1+ CD49+


title: Liver NK1.1+ CD49- rep3

value: Liver NK1.1+ CD49-


title: Spleen DX5+ rep1


title: Liver NK1.1+ CD49- rep1


title: Liver NK1.1+ CD49+ rep1


title: GEK-45

status: Public on Apr 25 2014

city: Porto Alegre

first: Rogerio

last: Margis

state: RS

address: Av. Bento Goncalves 9500

department: Centro de Biotecnologia

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

data_processing:
Illumina Casava1.7 software used for basecalling.
low quality reads with 'n' were removed using PrinSeq script (Schmieder and Edwards, 2011)
Unique raw reads counted obtained with perl scripts
Supplementary_files_format_and_content: tab-delimited text files with abundance of unique sequences

organism: Vriesea carinata

source_name: leaf

growth_protocol: Adult individual

extract_protocol: Total RNA were isolated from Vriesea carinata leaves using Trizol reagent (Invitrogen, CA, USA), according to manufacturer’s protocol and the RNA quality was evaluated by electrophoresis on a 1% agarose gel. Total RNA (> 10 μg) was sent to Fasteris Life Sciences SA (Plan-les-Ouates, Switzerland) for processing. One mRNA library was constructed and it was sequenced by Illumina HiSeq2000. Briefly, the polyadenylated transcript sequencing (mRNA-seq) was performed using the following successive steps: Poli-A purification, cDNA synthesis using Poli-T primer shotgun to generate inserts of 500 nt, 3p and 5p adapters ligations, pre-amplification, colony generation and sequencing. The Illumina output data were sequence tags of 100 bases.

tag: sample

value: single

value: adult

value: leaf


title: ERG_JQ1_exp1

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

data_processing:
Basecalls performed using RTA 1.17.21.3 and CASAVA version 1.8.2
Reads were aligned to the HG19 genome using Bowtie2 with all default settings.
Resulting BAM files were sorted and duplicates were removed using samtools
Coverage profiles were calculated using bedtools genomecov as BedGraph files
BedGraph files wer converted to BigWig using BedGraphToBigWig from Kent Utils
Genome_build: hg19
Supplementary_files_format_and_content: Coverage profiles are normalized to sequencing depth

source_name: Prosate cancer cells

growth_protocol: Cells were grown in DMEM containing 10% FBS

extract_protocol:
ChIP was performed using HighCell ChIP kit following manufacturers protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight followed by wash and reversal of cross-linking.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E.coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3’ to 5’ exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2000 Sequencer (100 nucleotide read length).

treatment_protocol: For BRD2/3/4 and ERG ChIP-seq experiments (sample21-33) with BET inhibitors, VCaP cells were treated with DMSO, 500 nM JQ1 or I-BET762 for 12hrs. For AR signaling ChIP-seq experiments (sample1-20), VCaP cells were grown in charcoal-stripped serum containing media for 48hrs. followed by 6hrs. pre-treatment with vehicle or 500nM JQ1 or 10µM MDV3100 or 25µM Bicalutamide and then stimulated with 10nM DHT for 12hrs

value: vertebral metastatic lesion derived prostate cancer cells

tag: cell line

value: VCaP

value: ERG (Epitomics, 2805-1)


title: ERG_DMSO_exp2

description: DMSO


title: Spleen NK1.1+ CD49- rep1


title: ERG_JQ1_exp2


title: Liver DX5+ rep2


title: IgG

value: IgG (diagenode kit)


title: BRD4_I-BET762

value: BRD4 (Bethyl, A301-985A)


title: H3K27ac

value: H3K27ac (Abcam, ab4729)


title: ERG_DMSO_exp1

description: DMSO


title: BRD4_DMSO

description: DMSO


title: BRD3_I-BET762

value: BRD3 (Bethyl, A302-368A)


title: Liver NK1.1+ CD49- rep2


title: BRD2_JQ1

value: BRD2 (Bethyl, A302-583A)


title: BRD3_JQ1


title: BRD4_JQ1


title: BRD3_DMSO

description: DMSO


title: BRD2_I-BET762


title: BRD2_DMSO

description: DMSO


title: RNA PolII_MDV3100+DHT

value: RNA PolII (Abcam, ab5408)


title: RNA PolII_JQ1+DHT


title: RNA PolII_ vehicle control

description: vehicle control


title: BRD4_Bicalutamide+DHT

description: Bicalutamide+DHT


title: RNA PolII_DHT

description: DHT


title: BRD4_MDV3100+DHT


title: RNA PolII_Bicalutamide+DHT

description: Bicalutamide+DHT


title: BRD4_ JQ1+DHT


title: 4C_EScells_Hoxb13

department: School of Life Sciences

value: Embryonic stem cells

value: WT


title: Liver DX5-CD49+ rep1

value: liver

value: Liver DX5-CD49+ NK cells


title: BRD4_DHT

description: DHT


title: AR_Bicalutamide+DHT_exp1

description: Bicalutamide+DHT

value: AR (Millipore, 06-680)


title: AR_MDV3100+DHT_exp2


title: AR_MDV3100+DHT_exp1


title: AR_Bicalutamide+DHT_exp2

description: Bicalutamide+DHT


title: AR_JQ1+DHT_exp2


title: BRD4_vehicle control

description: vehicle control


title: AR_JQ1+DHT_exp1


title: AR_DHT_exp1

description: DHT


title: HUES9 control ES cell

city: La Jolla

first: Hai-Ri

last: Li

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
HUES9.bed: hg19

source_name: Human embryonic stem cell line

growth_protocol: iPS cells and HUES9 cells were passaged on ES matrigel-coated plates and cultured in feeder-free condition with STO feeder conditioned medium prepared from ES culture medium containing KO-DME/20%KSR/NEAA/2-Mercaptoethanol/Pen/Strep/bFGF. BJ cells were cultured in DMEM/10%FBS/NEAA/Pyruvate/Pen/Strep.

extract_protocol: RNAs were extracted from cultured cells using TRIzol Reagent (Life Technologies, cat# 15596-026) . The cDNAs were synthesized with biotinylated P7-dT(20) oligos by reverse transcription and captured to solid phase. The second strand cDNAs were made with Adpator-hexamer by extension using DNA polymerase. The second strand cDNAs were PCR amplified with P7 and P5-index-Adaptor primers. The PCR products were size-selected, pooled and subjected to Illumina sequencers, reading target sequences followed by reading index (Genomics. 2011:98;266)

value: Human embryonic stem cell line


title: BJ-OKS-iG#2

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ-OKS-iG2.bed: hg19

source_name: iPS cell derived from BJ

value: iPS cell derived from BJ


title: BJ-OKS-iM#21

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ-OKS-iM21.bed: hg19

tag: karyotype

value: Normal


title: BJ-OKS-iM#2

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ-OKS-iM2.bed: hg19


title: BJ-OKS-iG#5

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ-OKS-iG5.bed: hg19


title: AR_vehicle control _exp2

description: vehicle control

value: vertebral metastatic lesion derived prostate cancer cells

tag: chip antibody


title: 4C_EScells_Hoxd4


title: AR_vehicle control _exp1

description: vehicle control

value: VCaP


title: CME185_Klf4OE_ChIP-seq

city: Lyon

first: Irene

last: Aksoy

address: 18 avenue du Doyen Lepine

institute: Stem Cell and Brain Research Institute

data_processing:
ChIP-Seq reads were aligned using the Eland software to NCBI build 37 (mm9) of the mouse genome.
The MACS program (version 1.4) was used to detect peaks of ChIP enrichment. It was run with the default settings using a tag size of 35 and band width 280.
Genome_build: mm9
Supplementary_files_format_and_content: bed format. Chrom, ChromStart, ChromEnd, Name and Score.

source_name: mouse ESCs

growth_protocol: ES cells were grown with in standard media composed of  DMEM supplemented with ES qualified FBS and Leukemia Inhibitory Factor (LIF). Cells overexpressing Klf4 or Klf5 were grown in the same media but without LIF.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 min at room temperature, and formaldehyde was inactivated by the addition of 125 mM glycine. Chromatin from each cell line was sonicated to a length of around 250-500bp and immunoprecipitated using custom made antibodies provided bu Huck-Hui Ng. Samples were sequenced using the SOLEXA platform.
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 (3' to 5' exo minus) and dATP. 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.

value: Undifferentiated mouse ESCs


title: Parent BJ cell

data_processing:
Illumina OLB-1.9.0 software used for basecalling.
For gene counts for expression, sequenced reads were mapped to refMrna(hg19) using bowtie v0.12.7 and counted for each genes(Genomics. 2011;98(4):266-71)
For bed files, sequenced reads were mapped to hg19 using bowtie v0.12.7 and the bed files were made based on the mapping information.
Genome_build: hg19
BJ.bed: hg19

source_name: Human fibroblast

value: Human fibroblast


title: CME210_Klf5OE_ChIP-seq