title: P1_rep2

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

data_processing:
50 bp reads were truncated to 36 bp. Sequencing reads were filtered for primer and adapter sequences and a minimal quality score of 20 using Tagdust (Version 1.12) and FASTQC.
Sequences were aligned to the C. elegans ce10 genome using Tophat (1.4.0)
Alignment files were quantified using HT-Seq (0.5.3) and the RefSeq gene annotation for WS220 downloaded March 23, 2012 and reads were assigned per gene model
The significance of differentially represented transcripts were quantified by DESeq (1.2.1) in R 2.12 using size estimation normalization
Genome_build: ce10
Supplementary_files_format_and_content: AB_average.wig.gz and "P1_average.wig.gz": Individual .wig files were normalized to size distribution (DESeq) and averaged together per blastomere type; "ABP1_Nishimura_raw_matrix.txt.gz": ColumnA-E=Gene Identifiers (XLOC, WBID, WB public name, Seq name, refseq name), ColumnF=Location, ColumnG-L=Raw Counts for all samples; "ABP1_Nishimura_normalized_matrix.txt.gz": ColumnA-E=Gene Identifiers (XLOC, WBID, WB public name, Seq name, refseq name), ColumnF=Location, ColumnG-L=Normalized Counts for all samples normalized in DESeq by EstimateSizeFactors.

organism: Caenorhabditis elegans

source_name: P1 cells

growth_protocol: N2 worms were grown at 20° C on NGM plates spotted with a thin lawn of OP50 E. coli. Worms were grown to gravid adult stages.

extract_protocol:
Trizol-stored blastomeres were thawed and re-frozen up to three cycles to lyse them. RNA extraction was performed using a Trizol/chloroform extraction followed by RNeasy Micro (Qiagen) preparation using On Column DNaseI Digestion (Qiagen).
mRNA was amplified using in vitro transcription (TargetAmp aRNA Amplification Kit, Epicentre). Standard RNA-seq protocol  (Illumina mRNA Sequencing Sample Preparation Guide, September 2009) was used to sequence amplified aRNA. Magna beads were used for final purification in lieu of gel purification.

treatment_protocol: Blastomere isolations were performed by embryo isolation, eggshell degradation and micromanipulation using a mouth pipette. We used 3 min incubation in 10 - 20 % bleach followed by 5 min incubation in chitinase chymotrypsin solution from Streptomyces griseus (Sigma, C6137) at 10 U/ml to degrade the eggshells. Isolated AB and P1 cells were dropped directly into Trizol solution and stored at -80°C.

tag: strain

tag: replicate


title: P1_rep3

status: Public on Mar 05 2015

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

tag: cell type


title: AB_rep2

source_name: AB cells

value: AB


title: Astro1

city: San Francisco

first: Robert

last: Blelloch

state: CA

address: 35 Medical Center Way

department: Urology

institute: University of California, San Francisco

description: v6.5 ESCs; ES-derived GPCs

data_processing:
Adapters were clipped from the fastq file using in house perl scripts.
Mapping to microRNA hairpins from mirbase using Bowtie.
Supplementary_files_format_and_content: Sequence files following adapter clipping were mapped to miRNA hairpins from mirbase. Read counts were summarized for each miRNA and are provided in the processed data file.

organism: Mus musculus

source_name: astrocytes

growth_protocol: All GPCs were grown in N2 media + EGF and FGF as per the protocol of Okabe et al, 2000.

extract_protocol:
RNA was extracted with the standard Trizol protocol
Library was constructed using the standard Illumina protocol with in house reagents.

treatment_protocol: For differentiation, growth factors (EGF & FGF) were removed and 1% FBS and B27 were added.

value: astrocytes


title: AB_rep1


title: P1_rep1


title: Astro2

description: v6.5 ESCs; ES-derived GPCs


title: SIBAS3

city: Philadelphia

first: Santanu

last: Banerjee

state: PA

address: 421 Curie Blvrd

department: Cell and Developmental Biology

institute: University of Pennsylvania

data_processing:
Illumina Casava1.7 software used for basecalling.
Aligned and Quantified with RUM (v2.0.5_05), Quantification was used on the gene level
Normalization was performed with RPKM
fold changes were calculated between SIB and MUT and the two different tissues
Genome_build: Zv9/danRer7
Supplementary_files_format_and_content: RPKMs for each sample and normalized fold changes between conditions.

organism: Danio rerio

source_name: anterior somitic segments

growth_protocol: All embryos and larvae used in this study were  raised in E3 fish medium at 28ºC for the required amount of time.

extract_protocol:
For RNA-seq, mRNA was extracted from 38-40 hpf old embryos. We isolated wild type and foxc1a mutant samples by dissecting the entire the first 6 anterior somitic segments (AS) through which the fin nerves migrate, and the adjacent posterior segments (PS; segments 7 through ~12) devoid of fin innervating nerves. Heads and yolks were excluded from all samples.  Tissues were stored in RNAlater solution (Life Technologies) for up to 2 days at 4 degree before RNA was extracted using the RNAeasy kit (Qiagen) according to the manufacture’s protocol. RNA was tested for integrity using a Bioanalyzer (Agilent technologies). RNA samples showing RIN value of 8 or higher were used for generating cDNA libraries as described in the TruSeq® Stranded mRNA sample preparation guide.
RNA samples showing RIN value of 8 or higher were used for generating cDNA libraries as described in the TruSeq® Stranded mRNA sample preparation guide. At the final stage, 15 cycles of PCR amplifications was performed. Barcoded libraries representing duplicates of AS and PS samples of wild type and mutants were validated using Bionalyzer (Agilent Technology).
Barcoded libraries representing duplicates of AS and PS samples of wild type and mutants were validated using Bionalyzer (Agilent Technology) and finally sequenced in Illumina HiSeq 2500 yielding paired end reads of 101bp.

treatment_protocol: All embryos and larvae were raised as above with no special treament.

tag: age

value: 38-40 hpf old embryos

tag: tissue

value: anterior somitic segments

tag: genotype


title: GPC1

description: v6.5 ESCs; ES-derived GPCs

source_name: GPCs

value: glial progenitor cell


title: SIBPS3

source_name: posterior somitic segments

value: posterior somitic segments


title: MUTPS3


title: GPC2

description: v6.5 ESCs; ES-derived GPCs


title: AB_rep3


title: SIBAS


title: MUTPS


title: Input DNA

city: Haining

first: Jian

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.

department: Zhejiang University - University of Edinburgh Institute

country: China

institute: Zhejiang University

description: lung from Ptend/d mouse

library_source: genomic

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (36 nt reads, single end) were aligned to the mouse genome (mm9) using the BWA algorithm (default parameters).
Aligns were extended in silico at their 3’-ends to a length of 150 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in BAR files.
Peak locations were determined using the MACS algorithm (v1.3.7.1) with a cutoff of pvalue = 1E-10.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated

molecule: genomic DNA

source_name: lung

growth_protocol: normal feed condition

extract_protocol:
lungs were removed from the Ptend/d mice, snap frozen in liquid N2 and stored at -80°C until shipment on dry ice to ActiveMotif company. For fixation, lungs were cut into small pieces in PBS + 1% formaldehyde and incubated at room temperature for 15 minutes. Fixation was stopped by the addition of 0.125 M glycin (final) and tissue pieces were treated with a TissueTearer. Chromatin was isolated by disrupting the cells with a Dounce homogenizer. Lysates were sonicated using a Misonix Sonicator 3000 equipped with a microtip in order to shear the DNA to an average length of 300-500 bp. Lysates were cleared by centrifugation and stored at -80 C. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNaseA, proteinase K and heat for de-crosslinking, followed by phenol/chloroform extraction and ethanol precipitation. Purified DNA was quantified on a NanoDrop spectrophotometer. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reactions were set up using precleared chromatin and antibodies and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed two times each with a series of buffers consisting of the deoxycholate sonication buffer, high salt buffer, LiCl buffer, and TE buffer. Immune complexes were eluted from the beads with SDS buffer, and subjected to RNase treatment and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
ChIP and Input DNAs were prepared for amplification by converting overhangs into phosphorylated blunt ends and adding an adenine to the 3’-ends. Illumina genomic adapters were ligated and the sample was size-fractionated (200-250 bp) on a 2% agarose gel. After a final PCR amplification step (18 cycles), the resulting DNA libraries were quantified and sequenced on HiSeq 2000.

treatment_protocol: no treatment

value: mixed background

value: Ptend/d mouse

value: 7 months

tag: tumors

value: no

tag: chip antibody

value: lung


title: MUTAS3


title: Smad4_ChIPSeq

description: lung from Ptend/d mouse

value: Smad4 R&D Systems, cat.# AF2097, Lot# KUH0311081


title: APP-3

city: Shenzhen

first: Jun

last: Wan

state: Guangdong Province

address: No. 1120, Lianhua Road

institute: Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed  adaptor sequence, and masked  low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Clean miRNA reads were aligned to the miRBase database version 19.0  using CLC workbench  version 4.5.0  with perfect match
miRNA abundance measurements were generationed and normalized  using CLC workbench  version 4.5.0 ; The normalized standard were Transcripts Per Million Reads (TPM)
Differential miRNA expression were analysed  using DEGseq function package in R program version 2.10.0
Genome_build: UCSC mm9
Supplementary_files_format_and_content: tab-delimited text files include normalized TPM values and raw reads for each Sample

source_name: Brain cortex

growth_protocol: APPswe/PS1deltaE9 transgenic mice were keep in SPF level enviroment for 9 months.

extract_protocol:
Total RNA was extracted by Trizol.
Following "TruSeq Small RNA Sample Preparation Guide".

treatment_protocol: The mice were anesthetized with pentobarbital (50 mg/kg) followed by the removing and dissection of the brain tissues. The cortexes of the brains were frozen in liquid nitrogen for the further RNA extraction.

value: brain cortex


title: WT-2

value: wild type


title: MUTAS


title: SIBPS


title: D2_RING1B_Fbxl10_Exp.2

status: Public on Mar 04 2015

city: meguro-ku

first: Takeshi

last: Inagaki

state: Tokyo

address: 4-6-1 Komaba

country: Japan

institute: Univ of Tokyo

description: Day 2 of differentiation

data_processing:
All DNA-fragments binding were mapped onto build mm9 (NCBI Build 37) by a mapping program ELAND (http://support.illumina.com/sequencing/sequencing_software/casava.html) based on the 5’-side 36 bp sequences.
Genome_build: mm9
Supplementary_files_format_and_content: bar. formatted file

growth_protocol: 3T3-L1 mouse preadipocytes (CL-173, American Type Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37°C in 5% CO2.

extract_protocol:
DNA was extracted using ISOGEN following manufacturer's protocol
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 3T3-L1 cell lines transduced with the retroviral vector for V5-tagged Fbxl10 or its dF-box mutant. For adipocyte differentiation, two days after reaching confluence (day 0), 3T3-L1 preadipocytes were treated with differentiation medium containing insulin (1 ug/ml), 0.25 μM dexamethasone, and 0.5 mM isobutylmethylxanthine (MDI cocktail) for 48 h.

tag: cell line

tag: antibody

tag: protocol

value: V5-tagged Fbxl10


title: WT-1


title: D2_V5_Fbxl10-1_peaks

description: Day 2 of differentiation


title: ChIP-seq_Input_E2_rep2

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

description: ChIP 5% Input from MCF7 cells  after 40min of E2 treatment

data_processing:
Alignment: Short-reads were aligned to the human reference genome (hg19). Bowtie software package (Langmead et al., 2009) was used to align reads and the output was processed using custom Perl scripts, and imported into R for most the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: bed

organism: Homo sapiens

growth_protocol: MCF-7 breast cancer cells were obtained from the ATCC and maintained in Minimum Essential Medium Eagle supplemented with 5% calf serum.

extract_protocol:
ChIP-seq libraries were generated from two biological replicates for each condition.  The immunoprecipitated DNA was purified using a MiniElute PCR Purification Kit from Qiagen.  After purification, 50 ng of ChIPed DNA for each condition was used to generate libraries for deep sequencing, as previously described (Quail et al., 2008), with some modifications.  Briefly, the DNA was end-repaired and a single “A”-base overhang was added using the Klenow fragment of E. coli DNA polymerase.  The A-modified DNA was ligated to Illumina sequencing adaptors using the Illumina TruSeq DNA Sample Prep Kit.  The ligated DNA (250-300 bp) was size-selected by agarose gel electrophoresis and purified using a Qiagen Gel Extraction Kit.
The size-selected fragments were amplified using Illumina TruSeq P5 and P7 PCR primers, and purified using AMPure beads (Beckman Coulter).  Quality control was performed to determine the size, purity, and concentration of the final libraries, which were sequenced using an Illumina HiSeq 2000 per the manufacturer’s instructions.

treatment_protocol: Prior to all treatments, the cells were grown for 3 days in phenol red-free MEM Eagle medium supplemented with 5% charcoal-dextran-treated calf serum.  All treatments were performed for 40 min with 100 nM 17β-estradiol, 25 ng/mL TNFα, or both.

value: ER Positive Breast Cancer Cells

tag: treatment

value: input


title: D2_RING1B_Fbxl10_Exp.1

description: Day 2 of differentiation


title: D2_RING1B_Empty_Exp.2

description: Day 2 of differentiation

value: Empty


title: D2_RING1B_dFbox_Exp.2

description: Day 2 of differentiation

value: V5-tagged dF-box mutant Fbxl10


title: D2_RING1B_Empty_Exp.1

description: Day 2 of differentiation


title: CPE Mock, 2

city: Chicago

first: Alex

last: Ruthenburg

address: 920 E. 58th Street

institute: University of Chicago

data_processing:
Alignment with Tophat2
de novo assembly and initial abundance estimates of Chromatin RNA samples were performed using Cufflinks2. Nuclear RNA samples were quantified against the Gencode (v19) reference genome also using Cufflinks2.
differential abundance was between Chromatin and Nuclear samples was performed using Cuffdiff, and geometric mean normalization.
For +/- DRB experiments, coverage in each fraction was normalized to the number of reads mapped to XIST in that fraction
Genome_build: hg19
Supplementary_files_format_and_content: gene_exp.txt and isoform_exp.txt files contain abudances (FPKM) of each 'gene' or transcript isoform in the chromatin pellet extract (CPE) vs. soluble nuclear extract (SNE), and whether the differences are significant.

molecule: nuclear RNA

source_name: Human Embryonic Kidney_chromatin_pellet_extract (cpe)_mock

growth_protocol: 37° C, 5% CO2. Adherent growth

extract_protocol:
Nuclear Fractionation
Illumina TruSeq Stranded Total RNA

treatment_protocol: 37° C, 5% CO2. Adherent growth

tag: rna fraction

value: chromatin RNA


title: CPE + DRB, 2

description: plus DRB

source_name: Human Embryonic Kidney_chromatin_pellet_extract (cpe)_plus DRB


title: CPE 3

source_name: Human Embryonic Kidney_chromatin_pellet_extract (cpe)


title: D2_RING1B_dFbox_Exp.1

description: Day 2 of differentiation


title: CPE + DRB, 1

description: plus DRB


title: APP-4


title: CPE 2


title: CPE 1


title: SNE 3

source_name: Human Embryonic Kidney_soluble_nuclear_extract (sne)

value: nuclear RNA


title: SNE 2


title: SNE 1


title: MCF7_E2_1280min_RNASeq

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

data_processing:
ChIP-seq reads were mapped to hg19 using Genomatix Mapping Station.
ChIP-seq data were summarised by counting the fraction of reads in 200 bp bins forming the last 20% of the annotated gene region, background corrected by subtracting an average over manually selected inactive regions and normalised by the total number of reads and using the geometric median normalisation of Anders and Huber (2010).
RNA-seq reads were mapped to Ensembl v68 transcriptome complemented by pre-mRNA sequences using bowtie.
RNA-seq expression estimates (means and variances) were obtained using BitSeq.
RNA-seq data were normalised using the geometric median method of Anders and Huber (2010).
Genome_build: hg19
tsv, summary of PolII activity at the last 20% of each gene for PolII, summary of gene expression (mean and standard deviation) for each gene for RNA-seq; wig, reads with unique PolII ChIP-seq alignments as fractions in 200 bp bins over the gene; wig, reads with unique alignments to pre-mRNA as fractions in 200 bp bins over the pre-mRNA transcript

source_name: Breast cancer cells

growth_protocol: MCF-7 cells were cultured in DMEM with 10% FCS at 37 °C. Cells were maintained in DMEM w/o phenol red and 5% charcoal stripped FCS for 72 hours before induction

extract_protocol:
For DNA-Seq: lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For RNA-Seq: total RNA was isolated using TRIzol according to the manufacturer's recommendations, followed by DNaseI treatment. 100–250 ng total RNA was subjected rRNA depletion with the Ribo-Zero Magnetic Gold Kit and processed further for strand specific RNAseq.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MCF-7 cells were mock treated or with 10nM 17b-E2 to nine time points (5', 10', 20', 40', 80', 160', 320', 640' and 1280')

tag: time

tag: sample type

value: Pleural effusion

tag: passages


title: MCF7_E2_640min_RNASeq

value: 640 min


title: MCF7_E2_160min_RNASeq

value: 160 min


title: MCF7_E2_40min_RNASeq

value: 40 min


title: MCF7_E2_320min_RNASeq

value: 320 min


title: MCF7_E2_80min_RNASeq

value: 80 min


title: MCF7_E2_20min_RNASeq

value: 20 min


title: MCF7_untreated_RNASeq

value: untreated


title: MCF7_E2_1280min_Pol_II

value: Homemade Anti-Pol II Monoclonal


title: MCF7_E2_5min_RNASeq

value: 5 min


title: MCF7_E2_160min_Pol_II


title: MCF7_E2_80min_Pol_II


title: MCF7_E2_320min_Pol_II


title: MCF7_E2_640min_Pol_II


title: Lib2_Gcn4_or_Gal4

city: Rehovot,

first: Michal

last: Levo

address: Herzl Street 234

country: Israel

institute: Weizmann Institute of Science

description:
See the specific bands included in this sample and their band barcodes in the overall design field above
EXP4

data_processing:
Based on the frist 5bps assign each read to an originating band
Bands were normalized to have the same sum of reads
Sequences were mapped based on an internal variant barcode (bps 20-to-29) to a designed variant
The frequency of each variant in each band was computed
Variants that are lowly represneted in the no-protein band (i.e. in the initial input library) were discarded from future analysis
For each varaint and each bound band a binding score was computed, that is the frequency of that sequence in this bound band divided by its frequency in the no-protein band
Genome_build: synthetic construct
Supplementary_files_format_and_content: Tab delimited file that holds the sequence variant id number, its sequence and the binding score in the band specified in the header of the column

organism: synthetic construct

source_name: synthetic DNA construct

extract_protocol:
The material for sequencing was obtained with a newly developed protocol, BunDLE-seq that enables quantitative measurements of TF (or histones) binding to a pool of thousands of designed sequences, in a single experiment. In this assay, we design a library of sequence variants, up to 200 bp in length, that is then synthesized on Agilent programmable microarrays. Next, we incubate the obtained DNA with a buffer alone (no protein present) or with different concentrations of the examined TF, run the products of this incubation on gel, and extract the DNA from each of the bands detected, corresponding to either naked DNA or DNA bound to different numbers of TF molecules. We amplify the DNA with a unique barcode, marking the originating band, join all samples together and send them to high-throughput sequencing.
10 ng were used for library preparation for sequencing (protocol adopted from (Blecher-Gonen et al. 2013)). The DNA amplified using 14 amplification cycles and sequenced on a 50 bp single read or 100 bp paired-end flowcell on Illumina HiSeq-2000 sequencer

tag: input sequnces libarary

tag: proteins used

value: Gcn4 or Gal4


title: CPE Mock, 1


title: MCF7_E2_10min_Pol_II

value: 10 min


title: MCF7_E2_20min_Pol_II


title: MCF7_E2_5min_Pol_II


title: MCF7_untreated_Pol_II


title: Lib1_Gcn4

description:
See the specific bands included in this sample and their band barcodes in the overall design field above
EXP2


title: Lib1_Gal4

description:
See the specific bands included in this sample and their band barcodes in the overall design field above
EXP3


title: Lib1_Gcn4_or_histones

description:
See the specific bands included in this sample and their band barcodes in the overall design field above
EXP1

value: Gcn4 or histones


title: 293T_Input

city: Davis

first: Henriette

last: O'Geen

address: 1 Shields Ave

department: Genome Center

institute: Uc Davis

description: Input

data_processing:
Illumina Casava1.8 software used for basecalling and demultiplexing.
ChIP-seq reads were aligned to the mouse (mm9) or human (hg19) genome using  Bowtie2. All reads mapping with two or fewer mismatches were retained. Peak detection was performed using MACS1.4 with a chromatin input library as the control data set.
Genome_build: mm9 or hg19
Supplementary_files_format_and_content: MACS_peak.txt file (chromosome; peak start;peak end; PeakID; ChIP enrichment value assigned by the MACS1.4 software)

source_name: Input

growth_protocol: The mouse neuroblastoma cell line Neuro-2a (ATCC #CCL-131) was grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum (BCS). Neuro-2a cells were grown to 70% confluency and transfected using Lipofectamine 2000 (Life Technologies). HEK293T cells were grown under the same conditions, except DMEM media was supplemented with 10% BCS and 1% penicillin/streptomycin.

extract_protocol:
ChIP assays were performed as previously described with minor modifications (O'Geen et al. 2010). 50 μg of sonicated chromatin was incubated with 3 μg of monoclonal anti-Flag antibody (SIGMA M2 F1804).  After incubation with 3 μg of rabbit anti mouse serum, StaphA cells (Sigma-Aldrich) were used to collect the immunoprecipitates. After washes and reversal of DNA-RNA-protein cross-links
The entire ChIP sample was used to create an Illumina sequencing library using the KAPA library preparation kit (KAPA Biosystems) and NEXTflex DNA barcodes (BIOO Scientific).

treatment_protocol: Transient transfection using lipofectamine 2000: For ChIP-seq, cells were transfected with 7.5 μg gRNA-expressing plasmid and either 1 μg or 7.5 μg Flag-tagged dCas9 plasmid per 10-cm dish. Cells were cross-linked 24 or 48 hours post transfection (for transfections with 1 μg or 7.5 μg Flag-tagged dCas9 plasmid, respectively) by incubation with 1% formaldehyde solution for 10 minutes at room temperature. Cross-linked cell pellets were stored at -80°C.

value: kidney

value: HEK 293T


title: 293T_noED_VEGFA_rep2

description: dCas9-noED +VEGFA TS3 gRNA

source_name: dCas9-noED +VEGFA TS3 gRNA

value: Flag (SIGMA M2 F1804)


title: 293T_Control_EV

description: dCas9-noED +VEGFA TS3 gRNA


title: RNA KO2 30 min SDF stim

city: London

first: Francesco

last: Gualdrini

address: 44 Lincoln's Inn Fields

country: United Kingdom

institute: Francis Crick Institute

description: RNA-Seq

data_processing:
RNASeq: Alignments were performed using bwa version 0.5.9-r16
Genome_build: MM9
Supplementary_files_format_and_content: RNASeq: wig files generated by MACS at 1bp resolution

extract_protocol:
Lin- lo c-kit+ sca-1+ LSK cells FACS sorted from female pools of E14.5 fetal liver.
RNA-Seq: Total RNA was extracted using Genelute (Sigma). RNA samples were quality controlled (QC) using the 6000 Nano RNA Chip on the BioAnalyser 2100 (Agilent). Libraries were prepared using the Directional mRNA-Seq Library Prep. v1.0. Pre-Release Protocol from Illumina with minor adjustments. To minimise the ribosomal content of the samples a DSN treatment of the cDNA RNA-seq libraries was used (Evrogen JSC).The Illumina kit Phusion enzyme was replaced by Kapa HiFi HotStart ready mix which reduced the overall volume of the PCR and the ratio for the Agencourt AMPure XP beads was adjusted accordingly.  The standard PCR cycling was also changed to match the concentration of the total RNA from the initial QC. After passing the final QC, the libraries were subjected to cluster formation and then 72bp single end sequencing on the GAIIx analyser.

treatment_protocol: Each genoype (two SRF+ and two SRF-) of sorted LSK cells (300,000) were resuspended RPMI / 10% FCS, then divided into two media coated eppendorfs. Cells were rested for 1 hour at 37oC in a humidified incubator. Where indicated,  cells were stimulatated with 100ng SDF . Where indicated, cells were stimulated for 30 minutes with 100ng/mlrecombinant  SDF-1 (PMC1354)

value: SRF knockout (SRF-)

tag: cell markers

value: LSK

value: liver

tag: developmental stage


title: RNA KO2 no stim

description: RNA-Seq

source_name: Sorted LSK cells_SRF_KO_no_stimulation


title: MCF7_E2_10min_RNASeq

value: Pleural effusion


title: RNA WT2 30 min. SDF stim

description: RNA-Seq

value: wildtype (SRF+)


title: RNA KO1 no stim

description: RNA-Seq


title: RNA WT2 no stim

description: RNA-Seq


title: RNA WT1 30 min. SDF stim

description: RNA-Seq


title: RNA KO1 30 min SDF  stim

description: RNA-Seq


title: RNA WT1 no stim

description: RNA-Seq


title: MCF7_E2_40min_Pol_II

value: 40 min


title: lymphoma_1

city: La Jolla

first: Kazuko

last: Miyazaki

address: 9500 Gilman Drive

department: Division of Biological Sciences

institute: University of California, San Diego

description: Sample 15

data_processing:
Illumina Casava1.8 software used for basecalling.
Alignment and trimming of reads was performed using the OSA algorithm against the mm10 mouse genome reference in Arraystudio.
RNA transcripts were quantified using RSEM methods as implemented in Arraystudio
Principal Component Analysis (PCA) was then performed to check for possible batch effects.
Abundance values (counts) were normalized and compared using DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes the comparison abundance values of control (5 samples), Tfh (3 samples),  Id3 KO (3 samples), dKO (3 samples) and lymphoma (6 samples) with P-value.

source_name: sorted lymphoma cells

extract_protocol:
Total RNA was isolated from sorted cells using the RNeasy-Mini Kit (Qiagen). mRNA was purified using Dynabeads mRNA purification kit (Invitrogen). The mRNA was then subjected to first-strand cDNA synthesis using a combination of random hexamers and oligo-dT. Second-strand synthesis was performed using dUTP instead of dTTP. The double stranded cDNA was sonicated using S220 Focused-ultrasonicator (Covaris).
Sonicated cDNA was next ligated to adaptors and size selected. The size-selected cDNA was treated with Uracil-N-Glycosylase and then multiplex amplified by PCR. cDNA libraries were sequenced with a HiSeq 2500 sequencer (Illumina).

tag: strain background

tag: genotype/variation

value: Thymus

tag: cell type

value: CD3+TCRb+CD8+ cell


title: lymphoma_5

description: Sample 19

tag: tissue

value: Spleen

value: CD3+TCRb+CD4+ cell


title: lymphoma_2

description: Sample 16

value: Lymph node


title: lymphoma_6

description: Sample 20


title: CD4SP_dKO_2

description: Sample 13

source_name: sorted CD4 SP cells

value: CD4+TCRb+CD8– cell


title: CD4SP_Id3KO_3

description: Sample 11

value: Id3 KO


title: hfq_37_2

city: Helsinki

first: Päivi

last: Saavalainen

address: Haartmaninkatu 8

department: TRIMM

country: Finland

institute: University of Helsinki

data_processing:
Clean and merge reads using the adapter sequences and discarding the shortest ones; TOOL=SeqPrep; VERSION=v0.4-5-gb62f433; PARAMETERS=-f reads_1.fq -r reads_2.fq -1 reads_adapterClean_1.fq.gz -2 reads_adapterClean_2.fq.gz -s reads_adapterClean_pairedSingle.fq.gz -L 35 -y I -A CTGTCTCTTATAC -B CTGTCTCTTATAC
Filter out reads with homopolymers (>70% read length) and trim the bases at the end of the read with lower quality values (<20); TOOL=At-home perl script; PARAMETERS=--quality_threshold 20 --homopolymer_threshold 70
Filter reads aligning to rRNA or tRNA; TOOL=bowtie2; VERSION=2.1.0; PARAMETERS=-D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -k 20 --local  --score-min L,-0.6,-0.6
Alignment of the reads to reference genome; TOOL=Tophat2; VERSION=v2.0.8b; PARAMETERS= --bowtie1  --mate-inner-dist NNN --mate-std-dev NN -G organism.gtf --library-type fr-secondstrand --no-discordant
Estimation of gene FPKM values; TOOL=Cufflinks; VERSION=v2.0.2; PARAMETERS=--library-type fr-secondstrand --frag-bias-correct genome.fa -b genome.fa --GTF organism.gtf
Genome_build: NCBI GenBank | FR729477 | Yersinia enterocolitica subsp. palearctica Y11.
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM values for each sample separately

organism: Yersinia enterocolitica

source_name: bacteria

growth_protocol: Overnight cultures were diluted in fresh sterile LB broth and incubated at either 22°C or 37°C with vigorous shaking till the OD = 0.6 was reached.

extract_protocol:
The total RNA was isolated using the SV Total RNA Isolation System (Promega). The qualities of the isolated RNA, as well as the rRNA profiles were determined using Bioanalyzer (Agilent).
The ribosomal RNA was removed using Ribo-ZeroTM rRNA Removal Kit for Gram-negative Bacteria (Epicentre); RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: growth phase

value: logarithmic phase

value: hfq mutant

tag: temperature


title: CD4SP_Id3KO_2

description: Sample 10


title: CD4SP_dKO_1

description: Sample 12


title: hfq_37_1


title: 293T_noED_VEGFA_rep1

description: dCas9-noED + control gRNA

source_name: dCas9-noED + control gRNA

value: kidney

tag: cell line

value: HEK 293T

tag: chip antibody


title: CD4SP_Id3KO_1

description: Sample 9


title: hfq_22_2


title: Tfh_3

description: Sample 8

source_name: sorted Tfh1 cells

value: wild type

value: CD4+TCRb+CD44highCXCR5+ cell


title: hfq_22_1


title: Tfh_2

description: Sample 7


title: lymphoma_4

description: Sample 18


title: N2A_Input

description: Input

value: neuroblastoma


title: N2A_Control_EV

description: dCas9-noED + control gRNA

value: Flag (SIGMA M2 F1804)


title: Tfh_1

description: Sample 6


title: rfaH_37_1

value: rfaH mutant


title: rfaH_22_2


title: CD4SP_dKO_3

description: Sample 14


title: rfaH_22_1


title: CD4SP_Control_4

description: Sample 4


title: WT_37_2


title: N2A_KRAB_S2

description: dCas9-KRAB + S2 gRNA

source_name: dCas9-KRAB + S2 gRNA


title: N2A_KRAB_S1

description: dCas9-KRAB + S1 gRNA

source_name: dCas9-KRAB + S1 gRNA


title: WT_37_1


title: WT_22_2


title: YeO3_R1_22_2

value: O-antigen negative mutant


title: N2A_noED_S2_rep1

description: dCas9-noED + S2 gRNA

source_name: dCas9-noED + S2 gRNA


title: CD4SP_Control_2

description: Sample 2

value: Thymus


title: CD4SP_Control_1

description: Sample 1


title: rfaH_37_2


title: N2A_noED_S1_rep2

description: dCas9-noED + S1 gRNA

source_name: dCas9-noED + S1 gRNA


title: WT_22_1


title: mock-challenged plants; CK, T1

city: Changsha

first: Yongting

last: Yu

address: No 348, Xianjiahu West Rd.

institute: Institute of Bast Fiber Crops, Chinese Academy of Agricultural Science

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 processed data files contain the transcript IDs, gene length, RPKM value, the number of total reads and the number of unique reads. Series supplementary files contain transcript sequences and annotations.

organism: Boehmeria nivea

source_name: CK, T1

growth_protocol: The seedlings were prepared with shoot-cutting reproduction method. The rooted seedlings were each transplanted in a pot (15 cm in diameter and 12 cm in depth) with nutritious soils (clay: sand: organic matter = 1:1:1, v/v) and cultured in a climate-controlled chamber (14 h light photoperiod; 80% RH; 26 ± 2°C).

extract_protocol:
To prepare samples for Illumina sequencing, total RNA of each sample was extracted using an EASYspin plus Total RNA kit (Aidlab, Beijing, China) following the protocol. Quality and yield of RNA were determined by agarose gel electrophoresis and Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Wilmington, DE, USA), respectively.
RNA of CK (equally mixed RNA of 4 time points) and CH (equally mixed RNA of 4 time points) samples were used to construct the cDNA library, respectively, 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: For preparing challenge (CH) and mock-challenge plants (CK), two J2 larvae were transferred onto the 4 rd leave from the shoot apex of ramie seedling. To excite their appetite, they were fasting for 12 h before inoculation. 12, 24, 48, 72 h after inoculation, the topmost undamaged 2 leaves were sampled, and the unchallenged (CK) plants were sampled synchronously. There were 5 replicates (plants) per treatment. Leaves of 5 CK or CH plants sampled at the same time point were pooled and regarded as one sample and yielded 8 samples (CK 12, CK 24, CK 48, CK72, CH12, CH24, CH 48 and CH72).

tag: cultivar

value: Chuanzhu No.8

value: Leaf


title: N2A_noED_S1_rep1

description: dCas9-noED + S1 gRNA


title: CD4SP_Control_5

description: Sample 5


title: challenged plants; CH, T2

source_name: CH, T2


title: MED152_T12_Rep_3

status: Public on Mar 03 2015

city: Lewes

first: Matthew

last: Cottrell

address: 700 Pilottown Rd

institute: University of Delaware

description: Polaribacter MED152

data_processing:
HiSeq Control Software
Rockhopper software (http://cs.wellesley.edu/~btjaden/Rockhopper/)
Genome_build: Candidatus Pelagibacter ubique HTCC1062, complete genome (NC_007205.1),  Polaribacter sp. MED152, complete genome (CP004349.1),  Ruegeria pomeroyi DSS-3, complete genome (NC_003911.12), Ruegeria pomeroyi DSS-3 megaplasmid (NC_006569.1), marine gamma proteobacterium HTCC2207 scaffolds (NZ_CH672400,NZ_CH672399,NZ_CH672398,NZ_CH672397,NZ_CH672396)
Supplementary_files_format_and_content: Excel file containing Rockhopper output

organism: Polaribacter sp. MED152

source_name: Heterotrophic marine bacteria

growth_protocol: Batch culture, 19°C, aerated in darkness

extract_protocol:
Bacterial biomass was collected by vacuum filtration using 0.2 µm-pore-size Durapore filters.  The filters were stored at -80°C in RLT buffer until DNA and RNA were extracted using the AllPrep DNA/RNA (Qiagen) kit following the manufacturer's instructions.
RNA libraries were prepared for sequencing using Ribo-Zero rRNA Removal Kit (Bacteria) and TruSeq RNA Sample Prep Kit following Illumina protocols

value: slow growth


title: MED152_T12_Rep_1

description: Polaribacter MED152


title: mDC_RNAseq

city: Shanghai

first: PIN

last: WANG

address: Xiangyin Road 800

institute: SMMU

data_processing:
Illumina Casava1.6 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads) as described in article: Mortazavi, A., B. A. Williams, et al. (2008). Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5(7): 621-8.
A strict algorithm was developed to identify differentially expressed genes refering to Audic, S. and J. M. Claverie (1997). The significance of digital gene expression profiles. Genome Res 7(10): 986-95.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Mouse BMDC

growth_protocol: Mouse bone marrow cells were cultrued in  in RPMI-1640 medium with recombinant mouse GM-CSF (10ng/ml) and IL-4(1ng/ml) for 6 days

extract_protocol:
RNA was harvested using Trizol reagent，and isolated using an RNA isolation kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: sample 2 was treated with LPS(100ng/ml)for 24h in RPMI 1640 with recombinant mouse GM-CSF (10ng/ml) and IL-4(1ng/ml). And both samples were sorted by Moflo XDP(Dako Cytomation) based on surface marker CD86 and Iab.

value: bone marow derived dendritic cells

value: mature DC


title: MED152_T10_Rep_1

description: Polaribacter MED152


title: imDC_RNAseq

value: immature DC


title: CD4SP_Control_3

description: Sample 3

value: CD4+TCRb+CD8– cell


title: MED152_T10_Rep_3

description: Polaribacter MED152


title: MED152_T9_Rep_3

description: Polaribacter MED152

value: rapid growth


title: MED152_T9_Rep_1

description: Polaribacter MED152


title: MED152_T5_Rep_1

description: Polaribacter MED152


title: SAR92_T8_Rep_2

description: Gammaproteobacteria SAR92 (HTCC2207)

organism: gamma proteobacterium HTCC2207


title: lymphoma_3

description: Sample 17

value: Lymph node

value: CD3+TCRb+CD8+ cell


title: MED152_T5_Rep_3

description: Polaribacter MED152


title: N2A_noED_S2_rep2

description: dCas9-noED + S2 gRNA


title: SAR92_T6_Rep_3

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T8_Rep_3

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T6_Rep_2

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T6_Rep_1

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T5_Rep_3

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T5_Rep_1

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T4_Rep_1

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T4_Rep_2

description: Gammaproteobacteria SAR92 (HTCC2207)


title: SAR92_T4_Rep_3

description: Gammaproteobacteria SAR92 (HTCC2207)


title: CENH3-ChIPseq-derivative3-3-6

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using Illumina CASAVA.
ChIP-seq reads were mapped to maize B73 genome with BWA version 0.6.1 with the following configurations.
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v3
Supplementary_files_format_and_content: bedGraph files were generated using bedtools.

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse or in the field for ChIP experiments.

extract_protocol:
Extracted nuclei were digested with micrococcal nuclease (Sigma-Aldrich) for ChIP experiments using the maize CENH3 antibody.  The maize CENH3 antibody is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits. Anti-CENH3 polyclonal antibodies were affinity-purified using the peptides conjugated to Sulfo-link coupling Gel (Pierce) performed by GL Biochem (Shanghai) Ltd.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

value: young leaves


title: CENH3-ChIPseq-derivative3-3-11


title: SAR92_T8_Rep_1

description: Gammaproteobacteria SAR92 (HTCC2207)


title: CENH3-ChIPseq-telo2-2


title: CENH3-ChIPseq-TB-9Sb

value: control


title: 4-target

city: Nanjing

first: xue

last: cao

address: Xuanwu District No. 1

institute: Nanjing Agricultural University

description: degradome

data_processing:
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: SOL Genomics Network (SGN)

organism: Solanum habrochaites

source_name: tomato leaves

growth_protocol: Seedlings of ‘LA1777’ (S. habrochaites) at the five-leaf stage were used.

extract_protocol: To construct two small RNA libraries, samples from the two treatments harvested at different time points were individually subjected to small RNA extraction using an Illumina Truseq Small RNA Preparation kit (LC Sciences, Hangzhou, China). Equal quantities of small RNA extracted from different time points in one treatment group were pooled as one small RNA library, and the two small RNA libraries were then constructed. Following isolation and ligation, the small RNAs were reverse transcribed to cDNA. The purified cDNAs from the two RNA libraries were used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis.  Two degradome libraries were constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of conserved and novel miRNA.

treatment_protocol: The seedlings were divided into two groups for treatment; one group was exposed to 4°C/4°C for chilling treatment, while the other group was not treated with chilling stress(25°C/20°C).The third leaf from the stem apex was harvested at 1, 4, 8, 12, 24 and 48 h after treatment.

tag: development

value: five-leaf stage

value: leaves

tag: treatment

value: 1, 4, 8, 12, 24 and 48 h after chilling treatment(4°C/4°C)

value: S. habrochaites.cv. LA1777


title: CK-miRNA

value: 1, 4, 8, 12, 24 and 48 h after normal treatment(25°C/20°C)


title: ck-target

description: degradome


title: YeO3_R1_22_1

value: logarithmic phase

value: O-antigen negative mutant


title: Retr_T3_S_rep3

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

data_processing:
Illumina bcl2fastq 1.8.4 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.2.2. Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Trichoderma Reeseii reference genome using Bowtie mapper (version 0.12.7) using the "-n 2 -l 34 -e 70 -k 2 --best" parameters. Only one alignment were kept in a given locus for each read and reads alignments matching on more than one locus were removed. To compute gene expression, Trichoderma Reesei genome annotation was used.
Genome_build: Trichoderma Reesei reference genome (Trire2, JGI depository http://genome.jgi-psf.org/Trire2/Trire2.home.html)
Supplementary_files_format_and_content: tab-delimited text files include transcripts (JGI IDs) counting for each Sample

organism: Trichoderma reesei

source_name: Retransformed kap8

growth_protocol: Both strains were grown for 24 hrs in Mandels-Andreotti (MA) medium (Mandels MM, Andreotti RE: The cellulose to cellulase fermentation. Proc Biochem 1978, 13:6-13.), using glycerol as sole carbon sources at final concentrations for up to 1% w/v. They were then filtered and replaced to the same medium containing 1.8 mM sophorose as a th only carbon source, and further incubated for 3 hrs

extract_protocol:
Mycelium were harvested and shock frozen in liquid nitrogen. Mycelia were ground to a fine powder under liquid nitrogen and total RNA was isolated using the guanidinium thiocyanate method (Sambrook, 2001).
Illumina TruSeq Stranded RNA

value: Retransformed kap8

tag: growth

value: T3h Sophorose


title: Retr_T0_G_rep1

value: T0 glycerol


title: Retr_T3_S_rep2


title: Retr_T3_S_rep1


title: 4-miRNA


title: CENH3-ChIPseq-telo3-3


title: CENH3-ChIPseq-derivative3-3-7


title: Retr_T0_G_rep3


title: Dkap8_T3_S_rep3

source_name: Tu-6 DeltaKap8

value: Tu-6 DeltaKap8


title: Dkap8_T0_G_rep1


title: Dkap8_T0_G_rep3


title: Retr_T0_G_rep2


title: Dkap8_T0_G_rep2


title: Dkap8_T3_S_rep2


title: Dkap8_T3_S_rep1


title: mES ATAC-Seq

city: Worcester

first: Barbara

last: Tabak

state: MA

address: 55 Lake Avenue North

department: Molecular Medicine

institute: University of Massachusetts Medical School

data_processing:
reads were mapped to the genome using bowtie2 version 2.1.0 using --phred33  -5 9 -3 2 parameters
Genome_build: GRCm38
Supplementary_files_format_and_content: bigwig

source_name: Embryonic Stem Cells

growth_protocol: V6.5 mouse ES cells were grown on 0.1% gelatinized plates and maintained in 2i media

extract_protocol:
Cells were harvested with 0.25% trypsin for 5 minutes, collected, and counted. 50,000 cells were spun down at 500xg for 5 minutes at 4°C and washed once with 50µL of cold PBS
ATAC-Seq


title: IDG-SW3 Control  rep3

city: San Antonio

first: stephen

middle: e

last: harris

address: 7703 Floyd Curl Drive

department: Periodontics

institute: U. of Texas Health Sci Center at San Antonio

description: RNA Seq analysis was carried out using 6 barcoded libraries run on one lane

data_processing:
Initial analysis was with Illumina RTA 1.13.48 software. Base calling was carried out with the Casava 1.8. 2 software package and the resulting fastq files were further analyzed with  NGS software programs in our Unix based Alamo Cluster at UTHSCSA with over 350 nodes.
The fastq files were loaded into U. of Texas Health Science Ctr at SanAntonio Alamo Supercomputer with preload NGS software and our Python Scripts. We used the TopHat-2 and Bowtie-2 for sequence alignments to the mouse mm9 genome
The resulting .bam files were further analyzed using Cufflink-2, CuffCompare, and differential expression between Cont and PTH was determined using CuffDiff-2 program
The accepted_hits .bam files from TopHat-2 analysis were also  converted  to bedgraph files (bamtools), and then to bigWig files (bedGraphToBigWig tools) for loading into UCSC Browser or other genomic  browsers.
The 3 control  or 3 PTH accepted_hits.bam files were also merged with merge function in SamTools, then converted to bedgraph and bigWig files for overall analysis and presentation of effect of PTH using the UCSC or other genome browsers.
Also, included in the processed data analysis is the CuffDiff data with p and q values for differentially expressed genes between Cont and PTH treated samples, with an n=3.
Genome_build: mm9
Supplementary_files_format_and_content: Each of the 6 .xls files (3 Cont and 3 PTH) contain the gene_id, transcription start site symbol for the gene, the chromosome location and position, and the fpkm with confidence level. Also included are the the 6 bigWig files for loading into UCSC or other genomic Browser. The merged Cont and PTH data as bigwig files is also included where the 3 Cont or 3 PTH bam files were sorted, index, and merged, converted to bedgraph and then bigWig  (bw) files.

source_name: IDG-SW3 Cell Line derived from long bones of Dmp1-GFP positive/temperature sensitive T-antigen positive  mice (Woo et al, 2011, J. BoneMin.Res 26:2634-2646)

growth_protocol: IDG-SW3 cells were plated a density of 4x104/cm2 in a 6 well plate and cultured for 24 hours until confluent. The cells were then cultured for a further 28 days in differentiation/mineralizing media containing 50µg/ml ascorbic acid and 4mM betaglycerophosphate.

extract_protocol:
The total RNA was harvested in TRI-Zol reagent (1ml per well). RNA was extracted using phenol/chloroform as per the manufacturer's instructions.
The Illumina TruSeq_RNA-Seq_v2 library construction kit was used as per instructions using 2-3 ug of Total RNA as starting material after DNase1 digestion.

treatment_protocol: The mature, differentiated cells were treated with 50nM bovine PTH (1-34). The control cultures were treated with the same volume (0.5µl) of PBS. The cells were then cultured for 24hours before the total RA was harvested.

tag: time point

value: Day 28

tag: agent

value: Control

tag: sample id

tag: index

value: TTAGGC


title: SAR92_T5_Rep_2

description: Gammaproteobacteria SAR92 (HTCC2207)

value: slow growth


title: IDG-SW3 Control  rep2

value: CGATGT


title: IDG-SW3 Control  rep1

value: ATCACG


title: IDG-SW3 50nM PTH (1-34) rep 2

value: PTH

value: ACAGTG


title: WT_IP_IMP2: Sample 25

city: Cambridge

first: Diego

last: Borges-Rivera

address: 7 Cambridge Center

institute: Broad Institute

description: IP RNA WT using IMP2 Ab

data_processing:
Library strategy: RIP-Seq
Alignment: Tophat version 2.0.8
QC: RNASeQC version 1.1.7
Quantification: Cufflinks version 2.1.1
Quantification of RIP-seq: GenomicFeatures R
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks standard

source_name: Brown Adipose Tissue

growth_protocol: Imp2-/- mice and wildtype littermates were maintained on C57Bl/6J background in a specific pathogen-free facility with 12:12 light:dark cycle.  All animals used for experiments are bred by Imp2 +/-;Imp2 +/- mating.

extract_protocol:
RNA was isolated using the Trizol reagent and Qiagen RNase kit (Qiagen). RNA samples were examined for the integrity by bioanalyzer before library construction.
The library construction was followed by instruction of Illumina TruSeq DNA LT Sample Prep kit.

treatment_protocol: Imp2+/+ and Imp2-/- mice were weaned onto normal chow or a HFD, and sacrificed one week later for liver gene expression study. For brown fat IMP2 RIP-seq experiments, 10-weeks-old male mice fed NCD were placed at 4°C overnight and sacrified for study.

tag: genotype

value: WT

value: Brown Adipose Tissue

tag: diet

value: Normal Chow Diet

tag: supplementary file


title: WT_total: Sample 20

description: Total RNA WT BAT

tag: tissue


title: KO_IP_IMP2: Sample 23

description: IP RNA KO using IMP2 Ab


title: KO_total: Sample 19

description: Total RNA KO BAT


title: WT_total: Sample 15

description: Total RNA WT BAT


title: WT_IP_IgG: Sample 26

description: IP RNA WT using IgG


title: WT_IP_IMP2: Sample 22

description: IP RNA WT using IMP2 Ab


title: KO_HFD_Liver_6: sample105

data_processing:
Alignment: Tophat version 2.0.8
QC: RNASeQC version 1.1.7
Quantification: Cufflinks version 2.1.1
Quantification of RIP-seq: GenomicFeatures R
Genome_build: mm10
Supplementary_files_format_and_content: Cufflinks standard

source_name: Liver

value: Liver

value: High Fat Diet


title: KO_HFD_Liver_6: sample104


title: KO_HFD_Liver_6: sample106


title: WT_HFD_Liver_6: sample107


title: KO_IP_IMP2: Sample 24

description: IP RNA KO using IMP2 Ab


title: KO_total: Sample 18

description: Total RNA KO BAT


title: WT_HFD_Liver_6: sample109


title: WT_total: Sample 16

description: Total RNA WT BAT


title: WT_HFD_Liver_6: sample108


title: WT_total: Sample 17

description: Total RNA WT BAT


title: IDG-SW3 50nM PTH (1-34) rep 1

value: TGACCA


title: IDG-SW3 50nM PTH (1-34) rep 3

value: GCCAAT


title: Wt spg-7 no antibody

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The raw sequence data obtained by sequencing was first clipped for adapter sequences and then mapped to the C. elegans genome (ce6 from UC Santa Cruz) using BWA MEM (ver 0.7.5). The output SAM files were processed and sorted with the Picard tools and then peaks were determined using MACS version 1.4 with the no-model parameter.
Genome_build: C. elegans genome (ce6 from UC Santa Cruz)
Supplementary_files_format_and_content: tabular file which contains information about called peaks

source_name: whole worm lysate

growth_protocol: Wildtype adult worms are bleached at day 3

extract_protocol:
Cross-linking of DNA and protein was performed by treating the worms with 11% formaldehyde at 4°C for one hour. The worms were then lysed via Teflon homogenizer and sonicated to obtain 500-1000 base pair DNA fragments.
ATFS-1 was then immunopreciptated from 500 mg of lysate using ATFS-1 antibodies [PMID 22700657] and protein A sepharose beads (Invitrogen). The cross-links were reversed by incubation at 65°C for 5 hours. The DNA fragments were then ethanol-precipitated and purified using QiaQuick Spin Columns (Qiagen). The DNA fragments were sequenced using the Hi-Seq Illumina platform.

treatment_protocol: The eggs harvested from the bleaching protocol are then grown in the presence of spg-7(RNAi). Worms are then harvested at L4 stage (~48 hrs)

tag: background genotype

value: Wildtype

tag: treated with

value: No Antibody


title: WT_IP_IMP2: Sample 21

description: IP RNA WT using IMP2 Ab


title: WT_HFD_Liver_6: sample102


title: KO_NCD_Liver_6: sample99


title: WT_NCD_Liver_6: sample98


title: Wt spg-7 with antibody

value: ATFS-1 antibody

tag: chip antibody ref.


title: KO_HFD_Liver_6: sample103


title: Ruegeria_T9_Rep_3

description: Ruegeria pomeroyi (DSS-3)

organism: Ruegeria pomeroyi DSS-3

tag: strain

tag: growth phase


title: KO_NCD_Liver_6: sample96


title: Ruegeria_T9_Rep_2

description: Ruegeria pomeroyi (DSS-3)


title: WT_NCD_Liver_6: sample95


title: Ruegeria_T9_Rep_1

description: Ruegeria pomeroyi (DSS-3)


title: Ruegeria_T7_Rep_3

description: Ruegeria pomeroyi (DSS-3)


title: Ruegeria_T7_Rep_1

description: Ruegeria pomeroyi (DSS-3)


title: csbUV10J6h1

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan

description: molecule: bru-labeled RNA

data_processing:
Library strategy: BruSeq
Illumina Casava v1.8.2 software used for basecalling.
Reads were mapped to the Human ribosomal DNA complete repeating unit (U13369.1) using bowtie v.0.12.8 and parameters -n 3 -k 1 -m 1
Reads that did not map to the ribosomal DNA were mapped to the hg19 genome using TopHat v1.4.1 and parameters –min-isoform-fraction 0, --max-multihits 1, --no-closure-search, --no-coverage-search, --bowtie-n, --initial-read-mismatches 3
A coverage determination was then made for every base in the genome using Bedtools v.2.16.2 such that a base covered by one read was recorded as having a coverage of 1/read_length
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: The columns of the abundance measurement files indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) score; (6) strand; (7) gene length; (8) feature type – exon, intron, etc; (9) number of introns and exons; (10) feautre length; (11) hits count; (12) density – count/length; (13) RPKM - count/(length/1E3)/(mapped read count/1E6)

source_name: Cockayne syndrome group B fibroblasts (CS1AN  - GM00739)

growth_protocol: All cell lines were grown as monolayers in MEM supplied with 10% fetal bovine serum and antibiotics (Invitrogen) and maintained at 37 C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated by using TRIzol reagent (Invitrogen), and Bru-labeled RNA was isolated from the total RNA by incubation with anti-BrdU antibodies (BD Biosciences) conjugated to magnetic beads (Dynabeads, Goat anti-Mouse IgG; Invitrogen) under gentle agitation at room temperature for 1 h. For more detail, see Paulsen et. al 2013
Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then  synthesized, in the presence of Actinomycin D to result in strand specific reads (only applicable to certain samples as indicated in sample table above). After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, after which the Illumina TruSeq RNA Sample Prep Kit was used to repair the cDNA ends, adenylate and ligate adaptors to the cDNA. The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then the Illumina TruSeq Kit PCR reagents were used to enrich the DNA fragments. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.

treatment_protocol: Cells were washed in PBS and irradiated in 100 ul PBS on 100 mm plates with a UVC lamp producing 1 J/m2/s.  Cells were then incubated in conditioned media for different periods of time (0, 6, 24h) before being incubated with 2 mM bromouridine (BrU) at 37C for a 30 min.

tag: cell line

tag: uv exposure

tag: time between uv exposure and bru labeling

value: 5.5 hours

tag: bru labeling time

value: 0.5 hours

tag: time between uv exposure and rna extraction

value: 6 hours

tag: labeling agent

value: Bromouridine (Bru)


title: KO_NCD_Liver_6: sample94


title: csbUV10J24h1

description: molecule: bru-labeled RNA

value: 23.5 hours

value: 24 hours


title: Ruegeria_T7_Rep_2

description: Ruegeria pomeroyi (DSS-3)

value: slow growth


title: Ruegeria_T4_Rep_2

description: Ruegeria pomeroyi (DSS-3)

value: rapid growth


title: Ruegeria_T4_Rep_1

description: Ruegeria pomeroyi (DSS-3)


title: xpcUV10J2h1

description: molecule: bru-labeled RNA

source_name: Xeroderma pigmentosum, complementation group C skin fibroblast (GM14867)

value: 1.5 hours

value: 2 hours


title: Ruegeria_T5_Rep_2

description: Ruegeria pomeroyi (DSS-3)


title: csbUV10J0h1

description: molecule: bru-labeled RNA

value: 0 hours


title: Pelagibacter_T11_Rep_3

description: Candidatus Pelagibacter ubique (HTCC1062)

organism: Candidatus Pelagibacter ubique HTCC1062


title: xpcUV10J24h1

description: molecule: bru-labeled RNA


title: xpcUV10J6h1

description: molecule: bru-labeled RNA


title: WT_NCD_Liver_6: sample97

value: WT

value: Liver

value: Normal Chow Diet


title: csb0h1-

description: molecule: bru-labeled RNA

value: No exposure


title: xpc0h1

description: molecule: bru-labeled RNA


title: Pelagibacter_T11_Rep_2


title: case2 w/ EP

city: Ube

first: Isao

last: Tamura

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

institute: Yamaguchi University Graduate School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
Tophat version 2.0.9 with the default parameters was used to map onto the human hg19 assembly
Cufflinks version 2.1.1 with -G option was used to quantify the gene expression levels.
Genome_build: hg19
Supplementary_files_format_and_content: Text file with FPKMs

source_name: Human endometrial stromal cells

growth_protocol: Human primary endometrial stromal cells (ESC) were isolated by the enzymatic digestion of minced endometrial tissues with collagenase followed by the separation using a 70 µm nylon mesh filter.  ESC were seeded at 105 cells/cm2 in 75 cm2 tissue culture flasks and incubated in Phenol Red-free DMEM containing glutamine, antibiotics, and dextran-coated charcoal-stripped FBS.

extract_protocol:
Total RNA was isolated from cultured cells with Isogen (Wako Pure Chemical Industries Ltd).
The library for mRNA-seq was generated by the modified Illumina protocol using a mRNAseq preparation kit (Illumina).  Briefly, 1 µg of total RNA was enriched for polyA RNA by two successive rounds of oligo (dT) selection.  The polyA RNA was then fragmented, and first-strand cDNA synthesis was performed using random hexamer priming.  Following second-strand cDNA synthesis, dsDNA was repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase (PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end.  After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel.  The samples were purified using the QIAquick MinElute kit (QIAGEN, Inc.) at each preparation step.  After the quality of the library was validated using the Agilent Bioanalyzer 2100 (Agilent Technologies), the samples were subjected to sequencing with a next-generation sequencer (Genome Analyzer GAIIx, Illumina).

treatment_protocol: To induce decidualization, ESC were incubated with or without E (10-8 mol/l) and MPA (10-6 mol/l) for 14 days.

value: Endometrial stromal cells

tag: condition

value: induction with estradiol (10-8 M) and medroxyprogesterone acetate (10-6 M)


title: Pelagibacter_T11_Rep_1


title: nfUV10J24h1

description: molecule: bru-labeled RNA

source_name: Foreskin fibroblasts (HF1)


title: case1 control

value: control (without any induction)


title: Ruegeria_T4_Rep_3

description: Ruegeria pomeroyi (DSS-3)


title: csbUV10J2h1

description: molecule: bru-labeled RNA

value: 0.5 hours


title: Ruegeria_T5_Rep_3

description: Ruegeria pomeroyi (DSS-3)


title: case1 w/ EP


title: xpcUV10J0h1

description: molecule: bru-labeled RNA


title: nfUV10J6h1

description: molecule: bru-labeled RNA

value: 5.5 hours

value: 6 hours


title: Pelagibacter_T8_Rep_3


title: case2 control


title: Pelagibacter_T8_Rep_2


title: nf0h6

description: molecule: bru-labeled RNA

value: Bromouridine (Bru)


title: Ruegeria_T5_Rep_1

description: Ruegeria pomeroyi (DSS-3)


title: Input case2 control

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 1.0.0 with the default parameters
Identification of differentially modified regions:
To examine whether histone modification statuses are altered throughout the genome during decidualization in ESC, histone modification signlas were searched in 1-kb intervals between -10 kb from transcription start site and +10 kb from transcription termination site. Then the difference in the signals between control ESC and decidualized ESC was evaluated by log2-transformed FPKM values. We defined the regions with more than 2-fold changes in the FPKM values as the differentially modified regions.
Genome_build: hg19
Supplementary_files_format_and_content: .bedgraph files; peak files in BED format

extract_protocol:
Lysates were clarified from sonication/enzymatic digested nuclei and histone-DNA complexes were isolated with antibody.
The ChIP DNA and the Input DNA ends were repaired using T4 DNA polymerase, Klenow enzyme, and T4 polynucleotide kinase(PNK) (New England Biolabs), followed by treatment with Klenow exo- to add an A base to the 3’ end. After ligation of the Solexa adaptor using TaKaRa ligation Mix (TaKaRa), the adaptor-ligated DNAs were amplified using Solexa PCR primers for 18 cycles, and the amplified library was isolated from an agarose gel. The samples were purified using the QIAquick MinElute kit (Qiagen) at each preparation step. The purified library was used for cluster generation and sequencing analysis using the Genome Analyzer GAIIx (Illumina).

tag: chip antibody


title: Pelagibacter_T6_Rep_2


title: nfUV10J0h1

description: molecule: bru-labeled RNA


title: H3K4me1 case2 control

value: H3K4me1 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: H3K27me3 case2 control

value: H3K27me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: Pelagibacter_T6_Rep_1

value: rapid growth


title: nfUV24h1

description: molecule: bru-labeled RNA

value: 23.5 hours

value: 24 hours


title: Pelagibacter_T6_Rep_3


title: nfUV60h1

description: molecule: bru-labeled RNA


title: H3K27ac case2 control

value: H3K27ac (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: Pelagibacter_T8_Rep_1

value: slow growth


title: H3K4me3 case2 control

value: H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: nfUV20h1

description: molecule: bru-labeled RNA

value: 1.5 hours

value: 2 hours


title: Pelagibacter_T5_Rep_3


title: nfUV00h1

description: molecule: bru-labeled RNA

value: 0 hours


title: Pelagibacter_T5_Rep_2


title: nfUV10J2h1

description: molecule: bru-labeled RNA


title: H3K27me3 case2 w/ EP

value: Endometrial stromal cells

value: induction with estradiol (10-8 M) and medroxyprogesterone acetate (10-6 M)


title: nf0h5

description: molecule: bru-labeled RNA

value: No exposure

value: 0.5 hours


title: Pelagibacter_T5_Rep_1


title: H3K4me1 case2 w/ EP


title: H3K4me3 case2 w/ EP


title: Input case1 control

value: control (without any induction)


title: RRBS F3D31

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA version 1.8.2 was used to export raw sequencing data in fastq format.
Illumina paired-end adapter sequences were removed using Trim Galore! version 0.3.3 with implemented Cutadapt version 1.1
Reads were mapped using Bismark version 0.10.1
Methylation calls from Bismark were extracted the Bismark methylation_extractor script
The extracted methylation data was further compiled using a custom R script
Genome_build: mm10
Supplementary_files_format_and_content: Each processed file contains a column for chromosome, position and extracted methylation data for the respective sample. For each CpG position observed the number of methylated / unmethylated reads is listed.

source_name: C57Bl/6 Mouse

extract_protocol: 100 ng of DNA was used for RRBS library preparation using a published protocol with minor modifications (Smith et al, 2009). Briefly, genomic DNA was digested with MspI (NEB, Ipswich, MA, USA) end-repaired and A-tailed with the Klenow-fragment enzyme (NEB), and ligated (NEB) with Illumina TruSeq adapters (Illumina Inc., San Diego, CA). Fragments in a range of 40 to 280 bps insert size were purified from a SYBR gold (Invitrogen) pre-stained agarose gel (NuSieve 3:1 Agarose, Lonza, Allenda, NJ, USA). Libraries were bisulfite converted using the EZ DNA Methylation™ Kit (ZymoResearch, Irvine, CA, USA) and amplified using PfuTurboCx polymerase (Agilent, Santa Clara, CA, USA). The libraries were sequenced on an Illumina HiScanSQ instrument with version 3 sequencing chemistry. Libraries were spiked with 45% PhiX DNA to counteract the imbalance in nucleotide representation.

tag: generation

tag: agent

value: decitabine


title: H3K27me3 case1 control


title: RRBS F3C30

value: control


title: RRBS D13

value: parental


title: RRBS F3D7


title: H3K4me1 case1 control

value: H3K4me1 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: RRBS D10


title: RRBS F3C9


title: RRBS F3D1


title: H3K27ac case2 w/ EP


title: Input case2 w/ EP


title: H3K4me3 case1 control


title: H3K27me3 case1 w/ EP

value: H3K27me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: C57BL6-BALB/c WT

city: Paris

first: Laurent

last: Jourdren

institute: École Normale Supérieure

description: Sample 1

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
RNA-Seq data analysis was done using the Eoulsan software version 1.1.6. Before mapping, poly N read tails were trimmed, reads ≤11 bases were removed, and reads with quality mean ≤12 were discarded. Reads were then aligned against the Mus musculus genome (mm10 genome assembly from UCSC) using the Bowtie mapper (version 0.12.7). Alignments from reads matching more than once on the genome were removed. Mus musculus GFF3 genome annotation from UCSC (mm10) was used to compute gene expression. All overlapping regions between alignments and referenced exons were counted.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include transcripts counting for each Sample.

source_name: Brain vessel

extract_protocol:
Total RNA was extracted using the RNeasy Lipid tissue kit (Qiagen). PolyA+ RNAs were purified from 1 µg of total RNA using oligo(dT).
Libraries were prepared using the bi-directional RNA-Seq library preparation TruSeq RNA Sample Prep Kits v2 (Illumina).

tag: strain/background

tag: age

value: 3 months

tag: genotype/variation

value: WT

value: brain vessel


title: H3K27ac case1 control

tag: tissue

value: H3K27ac (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: RRBS D11


title: Input case1 w/ EP


title: RRBS C14


title: RRBS C8


title: C57BL6 Cx30-/-

description: Sample 4

value: Cx30-/- (Cx30 deleted)


title: H3K4me1 case1 w/ EP


title: H3K27ac case1 w/ EP


title: C57BL6_control WT

description: Sample 3


title: Apoptosis IMR90 Input 2

status: Public on Mar 02 2015

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: E1A/RasG12V overexpressing IMR90 Input

data_processing:
Single-end reads were aligned against the Human Reference Genome (assembly hg18, NCBI Build 36) using BWA version 0.5.5. Reads were filtered by removing those with a BWA alignment quality score less than 15. A further filtration was carried out by removing reads falling into the 'blacklist' regions identified by ENCODE.
Principle Component Analysis (PCA) was used to assess the prevalence and quality of read data in TSS regions. Counts were normalized between samples by dividing by effective library size (bin count sums).
The MACS algorithm version 1.4.1 was used together with hg18 aligned, sequence read BAM files for identifying peak regions representing p53 binding sites.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

source_name: diploid fibroblast

growth_protocol: cultured in 5%O2 in DMEM with 10% FBS and Pen/Strep and Glutamine

extract_protocol: immunoprecipitated DNA was end-repaired, A-tailed, ligated to the sequencing adapters, amplified by 18 cycles of PCR and size selected (200-300 bp) followed by single end 4 sequencing on an Illumina Genome Analyzer according to the manufacturer’s recommendationas described in Chandra, T. et al. Independence of Repressive Histone Marks and ChromatinCompaction during Senescent Heterochromatic Layer Formation. Mol Cell 47, 203–214 (2012)

treatment_protocol: 24 hours Etoposide (100microM),pBabe-Puro H-RasG12V, pWXL-Hygro E2A, H-RasG12V, pLNCX-Neo ER:H-RasG12V overexpression

tag: factor

value: Input

value: pAPO


title: Ras Senescence IMR90 Input 2

description: RasG12V overexpressing IMR90 Input

value: RIS


title: Checkpoint IMR90 p53 r3

description: 24 hour Etoposide treated IMR90 anti p53 mouse monoclonal antibody (DO-1) ChIP Seq

value: DDR

tag: antibody

value: anti p53 mouse monoclonal (DO-1) Sigma


title: IMR90 MNase-seq

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Reads were aligned to the human genome (hg18) with bowtie (v0.12.8) using the parameters "-m 1 -best -strata" retaining only the uniquely mapping reads
The wig files represent single nucleotide genome coverages of the 5' ends of the reads.
Two wig files are provided, each containing either alignments from the plus or the minus strand
Genome_build: hg18

growth_protocol: IMR90 were grown in DMEM medium, 10% FCS

extract_protocol:
Chromatin isolation was performed under native conditions. MNase treatment was performed with 5 U at 37°C for 30 min per 1 million cells and the mononucleosomal band was extracted from2% agarose gel.
Library preparation was performed using Illumina Genomic DNA Sample Preparation Guide starting with 2 μg of mononucleosomal fraction DNA.
Single End Genomic Adapter Oligo Mix was used and the library was amplified for 10 cycles.

tag: cell type

value: IMR90 fetal lung fibroblasts


title: Apoptosis IMR90 p53 r3

description: E1A/RasG12V overexpressing IMR90 anti p53 mouse monoclonal antibody (DO-1) ChIP Seq


title: Apoptosis IMR90 p53 r2


title: Apoptosis IMR90 Input 1

description: E1A/RasG12V overexpressing IMR90 Input


title: Ras Senescence IMR90 p53 r3

description: RasG12V overexpressing IMR90 anti p53 mouse monoclonal antibody (DO-1) ChIP Seq


title: Growing IMR90 Input 1

description: Growing IMR9 Input

value: Growing


title: TG biological rep4

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

description: Biological replicate 4 of 5 Epac1-PLN transgenic cardiomyocytes

data_processing:
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
The Alignment was performed using STAR 2.3.0 to mm10. Reads per gene were counted via htseq version 0.5.4.p3. Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading DESeq, gplots and goseq packages.
Candidate genes were filtered to a minimum of 2x fold change and FDR-corrected pvalue<0.05. For functional analysis gene ontology enrichment was tested accounting for gene length via R-package goseq.
Genome_build: mm10
Supplementary_files_format_and_content: NormData.xls: Excel file containing read counts after normalization by DESeq2
Supplementary_files_format_and_content: RawData.xls: Excel file containing read counts determined by htseq-count

source_name: adult cardiomyocytes

extract_protocol:
Adult wildtype and transgenic mouse cardiomyocytes were isolated via the Langendorff perfusion method. Total cardiomyocyte RNA was then isolated using the RNeasy purification Kit (Qiagen) according to the manufacturer protocol.
Library preparation for RNA-Seq was performed using the TruSeq RNA Sample Preparation Kit (Illumina, Cat. N°RS-122-2002) starting from 500 ng of total RNA according to Illumina's instructions. Accurate quantitation of cDNA libraries was performed by using the QuantiFluor™ dsDNA System (Promega). The size range of final cDNA libraries was determined applying the DNA 1000 chip on the Bioanalyzer 2100 from Agilent (280 bp). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000  following the manufacturer's protocols.

treatment_protocol: no treatment

tag: strain

value: FVB/N

tag: gender

value: female

value: adult cardiomyocytes

tag: genotype

value: Epac1-PLN transgenic


title: TG biological rep1

description: Biological replicate 1 of 5 Epac1-PLN transgenic cardiomyocytes

value: male


title: Growing IMR90 p53 r1

description: Growing IMR90 anti p53 mouse monoclonal antibody (DO-1) ChIP Seq


title: Ras Senescence IMR90 p53 r1


title: Apoptosis IMR90 p53 r1


title: Ras Senescence IMR90 p53 r2


title: Checkpoint IMR90 p53 r2


title: Checkpoint IMR90 p53 r1


title: WT biological rep5

description: Biological replicate 5 of 5. Control wildtype cardiomyocytes

value: wildtype


title: TG biological rep5

description: Biological replicate 5 of 5 Epac1-PLN transgenic cardiomyocytes


title: WT biological rep2

description: Biological replicate 2 of 5. Control wildtype cardiomyocytes


title: Ras Senescence IMR90 Input 1

description: Growing IMR9 Input


title: TG biological rep2

description: Biological replicate 2 of 5 Epac1-PLN transgenic cardiomyocytes


title: WT biological rep4

description: Biological replicate 4 of 5. Control wildtype cardiomyocytes


title: WT biological rep3

description: Biological replicate 3 of 5. Control wildtype cardiomyocytes


title: Mmu aRG Tis+ replicate 2

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

description:
Mmu_aRGp_2
mmu_fpkm_matrix.txt

data_processing:
Basecalls performed using CASAVA version 1.8
Reads were trimmed with cutadapt (-m 20 -q 25)
Trimmed Reads were mapped using tophat v2.0.11 (-G $gtfFile -g1)
Abundance estimation was performed using cuffdiff (v2.2.1)
Genome_build: mm10, hg19
Supplementary_files_format_and_content: FPKM normalized expressoin score tables as provided by cummerbund::countMatrix

source_name: aRG Tis+

extract_protocol:
Total RNA was extracted using the RNAeasy Mini kit (Qiagen) according to the manufacturer's instructions.
Complete cDNA was synthesized from half of the isolated mRNA with SmartScribe reverse transcriptase (Clontech) using a universally tailed poly-dT primer and template switching oligos. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase (12 cylces). After ultrasonic shearing of the amplified cDNA (Covaris S2), samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs), in brief: fragments were end repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Subsequently, the NGS libraries were finalized by a universally primed PCR amplification (15 cycles). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75-bp single end sequencing on the Illumina HiSeq 2000 platform providing on average 35 Mio reads per sample.


title: WT biological rep1

description: Biological replicate 1 of 5. Control wildtype cardiomyocytes


title: Mmu aRG Tis+ replicate 1

description:
Mmu_aRGp_1
mmu_fpkm_matrix.txt


title: Mmu aRG Tis+ replicate 3

description:
Mmu_aRGp_3
mmu_fpkm_matrix.txt


title: Mmu aRG Tis- replicate 4

description:
Mmu_aRGm_4
mmu_fpkm_matrix.txt

source_name: aRG Tis-


title: Mmu aRG Tis+ replicate 0

description:
Mmu_aRGp_0
mmu_fpkm_matrix.txt


title: H3K4me3 case1 w/ EP

value: Endometrial stromal cells

value: induction with estradiol (10-8 M) and medroxyprogesterone acetate (10-6 M)

value: H3K4me3 (generous gifts from Dr. H. Kimura, Osaka University, Osaka, Japan).


title: Checkpoint IMR90 Input 1

description: 24 hour Etoposide treated IMR90 Input


title: TG biological rep3

description: Biological replicate 3 of 5 Epac1-PLN transgenic cardiomyocytes


title: Oct4 ChIP-seq

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

description: Illumina Hiseq 2000

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (mm).
Supplementary_files_format_and_content: peaks.bed

source_name: mouse embryonic stem cells (E14)

growth_protocol: The E14 mESC line was cultured on Mouse Embryonic Fibroblast (MEF) feeder cells as previously described26. The medium contained DMEM supplemented with 15% FBS, GlutaMAX™-I (2mM), sodium Pyruvate (1mM), MEM nonessential amino acid (0.1 mM), Penicillin/Streptomycin (50 ug/ml each), β-mercaptoethanol (100 uM) and ESGRO-LIF (Millipore, ESG1106; 1000 U/ml).

extract_protocol:
2×107 mouse ES cells were cross-linked with 1% formaldehyde at 25°C for 10 min and sonicated to generate chromatin fragments of 100–500 bp. Chromatin fragments from 2×107 cells were immunoprecipitated using Nanog, Oct4 and Sox2 antibody
25ng of input genomic DNA or experimental enriched DNA were utilized for each library construction. 150-300 bp DNA fragments were selected by AMPure XP Beads (Beckman Coulter) after the adapter ligation. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA, qPCR was applied to accurately quantify the library concentration. 20 pM diluted libraries were used for sequencing. 50-cycle single-end sequencings were performed using Illumina HISeq 2000. Image processing and sequence extraction were done using the standard Illumina Pipeline.

value: mouse embryonic stem cells (E14)

tag: passages

tag: chip antibody vendor/catalog

value: Abcam ab19857


title: Mmu bIP replicate 3

description:
Mmu_IPC_3
mmu_fpkm_matrix.txt

source_name: bIP


title: Mmu bIP replicate 2

description:
Mmu_IPC_2
mmu_fpkm_matrix.txt


title: Mmu N replicate 2

description:
Mmu_N_2
mmu_fpkm_matrix.txt

source_name: Neuron


title: Mmu aRG Tis- replicate 3

description:
Mmu_aRGm_3
mmu_fpkm_matrix.txt


title: Mmu bIP replicate 1

description:
Mmu_IPC_1
mmu_fpkm_matrix.txt


title: Mmu N replicate 1

description:
Mmu_N_1
mmu_fpkm_matrix.txt


title: Mmu aRG Tis- replicate 2

description:
Mmu_aRGm_2
mmu_fpkm_matrix.txt


title: Mmu bRG replicate 2

description:
Mmu_bRG_2
mmu_fpkm_matrix.txt

source_name: bRG


title: Mmu N replicate 3

description:
Mmu_N_3
mmu_fpkm_matrix.txt


title: Mmu N replicate 0

description:
Mmu_N_0
mmu_fpkm_matrix.txt


title: Mmu aRG Tis- replicate 1

description:
Mmu_aRGm_1
mmu_fpkm_matrix.txt


title: Mmu aRG replicate 3

description:
Mmu_aRG_3
mmu_fpkm_matrix.txt

source_name: aRG


title: Mmu bRG replicate 0

description:
Mmu_bRG_0
mmu_fpkm_matrix.txt


title: Mmu bRG replicate 3

description:
Mmu_bRG_3
mmu_fpkm_matrix.txt


title: smallRNA #9

city: Vienna

first: Andreas

middle: B

last: Diendorfer

address: Muthgasse 18

department: Department of Biotechnology

country: Austria

institute: University of Natural Resources and Life Sciences

description: Temperature shift

data_processing:
3' Adapter was cleaved. Reads shorter than 17 nt or longer than 26 nt were discarded
Reads were collapsed to remove redundant sequences. Read count for each sequences was saved in header
Supplementary_files_format_and_content: Fasta file containing collapsed reads from all lanes with a max. length of 26 nt. The header contains a unique ID of the sequence and the read count (separated with a dash).

organism: Cricetulus griseus

growth_protocol: CHO cells were grown in a 2L bioreactor as a batch culture.

extract_protocol:
RNA was extracted with Trizol reagent. RNA integrity was tested on an Agilent chip
Standard Illumina TrueSeq protocol for small RNA. 12 Barcoded samples were put on one lane. Sequencing of ready to load libraries was conducted by GATC, Germany on a Illumina HiSeq Analyser.

treatment_protocol: In the middle of the exponential growth phase, temperature was shifted

tag: cell line

value: chinese hamster ovary cells


title: smallRNA #8

description: Temperature shift


title: Mmu aRG Tis+ replicate 4

description:
Mmu_aRGp_4
mmu_fpkm_matrix.txt


title: smallRNA #7

description: Temperature shift


title: Mmu aRG replicate 2

description:
Mmu_aRG_2
mmu_fpkm_matrix.txt


title: smallRNA #12

description: Temperature shift


title: Mmu bRG replicate 1

description:
Mmu_bRG_1
mmu_fpkm_matrix.txt


title: Mmu aRG replicate 1

description:
Mmu_aRG_1
mmu_fpkm_matrix.txt


title: Mmu aRG Tis- replicate 0

description:
Mmu_aRGm_0
mmu_fpkm_matrix.txt


title: smallRNA #3

description: contol run


title: Time-course_mut_24hr

data_processing:
For each read, the 3′ adaptor TGGAATTCTCGGGTGCCAAGG was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least seven or ten bases, respectively. Reads with Low-complexity were filtered out based on their dinucleotide entropy (removing <1% of the reads). Only reads with a minimum length of 14nt were retained. Alignments to the rat miRNA database miRBase release 20 (http://www.mirbase.org/) were performed by the software bowtie (version 0.9.9.1) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Reads that mapped to a miRNA but at the same time also mapped with fewer mismatches to the genome (rn4) were filtered out. The expression of each miRNA was determined by counting the number of associated reads. To compensate for differences in the read depths of the individual libraries, each sample was divided by its total number of counts and multiplied by the ave  rage sample size. The resulting values were log2 transformed using a pseudocount of 8 (y=log2(x+8)). The two experiments “Syn-Target” and “Time-course” were normalized separately.
genome build: rn4 (UCSC)
Supplementary_files_format_and_content:MiRNA expression table (all samples)

organism: Rattus norvegicus

source_name: Primary hippocampal neurons

growth_protocol: Primary dissociated hippocampal neurons were routinely generated by removing hippocampi from embryonic day 18.5 (E18.5) rats and treated with 0.05 % trypsin (Sigma) for 15 min at 37 °C, followed by washing and trituration. Dissociated cells were plated at 30,000 cells/cm2 on poly-D-lysine coated plates (BD biosciences) and cultured in Neurobasal medium (Gibco) supplemented with 2 mM Glutamax (Invitrogen), and 2% B-27 supplement (Invitrogen).

extract_protocol:
Total RNA and Ago-associated RNA (FLAG-IP fraction) were extracted using Trizol reagent.
Small RNA libraries were prepared for sequencing using Illumina TruSeq Small RNA Sample Prep Kits (Cat # RS-200-0024).

treatment_protocol: Neurons were transduced with lentiviruses 9 days after plating (DIV9) at a multiplicity of infection (MOI) of 1-5, and analyzed 5-6 days after infection (DIV15-16). Immunoprecipitation of FLAG/HA-Ago2 was performed with Anti-FLAG M2 Magnetic Beads (Sigma. Cat # M8823).

value: Sprague Dawley

tag: embryo stage for culture prep

tag: days of in vitro culture (div)


title: smallRNA #2

description: contol run


title: smallRNA #1

description: contol run


title: Mmu aRG replicate 0

description:
Mmu_aRG_0
mmu_fpkm_matrix.txt


title: smallRNA #11

description: Temperature shift


title: Growing IMR90 p53 r2

tag: condition


title: smallRNA #10

description: Temperature shift


title: Time-course_WT_72hr


title: smallRNA #6

description: contol run


title: Time-course_mut_72hr


title: Syn-Target_Seed_miR-132_mut-1


title: Syn-Target_Seed_miR-132_WT-1


title: Syn-Target_Seed_miR-124_mut-2


title: Syn-Target_Seed_miR-124_mut-1


title: Syn-Target_Seed_miR-132_WT-2


title: Time-course_mut_4hr


title: smallRNA #4

description: contol run


title: Time-course_mut_8hr


title: Mmu bIP replicate 0

description:
Mmu_IPC_0
mmu_fpkm_matrix.txt


title: Syn-Target_Seed_miR-124_WT-1


title: Time-course_mut_0hr


title: Syn-Target_Ext_miR-132_WT-2


title: Time-course_WT_24hr


title: Syn-Target_Ext_miR-132_mut-1


title: Syn-Target_Ext_miR-124_mut-2


title: Time-course_WT_4hr


title: S. pombe wildtype mononucleosomes

city: Hamburg

first: Babett

last: Steglich

address: Martinistrasse 52

institute: Universitätsklinikum Hamburg-Eppendorf

description: WT

data_processing:
Alignment to the S. pombe genome was carried out using Bowtie2 with standard parameters for paired-end data.
Removal of clonal reads, read length adjustment, quantile normalization and calculation of differences in nucleosome occupancy were carried out with DANPOS (doi:10.1101/gr.142067.112).
Illumina MiSeq v.3.
Genome_build: Ensembl Genome Build ASM294v2.2, retrieved March 21, 2014, from http://www.pombase.org/downloads/datasets .
Supplementary_files_format_and_content: Processed fixed step WIG files contain nucleosome occupancy scores (WT.wig and Fft2DFft3D.wig) and differential scores (+/- log10 of Poisson test p-values) as calculated by DANPOS with a step size of 10bp.

organism: Schizosaccharomyces pombe

source_name: mononucleosomes, WT

extract_protocol:
Mononucleosomal DNA was prepared as described in Lantermann et al., Methods, 48(3), 218–225. doi:10.1016/j.ymeth.2009.02.004.
NEBNext® ChIP-Seq Library Prep Master Mix Set for Illumina®.

tag: culture type

value: log-phase liquid culture


title: Time-course_WT_2hr


title: smallRNA #5

description: contol run


title: Syn-Target_Ext_miR-124_mut-1


title: Syn-Target_Ext_miR-124_WT-1


title: Syn-Target_Seed_miR-132_mut-2


title: Time-course_WT_0hr


title: Time-course_mut_2hr


title: sta1

city: Beijing

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced clean reads were mapped to Arabidopsis thaliana (tair10) whole genome using tophat v2.0.12 with parameters --bowtie1 --no-coverage-search --segment-length 20 -g 10 -p 10
Gene annotation and calculation of FPKM values was carried out using Cufflinks (v2.0.1) with the provision of a GTF annotation file (tair10).
Gene expression differences were assessed by Cuffdiff use upper-quartile normalization, with false discovery rate correction for multiple testing.
Genome_build: tair10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized and placed on MS (Murashige and Skoog) agar medium. Then the MS plates were incubated at 23ºC with 16-h-light and 8-h-dark for 10 days.

extract_protocol:
Seeding materials was ground into powder in liquid nitrogen; total RNA was harvested using RNeasy Plant Mini Kit (QIAGEN); then total RNA samples were treated with DNase I and the mRNA is enriched by using the oligo(dT) magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: ecotype


title: zop1


title: C24


title: Time-course_WT_8hr


title: Syn-Target_Seed_miR-124_WT-2


title: S. pombe Fft3D mononucleosomes

source_name: mononucleosomes, Fft3D

tag: strain/background

value: h+ fft3D::hphMX ura4D18 leu1-32 ade6-216


title: Syn-Target_non-infected cells_1


title: Sample9_ColA9xC24_Rep3

city: Davis

first: Luca

last: Comai

state: Calif

address: 451 Health Sciences Dr

institute: UC Davis

description:
Samples 1-4 were standard RNA-seq. Samples 5-9: mRNA amplicons, PCR sequence data for validation
Seed from 3 DAP ColA9 X C24 crosses

data_processing:
All sequence preprocessing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). Sequences were divided according to barcodes and barcodes were removed. The Illumina 1.5+ format (fastq) reads were trimmed for adaptor contamination and bases with a quality score lower than Phred 20 were also excluded using a custom python script. Reads that were shorter than 40 base pairs (for 80-bp or 100-bp). The Illumina quality scores were converted to Sanger, which is compatible with most aligners. Biological replicates were pooled for greater sequence depth.
Processed and pooled sequences were aligned to A. thaliana TAIR10 cDNA all gene models using Burrows-Wheeler Aligner (BWA) version 0.5.8c and SAM files and parsed pileups were generated using Samtools version 0.1.7 [58] as well as custom python scripts..
Read counts were generated using a custom python script available for download at http://comailab.genomecenter.ucdavis.edu/index.php/Hybrid_Transcriptome.
Genome_build: TAIR10 cDNA (all gene models)

source_name: Arabidopsis seeds

growth_protocol: Wild type Col-0 (CS6673) and C24 (CS22620), as well as male sterile lines that were hemizygous for a male sterility construct, were grown in 16 hours of light at 21°C and 8 hours of dark at 18°C in a controlled environment fascility. The male-sterile A. thaliana lines (ColA9 and C24A9) were pollinated by either wild type Col-0 or C24. Two biological replicates for each condition (ColA9 X C24 or C24A9 X Col-0) were used in these experiments. No emasculation was needed because all egg donors had a sterility construct.

extract_protocol: RNA processing for Illumina sequencing was performed using a homemade kit (see Burkart-Waco et al. 2013 for technical details). RNA was sequenced according to Illumina's specifications on HiSeq2000 (Illumina, San Diego) (100-bp paired-end reads).

treatment_protocol: Seeds were harvested fresh from ColA9 X C24 and C24A9 X Col-0 and frozen on dry ice. RNA isolation using Invitrogen's Plant RNA Reagent was described by Burkart-Waco et al. (2013).

value: A. thaliana eco. ColA9 X C24

value: whole seeds

tag: time

value: 3 days after pollination


title: Syn-Target_Ext_miR-132_mut-2


title: Syn-Target_Ext_miR-132_WT-1


title: Syn-Target_Ext_miR-124_WT-2


title: Sample3_C24A9XCol-0_Rep1

description:
Samples 1-4 were standard RNA-seq. Samples 5-9: mRNA amplicons, PCR sequence data for validation
Seed from 3 DAP C24A9 X Col-0 crosses

data_processing:
All sequence preprocessing was done with custom python scripts available at the Comai lab wiki (http://comailab.genomecenter.ucdavis.edu/index.php/Barcoded_data_preparation_tools). Sequences were divided according to barcodes and barcodes were removed. The Illumina 1.5+ format (fastq) reads were trimmed for adaptor contamination and bases with a quality score lower than Phred 20 were also excluded using a custom python script. Reads that were shorter than 40 base pairs (for 80-bp or 100-bp). The Illumina quality scores were converted to Sanger, which is compatible with most aligners. Biological replicates were pooled for greater sequence depth.
Processed and pooled sequences were aligned to A. thaliana TAIR10 cDNA all gene models using Burrows-Wheeler Aligner (BWA) version 0.5.8c and SAM files and parsed pileups were generated using Samtools version 0.1.7 [58] as well as custom python scripts..
Read counts were generated using a custom python script available for download at http://comailab.genomecenter.ucdavis.edu/index.php/Hybrid_Transcriptome.
Genome_build: TAIR10 cDNA (all gene models)
Supplementary_files_format_and_content: .txt (count file)
The N libraries are normalized libraries of the Sample 1 and Sample 3

value: A. thaliana eco. C24A9 X Col-0

tag: tissue


title: Sample7_ColA9xC24_Rep1


title: Sample2_ColA9xC24_Rep2


title: Syn-Target_non-infected cells_2


title: Sample8_ColA9xC24_Rep2


title: Sample1_ColA9xC24_Rep1


title: Sample6_ColA9xAa_Rep2

description:
Samples 1-4 were standard RNA-seq. Samples 5-9: mRNA amplicons, PCR sequence data for validation
Seed from 3 DAP ColA9 X A. arenosa

organism: Arabidopsis thaliana x Arabidopsis arenosa

value: A. thaliana eco. ColA9 X A. arenosa eco. Strecno


title: Sample5_ColA9xAa_Rep1


title: prp31

tag: genotype/variation