title: mbd7-2_CS876032_MethylC-Seq

city: West Lafayette

first: Jian-Kang

last: Zhu

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: treated with bisulfite

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

source_name: Seedlings

extract_protocol:
The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen.
5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.

tag: background

value: mbd7-2 mutant

value: seedling


title: Col-0_MethylC-Seq

status: Public on Jun 01 2017

type: SRA

state: IN

country: USA

description: treated with bisulfite

library_source: genomic

molecule: genomic DNA

organism: Arabidopsis thaliana

tag: genotype/variation

value: wild type

tag: tissue


title: 0 Gy cell 2

city: Hangzhou

first: Ling

last: Yang

address: 34th, Yanguan alley

country: China

institute: Hangzhou cancer institute

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T02.bam

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Repeated 12 Gy sequencing reads were combined. Then all reads were mapped to gencode v22 whole genome using tophat v2.0.14 with default parameters.
Reads count were calculated using Rsubread 1.2.0. The raw data was cleaned by scde package. The normalized number of reads count falling in the exons of this meta-transcript were generated by the DESeq2 package.
Genome_build: gencode v22
Supplementary_files_format_and_content: normalized reads counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Esophageal squamous cell carcinoma

extract_protocol:
Cells were directly lysed and amplified with smart-seq2 kit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Esophageal squamous cell carcinoma line KYSE-180

value: Esophagus

tag: irradiation

value: 0 Gy


title: Pineal Day rep3

city: New York

first: Marjan

last: Bozinoski

state: NY

address: 1305 York Avenue, Box 140

department: Physiology and Biophysics

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were aligned with the RNA-STAR aligner (v. 2.3.0e) , using a rhesus rheMac3 genome build. STAR aligner parameters used: --runThreadN 8 --outFilterMultimapNmax 1 --outSAMunmapped Within --outStd SAM. Quality control metrics were calculated and visualized using FastQC software and in-house written scripts, and no major artifacts or abnormalities were found
Gene read counts were provided by R subreads package, (featureCounts function) with parameters specifying: paired-end reads, and reverse-complement for the second strand (-p, -S2). Annotation for assigning the reads was derived from Gencode v.19 human annotation. Gene coordinates were lifted over using RheMac3/hg19 liftover chains, and only sequences that shared no less than 95% homology were kept, resulting in total of 50308 genes. Differential expression analysis was performed using DESeq2 software package.
Genome_build: RheMac3
Supplementary_files_format_and_content: retina_pineal_control.xlsx file includes FPKM values for all of the Samples, pineal_DE.xlsx includes the differential expression analysis for pineal gland, Retina_DE.xlsx includes the differential expression analysis for retiina

organism: Macaca mulatta

source_name: Pineal Day

extract_protocol:
Twelve adult rhesus macaques (Macaca mulatta, 3 to 33 years of age, male and female, 4 to 10.3 kg) were obtained through the Veterinary Resources Program Primate Recycle Program of NIH over a period of 11 years.     All protocols and handling of the animals conformed to the Guidelines for Care and Use of Laboratory Animals (NIH Publication 80-23; Protocols 99-012 and 11-055 ). Animals were housed under a 12-h light, 12-h dark lighting regimen (lights on at 0600 h) in NIH facilities for at least 6 wk. The light level in the cages was approximately 325 Lux.   Animals (three per time point) were sacrificed between 1100 and 1300 (day) , 1700 and 1900 (dusk), 2300 and 0100 (night) and 0500 and 0700 (dawn).  Animals were anesthetized (ketamine, 0.1 ml/kg body weight) and a catheter was placed in the saphenous vein prior to transport to the procedure room.   Animals were sacrificed using Euthasol (Virbac, Fort Worth, TX)  or Beuthanasia D ( Schering Plough, Union, NJ).   Animals sampled at night  or dusk  were anesthesized  under dim red light and  blindfolded; euthanasia was done under dim white light and  the blindfold was removed  after decapitation. Removal of tissues, including the pineal gland, retina, and others (corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine,  testis and  ovary) was complete within 45 minutes following euthanasia; immediately following removal, samples  of each tissue were obtained and placed on solid  CO2.  Tissue was store at -80° C. Total RNA was extracted from individual pineal glands or pieces of other tissues (  2 to 4 mm 3 pieces) with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: Day

value: pineal gland


title: 0 Gy cell 1

description: Corresponds to Normalized_counts.txt column: Unkonwn.180.T01.bam


title: CS_7days_rep1

city: Denver

first: Irina

last: Petrache

state: CO

address: 1400 Jackson St, Molly Blank Building, J203

department: Division of Pulmonary, Critical Care and Sleep Medicine

institute: National Jewish Health

description:
RNA from mouse x26 (treatment CS after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

data_processing:
Sequences were mapped to the Mus musculus reference genome (mm10) using GSNAP version 2013-11-27 with SNP version 137
Uniquely mapped reads were quantified with HTSeq (version 0.5.4p3) using the “intersection-nonempty” mode; counts from the four sequencing lanes for each sample were added up.
Low expression genes were filtered across the entire time series using HTSFilter (version 1.8.0) and DESeq normalization applied from with HTSFilter. Month 9 cessation data was filtered separately for additional analysis
For DEXseq analysis, uniquely mapped reads were quantified using exon part derived from Ensembl annotation (version 78 for mouse) with HTSeq (version 0.6.0) and the dexseq_count.py script supplied by the DEXSeq package.  Counts from the four sequencing lanes for each sample were added up.
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file containing raw read counts; first column contains gene names, first row contains mouse IDs (see Samples for details)
Supplementary_files_format_and_content: DEXSeq-counts.txt: raw counts for exonic parts
Supplementary_files_format_and_content: mouse126_all_reads.csv: CSV; raw read counts, all genes
Supplementary_files_format_and_content: mouse126_filtered_reads.csv: CSV; raw read counts, filtered genes
Supplementary_files_format_and_content: mouse126_filtered_9month_reads.csv: CSV; raw read counts, filtered separately for 9 month cessation data

organism: Mus musculus

source_name: Whole lung

extract_protocol:
Whole lung tissue was snap-frozen and stored at -80 °C.   RNA was extracted using RNeasy Mini Kits (Qiagen, # 74104) following standard protocols.
Total RNA (500ng per sample) was used to construct sequencing libraries with the Illumina TruSeq Stranded mRNA LT Library Construction Kit (catalog # RS-122-2101, Illumina Inc., San Diego, CA) following standard protocols.  Each library was sequenced on 4 lanes spread over two different flow cells on an Illumina HiSeq 2000 sequencer.

tag: mouse id

value: whole lung

tag: time point

value: 7 days

tag: treatment

value: CS

tag: strain


title: Pineal Day rep2


title: 174a

city: Los Angeles

first: Tracy

last: Grikscheit

state: California

address: 4650 Sunset Boulevard Mailstop#100

institute: Children's Hospital Los Angeles

data_processing:
Sequencing QC: FastQC
Trimming of reads for quality: Trimmomatic
Alignment: STAR
Read binning: Htseq-count
Differential Gene Expression: RUVSeq, edgeR
Genome_build: GRCh38.p3 (Gencode 24)
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values, counts, DE statistics and Annotation

source_name: full thickness intestine

extract_protocol:
Full thickness section of intestine was removed, and RNA was harvested using Trizol reagent. RNA integrity was checked with the PIco chip in the BioAnalyzer.
Kapa stranded RNA kit was used with 1 ug of total RNA for the construction of sequencing libraries. ERCC spikes ins were added based on manufacturer recommendations

tag: age

value: 3 month

tag: status

value: fed

tag: diagnosis

value: necrotizing enterocolitis


title: 174b

value: unfed


title: CS_1day_rep4

description:
RNA from mouse x148 (treatment CS after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 day


title: CS_7days_rep5

description:
RNA from mouse x30 (treatment CS after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: 166b

value: 10 month


title: Pineal Day rep1


title: CS_1day_rep3

description:
RNA from mouse x139 (treatment CS after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: 166a


title: CS_1day_rep2

description:
RNA from mouse x138 (treatment CS after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: Pineal Dawn rep3

source_name: Pineal Dawn

value: Dawn


title: Pineal Dawn rep2


title: Symp RNAi RNA-seq rep2

city: St. Louis

first: Mindy

last: Steiniger

address: 1 University Blvd.

institute: University of Missouri-St. Louis

data_processing:
All adapter sequences were trimmed and the libraries cleaned using Cutadapt (MARTIN 2011).We aggressively trimmed the siRNA reads to 25 nts from the 5’ end following adapter removal to filter remaining rRNAs, snoRNAs, snRNAs and tRNAs out of the data set before mapping. All data sets were mapped using the RNA-seq Unified Mapper (RUM) (GRANT et al. 2011). The NEB kit used to prepare the RNA-seq samples produces libraries with high directionality and RUM utilized this feature to strand specifically map the RNA-seq reads. RUM separated unique and non-uniquely mapping sequences into separate output files that could be further analyzed. The UCSC genome browser (www.genome.ucsc.edu) was used to visualize the non-uniquely mapping bedgraph output files.
Genome_build: dm3
Supplementary_files_format_and_content: Text files with normalized readcounts unique and non-unique RNA-seq and small RNA-seq reads.

organism: Drosophila melanogaster

source_name: Symp RNAi RNA-seq

growth_protocol: Dmel-2 cells were grown in Sf-900 serum free media.

extract_protocol:
Total RNA from 8 x 10^6 Drosophila Dmel-2 tissue culture cells was isolated using QIAzol Lysis Reagent (Qiagen). Total RNA was fractionated into large (>200 nts) and small (<200 nts) fractions using RNeasy Mini spin columns and RNeasy MinElute spin columns, respectively (Qiagen). DNA was removed from the large fraction by on-column DNase digestion (Qiagen). 28S, 18S and 5S rRNAs were depleted from 5 µg of each large RNA fraction using the Ribo-Zero Magnetic Kit (Epicentre). 2S rRNA was depleted from the small RNA fraction according to Seitz et al.  (SEITZ et al. 2008) with the following modifications. 0.1 nMoles 2S rRNA complementary oligo were bound to 500 µg streptavidin beads in 1 mL 0.5x SSC for one hour at 4oC. The beads were then washed 5X in 0.5X SSC followed by 5 minute incubation at 65oC to remove secondary structure. 2 µg of the small RNA fraction were diluted to 12.5 ng/µl and 160 µl were added to the bead slurry.
RNA-seq libraries were prepared in triplicate from 35 ng of the rRNA-depleted large RNA fraction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). smRNA-seq libraries were prepared in triplicate from ~475 ng of the 2S rRNA-depleted small RNA fraction using the NEBNext Small RNA Library Prep Set for Illumina (NEB).

treatment_protocol: RNAi was performed as described (Sullivan, et. al., Mol. Cell, 2009)

tag: RNAi

value: Symp RNAi

tag: molecule subtype

value: rRNA depleted Large RNA


title: CS_1day_rep1

description:
RNA from mouse x137 (treatment CS after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: Symp RNAi RNA-seq rep3


title: Symp RNAi RNA-seq rep1


title: 149b

value: focal intestinal perforation


title: 149a


title: AC_9months_rep5

description:
RNA from mouse x122 (treatment AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv

value: 9 months

value: AC


title: CPSF73 RNAi RNA-seq rep3

source_name: CPSF73 RNAi RNA-seq

value: CPSF73 RNAi


title: 136b

value: 2 month


title: Pineal Dawn rep1

value: pineal gland


title: CPSF73 RNAi RNA-seq rep2


title: AC_9months_rep3

description:
RNA from mouse x104 (treatment AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv

value: whole lung


title: Control Night

source_name: Control Night

value: Night

value: mixed (corpus callosum, frontal cortex, cerebellum, thalamus, hippocampus, caudate, medulla, pituitary, heart, liver, lung, kidney, skeletal muscle, small intestine, testis and ovary)


title: CPSF73 RNAi RNA-seq rep1


title: AC_9months_rep2

description:
RNA from mouse x103 (treatment AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: AC_6months_rep4

description:
RNA from mouse x94 (treatment AC after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 6 months


title: Control Day

source_name: Control Day

value: Day


title: 117a

value: 3 month

value: fed


title: 136a

value: necrotizing enterocolitis


title: UtestesM_g3

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

country: France

institute: IRSN

description: Testies dissected from depleted uranium exposed adult males

data_processing:
Base call with CASAVA v1.7
Mapping with RNASTAR and the exon-exon reference from ensembl v85
Quantification of reads to genes from RNASTAR output in --quantMode GeneCounts
Genome_build: Zv10
Supplementary_files_format_and_content: Non-normalized read count at the gene levels (ensembl gene identifier from release 85)

organism: Danio rerio

source_name: adult testis

extract_protocol:
total RNA extracted from mouse tissu in Trizol (Life Technologies)
TruSeq mRNA version 2

treatment_protocol: exposure of adults to 20µg/L of depleted uranium for 10 days

tag: developmental stage

value: adult

value: testis

tag: genotype

value: wild type AB

value: 20µg/L depleted uranium


title: Blank RNAi RNA-seq rep1

source_name: Blank RNAi RNA-seq

value: Blank RNAi

value: rRNA depleted Large RNA


title: UtestesM_g1


title: Blank RNAi RNA-seq rep3


title: Retina Dusk rep2

source_name: Retina Dusk

value: Dusk

value: retina


title: Brain-AD

city: Ann Arbor

first: Kin Fai

last: Au

state: MI

address: 100 Washtenaw Avenue

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
Hisat2 (version 2.0.0-beta) was used to align Illumina short reads to reference genome with the parameters (“-k 1 - -rna-strandness RF - -no-mixed - -no-discordant”) for paired-end strand-specific data.
The SMRT Analysis software (version 2.3.0) was used to process PacBio long read data. In brief, Reads of Insert (ROI) were extracted from raw sequencing data requiring full passes ≥0 and predicted accuracy ≥70. Full-length non-chimera ROI and non-full-length non-chimera ROI were used for alignment. GMAP (version 2016-06-09) was used to align long reads to reference genome with the parameter “- -max-intronlength-middle 500000 - -max-intronlength-ends 500000 -z sense_force -n 0 -f samse - -split-output”.
IDP-APA (with PacBio long reads and Illumina short reads) was run using a reference isoform annotation library (GENCODE, version 25) to construct expressed isoforms and identify polyA sites.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includ identified polyA sites for each expressed gene isoforms

molecule: polyA RNA

source_name: human brain tissue from a patient with Alzheimer’s disease

growth_protocol: For human embryonic stem cells (H1-hESC cell line; WiCell), cells were cultured in mTeSR1 (Stem Cell Technologies) on Matrigel matrix (BD) and were harvested between passages 50 and 55. For Brain-AD sample, total RNA materials (BioChain, Lot No. A703252) was provided by Elizabeth Tseng (PacBio Inc.) and Ting Hon (PacBio Inc.) as a gift.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN). Agilent RNA 6000 Pico Kit (Agilent) was used to assess the RNA quality, and Qubit RNA BR Assay Kit (ThermoFisher Scientific) was used to quantify the extracted RNA.
For Illumina sequencing, TruSeq Stranded mRNA Library Prep Kit was used to prepare library. For PacBio SMRT seqeuncing, library was prepared following Iso-Seq protocol (PacBio Inc.). For size selection of PacBio SMRT seqeuncing, the full-length cDNA was fractioned into four contiguous size ranges (0–1kb, 1–2kb, 2–3kb, >3kb) on a Sage ELF (Sage Science) before constructing SMRTbell templates.

value: brain from Alzheimer's disease patient


title: Retina Night rep3

source_name: Retina Night


title: 117b

value: unfed

value: focal intestinal perforation


title: Retina Dusk rep1


title: AC_9months_rep1

description:
RNA from mouse x101 (treatment AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv

value: whole lung

value: 9 months

value: AC


title: UovaryF_g4

description: Ovaries dissected from depleted uranium exposed adult females

source_name: adult ovary

value: ovary


title: Retina Night rep2

value: Night


title: H1-hESC

source_name: human embryonic stem cells

value: human embryonic stem cell line H1


title: Blank RNAi RNA-seq rep2


title: Retina Night rep1


title: Retina Dusk rep3


title: AC_6months_rep3

description:
RNA from mouse x83 (treatment AC after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 6 months


title: UtestesM_g5

value: adult

value: testis


title: UbrainM_b3

description: Brain dissected from depleted uranium exposed adult males

source_name: adult brain

value: brain

value: wild type AB

value: 20µg/L depleted uranium


title: AC_6months_rep2

description:
RNA from mouse x82 (treatment AC after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: AC_3months_rep2

description:
RNA from mouse x63 (treatment AC after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 3 months


title: AC_6months_rep1

description:
RNA from mouse x81 (treatment AC after 6 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: AC_3months_rep1

description:
RNA from mouse x62 (treatment AC after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: UovaryF_g1


title: AC_3months_rep5

description:
RNA from mouse x74 (treatment AC after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: AC_3months_rep4

description:
RNA from mouse x65 (treatment AC after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: Selex_7_cyc

city: Vienna

first: Philipp

last: Rescheneder

address: Dr. Bohr Gasse 9

country: Austria

institute: MFPL

description: SELEX RNA library

data_processing:
Reads were trimmed using trimmomatic (Bolger et al., 2014)
Mapped against the reference genomes of the E. coli strain K12 (substrain MG1655, GenBank ID: U00096.3) using NextGenMap (Sedlazeck et al., 2013). Read mapping was conducted with permissive settings that allowed up to 20% sequence divergence in order to account for the considerable amounts of sequence alterations introduced by the SELEX procedure (Zimmermann et al., 2010a, 2010b). The mapped reads were then filtered for a minimum mapping quality of 20.
Peak finding: Strand-specific coverage signals from K12 alignments were extracted and a custom peak-finding method was applied to these signals in order to identify the originating genomic regions of mRNA-fragments that were found to be enriched in the respective SELEX cycle. Briefly, our peak-calling method consists of the following steps: (1) signal smoothing using a moving Gaussian kernel, (2) approximation of the first derivative at each signal position by cubic Hermite interpolation, (3) calling peaks based on derivative sign-changes and defined minimum/maximum peak dimensions (minimum width: 10bp, maximum width: 500bp, minimum (smoothed) peak height: 8).
Genome_build: E. coli strain K12 (substrain MG1655, GenBank ID: U00096.3)
Supplementary_files_format_and_content: BED file containing the locations and strand of all identified RAPs

organism: Escherichia coli

source_name: Escherichia coli

extract_protocol:
For cloning, reporter protein assays and maintaining strains: cultures were grown in LB or LB-agar media at 37°C and, when required, supplemented with ampicillin (100 µg/ml; Sigma-Aldrich), kanamycin (30 µg/ml; Sigma-Aldrich), erythromycin (1.5 µg/ml; Sigma-Aldrich) and/or bicyclomycin (BCM; Astellas Corporation) (8-10 µg/ml – low concentration used for extended treatments, minimally affects bacterial growth). When grown in liquid media, cells were cultivated with constant aeration (shaking at 200 rpm).
The RNA library from SELEX cycle 7 was first reverse transcribed to cDNA and amplified by 16 cycles of PCR with Phusion High-Fidelity DNA polymerase (New England Biolabs) using primers with fixed part and added barcode for multiplexing according to (Parameswaran et al., 2007), (Windbichler et al., 2008)  (fixFW: TATAGGGGAATTCGGAGCGGG, fixRV_multi: TAGCCCGGGATCCTCGGGGCTG (Sigma)). Library preparation (adapter ligation step) and deep sequencing were performed at the CSF NGS unit http://csf.ac.at/. The SELEX library was multiplexed and sequenced with the Solexa technology on a GAIIx with paired-end 76 base-pair reads.


title: UbrainM_b5


title: AC_3months_rep3

description:
RNA from mouse x64 (treatment AC after 3 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: AC_1month_rep4

description:
RNA from mouse x44 (treatment AC after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 month


title: UbrainF_b4

description: Brain dissected from depleted uranium exposed adult females


title: UbrainF_b2


title: Retina Day rep2

source_name: Retina Day

value: Day

value: retina


title: Retina Day rep1


title: AC_1month_rep2

description:
RNA from mouse x42 (treatment AC after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

source_name: Whole lung


title: JS_RNA-seq

city: Taipei

first: Moloya

last: Gohain

state: Taipei

address: 128, SEC.2 ACADEMIA ROAD, NANGANG DISTRICT

department: INSTITUTE OF PLANT AND MICROBIAL BIOLOGY

country: Taiwan

institute: ACADEMIA SINICA

description: RNA-Seq

data_processing:
The quality of reads was checked with FastQC (Andrews, 2010), reads were mapped to Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie (Langmead et al., 2009) allowing up to two mismatches and only unique alignments were retained. The alignment file was processed and differential expression was calculated using Tophat (Langmead et al., 2009) to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene by applying 4-fold cut-off .
We identified differentially expressed genes (DEGs) using Tophat to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene. The transcripts showing at least four-fold change with P-value less than 0.05 were identified as DEGs.
genome build: MSU7
processed data files format and content: Excel file with FPKM values.

organism: Oryza sativa Japonica Group

source_name: Callus

growth_protocol: Seeds of TNG67 and IR64 were surface-sterilized in 70% ethanol for 1 min and rinsed with distilled water. The sterilized seeds were soaked in 2.5% sodium hypochlorite (NaClO; The Clorox Co., Oakland, CA, USA) containing 0.2% Tween 20 (Sigma-Aldrich, St. Louis, MO, USA) for 15 min in a rotator followed by washing with sterile ddH2O. After surface sterilization, seeds were sown on N6D media (N6 salt, Vitamin B5, 3% sucrose, 2.5 mg/L 2,4-D pH 5.8 0.4% gelsite) for callus induction.

extract_protocol:
Total RNA was extracted & quantified using Qubit RNA assay 100 ng RNA was used as starting material for each sample. Total RNA are treated with DNase I (Roche), and cleaned up with phenol-chloroform and precipitated with ethanol.
RNA–Seq libraries were prepared following standard Illumina protocols. Resulted libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2000 sequencers (at National Center for Genome Medicine, Academia Sinica). The quality of reads was checked with FastQC (Andrews, 2010), reads were mapped to Os-Nipponbare-Reference-IRGSP-1.0 using Bowtie (Langmead et al., 2009) allowing two mismatches and only unique alignments were retained. The resulted alignment file was processed and differential expression was calculated using Tophat (Langmead et al., 2009) to generate Fragments Per Kilo Base Per Million mapped reads (FPKM) per gene by applying 4-fold cut-off.

treatment_protocol: The callus samples were collected at different time points of culture starting with embryonic stage (T0).  N6D medium was used for callus induction of both cultivars; induced calli were transferred to fresh N6D medium for subsequent callus growth. Finally calli were transferred to REIII M2 medium (MS salt with vitamin, 1g/L casein hydrolysate, 3% sucrose, 3% sorbitol, 0.02 mg/L NAA, 2mg/L BAP, pH5.8 0.4% gelrite) for regeneration.

tag: rice cultivar

value: Tainung 67

tag: tissue culture stage

value: Successful Regeneration

value: TS


title: Retina Dawn rep3

source_name: Retina Dawn

value: Dawn

tag: tissue


title: AC_1month_rep1

description:
RNA from mouse x41 (treatment AC after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: whole lung

value: AC


title: U96hpf_l1

description: 96hpf larvae obtaiend from depleted uranium exposed adult

source_name: 96 hpf larvae

value: 96 hpf larvae

value: whole larvae

value: progeny of adult exposed fish


title: J2_RNA-seq

description: RNA-Seq

value: Subculture


title: Retina Dawn rep2


title: UbrainM_b2

value: adult

value: brain


title: Retina Day rep3


title: J1_RNA-seq

description: RNA-Seq

extract_protocol:
Rice calli were ground using pestle and mortar in the presence of liquid nitrogen for extraction of genomic DNA (gDNA) followed by purification using DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany).
To obtain fragments ranging between 50 and 350 bp the gDNA was sonicated. The fragmented DNA was then used for library preparation using Illumina's library preparation kits. Premethylated adapter ligated fragments were bisulfite converted using the EZ DNA methylation kit (Zymo Research). Resulted libraries were then subjected to PCR amplification prior to sequencing on the Illumina HiSeq 2000 sequencers at National Center for Genome Medicine at Academia Sinica. The genome size of rice is about 466 MB and sequencing was done in enough lanes to reach >20x per sample

value: Callus Induction


title: UbrainF_b5

value: wild type AB

value: 20µg/L depleted uranium


title: Retina Dawn rep1


title: AC_1month_rep5

description:
RNA from mouse x53 (treatment AC after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 month


title: J0_RNA-seq

description: RNA-Seq

source_name: Embryo

value: Embryo


title: AC_1month_rep3

description:
RNA from mouse x43 (treatment AC after 1 month)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: U96hpf_l3


title: AC_7days_rep3

description:
RNA from mouse x25 (treatment AC after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 7 days


title: AC_7days_rep1

description:
RNA from mouse x22 (treatment AC after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: AC_7days_rep5

description:
RNA from mouse x35 (treatment AC after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: U96hpf_l2


title: AC_7days_rep4

description:
RNA from mouse x31 (treatment AC after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: U2cells_r5

description: Two cells embryos obtained from depleted uranium exposed adult

source_name: 2 cells embryos

value: 2 cells embryos

value: whole embryo


title: U2cells_r3


title: U2cells_r1


title: CtestesM_g3

description: Testies dissected from non exposed adult males

value: testis


title: AC_7days_rep2

description:
RNA from mouse x24 (treatment AC after 7 days)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: whole lung


title: CtestesM_g5


title: AC_1day_rep4

description:
RNA from mouse x142 (treatment AC after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 day

value: AC


title: AC_1day_rep3

description:
RNA from mouse x134 (treatment AC after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: IS_RNA-seq

description: RNA-Seq

organism: Oryza sativa Indica Group

value: Indica Rice 64

value: Successful Regeneration

value: TS


title: IF_RNA-seq

description: RNA-Seq

value: Failed Regeneration

value: TF


title: j1_BS-seq

description: BS-seq

data_processing:
BS-Seq reads were aligned to the MSU7 genome using BS Seeker2
genome build: MSU7
processed data files format and content: Processed data (CGmap) is in text format.  column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

value: Tainung 67

value: Callus Induction


title: j2_BS-seq

description: BS-seq

value: Subculture


title: AC_1day_rep5

description:
RNA from mouse x144 (treatment AC after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: jF_BS-seq

description: BS-seq


title: JF_RNA-seq

description: RNA-Seq


title: CovaryF_g5

description: Ovaries dissected from non exposed adult females

value: adult

value: ovary

value: wild type AB

value: 20µg/L depleted uranium


title: CtestesM_g1


title: I0_RNA-seq

description: RNA-Seq

value: Embryo


title: CovaryF_g2


title: j0_BS-seq

description: BS-seq


title: CovaryF_g1


title: AC_1day_rep1

description:
RNA from mouse x131 (treatment AC after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv


title: CbrainM_b5

description: Brain dissected from non exposed adult males

value: brain


title: jS_BS-seq

description: BS-seq


title: I2_RNA-seq

description: RNA-Seq


title: 6CS+3AC_9months_rep5

description:
RNA from mouse x120 (treatment 6CS+3AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv

value: whole lung

value: 9 months


title: 6CS+3AC_9months_rep4

description:
RNA from mouse x119 (treatment 6CS+3AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: i0_BS-seq

description: BS-seq


title: 6CS+3AC_9months_rep3

description:
RNA from mouse x118 (treatment 6CS+3AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: AC_1day_rep2

description:
RNA from mouse x132 (treatment AC after 1 day)
mouse126_all_reads.csv
mouse126_filtered_reads.csv

value: 1 day

value: AC


title: I1_RNA-seq

description: RNA-Seq

value: Indica Rice 64


title: CbrainF_b5

description: Brain dissected from non exposed adult females


title: CbrainM_b1


title: iS_BS-seq

description: BS-seq

value: Successful Regeneration

value: TS


title: 6CS+3AC_9months_rep2

description:
RNA from mouse x113 (treatment 6CS+3AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: 6CS+3AC_9months_rep1

description:
RNA from mouse x112 (treatment 6CS+3AC after 9 months)
mouse126_all_reads.csv
mouse126_filtered_reads.csv
mouse126_filtered_9month_reads.csv


title: C96hpf_l3

description: 96hpf larvae obtaiend from non exposed adult

value: 96 hpf larvae

value: whole larvae

value: progeny of adult exposed fish


title: C96hpf_l1


title: i2_BS-seq

description: BS-seq

value: Subculture


title: C96hpf_l2


title: C2cells_r4

description: Two cells embryos obtained from non exposed adult

value: 2 cells embryos

value: whole embryo


title: siTUNAR + 1-AKP #2

city: Mölndal

first: Alex-Xianghua

last: Zhou

state: - If in U.S, Select a State -

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca R&D Gothenburg

data_processing:
Data were processed by BGI-Tech
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file. Those FASTQ files are the original data provided for users, and they include the detailed read sequences and the read quality information.
Filtering steps are as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define low quality base as the base whose sequencing quality is no more than 5.)
Clean reads were mapped to reference sequences and/or reference gene set. BWA (Li, H. and Durbin, R., 2009) was used to map clean reads to genome reference and Bowtie (Langmead B, et al., 2009) was used to gene reference.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N.,  2011) computes maximum likelihood abundance estimates using the Expectation-Maximization (EM) algorithm for its statistical model, including  the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are  isoforms of the same gene.
Genome_build: Human GRCh37/hg19
Supplementary_files_format_and_content: txt files include FPKM values for each sample.

source_name: EndoC-βH1 cell line

growth_protocol: Human EndoC-βH1 Cells were cultured on Matrigel-fibronectin–coated (100 μg/mL and 2 μg/mL, respectively, Sigma-Aldrich) plates in DMEM containing 5.5 mM glucose, 2% BSA fraction V (Roche Diagnostics), 50 μM 2-mercaptoethanol, 10 mM nicotinamide (Calbiochem), 5.5 μg/mL transferrin (Sigma-Aldrich), 6.7 ng/mL selenite (Sigma-Aldrich), 100 U/mL penicillin, and 100 μg/mL streptomycin.

extract_protocol:
Total RNA of human EndoC-βH1 cells was extracted using QIAGEN RNeasy mini kit with DNase treatment.
PolyA-tailed RNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the polyA-tailed RNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

treatment_protocol: EndoC-βH1 cells were transfected with siRNAs using Lipofectamine RNAiMAX (Thermo Fisher Scientific). AllStars Negative Control siRNA (QIAGEN) was used as control. FlexiTube pre-designed siRNAs targeting TUNAR were purchased from QIAGEN. After two days of transfection, cells were treated with 1-AKP 5 uM or DMSO (1:1000) for 24 hours.

tag: passages

tag: sirna

value: TUNAR siRNAs


title: siTUNAR + 1-AKP #3


title: C2cells_r2

value: wild type AB


title: CbrainM_b4

value: adult

value: 20µg/L depleted uranium


title: siTUNAR + 1-AKP #1


title: Neg siRNA + 1-AKP #3

value: Scramble siRNA


title: C2cells_r1


title: Neg siRNA + 1-AKP #2


title: sample6-4

city: Bergen

first: Kai

middle: Kristoffer

last: Lie

state: Hordaland

address: Pobox 2029 Nordnes

department: Feed Safety

country: Norway

institute: Institute of Marine research

data_processing:
Image analysis and base calling were both performed using Illumina's RTA software version 1.17.21.3. Reads were filtered to remove those with low base call quality using Illumina's default chastity criteria.
Sequence adaptors were removed using Cutadapt (Martin, 2011) and default parameters.
Bad reads and sequence regions were filtered and trimmed using Sicle (https://github.com/najoshi/sickle) with a 40 bp minimum remaining sequence length, Sanger quality of 20 and no 5’ end trimming
Prior to assembly, quality of reads were investigated using fastQC version 0.9.2 (The FastQC project, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure improvement compared to the raw data
Each gut segment RNA-seq library was mapped individually to the de novo labrus genome assembly (European Nucleotide Achive accession number: PRJEB13687) using the Tophat short read aligner (Langmead et al., 2009).
Counted reads of the intestinal segment samples were further processed and analyzed using the Bioconductor - DESeq2 analysis package (Love et al., 2014). Genes of which read counts < 1 in all samples were initially excluded from further analysis prior to normalization and differential expression (DE) analysis leaving a total of 27 392 transcripts for further downstream analysis.
Transcripts abundance were estimated using the FeatureCounts (Liao et al., 2014) software embed in the Subread package (http://subread.sourceforge.net/). An average of 67 ± 3 % of the reads in each sample were mapped to the de novo genome assembly by Tophat and counted by FeatureCounts.
Genome_build: ENA accession number PRJEB13687
Supplementary_files_format_and_content: The processed data file is a tab separated text file (txt) file containing normalized read counts.

organism: Labrus bergylta

source_name: Labrus bergylta intestinal segment

growth_protocol: Ballan wrasse were sampled from a commercial farm in Øygarden

extract_protocol:
RNA was extracted using a BioRobot® EZ1 and RNA Tissue Mini Kit (Qiagen, Hilden, Germany)
Libraries were prepared using TruSeq RNA v2 reagents (Illumina) according to manufacturer’s instructions.

treatment_protocol: RNA was extracted from four segments from different fish six fish. The sample number is given as Sample_Lie-wrasseRNA-X-X, where the first number represents the fish number and the second represents the segment. For example Sample_Lie-wrasseRNA-1-4. is take from the fourth segment in fish number one.

tag: individual

value: fish number 6

value: intestine

tag: intestinal segment


title: iF_BS-seq

description: BS-seq

value: Failed Regeneration

tag: time point

value: TF


title: sample6-2


title: siTUNAR #3

tag: treatment

value: DMSO


title: sample6-3


title: sample6-1


title: sample5-4

value: fish number 5


title: siTUNAR #2


title: Neg siRNA #3


title: siTUNAR #1


title: CbrainF_b3

value: brain


title: i1 _BS-seq

description: BS-seq

value: Indica Rice 64

value: Callus Induction


title: CbrainF_b2


title: sample5-2


title: sample5-3


title: Neg siRNA #1


title: sample5-1


title: Neg siRNA #2


title: sample4-4

value: fish number 4


title: RNA-seq_Uninduced_ATMi_treated

city: Milan

first: Fabrizio

last: d'Adda di Fagagna

state: Mi

address: Via Adamello 16

country: Italy

institute: IFOM - The FIRC Institute of Molecular Oncology

description: Barcode: ACTGAT

data_processing:
BLISS: reads were mapped to the human genome (GRCh37/hg19) using BWA. At most one mismatch per read was allowed and duplicated reads were removed using rmdup of SAMtools. All reads uniquely mapping were scanned for the presence of the proximal linker barcode with ad-hoc scripts written in bash and R languages. Finally, all reads within 100 bp of the AsiSI sites identified by BEDtools intersect, were considered on target and retained for further analysis. In order to rank the cutting efficiency at individual AsiSI sites, a four steps normalization procedure was applied. In order to identify the AsiSI sites that where cut upon AsiSI induction, we compared the cutting efficiency at individual AsiSI sites in induced and uninduced samples.
RNA-seq: reads were aligned to the GRCh37/hg19 assembly human reference genome using the STAR aligner. For differential testing we used the package DESeq2, in particular we used the regularized-logarithm transformation (rlog) that stabilizes the variance across the mean.
Bru-seq: reads were aligned to the human ribosomal DNA complete repeating unit (U13369.1) using Bowtie (v0.12.8) and the reads that remained unaligned were mapped to the human genome build hg19/GRCh37 TopHat (v1.4.1). Bru-seq data from induced samples were compared to uninduced samples and fold differences determined.
CAGE: data were analysed with the CAGEr package. After bam file preprocessing and quality (mappingQ ≥ 20) filtering, CAGE tags were normalized and TSSs distance-based clustering (20 bp distance) was performed. Then aggregate tag clusters across all CAGE datasets were computed and finally promoters were grouped into expression classes by applying k-means unsupervised clustering algorithm.
gamma-H2AX ChIP-seq: reads were mapped to the human genome (GRCh37/hg19) using BWA.Clusters were generated by “connecting” γH2AX peaks (windows of 250 bp or multiples thereof in which γH2AX ChIPseq signal is significantly  zscore > 3  enriched over background) if their distance is less than a “window size” n. In other words, two adjacent γH2AX peaks A and B, whose midpoints are m nucleotides apart on the same chromosome, will be collapsed into a single cluster  covering peaks A, B and the distance in between  if m is smaller than or equal to n. The cluster may be further extended if there is another gamma-H2AX peak C equal to or less than n nucleotides away from the midpoint of peaks A or B (and so on). If, for a given gamma-H2AX peak C, the distance to its nearest neighbour peak is bigger than n (or if there were no other peak on that chromosome), the resulting cluster will be equivalent to C itself. Finally, we introduced a gamma-H2AX rank score as an indicator of the likelihood of a given site to be in a cleaved state upon AsiSI induction.
RNAPII ChIP-seq: preliminary sequencing quality assessment was performed using FastQC. The samples passing the quality standards were aligned on the human genome (GRCh37/hg19) using BWA. In order to maintain the collinearity between the read signal and the protein occupancy on the genome, multiple-matching reads were eliminated using ad hoc SAMtools and UNIX shell integrated scripts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were generated using the BEDtools suite
Supplementary_files_format_and_content: 214_AsiSI_BLISS_hg19.bed: Genomic coordinates on GRCh37/hg19 genome build of the 214 AsiSI cut sites detected by BLISS.

source_name: DiVA (AsiSI-ER-U2OS) cells

growth_protocol: DIvA (AsiSI-ER-U20S) cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) without phenol red, supplemented with glutamine, pyruvate, HEPES and 10% fetal bovine serum (FBS, Euroclone). Cells were grown at 37°C under a humidified atmosphere with 5% CO2 and selected on a semi regular basis with puromycin at a final concentration of 1 μg/ml.

extract_protocol:
BLISS: Briefly, after fixation, cells were lysed and submitted to in situ DNA ends blunting (with Quick Blunting kit, NEB), followed by in situ DNA ends ligation with BLISS linker. After washing, genomic DNA was extracted and sonicated with Covaris S220 (10% duty factor, 175W peak incident power, 200 Cycles/burst, 105s) to obtain a pool of 300 bp fragments. Afterwards, fragmented DNA was in vitro transcribed using MessageAmpII kit (Ambion) for 14h at 37°C. After RNA purification and ligation of the 3’ Illumina adapter, the RNA was reverse-transcribed.
CAGE: we used the mirVana Kit (Ambion) according to the manufacturer’s instructions for the collection of total RNA.
RNA-seq: total RNA was isolated using the mirVana Kit (Ambion), according to the manufacturer’s instructions.
RNA-seq of DMSO- and ATMi-treated cells: total RNA was isolated using the RNeasy Kit (QIAGEN), according to the manufacturer’s instructions.
Bru-seq: cells were incubated at different times after AsiSI induction in 2 mM bromouridine (Bru) for 30 min and total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
ChIP-seq: Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with specific antibody against total RNAPII (Millipore, 05-623) or RNAPII pSer2 (Abcam, 5095).
BLISS: The final step of library indexing and amplification was performed using the TruSeq Small RNA Library Prep Kit (Illumina, RS-200-0012).
Bru-seq: strand-specific DNA libraries with the Illumina TruSeq Kit (Illumina).
ChIP-seq: library preparation and sequencing using standard Illumina TruSeq for HiSeq 2000 reagents.
RNA-seq: strand-specific library preparation was performed using ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre). rRNAs were removed using Ribo-Zero Magnetic Kit (Epicentre).
RNA-seq of DMSO- and ATMi-treated cells: strand-specific library preparation was performed using Illumina TruSeq kit.
CAGE: cap analysis of gene expression (CAGE) for high-throughput gene expression profiling was performed following nAnT-iCAGE protocol workflow (Murata et al., 2014).

treatment_protocol:
For AsiSI-dependent DSB induction, cells were treated with 300 nM 4-Hydroxytamoxifen (4OHT, Sigma; H7904) for 4h. For experiments with ATM inhibitor, cells were treated with DMSO or ATMi (KU-60019; Sigma SML1416) at a final concentration of 10 μM simultaneously with 4OHT treatment.
BLISS was performed on DIvA (AsiSI-ER-U20S) cells mock treated or induced with 4-OHT using one coverslip per condition (11 millimiters), containing ~30.000 adherent cells. 4 h after induction, cells were washed with PBS and fixed in 4% PFA for 10 minutes at room temperature.
Cells were treated with DMSO or ATMi (KU-60019; Sigma SML1416) at a final concentration of 10 μM simultaneously with 4OHT treatment for 4 hours.

tag: cell line

value: DiVA (AsiSI-ER-U2OS) cells

tag: cell type

value: U2OS-derived cells

value: Uninduced, ATMi


title: sample4-3


title: RNA-seq_Induced_ATMi_treated

description: Barcode: GTCCGC

value: Induced; ATMi


title: Neg siRNA + 1-AKP #1


title: sample4-2


title: RNA-seq_Uninduced_DMSO_treated

description: Barcode: TAGCTT

value: Uninduced, DMSO


title: RNA-seq_Induced_DMSO_treated

description: Barcode: ACTTGA

value: Induced; DMSO


title: sample3-3

value: fish number 3


title: CAGE_Uninduced

value: Uninduced


title: sample3-2

value: intestine


title: CAGE_Induced

value: Induced


title: sample3-1


title: Bru-seq_Uninduced

data_processing:
Library strategy: Bru-seq
BLISS: reads were mapped to the human genome (GRCh37/hg19) using BWA. At most one mismatch per read was allowed and duplicated reads were removed using rmdup of SAMtools. All reads uniquely mapping were scanned for the presence of the proximal linker barcode with ad-hoc scripts written in bash and R languages. Finally, all reads within 100 bp of the AsiSI sites identified by BEDtools intersect, were considered on target and retained for further analysis. In order to rank the cutting efficiency at individual AsiSI sites, a four steps normalization procedure was applied. In order to identify the AsiSI sites that where cut upon AsiSI induction, we compared the cutting efficiency at individual AsiSI sites in induced and uninduced samples.
RNA-seq: reads were aligned to the GRCh37/hg19 assembly human reference genome using the STAR aligner. For differential testing we used the package DESeq2, in particular we used the regularized-logarithm transformation (rlog) that stabilizes the variance across the mean.
Bru-seq: reads were aligned to the human ribosomal DNA complete repeating unit (U13369.1) using Bowtie (v0.12.8) and the reads that remained unaligned were mapped to the human genome build hg19/GRCh37 TopHat (v1.4.1). Bru-seq data from induced samples were compared to uninduced samples and fold differences determined.
CAGE: data were analysed with the CAGEr package. After bam file preprocessing and quality (mappingQ ≥ 20) filtering, CAGE tags were normalized and TSSs distance-based clustering (20 bp distance) was performed. Then aggregate tag clusters across all CAGE datasets were computed and finally promoters were grouped into expression classes by applying k-means unsupervised clustering algorithm.
gamma-H2AX ChIP-seq: reads were mapped to the human genome (GRCh37/hg19) using BWA.Clusters were generated by “connecting” γH2AX peaks (windows of 250 bp or multiples thereof in which γH2AX ChIPseq signal is significantly  zscore > 3  enriched over background) if their distance is less than a “window size” n. In other words, two adjacent γH2AX peaks A and B, whose midpoints are m nucleotides apart on the same chromosome, will be collapsed into a single cluster  covering peaks A, B and the distance in between  if m is smaller than or equal to n. The cluster may be further extended if there is another gamma-H2AX peak C equal to or less than n nucleotides away from the midpoint of peaks A or B (and so on). If, for a given gamma-H2AX peak C, the distance to its nearest neighbour peak is bigger than n (or if there were no other peak on that chromosome), the resulting cluster will be equivalent to C itself. Finally, we introduced a gamma-H2AX rank score as an indicator of the likelihood of a given site to be in a cleaved state upon AsiSI induction.
RNAPII ChIP-seq: preliminary sequencing quality assessment was performed using FastQC. The samples passing the quality standards were aligned on the human genome (GRCh37/hg19) using BWA. In order to maintain the collinearity between the read signal and the protein occupancy on the genome, multiple-matching reads were eliminated using ad hoc SAMtools and UNIX shell integrated scripts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were generated using the BEDtools suite
Supplementary_files_format_and_content: 214_AsiSI_BLISS_hg19.bed: Genomic coordinates on GRCh37/hg19 genome build of the 214 AsiSI cut sites detected by BLISS.


title: sample2-4

value: fish number 2


title: Bru-seq_Induced_240min_after_induction

tag: time


title: sample2-3


title: Bru-seq_Induced_150min_after_induction


title: Bru-seq_Induced_60min_after_induction


title: sample1-4

value: fish number 1


title: sample2-1


title: Bru-seq_Induced_30min_after_induction


title: RNA-seq_Uninduced


title: sample2-2


title: RNAPII_input DNA_Uninduced

tag: chip antibody


title: RNA-seq_Induced


title: sample1-2


title: sample1-3


title: sample4-1


title: sample3-4


title: sample1-1


title: IgG_iRIP-Seq_Rep2

city: Beijing

first: Wanjin

last: Li

address: No. 38, Xueyuan road.

institute: Peking University Health Science Center

description: IgG data of iRIP-Seq data replicate1.

data_processing:
base-calling: Phred.
alignment: bowtie2 for ChIP-Seq; TopHat2 for RIP-Seq.
peak-calling: MACS2 for ChIP-Seq; CIMS and Piranha for RIP-Seq.
ChIPseeker for the annotation of peaks.
Genome_build: ChIP-Seq: hg19; RIP-Seq: hg38.
Supplementary_files_format_and_content: bigwig (bw): The signal intensity of binding. Bed files for RIP-Seq.

source_name: MCF-7 Cell

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
chloroform extraction
One microliter of glycogen (10 mg/ml stock) was added and RNAs were precipitated by adding 3 volumes of ethanol and dissolved in 10.5 μl water. The recovered RNAs were used to generate paired-end sequencing library with Truseq small RNA library preparation kit (Illumina) following the manufacturer’s instruction.


title: RNAPII-Ser2_ChIPSeq_Uninduced

value: RNAPII_Ser2 antibody (Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody; vendor:Abcam; clonality:Rb Polyclonal; catalog number:ab5095; lot:GR124547-2)


title: IgG_iRIP-Seq_Rep1

description: IgG data of iRIP-Seq data replicate1.


title: RNAPII-Ser2_ChIPSeq_Induced


title: totRNAPII_ChIPSeq_Uninduced

value: RNAPII_CTD4H8 antibody (Anti-RNA polymerase II antibody, clone CTD4H8; vendor:Millipore; clonality:M MONOCLONAL (clone CTD4H8); catalog number:05-623; lot:2282159)


title: FOXN3_iRIP-Seq_Rep1

description: iRIP-Seq data for FOXN3 replicate1.

treatment_protocol: Treated with antibodies against FOXN3.


title: FOXN3_iRIP-Seq_Rep2

description: iRIP-Seq data for FOXN3 replicate2.


title: gH2AX_input DNA_Uninduced


title: totRNAPII_ChIPSeq_Induced


title: SIN3A_ChIP-Seq

description: ChIP-Seq data for SIN3A.

extract_protocol:
Chromatin DNAs precipitated by polyclonal antibodies against SIN3A were purified with the Qiagen PCR purification kit.
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 10e7 cells were used for each ChIP-seq assay. Chromatin DNAs precipitated by polyclonal antibodies against SIN3A were purified with the Qiagen PCR purification kit.

treatment_protocol: Treated with antibodies against SIN3A.


title: FOXN3_ChIP-Seq

description: ChIP-Seq data for FOXN3.

extract_protocol:
Chromatin DNAs precipitated by polyclonal antibodies against FOXN3 were purified with the Qiagen PCR purification kit.
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 10e7 cells were used for each ChIP-seq assay. Chromatin DNAs precipitated by polyclonal antibodies against FOXN3 were purified with the Qiagen PCR purification kit.


title: gH2AX_ChIPSeq_Uninduced

value: gH2Ax antibody (Anti-gamma H2A.X (phospho S139) antibody; vendor:Abcam; clonality:Rb Polyclonal; catalog number:ab2893; lot:GR220924-5)


title: gH2AX_input DNA_Induced


title: BLISS_Uninduced

description: Barcode: CTTGTA

data_processing:
Library strategy: BLISS
BLISS: reads were mapped to the human genome (GRCh37/hg19) using BWA. At most one mismatch per read was allowed and duplicated reads were removed using rmdup of SAMtools. All reads uniquely mapping were scanned for the presence of the proximal linker barcode with ad-hoc scripts written in bash and R languages. Finally, all reads within 100 bp of the AsiSI sites identified by BEDtools intersect, were considered on target and retained for further analysis. In order to rank the cutting efficiency at individual AsiSI sites, a four steps normalization procedure was applied. In order to identify the AsiSI sites that where cut upon AsiSI induction, we compared the cutting efficiency at individual AsiSI sites in induced and uninduced samples.
RNA-seq: reads were aligned to the GRCh37/hg19 assembly human reference genome using the STAR aligner. For differential testing we used the package DESeq2, in particular we used the regularized-logarithm transformation (rlog) that stabilizes the variance across the mean.
Bru-seq: reads were aligned to the human ribosomal DNA complete repeating unit (U13369.1) using Bowtie (v0.12.8) and the reads that remained unaligned were mapped to the human genome build hg19/GRCh37 TopHat (v1.4.1). Bru-seq data from induced samples were compared to uninduced samples and fold differences determined.
CAGE: data were analysed with the CAGEr package. After bam file preprocessing and quality (mappingQ ≥ 20) filtering, CAGE tags were normalized and TSSs distance-based clustering (20 bp distance) was performed. Then aggregate tag clusters across all CAGE datasets were computed and finally promoters were grouped into expression classes by applying k-means unsupervised clustering algorithm.
gamma-H2AX ChIP-seq: reads were mapped to the human genome (GRCh37/hg19) using BWA.Clusters were generated by “connecting” γH2AX peaks (windows of 250 bp or multiples thereof in which γH2AX ChIPseq signal is significantly  zscore > 3  enriched over background) if their distance is less than a “window size” n. In other words, two adjacent γH2AX peaks A and B, whose midpoints are m nucleotides apart on the same chromosome, will be collapsed into a single cluster  covering peaks A, B and the distance in between  if m is smaller than or equal to n. The cluster may be further extended if there is another gamma-H2AX peak C equal to or less than n nucleotides away from the midpoint of peaks A or B (and so on). If, for a given gamma-H2AX peak C, the distance to its nearest neighbour peak is bigger than n (or if there were no other peak on that chromosome), the resulting cluster will be equivalent to C itself. Finally, we introduced a gamma-H2AX rank score as an indicator of the likelihood of a given site to be in a cleaved state upon AsiSI induction.
RNAPII ChIP-seq: preliminary sequencing quality assessment was performed using FastQC. The samples passing the quality standards were aligned on the human genome (GRCh37/hg19) using BWA. In order to maintain the collinearity between the read signal and the protein occupancy on the genome, multiple-matching reads were eliminated using ad hoc SAMtools and UNIX shell integrated scripts.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bigwig files were generated using the BEDtools suite
Supplementary_files_format_and_content: 214_AsiSI_BLISS_hg19.bed: Genomic coordinates on GRCh37/hg19 genome build of the 214 AsiSI cut sites detected by BLISS.


title: gH2AX_ChIPSeq_Induced


title: SK-Hep1 TuD rep2

city: San Diego

first: Vivek

last: Kaimal

state: CA

address: 10614 Science Center Dr.

department: Bioinformatics

institute: Regulus Therapeutics

description: Gene expression data from SK-Hep1 HCC cell line expressing miR-17 TuD

data_processing:
FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), a quality control tool for high throughput sequence data, was used for checking q-scores and reads were not trimmed prior to alignments.
The data were aligned against UCSC human genome version hg19 using STAR aligner (Dobin, A. et al., Bioinformatics, 2013).
From BAM files, gene-level counts of uniquely mapped reads were computed using SAMTools (Li H. et al, Bioinformatics, 2009) and HTSeq v0.5.4p5 (Anders S. et al, bioRxiv preprint, 2014).
Gene level counts were then normalized with the R/Bioconductor package limma (Smyth, G. K., Springer, 2005) using the voom (Law CW, et al. Genome Biology, 2014) /variance stabilization method
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with gene counts for each sample
Supplementary_files_format_and_content: tab-delimited text file with normalized Log2 transformed data matrix

source_name: SK-Hep1 HCC cell line, miR-17 TuD

growth_protocol: HepG2 or SK-Hep1 HCC cells were grown in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA were prepared from cells using the mRNA isolation RNeasy Mini kit (Qiagen) according to the manufacturer's instructions. RNA quality was assessed using BioAnalyzer (Agilent). Illumina’s TruSeq RNA Sample Preparation v2 kit was used to construct libraries. Briefly, 150ng of total RNA input was used. The libraries were quantified using KAPA library quantification kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HepG2 or SK-Hep1 HCC cells were incubated with viral particles encoding miR-17 or NC TuD (Sigma-Aldrich) at multiplicity of infection 5 in medium with 10.0 μg/mL polybrene at 37°C for 48 hours, Cells were then selected by culturing in medium supplemented with 1.0 μg/mL puromycin (Life Technologies). After 2 weeks in culture, puromycin-resistant colonies were pooled to establish stable cell lines.

value: SK-Hep1 HCC cell line

tag: expressing

value: miR-17 TuD


title: HepG2 NC TuD rep2

description: Gene expression data from HepG2 HCC cell line expressing NC TuD

source_name: HepG2 HCC cell line, NC TuD

value: HepG2 HCC cell line

value: NC TuD


title: BLISS_Induced

description: Barcode: GCCAAT

value: DiVA (AsiSI-ER-U2OS) cells

value: U2OS-derived cells


title: HepG2 NC TuD rep3


title: SK-Hep1 NC TuD rep1

description: Gene expression data from SK-Hep1 HCC cell line expressing NC TuD

source_name: SK-Hep1 HCC cell line, NC TuD


title: SK-Hep1 TuD rep1


title: RNAPII_input DNA_Induced


title: HepG2 NC TuD rep1


title: HepG2 TuD rep2

description: Gene expression data from HepG2 HCC cell line expressing miR-17 TuD

source_name: HepG2 HCC cell line, miR-17 TuD


title: HepG2 TuD rep3


title: HepG2 TuD rep1


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_9

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

data_processing:
Quality checking with FASTQC
Alignment and quantification with R package Rsubread
FPKM normalization with edgeR and limma
TPM normalization from the FPKM values
log2 values of the TPM normalized gene counts
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Raw sequence files as .fastq.gz, TPM-log2 normalized gene count processed file is a tab-delimited .txt file

source_name: Breast

growth_protocol: Human mammary epithelial cells, grown in Stemgent WIT-P culture medium at 3% CO2 and 37°C

extract_protocol:
Cells were scraped into RNA-Later and stored on ice until processing.  Then RNA was isolated from pelleted cells using a Qiagen Rneasy mini kit (with Rnase-free DNase set) and QIAshredders.
Illumina TruSeq stranded mRNA kit

treatment_protocol: Genes were introduced for over-expression by way of adenovirus.  Cells were infected with MOI 500 Adenovius for 18 hours for GFP18, AKT, BAD, HER2, IGF1R and RAF1; for 30 hours for GFP30 and KRAS(G12V).

value: Human mammary epithelial cells


title: Input_ChIP-Seq

description: Input data of ChIP-Seq.

extract_protocol:
Chromatin DNAs were purified with the Qiagen PCR purification kit.
MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum. Approximately 5 x 10e7 cells were used for each ChIP-seq assay. Chromatin DNAs were purified with the Qiagen PCR purification kit.


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_3


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_5


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_1


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_8


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_6


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_2


title: GFP control, overexpressed in HMEC cells GFP30_control_9


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_7


title: human KRAS G12V mutant form overexpressed in HMEC cells KRAS_G12V_overexpressed_4


title: GFP control, overexpressed in HMEC cells GFP30_control_8


title: GFP control, overexpressed in HMEC cells GFP30_control_6


title: GFP control, overexpressed in HMEC cells GFP30_control_5


title: SK-Hep1 NC TuD rep2


title: GFP control, overexpressed in HMEC cells GFP30_control_4


title: GFP control, overexpressed in HMEC cells GFP30_control_3


title: GFP control, overexpressed in HMEC cells GFP30_control_1


title: GFP control, overexpressed in HMEC cells GFP30_control_2


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_6


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_3


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_5


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_2


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_5


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_1


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_6


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_4


title: GFP control, overexpressed in HMEC cells GFP30_control_7


title: Hi-C_washoff-2days_rep1

city: San Francisco

first: Elphege

last: Nora

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

data_processing:
Hi-C. We mapped the sequence of Hi-C molecules to reference mouse genome assembly mm9 using Bowtie 2.2.8 and the iterative mapping strategy, as described in  (Imakaev et al., 2012; Lajoie et al., 2015). Upon filtering PCR duplicates and reads mapped to multiple or zero locations, we aggregated the reads pairs into 20kb and 100kb genomic bins to produce Hi-C contact matrices. To remove the short-range Hi-C artifacts - unligated and self-ligated Hi-C molecules - we ignored the contacts mapping to the same or adjacent genomic bins in all downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: 20kb and 100kb ICE corrected matrices are provided as .cool files, which can be handled with the Cooler package https://github.com/mirnylab/cooler

source_name: mouse ES cells

extract_protocol: ChIP libraries were prepared using standard Illumina protocols; RNA-seq libraries were assembled using the non-stranded kit E7530L from NEB; 5C (in situ ligation) and Hi-C (HindIII dilution ligation) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of Nora et al. 2017 Cell

tag: strain

value: CTCF-AID, Tir1

tag: restriction enzyme

value: HindIII


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_3


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_6


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_5


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_4


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_2


title: human HER2/ERBB2, overexpressed in HMEC cells HER2_overexpressed_5


title: -/- rep 3

city: Cardiff

first: Fraser

last: Young

address: Maindy Road

department: Neuroscience and Mental Health Research Institute

country: United Kingdom

institute: Cardiff University

description: all.markdup.featurecount

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mm10 (GRCm38) whole genome using BWA v0.5.9
Individual gene read counts were calculated using FeatureCounts v1.4.6
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Single tab delimited text file containing read counts for all 6 samples matched to Ensembl ID

source_name: Neural progenitor cells

growth_protocol: mESCs were maintained under routine culture conditions (0.1% gelatin-coated plates in GMEM + 10% FBS + LIF)

extract_protocol:
RNA was extracted on day 8 of differentiation and purified using the PureLink RNA Mini Kit (Thermofisher Scientific). TruSeq Stranded mRNA kit (Illumina) was used to prepare libraries from 1 µg RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: ESCs were seeded at 10 000 cells/cm2 in gelatin-coated 6 well plates and cultured in N2B27 medium. Differentiation medium was supplemented with 100 nM LDN193189, 10 µM SB431542 from days 0 to 4, 1 µM XAV939 from day 0 to 6  and 1 µM cyclopamine between days 2 and 10. On day 5  of differentiation, neural progenitor cells were dissociated using Trypsin/EDTA and replated onto poly-D-lysine/laminin coated surface at a density of 50,000 cells/cm2 for neuronal differentiation and maturation.

tag: genotype/variation

value: ESC-derived neural progenitor cells

tag: day of differentiation

value: day 8


title: -/- rep 1

description: all.markdup.featurecount


title: human HER2/ERBB2, overexpressed in HMEC cells HER2_overexpressed_4


title: flox/flox rep 3

description: all.markdup.featurecount

value: flox/flox


title: flox/flox rep 2

description: all.markdup.featurecount


title: human HER2/ERBB2, overexpressed in HMEC cells HER2_overexpressed_2


title: flox/flox rep 1

description: all.markdup.featurecount


title: MG-83

first: Manu

last: Dubin

address: Dr. Bohr-Gasse 3

institute: Gregor Mendel Institute, Austrian Academy of Sciences

data_processing:
Casava versions 1.7 and 1.8.2  were used for base-calling
Reads were aligned to the reference genome Lj3.0 using using NexGenMap version 0.4.12 with the following settings -p -i 0.90 -R 45 --bs-mapping --silent-clip
Genome_build: Genome_build: Lotus japonicus v3.0 (Lj3.0)
Supplementary_files_format_and_content: A TSV (tab separated values) detailing the methylation levels at each cytosine was generated using the methratio.py script from the BSMAP (version 2.73) using the -z and -u flags

organism: Lotus japonicus

source_name: aerial tissue

growth_protocol: Seeds were sown on soil moist filter paper and allowed to germinate. Seedlings were then transfered to single pots transferred to a greenhouse set at 20C under long day conditions (04:00-20:00) and individual seedlings were transplanted to single pots after one week. After 6 weeks growth the arial tissues of the plant were harvested and flash frozen in liquid nitrogen.

extract_protocol:
Total DNA was extracted from frozen tissue using the Macherey-Nagel Nucleomag96 Plant kit according to the manufacturer's instructions
Libraries were prepared according to Lister et al., 2008 (Cell) with the following modifications: Bisulfite conversion was performed using Qiagen epitech kit. PCR amplification was done using KAPA HIFI Uracil plus polymerase together with bar-coded primers (containing Illumina Tru-seq barcodes 1-48) to allow muiltiplexing.

tag: accession

value: leaf

tag: age

value: 21 weeks old


title: MG-85

tag: tissue

value: 22 weeks old


title: MG-93

value: 25 weeks old


title: MG-92

value: 23 weeks old


title: human BAD, overexpressed in HMEC cells BAD_overexprewssed_1


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_3


title: Hi-C_washoff-2days_rep2

tag: genotype


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_1


title: MG-79

value: 20 weeks old


title: -/- rep 2

description: all.markdup.featurecount


title: human HER2/ERBB2, overexpressed in HMEC cells HER2_overexpressed_1


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_6


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_5


title: MG-78b

value: 19 weeks old


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_3


title: MG-75

value: 17 weeks old


title: MG-78

value: 18 weeks old


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_4


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_1


title: MG-27

value: 14 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_12


title: MG-34

value: 15 weeks old


title: human AKT1, overexpressed in HMEC cells AKT1_overexpressed_4

value: Human mammary epithelial cells


title: MG-25

value: 13 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_11


title: GFP control, overexpressed in HMEC cells GFP18_control_10


title: MG-22

value: 12 weeks old


title: MG-20

value: 11 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_9


title: MG-16

value: 10 weeks old


title: MG-132

value: 9 weeks old


title: MG-92b

value: leaf

value: 24 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_7


title: MG-107

value: 8 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_8


title: GFP control, overexpressed in HMEC cells GFP18_control_6


title: MG-101

value: 7 weeks old


title: MG-10

value: 6 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_5


title: humanIGF1R, overexpressed in HMEC cells IGF1R_overexpressed_2


title: InVitro031212_MNaseSeq

city: La Jolla

first: Graham

last: McVicker

address: 10010 N Torrey Pines Rd

institute: Salk Institute

description:
MNase-seq on in vitro reconstituted nucleosomes. Histone octamers were isolated from chicken erythrocytes and reconstituted with genomic DNA from Drosophila S2 cells
solid0774_20120327_PE_WIDOM_28_WIDOM_031212_RLM_S2_InVit

data_processing:
Paired-end SOLiD Reads were aligned to the dm3 Drosophila melanogaster reference genome using BioScope
Only uniquely mapping, paired DNA fragments, and read pairs with inferred insert size outside of the range 101-191 were discarded
Midpoints of mapped reads pairs were used as estimates of nucleosome midpoints (dyads)
Genome_build: dm3
Supplementary_files_format_and_content: counts of nucleosome midpoints in wiggle format

source_name: in vitro reconstituted chromatin

growth_protocol: The cells were cultured in their recommended culture media at 24 °C. S2 cells were cultured in Schneider's Drosophila medium (Invitrogen) supplemented with 10% FCS (Hyclone); Cme-L1 cells were maintained in M3 (sigma-aldrich) + 2% FCS + 5 µg/ml insulin (sigma) + 2.5% fly extract, while ML-DmD11, ML-DmD20 and ML-DM17 cells were maintained in M3+BPYE + 10% FCS + 10 µg/ml insulin.

extract_protocol:
For in vivo extraction, ~100 million cells were collected from healthy cell cultures, pelleted and washed with ice-cold PBS. Cells were resuspended in NP-40 lysis buffer (10 mM Tris-Cl, pH 7.4; 10 mM NaCl; 3 mM MgCl2; 0.5% NP-40; 0.15 mM spermine; 0.5 mM spermidine). PMSF and BZA (Sigma) were added to final concentrations of 1 mM and 0.4 mM respectively. Cells were lysed by a 5-minute incubation on ice, the nuclei were pelleted and then washed once with PBS. After gentle resuspension in MNase digestion buffer (10 mM Tris-Cl, pH 7.4; 15 mM NaCl; 60 mM KCl; 0.15 mM spermine; 0.5 mM spermidine; 1 mM CaCl2), chromatin was digested with Micrococcal nuclease (Sigma N3755) for 10 minutes at room temperature. Digestion was stopped with MNase stop solution (0.25 M EDTA, 5% SDS added to a final ratio of 1:10 buffer volume) and 5 M NaCl (added to a ratio of 1:5 buffer volume). MNase-digested DNA was isolated from histones and other DNA binding proteins by phenol/chloroform extraction and ethanol precipitation. 10 mg/mL RNAse was added and the purified DNA was incubated for 30 minutes at 37* C to remove any residual RNA. Digested DNA was sized by running on a 3% agarose gel (NuSieve Lonza). Nucleosomal DNA bands were visualized by UV illumination and mononucleosomal DNA (mnDNA) corresponding in size to 150 bp was excised from the gel. mnDNA was recovered by a mild “crush and soak” protocol [17]. Briefly, excised gel slices were covered in crush and soak buffer (300mM NaOAc and 1mM EDTA, pH 8.0), and crushed with a microtube pestle inside the centrifuge tube. The gel and buffer slurry was then incubated at room temperature for 48 hours on a bench rocker to allow DNA to passively diffuse into the buffer. Solubilized DNA was separated from the agarose using spin-filters (Amicon Ultrafree-CL filter), centrifuged at 5000g for 3 minutes and purified (QIAquick PCR purification kit, Qiagen 28104).
For in vitro extraction, the reconstituted chromatin was collected from the dialysis tubing and and residual RNA was removed by incubating in 20mg/mL RNaseA at 37°C for 1 hour. Protein was subsequently removed by incubating with 100mg/mL Proteinase K for 3 hours at 50°C. Reconstituted chromatin was then suspended in MNase buffer (10mM Tris-Cl (pH 7.4), 15mM NaCl, 60mM KCl, 0.15mM spermine, 0.5mM spermidine, 1mM CaCl2) and digested with 1ug/uL MNase (Worthington) for 10μg of genomic DNA present for 10 min at room temperature. Digestion was stopped using 1/5 vol. 0.125M EDTA, and samples were purified via phenol/chloroform extraction and ethanol precipitation. DNA sized at ~147bp were excised from a 5% polyacrylamide gel and purified via crushing in “crush and soak buffer” (300mM NaOAc and 1mM EDTA, pH 8.0), with a microtube pestle inside the centrifuge tube. The gel and buffer slurry was then incubated at room temperature for 48 hours on a bench rocker to allow DNA to passively diffuse into the buffer. Solubilized DNA was separated from the agarose using spin-filters (Amicon Ultrafree-CL filter), centrifuged at 5000g for 3 minutes and purified (QIAquick PCR purification kit, Qiagen 28104).
ABI SOLiD adaptor ligation and fragment library preparation was then performed per manufacturer’s protocol (Invitrogen 4464411) before sequencing.

treatment_protocol: For in vitro reconstitution, Drosophila melanogaster S2 cells, a late embryonic stage cell line, were cultured in Schneider’s insect media (Invitrgoen) supplemented with 10% FBS (HyClone) and grown to semi-confluency; a density of approximately 0.5 - 1×106 cells/ml. Cells were harvested by gentle agitation and pelleted by centrifugation at 1200 x g before washing three times with PBS. Genomic DNA was purified from approximately 100 million S2 cells using QIAGEN Genomic-tips (500/G PN 10262). Purified histone octamer, derived from chicken erythrocytes, was mixed with  genomic DNA from S2 cells in a 3:10(histone:DNA) molar ratio in reconstitution buffer (2M NaCl; 5mM Tris; 1mM benzolamide; 0.5mM PMSF; 0.5mM EDTA) and loaded into a 12-14kDa, 10mm diameter dialysis tubing, which was then placed into a larger 6-8kDA 100mm dialysis bag filled with 100mL of reconstitution buffer. This assembly was then dialyzed against 4 liters of low salt dialysis buffer (5mM Tris; 1mM benzolamide; 0.5mM PMSF; 0.5mM EDTA) at 4°C for a minimum of 24 hours. After 24 hours the 4 liters of cold dialysis buffer were replaced and dialyzed for an additional 24 hours, and the process repeated for a total of 5 dialysis incubations

tag: sample type

value: purified genomic DNA (from S2 cells) and purified histones (from chicken erythrocytes)

tag: passages


title: MG-42

value: 16 weeks old


title: GFP control, overexpressed in HMEC cells GFP18_control_4


title: GFP control, overexpressed in HMEC cells GFP18_control_3


title: GFP control, overexpressed in HMEC cells GFP18_control_2


title: ML-DmD20_MNaseSeq

description:
MNase-seq from antenna cell line
Drosophil_CTGTTA

source_name: antenna cell line

value: antenna imaginal disc cell line

value: less than 10


title: ML-DmD17_MNaseSeq

description:
MNase-seq from haltere cell line
Drosophil_CGTTGG

source_name: haltere cell line

value: haltere imaginal disc cell line


title: Symp RNAi sm RNA-seq rep3

data_processing:
All adapter sequences were trimmed and the libraries cleaned using Cutadapt (MARTIN 2011).We aggressively trimmed the siRNA reads to 25 nts from the 5’ end following adapter removal to filter remaining rRNAs, snoRNAs, snRNAs and tRNAs out of the data set before mapping. All data sets were mapped using the RNA-seq Unified Mapper (RUM) (GRANT et al. 2011). The NEB kit used to prepare the RNA-seq samples produces libraries with high directionality and RUM utilized this feature to strand specifically map the RNA-seq reads. RUM separated unique and non-uniquely mapping sequences into separate output files that could be further analyzed. The UCSC genome browser (www.genome.ucsc.edu) was used to visualize the non-uniquely mapping bedgraph output files.
Genome_build: dm3
Supplementary_files_format_and_content: Text files with normalized readcounts unique and non-unique RNA-seq and small RNA-seq reads.

source_name: Symp RNAi sm RNA-seq

extract_protocol:
Total RNA from 8 x 10^6 Drosophila Dmel-2 tissue culture cells was isolated using QIAzol Lysis Reagent (Qiagen). Total RNA was fractionated into large (>200 nts) and small (<200 nts) fractions using RNeasy Mini spin columns and RNeasy MinElute spin columns, respectively (Qiagen). DNA was removed from the large fraction by on-column DNase digestion (Qiagen). 28S, 18S and 5S rRNAs were depleted from 5 µg of each large RNA fraction using the Ribo-Zero Magnetic Kit (Epicentre). 2S rRNA was depleted from the small RNA fraction according to Seitz et al.  (SEITZ et al. 2008) with the following modifications. 0.1 nMoles 2S rRNA complementary oligo were bound to 500 µg streptavidin beads in 1 mL 0.5x SSC for one hour at 4oC. The beads were then washed 5X in 0.5X SSC followed by 5 minute incubation at 65oC to remove secondary structure. 2 µg of the small RNA fraction were diluted to 12.5 ng/µl and 160 µl were added to the bead slurry.
RNA-seq libraries were prepared in triplicate from 35 ng of the rRNA-depleted large RNA fraction using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). smRNA-seq libraries were prepared in triplicate from ~475 ng of the 2S rRNA-depleted small RNA fraction using the NEBNext Small RNA Library Prep Set for Illumina (NEB).

tag: RNAi

value: Symp RNAi

tag: molecule subtype

value: rRNA depleted Small RNA


title: GFP control, overexpressed in HMEC cells GFP18_control_1

value: Human mammary epithelial cells


title: ML-DmD11_MNaseSeq

description:
MNase-seq from eye cell line
Drosophil_TCGTTA

source_name: eye cell line

value: eye imaginal disc cell line


title: Cme-L1_MNaseSeq

description:
MNase-seq from leg cell line
Drosophil_nobarcode

source_name: leg cell line

value: leg imaginal disc cell line


title: Symp RNAi sm RNA-seq rep2

tag: cell line


title: CPSF73 RNAi sm RNA-seq rep3

source_name: CPSF73 RNAi sm RNA-seq

value: CPSF73 RNAi


title: human RAF1, overexpressed in HMEC cells RAF1_overexpressed_2

tag: cell type


title: R48-L3-Input-Sequences

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

description: Sample 1

data_processing:
Base-calls were made using RTA  version 1.12.4.2
Reads were aligned to human genome hg19 using Bowtie version 0.12.7, only uniquely aligning reads were retained (-m 1)
Bam file were converted to BED using Bedtools (bamToBed v2.11.2)
Peaks were called using SICER (v1.1), with input aligned sequences as the control file, and FDR <.05
Galaxy was used for further data analysis (performing intersection/subtraction analysis, extracting features)
Genome_build: Human hg19
Supplementary_files_format_and_content: interval files from galaxy, containing chromosome and coordinates of peak locations (column headers; chromosome, start, stop, ChIP read count, Control read count, p value, fold change, and FDR threshold)

source_name: Human corneal epithelial cells (HCE)

growth_protocol: HCE cells were grown in OccuLife medium (LifeLine Cell Technology) at 37C, 5%CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the Grhl3 antibody.
Sequencing libraries were generated for the H3K4me1, H3K4me3, H3K27ac, and Input samples using the NEB Next reagents and Illumina adaptors and oligos, according to the Illumina protocol for ChIP-Seq library preparation, with some modification. After adaptor ligation, PCR amplification was performed prior to size selection of the library (Schmidt, 2009). Clustering and 50-cycle single end sequencing were performed on the Illumina Hi-Seq 2000 Genome Analyzer.
Libraries were sequenced on the Illumina Hi-Seq 2000, with 50bp single end sequencing

treatment_protocol: Cells were fixed and collected at approximately 50% confluence

value: Human corneal epithelial cells (HCE)

value: Input


title: R48-L5-H3K4me3-Sequences

description: Sample 3

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: R48-L4-H3K4me1-Sequences

description: Sample 2

tag: chip antibody

value: Abcam


title: R48-L6-H3K27ac-Sequences

description: Sample 4


title: IAA rep1

city: Novosibirsk

first: Daniil

last: Wiebe

address: Lavrentyeva 10

country: Russia

institute: ICG SBRAS

data_processing:
Raw reads were mapped onto the Arabidopsis genome (TAIR10) using SHRiMP (v2.2.3)
Uniquely mapped reads were counted using the htseq-count program with the annotation file from TAIR10
The DEGs were detected using the Bioconductor package DESeq
Genome_build: TAIR10

growth_protocol: Arabidopsis Col-0 seeds were surface-sterilized and vernalized for 7 days at 4°C. Seedlings were grown vertically at 22°C and 150 µmol m-2 s -1 under a 16-h light/8-h dark cycle on 1/2 Murashige and Skoog (MS) media (Sigma).

extract_protocol:
Roots were collected in liquid nitrogen. Each replicate contained approximately 100 roots. Total RNA from the roots was extracted using TRIzol® Reagent (Ambion, Cat. Num. 15596-018) and DNaseI (Promega), and total RNA yields were measured using an Invitrogen® Qubit™ fluorometer and Agilent Bioanalyzer 2100 microfluidics (Agilent, Santa Clara, CA). Complementary DNA was synthesized using a Revert Aid First Strand cDNA Synthesis Kit (Thermo SCIENTIFIC, USA).
Ribosomal RNA depletion was performed using a RiboMinus™ Plant Kit for RNA-Seq (Invitrogen™), according to the manufacturer’s instructions. Five micrograms of RNA with an RNA integrity number (RIN) of 7.9-9.0 was used. Three hundred nanograms of ribo-depleted RNA was taken for SOLiD cDNA barcoded fragment library construction using a SOLiD™ Total RNA-Seq Kit (Applied Biosystems™). cDNA libraries were amplified by PCR with 16 cycles following the recommendations of the sample preparation protocol. Library concentrations and quality were assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, USA) and had an average length of ~250 bp. e-PCR (emulsion quantitative polymerase reaction) was performed with a library concentration of 60 pmol.

treatment_protocol: Three days after germination (dag), seedlings were incubated in liquid 1/2 MS and 1/2 MS supplemented with 1 µM IAA for 6 h.

tag: strain

value: wild type

value: 3 days after germination

value: root

tag: treated with

value: 1 µM IAA for 6 h


title: IAA rep3

tag: genotype/variation


title: human HER2/ERBB2, overexpressed in HMEC cells HER2_overexpressed_3


title: Symp RNAi sm RNA-seq rep1

first: Mindy

last: Steiniger

address: 1 University Blvd.

institute: University of Missouri-St. Louis


title: xrn1 rat1-1 rep2

city: Martinsried

first: Sittinan

last: Chanarat

address: Am Klopferspitz 18

country: Germany

institute: MPI biochemistry

description: RNA-seq analysis

data_processing:
Basecalls performed using CASAVA 1.8.2 and filtered to only sequences passing the Illumina QC filter
Sequenced reads were mapped to yeast genome reference using Tophat2 (ver. 2.0.14) with default settings
Cufflinks (ver.2.2.1) was performed with -g option to obtain information of any novel isoforms, otherwise with default parameters.
spliceR (ver 1.14.0) was then used with default settings to generate isoform fraction value of each transcript, which was then compared between samples as intron read value (IR)
Genome_build: Yeast S288C
Supplementary_files_format_and_content: tab-delimited text file includes introns with their positions and features for  HUB1-OE vs wildtype. No splicing differences were detected in the analysis of delta hub1 vs wildtype. Therefore, processed data is presented only for  HUB1-OE vs wildtype.

organism: Saccharomyces cerevisiae

source_name: mid-exponential phase

growth_protocol: Yeast strains were grown at 33˚C to mid exponential phase (OD600=0.8) in synthetic complete medium

extract_protocol:
Total RNA was extracted using High Pure RNA Isolation Kit (Roche),
Transcript libraries were generated using TruSeq RNA Sample Kit (Illumina) according to the manufacturer's instructions.

tag: phenotype

value: wildtype

tag: growth phase

value: mid-exponential phase


title: xrn1 rat1-1 HUB1-OE rep1

description: RNA-seq analysis

value: HUB1 over-expression


title: xrn1 rat1-1 HUB1-OE rep2

description: RNA-seq analysis


title: IAA rep2

tag: age

tag: tissue


title: CPSF73 RNAi sm RNA-seq rep2

city: St. Louis


title: Control rep3

value: none (control)


title: Blank RNAi sm RNA-seq rep2

source_name: Blank RNAi sm RNA-seq

value: Blank RNAi

value: rRNA depleted Small RNA


title: CPSF73 RNAi sm RNA-seq rep1


title: E. coli 3' RACE Rep2

description: RNA (RACE)

data_processing:
50 bp single-end reads, were mapped to the genome with using bowtie2(Langmead and Salzberg, 2012) using default parameters. Alignments with bowtie2 mapping quality values lower than 40 were not retained for further analysis, leaving 128,413,654 and 76,508,335 reads.
In order to distinguish between 3’ ends of transient products of RNA metabolism and stable 3’ ends, we developed an algorithm to call coverage peaks. The algorithm will be discussed in detail in an upcoming manuscript, and the scripts used are available upon request from the authors. In short, positions in the E. coli genome were considered in descending order of coverage and assigned a p-value based on a Poisson distribution parameterized by the mean coverage of all covered bases in the genome. Peaks were rejected if their p-values exceeded 1e-4 or if there existed a >10-bp window containing the peak in which all positions were within 2-fold coverage of the peak position. Parameters were chosen based on analysis of annotated 3’ ends as well as qualitative analysis of peaks. This resulted in 20,019 peaks.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: GFF file containing 3' end annotations
Supplementary_files_format_and_content: BIGWIG file containing coverage tracks from 3' RACE data

source_name: Escherichia coli

extract_protocol:
Total RNA was isolated using the hot phenol method as described in (Lybecker et al., 2014).
total DNaseI treated RNA was depleted of ribosomal RNA using the Ribo-Zero™ RNA removal kit for Gram-negative bacteria (Epicentre). A 3' RNA adapter, based on the Illumina multiplexing adapter sequence (Oligonucleotide sequences © 2007-2014 Illumina, Inc. All rights reserved) blocked at the 3' end with an inverted dT (5'-GAUCGGAAGAGCACACGUCU[idT]-3'), was phosphorylated at the 5' end using T4 PNK (New England Biolabs) per the manufacturer’s protocol. The 3' RNA adapter was ligated to the 3' ends of the rRNA depleted RNA using T4 RNA ligase I (New England Biolabs). 1.5 mg of RNA was incubated at 20°C for 6 hours in 1X T4 RNA ligase reaction buffer with 1 mM ATP, 30 µM 3' RNA adapter, 10 % DMSO, 10 U of T4 RNA ligase I, and 40 U of RNasin (Promega) in a 20 ml reaction. RNA was then fragmented in equivalents of 100 ng using the RNA fragmentation reagents (Ambion®) per the manufacturer’s protocol at 70°C for 3 min and subsequently phosphorylated at the 5' ends using T4 PNK (New England Biolabs) per the manufacturer’s protocol to allow for ligation of the 5' adapter. RNA was size-selected (≈ 150-300 nt) and purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel. Gel slices were incubated in RNA elution buffer (10 mM Tris-HCl, pH 7.5, 2 mM EDTA, 0.1 % SDS, 0.3 M NaOAc) with vigorous shaking at 4°C overnight. The supernatant was subsequently ethanol precipitated using glycogen as a carrier molecule. The Illumina small RNA 5' adapter (5'-GUUCAGAGUUCUACAGUCCGACGAUC-3') was ligated to the RNA as described before except the concentration of the adapter was 52 mM and 20 U of T4 RNA ligase I was used in total volume of 25 µl. The ligated RNAs were size-selected (≈ 200-300 nt) and gel-purified over a denaturing 8 % polyacrylamide/8 M urea/TBE gel (as described above). The di-tagged RNA libraries were reverse-transcribed with SuperScript®II reverse transcriptase (Invitrogen) using random nonamers per the manufacturer’s protocol. RNA was removed using RNase H (Promega) per the manufacturer’s protocol and cDNA was amplified in PCR carried out using Phusion® High-Fidelity Polymerase (New England Biolabs). cDNA was amplified with modified designed Illumina-compatible PCR primers (3’ library Forward 5’-CAAGCAGAAGACGGCATACGACAGGTTCAGAGTTCTACAGTCCGA-3’; Reverse 5’-AATGATACGGCGACCACCGAGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) by 18 cycles of PCR. The products were purified using Agencourt AMPure XP beads (Beckman) and analyzed on an Agilent 2100 Bioanalyzer. 3’ end enriched cDNA libraries were sequenced on individual Genome Analyzer IIx lanes (36 bp, single-end) or on HiSeq 2000 lanes (50 bp, single-end) using primer based on Illumina Multiplexing Read 2 Sequencing Primer (5’-GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3’) at the CSF NGS unit http://csf.ac.at/.


title: Blank RNAi sm RNA-seq rep1


title: Control rep2


title: E. coli 3' RACE Rep1

description: RNA (RACE)


title: Control rep1


title: Day 8 replicate 3

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-3-SLX-8483.L2DRBC08.bam-FPKM

data_processing:
Reads were aligned to the Rnor5.0/Ensembl V75 transcriptome using Tophat v2.0.8 with default parameters
Counts and differential gene expression were determined using CuffLinks v2.2.1 using default parameters
Genome_build: Rnor 5.0
Supplementary_files_format_and_content: Fastq files for raw data and FPKM values in tab-delimted txt format

organism: Rattus norvegicus

growth_protocol:
Cortical neurons were derived from E18 Sprague Dawley rat cortex, and were plated at the density of 100-150 cells/mm2. The medium used for plating was a combination of fresh B27 medium (neurobasal medium supplemented with 2% B27 and 1% Glutamax) and B27 medium conditioned by astrocytes.
Astrocytes were derived from P0-2 Sprague Dawley rat cortex, and were grown for 7-8 days before being frozen for future use. They were then thawed and further grown for another 5-6 days before being combined with neurons as co-culture, or used for B27 medium conditioning.

extract_protocol:
Total RNA was extracted from 1, 4, 8, 16, and 24 DIV cultures by using the Qiagen RNeasy Micro Kit (Qiagen, 74004)
RNA was subjected to whole-transcriptome amplification using NuGEN RNAseq v2 System followed by fragmentation to 200bp with a Diagenode Bioruptor Pico sonicator, The resulting fragments were then used to make bar-coded libraries using NuGEN Ovation Rapid DR Multiplex System

value: Sprague Dawley

tag: developemental stage

value: Brain cortex

value: Embryonic cortical neurons

tag: co-cultured with

value: primary rat astrocytes from P0-2 rats

tag: time point

value: 8 days after plating


title: xrn1 rat1-1 rep3

description: RNA-seq analysis


title: xrn1 rat1-1 rep1

description: RNA-seq analysis


title: Day 8 replicate 4

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-4-SLX-9155.L2DRBC09.bam-FPKM


title: BalillaORF3+ORF5+_S3_rep1

city: shenzhen

first: yiming

last: yu

state: --- Select a state ---

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology

data_processing:
Raw reads was produced by Illumina HiSeq 2000
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
All the reads in sanger fastq format were mapped to the genome of Oryza sativa Japonica Group cultivar Nipponbare with Tophat. (IRGSP-1.0)
Cufflinks are used to assemble transcripts and estimate their abundances with default parameters.
Cuffdiff was used to find differential expressed genes with default parameters.

organism: Oryza sativa

source_name: pistil

growth_protocol: All the rice plants were grown in the fields of experimental station of Huazhong Agricultural University, Wuhan, China.

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) according to the manual. RNA yields and quality were measured using Nanodrop 2000 (Thermo Scientific), and further quantified using Qubit2.0 Fluorometer (Invitrogen). RNA integrity was evaluated using Experion RNA Analysis Kits (Bio-rad) and Experion Automated Electrophoresis Station (Bio-rad)
Each library was constructed using 3 μg total RNA using the TruSeq RNA Library Preparation Kit v2 (Illumina).

tag: Stage


title: xrn1 rat1-1 HUB1-OE rep3

description: RNA-seq analysis


title: Day 8 replicate 0

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-0-SLX-8483.L2DRBC05.bam-FPKM


title: Blank RNAi sm RNA-seq rep3

growth_protocol: Dmel-2 cells were grown in Sf-900 serum free media.

tag: cell line

tag: RNAi

tag: molecule subtype


title: Day 8 replicate 2

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-2-SLX-8483.L2DRBC07.bam-FPKM

tag: cell type


title: Day 4 replicate 4

description:
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-4-SLX-9155.L2DRBC07.bam-FPKM

value: 4 days after plating


title: BalillaORF3+ORF5+_S2_rep2


title: BalillaORF3+ORF5+_S3_rep2


title: Day 8 replicate 5

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-5-SLX-9155.L2DRBC10.bam-FPKM


title: BalillaORF3+ORF5+_S1_rep1


title: Day 8 replicate 1

description:
RNA harvested from cultured rat embryonic neurons 8 days after plating
D8-1-SLX-8483.L2DRBC06.bam-FPKM


title: BalillaORF3+ORF5+_S2_rep1


title: BalillaORF5+_S3_rep2


title: Day 4 replicate 3

description:
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-3-SLX-8483.L2DRBC04.bam-FPKM


title: Day 4 replicate 1

description:
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-1-SLX-8483.L2DRBC02.bam-FPKM


title: Day 4 replicate 2

description:
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-2-SLX-8483.L2DRBC03.bam-FPKM


title: BalillaORF5+_S2_rep2


title: Day 24 replicate 3

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-3-SLX-8483.L2DRBC16.bam-FPKM

value: 24 days after plating


title: Day 24 replicate 5

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-5-SLX-9155.L2DRBC14.bam-FPKM


title: Day 4 replicate 0

description:
RNA harvested from cultured rat embryonic neurons 4 days after plating
D4-0-SLX-8483.L2DRBC01.bam-FPKM


title: Day 24 replicate 2

description:
RNA harvested from cultured rat embryonic neurons 24 days after plating
D24-2-SLX-8483.L2DRBC15.bam-FPKM