title: Vv egg stage

city: Fuzhou

first: Baogui

last: Xie

state: Fujian

address: Shangdian Road

department: Mycological Research Center

institute: mrcfafu

description: 3'-tag digital gene expression (DGE)

data_processing:
Illumina Cluster Station and Illumina HiSeq™ 2000 instrument used for basecalling.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences.All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Genome_build: V.volvacea strain PYd21 genome data
Supplementary_files_format_and_content: tab-delimited text files include tag sequences,tag number and TPM values for each strain.

organism: Volvariella volvacea

source_name: Mushroom

growth_protocol: Culture spawn was prepared by growing mycelium on (w/w) 84% cotton seed hull, 9% wheat bran, 1% light Calcium Carbonate, 1% lime, 1% bagasse with 60-65% of relative humidity. Fruiting body production of V. volvacea was carried out in bed load. The cultivation substrate was composed of 25.5kg straw, 1.5kg cattle manure, and 0.5kg lime in 1m2 areas. Firstly, add the dry straw on the wood bed per square, and spray four days continuously. Then sprinkled the cattle manure on the straw bed surface with the lime. Secondly, after pasteurization by heating at 65℃ for 24–34h and cooling to around 32℃, the cultivation substrate was inoculated with the culture spawns of V. volvacea strains. Each V. volvacea strains were randomly arranged to cultured in triplicate with 5cm gap. Culture about six days at the temperature 32-32℃ with ventilating 2-3 times every day. Thirdly, open all doors and windows ventilation and cooling, while playing the fruiting water. Continue to training 2-3 days, fruiting bodies (primordium) usually emerged, but in others they were delayed for 2-4 weeks after the spawn was introduced.

extract_protocol:
Total RNA was extracted from mycelia using pBIOZOL Plant Total RNA Extraction Reagent, according to the manufacturer’s protocol (BioFlux). The isolated RNA was treated with RNeasy plant mini kit to remove potential genomic DNA contamination, according to the manufacturer’s protocol (QIAGEN, Germany). RNA integrity and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (6 μg) from each development stage of V. volvacea was submitted to BGI-Shenzhen (Shenzhen, China) for library construction and sequencing.
Sequence tag preparation was carried out using the Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol.

value: Stipe of fruiting body

tag: Stage

value: egg


title: Vv elongation stage

status: Public on Dec 19 2014

type: SRA

country: China

description: 3'-tag digital gene expression (DGE)

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: tissue

value: elongation


title: Vv maturation stage

description: 3'-tag digital gene expression (DGE)

value: maturation


title: Vv button stage

description: 3'-tag digital gene expression (DGE)

value: button


title: iWAT518_day0

city: Odense

first: Qin

last: Hao

address: kanslergade 1

country: Denmark

institute: Copenhagen University

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence by using cutadapt with parameters -m 15 -e 0.05, then mapped to refMrna downloaded from UCSC using bwa with parameters -n 1
The number of reads which uniquely mapped to the RefSeq transcripts were counted for each gene, then merged into one file for each tissue.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include tag counts for each sample ...

organism: Mus musculus

extract_protocol:
Adipose tissues were dissected, snap frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were kept at thermoneutrality for 8 days acclimation before treatment. Mice were divided into 3 groups. Two groups were transferred to 4 degree for 2 and 4 days. The third group was sacrificed without cold exposure.

tag: age

value: 8 weeks

tag: gender

value: male

value: inguinal white adipose tissue

tag: treatment

value: 0 day in cold exposure


title: Vv primordia

description: 3'-tag digital gene expression (DGE)

value: Fruiting body

value: primordia


title: Embryo_adar_mavs

city: Edinburgh

first: Liam

last: Keegan

address: Crewe Road South

department: MRC Human Genetics Unit, MRC IGMM at the University of Edinburgh

country: United Kingdom

institute: University of Edinburgh

data_processing:
Sequence reads were mapped to the mm9 genome assembly using Tophat v1.4.0 and allowing no mismatches, insertions or deletions.
Transcripts were then assemlbed separately for each tissue sample and genotype using Cufflinks v2.2.1.
Differences in read abundance between datasets were identified using edgeR v3.4.2.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Whole embryo

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Adar1-/-; Mavs-/-


title: iBAT550_day4

value: interscapular brown adipose tissue

value: 4 day in cold exposure


title: wt ccdb

city: Stanford

first: Justin

middle: William

last: Chartron

state: California

address: Clark Center E200, 318 Campus Drive

department: Biology

country: USA

institute: Stanford University

data_processing:
Library strategy: ribosome profiling
Base calls performed by Illumina CASAVA
3' adaptor sequence was trimmed using Cutadapt 1.3
ribosomal RNA reads were removed by alignment to reference sequences using Bowtie 2
Open reading frame reads were aligned to coding sequences flanked by 21 nucleotides using Bowtie 2. Coding sequences for which >20% of reads have greater than one match were excluded
Reads were assigned to codon position at center of read
Total reads per open reading frame were determined by summing codon reads from position start+2 to stop-2.
Genome_build: sacCer3
Supplementary_files_format_and_content: File containing open reading frame name, total codon reads, and reads per kilobase per million dataset reads (RPKM).

organism: Saccharomyces cerevisiae

source_name: Wild-type yeast

growth_protocol: Yeast were grown in synthetic defined media to early-log phase. Expression of plasmid-encoded open reading frames is induced for two hours. Yeast are harvested by fast filtration and plunged in liquid nitrogen.

extract_protocol:
Cells were lysed using a cryogenic mixer mill. Lysates were clarified by centrifugation, and digested using Rnase I. Ribosomes were isolated by ultracentrifugation through a sucrose cushion, and RNA was extracted from the pellet.
RNA fragments of approximately 30 nucleotides were extracted from a polyacrylamide gel. A DNA adapter was ligated to the 3' of fragments and used to prime reverse transcription. cDNA were circularized and rRNA-originating fragments were removed using biotinylated subtraction oligonucleotides. The library was barcoded during PCR amplification.

value: whole cell lysate

tag: vps35 genotype

value: wild type

tag: plasmid

tag: assayed molecue

value: Ribosome protected mRNA


title: vps35 tif

source_name: vps35 deletion overexpressing TIF4631


title: Embryo_adar


title: vps35 ccdb

source_name: vps35 deletion


title: wt tif

source_name: Wild-type yeast overexpressing TIF4631


title: Liver_adar_mavs

source_name: Embryonic liver


title: BMI1_mBrain_ChIPseq

status: Public on Dec 18 2014

city: New york

first: Zhonghua

last: Gao

state: NY

address: 522 1st Avenue, SML 203

department: Biochemistry and Molecular Pharmacology

institute: New York University School of Medicine

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 or hg19 genome assembly using Bowtie with -m1 -v2.
Duplicated reads were removed with samtools rdup.
peaks were called using QESEQ.
ChIP-seq read density files were generated using igvtools
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: txt: called peaks

molecule: genomic DNA

source_name: brain

growth_protocol: 293T-REx stable lines transfected with HA-tagged PRC1 subunits or an empty vector were grown in standard conditions (DMEM 10% FBS) and kept in selection with zeocin

extract_protocol:
For ChIP-seq in mouse brain, the whole brains were homogenized with a glass douncing homogenizer. The cell homogenate was fixed with 1% paraformaldehyde for eight min at room temperature and quenched with 0.125 M glycine for five min at room temperature, followed by centrifugation through a 29% iodixanol cushion. The nuclei pellet was resuspended and sonicated using a Diagenode Bioruptor to an average size of ~250 bp. After pre-clearing with BSA-blocked protein G Sepharose, chromatin was incubated with antibodies at 4°C overnight. The chromatin immunocomplexes were recovered with the same BSA-blocked protein G beads.For ChIP-seq in 393T-REx cells, cells were crosslinked with 1% formaldehyde for eight min at room temperature and the nuclei were then isolated. As described above, following sonication and pre-clearing, chromatin IP was performed to isolate associated DNA.
For ChIP-seq library construction, 5-10 ng of DNA extracted from the chromatin immunocomplexes. Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters with LigaFast (Promega, city, state #M8225). Fragments of 350±50 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB M0530).

tag: mouse strain

tag: antibody


title: H3K27me3_mBrain_ChIPseq


title: H2AK119ub1_mBrain_ChIPseq

value: H2AK119ub1 (Cell Signaling, 8240, lot# 1)


title: H3K36me3_mBrain_ChIPseq


title: P300_mBrain_ChIPseq

value: P300 (Santa Cruz, sc585, lot# B0413)


title: H3K27ac_mBrain_ChIPseq


title: mBrain_RNAseq

data_processing:
The raw data were mapped to mm9 genome using bowtie with -v 2 and -m 1 parameters
Mapped data were sorted and PCR duplicates were filtered out.
The unique mapped reads were considered for reads count by using htseq.
The reads were averaged and normalized to reads per millions reads per kb of gene length
Genome_build: mm9
Supplementary_files_format_and_content: xls: RPKM

extract_protocol:
Total RNA was extracted from brain using TRIzol
Poly-A+ RNA was isolated with OligodT25 dynabeads (Invitrogen, #610-02) from 2 ug total RNA of each sample. Reverse transcription was performed with random hexamers and Superscript III reverse transcriptase (Invitrogen), followed by the second strand synthesis with E. coli DNA PolI (Invitrogen). Double stranded cDNA was purified with Qiaquick PCR purification kit (Qiagen), and sheared with a nebulizer (Invitrogen) to 100-500 bp fragments. These fragments were then end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB, #M0212), and ligated to custom adapters with T4 DNA ligase (Enzymatics, #L603-HC-L). Fragments of 200±20 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Phusion DNA polymerase (NEB, #M0530).


title: H3K4me3_mBrain_ChIPseq


title: PolII_mBrain_ChIPseq

value: PolII (Santa Cruz, sc899, lot#, G2414)


title: INPUT_mBrain


title: HL-1 + BRL rep 3

city: Madrid

first: David

last: Sanz-Rosa

address: 3, Melchor Fernandez Almagro

department: DEAIC

country: Spain

institute: CNIC

data_processing:
Illumina Casava1.7 software used for basecalling.
fastq Phred33 produced by illumina2bam.jar software
Sequenced reads were demultiplexed and trimmed for adaptor sequence using cutadapt software
Reads were assigned to genes using RSEM version 1.17 which uses Bowtie for alignment with default parameters
NCBIM37.v64 Ensembl genome build was used for read alignment.
Genome_build: MGSCv37
Supplementary_files_format_and_content: tab-delimited text files include counts per gene per sample as provided by RSEM (without normalization). The provided normalized values are the log2 normalized counts per million, calculated using calcNormFactors() multiplied by the library size as provided by the EdgeR package (http://genomebiology.com/2010/11/3/R25).

source_name: HL-1 cardiomyocyte

growth_protocol: HL-1 cardiomyocytes were grown in Claycomb Medium.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen). Illumina TruSeq RNA Sample Prep v2 Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Either 5µM BRL or vehicle was added to the cell culture medium.

value: heart

tag: cell type

value: HL-1 cardiomyocyte

tag: agent


title: HL-1 + BRL rep 2


title: dKO_5

city: Rotterdam

first: Harmen

middle: Jan George

last: van de Werken

address: Wytemaweg 80

department: Urology

country: Netherlands

institute: Erasmus MC

data_processing:
The sample was sequenced for 36bp on a HiSeq 2000 and demultiplexed using Narwhal [Brouwer et al., 2012].
The reads were aligned using Tophat version 2.0.8 (Trapnell and Schatz, 2009) against the UCSC mm10 reference genome, using Ensembl genes.gtf annotation version 73 (Ensembl 2014 Nucleic Acids Research 2014)
Read counts on ensemble annotation were computed using the htseq-count version 0.5.4. using -m union -s no -a 20
The differentially expressed genes were called using a generalized linear negative binomial model with controlling the effect of the RNA sample preparation date. The calculations were performed by the DESeq2 R package (Anders and Huber, Genome Biology 2010)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Id  and read count

molecule: polyA RNA

source_name: Megakaryocytes

growth_protocol: Bone marrow was isolated from the femur and a single cell suspension was made by straining through a 40 mm filter (BD Falcon). Cells were cultured in StemSpan medium (Stem Cell technologies) supplemented with 10% heat-inactivated fetal calf serum, Penicillin/Streptavidin, 2% low densitiy lipoprotein (Sigma-Aldrich) at a concentration of 2x10E6 cells/ml complemented with stem cell factor 1:100, 20ng/ml TPO, 1 unit/mL Erythropoietin. Cells were washed at day 2 and 4 and an increasing concentration of TPO was added, i.e. 50ng/mL at day 2 and 100ng/mL at day 4. At day 7 the cells were harvested for RNA extraction

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq was performed at the Erasmus MC Center for Biomics (Rotterdam, The Netherlands) according to manufacturer’s instructions (Illumina). The TruSeq RNA sample prep kit v2 was used. Briefly, polyA containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification, the mRNA was fragmented into ~200 bp fragments using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand synthesis using DNA polymerase I and RNaseH treatment. These cDNA fragments were end repaired, a single A base was added and Illumina adapters were ligated. The products were purified and size selected on gel and enriched by PCR. The PCR products were purified by Qiaquick PCR purification and used for cluster generation according to the Illumina cluster generation protocols (www.illumina.com).

value: Megakaryocytes

value: post natal week 12

value: Pf4-Cre::Sp1fl/fl::Sp3fl/fl (dKO)

tag: rna isolation date


title: WTlox_6

value: Sp1fl/fl::Sp3fl/fl (WTlox)


title: HL-1 + BRL rep 1


title: WTlox_3


title: HL-1 + Vehicle rep 2

value: control


title: MEF_Male_1

city: Cambridge

first: Rahul

last: Karnik

state: MA

address: 419 Broadway

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9) using MAQ bisulfite alignment mode.
Aligned bam files were processed using custom software (PMID:20852634).
Genome_build: mm9
Supplementary_files_format_and_content: chrom, chromstart, chromend,'number methylated cytosines/number total cytosines',score,strand,number methylated cytosines,number total cytosines

extract_protocol:
Please see Gu et al., 2011 and Smith et al., 2012
RRBS was performed according to a previously published protocol (Smith et al., 2009) with some optimizations for small cell numbers (Gu et al., 2010)

value: MEF

value: male


title: MEF_Male_2


title: HL-1 + Vehicle rep 1


title: Liver_adar


title: WTlox_10

value: post natal week 17


title: RING1B_mBrain_ChIPseq

value: RING1B (form Luciano Di Croce)


title: MEF_Female_3

value: female


title: Input-Mock-1

city: Vienna

first: Maximilian

last: Kauer

address: Zimmermannplatz 10

department: Molecular Biology

country: Austria

institute: CCRI, St.Anna Children Cancer Research Institute

description: small RNA isolated from input fraction

data_processing:
Illumina Casava1.8.2 pipeline was used for basecalling.
adapters were trimmed using cutadapt 1.0
alignment to hg19 was done using GSNAP (version 2012-11-27), with settings: -n 5 -m 0
counting of microRNAs was done using miRanalyzer (http://bioinfo5.ugr.es/miRanalyzer/miRanalyzer.php) with default settings (06/Feb/2014)
further processing was done in R statistical environment: for differential expression analysis the DESeq2 package was used
Genome_build: hg19
Supplementary_files_format_and_content: miRcount output from miRanalyzer, tab separated file with counting occurence for each microRNA

organism: Homo sapiens

source_name: A549 cells

extract_protocol:
RNA was extrated using TRIzol according to the manufacturer's instructions (Life Technologies).
small RNA libraries were prepared for sequencing using standard Illumina protocols.
Small RNA libraries for RNA-seq; sequenced on a Illumina HiSeq2000 platform; 50 nt single-reads.

tag: cell line

value: human lung epithelial

tag: infection

value: infected with mock control


title: MEF_Female_4


title: IP-Mock-1

description: small RNA isolated from mock IP


title: MEF_Female_1


title: IP-Mock-2

description: small RNA isolated from mock IP


title: IP-Adv-rep2

description: small RNA isolated from immunoprecipitated  RISC

value: infected with human adenovirus 5


title: dKO_9


title: Vv heterokaryon strain H1521

description: Sample 3

data_processing:
Illumina Cluster Station and Illumina HiSeq™ 2000 instrument used for basecalling.
Raw sequences have 3' adaptor fragments as well as a few low-quality sequences and several types of impurities. Raw sequences are transformed into Clean Tags after certain steps of data-processing.
A virtual libraries containing all the possible CATG+17 bases length sequences of the reference gene sequences. All clean tags were mapped to the reference sequences and only 1bp mismatch is considered. Clean tags mapped to reference sequences from multiple genes were filtered. Remainder clean tags were designed as unambiguous clean tags. The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags). ('t Hoen, Ariyurek, et al. 2008; Morrissy, Morin, et al. 2009).
Genome_build: V.volvacea strain PYd21 genome data
Supplementary_files_format_and_content: tab-delimited text files include tag sequences,tag number and TPM values for each strain.

growth_protocol: V. volvacea strains were routinely grown at 32 °C on potato dextrose agar medium (PDA) (200 g.L-1 of potato tissue, 20 g.L-1 glucose,20 g.L-1 agar). Liquid cultures were prepared in potato dextrose broth by shaking at 150 rpm for 7 days.

extract_protocol:
Total RNA was extracted from mycelia using pBIOZOL Plant Total RNA Extraction Reagent, according to the manufacturer’s protocol (BioFlux). The isolated RNA was treated with RNeasy plant mini kit to remove potential genomic DNA contamination, according to the manufacturer’s protocol (QIAGEN, Germany). RNA integrity and concentration were evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). RNA (6 μg) from each of the three strains was submitted to BGI-Shenzhen (Shenzhen, China) for library construction and sequencing.
Sequence tag preparation was carried out using the Illumina Gene Expression Sample Prep Kit according to the manufacturer’s protocol.
library strategy: 3'-tag digital gene expression (DGE)

tag: nuclear condition

value: heterokaryotic

tag: strain info

value: hybrid strain of PYd15 and PYd21

value: Mycelia


title: Vv homokaryon strain PYd15

description: Sample 2

tag: strain

value: homokaryotic

tag: tissue


title: SSEA1_Neg_2

tag: gender


title: SSEA1_Neg_1


title: Vv homokaryon strain PYd21

description: Sample 1


title: IP-Adv-rep1


title: HL-1 + Vehicle rep 3

value: heart

value: HL-1 cardiomyocyte


title: SSEA1_Pos_2


title: Input-Adv-rep1

description: small RNA isolated from input fraction


title: SSEA1_Pos_1


title: Input-Adv-rep2

description: small RNA isolated from input fraction


title: iPS_Female_2

value: iPSC


title: H3K4me3_293TREx_ChIPseq

source_name: 293T-Rex mock control cells

value: Human embryonic kidney cells stably expressing the tetracycline repressor protein

tag: Stage


title: MEF_Female_2


title: Input-Mock-2

description: small RNA isolated from input fraction


title: H3K36me3_293TREx_ChIPseq


title: H3K27ac_293TREx_ChIPseq


title: iPS_Female_1


title: HA-AUTS2_293TREx_ChIPseq

source_name: 293T-Rex cells expressing FLAG/HA-tagged AUTS2


title: ESC_Female_2

value: ESC


title: INPUT_293TREx


title: ESC_Female_4


title: ESC_Female_3


title: ESC_Male_1


title: ESC_Male_2


title: PolII_293TREx_ChIPseq

value: PolII (Santa Cruz, sc899, lot#, G2414)


title: dKO_4

value: Megakaryocytes

tag: age

value: post natal week 12

tag: genotype

value: Pf4-Cre::Sp1fl/fl::Sp3fl/fl (dKO)


title: ESC_Female_1

value: female


title: WT_RNASeq_P53_12h_A

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

data_processing:
Illumina Casava1.7 software used for basecalling.
The processing of reads included elimination of contaminant adaptar substrings with Scythe and quality-based trimming using Sickle. The alignment of reads to the human genome (hg19) was performed using Tophat2 mapper.
The transcript assembly  and quantification using FPKM of transcripts was carried out using Cufflinks2.
Annotation of the gene locus obtained was performed using Cuffmerge with Gencode v19 as reference.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample using cufflinks and GENCODE v19

source_name: HCT116 colon cancer cell lines

growth_protocol: HCT116 colon cancer cell were treated with DNA damage 5FU for two different time point. RNA was isolate with trizol and purificated with the Giagen kit colunm

extract_protocol:
RNA was isolate with trizol and purified with the Giagen kit throught the colunm.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were treated with 350uM 5FU for 4 and 12h.

tag: passages

tag: dna-damage

value: 5-fluorouracil for 12h


title: WT_RNASeq_P53_0h

value: 5-fluorouracil for 0h


title: WT_RNASeq_P53_4h

value: 5-fluorouracil for 4h


title: ALL-54 Dexamethasone treated AcHistone

city: Sydney

first: Dominik

last: Beck

state: NSW

address: Level 10, UTS Building 11 (CB11 81-113, Broadway, Ultimo)

department: School of Biomedical Engineering

country: Australia

institute: University of Technology Sydney

data_processing:
Base-calling: Illumina Real Time Analysis, scoring metric v1.5
Raw reads were prefiltered to remove all reads that have 3 or more bases with a quality score of less than Q13 and adaptors have been removed.
Alignments were all made against hg19 using bwa (version 0.6.1-r104) with default parameters. ChIP-seq peaks were called using HOMER (FDR 1e-3 and 1e-2) , MACS (p<1e-5 and p<1e-9) and SPP (FDR 1e-2 and FDR 1e-5)as previously described (Chacon D, Beck D, Perera D, Wong JW, Pimanda JE. 2014. BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells. Nucleic acids research 42(Database issue): D172-177.) BigWig files were created using tools from the UCSC Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain coordinates of identified peaks.

source_name: Human patient-derived xenograft cells

extract_protocol:
ALL xenograft cells were inoculated by tail-vein injection into NOD/SCID mice, and engraftment was monitored weekly as previously described25. When >70% %huCD45+ engraftment in the peripheral blood was apparent, which occurred 8-10 weeks post-transplantation, mice were treated with either dexamethasone (15 mg/kg) or vehicle control by intra-peritoneal (IP) injection, and culled at 8 hours following the treatment. Cell suspensions of spleens were prepared and mononuclear cells enriched to >97% human by density gradient centrifugation. The spleen-harvested cells were used for ChIP-seq assay.
ChIP DNA was fragmented to 100-500bp by sonication or micrococcal nuclease digestion. DNA-end was repaired to overhang a 3'-dA, then adapters were ligated to the end DNA fragments. DNA fragments with proper size (usually 100-300bp, including adaptor sequence) were selected after PCR amplification.

tag: host organism

value: mus musculus

tag: chip antibody

value: Acetyl-Histone H3 (lys9/14)

tag: antibody manufacturer

value: Millipore

tag: catalog number


title: WT_RNASeq_P53_12h_B


title: ALL-54 Dexamethasone treated IgG

value: IgG control

value: Sigma


title: ALL-54 Dexamethasone treated GR

value: GR

value: Cell Signaling


title: ALL-54 Control IgG


title: ALL-54 Control AcHistone


title: AGO-3-AGTCAA

city: Chapel Hill

first: Sara

middle: Rebecca

last: Selitsky

state: NC

address: 120 Mason Farm Rd., 5100H Genetic Medicine Building

department: Genetics

institute: University of North Carolina-Chapel Hill

description: Small RNA from AGO-2 pull-down

data_processing:
Trimmed reads: cutadapt -e .1 -O 10 -m 14
Organized reads by sequence
Downloaded tRNA sequences from the Genomic tRNA database and aggregated tRNAs by sequence, giving each tRNA sequence a unique ID
Aligned organized reads to aggregated tRNA sequences
Genome_build: hg19
Supplementary_files_format_and_content: Format: length, sequence, count, each tRNA the sequence mapped to, each tRNA the sequence mapped to, length of tRNA, offset from the first nucleotide

source_name: Small RNA from AGO-2 pull-down

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO7

extract_protocol:
miRNeasy Mini Kit
Illumina TruSeq Library Preparation, barcode listed in sample title and characteristic

treatment_protocol: Three technical replicates of 1x10^7 FT3-7 cells were harvested in lysis buffer [150 mM KCl, 25 mM Tris-HCl (pH 7.4), 5 mM EDTA, 1% Triton X-100, 5 mM DTT, Complete protease inhibitor mixture (Roche), and 100 U/mL RNaseOUT (Invitrogen)]. Lysates were centrifuged for 30 min at 17,000 × g at 4 °C and filtered through a 0.22-um filter. Filtrates were incubated with anti-AGO2 mAb (MBL) or isotype control IgG (ABCAM) at 4 °C for 2 h, followed by addition of 30 μL of Protein G Sepharose (GE Healthcare) for 1 h. The Sepaharose beads were washed three times in lysis buffer.

tag: barcode

value: AGTCAA

value: FT3-7 cells


title: AGO-2-CTTGTA

description: Small RNA from AGO-2 pull-down

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO6

value: CTTGTA

tag: cell line


title: IGG-1-GATCAG

description: Small RNA from IgG pull-down

source_name: Small RNA from IgG pull-down

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO8

value: GATCAG


title: IGG-3-TAGCTT

description: Small RNA from IgG pull-down

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO9

value: TAGCTT


title: ALL-54 Control GR


title: AGO-1-GGCTAC

description: Small RNA from AGO-2 pull-down

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO5

value: GGCTAC


title: HCV-cancer-16-ACTTGA

description: Cancer tissue from patient with chronic hepatitis C associated cancer

extract_protocol:
mirVana miRNA isolation kit
Illumina TruSeq Library Preparation, barcode listed in sample title and characteristic

value: Hepatocellular carcinoma tissue

value: ACTTGA


title: TOTAL-1-AGTTCC

description: Total small RNA from FT3-7 cells

source_name: Total small RNA from FT3-7 cells

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO2

value: AGTTCC


title: TOTAL-2-ATGTCA

description: Total small RNA from FT3-7 cells

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO3

value: ATGTCA


title: WT_ChIPSeq_P53_0h

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie2 using default parameters.
Peak calling were performed using MACS version 1.4.2 with default settings without input signal.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using MACS; Scores represent filtered read coverage

source_name: HCT116 colon cancer cell line

growth_protocol: HCT116 colon cancer cell were treated with DNA damage 5FU for two different time point. ChIP was performed with the p53 human antibody  FL636 from SC-6243

extract_protocol:
Lysates were sonicated and p53 binding sites were isolated with antibody (SC- 6243)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were treated with 350uM 5FU for  12h.

tag: antibody

tag: treatment

value: 5FU for 0h


title: HCV-cancer-9-GCCAAT

source_name: Cancer tissue from patient with chronic hepatitis C associated cancer

value: GCCAAT


title: HCV-cancer-11-CAGATC

value: CAGATC


title: HCV-non-cancer-9-ACTTGA

description: Non-cancer liver tissue from patient with chronic hepatitis C and associated cancer

value: Non-cancer liver


title: HCV-non-cancer-5-CAGATC

source_name: Non-cancer liver tissue from patient with chronic hepatitis C and associated cancer


title: HCV-non-cancer-11-GATCAG


title: HCV-non-cancer-16-TAGCTT


title: HCV-cancer-5-ACAGTG

value: ACAGTG


title: HBV-cancer-10-TGACCA

description: Cancer tissue from patient with chronic hepatitis B associated cancer

value: TGACCA


title: HBV-cancer-6-TTAGGC

source_name: Cancer tissue from patient with chronic hepatitis B associated cancer

value: TTAGGC


title: HBV-non-cancer-6-GTTTCG

description: Non-cancer liver tissue from patient with chronic hepatitis B and associated cancer

value: GTTTCG


title: HBV-non-cancer-3-GTGGCC

source_name: Non-cancer liver tissue from patient with chronic hepatitis B and associated cancer

value: GTGGCC


title: HBV-cancer-1-ATCACG

value: ATCACG


title: HBV-cancer-2-CGATGT

value: CGATGT


title: HBV-non-cancer-10-CGTACG

value: CGTACG


title: HBV-non-cancer-1-GTGAAA

value: GTGAAA


title: Uninfected-8-GGTAGC

description: Liver tissue from control subject

source_name: Liver tissue from control subject

value: Liver

value: GGTAGC


title: WT_ChIPSeq_P53_12h

value: 5FU for 12h


title: Uninfected-4-GAGTGG

description: Liver tissue from control subject

value: GAGTGG


title: Uninfected-6-CTTGTA

description: Liver tissue from control subject

value: CTTGTA


title: Uninfected-3-GGCTAC

description: Liver tissue from control subject

value: GGCTAC


title: TOTAL-3-CCGTCC

description: Total small RNA from FT3-7 cells

growth_protocol: FT3-7 cells were grown in Dulbecco’s modified Eagle’s medium (Gibco-BRL) and supplemented with 10% fetal calf serum and 2 mM GlutaMAX (Life Technologies). Cells were cultured in a humidified incubator at 37 C and 5% CO4

value: CCGTCC

value: FT3-7 cells


title: hom_RNF17 round spermatids_3rd_replicate

status: Public on Dec 17 2014

city: Cold Spring Harbor

first: Vasily

last: Vagin

address: 1 Bungtown Rd

institute: Cold Spring Harbor

description: 19-33 nt size fractionated RNA

data_processing: Unmapped reads were re-mapped using STAR (Dobin et al.29;15-21 2013 Bioinformatics) with the same criteria to extract spliced reads (Dobin et al.29;15-21 2013 Bioinformatics)

source_name: male pachytene cells

growth_protocol: mice were maintained according to the guidelines of the Cold Spring Harbor Laboratory Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA prepared with Trizol reagent (Invitrogen) was size selected (19-33nt) on 15% vertical polyacrylamide/urea gel.
small RNA libraries were prepared according (Malone et al. Cold Spring Harb Protoc. 2012). Size selected RNA was ligated with 3' adaptor Modban oligonucleotide with mutant T4 RNA ligase 2, truncated (home made). The ligated products were sized fractionated on 15% vertical polyacrylamide/urea gel and ligated with 5’ adaptor with T4 RNA ligase (Ambion). Then ligated products were separated on 15% vertical polyacrylamide/urea gel and used for reverse transcription with random hexamers and Superscript lll reverse transcriptase (Invitrogen). cDNA was amplified using Illimina primers and used for following sequencing on Illumina platforms.

value: 10 weeks old

tag: genotype/variation

value: homozygous RNF17


title: het_RNF17 round spermatids_3rd_replicate

description: 19-33 nt size fractionated RNA

value: heterozygous RNF17

tag: strain


title: hom_RNF17 round spermatids_2nd_replicate

description: 19-33 nt size fractionated RNA


title: het_RNF17 pachytene cells_3rd_replicate

description: 19-33 nt size fractionated RNA


title: hom_RNF17 pachytene cells_3rd_replicate

description: 19-33 nt size fractionated RNA


title: het_RNF17 round spermatids_2nd_replicate

description: 19-33 nt size fractionated RNA


title: het_RNF17 gonia cells_2nd_replicate

description: 19-33 nt size fractionated RNA

source_name: male gonia sorted cells


title: hom_RNF17gonia cells_2nd_replicate

description: 19-33 nt size fractionated RNA


title: Wild

city: Shenzhen

first: Hong

middle: zhi

last: Cao

state: Guangdong

address: F5, Main Building, Beishan Industrial Zone, Beishan Road, Yantian District

department: Bioinformatics

institute: BGI-SHENZHEN

description: Sequenced reads were generated from the mantle of the wild individual.

data_processing:
Used the inbred individual genome of Pacific oyster as reference. BS-Seq reads were aligned onto the corresponding reference using soap v2.21 with default parameters except -m 175 -x 325 -s 40 -l 32 -v 8.
Genome_build: Inbred individual genome.
Supplementary_files_format_and_content: Cdepth: Tab-delimited text file that contains all of the cytosines of the whole genome, one cytosine per line. For additional details on the generation of the Cdepth files, please see the 'GSE40302_Cdepth_readme.txt' file, which is linked to the Series record as a supplementary file.

organism: Magallana gigas

source_name: mantle of the wild individual

extract_protocol: Up to 5 μg of total genomic DNA were isolated from the mantle tissue of inbred and wild individuals using standard molecular biology techniques. DNA was fragmented by sonication with a Covaris S2 system (Covaris, MA), followed by end-repair, 3'-end addition of dA, and adapter ligation. Methylated adapters were used according to the manufacturer's instructions (Illumina). The bisulfite conversion of sample DNA was carried out using a modified NH4HSO3-based protocol and amplified by 9 cycles of PCR. Paired-end sequencing was carried out using Illumina HiSeq 2000.

treatment_protocol: The bisulfite conversion of sample DNA was carried out using a modified NH4SO4-based protocol.

tag: individual type

value: wild

tag: tissue

value: mantle


title: Inbred

description: Sequenced reads were generated from the mantle of the inbred individual.

source_name: mantle of the inbred individual

value: inbred

tag: gender

value: female

tag: sample type

value: reference


title: hom_RNF17 pachytehe cells_2nd_replicate

description: 19-33 nt size fractionated RNA

tag: age


title: hom_RNF17gonia cells_1st_replicate

description: 19-33 nt size fractionated RNA

source_name: gonia sorted cells


title: hom_RNF17 testes_2nd_replicate

description: 19-33 nt size fractionated RNA

source_name: testis

value: 6 weeks old


title: het_RNF17 testes_2nd_replicate

description: 19-33 nt size fractionated RNA


title: het_RNF17 gonia cells_1st_replicate

description: 19-33 nt size fractionated RNA


title: MIWI_IP_homtRNF17 testes

description: 19-33 nt size fractionated RNA

data_processing:
clip 3' end adaptor GATCGGTACAGTTGCAGTAAGAGC, keep reads with min length 15nt
reads mapped to mm9 mouse genome release using Bowtie (Langmead et al. Genome Biol 2009, ) with up to 2 mis-matches and a maximum of 100 multiple alignments (otherwise suppressed)
Unmapped reads were re-mapped using STAR (Dobin et al.29;15-21 2013 Bioinformatics) with the same criteria to extract spliced reads (Dobin et al.29;15-21 2013 Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: txt files with all mappers, their reads number and genomic annotation

source_name: 6 week old testis lysate

extract_protocol:
RNA was size selected (19-33nt) on 15% vertical polyacrylamide/urea gel.
small RNA libraries were prepared according (Malone et al. Cold Spring Harb Protoc. 2012 ). Size selected RNA was ligated with 3' adaptor Modban oligonucleotide with mutant T4 RNA ligase 2, truncated (home made). The ligated products were sized fractionated on 15% vertical polyacrylamide/urea gel and ligated with 5’ adaptor with T4 RNA ligase (Ambion). Then ligated products were separated on 15% vertical polyacrylamide/urea gel and used for reverse transcription with random hexamers and Superscript lll reverse transcriptase (Invitrogen). cDNA was amplified using Illimina primers and used for following sequencing on IIllimina platphorms.

treatment_protocol: IP with MIWI and MILI antibodies were done according (Aravin et al. 2008 Mol. Cell). Manually dissected testes were homogenized in lyses buffer and diluted 5 times in IP buffer NT2 with MIWI or MILI antibodies diluted 1:500 and incubated for 10 hours at 4C. Then protein A agarose beads (Roche) were added and incubated for 2 more hours at 4C. After 5 washes with NT2 buffer total RNA from immunoprecepitates was isolated by proteinase K treatment with following Phenol/Chloroform pH 4.8 (Ambion) extraction.

tag: antibodies

value: MILI N2 antibodies (Vagin et al. G&D2009)


title: wtSOD1 transgenic_3d_B6

city: New York

first: Mariano

middle: Javier

last: Alvarez

address: 1130 St. Nicholas ave.

department: Systems Biology

institute: Columbia University

data_processing:
OLB-1.9.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using TopHat (version 1.3.3) with default parameters.
Reads mapping to known genes, based on entrez gene identifiers, were counted using the GenomicFeatures R-system package (Bioconductor).
The expression data was normalized and the variance stabilized based on the negative binomial distribution with the DESeq R-system package (Bioconductor).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files with 4 columns: Entrez Gene ID (GeneID), Entrez gene symbol (symbol), Number of mapped reads (Reads), Variance Stabilized normalized expression (VSE).

source_name: ES-MN_wtSOD1 transgenic_3d

growth_protocol: ES cells were derived from transgenic Hlxb9-GFP1Tmj mice expressing eGFP or eGFP and CD2 driven by the mouse HB9 promoter. These cells were then differentiated into MNs as described previously by Wichterle et al. (Cell 110(3):385-97). The produced cell suspensions were resuspended in PBS containing 1% BSA at the concentration of 2E+7 cells per ml to be processed by MACS. Cell suspensions were incubated with 80 ul of L15 medium and 10 ul of anti-rat CD2 antibody (Invitrogen; per 15 million dissociated cells) for 20 min at 4 degC.  After washing again with L15 medium, cells were then incubated with anti-mouse magnetic microbeads (Miltenyi Biotec) for 20 min at 4 degC.  Finally, cells were passed through a magnetic column to separate CD2-GFP+ cells from the other types.  Post-sorting, the cells were collected in MN medium and were plated for culture.

extract_protocol:
At 1 day and 3 days of exposure to astrocytes conditioned media, total mRNA samples from purified ES-MNs were extracted using TRI Reagent Solution (Ambion) and isolated with MagMAX-96 total RNA Isolation kit (Ambion). Total RNA samples were, then, quantified by Nanodrop (Thermo Scientific) and their RNA integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Astrocyte monolayers were prepared from spinal cords or cortices of newborn mouse pups, obtained from the matings of transgenic mice overexpressing either G93A mutant SOD1 (mSOD1) or wtSOD1 with non-transgenic mice. After 2 weeks, these cultures contained 95% GFAP+ astrocytes, 5% of CD11b+ microglia, and no neurons or oligodendrocytes as indicated by the lack of, respectively, MAP2 or 2'-3'-cyclic nucleotide phosphohydrolase immunoreactivity. Residual microglia were eliminated by mechanical agitation. Then, ACMs were prepared from astrocyte cultures of different genotypes, collected and frozen in several aliquots. On the day of the assay, ACM was supplemented with 4.5 mg/ml D-glucose (final concentration), penicillin/streptomycin, and a cocktail of trophic factors composed of 0.5 ng/ml GDNF, 1 ng/ml BDNF and 10 ng/ml CNTF (trophic factor cocktail, R&D Systems). The ACM was then filtered (0.22 μm cellulose acetate membrane filter, Nalgene) before being added to the MN cultures.

value: transgenic Hlxb9-GFP1Tmj

value: ES-derived motor neurons (ES-MN)

tag: exposed to

value: wt SOD1 transgenic astrocyte condition media for 3 days

tag: experiment


title: wtSOD1 transgenic_3d_B3


title: wtSOD1 transgenic_3d_B4


title: mSOD1 transgenic_3d_B6

source_name: ES-MN_mSOD1 transgenic_3d

value: G93A mutant SOD1 transgenic astrocyte condition media for 3 days


title: wtSOD1 transgenic_3d_B5


title: MILI_IP_het_RNF17 testes

description: 19-33 nt size fractionated RNA

value: MIWI N2 antibodies( Vagin et al. G&D2009)


title: MILI_IP_homtRNF17 testes

description: 19-33 nt size fractionated RNA


title: MIWI_IP_het_RNF17 testes

description: 19-33 nt size fractionated RNA

value: MIWI N2 antibodies (Vagin et al. G&D2009)


title: mSOD1 transgenic_3d_B5


title: mSOD1 transgenic_3d_B4


title: het_RNF17 pachytene cells_2nd_replicate

description: 19-33 nt size fractionated RNA


title: hom_RNF17_6_week_old_adult_testis_smallRNA

description: 19-33 nt size fractionated RNA

source_name: adult testes of 6 week old mouse

extract_protocol:
Total RNA prepared with Trizol reagent (Invitrogen) was size selected (19-33nt) on 15% vertical polyacrylamide/urea gel.
small RNA libraries were prepared according (Malone et al. Cold Spring Harb Protoc. 2012). Size selected RNA was ligated with 3' adaptor Modban oligonucleotide with mutant T4 RNA ligase 2, truncated (home made). The ligated products were sized fractionated on 15% vertical polyacrylamide/urea gel and ligated with 5’ adaptor with T4 RNA ligase (Ambion). Then ligated products were separated on 15% vertical polyacrylamide/urea gel and used for reverse transcription with random hexamers and Superscript lll reverse transcriptase (Invitrogen). cDNA was amplified using Illumina primers and used for following sequencing on Illumina platforms.

value: testis


title: mSOD1 transgenic_3d_B3


title: het_RNF17_6_week_old_adult_testis_smallRNA

description: 19-33 nt size fractionated RNA


title: hom_RNF17_pachytene_cells_smallRNA

description: 19-33 nt size fractionated RNA

source_name: sorted pachytene cells

value: pachytene cells


title: hom_RNF17 _round_spermatids_smallRNA

description: 19-33 nt size fractionated RNA

source_name: sorted round spermatid cells

value: homozygous RNF17

value: spermatids


title: mSOD1 transgenic_3d_B1


title: Non-transgenic_3d_B5

value: non-transgenic astrocyte condition media for 3 days


title: wtSOD1 transgenic_3d_B1


title: Non-transgenic_3d_B3


title: Non-transgenic_3d_B6


title: het_RNF17_ MILI_IP_5RACE

data_processing:
Reads mapped to mm9 mouse genome release using Bowtie (Langmead et al. Genome Biol 2009, ) with up to 2 mis-matches and a maximum of 100 multiple alignments (otherwise suppressed)
Unmapped reads were re-mapped using STAR (Dobin et al.29;15-21 2013 Bioinformatics) with the same criteria to extract spliced reads (Dobin et al.29;15-21 2013 Bioinformatics). Then reads from fraction above and below 500bp were combined for the futher analysis.
Genome_build: mm9
Supplementary_files_format_and_content: txt files with all mappers, their reads number and genomic annotation

source_name: MILI IP from adult testes of 6 week old mouse

extract_protocol:
total RNA was extracted from manually dissected testes with Trizol reagent (Invitrogen)
5'RACE libraries were prepared according  (Karginov et al. 2010, Mol Cell 38: 781-788).  Poly(A)+ mRNAs were isolated from 100 g of total RNA using the Invitrogen Dynabeads mRNA Direct kit. The RNA was ligated to a 5 linker with T4 RNA ligase (Ambion). Reverse transcription reactions were carried out by handom hexamer priming SBS8-N6 primer and SuperScript III (Invitrogen). Template RNA was degraded by addition of 1 l RNase H (Invitrogen). PCR reactions on the resulting cDNAs were carried out using KOD Hot Start DNA polymerase (Novagen) with PE-P5-SBS3 and PE-P7-SBS8 primers. Products were run on a 2% low-melt agarose gel, and the 150500 bp (sometimes 1501000bp) range was purified.

value: heterozygous RNF17 knockout


title: het_RNF17_pachytene_cells_smallRNA

description: 19-33 nt size fractionated RNA

value: heterozygous RNF17


title: Non-transgenic_3d_B4


title: hom_RNF17_ MILI_IP_5RACE

value: homozygous RNF17 knockout


title: het_RNF17_ MIWI_IP_5RACE

source_name: MIWI IP from adult testes of 6 week old mouse


title: hom_RNF17_ MIWI_IP_5RACE


title: wtSOD1 transgenic_3d_B2


title: Non-transgenic_3d_B2


title: Non-transgenic_3d_B1


title: hom RNF17 RNF17IP rep2 RNAseq

data_processing:
First 8 nucleotides from 5 'end were trimmed and reverse-complemented before genomic mapping
Mapped to mm9 mouse genome release with STAR (Dobin et al.29;15-21 2013 Bioinformatics) with 2 mismatches and maximum of 100 multiple alignments.
DESeq was used according to (Anders and Huber 2010, Genome Biol 11: R106.)
Genome_build: mm9
Supplementary_files_format_and_content: results of DESeq analysis only for transcripts which are deferentially expressed between homozygous and heterozygous RNF17mutant 6 week old adult testes include fold change in raw counts normalized according to DESeq protocol (Anders and Huber 2010, Genome Biol 11:R106) (up- (fold change<0) or down-regulated (fold change>0)) and p-values. Number of reads that map to genes or uniquely or multiple times (2-99) to tranposable elements form RNF17 IP or total testes lysate.

source_name: RNF17 IP from lysate of 6 week old testes

extract_protocol:
total RNA was prepared with Trizol reagent (Invitrogen)
Transcriptome libraries were prepared according  (Armour et al. 2009, Nat Methods) using not-so-random priming (NSR). 1 ug total RNA was revere transcribed using SuperScript III enzyme with first-strand NSR primer. RNA template was removed with RNase H (Invitrogen) Then cDNA was mixed with exo− Klenow fragment (NEB) second-strand NSR primer to synthesize the second strand. For PCR amplification, purified second-strand synthesis reaction were mixed with ExpandPLUS enzyme (Roche) and PE-P5-SBS3 and PE-P7-SBS8 primers. Products were run on a 2% low-melt agarose gel, and the 350–500 bp. range were purified.

treatment_protocol: IP with RNF17 antibodies were done according (Aravin et al. 2008 Mol. Cell). Manually dissected testes were homogenized in lyses buffer and diluted 5 times in IP buffer NT2 with RNF17 antibodies diluted 1:500 and incubated for 10 hours at 4C. Then protein A agarose beads (Roche) were added and incubated for 2 more hours at 4C. After 5 washes with NT2 buffer total RNA from immunoprecepitates was isolated by proteinase K treatment with following Phenol/Chloroform pH 4.8 (Ambion) extraction.

value: RNF17 1774 antibody (Pan, J. et al. Development 2005)


title: het RNF17 RNF17IP rep2 RNAseq

value: 6 weeks old


title: hom RNF17 RNF17IP rep1 RNAseq


title: wtSOD1 transgenic_1d_B4

source_name: ES-MN_wtSOD1 transgenic_1d

value: wt SOD1 transgenic astrocyte condition media for 1 day


title: het RNF17 RNF17IP rep1 RNAseq


title: wtSOD1 transgenic_1d_B3

value: transgenic Hlxb9-GFP1Tmj


title: mSOD1 transgenic_3d_B2

value: ES-derived motor neurons (ES-MN)


title: het RNF17 6 week old adult testis rep2 RNAseq


title: wtSOD1 transgenic_1d_B2


title: wtSOD1 transgenic_1d_B5


title: wtSOD1 transgenic_1d_B1


title: hom RNF17 6 week old adult testis rep1 RNAseq


title: mSOD1 transgenic_1d_B6

source_name: ES-MN_mSOD1 transgenic_1d

value: G93A mutant SOD1 transgenic astrocyte condition media for 1 day


title: het_RNF17 _ round_spermatids_smallRNA

description: 19-33 nt size fractionated RNA


title: het RNF17 6 week old adult testis rep1 RNAseq


title: mSOD1 transgenic_1d_B4


title: mSOD1 transgenic_1d_B5


title: mSOD1 transgenic_1d_B3


title: Non-transgenic_1d_B6

value: non-transgenic astrocyte condition media for 1 day


title: mSOD1 transgenic_1d_B1


title: het_RNF17_ 5RACE_small and large500bp


title: stk2

city: Milano

first: IGNACIO

last: EZQUER

state: Italia

address: Via celoria 26

country: Italy

institute: MILANO UNIVERSITY

data_processing:
Base-calling and quality value calculations were performed using the Illumina data processing pipeline (version 1.8).
Raw reads were filtered to obtain high-quality reads by removing low-quality reads containing more than 30% bases with Q < 20. a quality control of the raw sequence data was performed using FastQC.
Gene expression value was based on reads per kilobase of exon model per million mapped reads (RPKM) values. The fold change and differential expression values between wild type and stk mutant was calculated in terms of RPKM of the corresponding transcripts.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: Arabidopsis inflorescences and siliques until 5 DAP

growth_protocol: Arabidopsis thaliana wild-type (ecotype Columbia) and stk mutant plants were grown at 22°C under short-day (8 h light/16 h dark) or long-day (16 h light/8 h dark) conditions.

extract_protocol:
Total RNA was extracted from two biological replicates from both wild-type and stk mutant inflorescences and siliques until 5 DAP with the Qiagen Kit according to the manufacturer's instructions. DNA contaminations were removed using the PROMEGA RQ1 RNase-Free DNase according to the manufacturer's instructions. RNA quality integrity was analyzed by electrophoresis gel and was validated on a Bioanalyzer 2100 (Aligent, Santa Clara, CA); RNA Integrity Number (RIN) values were greater than 7 for all the samples.
Sequencing libraries were prepared according to the manufacturer’s instructions by TruSeq RNA Sample Prep kit (Illumina Inc.)

value: Columbia

value: inflorescences and siliques

value: inflorescences and siliques until 5 DAP

tag: genotype

value: stk-/-


title: wtSOD1 transgenic_1d_B6


title: stk1


title: hom_RNF17_5RACE_small and large500bp


title: mSOD1 transgenic_1d_B2


title: hom RNF17 6 week old adult testis rep2 RNAseq

value: homozygous RNF17


title: Non-transgenic_1d_B5


title: wt2

value: wild type


title: RPE-WCE_for_MITF

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: Retinal pigment cells

growth_protocol: sciencell epithelial media

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
sonication

treatment_protocol: Fix 12 min

tag: cell type

value: Sciencell #6540

tag: chip antibody

tag: antibody vendor


title: Non-transgenic_1d_B4


title: wt1


title: Non-transgenic_1d_B3


title: Non-transgenic_1d_B2


title: Non-transgenic_1d_B1


title: RPE-LHX2_ChipSeq

growth_protocol: sciencell epithelail media

value: Santa Cruz

tag: antibody catalog#


title: RPE-PAX6_ChipSeq

value: Abcam


title: RPE-MITF_ChipSeq

value: MITF

value: Active motif


title: 35S::BBM-GFP

city: Wageningen

first: Kim

last: Boutilier

address: Droevendaalsesteeg 1

institute: Plant Research International

description: Processed data file: 35SL003vsL004bg2_t2.wig

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were mapped to TAIR10 whole genome using SOAPv2 -r 0.
CSAR (default parameter except backg=2) was used for the peak calling step.
Genome_build: TAIR10
Supplementary_files_format_and_content: wig; files to be visualized in a genome browser.

source_name: BBM induced embryogenic seedlings, 35S::BBM-GFP

extract_protocol:
Somatic embryo material was cross-linked using formaldehyde and ground prior to nuclear extraction. The nuclear pellet was sonicated and the lysate was used for immunoprecipitation with the µMACS GFP Isolation Kit (Miltenyi, cat.# 130-091-125, lot# 5130926275). After proteinase K treatment, the DNA was purified using the QIAquick kit (Qiagen).
The Illumina ChIP-Seq library preparation kit was used for library construction using the manufacturer's protocol, except that 1:10 dilutions were used of the adapters. Library fragments of 200-500 bp were excised from the gel and purified.

tag: ecotype

value: whole embryogenic seedlings

value: anti-GFP microbeads (Miltenyi µMACS GFP Isolation Kit)


title: 35S::BBM

source_name: BBM induced embryogenic seedlings, 35S::BBM

value: negative control


title: pBBM::BBM-YFP

description: Processed data file: pBBMBBMYFPvsNLSbg2_t2.wig

source_name: 2,4-D induced somatic embryos, pBBM::BBM-YFP

value: somatic embryo


title: pBBM::NLS-GFP

source_name: 2,4-D induced somatic embryos, pBBM::NLS-GFP


title: M421_DMSO

status: Public on Dec 16 2014

city: Los Angeles

first: Jennifer

last: Tsoi

state: CA

address: 570 Westwood Blvd, CNSI 4338

department: University of California, Los Angeles

institute: UCLA

data_processing:
Read mapping was performed using TopHat version 2.0.9 with the NCBI Build 37 reference genome.
Read counts per gene were quantified using HTSeq version 0.5.4.
The CQN R Package was used to compute FPKM by adjusting read counts for gene length and GC content and to obtain offsets for normalization and analysis using the DESeq2 R package.
Genome_build: NCBI Genome build 37
Supplementary_files_format_and_content: Matrix of gene expression measurements in FPKM

source_name: Melanoma

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells have been treated with DMSO for 48 hours.

value: Melanoma

tag: cell line


title: M417_DMSO


title: dme_maternal

city: Colchester

first: Antonio

last: Marco

address: Wivenhoe Park

department: School of Life Sciences

institute: University of Essex

description: small RNA

data_processing:
Adapters were removed with Cutadapt (https://code.google.com/p/cutadapt/)
Supplementary_files_format_and_content: TAB-delimited file of trimmed sequences and  number of reads

organism: Drosophila melanogaster

source_name: Unfertilized eggs small RNAs

extract_protocol:
Total RNA was extracted with TRIzol reagent (Life Technologies), following instructions given by the manufacturer, and dissolving the RNA in RNase-free water.
cDNA libraries were generated with TruSeq Small RNA Sample Preparation Kit (Illumina) following specifications from the manual. Amplified cDNA constructs were size selected in a 6% PAGE gel for 145 to 160 bp (fragments including RNA-derived sequences of size ~20-30 bp plus adapters). Size selected cDNAs were purified and precipitated with ethanol, and DNA integrity was checked with TapeStation (Agilent).

tag: source

value: Unfertilized eggs

value: Bloomington w[1118]


title: M420_DMSO


title: M411_DMSO


title: totalArab_nuc_rep2_DSN

city: Philadelphia

first: Sager

middle: Jayesh

last: Gosai

state: Pennsylvania

address: 433 S University Ave.

institute: Universiry of Pennsylvania

data_processing:
Basecalls performed with Bustard 1.9.3.
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed to a list of non-redundant sequence tags using an in-house perl (version 5.8.8) script
Untrimmed non-redundant sequence tags were aligned to the Arabidopsis thaliana genome (TAIR10) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
Isolated non-redundant, untrimmed sequence tags mapping to intron/exon juctions of first or last constitutively spliced  intron (per TAIR10) of all annotated mRNAs using bedtools suite
Calculated the fraction of isolated reads mapping to both exonic and intronic sequences (unspliced read) and fraction of reads with gaps mapping exactly to introns (spliced read) using bedtools
Genome_build: TAIR10
Supplementary_files_format_and_content: BAM files containing reads mapping to most 5' or most 3' constitutively spliced intron/exon junctions

source_name: Total seedlings

growth_protocol: The purified nuclei used in this study were extracted from 10-day-old seedlings of UBQ10:NTF/ACT2p:BirA Columbia-0 (Col-0) ecotype of Arabidopsis thaliana using the INTACT methodology. All plants were grown at 20°C, in a 16 h light/8 h dark cycle

extract_protocol:
For each sample, ~0.5 million INTACT purified nuclei were lysed in 850 ml RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 mM DTT; 1 tablet protease inhbitors and 0.5ml/ml RNaseOUT (Life Technologies; Carlsbad, CA)) by manual grinding. RNA was then isolated using the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
Purified RNA was used as the substrate for strand-specific sequencing library preparation (TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Zheng et al. 2010; Li et al. 2011), with the exception that we also include DSN library normalization per manufacturer instructions (Illumina; San Diego, CA).

treatment_protocol: 10-day-old seedlings of UBQ10:NTF/ACT2p:BirA underwent INTACT purification as previously described (Deal, 2010).

value: UBQ10:NTF/ACT2p:BirA (Col-0)


title: M416_DMSO


title: M410_DMSO


title: M409AR_DMSO


title: BMDBKCs-HiSeq

city: Shihezi

first: Qiang

last: Fu

state: Xinjiang

address: Bei 4 Road

institute: Shihezi University

data_processing:
Data cleaning and length distribution using a software developed by BGI
Common and specific sequences between samples
Mapping to genome  by SOAP
Summary of known miRNA alignment with miRBase18
Repeat associated RNA alignment using a software developed by BGI(tag2repeat)
Alignment to Genbank using blastall and blastn
Alignment to Rfam using blastall and blastn
Exon and intron alignment using a software developed by BGI(overlap)
Small RNA annotation using a software developed by BGI (tag2annotation)
Novel miRNA prediction using a software developed by BGI (Mireap)
Family analysis of known miRNA
Target prediction for novel miRNA candidates using  Mireap
miRNA base edit with miRBase18
GO enrichment analysis using GO terms (http://www.geneontology.org/)
KEGG pathway analysis in KEGG
Genome_build: bosTau7
Supplementary_files_format_and_content:
sig.txt  file contains differentially-expressed known miRNAs in BMDBKCs compared to MDBKCs;
stat.txt file contains differentially-expressed novel miRNAs in BMDBKCs compared to MDBKCs;
*match_hairpin.aln.txt contains miRNA precursor information (sequence, name, length, hairpin structure, structure, minimization of Gibbs free energy (MFE)) and mature miRNA information (sequence, ID, length).
*match_hairpin.txt contains results of blasting with miRBase17 (miRNA name, mature miRNA name, ID, count, count, position, sequence, sequence).
*miRNA.txt contains mature miRNA information (ID, length, count, sequence, mature miRNA name).
profile_total.xls contains miRNA profile information (name, expressed reads in BMDBKCs, expressed reads in MDBKCs).

organism: Bos taurus

source_name: MDBK cells infected with BVDV

growth_protocol: MDBK cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% heat-inactivated horse serum.

extract_protocol:
The cells were treated with BVDV NADL for 6 h, and total RNA was extracted using the Total RNA Extraction Kit (Tiangen).
First-strand cDNA was synthesized from 2 μg of total RNA using a Reverse Transcription Kit (Tiangen).
Differentially-expressed miRNAs in MDBK cells infected with bovine viral diarrhea virus compared to MDBK cells were sequenced using Solexa high-throughput sequencing technology (BGI, China).

treatment_protocol: BVDV NADL (100 TCID50/ 0.1 ml) for 6 h

value: Madin-Darby bovine kidney (MDBK) cells

tag: passages

tag: infected with

value: bovine viral diarrhea virus (BVDV) NADL (100 TCID50/ 0.1 ml) for 6 h


title: totalArab_nuc_rep4_ssRNase_protein

description:
totalArab_nuc_rep4_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed

data_processing:
Basecalls performed with Bustard 1.9.3.
3' adapter sequences were trimmed using cutadapt (version 1.2.1 with parameters -e 0.06 -O 6 -m 14)
Redundant reads were compressed using an in-house perl (version 5.8.8) script
Trimmed and untrimmed reads were aligned to the Arabidopsis thaliana genome (TAIR10) using Tophat (version 2.0.10 with parameters --library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive --transcriptome-max-hits 10 --no-coverage-search –no-novel-juncs)
Reads mapping to the mitochondria and chloroplast genomes were discarded and protein-protected sites (PPSs) were identified using a modified version of the CSAR software package (Muino et al. 2011). Specifically, read coverages were calculated for each base position in the genome and a Poisson test was used to compute an enrichment score for ‘protected’ versus ‘unprotected’ libraries. PPSs were then called as described (Muino et al. 2011) with an false discovery rate (FDR) of 5%
The "*_structScore_TH*.txt" files are tab-delimited text files containing the calculated "structure score" of every nucleotide of all annotated mRNA (TAIR10), pre-mRNA (TAIR10), or mRNA cleavage sites (Sherstnev A. et al., 2012) with sufficient dsRNA-seq and ssRNA-seq coverages, as well as other pertinent information such as their feature length and (weighted) clone number of the dsRNA-seq and ssRNA-seq reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: BED/peak format of protein protected sites (PPSs)

extract_protocol:
~Two million INTACT purified nuclei were lysed in 850 ml RIP buffer (25 mM Tris-HCl, pH = 7.4; 150 mM KCl, 5 mM EDTA, pH = 7.5; 0.5% NP40; 10 mM DTT; 1 tablet protease inhbitors and 0.5ml/ml RNaseOUT (Life Technologies; Carlsbad, CA)) by manual grinding. The resulting cell lysate was treated with RNase-free DNase (Qiagen; Valencia, CA). The lysates were then split and treated with either 100 U/ml of a single-stranded RNase (ssRNase) (RNaseONE (Promega; Madison, WI)) with 200 μg/ml BSA in 1X RNaseONE buffer for 1 hour at room temperature (RT), or 2.5 U/ml of a double-stranded RNase (dsRNase) (RNaseV1 (Ambion; Austin, TX)) in 1X RNA structure buffer for 1 hour at 37°C as previously described (Silverman, 2014). See Figure 1A for a schematic representation of library preparation. Proteins were then denatured and digested by treatment with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) for 15 minutes at RT. Proteinase digestion was followed by a 2 hour incubation at 65°C to reverse the RNA-protein cross-links. To determine whether nuclease resistant regions in RNAs are due to protein binding or specific secondary structures, we also determined the digestion patterns of ds- and ssRNases immediately following protein digestion. To do this, we performed the identical treatments as described above except that the cross-linked nuclear lysates were treated with 1% SDS and 0.1 mg/ml Proteinase K (Roche; Basel, Switzerland) and ethanol precipitated prior to being treated with the two RNases. In this way, the SDS and Proteinase K solubilized and digested the proteins allowing us to deduce PPSs within all detectable RNAs in the cells of interest (see Figure 1A for schematic).The digested RNA was then isolated using the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
Purified RNA was used as the substrate for strand-specific sequencing library preparation (TruSeq small RNA sequencing kit [illumina, Valencia, CA]), as previously described (Zheng et al. 2010; Li et al. 2011), with the exception that we also include DSN library normalization per manufacturer instructions (Illumina; San Diego, CA).

treatment_protocol: Immediately before nuclei purification, 10-day-old seedlings of UBQ10:NTF/ACT2p:BirA were crosslinked in nuclear purification buffer (20 mM MOPS (pH 7), 40 mM NaCl, 90 mM KCl, 2 mM EDTA, 0.5 mM EGTA) plus 1% (vol/vol) formaldehyde under vacuum for 10 minutes, followed by a five minute quench with 125 mM Glycine under vacuum for an additional five minutes.  Crosslinked seedlings then underwent INTACT purification as previously described (Deal, 2010).

tag: crosslinker

value: formaldehyde

tag: rnase

value: ssRNase (Rnase One)

tag: cultivar

tag: tissue

value: seedling

tag: protein-bound

value: yes


title: MDBKCs-HiSeq

source_name: MDBK cells

value: none (control)


title: totalArab_nuc_rep1_DSN


title: M406_DMSO


title: M407_DMSO


title: 500 μg/l BDE47 treatment

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
After obtained from the raw sequencing data, clean reads were mapped into reference zebrafish genome Zv9 assembly, and also H.sapiens hg19 assembly using BLAST to increase the subsequent annotation efficiency.
Trimmed mean of M-values of library size (TMM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: zv9
Supplementary_files_format_and_content: tab-delimited text files include TMM values for each Sample

organism: Danio rerio

source_name: 6 dpf larvae, 500 μg/l BDE47 treatment

extract_protocol:
Zebrafish larvae were homogenized, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Tuebingen

value: whole larvae

tag: age

value: 6 day post fertilization


title: totalArab_nuc_rep4_ssRNase_noprotein

description:
totalArab_nuc_rep4_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed
At_total_refTAIR10_cleavage_invivo_structScore_TH010.txt
At_total_refTAIR10_mRNA_invivo_structScore_TH100.txt
At_total_refTAIR10_pri_mRNA_invivo_structScore_TH100.txt

value: no


title: oblong_polyA_RNA_Seq

city: Jerusalem

first: Michal

last: Rabani

address: Hebrew University, Edmond J. Safra Campus, Silberman building

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
aligned reads to the zebrafish reference genome (DanRer 7, Zv9) using the TopHat aligner.
apply a newly developed method (DRiLL) to estimate precursor and mature RNA expression of annotated transcripts from mapped sequence reads and zebrafish expression source (Maternal or Zygotic)
Genome_build: zv9
Supplementary_files_format_and_content: expression_gene.zebrafish_oblong.txt text file contains DRiLL predicted expression levels of the precursor and mature RNA of early developmental genes.

source_name: zebrafish embryos, oblong staged

extract_protocol:
Zebrafish samples Total RNA was isolated using the standard Trizol (Invitrogen) protocol. Two rounds of PolyA+-RNA purification were performed for each sample, using the PolyA(Purist)TM-MAG kit (Ambion). The quality of the RNA and lack of contaminating ribosomal RNA were confirmed using the Agilent 2100 Bioanalyzer.
We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.

treatment_protocol: Zebrafish embryos were dechorionated at the 1-cell stage, followed by incubation at 28C for 3.5 hours.

tag: developmental stage

value: oblong

value: embryo

tag: hours post fertilization

value: 3.5 hours

tag: treatment

value: polyA+ selection


title: RPE-OTX2_ChipSeq

tag: cell type

value: Sciencell #6540

tag: chip antibody

tag: antibody vendor

value: Abcam


title: 5 μg/l BDE47 treatment

source_name: 6 dpf larvae, 5 μg/l BDE47 treatment


title: DMSO vehicle

source_name: 6 dpf larvae, DMSO vehicle


title: M397_DMSO

value: Melanoma

tag: cell line


title: M409_DMSO


title: totalArab_nuc_rep4_dsRNase_protein

description:
totalArab_nuc_rep4_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed

value: dsRNase (Rnase V1)


title: M403_DMSO


title: totalArab_nuc_rep4_dsRNase_noprotein

description:
totalArab_nuc_rep4_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed
At_total_refTAIR10_cleavage_invivo_structScore_TH010.txt
At_total_refTAIR10_mRNA_invivo_structScore_TH100.txt
At_total_refTAIR10_pri_mRNA_invivo_structScore_TH100.txt

value: formaldehyde


title: RNaseL_shRNA_IAV-Infected_A549

city: Aurora

first: Daphne

middle: A.

last: Cooper

state: CO

department: Department of Microbiology

institute: University of Colorado

description:
Host and viral RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from IAV-infected, RNase L shRNA-treated A549 cells at 24 hpi

data_processing:
Reads were trimmed for residual cDNA linker (IDT miRNA cloning linker 1)
Fastq datasets were trimmed for 8-base unique molecular identifier using umitools (github.com/brwnj/umitools).
Aligned to influenza and cellular RNA sequences using Bowtie2, unique UMIs counted using umitools, and using bedtools genomecov, bam converted to bedgraph format based on genomic (-) or anti-genomic (+) strand.
Aligned data normalized to the total number of aligned reads and depicted as a % of total aligned reads.
The 3'-dinucleotide from the read was obtained to characterize RNase specificity, and the % of total aligned reads was plotted for cleavage sites across the genome/sequence.
Genome_build: FLU_PB2: AF389115.1
Genome_build: FLU_PB1: AF389116.1
Genome_build: FLU_PA: AF389117.1
Genome_build: FLU_HA: AF389118.1
Genome_build: FLU_NP: AF389119.1
Genome_build: FLU_NA: AF389120.1
Genome_build: FLU_M: AF389121.1
Genome_build: FLU_delNS1: AF389122.1 (nucleotides 57-528 deleted)
Genome_build: 45S_prerRNA: NR_046235.1
Supplementary_files_format_and_content: Text files for + strand reads [genome, cleavage site -1, cleavage site, # of UMI reads, normalized value, 3'-dinucleotide] Text files for - strand reads [genome, cleavage site with + strand numbering, cleavage site with - strand numbering, # of UMI reads, normalized value, 3'-dinucleotide]

source_name: Lung Carcinoma Cells

extract_protocol:
Total RNA harvested at 24 hpi using Trizol.
Illumina TruSeq RNA linker with 8-base Unique Molecular Identifier (UMI) was attached with Arabidopsis thaliana tRNA ligase (recognizes RNAs with terminal 2', 3'-cyclic phosphates). cDNA was generated using a DNA primer specific to the Illumina linker, and the IDT miRNA cloning linker 1 was attached to the 3'-end of the cDNA. cDNAs were PCR amplified, pooled, and sequenced.
2', 3'-cyclic phosphate cDNA synthesis and Illumina sequencing were used to identify and quantify metal-ion-independent endoribonuclease cleavage sites in host and viral RNAs

treatment_protocol:
A549 cells were infected with the lentiviruses expressing control shRNA or RNase L shRNA.
Control or RNase L shRNA-treated A549 cells were left uninfected or infected at an MOI of 10 using IAVΔNS1.

value: A549 Lung Carcinoma Cells

tag: shRNA treatment

value: RNase L shRNA-Treated

tag: infection

value: Influenza A (A/PR/8/34) ΔNS1-Infected

tag: time

value: 24 hpi


title: RNaseL_shRNA_Uninfected_A549

description:
Host and viral RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from uninfected, RNase L shRNA-treated A549 cells at 24 hpi

value: Control shRNA-Treated

value: Uninfected


title: Control_shRNA_IAV-Infected_A549

description:
Host and viral RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from IAV-infected, control shRNA-treated A549 cells at 24 hpi


title: M399_DMSO


title: M395_DMSO


title: LPS_180min_RNA_4sU

description:
4sU-containing RNA
expression.4sUl.M.txt
expression.4sU.P.txt
gene_expression.4sU.M.txt
gene_expression.4sU.P.txt
rates.tx.txt
rates.px.txt
rates.dg.txt
gene_rates.tx.txt
gene_rates.px.txt
gene_rates.dg.txt

data_processing:
aligned reads to the mouse reference genome (NCBI 37, MM9) using the TopHat aligner.
used Trinity de novo transcript assembly and Cufflinks ab initio transcript reconstructionto reconstruct mature transcripts from available polyA+ sequencing data in DCs.
apply a newly developed method (DRiLL) to estimate precursor and mature RNA expression of annotated transcripts from mapped sequence reads and kinetic parameters
Genome_build: mm9
Supplementary_files_format_and_content: expression.M.txt text files contain DRiLL predicted expression levels of mature splicing junctions (one column per time point). expression.M.txt text files contain DRiLL predicted expression levels of precursor splicing junctions (one column per time point). gene_expression.M.txt contain median mature expression per gene. gene_expression.P.txt contain median precursor expression per gene. rates.*.txt contain DRiLL predicted rates per splicing junction: tx = transcription rates, px = processing rates, dg = degradation rates (one column per time point), and gene_rates.*.txt contain DRiLL predicted rates per gene (same rates, one column per timepoint)

source_name: Mouse dendritic cells

extract_protocol:
Total RNA was extracted with the miRNeasy kit's procedure (Qiagen). For preparation of RNA-Sequencing samples, we used 10 μg total RNA and removed rRNA with the RiboZero kit (Epicenter). After taking an aliquot of 100 ng ribosomal depleted total RNA, we followed with 4sU purification for the remainder of the sample as desceibed in Rabani et. al., Nat. Biotech., 2011
We prepared the RNA-Seq libraries using the dUTP second strand (strand specific) protocol as described in Levin et. al, Nat. Methods, 2010.

treatment_protocol: We collected RNA samples at 0h and until 3h after LPS stimulation in 15 minutes intervals. 4-thiouridine (Sigma) was added to a 500 μM final concentration for 10 minutes before RNA collection.

value: dendritic cell

tag: stimulation

value: LPS

tag: time post stimulation

value: 180 min

value: ribosomal delpetion, 4sU selection


title: totalArab_nuc_rep3_ssRNase_noprotein

description:
totalArab_nuc_rep3_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed
At_total_refTAIR10_cleavage_invivo_structScore_TH010.txt
At_total_refTAIR10_mRNA_invivo_structScore_TH100.txt
At_total_refTAIR10_pri_mRNA_invivo_structScore_TH100.txt

tag: crosslinker

tag: rnase

value: ssRNase (Rnase One)

tag: cultivar

value: seedling

value: no


title: Control_shRNA_Uninfected_A549

description:
Host and viral RNA fragments with 2’, 3’-cyclic phosphates
2', 3'-cyclic phosphate cDNA library derived from uninfected, control shRNA-treated A549 cells at 24 hpi


title: M381_DMSO


title: LPS_165min_RNA_4sU

tag: strain

value: 165 min


title: totalArab_nuc_rep3_dsRNase_protein

description:
totalArab_nuc_rep3_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed

tag: tissue

tag: protein-bound

value: yes


title: LPS_135min_RNA_4sU

value: 135 min


title: M395AR_DMSO

value: Melanoma


title: LPS_105min_RNA_4sU

value: 105 min


title: LPS_120min_RNA_4sU

value: 120 min


title: LPS_90min_RNA_4sU

value: 90 min


title: M370_DMSO


title: LPS_75min_RNA_4sU

value: 75 min


title: M308_DMSO


title: LPS_60min_RNA_4sU

value: 60 min


title: LPS_45min_RNA_4sU

value: 45 min


title: totalArab_nuc_rep3_ssRNase_protein

description:
totalArab_nuc_rep3_ssRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed

value: formaldehyde


title: M397AR_DMSO


title: M297_DMSO


title: totalArab_nuc_rep3_dsRNase_noprotein

description:
totalArab_nuc_rep3_dsRNase_mergedGapped.CSAR_PPS_FDR05.bed
totalArab_nuc_rep3and4_merged_mergedGapped.CSAR_PPS_FDR05.bed
At_total_refTAIR10_cleavage_invivo_structScore_TH010.txt
At_total_refTAIR10_mRNA_invivo_structScore_TH100.txt
At_total_refTAIR10_pri_mRNA_invivo_structScore_TH100.txt

value: dsRNase (Rnase V1)


title: ChIP-seq analysis of PolII in KB cells (PolII 5Z +IL1)

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings
Genome_build: hg19
Supplementary_files_format_and_content: coverage Wiggle files were generated with Mscs1.4 at 10 bp resolution. Wig files were converted to bigwig using the wigToBigWig utility (UCSC)

source_name: KB cells

growth_protocol: cells were cultured in DMEM, 10% FCS, to subconfluency

extract_protocol:
ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris pH 8.1, 1mM PMSF, Roche protease inhibitor mix), followed by IP and purification of DNA
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: IL-1 alpha and inhibitors PHA-408 and 5Z-oxozeaenol were added directly to the cell culture medium

value: 10ng/ml IL-1alpha for 1 h

value: 1µM 5Z-7-oxozeaenol for 1 h

tag: antibody

value: anti-PolII (Millipore, catalog# 17-620, Lot #1975094)


title: ChIP-seq analysis of PolII in KB cells (PolII 5Z)

description: ChIP-seq


title: ChIP-seq analysis of p65 in KB cells (p65 5Z IL1)

description: ChIP-seq

value: anti-p65 (Santa Cruz, catalog# sc-372, Lot #K2210)


title: LPS_30min_RNA_4sU

value: dendritic cell

value: LPS

value: 30 min

tag: treatment

value: ribosomal delpetion, 4sU selection


title: M263_DMSO

tag: cell type

value: Melanoma


title: LPS_0min_RNA_4sU

value: 0 min


title: LPS_180min_RNA_total

description:
expression.total.M.txt
expression.total.P.txt
gene_expression.total.M.txt
gene_expression.total.P.txt
rates.tx.txt
rates.px.txt
rates.dg.txt
gene_rates.tx.txt
gene_rates.px.txt
gene_rates.dg.txt

value: 180 min

value: ribosomal delpetion


title: ChIP-seq analysis of p65 in KB cells (p65 5Z)

description: ChIP-seq


title: LPS_150min_RNA_4sU

value: 150 min


title: LPS_15min_RNA_4sU

value: 15 min


title: LPS_165min_RNA_total

value: 165 min


title: Sequencing of input (Input IL1 5Z)

description: ChIP-seq


title: M255_DMSO


title: LPS_135min_RNA_total

value: 135 min


title: Sequencing of input (Input 5Z)

description: ChIP-seq


title: LPS_120min_RNA_total

value: 120 min


title: LPS_150min_RNA_total


title: M249_DMSO


title: LPS_90min_RNA_total

value: 90 min


title: M238_DMSO


title: M238AR_DMSO


title: LPS_105min_RNA_total

value: 105 min


title: ChIP-seq analysis of H3K27Ac in KB cells (H3K27Ac IL1 5Z)

description: ChIP-seq

value: 10ng/ml IL-1alpha for 1 h

value: 1µM 5Z-7-oxozeaenol for 1 h

value: Anti-H3K27Ac (Diagenode, catalog# 174-050, Lot #A7071-001P)


title: Sequencing of input (Input IL1)

description: ChIP-seq


title: LPS_0min_RNA_total

value: dendritic cell

value: LPS


title: LPS_30min_RNA_total

value: 30 min


title: LPS_75min_RNA_total

value: 75 min


title: Sequencing of input (Input)

description: ChIP-seq


title: LPS_60min_RNA_total

value: 60 min


title: LPS_45min_RNA_total

value: 45 min


title: M229_DMSO

value: Melanoma


title: M229AR_DMSO


title: ChIP-seq analysis of H3K4me1 in KB cells (H3K4me1 IL1 5Z)

description: ChIP-seq

value: Anti-H3K4me1 (Abcam, catalog# ab8895, Lot GR61280)


title: ChIP-seq analysis of H3K27Ac in KB cells (H3K27Ac IL1)

description: ChIP-seq


title: M262_DMSO_2


title: ChIP-seq analysis of H3K4me1 in KB cells (H3K4me1 IL1)

description: ChIP-seq


title: ChIP-seq analysis of PolII in KB cells (p(S5) PolII IL1 5Z)

description: ChIP-seq

value: anti-P(S5)-PolII (Abcam, catalog# ab5131, Lot GR138607-1)


title: ChIP-seq analysis of PolII in KB cells (p(S5) PolII 5Z)

description: ChIP-seq


title: ChIP-seq analysis of H3K4me1 in KB cells (H3K4me1 5Z)

description: ChIP-seq


title: ChIP-seq analysis of PolII in KB cells (p(S5) PolII IL1)

description: ChIP-seq


title: ChIP-seq analysis of p65 in KB cells (p65 PHA IL1)

description: ChIP-seq

value: 5µM PHA-408

value: anti-p65 (Santa Cruz, catalog# sc-372, Lot #K2210)


title: LPS_15min_RNA_total

value: 15 min

value: ribosomal delpetion


title: M233_DMSO


title: ChIP-seq analysis of H3K27Ac in KB cells (H3K27Ac 5Z)

description: ChIP-seq


title: RNA-seq in KB cells (IL1)

description:
RNA-seq
KB cells IL1

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Read mapping was done with Bowtie2 called from TopHat
The aligned reads were analyzed with Cufflinks and Cuffdiff  in order to obtain gene expression measures and to identify differentially expressed genes
Genome_build: hg19
Supplementary_files_format_and_content: Gene model specific output from cuffdiff analysis

extract_protocol:
TRIZOL
Single-end sequencing libraries were prepared from purified polyA-mRNA isolated from non-treated or IL-1 treated KB cells using ScriptSeqTM v2

treatment_protocol: IL-1 alpha was added directly to the cell culture medium


title: ChIP-seq analysis of p65 in KB cells (p65 PHA)

description: ChIP-seq


title: ChIP-seq analysis of p65 in KB cells (p65 DMSO )

description: ChIP-seq


title: RNA-seq in KB cells (control)

description:
RNA-seq
KB cells control


title: ChIP-seq analysis of H3K4me1 in KB cells (H3K4me1)

description: ChIP-seq


title: ChIP-seq analysis of PolII in KB cells (p(S5) PolII)

description: ChIP-seq


title: Myc_Control_ChIP_seq_Aero

status: Public on Dec 15 2014

city: Madison

first: Timothy

middle: J

last: Donohue

state: WI

address: 1552 University Avenue

department: Bacteriology

institute: University of Wisconsin - Madison

data_processing:
100 bp reads were trimmed to 70bp to remove unreliable base calls. 50bp reads were not trimmed
Mapping was done to the R. sphaeroides reference genome using SOAP version 2.21 allowing for 3 mismatches for 70bp reads and 2 mismatches for 50bp reads
Peaks were identified using MOSAiCS at a false discovery rate of 0.05 using a two-sample analysis with Input DNA or mock chip used as control.
Genome_build: Rhodobacter sphaeroides 2.4.1 GCA_000012905.2
Supplementary_files_format_and_content: Processed data files are provided as wig files with scores representing the normalized ratio of reads between a sample ChIP and INPUT DNA

organism: Cereibacter sphaeroides

source_name: Bacteria culture (SIS)

growth_protocol: R. sphaeroides strains that were grown in 500 ml cultures in roux bottles either photosynthetically (bubbling with 95% N2, 5% CO2) on Sistrom's minimal media and harvested at exponential phase. Where necessary 1 to 5μL of IPTG was added at the start of the culture to induce protein expression.

extract_protocol:
At midexponential phase (~2×108 colony-forming units/ml), formaldehyde and sodium phosphate were added to a final concentration of 1% and 10 mM, respectively. This mixture was incubated at 30 °C for 4 min before glycine was added to 100 mM, and the solution was placed on ice for 30 min with gentle agitation to quench excess formaldehyde. Cells were centrifuged at 3000g, washed twice with chilled phosphate buffered saline, centrifuged, and flash-frozen at −80 °C. About 2×1010 cells were suspended in 0.5 ml of 100 mM Tris (pH 8.0), 300 mM NaCl, 2% Triton X-100, RNase A (0.5 μg) and 1 mM phenylmethylsulfonyl fluoride, and sonicated in a Misonix water bath for 8 mins with 10s pulses and intervals. Cell debris was removed by centrifugation for 10 min at 12,000g, and an aliquot was removed to analyze DNA fragmentation by agarose gel eletrophoresis (desired size of ~200–1000 bp with enrichment for ~500-bp molecules). The resulting supernatant was incubated with gentle mixing with 20 μl of Staphylococcus aureus protein A Sepharose beads (Sigma-Aldrich, St. Louis, MO) for 3 h at 4 °C as pretreatment to remove potential nonspecific binding to the beads. After the beads had been removed by centrifugation (5 min at 3000g), one-tenth of the sample was removed and used as non-antibody-treated control. Five microlitre of Myc epitope antibody (ab9132, Abcam plc) or FnrL polyclonal antibody was added and the mixture was incubated overnight at 4 °C with gentle mixing before being incubated with protein A Sepharose beads (30 μl) for 3 h at 4 °C. The beads were recovered by centrifugation; washed once (4 °C) with 250 mM LiCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 600 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; washed twice with 300 mM NaCl, 100 mM Tris (pH 8.0), and 2% Triton X-100; and washed twice with TE buffer (10 mM Tris pH 8.0 and 1 mM EDTA). Protein–DNA complexes were eluted from the beads by incubating at 65 °C for 30 min in 50 mM Tris (pH 8.0), 10 nM EDTA, and 1% sodium dodecyl sulfate. The beads were removed by centrifugation, and protein–DNA cross-linking was reversed by incubating the samples for 12 h at 65 °C. DNA was purified using the QIAquick PCR Purification Kit. Samples were sent to UW-Madison Biotech center for further processing and sequencing.
Libraries were prepared according to Illumina's instructions by UW-Madison biotech center

tag: chip-antibody

value: Myc epitope antibody

tag: antibody manufacturer

value: Abcam plc

tag: antibody catalog number


title: RSP_2888_3xMyc_ChIP_Seq_Rep2

source_name: Bacteria culture (SIS - Photo)

value: ΔRSP_2888 complemented with 3xMyc tagged RSP_2888 from an IPTG inducible plasmid


title: Input_DNA_pairedEnd


title: FnrL_ChIP_Seq_Rep3

source_name: Bacteria culture (Acetate - Photo)

value: FnrL polyclonal antibody


title: PrrA_3xMyc_ChIP_Seq

value: PrrA3 complemented with 3xMyc tagged PrrA from an IPTG inducible plasmid


title: Input_DNA


title: RSP_2888_3xMyc_ChIP_Seq_Rep1


title: Myc_Control_ChIP_seq_Photo


title: E14.5 DRG (30ng, low volume)

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

data_processing:
The raw image data is converted to basecalls with Casava 1.8+ and the indexed samples are demultiplexed into individual gzipped fastQ files with proprietary demultiplexer algorithm.  The fastQ files are then aligned to the transcriptome and the whole-genome with TopHat version 2.0.8 using Bowtie2 version 2.1.0.
The RPKM values were derived from the unique alignments to transcripts by RPKM_count.py in the RSeQC version 2.3 package of RNA-seq QC tools.
Genome build: GRCm38.p1
Supplementary_files_format_and_content: Excel spreadsheet including RPKM values for each Sample.

source_name: E14.5 dorsal root ganglia (30ng low volume, total RNA, pooled sample)

extract_protocol:
1)  DRGs from eighteen E14.5 embryos were lysed in TRIzol-LS (Life Technologies, #10296-010).  2. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols).  3. Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to 100ng/ul and used as a master stock. This was used to make further dilutions as needed for the RNAseq experiments.
library_construction_protocol : 1) 3ng, 10ng or 30ng total RNA (in 1µl) was reverse transcribed and amplified using the SMARTer® Ultra™ Low RNA Kit for Illumina® Sequencing (Clontech, cat# 634936) according to the manufacturer’s instructions.  2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator.   3) The libraries were prepared using VeraSeq™ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles.  PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C.  The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer with the indexes can be viewed on the GUDMAP website (Jain Group protocols).

treatment_protocol: DRGs were dissected from 18 E14.5 C57BL/6J embryos, pooled and lysed in TRIzol-LS (Life Technologies, #10296-010) per manufacturer’s protocol.

tag: genotype

value: wild type

value: dorsal root ganglion

tag: theiler stage

tag: developmental stage

tag: Sex

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: Dorsal root ganglia from 18 embryos


title: CrpK_3xMyc_ChIP_Seq

value: ΔCrpK complemented with 3xMyc tagged CrpK from an IPTG inducible plasmid


title: Endogenous small RNAs from A. thaliana Col-0, aos mutant, 3-5week seedlings

city: Beijing

first: Zhiping

last: Jin

address: Chaoyang District, Beichenxilu

institute: Institute of Genetics and Developmental Biology Chinese Academy of Sciences

data_processing:
No-JA.unique_counts.txt; genome build: TAIR8
Low quality sequencing data and null reads including null 3' adaptor, null insert, 5' adaptor contaminant and improper size (<18nt) were wiped off by the Illumina 1G Genome Analyzer sequencer software. Small RNA sequences in length of 18-30nt were mapped to the Arabidopsis thaliana genome (TAIR8, www.arabidopsis.org). Only full-length complete matches were allowed. The relative abundance of each unique sRNA was determined by calculating (reads of the sRNA/total reads of the library)*1,000,000.

source_name: aos mutant, 3-5week seedlings

growth_protocol: The plants were grown under 16hours light/ 8hours dark, 22℃.

extract_protocol: Fifteen- to 30-nt siRNAs from 500 µg of total RNA were gel extracted from a 15% denaturing acrylimide gel (0.5´ TBE, 0.42 g/ml urea, 15% 19:1 acrylimide:bisacrylimide). After elution from the gel (twice incubated at 4°C in 0.3 M NaCl for several hours), siRNAs were precipitated. A 5' adapter was ligated to the siRNA (20 uM adapter, 15% DMSO, 50 mM Tris•HCl, pH 7.6, 10 mM MgCl2, 10 mM 2-ME, 0.2 mM ATP, 0.1 mg/ml BSA, 1 unit/µl T4 RNA ligase, 1 unit/µl RNase inhibitor) before gel extraction (30- to 50-nt fragments) and elution as above. After precipitation, a 3' adapter was ligated in the same manner, gel extracted (50-70 nt), and precipitated. Adapter-ligated siRNA was subjected to reverse transcription using standard protocols. RT was stopped by addition of 150 mM KOH, 20 mM Tris-base and neutralized with HCl (final volume approximately 180 µL). 50 µL of this was used as template for PCR. PCR products were gel extracted on a native polyacrylamide gel (0.5´ TBE, 10% 19:1 acrylimide:bisacrylamide). Ninety- to 105-nt products were excised and eluted. Purified amplicons were sent to BGI-Shenzhen for sequencing (Illumina 1G Genome Analyzer sequencer).

treatment_protocol: The 3- to 5-week-old wild type Arabidopsis seedlings were treated with 100 µM MeJA solution for 8, 16, 24h. The 3- to 5-week-old aos mutant seedlings were not treated as a control.

tag: ecotype background

value: Columbia-0 (Col-0)

value: aos mutant

value: seedlings

tag: age

value: 3-5 weeks

value: mixed


title: Endogenous small RNAs from A. thaliana Col-0, WT, 3-5week seedlings, treated with 100 µM MeJA solution for 8, 16, 24h

data_processing:
High-JA.unique_counts.txt; genome build: TAIR8
Low quality sequencing data and null reads including null 3' adaptor, null insert, 5' adaptor contaminant and improper size (<18nt) were wiped off by the Illumina 1G Genome Analyzer sequencer software. Small RNA sequences in length of 18-30nt were mapped to the Arabidopsis thaliana genome (TAIR8, www.arabidopsis.org). Only full-length complete matches were allowed. The relative abundance of each unique sRNA was determined by calculating (reads of the sRNA/total reads of the library)*1,000,000.

source_name: wild type, 3-5week seedlings, treated with JA

value: jasmonate (JA)


title: E14.5 DRG (3ng, high volume)

source_name: E14.5 dorsal root ganglia (3ng high volume, total RNA, pooled sample)

extract_protocol:
1)  DRGs from eighteen E14.5 embryos were lysed in TRIzol-LS (Life Technologies, #10296-010).  2. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols).  3. Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to 100ng/ul and used as a master stock. This was used to make further dilutions as needed for the RNAseq experiments.
library_construction_protocol : 1) 3ng, 10ng or 30ng total RNA (in 9µl) was reverse transcribed and amplified using the SMARTer® Ultra™ Low Input RNA for Illumina® Sequencing - HV (Clontech, cat# 634828) according to the manufacturer’s instructions.  2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator.   3) The libraries were prepared using VeraSeq™ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles.  PCR conditions were 98°C for 30s; 12 cycles of 98°C for 10s, 64°C for 30s, 72°C for 30s; 72°C for 5 minutes and then hold at 4°C.  The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer with the indexes can be viewed on the GUDMAP website (Jain Group protocols).

tag: strain