title: pUC19

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Bisulfite-Seq clean reads were aligned to the human reference genome (hg19) by BSMAP(v2.74) with the parameter “-u -v 5 -z 33 -p 6 -n 0 -w 20 -s 16 -r 0 -f 10 -L 140”.
Only the CpG sites with read depths >=4 were taken into consideration for DNA methylation level calculation.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: The cout.gz file for each cytosine context (CG, CHG, or CHH where H=A,T,C) with following tab-separated information: Chromosome, coordinate, strand, cytosine type, cytosine context, methylated cytosines reads and unmethylated cytosines reads.
Supplementary_files_format_and_content: The bedGraph format files for each cytosine context with following tab-separated information: Chromosome, start coordinate, stop coordinate, and methylation level (%) (#methylated cytosines reads/#total cytosines reads).

source_name: Human embryonic kidney cells

growth_protocol: Human embryonic kidney HEK293T cells were cultured in Dulbecco's modified Eagle's medium (DMEM, Life Technologies), 10% fetal bovine serum (Sigma), 1% penicillin-streptomycin (Sigma), 1X GlutaMAX (Life Technologies).

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 69506) according to the manufacturer’s instructions, and subject to WGBS SOP analysis in BGI tech.
For Bisulfite-Seq, genomic DNA was fragmented by sonication to a mean size of 250bp using a Bioruptor (Diagenode, Belgium). Bisulphite conversion was conducted with the EZ DNA Methylation-Gold kit (ZYMO). The libraries were sequenced on Illumina HiSeq X Ten. The 48502 bp lambda DNA was used as an extra reference for calculating the bisulphite conversion rate. Nearly complete (>99%) bisulfite conversion was documented in all libraries.

treatment_protocol: Unless stated elsewhere, cells were transfected with gRNAs (total 500 ng) and a CRISPRme expression vector (500 ng) in six-well plates using X-tremeGENE 9 DNA transfection reagent (Roche). For single gRNA or pUC19 control transfections, the amount of plasmid added was equivalent to the total amount of plasmid added for multiple gRNA transfections.

tag: cell line

tag: cell type

value: Human embryonic kidney cell line


title: e10.5_forelimb_H3K27me3

status: Public on Dec 14 2016

type: SRA

city: montreal

first: Rushikesh

last: Sheth

address: 110 avenue des pins ouest

department: Genetics and Development

country: Canada

institute: IRCM

description: Chromatin IP against H3K27me3

library_source: genomic

data_processing:
Reads were mapped to the mouse mm9 genome using Bowtie v0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS v1.4 (PMID: 18798982) with default parameters and --nomodel. Each IP was compared to experiment-matched input DNA.
In the case of e10.5 forelimb H3K27me3 sample, trimming of 56 bases at the 3' was performed before alignment. All the other samples were trimmed by 6 bases at their 3'.
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *_peaks.bed, list of the peaks called by MACS

molecule: genomic DNA

organism: Mus musculus

source_name: embryonic forelmb bud, H3K27me3 ChIP

growth_protocol: The Hoxa13 loss of function allele was generated by insertion of neomycine cassette in Hoxa13 coding region (PMID: 8898214). In Hoxd13 loss of function allele, a lacZ reporter transgene is inserted in the first exon of Hoxd13 (PMID: 10652274). The Hoxa13 and Hoxd13 mutant lines were maintained in a mixed background. Noon of the day the vaginal plug was observed was considered as embryonic day 0.5 (E0.5). Mice and embryos were genotyped by PCR using genomic DNA extracted from tail biopsies and yolk sacs, respectively

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 16630818) with some modifications. Briefly, E11.5 ZAP cells from wild type and mutant limbs were cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was cross-linked using formaldehyde as previously described except for HOXA13 ChIP for which we performed the cross-linking using a dual method using disuccinimidyl glutarate (DSG) and formaldehyde (PMID: 21123453). Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp. Protein A and G Dynabeads (Invitrogen) were incubated 6h at 4 C with 5 µg of antibody. The chromatin was then incubated with the beads overnight at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 65 C overnight. Samples were treated for 15 min RT with RNase A and then with Proteinase K for one hour at 55 C. Finally, the DNA was purified on QIAquick columns (Qiagen) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared by the IRCM functional genomics core facility using Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2000.

tag: strain

tag: developmental stage

value: gestational day e10.5

tag: tissue

value: forelimb bud

tag: antibody

value: anti-H3K27me3 (Cell Signaling, #9733)


title: ACondition2

city: Beijing

first: Lucas

last: Carey

state: Bejijng

address: 5 Yiheyuan Road

department: Center for Quantitative Biology

country: China

institute: Peking University

description:
AMPLICON
exp_log2_cond2 & cv2_log2_cond2 in expression_all_constructs.tab

data_processing:
Sequencing reads are from PCR amplicons of barcodes attached to promoters. Each read has two barcodes, an expression bin barcode (added via PCR after sorting cells by FACS) and a promoter-specific barcode. The first step is to build a matrix of the number of times each promoter barcode bin is seen, containing each condition-specific & expression level (FACS sorting) bin.
This matrix is N rows (# of promoters) by M columns (# of expression bins). One matrix per experiment. Rows are normalized to compute the relative counts per bin of each promoter.
The expression level of each promoter is then computed from these matricies. Details are in the paper, and in Sharon et al 2012.
Promoter-specific barcodes are in Sharon et al. 2012.
Supplementary_files_format_and_content: Tab files of calculated expression levels and promoter annotations.
expression_all_constructs.tab is a tab file with computed expression data for each of the barcoded promoter in each condition. Column exp reports expression level, cv2 reports the squared coefficient of variation.
annotation_all_constructs.tab is a tab file with annotation for each barcoded promoter

molecule: other

organism: Saccharomyces cerevisiae

source_name: Yeast grown in media w/ 1/4 amino acid concentration. Biological replicate A

growth_protocol: yeast were grown in synthetic media with varying amino acid concentrations

extract_protocol:
DNA barcodes were PCR amplified with condition-specific and expression-bin specific barcoded primers
PCR amplicons were used to prepare standard Illumina libraries by adding sequencing adapters via PCR

treatment_protocol: cells were sorted by YFP/mCherry expression ratios

tag: growth protocol

value: media w/ 1/4 amino acid concentration


title: dCas9-BFP-DNMT3A (50 ng) + uPA gRNA (50 ng)

country: Denmark

institute: Aarhus University

organism: Homo sapiens


title: dCas9-BFP-DNMT3A (500 ng)


title: dCas9-BFP-DNMT3B (500 ng)


title: dCas9-BFP-DNMT3B (500 ng) + uPA gRNA (500 ng)


title: dCas9-BFP-DNMT3A (50 ng) + TGFBR3 gRNA (50 ng)


title: dCas9-BFP-DNMT3B (500 ng) + TGFBR3 gRNA (500 ng)


title: dCas9-BFP-DNMT3A (500 ng) + uPA gRNA (500 ng)


title: dCas9-BFP-DNMT3A (500 ng) + TGFBR3 gRNA (500 ng)


title: BCondition2

source_name: Yeast grown in media w/ 1/4 amino acid concentration. Biological replicate B


title: WT rep1

city: Strasbourg

first: Patrice

last: Dunoyer

state: Alsace

address: 12 rue du général Zimmer

department: Ibmp

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence by Fasteris using a in-house developed script. Then we kept the reads of length 18 to 26 nt and we mapped those reads to the whole TAIR10 genome using bowtie v1.1.2 with parameters -t -q -y -e 50 -n 0 -a --best --strata -p 8 --phred33-quals --nomaqround
we removed multiple alignment with homemade python script (avalailable upon request)
bam files were transformed to bed files using bedtools suite v2.25.0
reads sharing tRNA and rRNA coordinates were removed (cordinate from TAIR10 gff file)
count of miR (miRBase, v23), EndoIR-siRNAs (loci predicted by Lindow et. al., Intragenomic Matching Reveals a Huge Potential for miRNA-Mediated Regulation in Plants. PLoS Comput Biol, 2007, which did not match miRBase miRNAs), loci-producing siRNAs in a polV-dependent manner (retrieve from Mosher et. al. polVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci USA, 2008) and of tasiRNA producing loci given by tasiRNAdb (last update September 1 2013)
normalisation : Data were normalized with there own conserved miRNA counts (miR156, 157, 159, 160, 162, 164, 165, 166, 167, 168, 169, 170, 171, 172, 319, 390, 391, 393, 394, 395, 396, 397, 398, 399, 403, 408, 472) under the assuption that they were globaly unaffected.
Genome_build: Col-0 TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw and normalised data for 21 to 24nt read long and for the main sRNA category (miRNA,tasiRNA,polV-siRNA and endoIR-derived siRNA

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Flowers

growth_protocol: Plant seeds were stratified for 2–4 days at 4°C before growth in soil under standard conditions at 22◦ C with a 16 h light/ 8 h dark cycle

extract_protocol:
Total RNA from two independent biological replicate of Col-0 and drb7.2 flowers was extracted with Tri-Reagent (Sigma) according to manufacturer’s instructions. A 6μg weight of total RNA was used for preparation of small-RNA libraries
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, a first acrylamide gel purification of small RNA between 18-30 was performed. The libraries were then constructed using the kit TruSeq Small RNA preparation kit from illumina following manufacturer's instructions and the libraries were sequenced using a Illumina HiSeq 2500 (Fasteris, Switzerland)

treatment_protocol: No treatment

tag: ecotype

value: Columbia

value: flower

tag: genotype

value: wild type


title: WT1

city: New York

first: Zhaohui

last: Yang

state: NY

address: 430 East 67th Street

country: USA

institute: Memorial Sloan Kettering Cancer Center

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner that maps reads genomically and resolves reads across splice junctions.
Partek Flow (www.partek.com/partekflow) was used to compute the expression count matrix from the mapped reads.
The raw count matrix was then processed using Partek Flow to normalize the full dataset and analyze differential expression between sample groups.
A heatmap was generated using Partek Flow. The data plot was the mean centered normalized log2 expression of the 288 significant genes with both p value and FDR below 0.05, and with normalized read counts over 10. Hierarchical clustering was generated with the Pearson correlation on the normalized log2 expression values.
Genome_build: mm9
Supplementary_files_format_and_content: xls file,  normalized count tables

source_name: Gli1-GFP positive stromal cells in normal mouse prostate

extract_protocol:
Mouse dorsal-lateral prostates were freshly dissected, dissociated using Collagenase into single-cell suspension, and Gli1-GFP positive cells were isolated using fluorescence activated cell sorting (FACS). RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
SMART-seq V4 (Clonetech) ultra low input RNA kit was used for library preparation. 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR.

tag: strain background

value: Swiss webster

tag: genotype/variation

value: Gli1-GFP/+; WT

value: Prostate

value: Gli1-GFP positive stromal cells


title: WT2


title: WT3


title: PBMYC2

source_name: Gli1-GFP positive stromal cells in PB-MYC mouse prostate tumor

value: Gli1-GFP/+; PB-MYC/+

value: Prostate tumor


title: PBMYC1


title: WGBS WT ND

city: Fukuoka

first: Yukihiro

last: Inoguchi

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

data_processing:
Reads were mapped to C-to-T and G-to-A converted mm10 genomic sequencis. by using Bismark.
CpG methylation levels were analyzed by using Bismark.
Genome_build: mm10
Supplementary_files_format_and_content: tab-divided plain text; chromosome, start, end, methylation rate (%), methylated reads, unmethylated reads

source_name: erthroblast

growth_protocol: In the LID-W regimen, WT mice and B1KO mice were fed a low iron-containing diet (LID) staring from 3 weeks upon weaning for 7 weeks. On the other hand, in the ND regimen, WT mice and B1KO mice were fed a ND until sacrifice.

extract_protocol:
Genomic DNAs were extracted using QIAamp® DNA Micro kit (QIAGEN).
Genomic DNAs were treated with bisulfite, then libraries were constructed by PBAT.
The PBAT libraries were sequenced on HiSeq 2500 sequencer equipped with HCS
v2.0.5 and RTA v1.17.20.

treatment_protocol: Bone marrow cells collected from the bilateral femur and tibia were suspended in staining buffer and CD71/Ter119 staining was performed. CD71 high and Ter119 positive cells (subset II) were sorted by FACS Aria II for DNA extraction.

value: erthroblast (WT)

tag: passage

tag: diet

value: Normal diet


title: WGBS WT LID-W

value: Low iron diet


title: PBMYC3


title: WGBS B1KO ND

value: erthroblast (Bach1 KO)


title: LN-CaP-SRC-Input

city: Buffalo

first: Jianmin

last: Wang

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina Casava-1.8.2 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version  v0.12.7 with parameters -m 1 -S hg19
Peaks were called MACS version 1.4
Genome_build: Hg19
Supplementary_files_format_and_content: Peak files are in bed file format generated using MACS

source_name: human prostate cancer  LN-CaP cell line

growth_protocol: Ten million cells were grown to 70–80% confluence in a 150 mm culture dish containing ADM for 48 h.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) as per the manufacturer’s instructions.
RNA was quantified by absorbance at 260 and 280nm using a NanoDrop ND-1000 (Wilmington, DE, USA). The quality of RNA was determined using an Agilent Bioanalyzer 2100 (Santa Clara, CA), requiring RIN (RNA Integrity Number) value of ≥6.5.  rRNA depletion (cytoplasmic and mitochondrial) was performed on 200-400 ng of total RNA using the RiboZeroGold kit (Illumina, San Diego, CA) as per the manufacturer’s instructions. The entire rRNA-depleted fraction (ranging 4-22 ng) was used as input for library preparation using the ScriptSeq V2 RNA Seq library preparation kit (Illumina, San Diego, CA) as per the manufacturer’s instructions. Briefly, rRNA-depleted samples were chemically fragmented using the StarScript Reverse Transcriptase Buffer and the cDNA Synthesis Primer was annealed to the RNA. 5′ end-tagged cDNA (equivalent to the 3′ end of the original RNA) was produced by random-primed cDNA synthesis. This was followed by 3′-Terminal Tagging of the cDNA using the Terminal-Tagging Oligo to produce a template for cDNA extension. The resulting “di-tagged” cDNAs were purified using Qiagen MinElute PCR Purification Kit (Hilden, Germany), ligated to the NEBNext Illumina-compatible adaptor 5’-poGATCGGAAGAGCACACGTCTGAACTCCAGTC-U-ACACTCTTTCCCTACACGACGCTCTT  CCGATC*T-3’ (*, phosphorothioate bond), and then indexed using the NEBNExt Universal primer, 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T-3’ plus 6-mer NEBNext indexed primer sets, 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTG ACTGGAGTTCAGACGTGTGCTCTTCCGATC*T-3’, to allow multiplexing. The size of all libraries was assessed using the 2100 Bioanalyzer and a high sensitivity DNA chip (Agilent Technologies, Inc, CA), and further quantified with the Qubit DNA Broad Range assay (Life Technologies, Carlsbad, CA).

treatment_protocol: 10nM DHT or vehicle 16 h

tag: genetic background

value: Expression of Src-527F

tag: treatment

value: Input

tag: chip antibody

value: IgG


title: V-CaP-Input

source_name: human prostate cancer  V-CaP cell line


title: LN-CaP-SRC-Control

value: Control

value: AR N-20 , Cat. #SC-816X, Santa Cruz


title: drb7.2 rep2

value: Columbia

value: flower


title: LN-CaP-SRC + DHT

value: dihydrotestosterone  (DHT)


title: LN-CaP + DHT

value: dihydrotestosterone (DHT)


title: WGBS B1KO LID-W


title: LN-CaP-Input


title: V-CaP-Control


title: WT rep2

value: wild type


title: Cas9-22

city: Yangling

first: Yuanpeng

last: Gao

state: Shaanxi

address: 3 Taicheng Road

department: College of Veterinary Medicine

institute: Northwest A&F University

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <20. The clean reads were then aligned to Bos Taraus genome (using the BWA program (0.7.8-r455). In alignment, preliminary experiments were performed to optimize the alignment parameters (bwa aln -n 2 -e 5 -t 7) [Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform.Bioinformatics. 2009;25:1754–1760. doi: 10.1093/bioinformatics/btp324.]
We applied the Peak calling between Case and Cas9-WT control based on the mapped reads utilizing MACS 1.4. [Zhang Y, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17.]
Genome_build: Btau_4.6.1_NCBI
Supplementary_files_format_and_content: peak files

organism: Bos taurus

source_name: bovine fetal fibroblast cells

growth_protocol: One million cells were seeded on to 6-cm plates on day 1, transfected with reformed sgRNAs-plasmids (or dCas9 plasmids without sgRNA) on day 2, transferred to 10-cm plates on day 3; and cross-linking was done on day 4 with about five million cells.

extract_protocol:
Then the transfected cells were subjected to standard ChIP protocol in Pierce Agarose ChIP Kit.
DNA fragments after ChIP were end-repaired, A-tailed and ligated with indexed adapters. The products were purified and enriched by PCR to create the final cDNA libraries. Target bands were harvested by 2% agarose gel electrophoresis and quantified by Agilent 2100. The tagged DNA libraries were pooled in equal ratios and used for 101-bp paired-end sequencing in a single lane of the Illumina HiSeq™ 2500 with 51 + 7 cycles.

tag: transfection

value: transfected with sgRNA 22

value: anti-FLAG,sigma F7425


title: Cas9-20

value: transfected with sgRNA 20


title: Cas9-38

value: transfected with sgRNA 38


title: drb7.2 rep1


title: Cas9-WT

value: Un-transfected BFFs


title: LN-CaP-Control


title: Cas9-con

value: transfected with Cas9 plasmid only


title: RNase_E-WT_44C_R2

city: Irvine

first: Lei

last: Li

state: CA

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
Fastq quality trimming using FASTX version 0.0.13 and a cut-off value of 20
Size filtering: discarding reads shorter than 12 nt (via READemption)
Read mapping using segemehl version 0.2.0 (READemption 0.3.5, Förstner et al., 2014)
Coverage calculation based on 5' end of mapped reads using the first_base_only option (READemption 0.3.5, Förstner et al., 2014)
Coverage was normalized as divided by the total number of aligned reads multiple per million mapped reads
Genome_build: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: wiggle

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

growth_protocol: Salmonella Thyphimurium strain rne-3071(rne-TS) and its isogenic rne-wt control strain were grown in LB-Lennox medium at 28°C with 220 rpm shaking

extract_protocol:
Bacterial cultures were mixed with 0.2 vol. STOP solution (95 % Ethanol, 5 % Phenol) and subjected to RNA extraction following the hot phenol protocol. In brief, bacteria were lysed at 64°C in 600 µl of lysozyme solution (0.5 mg/ml, pH 8.0) and 60 µl of 10% SDS. After adding 66 µl of 3 M NaOAc (pH 5.2), the lysate was extracted by phenol and followed by a chloroform extraction. Total RNA was precipitated in ethanol at -20°C, and subsequently treated with 5 units of DNase I at 37°C for 45 min. For in vitro assays, RNA were extracted using phenol:chloroform:isoamylalcohol (P:C:I, 25:24:1) and precipitated in ethanol at -20°C.
Total RNAs were converted to cDNA libraries at vertis AG (Munich, Germany) following a standard protocol described previously (Chao et al. EMBO J, 2012; Westermann et al. Nature, 2016). In brief, RNA was poly(A)-tailed using poly(A) polymerase, and the 5’PPP structure was removed using tobacco acid pyrophosphatase (TAP, epicenter). An RNA adaptor was ligated to the 5’P of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase, and purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

treatment_protocol: When cultures reached OD600 of 2.0, half of each culture was shifted from 28°C to 44°C water bath for 30 min, with 220 rpm shaking

value: Isogenetic control

tag: growth stage

tag: growth condition

value: at 28°C with heat treatment (44°C) for 30min


title: RNase_E-WT_44C_R1

tag: strain


title: MDA231-UCA1-MS2-RIP

city: Shantou

first: Zhou

last: Yanchun

state: Guangdong

address: Xinling Road

department: Pathophysiology

institute: Shantou University Medical College

description: miRNA profiling by RNA sequencing

data_processing:
Illumine bcl2fastq2.17 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, and mapped to human genome using BWA. Clean reads were compared with a miRBase database (version 21) and the copy numbers of each unique sequence were calculated. The analysis was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.
Genome_build: miRBase database (version 21)
Supplementary_files_format_and_content: txt files include RPM values for each Sample

growth_protocol: MDA231-UCA1-MS2 and MDA231-Con Cells were cultured in cultured DMEM supplemented with 10% fetal bovine serum, 100U/ml penicillin,  and 100 µg/ml streptomycin at 37 °C in a humid environment with 5 % CO2

extract_protocol:
Cells were lysed in an ice-cold lysis buffer (20mM Tris•Cl pH7.5, 50mM NaCl, 5 mM MgCl2, 0.5% NP-40) containing protease inhibitors and RNasin (200 U/mL).Lysates were centrifuged at 12,000 rpm at 4°C for 15 minutes, to remove cell debris.Supernatants were incubated with Amylose-resin-attached MBP-MCP (MS2 coat protein) at 4°C for 5 h with gentle rotation. After incubation, the supernatant was removed by a short centrifugation and the Amylose beads were washed three times in lysis buffer，Bound UCA1-MS2 RNP complexes were eluted with 100 µl lysis buffer containing 20 mM maltose. miRNAs associated with UCA1 were extracted and analyzed by miRNA-seq.
Libaries were prepared for sequencing according to Illumina's protocol. The experiment was performed by the Guangzhou RiboBio co. Ltd in Guangzhou, China.

tag: cell line

tag: parental cell line

tag: cell type

value: breast cancer cells


title: RNase_E-WT_28C_R2

value: at 28°C (without heat treatment (44°C) for 30min)


title: ChIP dCas9-BFP-DNMT3A (500 ng) + uPA gRNA (500 ng)

description: ChIP DNMT3A

data_processing:
Illumina Casava1.8 software used for basecalling.
ChIP-seq clean reads were mapped to human genome hg19 using SOAP2 with the parameter "-p 4 -v 2 -s 35".
Unique mapping reads was sampled randomly and equally (62723057 reads).
Peaks were called using MACS with P value 1e-3. Sequence motifs enriched within 70 bp of peak summits were identified using MEME-ChIP.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited MACS peak files

source_name: Human embryonic kidney

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen, 69506) according to the manufacturer’s instructions. For ChIP, transfected cells were subjected to chromatin immunoprecipitation (ChIP) with a commercially available kit ChIP-IT Express Enzymatic (53009-AF, ActivMotif, distributed by Nordic Biolabs) and an anti-HA tag antibody (C29F4, Cell Signaling) according to the manufacturer's instructions.
Library Preparation was followed by DNA-end repair, 3'-dA overhang and ligation of sequencing adaptors, PCR amplification and size selection (100-300bp, including adaptor sequence).

value: anti-HA tag antibody (Cell Signaling, catalog# C29F4, lot# 5 from 12/2014)


title: RNase_E-TS_44C_R2

value: Thermosensitive RNase E mutant


title: ChIP input

description: ChIP input


title: RNase_E-WT_28C_R1


title: MDA231_duiRIP

description: miRNA profiling by RNA sequencing


title: Cas9-45

value: transfected with sgRNA 45

tag: antibody


title: Cas9-34

value: transfected with sgRNA 34


title: RNase_E-TS_28C_R1


title: RNase_E-TS_44C_R1


title: V-CaP + DHT

source_name: human prostate cancer V-CaP cell line

value: dihydrotestosterone  (DHT)

value: AR N-20 , Cat. #SC-816X, Santa Cruz


title: SC27 P15

city: Los Angeles

first: Giovanni

last: Botten

state: California

address: 6525 MRL 675 Charles E. Young Dr. South

department: Microbiology, Immunology, & Molecular Genetics

institute: University of California, Los Angeles

data_processing:
Illumina Real-Time Analysis (RTA) Software v1.18.64 was used for base calling.
Sequenced reads were trimmed for adaptor reads then mapped to hg19 whole genome using TopHat v1.5.0 for Single-end library with most default parameters but with the following modifications...
Tophat parameter modifications: Library Type (FR First Strand) Indel Search (No) Max number of Alignments (1) Coverage Search (No)
SeqMonk v0.32.1 software was used to count reads per exon of mRNA transcript.
Reads per kilobase pair per million mapped reads (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008. Briefly, all exons from a gene were merged to create a meta-transcript. The number of reads falling in these exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: hNSPC

growth_protocol: hNSPCs were grown in proliferative conditions in the presence of DMEM/F12, BSA/Insulin/Transferrin (BIT-9500), Antibiotic/Antimycotic, and growth factors EGF, FGF, and PDGF-AB

extract_protocol:
hNSPCs were grown to confluency and RNA was harvested using Bio-RAD RNA Isolation kit (Cat#: G00065). Illumina TruSeq Stranded mRNA kit (Cat #: RS-122-2101) was used with 250 ng of Total RNA for the construction of sequencing libraries.
RNA lilbraries were prepared for sequencing using Illumina Stranded mRNA protocol.

treatment_protocol: hNSCs were kept in proliferative conditions prior to RNA isolation

tag: tissue

value: aborted postnatal cerebral cortex

tag: age of infant

value: 23 week gestation, 2-day-old premature infant

value: human neural stem/progenitor cells (hNSPC)

tag: passage number


title: SC27 P12


title: SC27 P17


title: Cas9-2

value: transfected with sgRNA 2

value: anti-FLAG,sigma F7425


title: 157EV2S (Npl3 IP 42°C)

status: Public on Dec 13 2016

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Basecalling and demultiplexing was performed using Illumina CASAVA 1.8.2
Sequences were aligned to the genome reference sequence of Saccharomyces cerevisiae (assembly R64-1-1, obtained from www.ensembl.org) using the STAR software (Dobin et al., 2012; version 2.4.2) allowing for 2 mismatches.
Filtering of unique hits and counting of reads overlapping with exons was conducted with featureCounts (Liao et al., 2014, subread version 1.5.0-p1, Ensembl annotation version 84).
Data was preprocessed in the R/Bioconductor environment (www.bioconductor.org) using the DESeq2 package (Love et al., 2014, version 1.8.2) to yield normalized read counts across all samples.
Only genes with at least 10 raw read counts in any of the samples were used for the downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: tab-delimited read counts per gene

growth_protocol: Yeast cells were grown at 25°C in YPD full medium to log phase. Cells were splitted into two parts and collected by centrifugation. Pellets were resuspended in 50mL YPD medium and incubated either at 25°C or 42°C in a petri dish for 30 min.  After subsequent UV cross-linking cells were harvested and further porcessed by RNA Co Immunoprecipitation (IP).

extract_protocol:
Eluates were purified via trizol-chloroform (Ambion® RNA by Life technologies™) extraction. Removal of contaminating DNA was performed using the TURBO DNA-free kit (Ambion® RNA by Life technologies™).
500 ng of total RNA were used as start material for library preparation. Quality and quantity of RIP RNA was determined by using the Fragment Analyzer (Advanced Analytical). We started directly with the fragmentation of the RIP samples (200 bp) and cDNA synthesis. mRNA enrichment or depletion of rRNA was avoided. The samples were prepared with the "TruSeq RNA Sample Prep Kit v2" protocol from Illumina. Libraries were validated by using the Fragment Analyzer for sizing and the QuantiFlur Kit from Promega for library quantitation.

treatment_protocol: RNA Co-IP: cell pellets were washed in 1 ml RIP buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 0,2 % (v/v) Triton X-100, 2 mM DTT, 10 U RiboLockTM RNase Inhibitor (Thermo Scientific)). One volume of the pellet was mixed with 1.5 volumes of RIP buffer, containing EDTA-free Protease inhibitor cocktail (Roche) and one volume of glass beads. Cells were lysed by vigorous mixing for 30 sec at 4 m/s using the FastPrep®-24 machine (MP Biomedicals).Co-immunoprecipitation experiments were performed at 4 °C for 4h by incubating the lysates with Protein G sepharose beads (Amersham Biosciences) bound to monoclonal c-myc (9E10) antibody (Santa Cruz) and GFP-Trap beads (Chromotek). Afterwards beads were washed five times with RIP buffer. Eluate sample was treated with 20 µg proteinase K at 55 °C for 20 min to remove RNA bound proteins.

value: HKY157 Cell lysate

tag: stress

value: heat stress (30 min, 42°C)

tag: ip


title: 1266EV2S (Mex67 IP 42°C)

value: HKY1266 Cell lysate


title: 157EV1S (Npl3 IP 42°C)


title: 1266EV1S (Mex67 IP 42°C)


title: 36EV2S (No tag control (42°C)

value: HKY36/381 Cell lysate


title: 1266EV2US (Mex67 IP 25C)

value: normal growth


title: 36EV1S (No tag control (42°C)


title: 1266EV1US (Mex67 IP 25°C)


title: 157EV2US (Npl3 IP 25°C)


title: 157EV1US (Npl3 IP 25°C)


title: 36EV2US (No tag control 25°C)


title: cond_2_rep3

city: Worcester

first: Nick

last: Rhind

state: MA

address: 364 Plantation St.

department: Biochemistry and Molecular Pharmalology

institute: UMass Med School

data_processing:
Basecalls performed using CASAVA version 1.4
We aligned sequencing reads to Ensembl/EF2 S. Pombe assembly and the EF2 transcriptome reference annotation (with GFP added) (Harrow et al. 2012) using TopHat2  (Trapnell, Pachter, and Salzberg 2009)  with options  -p 4    --library-type fr-firststrand  and -M.
We estimated transcript and gene abundances per REPLICATE as well as depletion/ enrichment calls using the Cuffdiff 2 with default options
We made significance calls using  Cuffdiff 2
Genome_build: ensemble EF2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample at gene and isoform level in addition to CuffDiff 2 generated p and q values with significance calls

organism: Schizosaccharomyces pombe

source_name: Asynchonous, log-phase cells

growth_protocol: Log-phase liquid culture in YES at 30˚C

extract_protocol:
RNA was extracted from the cells by bead beating with Trizol (Ambion), followed by isopropyl alcohol precipitation and ethanol wash.
To remove ribosomal RNA, we input 1ug of total RNA into the Ribo-Zero™ Magnetic Gold Kit (Yeast) Illumina cat #MRZY1324) followed by a cleanup using Agencourt RNAClean XP beads (Beckman Coulter, cat #A63987) and elution with 19.5 uL of Elute, Prime, Fragment mix from the TruSeq RNA Sample Preparation Kit (Illumina, cat #RS-122-2101). We performed library construction per the vendor’s instructions, starting with the “Incubate RFP” step. We pooled the resulting cDNA libraries and subjected them to paired-end sequencing on an Illumina miSeq --151  base pairs per read.

treatment_protocol: 3 hour incubation with 1 µm beta-estradiol in EtOH or vehicle

value: Asynchonous, log-phase cells


title: cond_1_rep3

value: control


title: cond_2_rep2


title: cond_1_rep1


title: cond_1_rep2


title: cond_2_rep1


title: 36EV1US (No tag control 25°C)


title: crpmutant.fis.me.input

city: Parul

first: Parul

last: Singh

address: 25-28, rue du Docteur Roux

institute: Institut Pasteur

description: crpmutant.fis.me.input

data_processing:
Samples were aligned to the E. coli K 12 MG1655 reference sequence (version NC000913.2), using BWA (version 0.5) WITH -q 30 parameter for trimming of reads below PHRED quality score of 30.
SAM files thus obtained were converted to BAM files using samtools view command
BAM files of each ChIP biological replicate and the input replicate samples were used in the MACS peak calling program with the -f BAMPE parameter
Genome_build: NC000913.2
Supplementary_files_format_and_content: peaks.bed

organism: Escherichia coli str. K-12 substr. MG1655

growth_protocol: Cells were inoculated from overnight culture in rich Lysogeny broth at 37 degrees in aerobic conditions.

extract_protocol:
Cells were fixed in the required growth phase in formaldehyde, quenched, washed and lysed. Fragmented DNA - protein complex were pulled using the monoclonal flag tag antibody. The complex was then washed, reverse cross-linked and obtained DNA purified using Qiagen min elute PCR purification kit.
Truseq ChIP kit was used for the library preparation. DNA was end repaired and adapters were ligated. After ligation, purify ligation products and then amplify.

tag: growth phase

value: Mid exponential

tag: background

value: crp mutant background, fis flag tag

value: Monoclonal ANTI-FLAG M2 antibody (F3165) -Sigma


title: RNase_E-TS_28C_R2

tag: genotype/variation

value: Thermosensitive RNase E mutant

value: at 28°C (without heat treatment (44°C) for 30min)


title: crpmutant.fis.me.chipseq

description: crpmutant.fis.me.chipseq


title: fis.ee.input

description: fis.ee.input

value: Early exponential

value: wild type, fis flag tag


title: fis.me.input

description: fis.me.input


title: crpmutant.fis.ee.input

description: crpmutant.fis.ee.input


title: crpmutant.fis.ee.chipseq

description: crpmutant.fis.ee.chipseq


title: fis.me.chipseq

description: fis.me.chipseq


title: fis.ee.chipseq

description: fis.ee.chipseq


title: crp.ee.chipseq

description: crp.ee.chipseq

value: wild type, crp flag tag


title: crp.ee.input

description: crp.ee.input


title: fismutant.crp.me.chipseq

description: fismutant.crp.me.chipseq

value: fis mutant background, crp flag tag


title: fismutant.crp.me.input

description: fismutant.crp.me.input


title: fismutant.crp.ee.chipseq

description: fismutant.crp.ee.chipseq


title: crp.me.input

description: crp.me,input


title: fismutant.crp.ee.input

description: fismutant.crp.ee.input


title: crp.me.chipseq

description: crp.me.chipseq


title: PCV2 uninfected commercial pig

first: Liyuan

state: China

address: No.2 of Yuanmingyuan West Road, Haidian District

department: Animal Sciencie and Technology

institute: China Agricultura University

data_processing:
Reads were sorted according to the barcode index and adapter sequences were trimmed. The remaining 18–30 nucleotide identical high-quality sequences were counted and the unique sequences with their associated read counts were mapped to the Sus scrofa genome assembly with no mismatches by SOAP  -v 0 -r 2 -M 0 -a clean.fa -D ref_genome.fa.index -o match_genome.soap
Known miRNA mapping through blastall -p blastn -F F -e 0.01 and tag2miRNA developed by BGI
Align small RNA tags to repeat associated RNA to find matched tags in the sample using software  - tag2repeat developed by BGI
Annotate the small RNA tags with rRNA, scRNA, snoRNA, snRNA and tRNA from Genbank and Rfam to get rid of matched tags from unannotated tags using blastall -p blastn -F F -e 0.01
Small RNA annotation using - tag2annotation developed by BGI
Genome_build: miRNABase 21.
Supplementary_files_format_and_content: miRNA length and number distribution

organism: Sus scrofa

source_name: Lung tissue

growth_protocol: Fifteen purebred Laiwu and fifteen Yorkshire/Landrace crossbred (YL), colostrum-fed pigs raised under identical conditions on the same farm and in the same barn were purchased from two herds that were tested routinely for major swine pathogens and were free of PCV2, PRRSV, Mycoplasma hyopneumoniae, and PPV infection. There was no evidence of PCV2-associated disease in the two source herd or in the multiplier herds supplied by this source. After waning of the maternal antibodies at approximately 42 days postnatal, the pigs were distributed randomly into uninfected and infected groups: PCV2-uninfected Laiwu pigs (Lw-un; n=5), PCV2-uninfected YL pigs (YL-un; n=5), PCV2-infected Laiwu pigs (Lw-i; n=10), PCV2-infected YL pigs (YL-i; n=10).

extract_protocol:
Total RNA was extracted through Trizol reagent
Briefly, the 18–30-nt fraction of total RNA was excised and purified by 15% Tris-borate-EDTA (TBE) denaturing polyacrylamide gel electrophoresis (PAGE). Subsequently, 3′ and 5′ RNA adaptors were ligated to the purified fragments using T4 RNA ligase. The adaptor-ligated sRNAs were amplified by RT-PCR, and the cDNA was amplified further by running 15 PCR cycles. The PCR products (90-bp sRNAs+adaptors) were purified on 4% agarose gels and used for sequencing analysis on an Illumina 1G Genome Analyzer (Illumina) at the BGI.

treatment_protocol: All 20 infected pigs were injected with PCV2-SD at a multiplicity of infection of 1 with 3 mL by intramuscular injection,and the uninfected ones were injected with phosphate buffer. Four pigs with similar clinical manifestations were selected from each of the four groups at 35 days post-infection (dpi) and slaughtered. Lung tissue was collected and snap-frozen in liquid nitrogen for sequencing

tag: age of injection

value: 6-week age

tag: age of slaughter

value: 11-week age

tag: breed

value: Yorkshire/Landrace crossbred

tag: group

value: PCV2 uninfected


title: Culture_SH15Mdup22PCB_rep2

city: Davis

first: Keith

last: Dunaway

address: 3318 Tupper Hall

department: MMI

institute: UC Davis

data_processing:
Filter using Illumina flag
Separate and trim reads based on adapter contamination
Align to hg38 using BSSeeker2
Combine aligned reads, both trimmed and no adapter contamination
Convert sam files to percent methylation bed files
Combine all chromosome percent methylation bed files into a single file
Genome_build: hg38
Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding

growth_protocol:
Grown in Dulbecco’s modified Eagle’s medium, DMEM/F12 medium supplemented with 15% fetal bovine serum (GIBCO, Gaithersburg, MD, U.S.A.) with the addition of 800 μg/ml G 418 to stably maintain 15M duplicated chromosome. Cells were maintained at 37°C in a saturated humidity atmosphere containing 95% O2 and 5% CO2. Cells were seeded at an initial density of 1.5 x 106 cells in T75 Flask.
None unless specified

extract_protocol:
Extracted and purified using the Qiagen Puregene kit
Five (5) μg of DNA was fragmented to ~300 bp using 28 cycles of 15 seconds on/15 seconds off on a Diagenode Bioruptor. DNA was end-repaired using 1× T4 DNA ligase buffer, 400 μM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 min at 20°C. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1× NEB 2 buffer, 200 μM dATP, and 15 U Klenow Fragment (3′ to 5′ exo-, NEB) for 30 min at 37°C. After another DNA purification using the PCR MinElute kit (Qiagen), 3 μL of Illumina's methylated sequencing adapters were ligated on using 1× ligase buffer and 5 μL Quick T4 DNA Ligase (NEB) for 30 min at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.

treatment_protocol:
1 μM PCB 95 in 0.1% DMSO for 40 days. Then, clonally isolated and grown for 21
None unless specified

tag: gender

value: Female

value: human neuroblastoma cell line with extra copy of part of maternal chr15 and part of chr22

tag: treated with

value: PCB 95 in DMSO for 10 days


title: Culture_SH15Mdup22PCB_rep3

tag: cell line


title: PCV2 infected commercial pig

value: PCV2 infected


title: IgG_ChIP_COLO829

city: Sydney

first: Rebecca

middle: C

last: Poulos

state: NSW

address: Level 2 ACP UNSW Australia

country: Australia

institute: UNSW Australia

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
All provided cleaned data have had adaptors clipped except the small RNA-seq data which still contains 5' adaptor:  5'-TGGAATTCTCGTATGCCGTCTTCTGCTTG
Alignments were all made against hg19 using bwa (0.7.5a-r405) with default parameters
Peaks were called using the Homer Suite with ‘factor’ as the style option and IgG as the background control
Genome_build: hg19
Supplementary_files_format_and_content: Bed files contain coordinates for CTCF peak calls

source_name: COLO829 cells

growth_protocol: COLO829 cells were cultured in RPMI medium supplemented with 10% fetal bovine serum, glutamax and penicillin/streptomycin.

extract_protocol:
Early passage cells were cross-linked in 1% formaldehyde and nuclei were extracted. Nuclei were lysed and DNA was sonicated for 6 hours in a Diagenode Pico Bioruptor (30 seconds on/ 30 seconds off). Chromatin was divided across two samples and incubated with polyclonal rabbit anti-CTCF antibody (Millipore 07-729) and rabbit immunoglobulin G (IgG; Sigma I5006) respectively. DNA was then purified, size selected and sequenced.
Library construction was performed as per Illumina protocol Rev A 11257047

tag: chip antibody

value: rabbit IgG (Sigma I5006)


title: CTCF_1_ChIP_COLO829

value: CTCF (Millipore 07-729)


title: CTCF_2_ChIP_COLO829


title: Culture_SH15Mdup22_rep3

treatment_protocol:
0.1% DMSO for 40 days. Then, clonally isolated and grown for 21 generations.
None unless specified

tag: cell type

value: DMSO for 40 days


title: Culture_SH15Mdup22PCB_rep1


title: Culture_SH15Mdup22_rep1


title: Culture_SH15Mdup22_rep2


title: PCV2 infected Laiwu pig

value: Laiwu


title: Culture_SHPCBclone_rep1

growth_protocol:
Grown in Dulbecco’s modified Eagle’s medium, DMEM/F12 medium supplemented with 15% fetal bovine serum (GIBCO, Gaithersburg, MD, U.S.A.). Cells were maintained at 37°C in a saturated humidity atmosphere containing 95% O2 and 5% CO2. Cells were seeded at an initial density of 1.5 x 106 cells in T75 Flask.
None unless specified

value: human neuroblastoma cell line


title: Culture_SHPCBclone_rep2


title: Culture_SHPCBclone_rep3


title: Culture_SH15MPCB_rep3

treatment_protocol:
1 μM PCB 95 in 0.1% DMSO for 10 days.
None unless specified

value: human neuroblastoma cell line with extra copy of part of maternal chr15


title: Culture_SH15MPCB_rep1


title: Culture_SHclone_rep2


title: Culture_SHclone_rep1


title: Culture_SH15MPCB_rep2


title: Culture_SH15M_rep1

treatment_protocol:
0.1% DMSO for 10 days.
None unless specified

value: DMSO for 10 days


title: Culture_SHPCB_rep3


title: Culture_SH15M_rep2


title: Culture_SHPCB_rep1


title: Culture_SH_rep1


title: Culture_SHPCB_rep2


title: Culture_SH_rep3


title: Culture_SH_rep2


title: PCV2 uninfected Laiwu pig


title: BraindfBA_Control_rep11

growth_protocol:
None: Post-mortem brain
None unless specified

tag: subject status

value: no diagnosed neurological disorders

value: Male

tag: age

tag: tissue

value: Brain

tag: tissue subtype/brodmann area


title: Brain_IdioAut_rep3

treatment_protocol:
None: Post-mortem brain
None unless specified

value: diagnosed with Idiopathic Autism


title: BraindfBA_Dup15_rep9

value: diagnosed with Dup15q Syndrome


title: BraindfBA_Control_rep10


title: Brain_IdioAut_rep5


title: Brain_Downs_rep2

value: diagnosed with Downs Syndrome


title: Brain_Downs_rep4


title: Brain_IdioAut_rep4


title: Brain_Downs_rep1


title: Brain_Angelman_rep3

value: diagnosed with Angelman Syndrome

value: Female


title: Brain_Angelman_rep1

value: 4 y


title: Brain_Downs_rep3


title: Brain_PWS_rep3

value: diagnosed with Prader-Willi Syndrome


title: Brain_PWS_rep4


title: Brain_PWS_rep2


title: Brain_Angelman_rep2


title: Culture_SH15M_rep3


title: Brain_Dup15_rep9


title: Brain_PWS_rep1


title: Brain_Dup15_rep5


title: Brain_IdioAut_rep2

value: 9 y


title: Brain_Dup15_rep4


title: Brain_Dup15_rep7


title: Brain_Dup15_rep3


title: Brain_Dup15_rep2


title: Brain_IdioAut_rep6


title: Brain_Dup15_rep6


title: Brain_Control_rep10


title: Brain_IdioAut_rep1


title: Brain_Control_rep9


title: Brain_Dup15_rep1


title: Brain_Control_rep7


title: Brain_Control_rep11


title: Brain_Control_rep8


title: Brain_Control_rep6


title: Brain_PWS_rep5


title: Brain_Control_rep1


title: Brain_Control_rep5


title: Brain_Control_rep4


title: Brain_Control_rep2


title: Brain_Dup15_rep8


title: Brain_Control_rep3


title: wt, NaCl, 60 min, 30C

city: Stockholm

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description:
sample3
Processed data file: Sample3 vs. Sample1.xlsx
Gene expression changes (fold changes) in NaCl-treated cells (60min) compared to untreated cells

data_processing:
Data processing was performed by Genewiz.
Sequence reads were trimmed to remove low quality bases at ends, mapped to the reference genome (C. crescentus NA1000), hit counts were calculated and RPKM values for genes determined
Samples were compared to determine relative changes in gene expression (fold changes)
Genome_build: C. crescentus NA1000
Supplementary_files_format_and_content: Excel files containing differentially expressed genes (fold-change of original RPKM values and the normalized RPKM values)

organism: Caulobacter vibrioides

source_name: Caulobacter crescentus_wt, NaCl, 60 min, 30C

growth_protocol: Cultures were grown in mid-log phase in rich medium (PYE) while shaking.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (done by Genewiz)

treatment_protocol: Mid-log cells were treated with 100 mM NaCl for 60 min before sampling.

tag: strain

tag: genotype

value: wildtype


title: wt, EtOH, 60 min, 30C

description:
sample5
Processed data file: Sample5 vs. Sample1.xlsx
Gene expression changes (fold changes) in EtOH-treated cells (60min) compared to untreated cells

source_name: Caulobacter crescentus_wt, EtOH, 60 min, 30C

treatment_protocol: Mid-log cells were treated with 4% EtOH for 60 min before sampling.


title: wt, no stress, 37C, 60 min

description:
sample6
Processed data file: Sample7 vs. Sample6.xlsx
Gene expression changes (fold changes) in divLts cells (37C) compared to the wild type (37C)

source_name: Caulobacter crescentus_wt, no stress, 37C, 60 min

treatment_protocol: Mid-log cells were shifted for 60 min to 37C before sampling.


title: divL_ts, 37C, 60 min

description:
sample7
Processed data file: Sample7 vs. Sample6.xlsx
Gene expression changes (fold changes) in divLts cells (37C) compared to the wild type (37C)

source_name: Caulobacter crescentus_divL_ts, 37C, 60 min


title: wt, EtOH, 30 min, 30C

description:
sample4
Processed data file: Sample4 vs. Sample1.xlsx
Gene expression changes (fold changes) in EtOH-treated cells (30min) compared to untreated cells

source_name: Caulobacter crescentus_wt, EtOH, 30 min, 30C

treatment_protocol: Mid-log cells were treated with 4% EtOH for 30 min before sampling.


title: wt, NaCl, 30 min, 30C

description:
sample2
Processed data file: Sample2 vs. Sample1.xlsx
Gene expression changes (fold changes) in NaCl-treated cells (30min) compared to untreated cells

source_name: Caulobacter crescentus_wt, NaCl, 30 min, 30C

treatment_protocol: Mid-log cells were treated with 100 mM NaCl for 30 min before sampling.


title: wt, no stress, 30C

description:
sample1
untreated cells
Processed data files: Sample2 vs. Sample1.xlsx, Sample3 vs. Sample1.xlsx, Sample4 vs. Sample1.xlsx, Sample5 vs. Sample1.xlsx

source_name: Caulobacter crescentus_wt, no stress, 30C

treatment_protocol: Cells were grown in mid-log phase at 30C.


title: Uninjured_Brain_Meninges_1

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

data_processing:
Base calling an quality scoring performed by real-Time Analysis (RTA) v2.
Raw FASTQ sequencing reads were chastity filtered to remove clusters having outlying intensity corresponding to bases other than the called base.
Filtered reads were assessed for quality using FastQC.
Reads were splice-aware aligned to the UCSC mm9 genome using STAR.
Reads overlapping Gencode mm9 gene regions were counted using HTSeq.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with the raw counts.

source_name: FACs sorted ILC2

growth_protocol: C57BL/6J mice were maintained in vivarium conditions

extract_protocol:
RNA was extracted using Arcturus PicoPure kit (Thermo Fisher)
Ovation RNA-Seq System V2 kit (Nugen) for initial RNA amplification. After purification, the cDNA was fragemented and further library steps performed.

treatment_protocol: Injured group received 80Kdyn spinal cord contusion 24hr prior to sacrifice

value: Brain Meninges

tag: stress

value: 10 week

value: Wild type


title: Uninjured_Brain_Meninges_2


title: Exhausted rep2, RNA-seq

city: La Jolla

first: James

last: Scott-Browne

address: 9420 Athena Circle

institute: La Jolla Institute

description:
processed data file: All_AVG_TPM.tsv
exhausted_2

data_processing:
Basecalls and demultiplexing performed in illumina basespace
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie v 1.0
Unmapped reads were trimmed of adapters and to a length of 36nt with trim_galore and remapped and merged with first bam file
bam files were filtered to extract fragments less than 100 nt, and peak summits were called using MACS2 with parameters
Peak summits from individual replicates were expanded to region of 500bp and overlapping regions from all samples were merged
Tn5 insertions sites per peak were computed for all replicates using all reads and normalized with DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tsv containing normalized counts per peak

source_name: Spleen CD8+ T cell_Exhausted_RNA-seq

extract_protocol:
ATAC-seq library preparations were performed essentially as described (Buenrostro et al., 2013), with minor modifications. Briefly, 50,000 cells were washed once in PBS before incubation for 30 minutes in lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3mM MgCl2, 0.1% NP-40). For one replicate of memory cells and d35 KLRG1+ cells, 10,000 cells were used. After lysis, cells were resuspended in 50 ul 1x TD Buffer containing 2.5 ul Nextera enzyme (Illumina, San Diego, CA).  Transposition reactions were incubated for 30 min at 37°C before purification with QiaQuick MinElute columns (Qiagen, Valencia, CA).
Purified DNA was amplified by PCR using Kapa Hi-Fi real-time library amplification kit (Kapa, Wilmington, Massachusetts) with 10-12 cycles, according to the manufacturer’s instructions with barcoded primers, as described previously (Buenrostro et al., 2013).  Amplified libraries were purified with QiaQuick MinElute columns (Qiagen, Valencia, CA) and quantitated with Kapa real-time library quantification kit (Kapa, Wilmington, Massachusetts). Paired-end sequencing was performed with the rapid run protocol with an Illumina HiSeq 2500 (Illumina, San Diego, CA) with 50 cycles in each direction.

value: Spleen CD8+ T cell

tag: phenotype

value: Exhausted

tag: infection

value: LCMV Cl13


title: Injured_Brain_Meninges_1

source_name: FACs sorted ILC2 at 1DPI

value: spinal cord injury


title: Injured_Brain_Meninges_2


title: Uninjured_Lung_1

value: Lung


title: Uninjured_Lung_2


title: Uninjured_Brain_Meninges_3


title: Uninjured_Lung_3


title: Exhausted rep1, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
exhausted_1


title: Effector rep1, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
effector_1

source_name: Spleen CD8+ T cell_Effector_RNA-seq

value: Effector

value: LCMV Arm5


title: Memory rep1, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
memory_1

source_name: Spleen CD8+ T cell_Memory_RNA-seq

value: Memory


title: Naïve rep2, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
naïve_2

source_name: Spleen CD8+ T cell_Naïve_RNA-seq

value: Naive


title: Effector rep2, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
effector_2


title: Naïve rep1, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
naïve_1


title: MPEC rep3, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8MPEC-Exp3-M-3-1-BC6_S6

data_processing:
library strategy: ATAC-seq
Basecalls and demultiplexing performed in illumina basespace
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie v 1.0
Unmapped reads were trimmed of adapters and to a length of 36nt with trim_galore and remapped and merged with first bam file
bam files were filtered to extract fragments less than 100 nt, and peak summits were called using MACS2 with parameters
Peak summits from individual replicates were expanded to region of 500bp and overlapping regions from all samples were merged
Tn5 insertions sites per peak were computed for all replicates using all reads and normalized with DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: tsv containing normalized counts per peak

source_name: Spleen CD8+ T cell_MPEC_ATAC-seq

value: MPEC


title: MPEC rep2, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8MPEC-Exp2-M-2-1-BC5_S5


title: MPEC rep1, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8MPEC-Exp1-M-1-1-BC4_S4


title: SLEC rep3, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8SLEC-Exp3-S-3-1-BC3_S3

source_name: Spleen CD8+ T cell_SLEC_ATAC-seq

value: SLEC


title: SLEC rep1, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8SLEC-Exp1-S-1-1-BC1_S1


title: invitro 10U PMAIonoCsA rep2, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC9_S9

source_name: Spleen CD8+ T cell_invitro 10U PMAIonoCsA_ATAC-seq

value: P14 TCR Calpha deficient (C57BL/6)


title: invitro 10U PMAIonoCsA rep1, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC4_S4


title: SLEC rep2, ATAC-seq

description:
processed data file: normCounts.tsv
d8CD8SLEC-Exp2-S-2-1-BC2_S2


title: invitro 10U rep1, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC1_S1

source_name: Spleen CD8+ T cell_invitro 10U_ATAC-seq


title: invitro 10U rep2, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC6_S6


title: Injured_Brain_Meninges_3


title: invitro 10U Iono rep2, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC7_S7

source_name: Spleen CD8+ T cell_invitro 10U Iono_ATAC-seq


title: invitro 10U PMAIono rep1, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC3_S3

source_name: Spleen CD8+ T cell_invitro 10U PMAIono_ATAC-seq


title: invitro 10U Iono rep1, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC2_S2


title: Memory rep2, RNA-seq

description:
processed data file: All_AVG_TPM.tsv
memory_2


title: invitro 100U rep2, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC10_S10

source_name: Spleen CD8+ T cell_invitro 100U_ATAC-seq


title: invitro 100U rep1, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC5_S5


title: naive rep2, ATAC-seq

description:
processed data file: normCounts.tsv
11-14-14-Renata-ATAC-BC4_S5

source_name: Spleen CD8+ T cell_naive_ATAC-seq


title: invitro NFAT CARIT rep1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-5-CD8-CARIT1_S9

source_name: Spleen CD8+ T cell_invitro NFAT CARIT_ATAC-seq

value: invitroNFATCARIT


title: invitro Mock rep1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-1-CD8-NT1_S5

source_name: Spleen CD8+ T cell_invitro Mock_ATAC-seq

value: invitroMock


title: invitro Mock rep2, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-2-CD8-NT2_S6


title: naive rep3, ATAC-seq

description:
processed data file: normCounts.tsv
naive-1_S3


title: naive rep4, ATAC-seq

description:
processed data file: normCounts.tsv
naive-2_S4


title: naive rep1tr2, ATAC-seq

description:
processed data file: normCounts.tsv
R4-BC-15_S4


title: invitro NFAT CARITDBDmut rep2, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-4-CD8-DBD2_S8

source_name: Spleen CD8+ T cell_invitro NFAT CARITDBDmut_ATAC-seq

value: invitroNFATCARITDBDmut


title: memory rep2, ATAC-seq

description:
processed data file: normCounts.tsv
CD8-d35il7rHi-rep2_S5

source_name: Spleen CD8+ T cell_memory_ATAC-seq


title: exhausted rep1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-7_S5

source_name: Spleen CD8+ T cell_exhausted_ATAC-seq


title: exhausted rep4, ATAC-seq

description:
processed data file: normCounts.tsv
exhausted-2_S2


title: naive rep1tr1, ATAC-seq

description:
processed data file: normCounts.tsv
R3-BC-24_S3


title: memory rep1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-10_S8


title: invitro 10U PMAIono rep2, ATAC-seq

description:
processed data file: normCounts.tsv
SaTr-ATAC-BC8_S8


title: d35 KLRG1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-11_S9

source_name: Spleen CD8+ T cell_d35 KLRG1_ATAC-seq

value: d35 KLRG1


title: effector rep2, ATAC-seq

description:
processed data file: normCounts.tsv
effector-BC5_S5

source_name: Spleen CD8+ T cell_effector_ATAC-seq


title: effector rep1tr1, ATAC-seq

description:
processed data file: normCounts.tsv
R1-BC-22_S1


title: effector rep1tr2, ATAC-seq

description:
processed data file: normCounts.tsv
R2-BC-23_S2


title: Prmt5cKO_1

city: Memphis

first: Michael

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

data_processing:
Sequences were trimmed to 100bp and aligned to mm10 using tophat (v 2.0.10) and bowtie (v 2.1.0) with parameters --b2-sensitive
Cufflinks/2.1.1 was used to assemble sequences to mm10, merge to assembled sequences and carryout differential expression analysis.
Differential expression data was analyzed using cummeRbund in R.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs.  Supplemental table reports differentially expressed genes.

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

value: mixed C57BL/6 and Swiss Webster

value: forelimb

tag: genotype/variation


title: Prmt5cKO_2


title: Control_3

source_name: Control

value: control


title: Control_2


title: Control_1


title: invitro NFAT CARITDBDmut rep1, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-3-CD8-DBD1_S7

value: Spleen CD8+ T cell


title: Control_1

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: RNA-Seq of untreated CD4+ T Cells

data_processing:
Raw data aligned using tophat2
Transcript abundance estimated using Cufflinks
Significantly differentially expressed genes calculated using cummeRbund
Genome_build: mm9
Supplementary_files_format_and_content: Results.csv comma separated value file.  Details significantly differentially expressed genes between both conditions
Supplementary_files_format_and_content: AllGenesFPKM.csv comma separated value file. FPKM data for each condition for each gene. AllGenesFPKM.csv contains gene names.

source_name: RNA from CD4+ T Cells isolated from the spleen

growth_protocol: Cells were preenriched from the spleens of Foxp3 reporter mice on C57BL/6 background using the StemCell CD4 T cell isolation kit and sorted for CD4+ Foxp3- CD25- CD45Rbhi cells. RNA was isolated using the Qiagen Rneasy mini kit according to the manufacturer's instructions.

extract_protocol:
RNA of CD4 T cells was extracted using the RNeasy Mini Kit from QIAGEN, following the manufacturer’s instructions.
RNA samples were quantified by qubit (Life Technologies) and quality by Agilent Bioanalyzer. All samples had RIN above 8. Libraries were prepared using TruSeq Stranded mRNA kit (Illumina). One hundred fifty nanograms from 6 RNA samples were purified for polyA tail containing mRNA molecules using poly-T oligo attached magnetic beads. Following purification, the RNA was fragmented. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using RNase H and DNA Polymerase I. A single “A” based was added and adapter ligated followed by purification and enriched with PCR to create cDNA libraries. Final cDNA libraries were size validated using Agilent Bioanalyzer and concentration validated by qPCR. All libraries were normalized to 10nM and pooled together. 10pM of pooled libraries were loaded onto Illumina cBot for cluster generation. Clustered flow cell was then sequenced Pair-end 100 cycles V3 using Illumina HighSeq 2000 to achieve a minimum of ~35 million reads per sample.

treatment_protocol: Parent animals were treated with 0.5 g/l of each Vancomycin, Streptomycin, Ampicillin and Metronidazole in the drinking water containing 4 g/l Splenda. Offspring mice were weaned at day 21 and kept on sterile drinking water until analysis. Control animals were conventionally raised (without antibiotics), weaned at day 21 and kept on regular drinking water until analysis.

tag: treatment


title: Control_2

description: RNA-Seq of untreated CD4+ T Cells


title: Control_3

description: RNA-Seq of untreated CD4+ T Cells


title: invitro NFAT CARIT rep2, ATAC-seq

description:
processed data file: normCounts.tsv
ReDe-ATAC-6-CD8-CARIT2_S10


title: exhausted rep3, ATAC-seq

description:
processed data file: normCounts.tsv
exhausted-1_S1

value: Exhausted

value: LCMV Cl13


title: Cocktail_1

description: RNA-Seq of Cocktail Treated CD4+ T Cells

value: Vancomycin, Streptomycin, Ampicillin and Metronidazole


title: Cocktail_3


title: c3_Vegetative

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR10
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

source_name: isolated nuclei from pollen

growth_protocol: A. thaliana plants were grown under 16h light/ 8h dark in a growth chamber (21°C, 70% humidity)

extract_protocol:
Sperm and vegetative nuclei were isolated by FACS as previously described (1). DNA was extracted with ChargeSwitch kit following the manufacturer’s instructions. Reference: 1. Ibarra CA, et al. (2012) Active DNA demethylation in plant companion cells reinforces transposon methylation in gametes. Science 337:1360-1364.
Libraries were prepared with Ovation Ultralow Methyl Seq kit following the manufacturer’s instructions.

tag: nuclei type

value: vegetative

tag: ecotype


title: Adult rat cardiomyocyte [adult_E]

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

data_processing:
Reads were aligned to the mouse reference genome using Tophat (2.1.0)
Aligned reads were assembled using Htseq-count
Differential expression analysis was performed using SCDE package and DEseq2 in R
Gene ontology analysis results were visualized using Revigo
Genome_build: mm10
Supplementary_files_format_and_content: rawcounts.csv contains the output of Htseq-count package with all genes with at least one read for 24 single cells. Each column represents and individual cell and the rows have the gene names.

organism: Rattus norvegicus

source_name: isolated from ventricular heart tissue

growth_protocol: ES cells were differentiated into cardiomyocytes and either transplanted into a neonatal rat heart or cultured in vitro for 30 days

extract_protocol:
Single cardiomyocytes were FACS sorted (SH800, Sony Technologies) or manually picked under a microscope.
Cells were placed into 96 well plates in water DNase I and RNase inhibitor. DNase was inactivated by increasing the temperature to 72 degrees Celsius for 3 minutes and then cells were placed on ice. SMARTscribe reverse transcriptase, RNase inhibitor, DTT, dNTP, MgCl2, and custom primers were used to convert the mRNA to cDNA. A custom designed PCR primer was used with Advantage2 taq polymerase and was added to the reverse transcription product and dNTP. This was amplified for 19 cycles and was purified using Ampure XP beads (Beckman-Coulter). 100 pg of total cDNA was added to a tagment DNA buffer and spiked with Tn5 (Epicenter) and incubated for 8 minutes at 55 degrees C, which was then stripped off by adding 0.2% SDS to a concentration of 0.05%. Libraries were enriched using KAPAHiFi with index primers and then multiplexed and sequenced.

value: WT

value: adult


title: c2_Sperm

value: sperm


title: Adult rat cardiomyocyte [adult_B]


title: Adult rat cardiomyocyte [adult_C]


title: Adult rat cardiomyocyte [adult_D]


title: c2_Vegetative


title: Adult rat cardiomyocyte [adult_A]


title: Adult rat cardiomyocyte [adult_H]


title: Adult rat cardiomyocyte [adult_G]


title: h1_Sperm


title: WT_Vegetative

value: wildtype


title: WT_Sperm


title: h1_Vegetative


title: Dawn + 21h Rep 3

city: Raleigh

first: Jigar

last: Desai

state: NC

address: 128 Polk Hall

department: Biochemistry

institute: NCSU

description:
SAMPLE 31
8-21h_C.2

data_processing:
Fastq files were trimmed by 10nts with seqtk
Trimmed files were aligned using tophat v2. Mismatches allowed was 2  read gap length was 2  library type was set firststrand  and the rest of the parameters remain as the default.
The resulting bam files were then piped to htseq count version 0.6.0. Using the options -f bam  -s reverse and -m intersection-nonempty counts per gene were generated
Counts were than normilized to counts per million
Genome_build: IRGSP-1.0.29
Supplementary_files_format_and_content: Comma-delimited files include CPM values for each Sample

organism: Oryza sativa

source_name: Rice Panicle

growth_protocol: An IR64 land variety was grown on a on a plot at IRRI in the Philippines. The plants were grown in the dry season of 2014.

extract_protocol:
Tissue samples were stored at -80C until needed. The panicle samples were first ground in liquid nitrogen with a metal pestle. The tissue then lyophilized at -60C overnight before RNA extractions.Total RNA was extracted using RNeasy Plant Mini Kit (Qiagen) with the recommended RLT lysis buffer. The RNA extraction provided protocol was followed the inclusion of DNase step. RNA concentration was then measured with NANOdrop 2000. 2ug of RNA was used with NEBNext Poly(A) Magnetic mRNA isolation kit (NEB). Oligo(dT) attached to magnetic beads isolate mRNA by attaching to poly(A) modified mRNA
Libraries were constructed using NEB ultra dircetional library preperation kit. Library quantification was done with both NEB library qRT quantification and bioanalyzers

treatment_protocol: Plants were grown in a field setting. This group of samples is untreated

tag: developmental stage

value: 50% flowering

value: Panicle

tag: time

value: Dawn + 21h


title: d1d2_Sperm


title: Dawn + 21h Rep 2

description:
SAMPLE 30
8-21h_C.1


title: Dawn + 21h Rep 4

description:
SAMPLE 32
8-21h_C.3


title: d1d2_Vegetative


title: Dawn + 21h Rep 1

description:
SAMPLE 29
8-21h_C


title: Cocktail_2


title: Dawn + 17.5h Rep 2

description:
SAMPLE 26
7-17.5h_C.1

value: Dawn + 17.5h


title: Dawn + 17.5h Rep 3

description:
SAMPLE 27
7-17.5h_C.2


title: Dawn + 17.5h Rep 4

description:
SAMPLE 28
7-17.5h_C.3


title: Dawn + 17.5h Rep 1

description:
SAMPLE 25
7-17.5h_C


title: Adult rat cardiomyocyte [adult_F]


title: Dawn + 14h Rep 4

description:
SAMPLE 24
6-14h_C.3

value: Dawn + 14h


title: Dawn + 14h Rep 2

description:
SAMPLE 22
6-14h_C.1


title: Dawn + 14h Rep 1

description:
SAMPLE 21
6-14h_C


title: c3_Sperm


title: Dusk Rep 4

description:
SAMPLE 20
5-Dusk_C.3

value: Dusk


title: Dawn + 10.5h Rep 3

description:
SAMPLE 15
4-10.5h_C.2

value: Dawn + 10.5h


title: Dusk Rep 3

description:
SAMPLE 19
5-Dusk_C.2


title: Dusk Rep 2

description:
SAMPLE 18
5-Dusk_C.1


title: Dawn + 10.5h Rep 1

description:
SAMPLE 13
4-10.5h_C


title: Dawn + 10.5h Rep 2

description:
SAMPLE 14
4-10.5h_C.1


title: Dusk Rep 1

description:
SAMPLE 17
5-Dusk_C


title: Dawn + 10.5h Rep 4

description:
SAMPLE 16
4-10.5h_C.3


title: Dawn + 7h Rep 1

description:
SAMPLE 9
3-7h_C

value: Dawn + 7h


title: Dawn + 7h Rep 4

description:
SAMPLE 12
3-7h_C.3


title: Dawn + 7h Rep 3

description:
SAMPLE 11
3-7h_C.2


title: Dawn + 3.5h Rep 4

description:
SAMPLE 8
2-3.5h_C.3

value: Dawn + 3.5h


title: Dawn + 3.5h Rep 2

description:
SAMPLE 6
2-3.5h_C.1


title: Dawn + 7h Rep 2

description:
SAMPLE 10
3-7h_C.1


title: Dawn Rep 4

description:
SAMPLE 4
1-Dawn_C.3

value: Dawn


title: Dawn Rep 2

description:
SAMPLE 2
1-Dawn_C.1


title: Dawn Rep 3

description:
SAMPLE 3
1-Dawn_C.2


title: Dawn Rep 1

description:
SAMPLE 1
1-Dawn_C


title: Dawn + 14h Rep 3

description:
SAMPLE 23
6-14h_C.2


title: Drosophila melanogaster Dis3L2 mutant testis total RNA replicate 2

city: CANBERRA

first: Jiayu

last: Wen

state: ACT

address: 133 Garran Rd

department: Department of Genome Science

institute: John Curtin School of Medical Research, The Australian National University

description: Sample name: G0035

data_processing:
3' adapter sequences were  trimmmed using Trimmomatic-0.36
Total RNA-seq paired-end reads from four datasets to UCSC Drosophila melanogaster (dm6) genome assembly using HISAT2
Genome_build: dm6
Supplementary_files_format_and_content: raw counts of genes

organism: Drosophila melanogaster

source_name: dissected testes

extract_protocol:
Total RNAs were isolated from w1118, Tailor, Dis3L2, and Tailor/Dis3L2 mutant 5 day old fly testes using Trizol. Two independent dissections were made to generate biologically replicate RNA samples, whose quality was assessed by Bioanalyzer
The Illumina Truseq Total RNA library Prep Kit LT was used to make RNAseq libraries from 650 ng of total RNA. Manufacturer’s protocol was followed except for using 8 cycles of PCR to amplify the final library instead of the recommended 15 cycles, to minimize artifacts caused by PCR amplification. All samples were pooled together, using the barcoded adapters provided by the manufacturer, over 2 flow cells of a HiSeq2500 and sequenced using pair-end PE50 at the New York Genome Center.

value: testes

value: Dis3L2 mutant


title: Drosophila melanogaster Tailor mutant testis total RNA replicate 2

description: Sample name: G0033

value: tailor mutant


title: Drosophila melanogaster Tailor/Dis3L2 double mutant testis total RNA replicate 2

description: Sample name: G0039

value: Tailor/Dis3L2 double mutant


title: Drosophila melanogaster Tailor/Dis3L2 double mutant testis total RNA replicate 1

description: Sample name: G0038


title: Drosophila melanogaster Dis3L2 mutant testis total RNA replicate 1

description: Sample name: G0034


title: Drosophila melanogaster Tailor mutant testis total RNA replicate 1

description: Sample name: G0032


title: Drosophila melanogaster w1118 testis total RNA replicate 2

description: Sample name: G0029


title: Drosophila melanogaster w1118 testis total RNA replicate 1

description: Sample name: G0028


title: mESC-CM cultured in vitro for 30 days [invitro_G]

source_name: stem cell-derived cardiomyocytes

value: mESCIsl1-Cre; Rosa-RFP; aMHC-GFP

value: 30 days in vitro


title: mESC-CM cultured in vitro for 30 days [invitro_H]


title: mESC-CM cultured in vitro for 30 days [invitro_F]


title: mESC-CM cultured in vitro for 30 days [invitro_E]


title: Dawn + 3.5h Rep 3

description:
SAMPLE 7
2-3.5h_C.2


title: Dawn + 3.5h Rep 1

description:
SAMPLE 5
2-3.5h_C


title: P1-1

city: Guangzhou

first: Zhenhui

last: Li

address: Tianhe District Wushan road

institute: South China Agricultural University

description: Ribosomal RNA removed

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences and low quality reads were filtered with the Trim Galore software (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Sequenced reads were assemblyed by Cufflinks, and mapped to chicken genome using Bowtie (http://bowtie-bio.sourceforge.net /index.shtml) and Tophat (Trapnell et al., Bioinformatics, 2009).
LncRNAs were annoted using CPC, HMMER+pfam and CPAT software.
The expression levels of the transcripts are expressed as FPKM (fragments per kilobase of transcript per million mapped reads) values
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: Microsoft Excel files include FPKM values for each sample.

organism: Gallus gallus

source_name: leg musle

extract_protocol:
Total RNAs were isolated by Trizol reagent (Invitrogen) and then Ribosomal RNA (rRNA) was removed from the total RNA using Epicentre Ribo-ZeroTM rRNA Removal Kit.
Total RNA samples (5 μg) were treated with the Epicentre RibozeroTM rRNA removel kit (Epicenter) to remove rRNA. RNA-seq libraries were prepared using the TruSeq® RNA LT Sample Prep Kit v2 (Illumina) following the manufacturer’s instructions.

value: 1 days post hatch

tag: breeds

value: Xinghua chicken

tag: Sex

value: female


title: P1-2

description: Ribosomal RNA removed


title: mESC-CM cultured in vitro for 30 days [invitro_A]


title: mESC-CM cultured in vitro for 30 days [invitro_B]


title: mESC-CM cultured in vitro for 30 days [invitro_D]


title: mESC-CM cultured in vitro for 30 days [invitro_C]


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_F]

value: 30 days in vivo


title: E11-2

description: Ribosomal RNA removed

value: 11 embryo age


title: E16-1

description: Ribosomal RNA removed

value: 16 embryo age


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_G]


title: E11-1

description: Ribosomal RNA removed


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_E]


title: ph_11559_alone-3

city: Ithaca

first: Olga

last: Lastovetsky

address: 334 Plant Science Building, 236 Tower Rd, Cornell University

institute: Cornell University

description:
edgeR_count_11559_ph_fungal
edgeR_count.xls.ph_11559_alone_vs_ph_11559_wb.edgeR.DE_results-annotated

data_processing:
Reads were quality controlled using FASTQ and trimmed with Trimmomatic to eliminate low quality reads and Illumina adapters
reads were aligned to the fungal genomes of R. microsporus ATCC 52813 (GenBank accession JOSV00000000) and R. microsporus ATCC 52814 (GenBank MCOJ00000000) using TopHat with following parameters tophat -p 11 -o outputdirectory -G genome.gff3 --transcriptome-index xxx --no-novel-juncs genomefile xxx_R1_paired.fq xxx_R2_paired.fq
Transcript abundances were quantified with CuffDiff and the counts file used for differential expression analysis with EdgeR
Genome_build: R. microsporus ATCC 52813 NCBI accession number: JOSV00000000
Genome_build: R. microsporus ATCC 11559 NCBI accession number: MCOJ00000000
Supplementary_files_format_and_content: tab-delimted text file with read counts generated by CuffDiff which was then used for differential expression analysis with EdgeR. EdgeR-generated tab-delimited text file with fold change, p- and and false discovery rate-values for all the genes.

organism: Rhizopus microsporus

source_name: vegetative mycelium

extract_protocol:
Total RNA was extracted with the Ambion ToTALLY Total RNA Isolation Kit (Life Technologies, Grand Island, NY) and rRNA was removed with RiboZero Magnetic Gold Kit (Epicentre, Madison, WI)
RNA sequencing libraries were prepared using the NEBNext® mRNA Library Prep Reagent Set for Illumina®

tag: isolate

value: non-host (ATCC 11559) isolate

tag: growth protocol

value: alone

tag: growth stage

value: 93h post inoculation

tag: cell type

value: vegetative mycelium


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_D]

tag: age


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_C]


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_B]


title: ph_11559_wb-3

value: wb


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_A]


title: ph_11559_wb-2


title: ph_13f_alone-3

description:
edgeR_count.txt_13_ph_fungal
13f_edgeR_counts_by_Rhimi_id.txt.ph_13f_alone_vs_ph_13f_wb.edgeR.DE_results

value: host (ATCC 52813) isolate

value: 67h post inoculation


title: ph_13f_alone-1


title: ph_13f_alone-2


title: E16-2

description: Ribosomal RNA removed


title: ph_13f_wb-3


title: mESC-CM injected into and isolated from neonatal rat heart [invivo_H]


title: ph_13f_wb-2


title: ph_13f_wb-1


title: 60'-2

status: Public on Dec 12 2016

city: Waltham

first: Xiao

last: Chen

address: 415 South St

department: Biology

institute: Brandeis University

description: Sample 24

data_processing:
cl2fastq v2.16.0.10 is used for base-calling
tophat for alignment
cufflinks for quantification
Genome_build: dm3
Supplementary_files_format_and_content: [fpkm_tracking] files generated by Cufflinks include FPKM values for each gene

source_name: BRAINS

growth_protocol: Drosophila were reared on standard cornmeal/agar medium supplemented with yeast under 12 hour LD cycles at 25 °C.

extract_protocol:
Brains were dissected and RNA immediately extracted with TRIzol.
Illumina mRNA library contruction protocol

treatment_protocol: Flies were reared at 18C and temperature shift to 29C for stimulation (for 0, 15, 30, 60min).

tag: strain

tag: temperature shift

tag: time (min)

value: young

value: pooled male and female

tag: tissue

value: BRAINS


title: 30'-2

description: Sample 23


title: 30'

description: Sample 19


title: elav-gal4 18C

description: Sample 29


title: elav-gal4 29c

description: Sample 30


title: elav-gal4 29c-2

description: Sample 32


title: 15'

description: Sample 18


title: Elav-TrpA1 0'-2

description: Sample 21


title: ph_11559_alone-1


title: 60'

description: Sample 20


title: elav-gal4 18C-2

description: Sample 31


title: ph_11559_alone-2


title: ph_11559_wb-1


title: PDF-EGFP 29C-2

description: Sample 83

source_name: PDF-EGFP 29C

extract_protocol:
Brains were dissected for neuron sorting and cells were stored in lysis buffer (Ambion, Dynabead mRNA extraction kit) at -80C.
refer to Abruzzi et al., 2014

treatment_protocol: Flies were reared at 18C and temperature shift to 29C for stimulation for 60min.

tag: temperature

value: PDF+ neurons


title: PDF-TRPA1 29C-4

description: Sample 79

source_name: PDF-TRPA1 29C


title: PDF-EGFP 18C-2

description: Sample 82

source_name: PDF-EGFP 18C


title: PDF-EGFP 18C

description: Sample 80


title: Elav-TrpA1 0'

description: Sample 17


title: PDF-TRPA1 29C-2

description: Sample 75


title: PDF-TRPA1 18C-4

description: Sample 78

source_name: PDF-TRPA1 18C


title: PDF-TRPA1 29C-3

description: Sample 77


title: PDF-TRPA1 29C

description: Sample 73


title: TH-EGFP 29C-2

description: Sample 69

source_name: TH-EGFP 29C

value: DA neurons


title: PDF-TRPA1 18C-2

description: Sample 74


title: PDF-TRPA1 18C

description: Sample 72


title: TH-EGFP 18C-2

description: Sample 68

source_name: TH-EGFP 18C


title: PDF-EGFP 29C

description: Sample 81


title: TH-EGFP 29C

description: Sample 67


title: TH-TRPA1 18C-2

description: Sample 60

source_name: TH-TRPA1 18C


title: TH-TRPA1 29C-3

description: Sample 63

source_name: TH-TRPA1 29C


title: TH-TRPA1 29C-2

description: Sample 61


title: TH-TRPA1 29C-4

description: Sample 65


title: TH-TRPA1 29C

description: Sample 59


title: TH-TRPA1 18C

description: Sample 58


title: Elav-TrpA1 0'

description: Sample 88

data_processing:
Library strategy: ATAC-seq
cl2fastq v2.16.0.10 is used for base-calling
Trim Galore is used to trim low quality bases (quality score < 20) on either end of the reads and remove adapter sequences
Bowtie2 {Langmead, 2012 #9002} was used to map the reads to reference genome with parameters “-D 20 -R 3 -N 1 -L 20”.
Alignments below a score of 10 were discarded, and PCR duplicates were removed using Picard (version 1.119).
Chromatin accessibility at TSS were pooled and averaged as described in {Menet, 2014 #7279}.
Genome_build: dm3
Supplementary_files_format_and_content: [bw] file for visualization

source_name: Elav-TrpA1 0'

extract_protocol:
Brains were dissected and lysed.
ATAC-seq nextera kit

treatment_protocol: Flies were reared at 18C and temperature shift to 29C for stimulation (for 0 and30 min).


title: Elav-TrpA1 30'

description: Sample 89

source_name: Elav-TrpA1 30'


title: Elav-GAL4 0'

description: Sample 86

source_name: Elav-GAL4 0'


title: ChIPSeq_WT_L1_CTCF

city: Bethesda

first: Michaela

last: Willi

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
Genome_build: mm9

source_name: Mammary

growth_protocol: C57BL/6 mice were purchased from Charles River. Were inter-bred to maintain homozygosity. Genotyping was confirmed by PCR followed by the DNA sequencing using genomic DNAs from a tail snip. All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.

extract_protocol:
Frozen-stored mammary tissues from p14, p16, and L1 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against H3K27ac (Abcam, Ab4729), STAT5A (Santa Cruz, sc-1081), CTCF (Millipore, 07-729) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: state

value: lactation day 1

tag: genotype

value: wild type

tag: chip antibody

value: CTCF (Millipore, 07-729)


title: ChIPSeq_WT_p16_STAT5A

description: ChIP-seq

value: pregnancy day 16

value: STAT5A (Santa Cruz, sc-1081)


title: PDF-TRPA1 18C-3

description: Sample 76


title: ChIPSeq_WT_p16_H3K27ac

description: ChIP-seq

value: H3K27ac (Abcam, ab4729)


title: ChIPSeq_WT_p14_H3K27ac

description: ChIP-seq

value: pregnancy day 14


title: YTHDF2-siYTHDF3-5-RIP-IP

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

institute: The University of Chicago

description:
full length RNA co-immunoprecipitated with YTHDF2
siYTHDF3_YTHDF12RIP.xlsx

data_processing:
General pre-processing of reads: All samples were sequenced by illumine Hiseq2000 or Hiseq4000 with single end 50bp read length. For libraries that generated from small RNA (PAR-CLIP and ribosome profiling), the adapters were trimmed by using FASTX-Toolkit. The deep sequencing data were mapped to Human genome version hg38 by Tophat version 2.0 without any gaps and allowed for at most two mismatches. RIP and Ribosome profiling were analyzed by DESeq to generate RPKM (reads per kilobase, per million reads).
Data analysis for each experiment: (1) PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings. Binding motif was analyzed by HOMER (v4.7); (2) for RIP, enrichment fold was calculated as log2(IP/input); (3) for ribosome profiling, only genes with RPKM >1 in input RNA sample and RPKM >0 in ribosome-protected fragments were used for analysis and the change fold was calculated as log2(siYTHDF3/siControl) or log2(siMETTL3/siControl);
Integrative data analysis and statistics: PAR-CLIP targets were defined as gene targets reproducible among three biological replicates (4,459). RIP targets (2,264) were genes with log2(IP/input) > 1 in both biological replicates. The overlap of PAR-CLIP and RIP targets were defined as high confident targets (1,239). For Figure 2 and Supplementary information, Figure S2, the three groups of transcripts are defined as the following: (1) YTHDF3 targets: high confident target of YTHDF3; (2) YTHDF1 unique: high confident target of YTHDF1 reported previously as “CLIP+IP” targets for YTHDF1 but not high-confident target of YTHDF3 [13]; (3) Non-target: non-target for a protein is defined as (a) complementary set of PAR-CLIP targets; (b) RIP enrichment fold <0; Non-target in the figure is defined as the intersection of YTHDF1’s non-target and YTHDF3’s non-target. For the comparison of PAR-CLIP and m6A peaks, at least 1 bp overlap was applied as the criteria of overlap peaks. Nonparametric Mann–Whitney U-test (Wilcoxon rank-sum test, two sided, significance level = 0.05) was applied in ribosome profiling data analysis as previous reported[48]. Gene Ontology (GO) term analyses were performed by DAVID[49,50]. Top terms were then selected for visualizations by the interactive graph function of REVIGO[51].
Supplementary_files_format_and_content: Excel files, see below

source_name: HeLa

growth_protocol: Human HeLa cell line used in this study was purchased from ATCC (CCL-2) and grown in DMEM (Gibco, 11995) media supplemented with 10% FBS and 1% 100 × Pen/Strep (Gibco).

extract_protocol:
Anti-Flag beads IP, and then rRNA removal with ribominus kit
Illumina TruSeq Stranded mRNA Library Prep Kit

tag: cell line

value: HeLa cells

tag: cell treatment

value: 40 nM siRNA knockdown for 48 hr in Flag-HA-YTHDF2 stable expression HeLa cell line


title: TH-EGFP 18C

description: Sample 66


title: YTHDF2-siYTHDF3-2-RIP-IP


title: NPCs biological repl2, technical repl 2

city: Milano

first: Yinxiu

last: Zhan

address: Via Adamello 16

country: Italy

institute: European Institute for Oncology

data_processing:
Single-end 51bp RNAseq reads from each sample were mapped to the mouse genomes using the QuasR software (v 1.8.4, qAlign function, default settings). Only unique alignments with a maximum of 2 mismatches were reported.
Transcriptome assembly was performed in all samples using QuasR software (v1.8.4, qCount function). Expression of each gene/transcript was measured in Reads Per Kilobase of transcript per Millions mapped reads (RPKM).
Differential expression analysis was performed using DESeq2 software (v1.10.0,). Technical replicates were pooled together.
Genome_build: mouse mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, foldchange and q-value for DE analysis from DESeq2 software

source_name: hybrid mouse ESC line F1-21.6

extract_protocol:
Total RNAs were prepared by Trizol (Invitrogen) extraction.
After ribosomal RNA depletion with Ribo-Zero (Illumina),  RNA-seq libraries were prepared using ScriptSeq v2 kit (Illumina)

tag: background strain

value: ES-derived neural precursor cells


title: YTHDF2-siControl-RIP-IP


title: YTHDF1-siYTHDF3-5-RIP-IP

description:
full length RNA co-immunoprecipitated with YTHDF1
siYTHDF3_YTHDF12RIP.xlsx

value: 40 nM siRNA knockdown for 48 hr in Flag-HA-YTHDF1 stable expression HeLa cell line


title: YTHDF1-siYTHDF3-2-RIP-IP


title: YTHDF1-siControl-RIP-IP


title: TH-TRPA1 18C-4

description: Sample 64

value: young

tag: Sex


title: NPCs biological repl2, technical repl 1


title: TH-TRPA1 18C-3

description: Sample 62

value: pooled male and female


title: NPCs biological repl1, technical repl 2


title: YTHDF2-siYTHDF3-5-RIP-input

description:
rRNA depleted RNA
siYTHDF3_YTHDF12RIP.xlsx

extract_protocol:
Extracted with Trizol, and rRNA removal with ribominus kit
Illumina TruSeq Stranded mRNA Library Prep Kit


title: NPCs biological repl1, technical repl 1


title: YTHDF2-siYTHDF3-2-RIP-input


title: Elav-GAL4 30'

description: Sample 87

source_name: Elav-GAL4 30'

value: BRAINS


title: YTHDF2-siControl-RIP-input


title: ESCs biological repl2, technical repl 1

value: Embyonic stem cell


title: YTHDF1-siYTHDF3-2-RIP-input


title: ESCs biological repl1, technical repl 1


title: YTHDF1-siYTHDF3-5-RIP-input


title: ChIPSeq_WT_p14_STAT5A

description: ChIP-seq


title: YTHDF1-siControl-RIP-input


title: Irf8 iChIP mTEC Lo

city: Rehovot

first: Jakub

last: Abramson

address: Herzl 234

department: Immunology

country: Israel

institute: Weizmann Institute

data_processing:
bcl2fastq/2.15.0.4
alignment using bowtiebowtie2/2.1.0 using default parameters
PCR duplication were removed using picard-tools (v1.108). In case of paired end samples if single end protocol was used a short read in R2 was used as a UMI
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: Immature mTECs from WT mice

growth_protocol: Mice were maintained under specific-pathogen-free conditions at the Weizmann Institute’s animal facility and sacrifised at 6weeks of age by CO2

extract_protocol:
Cells were crosslinked and FACS sorted into MACS buffer and Chromatin was analysed using iChIP (Lara-Aatiaso et al.) with our new modification iChIP-IVT
protocol developed by (Lara-Astiaso et al.)

value: Thymic EpCAM+Ly51-MHCIIlo

tag: mouse strain

value: Irf8 (Bethyl A303-BL12058)

value: 6 weeks-old


title: ESCs biological repl2, technical repl 2


title: Ribosome profiling-rep2-siYTHDF3-input

description:
rRNA depleted and fragmented RNA
siYTHDF3_RiboProfile.xlsx

data_processing:
Library strategy: Ribo-seq
General pre-processing of reads: All samples were sequenced by illumine Hiseq2000 or Hiseq4000 with single end 50bp read length. For libraries that generated from small RNA (PAR-CLIP and ribosome profiling), the adapters were trimmed by using FASTX-Toolkit. The deep sequencing data were mapped to Human genome version hg38 by Tophat version 2.0 without any gaps and allowed for at most two mismatches. RIP and Ribosome profiling were analyzed by DESeq to generate RPKM (reads per kilobase, per million reads).
Data analysis for each experiment: (1) PAR-CLIP data were analyzed by PARalyzerv1.1 with default settings. Binding motif was analyzed by HOMER (v4.7); (2) for RIP, enrichment fold was calculated as log2(IP/input); (3) for ribosome profiling, only genes with RPKM >1 in input RNA sample and RPKM >0 in ribosome-protected fragments were used for analysis and the change fold was calculated as log2(siYTHDF3/siControl) or log2(siMETTL3/siControl);
Integrative data analysis and statistics: PAR-CLIP targets were defined as gene targets reproducible among three biological replicates (4,459). RIP targets (2,264) were genes with log2(IP/input) > 1 in both biological replicates. The overlap of PAR-CLIP and RIP targets were defined as high confident targets (1,239). For Figure 2 and Supplementary information, Figure S2, the three groups of transcripts are defined as the following: (1) YTHDF3 targets: high confident target of YTHDF3; (2) YTHDF1 unique: high confident target of YTHDF1 reported previously as “CLIP+IP” targets for YTHDF1 but not high-confident target of YTHDF3 [13]; (3) Non-target: non-target for a protein is defined as (a) complementary set of PAR-CLIP targets; (b) RIP enrichment fold <0; Non-target in the figure is defined as the intersection of YTHDF1’s non-target and YTHDF3’s non-target. For the comparison of PAR-CLIP and m6A peaks, at least 1 bp overlap was applied as the criteria of overlap peaks. Nonparametric Mann–Whitney U-test (Wilcoxon rank-sum test, two sided, significance level = 0.05) was applied in ribosome profiling data analysis as previous reported[48]. Gene Ontology (GO) term analyses were performed by DAVID[49,50]. Top terms were then selected for visualizations by the interactive graph function of REVIGO[51].
Supplementary_files_format_and_content: Excel files, see below

extract_protocol:
Isolated according to illumina Truseq Ribo Profile kit: total RNA (>200 nt) extraction, rRNA removal, and fragmentation
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

value: 40 nM siRNA knockdown for 48 hr, then 100 ug/ml Cycloheximide (CHX) incubation


title: Ribosome profiling-rep2-siYTHDF3-RPF

description:
small mRNA fragments protected by stalled ribosome
siYTHDF3_RiboProfile.xlsx

extract_protocol:
Isolated according to illumina Truseq Ribo Profile kit: Nuclease digestion, Microspin S-400 column separation, RNA extration, TBE gel size selection
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®


title: Irf8 iChIP mTEC Hi

source_name: Mature mTECs from WT mice

value: Thymic EpCAM+Ly51-MHCIIhi


title: thermo-neutral 1

city: Barcelona

first: Francesc

last: Villaroya

address: Avda Diagonal 643

department: Facultat de Biologia

country: Spain

institute: Universitat de Barcelona

data_processing:
Sequencing reads were mapped to the Mus musculus genome (version GRCm38) using the program Tophat (http://ccb.jhu.edu/software/tophat/index.shtml) using default options and Ensembl 73 mouse annotation. The Tophat mapper reports all mappings and split-mappings.
GTF files: Mapped reads were used to quantify mouse transcripts from the Ensembl 73 reference database, using the Flux Capacitor approach that deconvolves reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations and thus obtains a number of reads specifically assigned to each alternative spliceform (http://flux.sammeth.net). All genes and transcripts have been assigned a relative coverage rate as measured in RPKM units ("reads per kilobase per million mapped reads").
Genome_build: GRCm38
Supplementary_files_format_and_content: The processed data files are in standard transcript GTF format (for the full format description see http://www.ensembl.org/info/website/upload/gff.html). The attributes column contains informations on the transcript length, transcript abundance quantification RPKM (reads per kilobase per million mapped reads) and the number of read that mapped to it.

molecule: polyA RNA

growth_protocol: eight adult male C57BL6 mice were maintained at thermoneutral temperature (29ºC). After two weeks, a subset of four mice was placed at 4ºC environment temperature for 24h

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen) which favors purification of all RNA molecules longer than 200 nucleotides; further sample preparation done as described by the manufacturer (Illumina, Eindhoven, The Netherlands)
mRNA was purified from 1 µg total RNA using oligo (dT) beads, before it was fragmented and randomly primed for reverse transcription followed by second-strand synthesis to create ds cDNA fragments. The generated cDNA had undergone paired-end repair to convert overhangs into blunt ends. After 39- monoadenylation and adaptor ligation, cDNAs were purified on a 2% agarose gel and 200 basepair (bp) products were excised from the gel. Following gel digestion, purified cDNA was amplified by PCR using primers specific for the ligated adaptors. The generated libraries were submitted to quality control with the Agilent bio- analyzer 2100 (Agilent Technologies, Wokingham, UK) before sequencing. The RNA integrity number (RIN) values for all samples were 7.5 and above. 1 µl cDNA was loaded on an Agilent DNA chip (DNA-1000) to verify cDNA quality and quantity. Only libraries reaching satisfactory conditions were used for sequencing, on an Illumina HiSeq 2000 system

tag: strain background

tag: gender

value: male

value: adult

tag: exposed to

value: thermoneutral temperature (29C)

value: Brown adipose tissue (BAT)


title: thermo-neutral 4

tag: age


title: thermo-neutral 2