title: Macrophage, intermittent hypoxia H3K27me3

first: David

last: Gozal

state: Illinois

address: KCBD, Room 4100, 900 E. 57th Street, Mailbox 4

department: Department of Pediatrics

institute: University of Chicago

data_processing:
trim adapter and low-quality sequence [trimmomatic (0.32); java -Xmx1G -jar trimmomatic-0.32.jar SE <input> <output> ILLUMINACLIP:<adapters>:1:20:7 SLIDINGWINDOW:3:25 LEADING:20]
align to reference [bwa (0.7.12); bwa aln -t 16  <genome.fa> <input.fq> > <output.sai>; bwa samse -n 1 -r <@RG tag>  <genome.fa> <input.sai> <input.fq> > <output.sam>]
convert sam to sorted bam [samtools (1.2); samtools view -h -F 4 -q 20 -u -b -t <genome.fai> <input.sam> | samtools sort -@ 8 -T <tmp_prefix> -O 'bam' -o <output.bam> -]
remove duplicates [picard (1.121); java -Xmx4g -jar MarkDuplicates.jar VALIDATION_STRINGENCY='SILENT' REMOVE_DUPLICATES='true' INPUT=<input.bam> OUTPUT=<output.bam> METRICS_FILE=<output.metrics>]
mask blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) [bedtools (2.23.0); bedtools intersect -wa -split -v  -abam <input.bam> -b <EncodeExclude/mm9-blacklist.bed> > <output.bam>]
index bam [samtools (1.2); samtools index -b <input.bam>]
find peaks with MACS2 [macs2 (2.1.0); macs2 callpeak -n <name> --outdir <output_dir> -f 'BAM' --gsize 1.87e9 --mfold 5 50 --pvalue 0.01 -t <IP.bam>]
filter narrowPeak file on column 9 > 2.0 (keep qval <0.01) [perl one-liner (); perl -ne "@a=split/\\t/; print if \$a[8] >=2.0;"]
call differential binding with ODIN [odin (0.1alpha); rgt-ODIN -n <name> -m <bamA> <bamB> <genome.fa> <mm9.chrom.sizes>]
clean odin bed file (remove inverted peak records) [perl one-liner (); perl -ne "(\$c, \$s, \$e) = split /\t/; print if \$e > \$s;]
merge macs2 peaks with same histone mark [bedops (2.4.2); bedops --merge --header  <A.narrowPeak> <B.narrowPeak> > <merged.bed>]
find differentially bound regions that intersect merged peaks [bedops (2.4.2); bedops --element-of -1 <odin_peaks.bed> <macs_peaks.bed> > <output.bed>]
annotate regions with nearest upstream and downstream genes [bedops (2.4.2); closest-features --dist --delim '*' <peaks> <mm9_UCSC_known_genes.bed> > <annotated_peaks>; cut -d '*' --output-delimiter=$'\t'  -f 2,3,1 <annotated_peaks> > <annotated_peaks.bed>; cut -d '*' --output-delimiter=$'\t'  -f 4,5,1 <annotated_peaks> >> <annotated_peaks.bed>]
get mappability scores for peak regions (http://hgdownload-test.cse.ucsc.edu/goldenPath/mm9/encodeDCC/wgEncodeMapability/) [bwtool (1.0-gamma); bwtool extract bed <input.bed> <wgEncodeCrgMapabilityAlign50mer.bigWig> <score-annotated_peaks.bed>]
filter out peak regions with any mappability score < 1.0 [perl script (); filterBwtoolExtractBed.pl <input> > <output>]
Genome_build: mm9
Supplementary_files_format_and_content: aligned read files in BAM format have been de-duplicated and reads aligning to blacklisted regions have been removed
Supplementary_files_format_and_content: peak regions in BED6 format are intersection of macs2 peaks with odin differentially bound regions, with any peaks in low-mappability regions filtered out.

source_name: macrophage from aorta

extract_protocol:
C57BL/6J were divided in two groups:  chronic intermittent hypoxia (CIH) and room air controls (RA). Mice from CIH groups housed in identical commercially designed chambers (30"x20"x20") that can accommodate 24 mice each, and are operated under 12 hour light-dark cycle (Oxycycler model A44XO, Biospherix). A custom oxygen concentration profile for the 12 daylight hours was originally extrapolated from the saturation recordings of an adult patient with moderate to severe obstructive sleep apnea, which consists of 90 sec of 6.1% O2 balance nitrogen alternating with 90 sec 21% O2 (room air for 12 hours during the light phase. The O2 concentration in the chambers was continuously monitored and automatically adjusted throughout the 12 hours of light time (07:00 a.m.-07:00 p.m.). For the remaining 12 hours of nighttime, oxygen concentrations were kept at 21% O2. Chronic intermittent hypoxia exposures lasted 20 weeks. Mice in the RA group were housed in matching cages and exposed to 21% O2 oscillations. Following exposures, mice were sacrificed using CO2 intoxication and exsanguination via cardiac puncture. Aortas were perfused with 5-10ml of ice-cold PBS supplemented with 20IU/ml heparin, dissected and cleaned under the microscope from surrounding adipose and lymphoid tissues.
Dissected aortas were minced and incubated with an aorta dissociation cocktail for 1hr on a shaker at a speed of 35 RPM at 37° C. The cocktail included 450u/ml of Collagenase type I (Worthington Biochemical, Lakewood, NJ, USA), 125 U/ml of Collagenase type XI, 60 U/ml of DNASE I and 60 U/ml of Hyaluronidase (all from Sigma-Aldrich, St. Louis, MO, USA), diluted in PBS + 20mM HEPES. Following incubation, the digestion reaction was stopped with 5% fetal bovine serum in PBS, cells were passed through 100 µm filter, washed and re-suspended for further processing in flow buffer (PBS with 2% FBS).
Next, CD11b+ cells were isolated using magnetic beads with an EasySep positive selection kit (STEMCELL Technologies Inc., Vancouver, Canada) per manufacturer’s protocol. Average yield per single mouse aorta was 2,000-4,000 cells. Cell pellets were stored at -80°C until processing. Macrophages were isolated from aortas of mice from CIH (n=20) or RA (n=20). Immediately after isolation, cells were crosslinked and chromatin immunoprecipitated using the True MicroChip kit (Diagenode, Denville NJ) and antibodies specific for H3K9ac and H3K27me3 histone modifications, according to manufacturer’s instruction. DNA was purified using MicroChip columns (Diagenode), according to manufacturer’s instruction.
Sequencing libraries from immunoprecipitated aorta macrophage DNA were prepared using the MicroPlex kit (Diagenode) according to the manufacturer’s protocol. In brief, immunoprecipitated DNA was quantified using Picogreen staining protocol (Quant-iT™ PicoGreen® dsDNA Assay Kit, ThermoFisher Scientific, Grand Island, NY) and 10 pg were used as input material. DNA was repaired and end-blunted by enzymatic treatment. Stem-loop adaptors with blocked 5’ ends were ligated to the 5’ end of the genomic DNA, leaving a nick at the 3’ end. The 3’ ends of the genomic DNA are extended to complete library synthesis and Illumina-compatible indexes were added through amplification. Libraries were purified using AMPure XP beads protocol (Beckman Coulter, Indianapolis, IN) and quantified using the KAPA Library Quantification Kit for Illumina Sequencing Platforms (Kapa Biosystems, Wilmington, MA). Libraries’ fragment size distribution was verified using the Bioanalyzer high sensitivity DNA chip (Agilent Technologies, Santa Clara, CA). Libraries were pooled and spike-in PhiX Control v3 (Illumina, San Diego, CA) was added.  Clusters were generated and sequenced using a HiSeq2000 instrument (Illumina).

value: macrophage from aorta

tag: condition

value: Induced Hypoxia

tag: antibody


title: Macrophage, room-air H3K72me3

status: Public on Jun 12 2017

type: SRA

city: Chicago

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

value: Room Air


title: CD4.WT.IFNb.24hr.si210

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

library_source: transcriptomic

data_processing:
abundance estimation, RNA-seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. To quantify transcript abundance we pseudo-aligned RNA-seq reads to ENSEMBL transcripts, using kallisto (v0.42.4, options: -b 50 --single -l 200 -s 30) (Bray et al., 2016)
alignment, RNA-seq: We aligned sequence reads from each RNA-seq library to the mouse genome (build mm10) using STAR (v2.4.2a, options: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout)(Dobin et al., 2013), guided by annotated transcript structures (cDNA sequences from ENSEMBL release 82 GRCm38) (Yates et al., 2016). We visualized these alignments by counting positional coverage across the genome (BEDTOOLS v2.15: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
alignment, ChIP-seq: We aligned ChIP-seq reads to the mouse genome (build mm10) with Bowtie (v1.1.2, options -m 1) (Langmead et al., 2009), allowing only uniquely aligning reads. We visualized each ChIP-seq dataset by counting positional coverage across the genome (BEDTOOLS v2.24; options: genomeCoverageBed -split -bg ) (Quinlan and Hall, 2010), scaling to 10M total read depth, converting to bigWig (wigToBigWig) (Kent et al., 2010), and viewing in IGV (Thorvaldsdottir et al., 2013)
peaks, ChIP-seq: We then identified peaks using MACS (v 1.4.3; default p-value threshold of 1E-5) (Y. Zhang et al., 2008) and GEM (v2.6; options: --k_min 6 --k_max 15) (Guo et al., 2012).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig and MACS peak calls for ChIP-seq.  bigWig track for selected RNA-seq samples, combined transcript abundance table including all RNA-seq samples.

molecule: total RNA

source_name: CD4+ T cells

extract_protocol:
RNA Sequencing (RNA-seq) was performed and analyzed as described previously. Total RNA was prepared from approximately 1 million cells by using TRIzol or mirVana miRNA Isolation Kit (Thermo Fisher Scientific Inc.). 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: 200 ng of total RNA was subsequently used to prepare RNA-seq library by using TruSeq SR RNA sample prep kit (FC-122-1001, Illumina) by following manufacturer’s protocol.
RNA-seq: The libraries were sequenced for 50 cycles (single read) with a HiSeq 2000 or HiSeq 2500 (Illumina)
ChIP-seq: Cells cultured as indicated were cross-linked for 10 minutes with 1% formaldehyde and harvested. Cells were lysed by sonication and immunoprecipitated with anti-T-bet (sc-21003, Santa Cruz Biotechnology), anti- STAT1 (sc-592, Santa Cruz Biotechnology), anti-STAT2 (ab124283, AbCam), anti-H3K4m1 (ab8895, AbCam) and anti-H3K27ac (ab4729, AbCam)
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt-ended, then phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.

treatment_protocol:
CD4+ T cells from spleens and lymph nodes of 6- to 8-week-old mice were purified by negative selection and magnetic separation (Miltenyi Biotec) followed by sorting of naïve CD4+CD62L+CD44-CD25- population using FACSAria III or FACSAria Fusion (BD).
RNA-seq in vitro culture protocol: All cells were cultured in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU/mL of penicillin, 0.1 mg/mL, of streptomycin and 20 mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen), 1 mM sodium pyruvate, nonessential amino acids (gibco), and 2 μM β–mercaptoethanol (Sigma-Aldrich). Naïve CD4 T cells were activated by plate-bound anti- CD3 (10 μg/mL, Clone: 145-2C11) and anti-CD28 (10μg/mL, 37.51) in media for 6hr to 3 days either under neutral conditions or with IFN-γ (100 ng/mL, R&D Systems) or IFN-β (5000 U/mL, PBL interferon source)
ChIP-seq in vitro culture protocol: All cells were cultured in RPMI medium with 10% (vol/vol) FCS, 2 mM glutamine, 100 IU/mL of penicillin, 0.1 mg/mL, of streptomycin and 20 mM HEPES buffer, pH 7.2-7.5 (all from Invitrogen), 1 mM sodium pyruvate, nonessential amino acids (gibco), and 2 μM β–mercaptoethanol (Sigma-Aldrich). Naïve CD4 T cells were activated by plate-bound anti- CD3 (10 μg/mL, Clone: 145-2C11) and anti-CD28 (10μg/mL, 37.51) in media for 3 days either under neutral conditions (anti-IL-4 (10 μg/mL, 11B11) and anti-IFN-γ antibodies (10 μg/mL, XMG1.2)) or IFN-γ condition (IFN-γ (100 ng/mL, R&D Systems) and anti-IL-4 antibody (10 μg/mL)) or IFN-β condition (IFN-β (5000 U/mL, PBL interferon source), anti-IL-4 (10 μg/mL), and anti-IFN-γ antibodies (10 μg/mL))
Toxoplasma gondii infection protocol: We generated chimeric Rag2-/- mice, reconstituted with ~5 million WT (CD45.1) and ~5 million Tbx21-/- (CD45.2) naïve CD4+ T cells sorted from Age- and Sex- matched mice (Fig. 4A), and 5 days later i.p. infected them with approximately 20 cysts of the avirulent ME49 strain of T. gondii as described previously (Jankovic et al., 2007). Splenocytes and peritoneal exudate cells (PEC) were harvested at day 7 after the infection, and WT and Tbx21-/- CD4+ CD62Llo CD44hi NK1.1- GR-1- T cells were sorted based on congenic surface markers (CD45.1/CD45.2) by flow cytometer
LCMV infection protocol: WT and Tbx21-/- mice were infected either with 2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong intraperitoneally or 2 x 10^6 PFU of LCMV Clone 13 intravenously. Eight and 7 days after inoculation, splenocytes were harvested and CD4+CD62Llo CD44hi memory T helper cell population was sorted by flow cytometer.

tag: genotype

value: WT

tag: culture condition

value: RNA-seq in vitro culture protocol (IFN-β, 24hr)


title: Macrophage, intermittent hypoxia H3K9ac


title: CD4.WT.IFNb.6hr.si195

value: RNA-seq in vitro culture protocol (IFN-β, 6hr)


title: s302a Den 1

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Male CUGBP1 s302a mouse given DEN at 50ug/g bodyweight at 3 weeks, and sacrificed at 30-38 weeks.

data_processing:
Following removal of primers and barcodes, reads were aligned to the mm10 genome using annotations provided by UCSC.
Raw reads were accurately aligned and quantified using Kallisto, in order to generate transcripts per million (TPM).
Raw counts were thresholded to 1, log2 transformed, normalized using a 75th percentile shift, and baselined to the median of all samples.
Genome_build: mm10 (MGSCv37)
Supplementary_files_format_and_content: Tab-delimited text files include TPM values.

source_name: Liver, CUGBP1 s302a, DEN

extract_protocol:
Total RNA was isolated using RNeasy Plus Mini kit (Qiagen) according to manufacturer's instructions.
RNA sequencing libraries were prepared using Illumina TruSeq RNA preparation kits and sequenced on HiSeq 2500.

treatment_protocol: 3-week-old mice (WT and CUGBP1 s302a knock-ins) were injected with DEN at 50ug/g bodyweight. Livers were collected 30-38 weeks later and stored at -80C.

tag: strain/background

tag: genotype/variation

value: CUGBP1 s302a

tag: Sex

value: Male

value: Liver

tag: treatment

value: DEN at 50ug/g bodyweight

tag: age at treatment

value: 3 weeks

tag: age at sacrifice

value: 33-41 weeks


title: WT Den 3

description: Male WT mouse given DEN at 50ug/g bodyweight at 3 weeks, and sacrificed at 30-38 weeks.

source_name: Liver, WT, DEN


title: s302a Den 3


title: WT Den 2


title: CD4.TbetKO.spleen.Toxo.si286

value: Toxoplasma gondii infection protocol (Spleen)


title: s302a Ctrl 3

description: Male CUGBP1 s302a mouse given no treatment at 3 weeks, and sacrificed at 30-38 weeks.

source_name: Liver, CUGBP1 s302a, untreated


title: CD4.WT.IFNb.24hr.si207


title: Macrophage, room-air H3K9ac


title: CD4.TbetKO.PEC.Toxo.si288

value: Toxoplasma gondii infection protocol (PEC)


title: CD4.TbetKO.nc.72hr.si296

value: RNA-seq in vitro culture protocol (neutral, 72hr)


title: CD4.TbetKO.PEC.Toxo.si284


title: CD4.TbetKO.nc.72hr.si133


title: WT Den 1


title: WT Ctrl 2

description: Male WT mouse given no treatment at 3 weeks, and sacrificed at 30-38 weeks.

source_name: Liver, WT, untreated


title: s302a Ctrl 1


title: CD4.TbetKO.na.naive.si289

value: cell isolation protocol


title: CD4.TbetKO.nc.72hr.si290


title: CD4.TbetKO.nc.72hr.si157


title: s302a Den 2


title: CD4.WT.IFNb.72hr.si124

value: RNA-seq in vitro culture protocol (IFN-β, 72hr)


title: CD4.TbetKO.na.naive.si278


title: WT Ctrl 1


title: CD4.TbetKO.spleen.Toxo.si282


title: input

city: Freiburg

first: Maria

middle: Josefina

last: Castex

address: BreisacherStrasse 66

country: Germany

institute: Freiburg Uniklinik

data_processing:
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie.
peaks were called using MACS
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using MACS

source_name: Trophoblast stem cells

growth_protocol: TSCs medium suplemented with Fgf4 and Heparin

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
NEBNextUltra library preparation kit without size selection

tag: cell type

value: trophoblast stem cells

tag: developmental stage

tag: passage

value: none (input)


title: Lsd1_ChIPSeq


title: WT Ctrl 3


title: CD4.TbetKO.IFNg.Iso.72hr.si291

value: RNA-seq in vitro culture protocol (IFN-γ, 72hr)


title: CD4.TbetKO.IFNg.Iso.72hr.si297


title: CD4.TbetKO.IFNg.aIFNAR_1.72hr.si299


title: s302a Ctrl 2


title: CD4.TbetKO.IFNg.aIFNAR_1.72hr.si293


title: CD4.TbetKO.IFNg.aIFNAR_10.72hr.si300


title: CD4.TbetKO.IFNg.aIFNAR_10.72hr.si294


title: GT added high-fat diet_mRNA_3

city: Gwangju

first: Ji-Young

last: Choi

address: 30, Chosundae 3-gil, Dong-gu

department: Food and Nutrition

country: South Korea

institute: Chosun University

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence
Mapped to M. musculus whole genome using STAR v2.4.0
Transcripts were assembled and quantitated using Cufflinks v2.1.1
Genome_build: M. musculus Ensembl 72
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for "ND","HFD", "GT" and "TJ" sample.

source_name: GT added high-fat diet_epididymal adipose tissue

growth_protocol: Forty male C57BL/6J mice (four-week-old, male) were obtained from the Jackson Laboratories (Bar Harbor, ME, USA). All mice were individually housed under a constant temperature (24°C) and 12-h light/dark cycle and, fed a normal chow diet for acclimation for 1 week after arrival.

extract_protocol:
Total RNA was extracted from the adipose tissue using TRIZOL reagent (Invitrogen Life Technologies, NY) according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.
Libraries were constructed from mRNA using the Illumina TruSeq RNA Sample Prep Kit following manufacturer's protocols.

treatment_protocol: At 5 weeks of age, they were randomly divided into 4 groups of 10 mice per each group and fed a normal diet (ND), high-fat diet (HFD), HFD + 0.25% (w/w) green tea ethanol extract (GT), HFD + 3% (w/w) Taeeumjowitang (TJ) for 12 weeks

tag: gender

value: male

tag: age

value: 17 weeks

value: High-fat diet, GT added

value: epididymal adipose tissue


title: TJ added high-fat diet_mRNA_3

source_name: TJ added high-fat diet_epididymal adipose tissue

value: High-fat diet, TJ added


title: TJ added high-fat diet_mRNA_1


title: TJ added high-fat diet_mRNA_2


title: GT added high-fat diet_mRNA_1


title: High-fat diet_mRNA_3

source_name: High-fat diet_epididymal adipose tissue

value: High-fat diet


title: GT added high-fat diet_mRNA_2


title: CD4.TbetKO.IFNg.aIFNAR_0.1.72hr.si298


title: High-fat diet_mRNA_2


title: CD4.TbetKO.IFNg.aIFNAR_0.1.72hr.si292


title: CD4.TbetKO.IFNg.72hr.si158


title: CD4.TbetKO.IFNg.6hr.si200

value: RNA-seq in vitro culture protocol (IFN-γ, 6hr)


title: CD4.TbetKO.IFNg.6hr.si203


title: CD4.TbetKO.IFNg.24hr.si215

value: RNA-seq in vitro culture protocol (IFN-γ, 24hr)


title: Normal diet_mRNA_2

source_name: Normal diet_epididymal adipose tissue

value: Normal diet


title: Normal diet_mRNA_1


title: CD4.TbetKO.IFNb.72hr.si301


title: High-fat diet_mRNA_1


title: Normal diet_mRNA_3


title: CD4.TbetKO.IFNb.72hr.si160


title: CD4.TbetKO.IFNb.72hr.si295


title: CD4.TbetKO.IFNb.72hr.si136


title: CD4.TbetKO.IFNb.6hr.si204

value: RNA-seq in vitro culture protocol (IFN-β, 6hr)


title: CD4.TbetKO.IFNb.24hr.si216

value: RNA-seq in vitro culture protocol (IFN-β, 24hr)


title: CD4.TbetKO.IFNb.24hr.si213


title: CD4.TbetKO.IFNg.24hr.si212


title: WT.ChIP_K27Ac.nc.3d

description:
WT.ChIP_K27Ac.nc.3d_scaled10M.bw
WT.ChIP_K27Ac.nc.3d_peaks.bed

value: WT

value: ChIP-seq in vitro culture protocol (nc)

tag: chip antibody

value: anti-H3K27ac, ab4729, AbCam


title: WT.ChIP_K27Ac.IFNg.3d

description:
WT.ChIP_K27Ac.IFNg.3d_scaled10M.bw
WT.ChIP_K27Ac.IFNg.3d_peaks.bed

value: ChIP-seq in vitro culture protocol (IFN-γ)


title: WT.ChIP_K27Ac.IFNb.3d

description:
WT.ChIP_K27Ac.IFNb.3d_scaled10M.bw
WT.ChIP_K27Ac.IFNb.3d_peaks.bed

value: ChIP-seq in vitro culture protocol (IFN-β)


title: wt.CD4.ChIP_Tbet.IFNb_3d

description:
wt.CD4.ChIP_Tbet.IFNb_3d_scaled10M.bw
wt.CD4.ChIP_Tbet.IFNb_3d_peaks.bed

value: anti-T-bet, sc-21003, Santa Cruz Biotechnology


title: WT.ChIP_input.nc.3d


title: WT.ChIP_input.IFNb.3d


title: wt.CD4.ChIP_STAT2.IFNg_3d

description:
wt.CD4.ChIP_STAT2.IFNg_3d_scaled10M.bw
wt.CD4.ChIP_STAT2.IFNg_3d_peaks.bed

value: anti-STAT2, ab124283, AbCam


title: wt.CD4.ChIP_STAT2.IFNb_3d

description:
wt.CD4.ChIP_STAT2.IFNb_3d_scaled10M.bw
wt.CD4.ChIP_STAT2.IFNb_3d_peaks.bed


title: wt.CD4.ChIP_STAT1.nc_3d

description:
wt.CD4.ChIP_STAT1.nc_3d_scaled10M.bw
wt.CD4.ChIP_STAT1.nc_3d_peaks.bed

value: anti- STAT1, sc-592, Santa Cruz Biotechnology


title: wt.CD4.ChIP_STAT1.IFNb_3d

description:
wt.CD4.ChIP_STAT1.IFNb_3d_scaled10M.bw
wt.CD4.ChIP_STAT1.IFNb_3d_peaks.bed


title: wt.CD4.ChIP_input.nc_3d


title: CD4.TbetKO.IFNb.6hr.si201


title: wt.CD4.ChIP_input.IFNg_3d


title: WT.ChIP_K4m1.IFNg.3d

description:
WT.ChIP_K4m1.IFNg.3d_scaled10M.bw
WT.ChIP_K4m1.IFNg.3d_peaks.bed

value: anti-H3K4m1, ab8895, AbCam


title: wt.CD4.ChIP_input.IFNb_3d


title: TbetKO.ChIP_K4m1.IFNg.3d

description:
TbetKO.ChIP_K4m1.IFNg.3d_scaled10M.bw
TbetKO.ChIP_K4m1.IFNg.3d_peaks.bed


title: wt.CD4.ChIP_Tbet.nc_3d

description:
wt.CD4.ChIP_Tbet.nc_3d_scaled10M.bw
wt.CD4.ChIP_Tbet.nc_3d_peaks.bed


title: WT.ChIP_input.IFNg.3d


title: TbetKO.ChIP_K27Ac.IFNb.3d

description:
TbetKO.ChIP_K27Ac.IFNb.3d_scaled10M.bw
TbetKO.ChIP_K27Ac.IFNb.3d_peaks.bed


title: TbetKO.ChIP_K27Ac.nc.3d

description:
TbetKO.ChIP_K27Ac.nc.3d_scaled10M.bw
TbetKO.ChIP_K27Ac.nc.3d_peaks.bed


title: wt.CD4.ChIP_Tbet.IFNg_3d

description:
wt.CD4.ChIP_Tbet.IFNg_3d_scaled10M.bw
wt.CD4.ChIP_Tbet.IFNg_3d_peaks.bed


title: TbetKO.ChIP_input.IFNb.3d


title: TbetKO.CD4.ChIP_STAT2.nc_3d

description:
TbetKO.CD4.ChIP_STAT2.nc_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT2.nc_3d_peaks.bed


title: wt.CD4.ChIP_STAT2.nc_3d

description:
wt.CD4.ChIP_STAT2.nc_3d_scaled10M.bw
wt.CD4.ChIP_STAT2.nc_3d_peaks.bed


title: TbetKO.ChIP_K27Ac.IFNg.3d

description:
TbetKO.ChIP_K27Ac.IFNg.3d_scaled10M.bw
TbetKO.ChIP_K27Ac.IFNg.3d_peaks.bed


title: TbetKO.ChIP_input.IFNg.3d


title: TbetKO.CD4.ChIP_STAT2.IFNg_3d

description:
TbetKO.CD4.ChIP_STAT2.IFNg_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT2.IFNg_3d_peaks.bed


title: TbetKO.ChIP_input.nc.3d


title: TbetKO.CD4.ChIP_STAT1.nc_3d

description:
TbetKO.CD4.ChIP_STAT1.nc_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT1.nc_3d_peaks.bed


title: TbetKO.CD4.ChIP_input.IFNb_3d

description: TbetKO.CD4.ChIP_input.IFNb_3d_scaled10M.bw


title: TbetKO.CD4.ChIP_STAT2.IFNb_3d

description:
TbetKO.CD4.ChIP_STAT2.IFNb_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT2.IFNb_3d_peaks.bed


title: TbetKO.CD4.ChIP_STAT1.IFNg_3d

description:
TbetKO.CD4.ChIP_STAT1.IFNg_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT1.IFNg_3d_peaks.bed


title: TbetKO.CD4.ChIP_STAT1.IFNb_3d

description:
TbetKO.CD4.ChIP_STAT1.IFNb_3d_scaled10M.bw
TbetKO.CD4.ChIP_STAT1.IFNb_3d_peaks.bed


title: wt.CD4.ChIP_STAT1.IFNg_3d

description:
wt.CD4.ChIP_STAT1.IFNg_3d_scaled10M.bw
wt.CD4.ChIP_STAT1.IFNg_3d_peaks.bed


title: TbetKO.CD4.ChIP_input.IFNg_3d

description: TbetKO.CD4.ChIP_input.IFNg_3d_scaled10M.bw


title: TbetKO.CD4.ChIP_input.nc_3d

description: TbetKO.CD4.ChIP_input.nc_3d_scaled10M.bw


title: EB_d14_shLuc_ctrl (RNA-Seq)

city: Detroit

first: Benjamin

middle: L

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

data_processing:
Basecalls performed using GAPipeline or CASAVA
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RPKM measure (read per kilo bases of exon model per million reads) was used to quantify the mRNA expression level of a gene from RNA-Seq data sets. The RBPM measure (read per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH, RPKM

molecule: polyA RNA

growth_protocol: ES cells were cultured on irradiated MEFs in DMEM, 15% FBS media containing LIF (ESGRO) at 37oC with 5% CO2. For RNA-Seq experiments ES cells were cultured on gelatin-coated dishes in ES cell media containing 1.5 µM CHIR9901 (GSK3 inhibitor) for several passages to remove feeder cells. ES cells were passed by washing with PBS, and dissociating with trypsin. For embryoid body (EB) formation, ES cells were cultured in low attachment binding dishes to promote 3D formation in ES cell media without LIF.

extract_protocol:
RNA was harvest using RNeasy and miRNeasy Qiagen kits.
Double-stranded cDNA was sonicated and end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

tag: cell line

value: R1 ES cell

tag: protocol

value: shLuc

value: EB

tag: differentiation time

value: day 14


title: EB_d10_shSmyd5 (RNA-Seq)

value: day 10


title: EB_d6_shSmyd5 (RNA-Seq)

value: day 6


title: EB_d10_shLuc_ctrl (RNA-Seq)


title: EB_d6_shLuc_ctrl (RNA-Seq)


title: EB_24h_shSmyd5 (RNA-Seq)


title: mES_shSmyd5 (RNA-Seq)

value: ES cells


title: mES_shLuc_ctrl (RNA-Seq)


title: EB_24h_shLuc_ctrl (RNA-Seq)


title: shSmyd5_HP1_mESC

description: Chromatin IP against HP1

data_processing:
Basecalls performed using GAPipeline or CASAVA
Sequence reads were obtained and mapped to the mouse (mm9) genomes with Bowtie2.
The RBPM measure (reads per base per million reads) was used to generate graph files.
Genome_build: mm9
Supplementary_files_format_and_content: BEDGRAPH

growth_protocol: shLuc and shSmyd5 ES cells were grown in ESC media (LIF and GSK3i) without feeders and in the presence of 1ug/mL puromycin.

extract_protocol:
ES cells were crosslinked with formaldehyde and subsequently sonicated. Sonicated cell extracts were used for ChIP assays.
ChIP-enriched DNA was end-repaired using the End-It DNA End-Repair kit (Epicentre), followed by addition of a single A nucleotide, and ligation of PE adapters (Illumina) or custom indexed adapters. PCR was performed using Phusion High Fidelity PCR master mix

value: mESC

value: Anti-HP1 antibody (Millipore)


title: shLuc_HP1_mESC

description: Chromatin IP against HP1


title: shSmyd5_Input_mESC (control for HP1 ChIP)

description: Direct sequencing following sonication of x-linked chromatin


title: mESC_SMYD5_FLAG

description: Chromatin IP against SMYD5

source_name: mESC

value: Anti-FLAG antibody (Sigma)


title: mESC_SMYD5_SA

description: Chromatin IP against SMYD5

value: Streptavidin bead


title: shLuc_Input_mESC (control for H3K9me3 ChIP)


title: mESC_Input (control for SMYD5 ChIP)


title: shSmyd5_Input_mESC (control for H3K9me3 ChIP)


title: shLuc_Input_mESC (control for HP1 ChIP)


title: shSmyd5_H3K9me3_mESC

description: Chromatin IP against H3K9me3

value: Anti-H3K9me3 antibody (Abcam; ab8898)


title: EB_d14_shSmyd5 (RNA-Seq)


title: shLuc_H3K9me3_mESC

description: Chromatin IP against H3K9me3


title: shSmyd5_Input_mESC (control for H4K20me3 ChIP)


title: shLuc_H3K9me2_mESC

description: Chromatin IP against H3K9me2

value: Anti-H3K9me2 antibody (Abcam; ab1220)


title: shLuc_H4K20me3_mESC

description: Chromatin IP against H4K20me3

value: Anti-H4K20me3 antibody (Abcam; ab9053)


title: RAW 264.7 Honaucin A 12 uM/LPS 180min replicate 2

city: La Jolla

first: Samantha

last: Mascuch

state: CA

address: 8622 Kennel Way

department: CMBB

institute: Scripps Institution of Oceanography

data_processing:
Sequencing adapters were removed from reads using the fastx toolkit clipper tool  (http://hannonlab.cshl .edu/fastx_toolkit/index.htmL)
Quality trimming was done using Prinseq (http://prinseq.sourceforge.net/).  All reads with a phred quality score less than 20 and all reads shorter than 55 base pairs after polyA trimming were excluded from subsequent analysis.
The ultrafast universal RNA-seq aligner STAR was used to map reads to the Ensembl Mus musculus GRCm38.75 reference genome (Dobin, 2013).
The Python package HTSeq, specifically htseq-count, was used to quantify the number of reads that mapped to each feature in the genome.
The R statistical package DESeq2 was used to perform differential expression analysis. This was accomplished by performing pair-wise comparisons of each treatment to its appropriate LPS control.
Genome_build: GRCm38.75 (mm10)
Supplementary_files_format_and_content: .csv files displaying gene identifier and abundance measurements

source_name: Abelson murine leukemia virus-induced tumor; ascites (immortalized cell line RAW 264.7; ATCC TIB-71)

growth_protocol: RAW 264.7 murine macrophages were grown in Dulbecco's Modified Eagle Medium (Gibco) supplemented with 10% fetal bovine serum, penicillin, and streptomycin. Cells were seeded in 6-well plates and grown to near confluency.

extract_protocol:
Total RNA was isolated and purified with TRIzol (Life Technologies) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: EtOH (vehicle) or honaucin A (4 μM or 12 μM) in EtOH were added to the appropriate wells and plates were incubated for 1 hour at 37 °C with 5% CO2. Lipopolysaccharide (0.5 μg/mL) was then added to all treatments. Three  replicates were prepared for each treatment. The treated cells were incubated for 30 minutes or 180 minutes.

value: RAW 264.7 macrophages

value: Abelson murine leukemia virus transformed macrophage

tag: strain

value: BALB/c

tag: morphology

value: monocyte/macrophage


title: RAW 264.7 Honaucin A 12 uM/LPS 180min replicate 3


title: RAW 264.7 Honaucin A 12 uM/LPS 180min replicate 1


title: RAW 264.7 Honaucin A 4 uM/LPS 180min replicate 1


title: RAW 264.7 Vehicle/LPS 180min replicate 1


title: RAW 264.7 Honaucin A 4 uM/LPS 180min replicate 2


title: RAW 264.7 Vehicle/LPS 180min replicate 3


title: RAW 264.7 Vehicle/LPS 180min replicate 2


title: RAW 264.7 Honaucin A 12 uM/LPS 30min replicate 2


title: RAW 264.7 Honaucin A 12 uM/LPS 30min replicate 3


title: shSmyd5_H3K9me2_mESC

description: Chromatin IP against H3K9me2

value: R1 ES cell


title: NHF1 6-4PP XR-seq_rep2

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
PP641h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
PP641h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw
The processed data files are the same as those linked at the foot of GSE67941.

data_processing:
Library strategy: XR-seq
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

organism: Homo sapiens

growth_protocol: Human GM12878 cells were cultured in RPMI 1640 medium (no phenol red) with 15% fetal bovine serum and 2 mM glutamine at 37 °C in a 5% CO2 humidified chamber.

extract_protocol:
Cells were lysed gently and small molecular weight DNA, consisting mostly of excised 26-27 mers was separated from chromosomal high molecular weight DNA by centrifugation
Briefly, the excised oligomers are immunopricipitated with anti-TFIIH (anti-XPB and anti-p62) antibodies because the excision product is released in a relatively stable complex with TFIIH, which also protects the excision product from degradation by non-specific nucleases. This is followed by extraction of the excised oligomers and ligation to adaptors and a second immunoprecipitation with either anti-CPD or anti-BPDE antibodies. Human DNA polymerases η and κ were used for primer extension in the presence of purified excised oligonucleotides containing either CPD or BPDE-dG damages, as polymerases η and κ can bypass CPD and BPDE-dG damage respectively in an error-free manner. This is followed by PCR amplification with index primers and NGS sequencing on HiSeq 2500 platform.

treatment_protocol: GM12878 cells were grown to about 80% confluence before UV irradiation or (±)-anti-BPDE (MRIGlobal) treatment. The UV (20 J/m2 at 254 nm) irradiation was performed as previously described(3), except 20 ml of GM12878 cells were irradiated in RPMI 1640 medium (no phenol red) in a 150 mm petri dish. BPDE stock solution (4 mM), which was freshly made by dissolving BPDE in DMSO, was added to the GM12878 cell suspension at a final concentration of 2 μM and cells were incubated for 1 h at 37 °C in a 5% CO2 humidified chamber.

tag: cell line source

value: normal newborn

value: foreskin fibroblast cell line

tag: uv exposure

tag: time between uv exposure and harvesting

tag: type of uv-induced dna damage

value: (6-4) pyrimidine-pyrimidone photoproduct ((6-4)PP)


title: shSmyd5_H4K20me3_mESC

description: Chromatin IP against H4K20me3


title: NHF1 CPD XR-seq_rep2

description:
Source of NHF1 cell line: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002).
Excised oligomer released in Nucleotide Excision Repair (XR-seq).
Processed data files:
CPD1h_Merged_MINUS_UNIQUE_NORM_fixedStep_25.bw
CPD1h_Merged_PLUS_UNIQUE_NORM_fixedStep_25.bw
The processed data files are the same as those linked at the foot of GSE67941.

source_name: NHF1, CPD

value: cyclobutane pyrimidine dimer (CPD)


title: RAW 264.7 Honaucin A 4 uM/LPS 30min replicate 4


title: NHF1 6-4PP XR-seq_rep1


title: RAW 264.7 Honaucin A 4 uM/LPS 30min replicate 3


title: RAW 264.7 Vehicle/LPS 30min replicate 3


title: NHF1 CPD XR-seq_rep1


title: RAW 264.7 Honaucin A 4 uM/LPS 30min replicate 2


title: shLuc_Input_mESC (control for H4K20me3 ChIP)

value: shLuc


title: RAW 264.7 Vehicle/LPS 30min replicate 4


title: RAW 264.7 Honaucin A 4 uM/LPS 30min replicate 1


title: antiUB_wt

city: New York

first: Xian

last: Zhang

address: 580 main st apt 138

institute: MSKCC

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie
peaks were called using deeptools bamcoverage
computematrix against glucose regulated genes
Genome_build: hg19
Supplementary_files_format_and_content: profile drew by deeptools plotprofiles and excel

source_name: Hep3B cells

growth_protocol: HEP3B cells cultred in the DMEM high glucose medium

extract_protocol:
CHIP-seq samples were prepared using the ChIP-IT kit from active motif
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HEP3B cells was first knocked down of H3.3A and H3.3B, then restored with Flag-H3.3 WT and Flag-H3.3 K23/36/37R by lentivirus

value: liver cancer

value: anti-Ub (FK2, millipore)


title: antiUB_3m


title: 48h_INTS12_D-siRNA_C_3

city: Cambridge

first: Alexander

last: Kheirallah

state: Cambridgeshire

address: Hills Road

department: Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description:
processed data file: 48h_metaMatrix.txt
C3

data_processing:
RNAseq alighnemnt performed using TopHat
RNAseq transcriptome assembly peroformed using Cufflinks
RNAseq differential gene expression performed using Cuffdiff (significant defined as q<0.05)
FPKM abundance per gene performed using Cuffnorm
ChIPseq alighnment performed with Bowtie2
ChIPseq peak calling perfmed with MACS2 (ChIP vs input control approach)
ChIPseq track signal performed by comparing ChIP vs input with fold enrichment option and total library size normalization. Generated bedGraphs were converted to wig files with 100bp resolution.
Genome_build: hg19
Supplementary_files_format_and_content: *metaMatrix.txt contains FPKM abundances per gene.
Supplementary_files_format_and_content: *.wig contains library size and background noise normalized signal tranck
Supplementary_files_format_and_content: *.narrowPeak contains inferred INTS12 binding sites at q<0.05

growth_protocol: Human bronchial epithelial cells HBECs were purchased from Clonetics-Biowhittaker (MD, USA). Cells were cultured in HBEC basal medium (BEGM) from Lonza (Berkshire, UK) prepared by addition of all the recommended supplements per manufacturer specifications excluding gentamicin. All laboratory experiments were performed using passage 3 cells. Prior to experiments cells were grown at 37oC with 5% CO2 until ~95% confluent with BEGM media change every ~48h

extract_protocol:
RNAseq: Total RNA was extracted using a mammalian total RNA prep kit with on-column DNaseI digestion
ChIP-seq: Unprecipitated genomic DNA (i.e. input control) was prepared from a pool of equal aliquots of the two donor samples. Genomic DNA regions of interest were isolated using 4 µg of antibody against INTS12 (Sigma cat. num. HPA03577) following manufacturer’s specifications (Active Motif).
RNA-seq: The sequencing libraries were prepared with Illumina TruSeq RNA Sample Prep Kit v2. mRNA was poly-A selected by capturing total RNA samples with oligo-dT coated magnetic beads. The mRNA was then fragmented and randomly primed. cDNA was synthesised using random primers. Finally a ready-for-sequencing library was prepared by end-repair, phosphorylation, A-tailing, adapter ligation and PCR amplification. Paired-end sequencing was performed on the HiSeq2000 platform (Illumina) using TruSeq v3 chemistry over 100 cycles yielding ~40 million reads per sample.
ChIP-seq: Libraries (Illumina) were prepared from the both ChIP and input DNAs and the resulting libraries were sequenced yielding ~40 million reads per two ChIP samples from each donor cells and one input control of both donors. DNA libraries obtained from single donor were sequenced on NextSeq 500 sequencing machine

treatment_protocol:
RNAseq: Effects of INTS12 depletion were assessed 120h and 48h after the initiation of interference.There were four experimental conditions: un-transfected cells, cells transfected with scrambled D-siRNA control, and cells transfected with D-siRNAs A and C. Each experimental condition was performed in three independent biological replicates.
ChIP-seq: Cells were formaldyhade fixed. Chromatin was isolated by the addition of lysis buffer. Genomic DNA for each replicate sample was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.

tag: donor

value: Human bronchial epithelial cells HBECs

tag: source

value: Lonza

tag: transfected with

tag: time point

value: 48h since the initiation of knockdown


title: Thy1-Nic-1

city: chongqing

first: jie

last: yang

address: 1 Youyi Road

country: China

institute: Chongqing Medical 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 mouse genome (version: GRCm38) using the Tophat  program.
Counts and RPKM was calculated based on the HTSeq
Genome_build: GRCm38
Supplementary_files_format_and_content: All_Fragments.txt

growth_protocol: Mice derived from two transgenic lines (GIN: # 003718 and YFPH: # 003782) were purchased from Jackson laboratory.  Mice were housed in the 12/12 h light/dark cycle and were given food and water ad libitum.

extract_protocol:
Cells (10 in each) were then transferred to 3.5 μl lysis buffer containing 2% Triton X-100 and 5% RNaseOUT (20U/μl, Invitrogen) in nuclease free water and were immediately stored at -80℃ for further processing. SMARTer Ultra Low Input RNA for Illumina Sequencing kit (Clontech) was used to amplify cDNA from cell lysates, according to manufacturer’s instruction. This kit allows high-quality cDNA synthesis in a single cell containing as low as 10pg RNA
The cDNA library was generated using Ovation® Ultralow DR Multiplex System (NuGEN). The amplified products were quantified by Qubit® 2.0 Fluorometer (Invitrogen) and validated by Agilent 2100 bioanalyzer (Agilent).

treatment_protocol: Male mice (20g, 5-7weeks) were implanted subcutaneously with an osmotic mini pump (model 2002; Alzet, Cupertino, CA) that delivered 48 mg/kg/d nicotine hydrogen tartrate (Sigma, St.Louis) or saline for 14 days

tag: strain background

value: male

tag: weight

value: 5-7 wks

tag: treated with

value: 48 mg/kg/d nicotine hydrogen tartrate for 14 days

tag: cell type

value: pyramidal neurons (cortex)


title: 48h_INTS12_D-siRNA_C_2

description:
processed data file: 48h_metaMatrix.txt
C2

tag: passage


title: Thy1-Nic-2

tag: gender

tag: age


title: Thy1-3

value: saline for 14 days


title: RAW 264.7 Honaucin A 12 uM/LPS 30min replicate 1

value: RAW 264.7 macrophages

value: Abelson murine leukemia virus transformed macrophage

tag: strain

value: BALB/c

value: monocyte/macrophage


title: 48h_scrambled_D-siRNA_3

description:
processed data file: 48h_metaMatrix.txt
NC3


title: Thy1-2


title: RAW 264.7 Vehicle/LPS 30min replicate 2

tag: morphology


title: 48h_INTS12_D-siRNA_A_3

description:
processed data file: 48h_metaMatrix.txt
A3


title: RAW 264.7 Vehicle/LPS 30min replicate 1


title: 48h_INTS12_D-siRNA_A_2

description:
processed data file: 48h_metaMatrix.txt
A2


title: RAW 264.7 Honaucin A 4 uM/LPS 180min replicate 3


title: 48h_INTS12_D-siRNA_A_1

description:
processed data file: 48h_metaMatrix.txt
A1


title: Thy1-Nic-3


title: 48h_INTS12_D-siRNA_C_1

description:
processed data file: 48h_metaMatrix.txt
C1


title: 48h_untransfected_3

description:
processed data file: 48h_metaMatrix.txt
UT3

value: none (untransfected)


title: 48h_scrambled_D-siRNA_2

description:
processed data file: 48h_metaMatrix.txt
NC2


title: 120h_INTS12_D-siRNA_A_3

description:
processed data file: 120h_metaMatrix.txt
A3

value: 120h since the initiation of knockdown


title: 48h_scrambled_D-siRNA_1

description:
processed data file: 48h_metaMatrix.txt
NC1


title: SST-1

value: FVB

value: somatostatin positive interneurons (cortex)


title: 120h_INTS12_D-siRNA_A_2

description:
processed data file: 120h_metaMatrix.txt
A2


title: SST-Nic-2


title: SST-Nic-1


title: 48h_untransfected_1

description:
processed data file: 48h_metaMatrix.txt
UT1


title: SST-Nic-3


title: Sgf73-Myc ChIPseq_2

first: Albert

middle: R.

last: La Spada

state: California

address: 2880 Torrey Pines Scenic Dr.

department: Pediatrics

institute: University of California San Diego

data_processing:
Bowtie 1.0.0 release (Langmead et al., 2009) was used to align ChIP-seq reads to the SacCer3 genome build.
Data filtering was done to limit tags per base pair to 1, effectively removing all duplicate reads that started at the same position.
Files were converted into a bedGraph formatted file using the HOMER tool suite (Heinz et al., 2010) v4.2  makeUCSCfile.
Peaks were called using HOMER tool suite v4.2 findPeaks with defualt settings and using the combined WT Myc ChIP runs as the background tag directory.
Genome_build: Saccharomyces cerevisiae, SacCer3, S288c GCA_000146055.2
Supplementary_files_format_and_content: Bed files were generated using HOMER tool suite v4.2, the file gives the chromosome, start, end, and relative ChIP-fragment density. Text files of peaks were generated using HOMER tool suite v4.2, the file gives the cordiantes of the called peaks (chromosome, start, and end position).

organism: Saccharomyces cerevisiae

source_name: yeast cells

growth_protocol: A 5 ml YPD culture from a single yeast colony grown overnight at 30¡C was diluted in 100 ml of YPD for harvest at ~A600 l/ml

extract_protocol:
Cells were lysed, lysates were sonicated, and protein DNA complexes were isolated using an anti-c-myc antibody.
Libraries for sequencing were generated using the ChIP’d fragments and the Ovation ultralow DR multiplex 1-8 library system (NuGEN – 0330) as described in the protocol.

treatment_protocol: Cells were fixed with 0.86% formaldehyde at room temperature (RT) for 25 min. The reaction was quenched with 125 mM glycine and 0.2% NH4OH for 5 min at RT.

value: Resgen

tag: tagged protein

tag: chip antibody

value: anti-c-Myc EZview resin (Sigma E6654)


title: 120h_INTS12_D-siRNA_A_1

description:
processed data file: 120h_metaMatrix.txt
A1

value: Human bronchial epithelial cells HBECs

value: Lonza


title: 120h_INTS12_D-siRNA_C_3

description:
processed data file: 120h_metaMatrix.txt
C3


title: IgG

first: Hong-wei

last: Sun

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
Sequence reads were obtained and mapped to the mouse mm10 genomes using Bowtie 1.1.2. All reads mapping with two or fewer mismatches were retained.
Peak detection was performed with MACS 1.4.2 using IgG as control and p-value threshold as 1e-5.
Bedgraph files where generated using Homer
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files contain the signal for each sequence experiment, the bed files contain the regions of the called peaks

source_name: Suprabasal Keratinocytes

extract_protocol:
Isolated Suprabasal keratinocytes were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibodies.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on HiSeq 2000 or 2500 following the manufacturer's protocols.

tag: genotype/variation

value: wild type

tag: background strain

value: adult

value: IgG


title: WT ChIPseq_2


title: 120h_scrambled_D-siRNA_2

description:
processed data file: 120h_metaMatrix.txt
NC2

tag: donor


title: SST-2

value: male

value: 5-7 wks


title: 48h_untransfected_2

description:
processed data file: 48h_metaMatrix.txt
UT2

tag: source

value: 48h since the initiation of knockdown


title: SST-3

value: saline for 14 days


title: Fertilised_embryo_2

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

data_processing:
fastq file processed by filering out low quality reads (<Q20) and llow quality bases (<Q20) with sickle. Adaptors were removed with cutadapt 1.0.
RNA-seq data have been aligned to mus musculus mm9 and X. Laevis genome 6.1 background genome using TopHat 2.0.6
ChIP-seq  data have been aligned to X. Laevis genome 6.1 mus musculus mm9 and X. Laevis genome 6.1 background genome using BWA 0.6.2 with default options. Duplicate reads were then removed
Differential analysis was conducted using EdgeR package
Genome_build: mus musculus mm9 and X. Laevis genome 6.1
Supplementary_files_format_and_content: text files contain RPKMs
Supplementary_files_format_and_content: bw files contain coverage across genome binned in 50bp windows

source_name: fertilised embryo

extract_protocol: RNA extractions were performed using  ARCTURUS PicoPure RNA Isolation Kit (Thermofischer) according to the manufacturer's protocol. Illumina TruSeq RNA sample prep kit for RNA-seq.

tag: transferred nucleus/sample type

value: mouse fertilised embryo

tag: starting material

value: pool of 10 embryos

tag: developmental stage/condition

value: mouse 2-cell stage embryos


title: Fertilised_embryo_1


title: 120h_INTS12_D-siRNA_C_2

description:
processed data file: 120h_metaMatrix.txt
C2

tag: transfected with

tag: time point

value: 120h since the initiation of knockdown


title: 120h_INTS12_D-siRNA_C_1

description:
processed data file: 120h_metaMatrix.txt
C1

tag: cell type


title: Ubp8-Myc ChIPseq_2


title: K4me3

value: BALB/c

tag: antibody vendor/catalog#

value: Diagenode C15410003


title: Dlx3

value: abcam ab178428


title: 120h_untransfected_3

description:
processed data file: 120h_metaMatrix.txt
UT3

tag: passage

value: none (untransfected)


title: ES_USP21_clone_1

source_name: ES transplanted to mouse egg expressing USP21

value: mES clone embryo


title: 120h_untransfected_2

description:
processed data file: 120h_metaMatrix.txt
UT2

value: Human bronchial epithelial cells HBECs

value: Lonza


title: ES_USP21_clone_2


title: Thy1-1

tag: strain background

tag: gender

tag: weight

tag: age

tag: treated with

value: pyramidal neurons (cortex)


title: ES_control_clone_3

source_name: ES transplanted to mouse egg


title: Sgf73-Myc ChIPseq_1

tag: strain

value: Resgen

tag: tagged protein

tag: chip antibody

value: anti-c-Myc EZview resin (Sigma E6654)


title: 120h_scrambled_D-siRNA_3

description:
processed data file: 120h_metaMatrix.txt
NC3

tag: donor

tag: source


title: ES_control_clone_2

tag: transferred nucleus/sample type

tag: starting material


title: H3K9me2_Con

city: Los Angeles

first: Cunyu

last: Wang

address: 10833 Le Conte Ave

department: School of Dentistry

institute: university of California, Los Angeles

data_processing:
Basecalls performed using  bcl2qfastq, version2.17.1.14
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie
peaks were called using algorithm described previously (Ferrari R et al.,  Genome Res. 2012:1212-21). The statistical cutoff for significant peaks was P < 10−3 and with two neighboring windows of the same significance
Genome_build: hg19
Supplementary_files_format_and_content: wig files reports significant normalized tag counts. bed files reports the position of significant peaks.

source_name: Human colorectal cancer HCT116 cells

growth_protocol: DMEM with 10% FBS, 37 degree with 5% CO2 culture for 2 days in 10cm dish

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Ovation Ultralow DR Multiplex System )

treatment_protocol: siRNA treatment followed by Invitrogen RNAimax protocol

tag: cell line

value: Human colorectal cancer

value: H3K9me2( Abcam, ab1220)


title: WT ChIPseq_1


title: ES_USP21_clone_3

tag: developmental stage/condition


title: 120h_untransfected_1

description:
processed data file: 120h_metaMatrix.txt
UT1

tag: cell type

tag: transfected with

tag: time point


title: ES_control_ clone_1


title: Input_KD


title: 120h_scrambled_D-siRNA_1

description:
processed data file: 120h_metaMatrix.txt
NC1

tag: passage


title: H3K9me2_KD


title: SSCs rep2

city: Shanghai

first: Ji

last: Wu

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

data_processing:
Alignment/mapping reads to reference genome by TopHat2
Transcripts assembling by Cufflinks
Merge assembles by Cuffmege
Coding potential calculation by CNCI and CPC
The  genes expression levels were estimated by FPKM (fragments per kilobase of exon per million fragments mapped) and assessed using Cuffdiff v2.1.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: RPKM values for novel lncRNAs

source_name: SSCs

extract_protocol:
Total RNA from the SSCs and FGSCs were isolated using TRIzol reagent (Invitrogen, life Technologies, USA) according to the manufacturer's protocol. Total RNA from each sample was quantified using Agilent 2100, and RNA integrity was assessed using Agilent 2100.
After extracting the total RNA from samples, mRNA and non-coding RNAs are enriched by removing rRNA from the total RNA with kit. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments (about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 when necessary.

tag: tissue

value: testis

value: spermatogonial stem cells

value: 3–5 days


title: input shNedd4 +Glucose

data_processing:
BCL files containing the sequence data were converted into “.fastq.gz” files and individual sample libraries were demultiplexed using CASAVA 1.8.2 with no mismatches.
3 nts from both ends were trimmed off and aligned to hg19 human assembly by Bowtie2.
sam files converted to bam files
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by bamcompare in Deeptools and normailzed to 1X genome coverage

source_name: Hep3B cells_input

growth_protocol: culture in DME/F12 medium

extract_protocol:
ChIP-IT High Sensitivity kit (Active motif) according to the manufacturer’s manual
Prepared using DNA Library preparation kit (KAPA, KK8232), as per the manufacturer’s protocol.  In brief, DNA was fragmented to a median size of 150bp by sonication. Fragmented DNA ends were polished and 5′-phosphorylated. After addition of 3′-A to the ends, indexed Y-adapters were ligated and the samples were PCR amplified.

treatment_protocol: glucose starvation in DMEM medium without glucose, then treat with glucose (4.5g/L)

tag: antibody

value: none (input)

tag: shRNA


title: KDM3B_Con

value: KDM3B (Millipore, 09-816)


title: FGSCs rep2

source_name: FGSCs

value: ovary

value: germline stem cells

tag: age

value: 6 days


title: SSCs rep1

tag: strain


title: input shLuc +Glucose

value: Luc


title: KDM3B_KD


title: FGSCs rep1


title: shLuc +Glucose H3K9ac ChIPseq

source_name: Hep3B cells_ChIP

value: anti-H3K9ac, Active Motif, 39917


title: Input_Con


title: SSCs rep3


title: YJE6 : pS6-IP from 100% heptanal stimulated olfactory epithelium

city: Durham

first: Kentaro

last: IKEGAMI

address: 213 Research Drive

institute: Duke University

data_processing:
we implemented a stepwise mapping scheme that allows reads aligned to multiple regions to be distributed proportionally to these regions based on the previous read counts from these regions (Mortazavi et al., 2008).
reads were aligned to mm10 by Bowtie with -m 20 -a, 100bp reads were trimmed to 50bp.
the resulted mapping file was separated into 20 sub-files that includes reads only mapped to 1, 2, ... , 20 regions respectively. BEDTools was used to first count reads mapped to coding exons of genes using only uniquely mapped reads. Reads mapped to two regions were distributed based on read counts from uniquely mapped reads.
Genome_build: mm10
Supplementary_files_format_and_content: the first column contains gene names. the next 20 columns are read counts corresponding to the 20 iterations described above.

source_name: Olfactory epithelium

extract_protocol:
homogenates of olfactory epithelium were incubated with pS6 antibody to immunoprecipitate mRNAs associated with pS6.
mRNAs were reverse-transcribed into cDNA, which was then amplified and constructed into sequencing biraries using Illumina Nextera library prep kit.

treatment_protocol: mice were stiumlated with heptanal or control for 1 hr.

value: Olfactory epithelium

tag: ip antibody

value: pS6 antibody

tag: developmental stage

value: post natal day 18


title: input shLuc -Glucose


title: YJE4 : pS6-IP from control olfactory epithelium


title: Drought_3 days_Replicate 1

city: YONGIN-SI

first: ANIL KUMAR

last: NALINI CHANDRAN

address: 1732, Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do

department: Graduate school of Biotechnology

institute: Kyung Hee University

data_processing:
Data obtained from illumina Hiseq 2000 platform
100-bp paired-end reads were assessed with a FastQC toolkit. Any adapter contaminations and low-quality reads (-phred33 and -q 20) were removed using both Cutadapt and its wrapper tool, Trimgalore.
Filtered reads were mapped to the International Rice Genome Sequencing Project (IRGSP) 1.0 reference genome using Tophat. Gene features were estimated based on the gff3 annotation file provided in the Rice Genome Annotation Project (RGAP) database.
Transcript abundance and differential expression analysis was done using Tophat pipeline (Trapnell et al. 2012)
Genome_build: International Rice Genome Sequencing Project (IRGSP) 1.0 reference genome
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample and differential expression

organism: Oryza sativa

source_name: Root

extract_protocol:
Root samples were collected and frozen in liquid nitrogen and RNA was collected using RNAiso kits (Takara Bio, Shiga, Japan). Illumina TruSeq RNA Sample Prep Kit was used  for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sub species

value: Japonica

value: 4 weeks old seedling

value: Root


title: Drought_3 days_Replicate 2


title: YJE5 : pS6-IP from 1% heptanal stimulated olfactory epithelium


title: YJE3 : pS6-IP from 100% heptanal stimulated olfactory epithelium

value: post natal day 21


title: shNedd4 +Glucose H3K9ac ChIPseq


title: YJE1 : pS6-IP from control olfactory epithelium


title: FGSCs rep3


title: YJE2 : pS6-IP from 1% heptanal stimulated olfactory epithelium


title: Drought_2 days_Replicate 2


title: shLuc -Glucose H3K9ac ChIPseq


title: YJC12 : pS6-IP from 100% heptanal stimulated olfactory epithelium

value: post natal day 22


title: TSC_Lsd1i_2

description:
TSC treated with inhibitor
processed data file: diff_edgeR_D0_Lsd1i.txt

data_processing:
Raw sequence files (.fastq files) were aligned to mouse genome (mm10) using TopHat
Counting of the aligned reads was performed using homer software (analyze RNA). Differentially expressed genes were identified with EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include processed raw counts, pvalues and fold changes

extract_protocol:
RNA was harvested using Qiagen kit. Strand-Specific RNA Seq with Agilent kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hrs with DMSO or Inhibitor changing media every 12 hrs; 8 days with DMSO or 4OHT

value: E 3.5 isolated trophoblast stem cells

tag: genotype/variation

value: +/+; TSC wild type

tag: treated with

value: inhibitor


title: YJC11 : pS6-IP from 1% heptanal stimulated olfactory epithelium


title: Drought_2 days_Replicate 1


title: YJC10 : pS6-IP from control olfactory epithelium


title: Control_Replicate 1


title: Muscle_HFD_veh

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

institute: Tsinghua University

data_processing:
All RNA-seq data sets were aligned to the mouse genome using TopHat
The mapped reads were further quantified as fragments per kilobase of transcript per million mapped reads (FPKM) based on the RefSeq database using the Cufflinks program
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Muscle

growth_protocol: Male C57BL/6J mice were fed on either a normal chow diet (NCD) or a high fat diet (HFD) from the age of 8 weeks to 17 weeks.

extract_protocol:
Fresh mouse tissues were isolated and snap frozen in liquid nitrogen. Total RNA was prepared using TRIzol reagent and quantified by NanoDrop-1000. Quality control was performed using Agilent 2100 bioanalyzer. 1 ug  total RNA was used for sequencing library construction.
RNA sequencing libraries were prepared according to the standard Illumina protocols

treatment_protocol: Drug treatment started from 10 weeks until 17 weeks.

tag: treatment

value: vehicle

value: Muscle

value: 17 weeks


title: DeltaCspCE_RNAseq2

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Reads were trimmed for a Phred quality of 20 using the FASTX toolkit version 0.0.13
Adapter trimming using Cutadapt version 1.3
Reads were mapped using the READemption pipeline (Förstner et al., 2014), segemehl, and the lack remapper to the SL1344 genome and associated plasmids (NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1 )
Coverage plots (wig files) and read quantifications were produced by READemption
Genome_build: NCBI references: NC_016810.1, NC_017718.1, NC_017719.1, NC_017720.1
Supplementary_files_format_and_content: text files are tab delimited including raw read counts; RIP-seq and RNA-seq contain fractional read counts for multimapping reads, while dual RNA-seq counts were generated solely from uniquely mapped reads.

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

source_name: OD 2

growth_protocol: Salmonella was routine grown in LB (220 rpm, 37C), supplemented with appropriate antibiotics. For RIP-seq, cultures were supplemented with 0.2% L-Arabinose at an OD of 0.2. Cultures were grown to OD 2.0 before harvesting RNA. For dual RNA-seq, OD 2 cultures were used to infect HeLa cells at a multiplicity of infection of 5 and centrifuged for 10 minutes. After 30 minutes at 37C, gentamicin was added to the media to kill extracellular bacteria, and RNA was harvested at the listed time points.

extract_protocol:
For RIP-seq: When the culture reached an OD600 of 2, bacteria were re-suspended in 800 µl of ice-cold lysis buffer (Tris, pH 8.0, 20 mM, KCl 150 mM, MgCl2 1 mM, DTT 1 mM), and disrupted with 1 ml glass beads (BioSpec Products, 0.1 mm diameter) by shaking at 30 Hz for 10 min. The cleared lysate obtained after centrifugation (16000 rcf, 15 min, 4°C) was incubated with 0.5 µl/OD anti-Flag antibody (Sigma, F1804) at 4°C for 30 min followed by incubation with 64 µl pre-washed Protein-A sepharose (Sigma, P6649) for another 30 min. After 5 washes with ice-cold lysis buffer, the sepharose was subjected to Phenol:Chloroform:Isopropanol extraction to isolate RNA (PCI 25:24:1, pH 4.5; Roth, X985.3). For RNA-seq: Total RNA was extracted with hot phenol and chloroform followed by DNase I treatment. For dual RNA-seq: Total RNA from the infected and sorted cells was isolated using the mirVana kit (Ambion).
The samples were rRNA depleted (RNA-seq and dual RNA-seq), then poly(A)-tailed using poly(A) polymerase and the 5’triphosphate (and eukaryotic cap) structures were removed using tobacco acid pyrophosphatase (TAP). Afterwards, an RNA adapter was ligated to the 5’monophosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the M-MLV reverse transcriptase (NEB). The resulting cDNA was PCR-amplified to about 20-30 ng/µL using a high fidelity DNA polymerase (barcode sequences for multiplexing were part of the 3’primers). The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Agilent Technologies).

tag: stategy

value: RNA-seq

value: deltaCE


title: DeltaCspCE_RNAseq3


title: Muscle_HFD_narciclasine

value: narciclasine


title: Liver_HFD_narciclasine

source_name: Liver

value: Liver


title: WT_RNAseq1

value: WT


title: WT_RNAseq2


title: Liver_NCD_veh


title: TSC_Ctrl_2

first: Maria

last: Castex

address: BreisacherStrasse 66

description:
TSC treated with DMSO
processed data file: diff_edgeR_D0_Lsd1i.txt

value: DMSO


title: Liver_HFD_veh


title: WT_RNAseq3


title: TSS_TAP_2

city: Daejeon

first: Yujin

last: Jeong

address: 291 Daehak-ro

institute: KAIST

description:
The rRNA-depleted RNA samples were treated with 20 U of RNA 5' polyphosphatase (TAP, Epicentre) without TEX treatment to generate the whole transcriptome library.
differential RNA-seq

data_processing:
CLC Genomics workbench 6.5 (CLC bio) was used for data trimming and read mapping.
For ssRNA-seq analysis, adapter sequences were trimmed and sequence reads shorter than 25 nucleotides were discarded.
For dRNA-seq analysis, the reads from two experiments were summed, whose TSS adapter sequence and N9 sequences were trimmed and sequence reads shorter than 25 nucleotides were also removed.
The retained sequence reads were mapped to the T. onnurineus NA1 (NC_011529) genome sequence using CLC genomics workbench (CLC bio, Aarhus, Denmark) with the following parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.9, and similarity = 0.9. Only sequence reads that aligned to unique genomic locations were retained.
Differentially expressed genes were identified using the DESeq package in R.
Genomic positions of the 5' ends of uniquely aligned dRNA-seq reads were considered to be potential TSSs. Only TSSs present in both TEX+ and TEX- libraries (within ± 5 bp) were retained.
potential TSSs within 150 bp were clustered together; they were then sub-clustered with the standard deviation <15. Clusters and sub-clusters with less than three reads were removed. The potential TSS with the most reads in a sub-cluster was selected as the TSS. If a cluster had several TSSs, the standard deviation of two adjacent TSSs was calculated. If the calculated standard deviation was less than 15, the one with lower reads was removed. The TSSs were then manually curated
Genome_build: NC_011529
Supplementary_files_format_and_content: tab-delimited text files include TSS or normalized expression values for each sample

organism: Thermococcus onnurineus

source_name: cell culture

extract_protocol:
Total mRNA was split into two samples for two different libraries: the library of the primary transcriptome and the library of whole transcriptome. Terminator 5’-Phosphate-Dependent Exonuclease (TEX, Epicentre) was used to treat one of the samples to enrich primary transcripts which have triphosphate at their 5’-ends, resulting in the preparation of the TEX-treated (TEX+) and non-treated (TEX-) samples. The triphosphates at the 5’-ends of mRNA were converted to monophosphate by treating RNA 5’-polyphosphatase (Epicentre). The mRNA was then purified by phenol-chloroform extraction and ethanol precipitation. 5’-RNA adaptor was ligated to the purified mRNA, then cDNA was synthesized using random 3’ overhanging primer (N9). Synthesized cDNA was purified using QIAquick PCR Purification Kit (Qiagen). The cDNA was purified again by ethanol precipitation. Purified cDNA was selected at a size range between 100 bp and 350 bp on a 2% agarose gel by Pippin Prep (Sage Science). Then the purified sequencing library was amplified by PCR with indexed primers for Illumina sequencing platform. After the enriched library was purified by ethanol precipitation, the library of size between 150 bp and 400 bp was extracted. The size-selected library was purified by ethanol precipitation. A second PCR amplification was carried out with a few PCR cycles to produce enough amount of library for Illumina sequencing. The final amplified library was purified by ethanol precipitation and those of size 150 bp to 400 bp were extracted from 2% agarose gel after electrophoresis. The final library was then purified using MinElute Gel Extraction Kit.
Cell cultures in the exponential growth phase were harvested and stored at −80°C prior to use. After thawing, the resulting cell pellet was used to obtain total RNA by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA). DNase I (Thermo Scientific Inc., Waltham, MA) treatment was performed at 37°C for 30 min to remove genomic DNA from the isolated total RNA. Total RNA was further purified by chloroform extraction and ethanol precipitation.
A Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI) was used to deplete rRNAs in accordance with the manufacturer’s protocol


title: Muscle_NCD_veh


title: Control_Replicate 2

value: Japonica


title: TSS_TEX_1

description:
The rRNA-depleted RNA samples were treated with 1 U of Terminator 5’-Phosphate-Dependent Exonuclease (TEX, Epicentre) to enrich primary transcripts.
differential RNA-seq


title: TSC_Lsd1i_1

institute: Freiburg Uniklinik


title: TSS_TEX_2


title: BAT_HFD_narciclasine

source_name: Brown adipose tissue

value: Brown adipose tissue


title: WAT_HFD_narciclasine

source_name: White adipose tissue

value: White adipose tissue


title: BAT_HFD_veh


title: TSS_TAP_1


title: WAT_HFD_veh


title: MEF_NT_BrUTP_Input_2

organism:
Xenopus laevis
Mus musculus

source_name: MEF transplanted to Xenopus oocyte injected with BrUTP

extract_protocol: For DNA extraction, sonicated chromatin was reverse crosslinked o/n at 65 degree in the presence of proteinase K, followed by  phenol/chloroform extraction and ethanol precipitation.

tag: transferred nucleus/sample type

tag: starting material

value: pool of  80 oocytes

tag: developmental stage/condition

value: stage 5-6 xenopus Nuclear transfer oocytes

value: H2Aub antibody (H2AK119U1, 8240, Cell Signalling)


title: MEF_NT_BrUTP_H2Aub_IP_2


title: MEF_NT_BrUTP_Input_1


title: PB1+Pi9 M.oryzae Treated R3

city: New Delhi

first: T

middle: R

last: Sharma

state: Delhi

address: Pusa Campus New

country: India

institute: NRCPB

data_processing:
CASAVA pipeline 1.7 was used for data processing, demultiplexing and Bcl conversion for all samples
The spliced read mapper Tophat v2.0.9 and Bowtie was used to map reads indiviually of each biological replicate(BR) in resistant and suceptible lines against O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
The aligned reads obtained from tophat were analyzed using Qualimap. The aligned reads were visualized on IGV. Cufflink v2.1.1 was used to  assemble aligned reads into transcript. Cufflink measures abundance in fragments per kilobase of exon per million fragments mapped (FPKM).  Cuffdiff was used to quantify transcript using the merged transcript assembly obtained from cuffmerge and to detect differentially expressed genes.
Genome_build: O. sativa Japonica Group cultivar Nipponbare; MSU release 7.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Leaf

growth_protocol: Growth conditions of 16 h light (115 μ Mol m–2 s–1) and 8 h dark photoperiod at 25 ± 2°C

extract_protocol:
Rice leaves were collected 24 hours  after M.oryzae infection from resistant and suceptible line, frozen on liquid nitrogen, and RNA was extracted using Spectrum™ Plant Total RNA Kit (Sigma).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: M.oryzae Conidia concentration was adjusted to 105spores/ml

value: Indica

value: Leaves from 4 leaf stage rice plant

value: 24 hours after M.oryzae spray

tag: genotype


title: BAT_NCD_veh

value: vehicle


title: TSC_Ctrl_1

tag: cell type

value: E 3.5 isolated trophoblast stem cells

tag: passage

value: +/+; TSC wild type


title: MEF_NT_BrUTP_H2Aub_IP_1

tag: antibody


title: WAT_NCD_veh

tag: tissue

value: 17 weeks


title: DeltaCspCE_RNAseq1

value: RNA-seq

value: deltaCE


title: MEF_NT_XLRing1B_Mutant_BrUTP_2

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with XLRing1B and with BrUTP

extract_protocol: RNA extractions were performed using Qiagen RNeasy Mini kit (Qiagen, 74106) according to the manufacturer's protocol including the on column DNAse step. Illumina TruSeq RNA sample prep kit for RNA-seq.

tag: pairing of samples

value: pool of  16 oocytes

value: anti-BrdUTP (Sc32323AC, Santa Cruz Biotechnology Inc)


title: MEF_NT_XLRing1B_Mutant_BrUTP_1

description: immunoprecipitated RNA


title: MEF-Ring1A&BdKO_NT_BrUTP_1

description: immunoprecipitated RNA

source_name: MEF-Ring1A&BdKO transplanted to Xenopus oocyte injected with BrUTP

value: 4-hydroxy-tamoxifen (OHT) treated Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 MEF


title: PB1+Pi9 Mock R3

tag: strain

tag: age

value: 24 hours after Gelatin spray


title: PB1+Pi9 M.oryzae Treated R2


title: PB1+Pi9 Mock R1


title: PB1+Pi9 M.oryzae Treated R1


title: MEF_NT_USP21_BrUTP_1_group3

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with USP21 and with BrUTP


title: MEF_NT_USP21_BrUTP_2_group4

description: immunoprecipitated RNA


title: PB1 M.oryzae Treated R2


title: MEF_NT_BrUTP_2_group4

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_K4d_K6b_USP21_BrUTP_2

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with K4d and K6b and USP21 and with BrUTP

value: Dnmt1N_p53minus_ MEF


title: PB1 M.oryzae Treated R1


title: PB1 Mock R1


title: PB1 Mock R2


title: PB1 Mock R3


title: Dnmt1N_MEF_NT_K6b_USP21_BrUTP_2

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with K6b and USP21 and with BrUTP


title: MEF_NT_BrUTP_1_group3

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_USP21_BrUTP_1

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with USP21 and with BrUTP


title: Dnmt1N_MEF_NT_USP21_BrUTP_2

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_K6b_BrUTP_2

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with K6b and with BrUTP


title: Dnmt1N_MEF_NT_K6b_BrUTP_1

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_K6b_USP21_BrUTP_1

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_K4d_BrUTP_2

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with K4d and with BrUTP


title: PB1+Pi9 Mock R2


title: MEF-Ring1A&BdKO_NT_BrUTP_2

description: immunoprecipitated RNA


title: Dnmt1N_MEF_NT_BrUTP_2

description: immunoprecipitated RNA

source_name: Dnmt1N_MEF transplanted to Xenopus oocyte injected with BrUTP


title: MEF_NT_K4d_K6b_USP21_BrUTP_2

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with K4d and K6b and USP21 and with BrUTP

value: p53minus_ MEF


title: Dnmt1N_MEF_NT_BrUTP_1

description: immunoprecipitated RNA

value: stage 5-6 xenopus Nuclear transfer oocytes


title: MEF_NT_K4d_K6b_USP21_BrUTP_1

description: immunoprecipitated RNA


title: PB1 M.oryzae Treated R3


title: MEF_NT_K6b_USP21_BrUTP_1

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with K6b and USP21 and with BrUTP


title: Sample_WT_2

city: WuHan

first: jin

middle: zhi

last: zhang

address: College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

institute: Huazhong Agricultural University

data_processing:
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis.    Filter steps:    Remove reads with adaptors;  Remove reads in which unknown bases are more than 10%;   Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
Denove
Genome_build: No
Supplementary_files_format_and_content: xls files were generated by Microsoft Excel, RPKM represent the expression of genes.

organism: Citrus trifoliata

source_name: Citrus

growth_protocol: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes of the MT and the WT 2-year-old trees were also collected at flower initiation (after self-pruning).

extract_protocol:
Total RNA was isolated from the WT and the MT (three biological replicates per genotype) using the Plant RNAiso Plus according to the manufacturer’s instructions (Takara, Kusatsu, Japan). Genomic DNA was removed from total RNA by DNase treatment (Promega, Madison, WI, USA). All RNA samples were quantified and examined for protein contamination and reagent contamination by a Nanodrop ND 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). Due to some lncRNAs lacking the poly(A) tail, total RNA was treated to remove rRNA by using Ribo-Zero rRNA Removal Kits (Plant) according to the manufacturer’s instructions (illumina, USA), retaining lncRNA both with and without a poly(A) tail.
Six strand-specific RNA libraries with an insert size of about 250–500 nucleotides were prepared according to a UTP method (Parkhomchuk et al., 2009), and submitted to the Beijing Genomics Institute (BGI, Shenzhen, China) for 125 bp paired-end sequencing on the Illumina HiSeq 2500, at a depth of approximately 90 million reads per library.

treatment_protocol: No treatment

tag: development stage

value: After self-pruning

tag: cultivar

value: Wild-type  trifoliate orange


title: Sample_WT_3

department: College of Horticulture and Forestry Science

value: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes


title: MEF_NT_K6b_USP21_BrUTP_2

description: immunoprecipitated RNA


title: MEF_NT_USP21_BrUTP_2_group2

description: immunoprecipitated RNA


title: Sample_WT_1


title: Sample_MT_3

value: Precocious trifoliate orange


title: MEF_NT_K6b_BrUTP_2

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with K6b and with BrUTP


title: MEF_NT_USP21_BrUTP_1_group1

description: immunoprecipitated RNA


title: MEF_NT_K4d_BrUTP_2

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with K4d and with BrUTP


title: Sample_MT_1


title: Sample_MT_2


title: Dnmt1N_MEF_NT_K4d_BrUTP_1

description: immunoprecipitated RNA


title: MEF_NT_K4d_BrUTP_1

description: immunoprecipitated RNA


title: MEF_NT_K6b_BrUTP_1

description: immunoprecipitated RNA


title: 5mMVanillin-Δyrr1-2A

city: Jinan

first: Xiaoming

last: Bao

state: Shandong

address: Shanda Nan Road 27

department: State Key Laboratory of Microbial Technology

institute: Shandong University

description: BY4741 deleted YRR1 as experimental strain cultured in SD medium with 5mM vanillin(Another parallel)

data_processing:
Raw reads was produced by Illumina HiSeqTM 4000.
Raw reads was subjected to quality control (QC).
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
If alignment result passes QC, we will proceed with downstream analysis including gene and isoform expression,deep analysis based on gene expression(PCA/correlation/screening differentially expressed genes and so on),exon expression, gene structure,refinement, alternative splicing, novel transcript prediction and annotation, SNP detection, Indel detection, gene fusion. Deep analysis based on DEGs,including Gene Ontology (GO) enrichment analysis,Pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcriptor were performed.
We define "dirty" raw reads as reads which contain the sequence of adapter, high content of unknown bases and low quality reads. They need to be removed before data analysis. Filtering steps are as follows to make clean data:
1) Remove reads with adapters;
2) Remove reads in which unknown bases are more than 10%;
3) Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 10).
Genome_build: R64
Supplementary_files_format_and_content: .txt files report FPKMs and differential expression of genes

organism: Saccharomyces cerevisiae BY4741

growth_protocol: The control medium was SD medium (1.7 g/L yeast nitrogen base(Sangon, China), 5 g/L ammonium sulfate(Sangon, China), CSM(MP Biomedicals,Solon,OH,USA) supplying 20 g/L glucose). The experimental medium was SD added 5mM vanillin. All the cultures were at 30℃,200rpm.

extract_protocol:
The pre-cultured cells of BY4741 and BY4741(yrr1Δ) in SD medium were transferred into fresh SD or SD added 5mM vanillin with an initial OD600 of 0.2. The cells were harvested during the log phase (OD600≈1.6-2.0) and quick frozen using liquid nitrogen. UNIQ-10 Trizol RNA Purification Kit (Sangon Biotech, China) was used to extract total RNA.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.

treatment_protocol: SD added 5mM vanillin

tag: stress

value: vanillin


title: MEF_NT_BrUTP_2_group2

description: immunoprecipitated RNA


title: 5mMVanillin-BY4741-2A

description: BY4741 as the control strain cultured in SD medium with 5mM vanillin(Another parallel)


title: 5mMVanillin-BY4741-1A

description: BY4741 as the control strain cultured in SD medium with 5mM vanillin


title: 5mMVanillin-Δyrr1-1A

description: BY4741 deleted YRR1 as experimental strain cultured in SD medium with 5mM vanillin


title: ES_NT _BrUTP_2

description: immunoprecipitated RNA

source_name: mES transplanted to Xenopus oocyte injected with BrUTP

value: mES 2i LIF


title: MEF_NT_BrUTP_1_group1

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte injected with BrUTP


title: YNB-Δyrr1-2A

description: BY4741 deleted YRR1 as experimental strain cultured in SD medium without stress(Another parallel)

value: control


title: YNB-Δyrr1-1A

description: BY4741 deleted YRR1 as experimental strain cultured in SD medium without stress


title: WT-mycelium-Light-R2

city: Irapuato

first: Alfredo

last: Herrera-Estrella

state: Guanajuato

address: Libramiento Norte Carretera Leon Km 9.6

department: LANGEBIO

country: Mexico

institute: LANGEBIO

data_processing:
100-base-pair-long reads were obtained and mapped to the P. blakesleeanus genome V2 using bowtie
We performed the mapping of the readings resulting from the RNAseq
experiment using the fasta file of the genome deposited at
http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Phybl2
Identifying the file as Phycomyces blakesleeanus NRRL1555 v2.0: Project:
401760, Phycomyces_blakesleeanus_v2_filtered_transcripts.fasta.gz 5 MB; Wed Mar 07 16:56:13 PST 2012.

The identifiers used are those appearing in the Phycomyces blakesleeanus
NRRL1555 v2.0 genome file and can be accessed individually at
http://genome.jgi.doe.gov/pages/search-for-genes.jsf?organism=Phybl2.
Alignment results were recorded in BAM format for further downstream analysis. Read counts per gene were calculated for each library using a shell script and collapsed into a table.
Differential expression analysis of gene expression in the wild type and madC strains in response to light was performed using the edgeR package
Enrichment analysis was performed on the differential genes using GOseq
Supplementary_files_format_and_content: read counts, differential expression

organism: Phycomyces blakesleeanus

source_name: WT strain exposed to light

growth_protocol: 104 activated spores (48 °C, 15 min) of each P. blakesleeanus strain were grown at 22 °C in minimal medium.

extract_protocol:
Mycelia were disrupted by two 0.5-min pulses in a cell homogenizer (FastPrep-24, MP Biomedicals) with 1.5 g of zirconium beads (0.5 mm diameter) using the RNeasy Plant Mini Kit (Qiagen) following the manufacturer procedure.
Libraries for RNAseq were prepared with RNA from mycelia of the wild type and the madC mutant strains using the TruSeq kit protocol (Illumina).

treatment_protocol: P. blakesleeanus dark-grown mycelia were exposed to blue light (2782.10 J/m2) at the age of 48 h for 30 min. After light exposure mycelia were collected and frozen in liquid nitrogen.

value: mycelium (Vegetative growth)


title: YNB-BY4741-2A

description: BY4741 as the control strain cultured in SD medium without stress(Another parallel)


title: YNB-BY4741-1A

description: BY4741 as the control strain cultured in SD medium without stress


title: WT-mycelium-Light-R3


title: WT-mycelium-Dark-R2

source_name: WT strain in dark


title: ES_NT_ BrUTP_1

description: immunoprecipitated RNA


title: RNA_CO

description: T. onnurineus NA1 cells were cultured anaerobically at 80°C. Modified minimal-formate (MMF) or -CO (MMC) media were prepared by adding 1% sodium formate or 1 bar CO gas into the modified minimal media (MM1) containing 0.1% yeast extract, 3.5% NaCl, 0.07% KCl, 0.39% MgSO4, 0.04% CaCl2·2H2O, 0.03% NH4Cl, 0.015% Na2HPO4, 0.003% NaSiO3, 0.05% NaHCO3, and 0.05% cysteine-HCl. The medium was supplemented with 0.1% (v/v) each of Holden’s trace element and Balch’s vitamin solution.

source_name: cell culture

extract_protocol:
The rRNA-depleted RNA samples were converted into sequencing libraries using a ScriptSeq RNA-seq library preparation kit (Epicentre). The samples were then sequenced using a MiSeq Genome Analyzer IIx in single-read mode with 38 cycles (Illumina Inc., San
A Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI) was used to deplete rRNAs in accordance with the manufacturer’s protocol


title: WT-mycelium-Light-R1


title: CspH_RIPseq

source_name: Arabinose-supplemented, OD 2

value: RIP-seq

tag: plasmid

tag: genotype/variation

value: WT

tag: fraction

value: anti-FLAG co-IPed RNA


title: WT-mycelium-Dark-R3


title: HUH-AAV_RNA-Seq

city: Westmead

first: Grant

middle: Joseph

last: Logan

address: 214 Hawkesbury Road

country: Australia

institute: CHildren's Medcial Research institute

data_processing:
Adaptor trimming using Trimmomatic with parameters: 2:30:10 LEADING:0 TRAILING:0 SLIDINGWINDOW:4:25 MINLEN:18
Alignment to the human genome (hg19) using RNA-STAR with parameters --outFilterMismatchNoverLmax 0.05 --twopassMode Basic --twopass1readsN -1.
Alignment to the AAV genome (J01901.1_modified) using RNA-STAR with parameters --outFilterMismatchNoverLmax 0.05 --twopassMode Basic --twopass1readsN -1.
Bedtools genomecov –d –split to determine the strand specific coverage on reads with flags 99 and 147 for the negative strand and flags 83 and 163 for the positive strand
Genome_build: J01901.1_modified. The fasta file for this genome is available on the series record.
Supplementary_files_format_and_content: genomic coverage for viral genome only generated by bedtools genomecov

organism: Adeno-associated virus

source_name: viral transcripts

growth_protocol: HuH-7 cells were seeded at 5 × 10(E)5 cells per T25 and cultured for 24 hours.

extract_protocol:
Cells were processed using an RNeasy kit (QIAGEN) to recover total RNA
Illumina TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Wild-type AAV serotype 2 was added at an MOI of 5000. Cells were cultured a further 48 hours before recovery using trypsin

tag: virus serotype

tag: cell line


title: RNA_Formate

description:
T. onnurineus NA1 cells were cultured anaerobically at 80°C. Modified minimal-formate (MMF) or -CO (MMC) media were prepared by adding 1% sodium formate or 1 bar CO gas into the modified minimal media (MM1) containing 0.1% yeast extract, 3.5% NaCl, 0.07% KCl, 0.39% MgSO4, 0.04% CaCl2·2H2O, 0.03% NH4Cl, 0.015% Na2HPO4, 0.003% NaSiO3, 0.05% NaHCO3, and 0.05% cysteine-HCl. The medium was supplemented with 0.1% (v/v) each of Holden’s trace element and Balch’s vitamin solution.
strand-specific RNA-seq

extract_protocol:
The rRNA-depleted RNA samples were converted into sequencing libraries using a ScriptSeq RNA-seq library preparation kit (Epicentre). The samples were then sequenced using a MiSeq Genome Analyzer IIx in single-read mode with 37 cycles (Illumina Inc., San Diego, CA).
Cell cultures in the exponential growth phase were harvested and stored at −80°C prior to use. After thawing, the resulting cell pellet was used to obtain total RNA by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA). DNase I (Thermo Scientific Inc., Waltham, MA) treatment was performed at 37°C for 30 min to remove genomic DNA from the isolated total RNA. Total RNA was further purified by chloroform extraction and ethanol precipitation.
A Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI) was used to deplete rRNAs in accordance with the manufacturer’s protocol


title: CspE_RIPseq

tag: stategy


title: RNA_YPS

description:
T. onnurineus NA1 cells were cultured anaerobically at 80°C in Yeast extract-peptone-sulfur (YPS) medium.
strand-specific RNA-seq

extract_protocol:
The rRNA-depleted RNA samples were converted into sequencing libraries using a ScriptSeq RNA-seq library preparation kit (Epicentre). The samples were then sequenced using a MiSeq Genome Analyzer IIx in single-read mode with 36 cycles (Illumina Inc., San Diego, CA).
Cell cultures in the exponential growth phase were harvested and stored at −80°C prior to use. After thawing, the resulting cell pellet was used to obtain total RNA by extraction with TRIzol reagent (Invitrogen, Carlsbad, CA). DNase I (Thermo Scientific Inc., Waltham, MA) treatment was performed at 37°C for 30 min to remove genomic DNA from the isolated total RNA. Total RNA was further purified by chloroform extraction and ethanol precipitation.
A Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI) was used to deplete rRNAs in accordance with the manufacturer’s protocol


title: MEF_NT_No_BrUTP_2

institute: University of Cambridge

description: immunoprecipitated RNA

source_name: MEF transplanted to Xenopus oocyte no BrUTP

tag: transferred nucleus/sample type

tag: starting material

value: pool of  16 oocytes

tag: developmental stage/condition

value: anti-BrdUTP (Sc32323AC, Santa Cruz Biotechnology Inc)


title: Prepub_2

city: Hefei

first: Fugui

last: Fang

state: Anhui

address: No. 130 of Changjiang West Road

department: College of Animal Sciences and Technology

institute: Anhui Agricultural University

data_processing:
Total RNA was used as input material for the RNA sample preparations. Ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA). Sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). Products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the libraries were  sequenced on an Illumina Hiseq 4000 platform and 150 bp paired-end reads were generated.
Inorder to identify the lncRNAs,the preliminary scanning was conducted by Scripture (beta2) and Cufflinks (v2.1.1) in a reference-based approach, follwed by coding poteintial analysis using CNCI (v2), CPC (0.9-r2) and Pfam Scan (v1.3).
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell,C.et al.2010).
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. The file lncRNA_sequence.txt contains the sequences for the lncRNA IDs contained in "lncRNA_FPKM.txt".

organism: Capra hircus

source_name: Hypothalamus

extract_protocol:
Hypothalamic tissues were surgically removed immediately frozen, and. RNA derived from goat hypothalamus was obtained using TRIzol Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Anhuai goats

value: Hypothalamus

value: Prepuberty


title: Prepub_3


title: MadC-mycelium-Light-R3

source_name: MadC mutant exposed to light

tag: cell type


title: CspB_RIPseq


title: CspD_RIPseq


title: CspC_RIPseq


title: MadC-mycelium-Light-R2


title: MadC-mycelium-Light-R1


title: MadC-mycelium-Dark-R2

source_name: MadC mutant in dark


title: Prepub_1

tag: tissue


title: MEF_NT_No_BrUTP_1

description: immunoprecipitated RNA

tag: pairing of samples

value: p53minus_ MEF

value: stage 5-6 xenopus Nuclear transfer oocytes

tag: antibody


title: MadC-mycelium-Dark-R1


title: MadC-mycelium-Dark-R3


title: Pub_1

tag: strain

value: Puberty


title: H30_mRNA

status: Public on Jun 11 2017

first: Yue

last: Hao

address: No.2 Yuanmingyuan West Road

institute: Institute of Animal Sciences, Chinese Academy of Agricultural Sciences

data_processing:
Raw data (i.e., raw reads) of fastq format were processed into clean data (i.e., clean reads) using Genome Analyzer Pipeline software (Illumina) by removing reads with ploy-N or 5’adapter contaminants; without 3’ adapter or insert tags; and with ploy A, T, G, or C.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the Sus scrofa draft genome assembly by Bowtie with no mismatches. Clean reads were aligned to the S. scrofa 10.2 reference genome using TopHat v1.4.0. The Cufflinks v1.3.0 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts using the TopHat alignment results.
Gene expression levels of mRNAs in CON and H30 were estimated and normalized by RPKM (Reads per Kilobase of exon model per million mapped reads). A corrected p-value of 0.05 was set as the threshold for significantly different expression.
Genome_build: Sus scrofa draft genome assembly (Sus_scrofa.Sscrofa10.2.70)
Supplementary_files_format_and_content: The fasta files were generated using Genome Analyzer Pipeline software (Illumina) by removing reads with poly-N or 5’adapter contaminants; without 3’ adapter or insert tags; and with poly A, T, G, or C. The FASTA file with novel gene sequences is available on the series record. the rpkm.txt file is in text format  and includes rpkm values for both samples.

organism: Sus scrofa

source_name: Skeletal muscle_30C_heat_stress

growth_protocol: 16 healthy crossbred barrows (DLY, originating from Duroc boars and Yorkshire-Landrace sows; body weight: 79.0±1.5 kg) from eight litters were selected.

extract_protocol:
Total RNAs were isolated from each sample using Trizol.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using the Illumina TruSeq RNA Sample Preparation Kit (Illumia, San Diego, CA). Briefly, mRNA was purified from the total RNA using poly-T oligo-attached magnetic beads. Fragmentation was performed using divalent cations under elevated temperatures in a proprietary Illumina fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and SuperScript II (Life Technologies Inc, Rockville, MD, USA). Second strand cDNA synthesis was then performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends using exonuclease and polymerase. After the adenylation of the 3' ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated in preparation for hybridization. To preferentially select cDNA fragments 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter, Beverly, MA). DNA fragments with adaptors ligated on both ends were selectively enriched using the Illumina PCR Primer Cocktail in a 10-cycle PCR reaction. The products were then purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system.

treatment_protocol: They were raised under constant ambient temperature at 22°C (CON, n = 8) or constant high ambient temperature at 30°C (H30, n = 8) for 21 days

value: Skeletal muscle

tag: muscle name

value: Longissimus dorsi

tag: breed

value: DLY


title: CON_mRNA

source_name: Skeletal muscle_22C_control


title: CspA_RIPseq