title: SU_DIPG_IV_JQ1_300nM_48h_rep2


title: B6_eWAT_12w_HFD+rosi_PPARg_4

status: Public on Feb 27 2017

type: SRA

city: Philadelphia

first: Raymond

last: Soccio

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Bowtie or GSNAP with default parameters
Peak bedGrpah was generated by HOMER
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph or bigWig

molecule: genomic DNA

organism: Mus musculus

source_name: eWAT

extract_protocol:
DNA was isolated using phenol/chloroform extraction and  NaCl/EtOH precipitated  with  20 μg  glycogen  carrier
ChIP-seq library was prepared for sequencing according to the amplification protocol from Illumina

tag: strain

tag: tissue

value: eWAT


title: SF8628_CTRL_rep1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

library_source: transcriptomic

data_processing:
Basecalls performed using bcl2fastq v2.17.1.14
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 1.1.2.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.1.0.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate. RNAseq bigwigs are split by strand.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

treatment_protocol: Treatment with JQ1 or DMSO was administrated only once

tag: cell type

value: Diffuse Intrinsic Pontine Glioma (DIPG)

tag: passages

value: Low passages (6-10)

tag: chip antibody

tag: agent

value: Cells lentiviral infected with control vector


title: SU_DIPG_IV_JQ1_300nM_12h_rep1

source_name: DIPG_SU_IV (H3.1K27M)

tag: time point


title: SU_DIPG_IV_JQ1_300nM_48h_rep1


title: SU_DIPG_IV_JQ1_300nM_12h_rep2


title: B6_eWAT_12w_HFD_PPARg_5


title: B6_eWAT_12w_HFD_PPARg_4


title: B6_iWAT_12w_HFD_control

source_name: iWAT

value: iWAT


title: B6_eWAT_12w_HFD+rosi_PPARg_5


title: SU_DIPG_IV_ JQ1_300nM_6h_rep1


title: 129_eWAT_12w_LFD_PPARg_1


title: SU_DIPG_IV_JQ1_300nM_3h_rep1


title: SU_DIPG_IV_ JQ1_300nM_6h_rep2


title: B6_eWAT_12w_LFD_PPARg_4


title: SU_DIPG_IV_JQ1_300nM_3h_rep2


title: SF8628_shSUZ12_rep1

value: Cells lentiviral infected with SUZ12 specific shRNA vector


title: SU_DIPG_IV_JQ1_300nM_24h_rep1


title: SU_DIPG_IV_ DMSO_300nM_6h_rep2

value: DMSO


title: SU_DIPG_IV_DMSO_300nM_12h_rep2


title: 129_eWAT_12w_HFD_PPARg_2


title: SU_DIPG_IV_DMSO_300nM_24h_rep2


title: B6_eWAT_12wk_LFD_Pol2_2


title: B6_eWAT_12w_LFD_H3K27ac_2


title: 129_eWAT_12w_LFD_PPARg_2


title: SU_DIPG_IV_DMSO_300nM_48h_rep2


title: 129_eWAT_12w_HFD_PPARg_1


title: B6_eWAT_12w_HFD_H3K27ac_2


title: B6_eWAT_12wk_HFD_Pol2_2


title: SU_DIPG_IV_DMSO_300nM_3h_rep1


title: SU_DIPG_IV_DMSO_300nM_48h_rep1


title: SU_DIPG_IV_DMSO_300nM_12h_rep1


title: B6_eWAT_12wk_LFD_Pol2_1


title: SF8628_JQ1_300nM_48h_rep2


title: SU_DIPG_IV_DMSO_300nM_3h_rep2


title: B6_eWAT_4w_LFD_PPARg_2


title: B6_eWAT_12w_HFD_H3K27ac_1


title: SU_DIPG_IV_DMSO_300nM_24h_rep1


title: B6_eWAT_12w_LFD_H3K27ac_1


title: B6_eWAT_4w_HFD_PPARg_2


title: B6_eWAT_4w_LFD_PPARg_3


title: SF8628_ JQ1_300nM_6h_rep2


title: SF8628_JQ1_300nM_3h_rep2


title: SF8628_JQ1_300nM_12h_rep2


title: B6_eWAT_4w_LFD_PPARg_1


title: SF8628_JQ1_300nM_24h_rep2


title: B6_eWAT_4w_HFD_PPARg_3


title: B6_eWAT_12wk_HFD_Pol2_1


title: SF8628_JQ1_300nM_48h_rep1


title: B6_eWAT_12w_HFD_PPARg_2


title: B6_eWAT_12w_HFD_PPARg_1


title: B6_eWAT_12w_LFD_PPARg_1


title: SF8628_JQ1_300nM_12h_rep1


title: B6_eWAT_12w_LFD_PPARg_2


title: SF8628_ JQ1_300nM_6h_rep1


title: SU_DIPG_IV_ DMSO_300nM_6h_rep1


title: B6_iWAT_12w_HFD_PPARg_1


title: SF8628_DMSO_300nM_24h_rep2


title: SF8628_JQ1_300nM_3h_rep1


title: B6_eWAT_12w_LFD_PPARg_3


title: SF8628_DMSO_300nM_12h_rep2


title: B6_iWAT_12w_LFD_PPARg_1


title: B6_eWAT_4wk_LFD_H3K27ac_2


title: SF8628_DMSO_300nM_48h_rep2


title: SF8628_DMSO_300nM_3h_rep2


title: SF8628_JQ1_300nM_24h_rep1


title: SF8628_DMSO_300nM_24h_rep1


title: B6_eWAT_2wk_HFD_H3K27ac_2


title: B6_eWAT_4wk_LFD_H3K27ac_1


title: SF8628_DMSO_300nM_48h_rep1


title: B6_eWAT_2wk_LFD_H3K27ac_2


title: B6_eWAT_4wk_HFD_H3K27ac_2


title: SF8628_ DMSO_300nM_6h_rep1


title: peritoneal_macrophages_PPARg

source_name: macrophage

value: macrophage


title: SF8628_DMSO_300nM_3h_rep1


title: B6_eWAT_4wk_HFD_H3K27ac_1


title: HCT_H3K27M_doxy_withdrawn_H3K27M

value: Colon cancer ectopically expressing H3.3K27M (expression inhibited by doxyxyclin withdrawal)

value: H3K27M (Millipore, ABE419)


title: 3T3L1_adipocyte_PPARg

value: adipocyte


title: B6_eWAT_12w_HFD_PPARg_3


title: B6_eWAT_2wk_HFD_H3K27ac_1


title: HCT_H3K27M_doxy_pos_H3K27M

value: Colon cancer ectopically expressing H3.3K27M


title: SF8628_ DMSO_300nM_6h_rep2


title: HCT_H3K27M_doxy_withdrawn_H3K27ac


title: F1_iWAT_LFD_rosi_5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat V2.1.0 with default parameters
Raw counts for every genes were caculated by HTSeq using UCSC mm9 RefSeq
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited matrix file including counts for all genes

extract_protocol:
Total RNA was extracted by using Trizol chloroform followed by purification with Qiagen RNeasey Mini kit. Ribosomal RNA was depleted by Ribo-Zero gold kit.
RNA libraries were prepared for sequencing using TruSeq RNA Sample Prep Kit

value: B6/129S1 F1 hybrid

tag: diet

value: LFD

value: rosi


title: B6_eWAT_4w_HFD_PPARg_1


title: B6_eWAT_2wk_LFD_H3K27ac_1


title: HCT_H3K27M_doxy_pos_H3K27ac


title: HCT_H3wt_H3K27ac

value: Colon cancer ectopically expressing H3.3


title: input_POS_CTRL


title: F1_iWAT_LFD_rosi_2


title: SF8628_DMSO_300nM_12h_rep1


title: F1_iWAT_LFD_control_5

value: control


title: H3.3_POS_CTRL


title: H3K27M_POS_CTRL


title: F1_iWAT_LFD_rosi_1


title: F1_iWAT_LFD_control_4


title: input_NEG_CTRL


title: F1_iWAT_LFD_control_3


title: H3.3_NEG_CTRL


title: HCT_input

value: Colon cancer


title: F1_iWAT_LFD_control_2


title: SF7761_H3.3

value: Diffuse Intrinsic Pontine Glioma (DIPG)


title: F1_iWAT_LFD_control_1


title: SF7761_H3K27M

value: Low passages (6-10)


title: SF7761_H3K27ac


title: 129_eWAT_HFD_control_4

value: eWAT

value: HFD


title: SU_DIPG_IV_input


title: 129_eWAT_HFD_control_3


title: SU_DIPG_IV_H3K4me1

value: Homemade (ref PMID:24081332)


title: F1_iWAT_LFD_rosi_3

value: iWAT


title: F1_iWAT_LFD_rosi_4


title: 129_eWAT_HFD_control_2


title: SU_DIPG_IV_Rna_Pol_II

value: RNA pol II (CST, 14958)


title: 129_eWAT_LFD_control_4


title: 129_eWAT_LFD_control_3


title: H3K27M_NEG_CTRL


title: SU_DIPG_IV_K27me3_rep1

value: Homemade (ref PMID:25170156)


title: 129_eWAT_LFD_control_2


title: 129_eWAT_HFD_control_1


title: SU_DIPG_IV_EZH2_rep2


title: SU_DIPG_IV_K27me3_rep2


title: SU_DIPG_IV_EZH2_rep1


title: 129_iWAT_HFD_rosi_3


title: SU_DIPG_IV_SUZ12_rep1


title: 129_iWAT_HFD_rosi_2


title: SU_DIPG_IV_SUZ12_rep2


title: 129_iWAT_HFD_rosi_4


title: SU_DIPG_IV_H3K27ac_rep2


title: SU_DIPG_IV_H3.3


title: 129_eWAT_LFD_control_1


title: 129_iWAT_HFD_control_4


title: SU_DIPG_IV_H3K27ac_rep1


title: 129_iWAT_HFD_rosi_1


title: 129_iWAT_HFD_control_2


title: SU_DIPG_IV_BRD4


title: 129_iWAT_HFD_control_3


title: SU_DIPG_IV_BRD2


title: B6_BAT_HFD_3

source_name: BAT

value: BAT


title: B6_BAT_HFD_4


title: SU_DIPG_IV_H3K27M_rep2

value: H3K27M (Millipore, ABE419)


title: SU_DIPG_IV_H3K27M_rep1


title: SF8628_input_rep2


title: 129_iWAT_HFD_control_1


title: B6_BAT_HFD_2


title: SF8628_input_rep1


title: B6_BAT_HFD_1


title: B6_iWAT_HFD_rosi_4


title: B6_iWAT_HFD_rosi_3


title: SF8628_H3K4me1


title: B6_iWAT_HFD_rosi_1


title: SF8628_BRD4_rep1


title: SF8628_BRD2_rep2


title: B6_iWAT_HFD_rosi_2


title: SF8628_H3.3_rep2


title: B6_iWAT_HFD_control_2


title: SF8628_H3.3_rep1


title: SF8628_H3K27me3_rep2


title: B6_iWAT_HFD_control_3


title: B6_iWAT_HFD_control_1


title: SF8628_BRD2_rep1


title: B6_iWAT_HFD_control_4


title: SF8628_H3K27me3_rep1


title: B6_iWAT_LFD_control_4


title: B6_iWAT_LFD_control_1


title: B6_iWAT_LFD_control_2


title: SF8628_EZH2_rep1


title: SF8628_EZH2_rep2


title: B6_eWAT_HFD_rosi_2


title: B6_eWAT_HFD_rosi_4


title: B6_eWAT_HFD_rosi_3


title: SF8628_SUZ12_rep2


title: SF8628_BRD4_rep2


title: SF8628_SUZ12_rep1


title: B6_eWAT_HFD_control_2


title: B6_eWAT_HFD_rosi_1


title: B6_eWAT_HFD_control_4


title: B6_eWAT_HFD_control_1


title: B6_eWAT_HFD_control_3


title: B6_eWAT_LFD_control_4


title: SF8628_H3K27ac_rep1


title: B6_eWAT_LFD_control_3


title: B6_eWAT_LFD_control_2


title: B6_iWAT_LFD_control_3


title: B6_eWAT_LFD_control_1


title: B6_eWAT_HFD_3


title: B6_eWAT_HFD_2


title: SF8628_H3K27M_rep2


title: SF8628_Rna_Pol_II_rep1


title: SF8628_Rna_Pol_II_rep2


title: B6_eWAT_HFD_4


title: B6_eWAT_HFD_5


title: SF8628_H3K27M_rep1


title: B6_eWAT_LFD_1


title: B6_eWAT_LFD_2


title: B6_eWAT_LFD_3


title: B6_eWAT_LFD_4


title: B6_eWAT_LFD_5


title: SF8628_H3K27ac_rep2


title: B6liver11

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: MBD-protein captured

data_processing:
FASTQ files were processed with FastQC tools (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to generate chip level reports with statistics on quality score distributions, complexity, length distributions, and PCR duplication level. This ensures that there are fewer technical problems that might be difficult to correct at a later stage.
Low-quality ends of reads were trimmed with Trimmomatic v0.30 (Bolger et al., 2014) using a Phred score of 15 (Q15), a 10 bp sliding window and a minimal read length of 40 bp. Trimmed reads were aligned against the mouse mm10 reference genome (Ensemble GRCm38) using the TMAP (https://github.com/iontorrent/TMAP) aligner with default settings.
Samtools was used to sort and index aligned (bam) files (Li et al., 2009). Reads with mapping quality of less than 10 were filtered from the bam file using ‘samtools –q 10’ command. For each sample, there were seven high quality bam files (each from the seven separate runs) and these were merged and indexed using samtools.
The generated Bam files were then analyzed using the MEDIPS R package (Chavez et al., 2010). Sequenced reads were  counted for every 500 bp non-overlapping window with normalization to the local CpG density (i.e., coupling factor CF). This process was done according to the following MEDIPS parameters: uniq=1, extend=300, shift=0, ws=500. This divided the mouse genome into 5451088 total bins with coverage counts at each bin. The read counts generated on the MEDIPS package were loaded to the EdgeR R package for differential methylation analysis (Robinson et al., 2010). Prior to statistical tests, we excluded the sex chromosomes. We also removed all bins with low coverage as these can provide no reliable statistics but will only add to the penalty for multiple testing. We filtered out regions with coupling factor (CF) below the genome-wide median of 3, and bins that had less than one count per million in 2 or more samples. This resulted in 466039 bins that have an average CpG count of 9.5 (minimum of 3 and maximum of 91) and mean count of 16.7 (minimum of 4 and maximum of 1167). We used this set of 466039 bins for statistical analysis
Genome_build: mm10
Supplementary_files_format_and_content: csv file; contains columns for bin name, chromosome (chr), start, end, CouplingFactor (CpG density), followed by qq columns with read counts for the 11 samples, and 11 columns with normalized relative methylation scores (rms) for 11 samples; after header rows, there are 466039 rows with methylation data

source_name: Liver

extract_protocol:
DNA was purified using the Qiagen AllPrep kit (http://www.qiagen.com) on the QIAcube system. NWe performed affinity-based enrichment using the MethylCap kit from Diagenode (https://www.diagenode.com). DNA in 110 µl TE buffer was ultrasonicated on a Covaris S2 machine (http://covarisinc.com) to an average fragment size of 300–400 bp. Enrichment was performed on 1µg of fragmented DNA according to the standard MethylCap protocol and captured DNA eluted in a single step using the High Elution Buffer.
Sequencing was done on the Life Technologies Ion Proton platform at the UTHSC Molecular Resource Center. The DNA fragments were used to prepare barcoded libraries employing the Ion XpressTM Plus Fragment Library Kit and the Ion XpressTM Barcode Kit from Life Technologies (http://www.thermofisher.com) according to protocol supplied by the manufacturer. After library preparation, the barcoded libraries were screened on an Agilent High Sensitivity DNA chip for size distribution. As an initial step, 1ul of each barcoded library was pooled and sequenced on an Ion Torrent PGM 314 chip. The read counts from the 314 chip were then used to prepare a final equalized pool. The final library pool was quantified by real-time polymerase chain reaction (PCR), used to prepare beads, and finally sequenced using the P1 chip on the Ion Torrent Proton sequencer. To avoid batch artifacts related to fragment library-processing steps and chip runs, we multiplexed the 11 samples and ran multiple chips to reach depth of ~30 million raw reads per sample. In total, seven P1 chips were used.

tag: Sex

value: F

tag: age in days


title: B6liver10

description: MBD-protein captured


title: B6liver9

description: MBD-protein captured

value: M


title: Total RNA from 2.5 days' conidia of Δdcl2

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

country: China

institute: Anhui Agricultural University

data_processing: quality control on clean data through drawing base composition chart and quality distribution chart.

organism: Metarhizium robertsii

growth_protocol: Conidia of WT and Δdcl2 were inoculated into SDAY medium at 1×107 conidia/ml at 25°C. Fungal samples were collected after 1 day (mycelium growth, MY) and 2.5 days (conidiogenesis, CO), respectively

extract_protocol:
Metarhizium robertsii wild type and Δdcl2 were ground into powder in liquid nitrogen,Powder was used to isolate total RNAs  using Trizol (Invitrogen, USA).
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then the first strand of cDNA is synthesized by using random hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library. The library products are ready for sequencing via Illumina HiSeqTM 2000.

value: ARSEF 23

tag: genotype/variation

tag: developmental stage

value: asexual

tag: age


title: Total RNA from mycelium of Metarhizium robertsii wild type

source_name: WT-MY

value: wild type


title: B6liver8

description: MBD-protein captured


title: B6liver7

description: MBD-protein captured


title: Total RNA from 2.5 days' conidia of Metarhizium robertsii wild type

source_name: WT-CO


title: B6_eWAT_HFD_1


title: D2liver5

description: MBD-protein captured


title: D2liver4

description: MBD-protein captured


title: D2liver6

description: MBD-protein captured


title: SF-Hg+TCDD-2.5uM+10nM-1

city: Tuxedo

first: Suresh

last: Cuddapah

state: New York

address: 57 Old Forge Road

department: Environmental Sciecne

institute: New York University Langone Medical center

description: Expt 4: BEAS2B cells treated with Hg+TCDD-2.5uM+10nM for 3 weeks

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-Seq data analysis was performed using Biowardrobe experimental management system. Breifly Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh37/hg19 whole genome using STAR version 2.4.oj using default parameters; multi hits removed
Gene expression levels were quantified as reads per kilobase of exon per million fragments mapped (RPKM) using Biowardrobe algorithm
Differential gene expression was calculated using DESeq2
More information on Biowardrobe suite can be found at https://www.biowardrobe.com/
Genome_build: Feb. 2009 (GRCh37/hg19)
Supplementary_files_format_and_content: csv file include RPKM values for each Sample

source_name: Bronchial epithelial cell

growth_protocol: BEAS-2B cells were cultured in Dulbecco’s Modified Eagle’s Medium (Cellgro).

extract_protocol:
Total RNA was isolated from treated cells  using RNeasy kit (Qiagen)
RNASeq libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit (RS-122-2002), according to the manufacturer’s instructions.

treatment_protocol: The cells were treated with different doses of HgCl2 (0, 0.5 and 2.5 MicroM) and TCDD (0, 2 and 10 nM) either individually or in combination (Hg 0.5 MicroM/TCDD 2.0 nM; Hg 2.5 microM/TCDD 10 nM) for 3 weeks

tag: treatment

value: Hg+TCDD-2.5uM+10nM for 3 weeks


title: SF-TCDD-10nM-2

description: Expt 3: BEAS2B cells treated with TCDD-10nM for 3 weeks

value: TCDD-10nM for 3 weeks


title: SF-TCDD-10nM-1


title: SF-Hg+TCDD-0.5uM+2nM-2

description: Expt 4: BEAS2B cells treated with Hg+TCDD-0.5uM+2nM for 3 weeks

value: Hg+TCDD-0.5uM+2nM for 3 weeks


title: Total RNA from mycelium of Δdcl2


title: SF-Hg+TCDD-0.5uM+2nM-1


title: D2liver1

description: MBD-protein captured


title: SF-TCDD-2nM-2

description: Expt 3: BEAS2B cells treated with TCDD-2nM for 3 weeks

value: TCDD-2nM for 3 weeks


title: D2liver2

description: MBD-protein captured


title: KO rep1

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

description: total RNA, Ribo-Zero

data_processing:
Base-Calling with Casava
RNA-Seq reads were initially trimmed using the Trimmomatic software to remove adapter sequences and poor quality bases.
Bowtie 2 was used to align reads to a sequence database composed of rRNAs, tRNAs,snRNAs, snoRNAs and other non-coding species which resulted to be overrepresented according to FastQC software; reads belonging to these sequences were filtered out.
The remaining reads were used for circRNA detection as follows: the two mates of each pair of reads (R1 and R2) were aligned separately to the reference genome (Bowtie 2 to GRCm38) and those mapping were discarded; the rest was used as input for find_circ (Memczak et al., Nature 2013). First, 20 nt long anchors were produced from the ends of each read, then anchors were aligned to the reference genome with Bowtie 2 and alignments of both R1- and R2-derived anchors were used by find_circ to identify and count circular and linear splicing events. Circular splicing events were then filtered, for each biological sample separately, for a few parameters, including: at least 2 unique reads mapping to head-to- tail junctions, distance between mapped anchors less than 100kb, mapping quality of the anchors of at least 35. Filtered circRNAs from each sample were then merged and, for all of them, reads mapping linearly to each of the two coordinates of the head-to- tail splice junction were parsed from the find_circ output and counted.
Genome_build: GRCm38
Supplementary_files_format_and_content: BED files containing genomic coordinates of filtered circRNAs found in each sample using find_circ.

source_name: in vitro differentiated motorneurons

growth_protocol: Differentiation Medium

extract_protocol:
Total RNA
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero treatment

tag: genotype

value: FUS -/-

tag: background strain

value: motor neuron


title: KO rep3

description: total RNA, Ribo-Zero


title: KO rep2

description: total RNA, Ribo-Zero


title: D2liver3

description: MBD-protein captured


title: WT rep3

description: total RNA, Ribo-Zero

value: WT


title: SF-TCDD-2nM-1


title: WT rep2

description: total RNA, Ribo-Zero


title: BLM14, rep1

city: Singapore

first: Melissa

middle: Jane

last: Fullwood

address: 14 Medical Drive, #12-01

department: Centre for Translational Medicine

country: Singapore

institute: Cancer Science Institute of Singapore

description:
4C-seq (miseq)
FourCSeq_results_BLM6_BLM14.txt

data_processing:
Library strategy: 4C-Seq
During the analysis of the reads generated by 4C-Seq it was found that multiple fragends were ligated together after the 2nd RE digestion therefore only reads that contain the primer for the tert promoter + HindII cut site (read 2 of the paired end reads) were used.
FastQC v0.11.3 was used to determine the quality of the 4C-Seq libraries and any adaptors were trimmed using scythe v0.991
Tagdust2.3 was used to extract reads that was sandwiched between the bait region (TERT-promoter + HindII) and a DpnII cut site
Extracted reads were aligned to the hg19 genome using bowtie2 with very sensitive parameters in unpaired mode. The aligned reads were filtered for a mapq of 30 and more.
r3CSeq (Thongjuea S et al., Nucleic Acids Research, 2013 ) in batch mode was used to call interactions for A375, BLM
The standard FourCSeq (Klein et al., Bioinformatics, 2015) protocol (with the change of zscore 2 instead of 3) was used to quantify the differential interactions between BLM6 and BLM14 using the aligned reads.
Genome_build: hg19
Supplementary_files_format_and_content: Bed 3 file that contains additional columns for the number of reads, normalized reads per million, p-value and q-value (FDR) generated by r3CSeq for A375, BLM, BLM6 and BLM14. A tab delimited file containing the coordinates of fragments 1Mb around the viewpoint with presence of interaction (TRUE/FALSE) and padjusted value of differential interaction between BLM6 and BLM14.

growth_protocol: Cells were cultured with DMEM suplemented with 10%FBS, penicillin and streptomycin using standard tissue culture techniques.

extract_protocol:
10 million cells were fixed with 1% formaldehyde and nuclei pellets were isolated after cell lysis with cold lysis buffer (50mM Tris-Hcl pH 7.5, 150mM NaCl, 5mM EDTA, 0.5% NP-40, 1% TritonX-100) supplemented with protease inhibitors. First step digestion was performed over-night at 37°C with 200unit HindIII enzyme. After phenol-chloroform extraction, DNA was ligated over-night at 16°C by T4 DNA ligase. Following de-crosslinking, DNA was processed for second digestion with 50units of DpnII enzyme for over-night at 37°C. After final ligation 4C template DNAs were quantified by Qubit dsDNA High sensitivity kit
4C library was prepared as described previously (Splinter et al. 2012). Tert promoter specific primers with Illimuna Nextera adapters were used for libraries.

treatment_protocol: There was no treatment.

value: Melanoma Cell

tag: tert promoter state

tag: cell line

tag: passage number


title: WT rep1

description: total RNA, Ribo-Zero

tag: cell type


title: SF-Hg-2.5µM-1

description: Expt 2: BEAS2B cells treated with Hg-2.5µM for 3 weeks

value: Hg-2.5µM for 3 weeks


title: SF-Hg+TCDD-2.5uM+10nM-2


title: SF-Hg-2.5µM-2


title: SF-Hg-0.5µM-2

description: Expt 2: BEAS2B cells treated with Hg-0.5µM for 3 weeks

value: Hg-0.5µM for 3 weeks


title: BLM14, rep2


title: BLM6, rep2


title: BLM6, rep1


title: SF-Hg-0.5µM-1


title: A375, rep2

description: 4C-seq (miseq)


title: SF-Veh_Control-2

description: Expt 1:BEAS2B cells vehicle control (Acetone) grown for 3 weeks


title: (p)ppGpp0 mutant rep2

city: Shanghai

first: Xianqing

last: Huang

address: DongChuan RD, Minhang District

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Illumina Casava1.82 software used for basecalling.
Sequenced reads were trimmed by Trimmomatic（v0.30） for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Pseudomonas protegens H78 whole genome using tophat (v2.0.9 ).
Fragments Per Kilobase per Megabase of library size (FPKM) were calculated using Htseq(V 0.6.1).
Genome_build: Pseudomonas protegens H78  (Genbank Accession No. CP013184)
Supplementary_files_format_and_content: Excel file include FPKM values for each sample and differential expression analysis of all genes in the ppGpp0 mutant relative to the wild-type H78 strain.

organism: Pseudomonas protegens

source_name: Pseudomonas protegens H78 (p)ppGpp0 mutant

growth_protocol: Pseudomonas protegens H78 and its (p)ppGpp0 relA/spoT mutant, which were grown to the late exponential phase (OD600 = 5.0 to 6.0) in the KMB media at 28 °C

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit (Cat.4106), purified by the Qiagen RNeasy micro kit (Cat.74004) and the Qiagen RNase-Free DNase Set (Cat.79254)
According to  standard Illumina protocols, mRNA was enriched by removing rRNA and further fragmented to be used for synthesizing the first and second strands of cDNAs and constructing the sequencing library.

tag: strain

value: (p)ppGpp0 relA/spoT mutant

tag: growth phase

value: the late exponential phase

value: (p)ppGpp0 mutant


title: (p)ppGpp0 mutant rep1


title: SF-Veh_Control_1

description: Expt 1: BEAS2B cells vehicle control (Acetone) grown for 3 weeks


title: BLM, rep2

description: 4C-seq (miseq)

source_name: BLM

value: BLM


title: A375, rep1

description: 4C-seq (miseq)


title: H78 WT rep2

source_name: Pseudomonas protegens H78

value: H78 wild-type

value: wild-type


title: H78 WT rep3


title: BLM, rep1

description: 4C-seq (miseq)


title: GC_1

status: Public on Feb 26 2017

city: Groningen

first: Ye

last: Yuan

state: Groningen

address: Hanzeplein 1

department: pathology

country: Netherlands

institute: UMCG

description: Small RNA sequencing

data_processing:
The read were trimmed for the Illumina truseq adapter using CLC Bio / Custom script adaptertrimmer.pl using the Illumina Truseq adapter’s 19 bp adjecent to the insert also known as  ‘TGGAATTCTCGGGTGCCAA’. Keeping the > 16 bp long reads.
The data was further processed using commandline tools, custom scripts and the MirDeep2.0.0.5 package (Friedlander et al.2008 https://www.mdc-berlin.de/38350089/en/research/research_teams/systems_biology_of_gene_regulatory_elements/projects/miRDeep/older_miRDeep2_versions/mirdeep2_0_0_5.zip) for the quantification and predication of novel miRNA’s versus the ucsc_hg19 genome builds and mirbase xxx?. Also removed reads <18 bp using miRDeep2.
Genome_build: UCSC hg19 and mirbase version 21 for mirna annotation.
Supplementary_files_format_and_content: Total read counts per sample were normalized to 1 million. Read counts for miRNAs transcripted from different loci or with the same mature sequence were merged. we did a cutoff of miRNAs with at least 50 read counts in the sum of all seven samples, that is the four samples of HL cell lines/BL cell lines and the three samples of GC-B cells.

growth_protocol: HL and BL cell lines were cultured in RPMI-1640 medium at 37℃ in an atmosphere containing 5% CO2. Germinal center B (GC-B) cells were sorted from tonsil tissue based on expression of CD20+lgD-CD38+.

extract_protocol:
RNA was isolated using miRNeasy mini kit (Qiagen, Hiden, Germany)
Small RNA libraries were generated from 2,000ng total RNA using TruSeq Small RNA Sample Preparation Kit and TruSeq small RNA indices (Illumina, San Diego, CA, USA).

tag: tissue

value: Germinal center B (GC-B) cells

tag: markers


title: GC_2

description: Small RNA sequencing


title: DG75

description: Small RNA sequencing

source_name: BL cell line

value: Burkitt lymphoma


title: H78 WT rep1


title: GC_3

description: Small RNA sequencing


title: CA46

description: Small RNA sequencing


title: L540

description: Small RNA sequencing

source_name: HL cell line

value: Hodgkin lymphoma


title: L1236

description: Small RNA sequencing


title: (p)ppGpp0 mutant rep3


title: ST486

description: Small RNA sequencing


title: L428

description: Small RNA sequencing


title: chdC-null 12H rep1 (RNA-seq)

city: Oxfors

first: James

last: Platt

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

data_processing:
Basecalls performed using CASAVA version 1.7
RNAseq reads were aligned using Tophat version 1.3.0 and Bowtie version 0.12.7 to the chromosomes 1-6 of the Ax4 dictyostelium genome masking the duplicated region on chromosome 2 (nucleotides 3,015,984 to 3,768,555) and gene models from dictybase.org
FPKM counts were calculated with HTseq and normalized and DEseq
Genome_build: Ax4_May2009
Supplementary_files_format_and_content: Pairwise comparisons with DESeq are uploaded

organism: Dictyostelium discoideum

source_name: Loose mound stage

growth_protocol: Cells were grown axenicly in HL5 + glucose media (Formedium)

extract_protocol:
RNA was extracted with TRIzol
Total RNA was isolated and mRNA was enriched using manufacurers protocol

treatment_protocol: Cells were developed on nitrocellulose filters until they reached loose-mound stage of development (10H for Ax2, 12H for ChdC null cells)

tag: development stage

value: 12H developed

value: chdC-null


title: chdC-null 12H rep2 (RNA-seq)


title: Ax2 10H rep1 (RNA-seq)

value: 10H developed

value: wild type Ax2


title: chdC-null 0H rep2 (RNA-seq)

source_name: Growing

value: Growing


title: Ax2 0H rep2 (RNA-seq)


title: Ax2 0H rep1 (RNA-seq)


title: SF-Control_2

description: Expt 1: BEAS2B cells control grown for 3 weeks

value: control grown for 3 weeks


title: Ax2 10H rep2

data_processing:
Basecalls performed using CASAVA version 1.7
Paired-end reads were aligned using bowtie version 0.12.7 to the chromosomes 1-6 of the Ax4 dictyostelium genome masking the duplicated region on chromosome 2 (nucleotides 3,015,984 to 3,768,555) and gene models from dictybase.org
Paired reads mapping with an isize of 150bp (+/- 20%) were selected as providing nucleosome position data
The centerpoint between the two paired reads was defined as the nucleosome dyad, the nucleosome dyads were then calculated genome wide in the resulting processed .sgr file.
Genome_build: Ax4_May2009
Supplementary_files_format_and_content: sgr

source_name: Dictyostelium

extract_protocol:
Briefly, 1 x 109 cells were washed in 100 mM sorbitol and resuspended in 400 ml digestion buffer [100 mM sorbitol, 50 mM NaCl, 10 mM Tris-HCl (pH 7.5), 5 mM MgCl2, 1 mM CaCl2, 1 mM 2-mercaptoethanol, 0.5 mM spermidine, 0.1% Nonidet P40] and transferred to a 1.5 ml microcentrifuge tube containing MNase (USB/Affymetrix) at a final concentration of 800 U/ml; incubation was at 37o C for 2 min. Digestion was stopped by addition of 40 ml stop buffer [5% SDS, 250 mM EDTA (pH 8.4)], followed by phenol/chlorophorm extraction of DNA. RNase A treatment was at 37o C for 30 min. The DNA was re-extracted with phenol/chloroform and precipitated with sodium acetate and 100% ethanol. Control digests used 10 mg of previously extracted undigested ‘naked’ DNA suspended in digestion buffer at 20o C for 30 sec. Three independent replicates for each sample were pooled, and separated on a 1.5% agarose gel. The 50-1000 bp gel region was extracted and libraries prepared with the Illumina paired-end kit.
Liibraries prepared with the Illumina paired-end kit


title: chdC-null 12H rep1


title: KMH2

description: Small RNA sequencing


title: chdC-null 0H rep2


title: DECAPseq_ESC_KO_polyA

status: Public on Feb 25 2017

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

institute: University of Torino

description:
RNA (polyA+)
Ribo and URNA depleted

data_processing:
Library strategy: Decapping-sequencing (DECAP-seq)
Basecalls performed using CASAVA version 1.8.
Reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters: --min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files were performed by using Wiggles tool.

source_name: E14 mESC Dnmt3b ko

growth_protocol: Mouse embryonic stem cells E14 were grown on 0.1% gelatin-coated plates and maintained in DMEM (4.5g/L D-Glucose), supplemented with 15% heat-inactivated FBS, 0.1mM NEAA, 1mM Sodium Pyruvate, 0.1mM 2-Mercaptoethanol, 25U/ml penicillin, 25 μg/ml streptomycin and 1,500U/ml LIF.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen).
Total RNA (or polyA RNA enriched using The NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB) following manufacturer instructions or cytosolic RNA) was first ribo- and URNA-depleted and then was chemically fragmented by using First Strand buffer of the SuperScript® II Reverse Transcriptase (Invitrogen). The fragmented RNA was Dephosphorylated of natural 5' and fragmentation-derived 3' phosphate by using Antarctic Phosphatase (AP, NEB). Dephosphorylated RNA was then treated with RNA 5' Pyrophosphohydrolase (RppH, NEB) in 1X Thermopol buffer (NEB) (for decapping and pyrophosphate removal from the 5' end of RNA to leave a 5' monophosphate RNA). 5' adapter was ligated, and 3' adapter was added by reverse transcription.

treatment_protocol:
Generation of Dnmt3b KO ESCs was performed using TALEN technology. In brief, cells were transfected with the two TALEN constructs targeting Exon 17 of murine Dnmt3b and after 16 hours were seeded as a single cell. After 1 week, clones were screened by Western blot analyses. Positive clones were analyzed by genomic sequencing of the TALEN target.
Transfection of mouse ESCs was performed using Lipofectamine™ 2000 Transfection Reagent according to manufacturer's protocol using equal amount of each plasmid (5 ug) in multiple transfections. For the Setd2 knockdown, cells were transfected with the specific shRNA constructs, and maintained in medium with puromycin selection (1ug/ml) for 48h.

value: mouse embryonic stem cells

tag: strain/background

value: Dnmt3b ko


title: Ax2 10H rep1


title: chdC-null 0H rep1


title: Ax2 10H rep2 (RNA-seq)


title: Ax2 0H rep2


title: Ax2 0H rep1


title: DECAPseq_ESC_KO_shDis3_Rrp6

description: Ribo and URNA depleted

source_name: E14 mESC Dnmt3b ko, Dis3/Rrp6 shRNA transfection

tag: cell treatment

value: transfection (Dis3/Rrp6 shRNA)


title: DECAPseq_ESC_KO_shCTR

description: Ribo and URNA depleted

source_name: E14 mESC Dnmt3b ko, CTR shRNA transfection

tag: genotype/variation

value: transfection (CTR shRNA)


title: DECAPseq_ESC_WT_shSetd2

description: Ribo and URNA depleted

source_name: E14 mESC wt, Setd2 shRNA transfection

value: wt

value: transfection (Setd2 shRNA)


title: DECAPseq_ESC_WT_rep1

description: Ribo and URNA depleted

source_name: E14 mESC wt


title: DECAPseq_ESC_KO_rep2

description: Ribo and URNA depleted


title: DECAPseq_ESC_WT_rep2

description: Ribo and URNA depleted


title: DECAPseq_ESC_WT_shCTR

description: Ribo and URNA depleted

source_name: E14 mESC wt, CTR shRNA transfection


title: DECAPseq_ESC_KO_rep1

description: Ribo and URNA depleted


title: chdC-null 0H rep1 (RNA-seq)


title: RNAseq_PolyA_ESC_WT_rep1

description: PolyA enriched

data_processing:
Basecalls performed using CASAVA version 1.8.
For RNA-seq, reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters: --min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files were performed by using Wiggles tool.

growth_protocol: Mouse embryonic stem cells E14 were grown on 0.1% gelatin-coated plates and maintained in DMEM (4.5g/L D-Glucose), supplemented with 15% heat-inactivated FBS, 0.1mM NEAA, 1mM Sodium Pyruvate, 0.1mM 2-Mercaptoethanol, 25U/ml penicillin, 25 ug/ml streptomycin and 1,500U/ml LIF.

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen).
For Ribo- RNA-seq library preparation, 2.5 ug of total RNA were depleted of ribosomal RNA using the RiboMinus Eukaryote System v2 kit (Invitrogen), following manufacturer instructions. Ribo- RNA was resuspended in 17ul of EFP buffer (Illumina), heated to 94°C x 8', and used as input for First Strand synthesis, using the TruSeq RNA Sample Prep kit, following manufacturer instructions. PolyA+ RNA-seq were performed by using the TruSeq RNA Sample Prep kit, following manufacturer instructions.

treatment_protocol:
Generation of Dnmt3b KO ESCs was performed using TALEN technology. In brief, cells were transfected with the two TALEN constructs targeting Exon 17 of murine Dnmt3b and after 16 hours were seeded as a single cell. After 1 week, clones were screened by Western blot analyses. Positive clones were analyzed by genomic sequencing of the TALEN target.
Transfection of mouse ESCs was performed using Lipofectamine™ 2000 Transfection Reagent according to manufacturer's protocol using equal amount of each plasmid (5 ug) in multiple transfections. For the Setd2 knockdown, cells were transfected with the specific shRNA constructs, and maintained in medium with puromycin selection (1ug/ml) for 48h.
For half-life measurements, wt and Dnmt3b-/- ESCs were treated with DRB at the concentration of 75uM for the indicated time.


title: RNAseq_PolyA_ESC_KO_rep2

description: PolyA enriched


title: RNAseq_PolyA_ESC_WT_rep2

description: PolyA enriched


title: Naked DNA digested with Mnase

tag: sample type

value: Naked DNA


title: chdC-null 12H rep2


title: RNAseq_PolyA_ESC_B77

description: PolyA enriched


title: DECAPseq_ESC_KO_cytosol

description:
RNA (cytosol)
Ribo and URNA depleted


title: RAMOS

description: Small RNA sequencing

value: RAMOS


title: RNAseq_total_ESC_WT_shSetd2_1

description: Ribo depleted

source_name: E14 mESC wt, Setd2 shRNA #1 transfection

value: transfection (Setd2 shRNA #1)


title: RNAseq_total_ESC_WT_shCTR

description: Ribo depleted

source_name: E14 mESC wt, ctr shRNA transfection

value: transfection (ctr shRNA)


title: RNAseq_total_ESC_WT_shSetd2_2

description: Ribo depleted

source_name: E14 mESC wt, Setd2 shRNA #2 transfection

value: transfection (Setd2 shRNA #2)


title: RNAseq_total_ESC_WT_rep2

description: Ribo depleted


title: RNAseq_total_ESC_WT_rep1

description: Ribo depleted


title: RNAseq_total_ESC_KO_shSetd2_2

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Setd2 shRNA #2 transfection


title: RNAseq_total_ESC_KO_rep2

description: Ribo depleted


title: RNAseq_total_ESC_KO_shCTR

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, ctr shRNA transfection


title: SF-Control_1

source_name: Bronchial epithelial cell


title: RNAseq_total_ESC_KO_Dnmt3b_VWRR

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Dnmt3b VWRR transfection

value: transfection (Dnmt3b VWRR)


title: RNAseq_total_ESC_KO_Dnmt3b_wt

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Dnmt3b WT transfection

value: transfection (Dnmt3b WT)


title: RNAseq_PolyA_ESC_KO_rep1

description: PolyA enriched


title: RNAseq_total_ESC_KO_B77

description: Ribo depleted


title: RNAseq_total_ESC_KO_Dnmt3b_V725G

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Dnmt3b V725G transfection

value: transfection (Dnmt3b V725G)


title: RNAseq_total_ESC_KO_Mock

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, empty vector transfection

value: transfection (empty vector)


title: RNAseq_total_ESC_KO_Dnmt3b_S277P

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Dnmt3b S277P transfection

value: transfection (Dnmt3b S277P)


title: ChIP-seq Dnmt3b [Dnmt3b-mut]

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1
Data were filtered using the following specifications: duplicate reads were filtered out
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were performed by using MACS tool

source_name: Mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells E14 were grown on 0.1% gelatin-coated plates and maintained in DMEM (4.5g/L D-Glucose), supplemented with 15% heat-inactivated FBS, 0.1mM NEAA, 1mM Sodium Pyruvate, 0.1mM 2-Mercaptoethanol, 25U/ml penicillin, 25 μg/ml streptomycin and 1,500U/ml LIF

extract_protocol:
For ChIP-seq, approximately 2 x 10E7 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in cold PBS. The cells were resuspended in Lysis Buffer 1 (50 mM Hepes-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100 and protease inhibitor) to disrupt the cell membrane and in Lysis Buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitor) to isolate nuclei. The isolated nuclei were then resuspended in SDS ChIP Buffer (20 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS and protease inhibitors). Extracts were sonicated using the Bioruptor H Twin (Diagenode) for 2 runs of 10 cycles [30 sec ‘‘ON’’, 30 sec ‘‘OFF’’] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Magnetic beads (Dynabeads® Rat Anti-Mouse IgM for anti-PolII-phospho-S5, Dynabeads®Protein G for all the other ChIPs, Life Technologies) were saturated with PBS/1% BSA and the samples were incubated with 2 micrograms of antibody overnight at 4°C on a rotator.  Next day samples were incubated with saturated beads for two hours at 4°C on a rotator. Successively immunoprecipitated complexes were washed five times with RIPA buffer (50 mM Hepes-KOH pH7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0,7% Na-Deoxycholate) at 4°C for 5 minutes each on a rotator. Elution Buffer was added and incubated at 65°C for 15 minutes. The decrosslinking was performed at 65°C overnight. Decrosslinked DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacture’s instruction.
For ChIP-seq, approximately 10 ng of purified ChIP DNA were end-repaired, dA-tailed, and adapter-ligated using the NEBNext ChIP-Seq Library Prep Master Mix Set (NEB), following manufacturer instructions.

treatment_protocol:
Generation of Dnmt3b KO ESCs was performed using TALEN technology. In brief, cells were transfected with the two TALEN constructs targeting Exon 17 of murine Dnmt3b and after 16 hours were seeded as a single cell. After 1 week, clones were screened by western blot analyses. Positive clones were analyzed by genomic sequencing of the TALEN target.
Transfection of mouse ESCs was performed using Lipofectamine™ 2000 Transfection Reagent in according to manufacturer’s protocol using equal amount of each plasmid (5 g) in multiple transfections.  For the Setd2 knockdown, cells were transfected with  the specific shRNA constructs, and maintained in medium with puromycin selection (1g/ml) for 48h.
For RNA PolII elongation inhibition, wt and Dnmt3b-/- ESCs were treated with DRB at the concentration of 75mM for 8h.

tag: strain background

tag: age

value: Mouse embryonic stem cells (mESCs)

tag: transfected with

value: Dnmt3b V725G

tag: chip antibody


title: ChIP-seq H3K4me3 [WT]

treatment_protocol: Generation of Dnmt3b KO ESCs was performed using TALEN technology. In brief, cells were transfected with the two TALEN constructs targeting Exon 17 of murine Dnmt3b and after 16 hours were seeded as a single cell. After 1 week, clones were screened by western blot analyses. Positive clones were analyzed by genomic sequencing of the TALEN target.

tag: developmental stage

value: WT

value: H3K4me3 (Upstate 07-473)


title: ChIP-seq H3K4me3 [Dnmt3b KO (cl. B126)]

value: Dnmt3b ko


title: ChIP-seq H3ac [Dnmt3b KO (cl. B126)]

value: H3ac (Upstate 06-599)


title: ChIP-seq H3ac [WT]


title: RNAseq_total_ESC_KO_shSetd2_1

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko, Setd2 shRNA #1 transfection

tag: cell line

value: mouse embryonic stem cells


title: ChIP-seq Dnmt3b [shCtr]

value: wild type

value: ctr shRNA


title: ChIP-seq H3K36me3 [shCtr]


title: ChIP-seq Dnmt3b [Dnmt3b-WT]

value: Dnmt3b WT


title: ChIP-seq H3K36me3 [shSetd2 #1]

value: Setd2 shRNA #1


title: ChIP-seq Dnmt3b [shSetd2 #1]


title: ChIP-seq Dnmt3b [shSetd2 #2]

value: Setd2 shRNA #2


title: RNAseq_total_ESC_KO_rep1

description: Ribo depleted

source_name: E14 mESC Dnmt3b ko


title: ChIP-seq H3K36me3 [shSetd2 #2]


title: ChIP-seq Ser5 DRB [WT]

value: DRB (8h)

tag: treated with

value: DRB for 8hrs

value: RNA Polymerase S5P (covance H14)


title: ChIP-seq Ser5 DRB [Dnmt3b KO (cl. B126)]

tag: cell type


title: ChIP-seq H3K36me3 [Dnmt3b KO (cl. B126)]


title: ChIP-seq RNA PolII DRB [Dnmt3b KO (cl. B126)]

value: RNA Polymerase (sc-899)


title: ChIP-seq RNA PolII [WT]


title: ChIP-seq RNA PolII [Dnmt3b KO (cl. B126)]


title: ChIP-seq H3K36me3 [WT]


title: ChIP-seq IgG [Dnmt3b KO (cl. B126)]

value: Control IgG (Millipore 12-370)


title: Input_CAPIP_KO

data_processing:
library strategy: CAP ImmunoPrecipitation (CAPIP)-seq
Basecalls performed using CASAVA version 1.8
Reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were performed by using Wiggles tool

extract_protocol:
Total RNA was extracted by using TRIzol reagent (Invitrogen).
For immunoprecipitation of mRNA for CAPIP-Seq experiments, 30ug of total RNA were fragmented by alkaline hydrolysis in ~200nt fragments and incubated with 5ug of mouse anti-CAP antibody (Anti-m3G-cap, m7g-cap, Clone H20, Millipore MABE419) (or IgG) overnight at 4°C in 0,5ml of IP Buffer (10mM Tris-HCl pH 7.5; 150mM NaCl; 0,1% Triton X-100) supplemented with 50U/ml RNaseOUT (Invitrogen), 50U/ml SuperaseIN (Invitrogen), and 50U/ml RNase Inhibitor (Ambion).  25ul of Dynabeads Protein G (Invitrogen) were saturated overnight at 4°C in IP Buffer supplemented with 150ug of Sonicated Salmon Sperm DNA (Qiagen). Following incubation, beads were washed two times in IP Buffer and incubated with the preformed RNA-antibody complexes at 4°C. After 3hrs, beads were washed 4 times with IP Buffer. Specific elution of recovered fragments were obtained by incubation of beads with 100μl Elution Buffer [5mM Tris pH7.5; 1mM EDTA; 0.05% SDS; 0.3mg/ml Proteinase K] for 1h 30’ at 50°C. Fragments were then purified by addition of 1ml TRIzol reagent (Invitrogen), and subjected to random-primed reverse transcription using the SuperScript III Reverse Trancriptase (Invitrogen) at 50°C for 1h. Resulting cDNAs were then used as input for the TruSeq RNA Sample Prep kit (Illumina), starting from the “Second Strand Synthesis” step, to produce the sequencing library, following manufacturer instruction.

value: Mouse embryonic stem cells (mESCs)

tag: rip antibody

value: Control Input


title: Input_CAPIP_WT


title: CAPIP_seq_WT_rep1

value: Anti-m3G-cap, m7G-cap (Millipore H-20)


title: CAPIP_seq_WT_rep2


title: ChIP-seq Dnmt3b [Mock]

value: empty vector


title: CAPIP_seq_KO_rep2

value: Dnmt3b ko


title: CAP_IgG_WT

value: Control IgG (Millipore 12-371)


title: ART_seq_WT_rep2

description: Ribosome profiling

data_processing:
library strategy: ART (Active mRNA Translation)-seq
Basecalls performed using CASAVA version 1.8
For ribosome profiling, only adapter containing reads were used in order to avoid total RNA contamination. Reads were clipped from adapters and mapped on rRNAs and tRNAs. Only reads not mapping on rRNA/tRNA genes were used for downstream analysis.
Reads were mapped on mm9 using TOPHAT v2.0.6 with the following parameters :--min-anchor=5 --min-isoform-fraction=0.01 --max-multihits=10 --bowtie1
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files were performed by using Wiggles tool

extract_protocol:
Ribosome profiling was performed using the ARTseq/TruSeq Ribo Profile (Illumina), with minor changes to the manufacturer protocol. Briefly, ~30 milions of cells were treated with 0.1μg/μl final Cycloheximide for 5’ at 37°C. Cells were then washed twice and harvested with ice-cold PBS (supplemented with 0.1μg/μl final Cycloheximide). Cells were lysed in 1ml Mammalian Lysis Buffer (supplemented with 0.5% final NP-40) by end-to-end rotation at 4°C for 10’. The lysate was then treated with 50 U of ART-seq Nuclease for 45’ at 25°C, with moderate shaking. 400μl of the digested lysate were then layered on the top of a 2.5ml sucrose cushion, and centrifuged at 265,000g for 5h at 4°C. After completely removing the supernatant, the pellet was resuspended in 100μl nuclease-free water, and purified on RNA Clean & Concentrator™-5 columns (Zymo Research).
5μg of the recovered monosomes RNA was then subjected to 2 consecutive rounds of rRNA depletion using the Ribo-Zero™ Gold Kit (Human/Mouse/Rat, Epicentre), and then run on a 10% TBE-Urea PAGE gel for 25’ at 200V. A gel slice corresponding to 28-30nt was then cut, crushed, and RNA was recovered by passive diffusion at 4°C for 16h.  The eluted RNA fragments were then end-repaired, ligated to the 3’ adapter, and reverse transcribed. The cDNA was run on a 10% TBE-Urea PAGE gel for 30’ at 180V, and a gel slice corresponding to fragments of ~70-80nt was cut, crushed, and cDNA was recovered by passive diffusion at 37°C for 16h with vigorous shaking. The eluted cDNA was then subjected to circularization, and the final library was obtained by 10 cycles of PCR. The final library was inspected on the Fragment Analyzer™ (Advanced Analytical), revealing a single sharp peak around 150bp.


title: CAPIP_seq_KO_rep1


title: CAP_IgG_KO


title: ART_seq_WT_rep1

description: Ribosome profiling


title: ChIP-seq RNA PolII DRB [WT]


title: ART_seq_KO_rep2

description: Ribosome profiling


title: nrpe1-11

city: Bloomington

first: Jered

last: Wendte

state: IN

address: 915 E. 3rd Street

institute: Indiana University

data_processing:
Reads were trimmed of adapters and filtered for size and quality using cutadapt v. 1.91. with the commands: cutadapt -a TGGAATTCTCGGGTGCCAAG -q 20 -m 15 -M60
Reads were first filtered of all structural RNAs (tRNAs, rRNAs, snRNAs, and snoRNAs) by mapping to a genome consisting of sequences corresponding to all genomic coordinates identified as structural RNAs on TAIR (www.arabidopsis.org) using bowtie2 default commands. All unmapped reads were saved for further analysis.
Filtered and cleaned reads were mapped to the Arabidopsis TAIR10 genome using ShortStack version 3.4 default settings.
sRNA counts for regions of interest were extracted from bam files using the ShortStack --locifile file function.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text file of raw read counts across regions that undergo Pol V-dependent CHH methylation

organism: Arabidopsis thaliana

source_name: nrpe1-11 mutant

growth_protocol: Plants were grown in soil in long day conditions (16 hours light, 8 hours dark)

extract_protocol:
RNA was extracted using Trizol
RNA of sizes 15-90 nucleotides was selected using a 15% denaturing polyacrylimide gel. Libraries were constructed using the Illumina TruSeq Small RNA Library prep kit.

tag: ecotype

tag: genotype

value: 2.5 week above ground tissues


title: ART_seq_KO_rep1

description: Ribosome profiling


title: six RNA samples of elderly donors were pooled 8E_S23

city: Warsaw

first: Zofia

last: Wicik

state: mazovia

address: Pawinskiego 5

department: Department of Human Epigenetics

country: Poland

institute: Mossakowski Medical Research Center

description:
Sex: 3F_3M
Blood donors were 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups: young (Y, n=24, age range 21-42 years, mean age 28.0±4.0 years) and long-lived (L, n=24, 90-102 years, 94.8±3.9 years). They were free of current infection and of any chronic diseases (type 2 diabetes, cardiovascular disease and its complications, neurodegeneration, cancer, etc.) however, in long-lived group a moderate hypertension and a mild degree physical and cognitive disability were allowed. All participants gave a written informed consent for participation in the study. The study was approved by the Bioethics Committee of the Medical University of Warsaw. ere 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups

data_processing:
adapter cutting - cutadapt, obtained sequences with the length of 15-28 nucleotides were subject to further analysis as potential miRNAs
alignment to reference sequences - bowtie
sam to bam format compression - samtools
reads counting for miRs: a number of all reads mapped to each reference sequence,R/Bioconductor ShortRead library
normalization - Reads Per Million (RPM)
Genome_build: fastq    files were aligned directly to the multifasta file including reference    sequences of 2042 human mature miRNAs from miRBase v19 avaiable at   ftp://mirbase.org/pub/mirbase/19/mature.fa.zip
Supplementary_files_format_and_content: xlsx file with raw counts

source_name: peripherial blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated according to the method of Neitzel (Neitzel 1986) with modifications. Briefly, 4 ml of full blood were centrifuged at 2500×g for 20 min at 4°C. The bottom layer of approximately 2 ml, containing all types of blood cells, was diluted in 4 ml of phosphate-buffered saline (PBS) and the resulting suspension was overlayed onto 3 ml of lymphocyte separation medium LSM 1077 (PAA Laboratories GmbH). The samples were centrifuged at 600×g for 20 min at 19°C. The layer of PBMCs was collected and washed twice with PBS.
Total RNA was extracted from PBMCs with TRIzol Reagent (Invitrogen) according to the manufacturer protocol. PBMCs were lysed in TRIZOL® Reagent by repetitive pipetting. The homogenized samples were incubated for 5 min at 15-30°C. Next, 0.2 ml of chloroform per 1 ml of TRIZOL® Reagent was added, samples were capped, shaken vigorously by hand for 15 s, incubated at 15-30°C for 2-3 min and centrifuged at no more than 12,000 × g for 15 min at 2-8°C. Total RNA was solely in 1 among 3 separated phases - the aqueous phase which then was transferred to a fresh tube and added 0.5 ml of isopropyl alcohol per 1 ml of TRIZOL® Reagent.  Afterwards, samples were incubated at 15-30°C for 10 min and centrifuged at no more than 12,000 × g for 10 min at 2-8°C. Supernatant was discarded and RNA pellet was washed by 1 ml of 75% ethanol per 1 ml of TRIZOL® Reagent. The sample was mixed by vortexing and centrifuged at no more than 7,500 × g for 5 min at 2-8°C. Obtained RNA pellet was briefly drained and subsequently dissolved in 20 ul of RNase-free water.
Equal amounts of total RNA from each study participant (250 ng per person)  were pooled, 4 pools of 6 RNA samples each per age group, and subjected to miRnome analysis. The quality and integrity of RNA was verified on Agilent 2100 Bioanalyzer (Agilent, CA, USA). The RIN of used RNA > 8. Small RNA library was prepared with TruSeq Small RNA Library Preparation kit (Illumina Inc., CA, USA). Total RNA was used for direct ligation of adapters to miRNAs. 3’ adapter in Illumina kit is modified, thus it binds only to 3’ hydroxyl group of small RNAs. Next ligated miRNAs were reverse transcribed, amplified with primers containing unique indexes and pooled. The fraction of small RNAs library was extracted using Pippin HT (Sage Science, MA USA) and sequenced on the Illumina NextSeq 500 platform. Small RNA fraction was sequenced and analyzed as described previously [Swierniak et al.,. 2013].

tag: age group

value: elderly

tag: median age

tag: Sex

value: pooled male and female

tag: median bmi

tag: pool number

tag: numbers of participants in the pool


title: six RNA samples of elderly donors were pooled 5E_S20


title: six RNA samples of long-lived donors were pooled 12L_S27

description:
Sex: 5F_1M
Blood donors were 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups: young (Y, n=24, age range 21-42 years, mean age 28.0±4.0 years) and long-lived (L, n=24, 90-102 years, 94.8±3.9 years). They were free of current infection and of any chronic diseases (type 2 diabetes, cardiovascular disease and its complications, neurodegeneration, cancer, etc.) however, in long-lived group a moderate hypertension and a mild degree physical and cognitive disability were allowed. All participants gave a written informed consent for participation in the study. The study was approved by the Bioethics Committee of the Medical University of Warsaw. ere 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups

value: long-lived


title: six RNA samples of young donors were pooled 4Y_S19

value: young


title: six RNA samples of long-lived donors were pooled 11L_S26

description:
Sex: 4F_2M
Blood donors were 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups: young (Y, n=24, age range 21-42 years, mean age 28.0±4.0 years) and long-lived (L, n=24, 90-102 years, 94.8±3.9 years). They were free of current infection and of any chronic diseases (type 2 diabetes, cardiovascular disease and its complications, neurodegeneration, cancer, etc.) however, in long-lived group a moderate hypertension and a mild degree physical and cognitive disability were allowed. All participants gave a written informed consent for participation in the study. The study was approved by the Bioethics Committee of the Medical University of Warsaw. ere 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups


title: six RNA samples of elderly donors were pooled 6E_S21

description:
Sex: 2F_4M
Blood donors were 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups: young (Y, n=24, age range 21-42 years, mean age 28.0±4.0 years) and long-lived (L, n=24, 90-102 years, 94.8±3.9 years). They were free of current infection and of any chronic diseases (type 2 diabetes, cardiovascular disease and its complications, neurodegeneration, cancer, etc.) however, in long-lived group a moderate hypertension and a mild degree physical and cognitive disability were allowed. All participants gave a written informed consent for participation in the study. The study was approved by the Bioethics Committee of the Medical University of Warsaw. ere 48 non-obese (BMI<30 kg/m2) Polish Caucasians belonging to either of the two age groups


title: six RNA samples of young donors were pooled 1Y_S16


title: six RNA samples of young donors were pooled 2Y_S17


title: six RNA samples of young donors were pooled 3Y_S18


title: ChIP-seq Dnmt3b [Dnmt3b KO (cl. B126)]

tag: strain background

tag: genotype/variation


title: six RNA samples of long-lived donors were pooled 9L_S24


title: six RNA samples of long-lived donors were pooled 10L_S25


title: nrpe1 Δ1251-1651 rep2

description: Index 7

data_processing:
Base-calling, adapter trimming, and size selection (>35bp) was completed with bcl2fastq v2.16.0.10
Methylation end bias was removed and reads were quality filtered using cutadapt v. 1.9.1 with the commands: cutadapt -U 7 -u 2 -q 25
Filtered reads were mapped to the TAIR10 genome and mapped reads were deduplicated using Bismark 0.16.1 using default settings.
Methylation status of each cytosine was extracted from mapped reads using Bismark_methylation_extractor with the commands: bismark_methylation_extractor -p --bedGraph --CX -cutoff 5 --cytosine_report --CX
Methylation status of each cytosine in the CHH context was extracted from the bismark_methylation_extractor output and used as input to the R package, methylkit v. 0.9.5 to define differentially methylated regions (DMRs) relative to Col-0. The genome was split into 300 base pair sliding windows with a step size of 200 base pairs and a minimum coverage requirement for each window of 10 informative cytosines with at least 5 read coverage each. Only regions that had coverage in each sample were utilized for calculation of DMRs. Significant hypo-DMRs were defined as those regions with a minimum 25% decrease in methylation relative to Col-0 and a q-value of less than or equal to 0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files that include methylation status of cytosines in the CHH context with at least 5 read coverage. Format for input to R package methylkit

source_name: nrpe1 Δ1251-1651 mutant

growth_protocol: Plants were grown in soil in long day conditions (16h light, 8 hours dark)

extract_protocol:
CTAB extraction of genomic DNA from 2.5 week above ground tissues
Illumina TruSeq DNA methylation Kit (product number: EGMK81312)

treatment_protocol: Transgenic lines were selected for by spraying with Basta herbicide

tag: background

value: nrpe1-11 mutant

tag: nrpe1 construct

tag: tissue


title: nrpe1 ΔSD rep2

description: Index 9

source_name: nrpe1 ΔSD mutant


title: nrpe1 Δ1251-1651 rep1

description: Index 11


title: nrpe1 Δ1251-1426 rep2

description: Index 3

source_name: nrpe1 Δ1251-1426 mutant


title: nrpe1 ΔSD rep1

description: Index 1


title: nrpe1 Δ1426-1651 rep2

description: Index 4

source_name: nrpe1 Δ1426-1651 mutant


title: nrpe1 Δ1251-1426 rep1

description: Index 7


title: nrpe1 Δ1851-1976 rep1

description: Index 6

source_name: nrpe1 Δ1851-1976 mutant


title: nrpe1 Δ1736-1976 rep1

description: Index 12

source_name: nrpe1 Δ1736-1976 mutant


title: nrpe1 Δ1851-1976 rep2

description: Index 2


title: RNAseq_ESC_WT_DRB_12h

description: PolyA enriched

source_name: E14 mESC wt, DRB, 12h

tag: cell line

value: mouse embryonic stem cells

tag: strain/background

value: wt

tag: cell treatment

value: DRB

tag: time point


title: nrpe1 Δ1736-1976 rep2

description: Index 8

tag: ecotype


title: nrpe1 Δ1651-1976 rep1

description: Index 5

source_name: nrpe1 Δ1651-1976 mutant


title: nrpe1 Δ1651-1976 rep2

description: Index 1


title: RNAseq_ESC_WT_DRB_6h

description: PolyA enriched

source_name: E14 mESC wt, DRB, 6h

tag: cell type


title: nrpe1 Δ1566-1976 rep2

description: Index 12

source_name: nrpe1 Δ1566-1976 mutant


title: RNAseq_ESC_WT_DRB_3h

description: PolyA enriched

source_name: E14 mESC wt, DRB, 3h


title: NRPE1 full length rep2

description: Index 6

source_name: nrpe1-11 mutant expressing a full length NRPE1 transgene


title: RNAseq_ESC_WT_DRB_0h

description: PolyA enriched

source_name: E14 mESC wt, DRB, 0h


title: nrpe1 Δ1251-1976 rep1

description: Index 2

source_name: nrpe1 Δ1251-1976 mutant


title: RNAseq_ESC_KO_DRB_3h

description: PolyA enriched

source_name: E14 mESC Dnmt3b ko, DRB, 3h


title: RNAseq_ESC_KO_DRB_12h

description: PolyA enriched

source_name: E14 mESC Dnmt3b ko, DRB, 12h


title: nrpe1 Δ1426-1976 rep2

description: Index 11

source_name: nrpe1 Δ1426-1976 mutant


title: nrpe1-11 rep2

description: Index 5

source_name: nrpe1-11 mutant


title: nrpe1 Δ1426-1651 rep1

description: Index 8


title: Col-0 rep1

description: Index 5

source_name: Col-0 wild type

value: wild type


title: nrpe1 Δ1251-1976 rep2

description: Index 10


title: nrpe1-11 rep1

description: Index 9


title: RNAseq_ESC_KO_DRB_6h

description: PolyA enriched

source_name: E14 mESC Dnmt3b ko, DRB, 6h


title: RNAseq_ESC_KO_DRB_0h

description: PolyA enriched

source_name: E14 mESC Dnmt3b ko, DRB, 0h


title: NRPE1 full length rep1

description: Index 10


title: ChIP-seq IgG [WT]

source_name: Mouse embryonic stem cells

tag: age

tag: chip antibody

value: Control IgG (Millipore 12-370)


title: TET2.FLT3_azaC_4 RNA-Seq

city: New York

first: Cem

last: Meydan

address: 1305 York

department: Physiology & Biophysics

institute: Weill Cornell Medical College

data_processing:
RNAseq bam files were aligned by STAR (v 2.4.0f1, with parameters chimSegmentMin=15  and chimJunctionOverhangMin=15) to mm9 and Gencode M1 transcriptome assembly.
RNAseq counts were annotated by using subread (v 1.4.5-p1) featureCounts.
Genome_build: mm9
Supplementary_files_format_and_content: processed files are in tab-separated text format giving raw counts and normalized fpkm values

molecule: polyA RNA

source_name: Hematopoietic stem cells

growth_protocol: Primary, uncultured cells.

extract_protocol:
RNA libraries were prepared for sequencing using SMARTer® Ultra® Low Input RNA for Illumina® Sequencing-HV
Libraries were prepared by the Weill Cornell Medicine Epigenomics Core per manufacturer's recommendations: https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=2&ved=0ahUKEwjruqSusYzLAhVkg4MKHcaZBTMQFggnMAE&url=http%3A%2F%2Fwww.clontech.com%2Fxxclt_ibcGetAttachment.jsp%3FcItemId%3D82347&usg=AFQjCNELhfN3rd9qBHZ1X-_MQqavkXH2BQ&sig2=SFKu-XNpO4_X8_3UpMbBig

treatment_protocol:
The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice.
AG-221 was administered twice daily using oral gavage at 100mg/kg single agent study and 40mg/kg combination agent study, suspended in 0.5% methyl cellulose and 0.2% Tween80, for 4-5 weeks
5-Aza was administered at 5mg/kg dissolved in PBS using IP injection daily for 5 days every 21 days, for four cycles

value: lin-Sca+cKit+

tag: genotype

tag: stain

tag: treatment


title: Col-0 rep2

description: Index 1


title: D42 ncRNA-Seq

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

description: small RNAs

data_processing:
Adaptor removal was performed using Cutadapt v1.4.2 (Martin, 2011)
Alignments to the Human reference genome GRCh37.75 were performed by Bowtie 2 v2.2.4 using parameters --very-sensitive-local and -k 10
Samtools v0.1.18 (Li et al., 2009) and HTSeq-count v0.6.0 (Anders and Huber, 2014) were used to count and compare aligned reads to annotated human genes
Mapped reads were aligned to the precursor and mature datasets from MirBase v21.0 (Griffiths‐Jones, 2004) using Bowtie 2 v2.2.4 (Langmead and Salzberg, 2012) using parameters -L 5 -N 1 -k 10 --local.
Samtools v0.1.18 (Li et al., 2009) and in-house Perl scripts were used to count aligned reads and to calculate the relative gene expression by dividing the read count for each gene, considering all non-coding (nc)RNA genes with at least 3 reads mapped within their location, by the raw read count ratio of D0 to D42 libraries.
Genome_build: Human genome GRCh37.75
Supplementary_files_format_and_content: Tab-delimited text files include normalized counts for both samples and alignments

source_name: Bone marrow of a Plasmodium vivax-infected patient

extract_protocol:
After collection of 4mL of bone marrow aspirate and 15mL of peripheral blood taken from a 46 years-old man who was diagnosed with P. vivax, treatment was immediately administered following National guidelines (chloroquine 1,500 mg for 3 days, primaquine.  30 mg/day for 7 days). At convalescence, 42 days after treatment, bone marrow aspirate and peripheral blood samples were obtained for comparison from this same individual. RNA was harvested using mirVana miRNA Isolation kit.
RNA libraries were prepared for sequencing using NEBNext Small RNA Library Prep Set for Illumina

tag: diagnosis

value: parasitaemia

value: 42 days after drug treatment


title: ChIP-seq Dnmt3b [WT]

tag: strain background

value: Mouse embryonic stem cells (mESCs)


title: TET2.FLT3_azaC_1 RNA-Seq


title: D0 ncRNA-Seq

description: small RNAs

value: untreated


title: TET2.FLT3_veh_4 RNA-Seq

value: vehicle


title: TET2.FLT3_azaC_2 RNA-Seq


title: nrpe1 Δ1566-1976 rep1

description: Index 4

value: 2.5 week above ground tissues


title: TET2.FLT3_veh_3 RNA-Seq


title: WGBS_ESC_KO

data_processing:
Basecalls performed using CASAVA version 1.8
Reads for WGBS_E14 were aligned to the mouse genome assembly using BSMAP v2.74 using the following parameters: -r 0 -n 1
Methylation status was peformed using Methratio tool of BSMAP.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of WGBS were performed using custom perl script.

extract_protocol:
DNA was purified using QIAQuick PCR Purification Kit (QIAGEN) according to the manufacture’s instruction. Total RNA was extracted by using TRIzol reagent (Invitrogen).
For whole-genome Bisulfite-Seq library preparation, 2.5 micrograms of ESCs genomic DNA, were spiked-in with 1ng of Escherichia coli genomic DNA, and sheared using a Bioruptor® Twin sonicator (Diagenode) for 3 runs of 10 cycles [30 s “ON,” 30 s “OFF”] at high power setting. Fragmented/digested DNA was then end-repaired, dA-tailed, and ligated to methylated adapters, using the Illumina TruSeq DNA Sample Prep Kit, following manufacturer instructions. DNA was loaded on an EGel Size select 2% agarose pre-cast gel (Invitrogen), and a fraction corresponding to fragments ranging from 180bp to 350bp was recovered. Purified DNA was then subjected to bisulfite conversion using the EpiTect Bisulfite Kit (Qiagen). Bisulfite-converted DNA was finally enriched by 15 cycles of PCR using Pfu Turbo Cx HotStart Taq (Agilent).

tag: genotype/variation

value: Dnmt3b ko


title: TET2.FLT3_veh_2 RNA-Seq


title: IDH2.FLT3_ag221_4 RNA-Seq

value: Idh2 R140Q;Flt3-ITD


title: WGBS_ESC_WT


title: TET2.FLT3_azaC_3 RNA-Seq


title: TET2.FLT3_veh_1 RNA-Seq


title: IDH2.FLT3_ag221_1 RNA-Seq


title: IDH2.FLT3_veh_3 RNA-Seq


title: IDH2.FLT3_veh_2 RNA-Seq


title: WT-1 RNA-Seq


title: WT-4 RNA-Seq


title: nrpe1 Δ1426-1976 rep1

description: Index 3

tag: background


title: IDH2.FLT3_veh_1 RNA-Seq


title: TET2.FLT3_ac220.azaC_1 RRBS

data_processing:
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Raw reads alignment and CpG methylation call were formed by using an in-house pipeline described in Akalin et al., PLoSGenetics, 2012.
Genome_build: mm9
Supplementary_files_format_and_content: methycall files are in .txt format

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
ERRBS libraries were prepared by the Weill Cornell Medicine Epigenomics Core according to a previously published protocol (Akalin et al., PLoSGenetics, 2012; Garrett-Bakelman, F.E. and Sheridan, C., JoVE, 2015). Briefly, high molecular weight DNA was disgested with MspI followed by end repair and adapter ligation. Size selection was perfomed for 150-400bp fragments ad bisulfite conversion was performed prior to PCR amplification.

treatment_protocol:
The hematopoietic stem cells, characterized by lin-, Sca+, and cKit+, were sorted from mice.
AC220 was administered daily using oral gavage with AC220 at 10 mg/kg, suspended in 5% 2-hydroxypropyl-β-cyclodextrin
AG-221 was administered twice daily using oral gavage at 100mg/kg single agent study and 40mg/kg combination agent study, suspended in 0.5% methyl cellulose and 0.2% Tween80, for 4-5 weeks
5-Aza was administered at 5mg/kg dissolved in PBS using IP injection daily for 5 days every 21 days, for four cycles


title: WT-3 RNA-Seq


title: TET2.FLT3_ac220.azaC_2 RRBS


title: TET2.FLT3_ac220.azaC_4 RRBS


title: TET2.FLT3_ac220.azaC_3 RRBS


title: WT-2 RNA-Seq


title: TET2.FLT3_azaC_3 RRBS


title: TET2.FLT3_azaC_1 RRBS


title: rrp6L1-2

data_processing:
Base-calling, adapter trimming, and size selection (>35bp) was completed with bcl2fastq v2.16.0.10
To ensure that only reads containing true 3’ end sequences were included in further analyses, reads were first selected for and trimmed of the 3’ RACE Primer 2 sequence using Cutadapt version 1.9.1 with the following commands: cutadapt -g ctactactaggccacgcgtcgactagtac -q 20,20 -m 15 --discard-untrimmed .
Reads were then selected for and trimmed of the artificially added poly-A tail with the following: cutadapt -g "t{210}" -m 15 --discard-untrimmed
Trimmed reads were then mapped to sequences extracted from the A. thaliana TAIR10 genome corresponding to the PCR target regions (consisting of genomic sequences from the following coordinates: Chr4: 2318164-2323164 (IGN5 top strand); Chr4: 2323282-2328282 (IGN5 bottom strand); Chr4: 2577970-2582970 (IGN23); Chr4: 5459147-5464147 (IGN25); Chr2: 15314824-15319824 (IGN29); Chr4: 6549057-6554057 (IGN35); Chr1: 13585635-13590635 (IGN17) using bowtie2 in local alignment mode
SAM output files were converted to bam files, sorted, indexed, and split into individual bam files for each PCR target region using samtools. Bam files were converted to bed files using bedtools
Bed files were further filtered for high quality mapping scores (MapQ >= 40) and reads that mapped to the appropriate strand, selected for by the GSP. Read coordinates in the bed files were used to calculate the 3’ end lengths relative to the coordinate of the 3’ end of the internal gene-specific primer.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files quantifying 3' end lengths

source_name: rrp6L1-2 mutant

extract_protocol:
RNA was extracted using Trizol
RNA was treated with Poly-A polymerase prior to reverse transcription. Reverse transcription was conducted with an oligo dT primer that inserted universal primer binding sites. Nested PCR was conducted with universal RACE primers and gene-specific primers to target Pol V transcripts of interest. Pooled and cleaned PCR products for each genotype (up to 1.2 µg) were prepared for Illumina sequencing with NEBnext end repair enzyme and Klenow fragment (3’-5’ exo -) from NEB according to the manufacturer’s protocols. After each enzyme treatment, products were cleaned with the Zymogen Clean and Concentrator-5 kit. Adapters (NextFlex PCR free DNA barcodes from BIOO Scientific) were ligated to end repaired, A-tailed PCR products using T4 DNA ligase (NEB) according to the manufacturer’s protocol at 16ºC for 2 hours. Libraries were cleaned using 1 volume AMPure XP beads (Beckman Coulter) according to the manufacturer’s instructions and quality checked and quantified with an Agilent Tapestation.


title: TET2.FLT3_ac220_1 RRBS


title: TET2.FLT3_ac220_2 RRBS


title: IDH2.FLT3_ag221_3 RNA-Seq


title: TET2.FLT3_ac220_4 RRBS


title: TET2.FLT3_ac220_3 RRBS


title: IDH2.FLT3_ag221_2 RNA-Seq


title: nrpe1-11


title: TET2.FLT3_azaC_2 RRBS


title: TET2.FLT3_azaC_4 RRBS


title: TET2.FLT3_veh_5 RRBS


title: rrp6L1-1

source_name: rrp6L1-1 mutant


title: TET2.FLT3_veh_2 RRBS


title: IDH2.FLT3_ag221.ac220_2 RRBS


title: IDH2.FLT3_ag221.ac220_3 RRBS


title: TET2.FLT3_veh_3 RRBS


title: TET2.FLT3_veh_1 RRBS


title: TET2.FLT3_veh_4 RRBS


title: TET2.FLT3_veh_6 RRBS


title: Col-0


title: p_Ib2

first: Selina

last: Chen-Kiang

state: NY

address: 1300 York Avenue, C338

data_processing:
Cluster generation, sequencing, and processing of the images were done using the Real-Time Analysis (RTA) software on the HiSeq2000 and post-processing with CASAVA (v.1.8.2).
To optimize library preparation we used a TACON high-throughput RNA prep-station. Raw data were filtered for high median quality (Q-value > 20) and then sent to Cornell’s High Performance Computing (HPC) cluster, to be run through our RNA-seq analysis pipeline.
Raw reads were trimmed for the first and last five base pairs before alignment to  remove low quality bases.
Our RNA-Seq analysis pipeline used BWA and SAMtools.
Processed Data files (RPKM values) were obtained using Genesifter (Geospiza), which uses SAMtools and the Genome Analysis Toolkit (GATK) for base quality score recalibration and local re-alignment for indels.
Genome_build: Human (Build 37.2)
Supplementary_files_format_and_content: .xls RPKM values

source_name: Lymph Node

growth_protocol: Mantle cell lymphoma (MCL) biopsies were obtained from patients at the New York-Presbyterian Hospital after informed consent as part of a study approved by the Institutional Review Board. Primary MCL cells were purified using MACS CD19 MicroBeads (Miltenyi Biotec). The percentage of MCL tumor cells (CD19+, CD5+, CD23-) was determined to be > 90% by flow cytometry.  B cells from healthy volunteers were isolated from peripheral blood (PBC)s using the same protocol. Primary MCL cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% heat-inactivated FBS (HyClone), 2 mM L-glutamine and 100 U/ml penicillin/streptomycin (Invitrogen)

extract_protocol:
For each experimental condition, 100 ng of high quality total RNA (RIN > 0.8 on the Agilent BioAnalyzer 2100) was isolated using the RNAEasy kit according to the manufacturer’s instructions (QIAGEN)
All RNAs were converted to cDNA, isolated with magnetic beads from the TruSeq mRNA prep kit (v2), and then ligated to Illumina adapters, as per the standard TruSeq Illumina protocol. Using these multi-plexed cDNA libraries, we generated clusters on the Illumina cBot station and paired-end sequenced each sample to 50x50 bp on the Illumina HiSeq2000 at the Weill Cornell Medical College (WCMC) Epigenomics Core

treatment_protocol: No treatment

value: Mantle cell lymphoma cells

tag: source

value: lymph node


title: IDH2.FLT3_ag221_3 RRBS


title: IDH2.FLT3_veh_1 RRBS


title: IDH2.FLT3_ag221_2 RRBS


title: p_Ib1


title: IDH2.FLT3_veh_3 RRBS


title: r_IbBM

source_name: Bone Marrow

value: bone marrow


title: IDH2.FLT3_veh_2 RRBS


title: IDH2.FLT3_ac220_2 RRBS


title: r_IbSP

source_name: Spleen


title: IDH2.FLT3_ag221_1 RRBS


title: IDH2.FLT3_ac220_3 RRBS


title: WT-3 RRBS


title: IDH2.FLT3_veh_4 RRBS


title: IDH2.FLT3_ac220_1 RRBS


title: IDH2.FLT3_ag221_4 RRBS


title: WT-4 RRBS


title: WT-2 RRBS


title: IDH2.FLT3_ag221.ac220_1 RRBS


title: Ribo-Zero total RNA fetal head 2

city: Klosterneuburg

first: Florian

middle: M

last: Pauler

address: Am Campus 1

country: Austria

institute: IST Austria

description:
Ribo-Zero total RNA, Trizol isolated
processed data file: FH.RefSeq_read_count.txt

data_processing:
Reads from each fastq file for CCE (reads provided here and from GSM718982) and fetal head (reads provided here and from GSM718983) were trimmed using trimmomatic v0.32 with these parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
All reads passing the filtering criteria were aligned using STAR v2.3 as single reads (paired information was not used), separtely for each tissue using these parameters: --outStd SAM, --outSAMmode Full, --alignIntronMax 200000, --outFilterIntronMotifs RemoveNoncanonical, --outSAMstrandField intronMotif, --outFilterMultimapNmax 1.
SAM output was converted to bam and sorted by position using samtools v 0.1.19. Reads Per Kb per Millions of reads (RPKM) expression values were calculated using the RPKM_count.py script from RSeQC v2.3.9 using the -u –e parameters.
Annotation: NCBI RNA reference sequences collection (RefSeq) obtained from the UCSC genome browser on the 17.07.2014
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimitted output from RPKM_count.py

source_name: 14.5dpc fetal head

growth_protocol: Cell were cultured and tissues obtained as described: Huang et al., PLoS ONE 2011, PMID:  22102886

extract_protocol:
RNA was prepared as described: Huang et al., PLoS ONE 2011, PMID:  22102886
Libraries were prepared as described: Huang et al., PLoS ONE 2011, PMID:  22102886

treatment_protocol: Cell were treated as described: Huang et al., PLoS ONE 2011, PMID:  22102886

tag: strain

value: FVB/N

value: fetal head dissected from 14.5dpc mouse embryo


title: Ribo-Zero total RNA CCE 2

description:
Ribo-Zero total RNA, Trizol isolated
processed data file: CCE.RefSeq_read_count.txt

source_name: Day5 differentiated CCE

value: differentiated ES cells induced by retinoic acid for 5 days


title: ago1 deleted cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks

organism: Schizosaccharomyces pombe

source_name: ago1 deleted cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30C.

extract_protocol:
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (epicentre)
ScriptSeq v2 RNA-Seq Library Preparation Kit was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Genomic deletion of ago1d, mmi1, and dcr1.

tag: growth stage

value: log growing cells

value: ago1 deletion


title: dcr1 deleted cells

source_name: dcr1 deleted cells

value: dcr1 deletion


title: mmi1 deleted cells

source_name: mmi1 deleted cells

value: mmi1 deletion within mei4 deletion background


title: wt deleted cells

source_name: wt deleted cells

value: Wild type


title: footprint SD

status: Public on Feb 24 2017

city: San Francisco

first: Jiashun

last: Zheng

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: ribosome protected mRNA

data_processing:
Library strategy: Ribosome Profiling
Illumina Casava1.7 software used for basecalling.
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S.cerevisiae rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the non-rRNA and non-tRNA reads were aligned against the S.cerevisiae genomic sequences.
reads with no alignment against S.cerevisiae genomics sequences were re-aligned against the library of S.cerevisiae processed protein-coding transcripts.
Genome_build: Recent genome build (03/14/2012) from the Saccharomces Genome Database (SGD)
Supplementary_files_format_and_content: wig

organism: Saccharomyces cerevisiae

source_name: SD

growth_protocol: Cells were cultured in SD media (Synthetic Defined (SD) Medium) before changing medium.

extract_protocol:
The RNA were extracted as described in Ingolia et al, 2011.
Deep-sequencing libraries were constructed as described in Ingolia et al, 2011.

treatment_protocol: Cells were separated from the media by spin-down at 3000 g for 5 minutes and re-suspended in SD and MetR media respectively. All samples were incubated for another hour before harvesting.

tag: medium

value: SD


title: mRNA MetR

description: polyA+ mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
The resulting sequences were aligned using the following method: the linker sequences at the 3’ends were removed prior to alignment.
The SOAP2.20 was used to align the sequence reads (allowing no more than 2 total mismatches)
Reads after linker removal were aligned against a library of S.cerevisiae rRNA and tRNA sequences. Reads with any alignment against rRNA and tRNA were eliminated from further analysis.
the non-rRNA and non-tRNA reads were aligned against the S.cerevisiae genomic sequences.
reads with no alignment against S.cerevisiae genomics sequences were re-aligned against the library of S.cerevisiae processed protein-coding transcripts.
Genome_build: Recent genome build (03/14/2012) from the Saccharomces Genome Database (SGD)
Supplementary_files_format_and_content: wig

source_name: MetR

value: MetR


title: Ribo-Zero total RNA CCE 1

description:
GSM718982
Ribo-Zero total RNA, Trizol isolated
processed data file: CCE.RefSeq_read_count.txt


title: mRNA SD

description: polyA+ mRNA


title: rnc-_time7.5

city: Madison

first: Gina

last: Gordon

state: WI

address: 1415 Engineering Dr

department: Chemical and Biological Engineering

institute: University of Wisconsin Madison

data_processing:
Adapters trimmed with Cutadapt (v1.12)
Aligned to NC_000913.3 with bwa version 0.7.7
Index and sort alignments with samtools version 1.2
Count reads aligned to each base IGVtools (version 2.3.71), window size = 1
Normalized decay values with average of stable genes ssrA, ssrS, and rnpB
Gave a pseudocount of 0.01 to all values of 0
Genome_build: NC_000913.3
Supplementary_files_format_and_content: In the .txt files the first column is the coordinate of the base corresponding to NC_000913.3 and the second column is the number of normalized reads at that position. All 0 values were given a pseudocount of 0.01. Counts are normalized so that the averages of ssrA, ssrS, and rnpB are stable throughout the decay from 0 to 20 minutes

organism: Escherichia coli

source_name: bacterial cells

growth_protocol: Cells were grown to exponential phase in Lysogeny broth, 37oC with shaking

extract_protocol:
Total RNA was extracted and DNase-treated according to published protocols (Khodurksy A, Bernstein J, Peter B, Rhodius V, Wendisch V, Zimmer D. Escherichia coli Spotted Double-Strand DNA Microarrays)
rRNA reduction with EpiCentre Ribo-Zero Gram Negative Ribosomal RNA reduction kit (2.5ug) & TruSeq RNA Library Prep

treatment_protocol: Cells were harvested after the addition of rifampicin  (250 μg/ml) to stop nascent transcription and quenched with stop solution (10% phenol in ethanol). The first timepoint was taken 3.5 minutes after addition of the antibiotic to give time for the diffusion of rifampicin into the cells and binding of the antibiotic to RNA polymerase. This sample was called 0 minutes, and further samples were taken at 2.5, 5, 7.5, 10, and 20 minutes from wild-type E. coli and the RNase III mutant. A partial biological replicate of wild-type was taken (0, 2.5, and 7.5 minutes), to examine the reproducibility between samples.

value: rnc- deletion mutant


title: WTB_time0

value: wild type


title: rnc-_time10


title: rnc-_time0


title: rnc-_time20


title: WTB_time7.5


title: rnc-_time5


title: WTA_time2.5


title: rnc-_time2.5


title: Ribo-Zero total RNA fetal head 1

description:
GSM718983
Ribo-Zero total RNA, Trizol isolated
processed data file: FH.RefSeq_read_count.txt


title: WTA_time10


title: footprint MetR

description: ribosome protected mRNA


title: WTA_time0


title: WTA_time7.5


title: WTA_time20


title: G142-M10_rRNA depleted_Hypophysectomized male liver + GH 90'_pool 1

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
Sample name: G142_M10
Ribosomal RNA depleted, strand-specific library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting  sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were cuantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: Excel spreadsheet with differential expression.

source_name: liver tissue

extract_protocol:
RNA was extracted from flash fozen liver by Trizol per the manufacturer's instructions.
RNA was partially depleted of rRNA using the NEB rRNA depletion kit (NEB, Ipswich, MA, Cat# E6310). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

treatment_protocol: Male and female CD-1 (ICR) mice were obtained from Charles River Labs (Wilmington, MA). Mice were intact or were hypophysectomized by the supplier at 7 wk of age. Hypophysectomized male mice were given a single ip injection of vehicle (control) without or with recombinant rat GH at 125 ng GH/g body weight

value: CD-1 (Charles River)

value: hypophysectomized + GH pulse (90 min)

tag: Sex

value: Male

value: 11 weeks

tag: tissue

value: liver


title: G142-M11_rRNA depleted_Hypophysectomized male liver + GH 90'_pool 2

description:
Sample name: G142_M11
Ribosomal RNA depleted, strand-specific library


title: G142-M12_rRNA depleted_Hypophysectomized male liver + GH 240'_pool 1

description:
Sample name: G142_M12
Ribosomal RNA depleted, strand-specific library

value: hypophysectomized + GH pulse (240 min)


title: ZUMA-0049-0050

city: Badalona

first: Miguel

middle: A.

last: Peinado

address: Can Ruti Campus

country: Spain

institute: IGTP

description: Tests on paired end sequencing

data_processing:
NSUMA technique is described in (Jordà, 2017) PMID:27999094
Pre-processing. Sequences were obtained from the Illumina instruments as fastq
Mapping. Paired-end reads were locally aligned against the hg19 canonocal chromosomes (22 autosomal, 2 sex) using bowtie2-2.2.6 with the -q --local --phred33 --sensitive-local  --no-discordant  --no-unal flags.
Post-processing. Primary aligned reads from concordant pairs (unaligned and discordant pairs discarded during mapping) were assigned to the NSUMA canonical universe using featureCounts from subread-1.5.1 with the following flags:  -F SAF -f -O -a slois_amplicons.saf –primary.
Genome_build: hg19
Supplementary_files_format_and_content: fastq, read counts (text files)

organism: Pan troglodytes

extract_protocol:
The method is based in the AUMA technique (Rodríguez, 2008; doi: 10.1093/nar/gkm1105), although important modifications were introduced to expand significantly the genomic coverage and to introduce internal controls that allow normalization and control of some technical biases. Briefly, one microgram of DNA was digested for 16 h at 25C with the methylation-sensitive restriction endonuclease SmaI  (Roche Diagnostics GmH, Mannheim, Germany) leaving blunt ends (CCC/GGG), followed by a second digestion with the methylation-insensitive restriction enzyme MseI (T/TAA)  (16h at 37C, Roche Diagnostics GmH, Mannheim, Germany) that leaves sticky ends. Adapters blunt-SmaI (ADPT-S1 GATAGTATGCCCGGGTGA plus the 5’ phosphorylated ADPT-S2 TCACCCGGGCATAC) and sticky-MseI (ADPT-M1 CTGAGGCTGGATCCCTG plus the 5’ phosphorylated ADPT-M2 TACAGGGATCCAGCCTCAG) were prepared by incubating the two oligonucleotides for 2 min at 65ºC and then cooling to room temperature for 30-60 min. Digested DNA and 2nmol of blunt and sticky adapters were ligated overnight at 16C using T4 DNA ligase (New England Biolabs, Beverly, MA). The product was purified using the Illustra GFX Purification kit (GE Healthcare, Buckinghamshire, UK) and eluted in 200 ul of bidistilled water. The ligation product consists of three types of molecules according to the flanking sites SmaI-SmaI, SmaI-MseI and MseI-MseI. Only the products containing SmaI adapters represent unmethylated fragments (Figure 1A). Next, a PCR (95ºC 2 min; 95ºC 30 sec, 60ºC 1 min, 72ºC 1min for 30 cycles; 72ºC 5min) was performed using two primers, one that anneals the MseI adapter (ADPT-M1A CTGAGGCTGGATCCCTGTAA) and another one homologous to the SmaI adapter plus TT at the 3’ end (ADPT-S1TT GATAGTATGCCCGGGTGAGGGTT) to enrich in Alu sequences. The final product appeared as a smear when run in an agarose gel and most of the amplicons ranged from 50 bp to 1000 bp.
The NSUMA PCR product was sheared by sonication with a Bioruptor (Diagenode) to a size of 100-300 bp. DNA fragments were blunt end repaired with T4 DNA polymerase and Klenow fragment (NEB) and purified with a QIAquick PCR purification kit (Qiagen). Thereafter, 3’-adenylation was performed by incubation with dATP and the Klenow (3´→5´ exo-) fragment of DNA polymerase I (NEB). DNA was purified using MinElute spin columns (Qiagen) and ligated to double-stranded adapters (GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT) using rapid T4 DNA ligase (NEB). The sample was purified again using a MinElute spin column and run on a 2% agarose gel, and fragments in the size range of interest, 150 bp plus 65 bp of adapters, were excised with a sterile single-use scalpel and recovered from the gel by QIAquick gel extraction. Then, adapter-ligated fragments were enriched, and adapters were extended, by selectively amplifying with an 18-cycle PCR reaction using Phusion DNA polymerase (Finnzymes), and primers 1.1 (5’ P- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and 2.0 (5’ P-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT) (library size of approximately 150 plus 92 bp of adapters). Finally, the quality of libraries was confirmed on the Agilent Technologies 2100 Bioanalyzer and by cloning into a blunt TOPO vector. Six colonies were sequenced by conventional Sanger method to verify correct adapter ligation and sequence match. Libraries were quantified by TaqMan Universal PCR No AmpErase kit (Applied Biosystems-Roche). DNA was loaded into a single read (SR) flow cell for cluster generation using a SR-cluster generation kit v4 (Illumina). During this process, DNA molecules were immobilized on the surface of the flow cell, amplified in situ to create same-sequence containing clusters, and following surface blocking and DNA denaturation, binding of sequencing primer was performed. The flow cell was then mounted on a  Illumina Hi-Seq 2000instrument for sequencing, and 35-50 sequencing cycles were carried out using v4 SBS kits.

value: Blood


title: G142-M13_rRNA depleted_Hypophysectomized male liver + GH 240'_pool 2

description:
Sample name: G142_M13
Ribosomal RNA depleted, strand-specific library


title: G142-M9_rRNA depleted_Hypophysectomized male liver + GH 30'_pool 2

description:
Sample name: G142_M9
Ribosomal RNA depleted, strand-specific library

value: hypophysectomized + GH pulse (30 min)


title: G142-M8_rRNA depleted_Hypophysectomized male liver + GH 30'_pool 1

description:
Sample name: G142_M8
Ribosomal RNA depleted, strand-specific library


title: G141-M15_rRNA depleted_Hypophysectomized male liver_pool 1

description:
Sample name: G141_M15
Ribosomal RNA depleted, strand-specific library

value: hypophysectomized


title: G142-M7_rRNA depleted_Hypophysectomized male liver_pool 2

description:
Sample name: G142_M7
Ribosomal RNA depleted, strand-specific library


title: G118-M18_PolyA+_Intact female liver pool 3

description:
Sample name: G118_M18
poly-A selected RNA, strand-specific library

data_processing:
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) mRNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene, Primary RNA transcripts (hnRNA) were quantified by counting reads that map to the intersection of all intronic sequences across all isoforms of a given gene; it thus excludes sequences found in an exonic region of at least one isoform of the gene.
Differential expression analysis for RefSeq genes was conducted using edgeR (Robinson, 2010, Bioinformatics)
Genome_build: mm9
Supplementary_files_format_and_content: excel spreadsheet with differential expression.

extract_protocol:
RNA was extracted from flash fozen mouse liver using Trizol per the manufacturer's instructions.
RNA was polyA-selected using the NEBNext Poly(A) mRNA magnetic isolation kit (NEB, Ipswich, MA, Cat# E7490). Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (NEB, Cat# E7420) and multiplexed using NEBNext Multiplex Oligos for Illumina (NEB, Cat# E7335, E7500), according to the manufacturer's instructions.

value: Intact

value: Female

value: 7-11 weeks


title: G118-M16_PolyA+_Intact female liver pool 1

description:
Sample name: G118_M16
poly-A selected RNA, strand-specific library


title: G118-M15_PolyA+_Intact male liver pool 3

description:
Sample name: G118_M15
poly-A selected RNA, strand-specific library

value: 7-9 weeks


title: G118-M17_PolyA+_Intact female liver pool 2

description:
Sample name: G118_M17
poly-A selected RNA, strand-specific library


title: WTA_time5

tag: time point


title: G118-M13_PolyA+_Intact male liver pool 1

description:
Sample name: G118_M13
poly-A selected RNA, strand-specific library